Starting phenix.real_space_refine
on Tue Mar  3 13:35:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8q_27254/03_2026/8d8q_27254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/03_2026/8d8q_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_27254/03_2026/8d8q_27254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2026/8d8q_27254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2026/8d8q_27254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2026/8d8q_27254.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.07, per 1000 atoms: 0.21
  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: 0.30
  Conformation dependent library (CDL) restraints added in 222.8 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: 0.15
  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: 0.78

  Time building geometry restraints manager: 0.41 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:             10.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.420
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.010
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG H  66 
 TYR   0.030   0.005   TYR A 489 
 PHE   0.015   0.004   PHE H  67 
 TRP   0.017   0.005   TRP A 436 
 HIS   0.003   0.001   HIS B  90 

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

*********************** 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  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   67 PHE cc_start: 0.6549 (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: 0.8347 (t) cc_final: 0.8092 (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: 0.0863
  time to fit residues: 24.3829
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  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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**
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.094151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.080881 restraints weight = 17994.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.083277 restraints weight = 10201.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.084897 restraints weight = 6845.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.086008 restraints weight = 5135.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.086811 restraints weight = 4141.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5335  Z= 0.166
  Angle     :  0.671  10.779   7245  Z= 0.360
  Chirality :  0.048   0.271    780
  Planarity :  0.005   0.044    927
  Dihedral  :  5.031  19.392    759
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.28 %
    Favored  : 97.57 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.33), residues: 659
  helix: -3.73 (0.62), residues: 33
  sheet:  0.62 (0.32), residues: 243
  loop :  1.69 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.016   0.002   TYR L  49 
 PHE   0.022   0.002   PHE C  29 
 TRP   0.015   0.002   TRP H 115 
 HIS   0.001   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5327)
  covalent geometry    : angle       0.66606 ( 7228)
  SS BOND              : bond        0.01055 (    7)
  SS BOND              : angle       1.47588 (   14)
  hydrogen bonds       : bond        0.04673 (  189)
  hydrogen bonds       : angle       6.66201 (  456)
  link_NAG-ASN         : bond        0.00472 (    1)
  link_NAG-ASN         : angle       2.61271 (    3)

*********************** 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
  176 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7758 (mmm) cc_final: 0.7445 (mmm)
REVERT: H   39 GLN cc_start: 0.7670 (pp30) cc_final: 0.7211 (pp30)
REVERT: H   43 LYS cc_start: 0.8505 (mptt) cc_final: 0.8288 (mmtm)
REVERT: H   46 GLU cc_start: 0.8206 (tt0) cc_final: 0.7725 (tt0)
REVERT: H  111 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7732 (mttt)
REVERT: H  113 ASP cc_start: 0.7130 (t70) cc_final: 0.6536 (p0)
REVERT: H  120 LEU cc_start: 0.8568 (tp) cc_final: 0.7790 (pp)
REVERT: L    3 VAL cc_start: 0.8251 (t) cc_final: 0.8027 (m)
REVERT: L   15 LEU cc_start: 0.8350 (mt) cc_final: 0.7619 (mt)
REVERT: L   48 MET cc_start: 0.7507 (mmm) cc_final: 0.6873 (mmm)
REVERT: L  103 LYS cc_start: 0.8558 (tttt) cc_final: 0.7967 (tptm)
REVERT: A  355 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7183 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8531 (m-30) cc_final: 0.8310 (m-30)
REVERT: A  402 ILE cc_start: 0.8829 (pt) cc_final: 0.8553 (pt)
REVERT: A  422 ASN cc_start: 0.8931 (m-40) cc_final: 0.8143 (m-40)
REVERT: B   14 SER cc_start: 0.7981 (m) cc_final: 0.7764 (t)
REVERT: B   49 TYR cc_start: 0.7551 (p90) cc_final: 0.7330 (p90)
REVERT: B  105 GLU cc_start: 0.4557 (tp30) cc_final: 0.4090 (tp30)
REVERT: C    4 LEU cc_start: 0.8210 (mt) cc_final: 0.7616 (mt)
REVERT: C   18 VAL cc_start: 0.8757 (p) cc_final: 0.8449 (p)
REVERT: C   36 TRP cc_start: 0.8910 (m100) cc_final: 0.8557 (m100)
REVERT: C   46 GLU cc_start: 0.8191 (tt0) cc_final: 0.7753 (tp30)
REVERT: C   71 ARG cc_start: 0.7803 (pmt-80) cc_final: 0.7036 (pmt-80)
REVERT: C   72 ASP cc_start: 0.8564 (t0) cc_final: 0.7851 (t70)
REVERT: C   73 MET cc_start: 0.6906 (pmm) cc_final: 0.6120 (pmm)
REVERT: C   82 LEU cc_start: 0.7924 (tp) cc_final: 0.7566 (tp)
REVERT: C   91 TYR cc_start: 0.9081 (m-80) cc_final: 0.8783 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0722
  time to fit residues: 16.0757
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  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  89 GLN
A 481 ASN
C  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.094988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082028 restraints weight = 17889.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.084332 restraints weight = 10326.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.085979 restraints weight = 6955.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.087136 restraints weight = 5196.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.087942 restraints weight = 4161.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   5335  Z= 0.121
  Angle     :  0.581   7.835   7245  Z= 0.317
  Chirality :  0.046   0.252    780
  Planarity :  0.004   0.042    927
  Dihedral  :  4.599  19.979    759
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.43 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  1.42 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.33), residues: 659
  helix: -3.63 (0.63), residues: 33
  sheet:  0.44 (0.32), residues: 242
  loop :  1.22 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 403 
 TYR   0.019   0.002   TYR L  91 
 PHE   0.025   0.002   PHE H  67 
 TRP   0.013   0.001   TRP B  96 
 HIS   0.001   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5327)
  covalent geometry    : angle       0.57637 ( 7228)
  SS BOND              : bond        0.00613 (    7)
  SS BOND              : angle       1.70914 (   14)
  hydrogen bonds       : bond        0.03902 (  189)
  hydrogen bonds       : angle       6.18861 (  456)
  link_NAG-ASN         : bond        0.00151 (    1)
  link_NAG-ASN         : angle       1.30768 (    3)

*********************** 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
  165 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8113 (mmm) cc_final: 0.7730 (mmm)
REVERT: H   39 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7229 (pp30)
REVERT: H   43 LYS cc_start: 0.8527 (mptt) cc_final: 0.8301 (mmtm)
REVERT: H   46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7670 (tt0)
REVERT: H   75 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8367 (mmtt)
REVERT: H  120 LEU cc_start: 0.8663 (tp) cc_final: 0.7927 (pp)
REVERT: L   48 MET cc_start: 0.7624 (mmm) cc_final: 0.7362 (mmm)
REVERT: A  355 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7240 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8776 (pt) cc_final: 0.8445 (pt)
REVERT: A  455 LEU cc_start: 0.8309 (tp) cc_final: 0.8099 (tp)
REVERT: B   14 SER cc_start: 0.7991 (m) cc_final: 0.7674 (t)
REVERT: B   17 GLU cc_start: 0.8552 (mp0) cc_final: 0.8306 (mp0)
REVERT: C   46 GLU cc_start: 0.8205 (tt0) cc_final: 0.7729 (tt0)
REVERT: C   56 ASN cc_start: 0.7631 (m110) cc_final: 0.7017 (p0)
REVERT: C   70 THR cc_start: 0.8524 (p) cc_final: 0.8243 (t)
REVERT: C   72 ASP cc_start: 0.8667 (t0) cc_final: 0.7659 (t70)
REVERT: C   82 LEU cc_start: 0.8048 (tp) cc_final: 0.7825 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0670
  time to fit residues: 14.3481
Evaluate side-chains
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0070
   chunk 1 optimal weight:    7.9990
   chunk 28 optimal weight:    0.2980
   chunk 9 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 38 optimal weight:   10.0000
   overall best weight:    0.6400

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
B 100 GLN
C   6 GLN
C  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.094981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.081868 restraints weight = 17746.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.084227 restraints weight = 10116.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.085879 restraints weight = 6762.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.086988 restraints weight = 5036.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.087763 restraints weight = 4051.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.4658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5335  Z= 0.113
  Angle     :  0.576   9.551   7245  Z= 0.314
  Chirality :  0.046   0.299    780
  Planarity :  0.004   0.039    927
  Dihedral  :  4.408  19.592    759
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  1.24 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.33), residues: 659
  helix: -3.50 (0.67), residues: 33
  sheet:  0.43 (0.32), residues: 245
  loop :  0.94 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.020   0.001   TYR H  79 
 PHE   0.024   0.001   PHE A 374 
 TRP   0.024   0.002   TRP A 353 
 HIS   0.001   0.000   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5327)
  covalent geometry    : angle       0.57107 ( 7228)
  SS BOND              : bond        0.00636 (    7)
  SS BOND              : angle       1.81951 (   14)
  hydrogen bonds       : bond        0.03553 (  189)
  hydrogen bonds       : angle       6.01726 (  456)
  link_NAG-ASN         : bond        0.00119 (    1)
  link_NAG-ASN         : angle       1.18554 (    3)

*********************** 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
  158 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.197 
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   34 MET cc_start: 0.8226 (mmm) cc_final: 0.7810 (mmm)
REVERT: H   39 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7160 (pp30)
REVERT: H   43 LYS cc_start: 0.8523 (mptt) cc_final: 0.8301 (mmtm)
REVERT: H   46 GLU cc_start: 0.8148 (tt0) cc_final: 0.7501 (tt0)
REVERT: L   30 TYR cc_start: 0.7792 (t80) cc_final: 0.7523 (t80)
REVERT: A  402 ILE cc_start: 0.8773 (pt) cc_final: 0.8428 (pt)
REVERT: A  409 GLN cc_start: 0.8356 (mp10) cc_final: 0.7955 (mp10)
REVERT: A  468 ILE cc_start: 0.8989 (pt) cc_final: 0.8434 (mm)
REVERT: B   14 SER cc_start: 0.8074 (m) cc_final: 0.7790 (t)
REVERT: C   36 TRP cc_start: 0.9118 (m100) cc_final: 0.8897 (m100)
REVERT: C   46 GLU cc_start: 0.8241 (tt0) cc_final: 0.7780 (tt0)
REVERT: C   70 THR cc_start: 0.8563 (p) cc_final: 0.8156 (t)
REVERT: C   71 ARG cc_start: 0.7280 (ppt170) cc_final: 0.6920 (ppt170)
REVERT: C   72 ASP cc_start: 0.8561 (t0) cc_final: 0.7432 (t70)
REVERT: C   85 GLU cc_start: 0.8338 (pm20) cc_final: 0.8005 (pm20)
REVERT: C   86 ASP cc_start: 0.7568 (m-30) cc_final: 0.7063 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0739
  time to fit residues: 14.7193
Evaluate side-chains
  107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
B  90 HIS
** 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 = 0.3513 r_free = 0.3513 target = 0.089619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076385 restraints weight = 18668.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.078544 restraints weight = 10825.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.080082 restraints weight = 7437.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.081131 restraints weight = 5667.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.081867 restraints weight = 4645.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.5156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5335  Z= 0.226
  Angle     :  0.679  11.912   7245  Z= 0.366
  Chirality :  0.047   0.304    780
  Planarity :  0.005   0.038    927
  Dihedral  :  4.937  19.132    759
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.33), residues: 659
  helix: -3.53 (0.80), residues: 27
  sheet:  0.37 (0.32), residues: 253
  loop :  0.44 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  18 
 TYR   0.034   0.002   TYR H  99 
 PHE   0.022   0.002   PHE A 374 
 TRP   0.020   0.002   TRP B  96 
 HIS   0.003   0.002   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 5327)
  covalent geometry    : angle       0.67498 ( 7228)
  SS BOND              : bond        0.01038 (    7)
  SS BOND              : angle       1.65133 (   14)
  hydrogen bonds       : bond        0.03902 (  189)
  hydrogen bonds       : angle       6.12278 (  456)
  link_NAG-ASN         : bond        0.00029 (    1)
  link_NAG-ASN         : angle       1.89065 (    3)

*********************** 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
  139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8076 (tt0) cc_final: 0.7498 (tt0)
REVERT: H   73 ASP cc_start: 0.8308 (m-30) cc_final: 0.7719 (m-30)
REVERT: L   30 LEU cc_start: 0.8491 (tp) cc_final: 0.8194 (tp)
REVERT: L   30 TYR cc_start: 0.8195 (t80) cc_final: 0.7706 (t80)
REVERT: L   85 ILE cc_start: 0.8739 (mm) cc_final: 0.7915 (tt)
REVERT: A  402 ILE cc_start: 0.8911 (pt) cc_final: 0.8590 (pt)
REVERT: A  455 LEU cc_start: 0.8428 (tp) cc_final: 0.8128 (tp)
REVERT: B   46 LEU cc_start: 0.8457 (tp) cc_final: 0.8193 (tp)
REVERT: C   46 GLU cc_start: 0.8132 (tt0) cc_final: 0.7647 (tt0)
REVERT: C   71 ARG cc_start: 0.7557 (ppt170) cc_final: 0.7241 (ppt170)
REVERT: C   72 ASP cc_start: 0.8586 (t0) cc_final: 0.7429 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0662
  time to fit residues: 12.1847
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  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0270
   chunk 43 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0670
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.9578

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.092622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.079506 restraints weight = 18405.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.081777 restraints weight = 10476.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.083363 restraints weight = 7061.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.084455 restraints weight = 5319.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.085202 restraints weight = 4302.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.5395

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= 0.122
  Angle     :  0.592   9.733   7245  Z= 0.319
  Chirality :  0.046   0.266    780
  Planarity :  0.004   0.039    927
  Dihedral  :  4.639  18.225    759
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.33), residues: 659
  helix: -3.81 (0.64), residues: 27
  sheet:  0.43 (0.33), residues: 246
  loop :  0.35 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  24 
 TYR   0.024   0.001   TYR H  99 
 PHE   0.011   0.001   PHE B  71 
 TRP   0.009   0.001   TRP H 115 
 HIS   0.000   0.000   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5327)
  covalent geometry    : angle       0.58951 ( 7228)
  SS BOND              : bond        0.00708 (    7)
  SS BOND              : angle       1.19788 (   14)
  hydrogen bonds       : bond        0.03561 (  189)
  hydrogen bonds       : angle       5.93645 (  456)
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       1.46515 (    3)

*********************** 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
  136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.204 
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: 0.8105 (mmm) cc_final: 0.7809 (mmm)
REVERT: H   46 GLU cc_start: 0.8001 (tt0) cc_final: 0.7485 (tt0)
REVERT: H   82 MET cc_start: 0.7392 (mmm) cc_final: 0.6560 (tmm)
REVERT: H   82 ASN cc_start: 0.8531 (m-40) cc_final: 0.8138 (p0)
REVERT: L   30 TYR cc_start: 0.8278 (t80) cc_final: 0.7898 (t80)
REVERT: L   55 GLU cc_start: 0.5874 (pt0) cc_final: 0.5349 (pt0)
REVERT: A  402 ILE cc_start: 0.8852 (pt) cc_final: 0.8508 (pt)
REVERT: A  455 LEU cc_start: 0.8324 (tp) cc_final: 0.8104 (tp)
REVERT: A  468 ILE cc_start: 0.9074 (pt) cc_final: 0.8491 (mm)
REVERT: B   46 LEU cc_start: 0.8265 (tp) cc_final: 0.8063 (tp)
REVERT: C   46 GLU cc_start: 0.8163 (tt0) cc_final: 0.7695 (tt0)
REVERT: C   71 ARG cc_start: 0.7492 (ppt170) cc_final: 0.7264 (ppt170)
REVERT: C   72 ASP cc_start: 0.8545 (t0) cc_final: 0.7416 (t70)
REVERT: C   86 ASP cc_start: 0.7580 (m-30) cc_final: 0.7122 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0684
  time to fit residues: 12.1442
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  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    0.0870
   chunk 32 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 60 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    2.2164

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.091193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.077935 restraints weight = 18569.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.080138 restraints weight = 10855.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.081684 restraints weight = 7465.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.082708 restraints weight = 5671.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.083428 restraints weight = 4651.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5335  Z= 0.173
  Angle     :  0.614   8.481   7245  Z= 0.333
  Chirality :  0.045   0.211    780
  Planarity :  0.004   0.040    927
  Dihedral  :  4.801  22.610    759
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.33), residues: 659
  helix: -3.75 (0.67), residues: 27
  sheet:  0.39 (0.34), residues: 233
  loop :  0.22 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.026   0.002   TYR C  59 
 PHE   0.031   0.001   PHE H  67 
 TRP   0.025   0.002   TRP A 353 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 5327)
  covalent geometry    : angle       0.61155 ( 7228)
  SS BOND              : bond        0.00908 (    7)
  SS BOND              : angle       1.10120 (   14)
  hydrogen bonds       : bond        0.03673 (  189)
  hydrogen bonds       : angle       5.86173 (  456)
  link_NAG-ASN         : bond        0.00071 (    1)
  link_NAG-ASN         : angle       1.61713 (    3)

*********************** 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
  126 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8214 (mmm) cc_final: 0.7886 (mmm)
REVERT: H   43 LYS cc_start: 0.8614 (mppt) cc_final: 0.8093 (mppt)
REVERT: H   46 GLU cc_start: 0.7980 (tt0) cc_final: 0.7378 (tt0)
REVERT: L   30 TYR cc_start: 0.8388 (t80) cc_final: 0.7973 (t80)
REVERT: L   55 GLU cc_start: 0.5985 (pt0) cc_final: 0.5457 (pt0)
REVERT: L   85 ILE cc_start: 0.8649 (mm) cc_final: 0.7770 (tt)
REVERT: L  103 LYS cc_start: 0.8511 (tttt) cc_final: 0.7992 (tptt)
REVERT: A  402 ILE cc_start: 0.8910 (pt) cc_final: 0.8644 (pt)
REVERT: A  455 LEU cc_start: 0.8297 (tp) cc_final: 0.8092 (tp)
REVERT: B   36 TYR cc_start: 0.8661 (m-80) cc_final: 0.8412 (m-10)
REVERT: B   46 LEU cc_start: 0.8350 (tp) cc_final: 0.8124 (tp)
REVERT: C   46 GLU cc_start: 0.8242 (tt0) cc_final: 0.7548 (tt0)
REVERT: C   72 ASP cc_start: 0.8623 (t0) cc_final: 0.7385 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0699
  time to fit residues: 11.6010
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  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
** B  89 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 = 0.3571 r_free = 0.3571 target = 0.092266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.079185 restraints weight = 18231.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.081411 restraints weight = 10542.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.082970 restraints weight = 7209.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.083997 restraints weight = 5443.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.084739 restraints weight = 4432.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5335  Z= 0.126
  Angle     :  0.579   6.592   7245  Z= 0.314
  Chirality :  0.045   0.193    780
  Planarity :  0.004   0.041    927
  Dihedral  :  4.665  21.911    759
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.33), residues: 659
  helix: -3.73 (0.67), residues: 27
  sheet:  0.38 (0.34), residues: 235
  loop :  0.12 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 357 
 TYR   0.022   0.001   TYR H  99 
 PHE   0.027   0.001   PHE H  67 
 TRP   0.018   0.001   TRP C  50 
 HIS   0.001   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5327)
  covalent geometry    : angle       0.57802 ( 7228)
  SS BOND              : bond        0.00576 (    7)
  SS BOND              : angle       0.61699 (   14)
  hydrogen bonds       : bond        0.03453 (  189)
  hydrogen bonds       : angle       5.81447 (  456)
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       1.45039 (    3)

*********************** 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
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8177 (mmm) cc_final: 0.7821 (mpp)
REVERT: H   46 GLU cc_start: 0.7728 (tt0) cc_final: 0.7222 (tt0)
REVERT: H  114 TYR cc_start: 0.7673 (m-80) cc_final: 0.7288 (m-80)
REVERT: H  120 LEU cc_start: 0.8836 (tp) cc_final: 0.7885 (pp)
REVERT: L   24 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7967 (tmmt)
REVERT: L   30 TYR cc_start: 0.8389 (t80) cc_final: 0.7992 (t80)
REVERT: L   49 TYR cc_start: 0.6810 (p90) cc_final: 0.6449 (p90)
REVERT: L   85 ILE cc_start: 0.8656 (mm) cc_final: 0.7838 (tt)
REVERT: L   87 TYR cc_start: 0.8275 (m-80) cc_final: 0.7996 (m-10)
REVERT: L  103 LYS cc_start: 0.8525 (tttt) cc_final: 0.8021 (tptt)
REVERT: A  396 TYR cc_start: 0.7922 (m-80) cc_final: 0.7715 (m-80)
REVERT: A  402 ILE cc_start: 0.8930 (pt) cc_final: 0.8655 (pt)
REVERT: A  455 LEU cc_start: 0.8371 (tp) cc_final: 0.8121 (tp)
REVERT: B   36 TYR cc_start: 0.8624 (m-80) cc_final: 0.8381 (m-10)
REVERT: C   46 GLU cc_start: 0.8241 (tt0) cc_final: 0.7571 (tt0)
REVERT: C   47 TRP cc_start: 0.8596 (t60) cc_final: 0.8213 (t60)
REVERT: C   72 ASP cc_start: 0.8615 (t0) cc_final: 0.7408 (t70)
REVERT: C   86 ASP cc_start: 0.7476 (m-30) cc_final: 0.7052 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0637
  time to fit residues: 10.9126
Evaluate side-chains
  96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 28 optimal weight:    0.0570
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.2302

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
** B  89 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 = 0.3560 r_free = 0.3560 target = 0.091895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.078744 restraints weight = 18424.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.080919 restraints weight = 10763.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.082435 restraints weight = 7358.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.083453 restraints weight = 5578.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.084182 restraints weight = 4561.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.6039

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= 0.127
  Angle     :  0.584   5.936   7245  Z= 0.315
  Chirality :  0.045   0.175    780
  Planarity :  0.004   0.040    927
  Dihedral  :  4.597  21.922    759
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.33), residues: 659
  helix: -3.67 (0.71), residues: 27
  sheet:  0.36 (0.34), residues: 235
  loop :  0.06 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 357 
 TYR   0.018   0.002   TYR H  99 
 PHE   0.015   0.001   PHE H  67 
 TRP   0.009   0.001   TRP C  50 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5327)
  covalent geometry    : angle       0.58336 ( 7228)
  SS BOND              : bond        0.00577 (    7)
  SS BOND              : angle       0.55335 (   14)
  hydrogen bonds       : bond        0.03450 (  189)
  hydrogen bonds       : angle       5.78445 (  456)
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       1.43719 (    3)

*********************** 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
  131 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.132 
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   34 MET cc_start: 0.8151 (mmm) cc_final: 0.7832 (mpp)
REVERT: H   46 GLU cc_start: 0.7842 (tt0) cc_final: 0.7211 (tt0)
REVERT: H   73 ASP cc_start: 0.8421 (m-30) cc_final: 0.8110 (m-30)
REVERT: H  114 TYR cc_start: 0.7619 (m-80) cc_final: 0.7358 (m-80)
REVERT: H  120 LEU cc_start: 0.8821 (tp) cc_final: 0.7893 (pp)
REVERT: L   30 TYR cc_start: 0.8361 (t80) cc_final: 0.7924 (t80)
REVERT: L   49 TYR cc_start: 0.6986 (p90) cc_final: 0.6521 (p90)
REVERT: L   70 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: L  103 LYS cc_start: 0.8498 (tttt) cc_final: 0.7943 (tptt)
REVERT: A  402 ILE cc_start: 0.8939 (pt) cc_final: 0.8661 (pt)
REVERT: A  455 LEU cc_start: 0.8438 (tp) cc_final: 0.8174 (tp)
REVERT: B   46 LEU cc_start: 0.8219 (tp) cc_final: 0.7889 (tp)
REVERT: C   10 GLU cc_start: 0.7665 (pp20) cc_final: 0.7032 (pp20)
REVERT: C   46 GLU cc_start: 0.8322 (tt0) cc_final: 0.7596 (tt0)
REVERT: C   71 ARG cc_start: 0.7552 (ppt170) cc_final: 0.7202 (ppt170)
REVERT: C   72 ASP cc_start: 0.8579 (t0) cc_final: 0.7397 (t70)
REVERT: C   73 MET cc_start: 0.6893 (pmm) cc_final: 0.6597 (ppp)
REVERT: C   86 ASP cc_start: 0.7421 (m-30) cc_final: 0.7006 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0663
  time to fit residues: 11.0634
Evaluate side-chains
  99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    0.2980
   chunk 46 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.4386

-------------------------------------------------------------------------------
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**
** 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 = 0.3520 r_free = 0.3520 target = 0.089765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076456 restraints weight = 18838.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.078582 restraints weight = 11095.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080011 restraints weight = 7682.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.081046 restraints weight = 5908.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.081764 restraints weight = 4850.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.6226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5335  Z= 0.176
  Angle     :  0.622   6.072   7245  Z= 0.334
  Chirality :  0.046   0.223    780
  Planarity :  0.005   0.051    927
  Dihedral  :  4.785  21.904    759
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.33), residues: 659
  helix: -3.67 (0.73), residues: 27
  sheet:  0.25 (0.34), residues: 235
  loop : -0.07 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 357 
 TYR   0.021   0.002   TYR H  99 
 PHE   0.019   0.002   PHE H  67 
 TRP   0.018   0.002   TRP B  96 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5327)
  covalent geometry    : angle       0.62173 ( 7228)
  SS BOND              : bond        0.00482 (    7)
  SS BOND              : angle       0.56949 (   14)
  hydrogen bonds       : bond        0.03638 (  189)
  hydrogen bonds       : angle       5.91771 (  456)
  link_NAG-ASN         : bond        0.00005 (    1)
  link_NAG-ASN         : angle       1.71448 (    3)

********************** 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
  119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.202 
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   34 MET cc_start: 0.8148 (mmm) cc_final: 0.7813 (mmm)
REVERT: H   46 GLU cc_start: 0.8173 (tt0) cc_final: 0.7520 (tt0)
REVERT: H  120 LEU cc_start: 0.8813 (tp) cc_final: 0.7884 (pp)
REVERT: L  103 LYS cc_start: 0.8405 (tttt) cc_final: 0.7914 (tptt)
REVERT: A  402 ILE cc_start: 0.9003 (pt) cc_final: 0.8759 (pt)
REVERT: A  455 LEU cc_start: 0.8526 (tp) cc_final: 0.8234 (tp)
REVERT: B   46 LEU cc_start: 0.8167 (tp) cc_final: 0.7949 (tp)
REVERT: C   10 GLU cc_start: 0.7744 (pp20) cc_final: 0.7085 (pp20)
REVERT: C   46 GLU cc_start: 0.8187 (tt0) cc_final: 0.7548 (tt0)
REVERT: C   71 ARG cc_start: 0.7709 (ppt170) cc_final: 0.7294 (ppt170)
REVERT: C   72 ASP cc_start: 0.8609 (t0) cc_final: 0.7478 (t70)
REVERT: C   73 MET cc_start: 0.7008 (pmm) cc_final: 0.6696 (ppp)
REVERT: C   86 ASP cc_start: 0.7565 (m-30) cc_final: 0.7113 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0650
  time to fit residues: 10.1829
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  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
H 117 GLN
** L  30DASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS
C   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.087385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.073938 restraints weight = 19104.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.076122 restraints weight = 11190.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.077528 restraints weight = 7713.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.078561 restraints weight = 5934.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.079303 restraints weight = 4883.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.6372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5335  Z= 0.223
  Angle     :  0.665   6.453   7245  Z= 0.356
  Chirality :  0.046   0.154    780
  Planarity :  0.005   0.054    927
  Dihedral  :  5.091  22.387    759
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.33), residues: 659
  helix: -3.65 (0.77), residues: 27
  sheet:  0.03 (0.34), residues: 236
  loop : -0.22 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 357 
 TYR   0.027   0.002   TYR H  99 
 PHE   0.028   0.002   PHE H  67 
 TRP   0.025   0.002   TRP B  96 
 HIS   0.005   0.002   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 5327)
  covalent geometry    : angle       0.66415 ( 7228)
  SS BOND              : bond        0.00465 (    7)
  SS BOND              : angle       0.74694 (   14)
  hydrogen bonds       : bond        0.03821 (  189)
  hydrogen bonds       : angle       6.10565 (  456)
  link_NAG-ASN         : bond        0.00062 (    1)
  link_NAG-ASN         : angle       1.93299 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1093.75 seconds
wall clock time: 19 minutes 36.81 seconds (1176.81 seconds total)