Starting phenix.real_space_refine
on Thu Jul  2 01:27:28 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8d8q_27254/07_2026/8d8q_27254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/07_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_27254/07_2026/8d8q_27254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2026/8d8q_27254.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2026/8d8q_27254.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2026/8d8q_27254.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2026/8d8q_27254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_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-6108/lib/python3.11/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 chiralities: 1
  Time building chain proxies: 1.27, per 1000 atoms: 0.24
  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: 0.39
  Conformation dependent library (CDL) restraints added in 153.5 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: 0.18
  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: 0.82

  Time building geometry restraints manager: 0.56 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: 2992
       16.62 -    33.25: 85
       33.25 -    49.87: 24
       49.87 -    66.49: 18
       66.49 -    83.11: 8
  Dihedral angle restraints: 3127
    sinusoidal: 1211
      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 3124 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:             12.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     6.510
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
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  : 11.072  83.112   1896
  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/Z
  covalent geometry    : bond        0.01151 /  0.62 ( 5327)
  covalent geometry    : angle       1.22975 /  0.85 ( 7228)
  SS BOND              : bond        0.04585 /  2.73 (    7)
  SS BOND              : angle       2.97151 /  1.55 (   14)
  hydrogen bonds       : bond        0.18854 / 12.40 (  189)
  hydrogen bonds       : angle       8.72196 /  5.96 (  456)
  link_NAG-ASN         : bond        0.06470 /  3.41 (    1)
  link_NAG-ASN         : angle       1.49950 /  0.86 (    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  : 0.200 
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: 0.0934
  time to fit residues: 26.6762
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  : 0.200 
-------------------------------------------------------------------------------
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...
** 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 = 0.3603 r_free = 0.3603 target = 0.094167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.080740 restraints weight = 18060.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.083093 restraints weight = 10385.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.084733 restraints weight = 7021.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.085850 restraints weight = 5283.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.086651 restraints weight = 4268.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5335  Z= 0.160
  Angle     :  0.668  10.829   7245  Z= 0.358
  Chirality :  0.049   0.289    780
  Planarity :  0.005   0.044    927
  Dihedral  :  5.043  19.516    738
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  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:  1.18 (0.33), residues: 659
  helix: -3.74 (0.62), residues: 33
  sheet:  0.60 (0.31), residues: 250
  loop :  1.61 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.018   0.002   TYR L  49 
 PHE   0.020   0.002   PHE C  29 
 TRP   0.016   0.002   TRP H 115 
 HIS   0.002   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 ( 5327)
  covalent geometry    : angle       0.66418 /  0.36 ( 7228)
  SS BOND              : bond        0.00491 /  0.25 (    7)
  SS BOND              : angle       1.21456 /  0.60 (   14)
  hydrogen bonds       : bond        0.04498 /  3.03 (  189)
  hydrogen bonds       : angle       6.62402 /  4.62 (  456)
  link_NAG-ASN         : bond        0.00176 /  0.09 (    1)
  link_NAG-ASN         : angle       2.87685 /  1.67 (    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  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7796 (mmm) cc_final: 0.7497 (mmm)
REVERT: H   39 GLN cc_start: 0.7756 (pp30) cc_final: 0.7365 (pp30)
REVERT: H   43 LYS cc_start: 0.8510 (mptt) cc_final: 0.8294 (mmtm)
REVERT: H  111 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7676 (mttt)
REVERT: H  113 ASP cc_start: 0.7106 (t70) cc_final: 0.6579 (p0)
REVERT: H  120 LEU cc_start: 0.8551 (tp) cc_final: 0.7778 (pp)
REVERT: L    3 VAL cc_start: 0.8247 (t) cc_final: 0.8016 (m)
REVERT: L   15 LEU cc_start: 0.8238 (mt) cc_final: 0.7534 (mt)
REVERT: L  103 LYS cc_start: 0.8588 (tttt) cc_final: 0.8000 (tptm)
REVERT: A  355 ARG cc_start: 0.7455 (ttt90) cc_final: 0.7186 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8559 (m-30) cc_final: 0.8303 (m-30)
REVERT: A  402 ILE cc_start: 0.8815 (pt) cc_final: 0.8533 (pt)
REVERT: A  422 ASN cc_start: 0.8936 (m-40) cc_final: 0.8134 (m-40)
REVERT: B   49 TYR cc_start: 0.7544 (p90) cc_final: 0.7321 (p90)
REVERT: B  105 GLU cc_start: 0.4642 (tp30) cc_final: 0.4154 (tp30)
REVERT: C   18 VAL cc_start: 0.8744 (p) cc_final: 0.8434 (p)
REVERT: C   36 TRP cc_start: 0.8922 (m100) cc_final: 0.8620 (m100)
REVERT: C   46 GLU cc_start: 0.8220 (tt0) cc_final: 0.7751 (tp30)
REVERT: C   71 ARG cc_start: 0.7771 (pmt-80) cc_final: 0.7031 (pmt-80)
REVERT: C   72 ASP cc_start: 0.8561 (t0) cc_final: 0.7854 (t70)
REVERT: C   73 MET cc_start: 0.6902 (pmm) cc_final: 0.6168 (pmm)
REVERT: C   82 LEU cc_start: 0.7934 (tp) cc_final: 0.7573 (tp)
REVERT: C   91 TYR cc_start: 0.9085 (m-80) cc_final: 0.8821 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0767
  time to fit residues: 17.1600
Evaluate side-chains
  111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.092329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.079071 restraints weight = 18115.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.081322 restraints weight = 10603.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.082937 restraints weight = 7208.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.084013 restraints weight = 5446.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.084750 restraints weight = 4437.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5335  Z= 0.169
  Angle     :  0.623   9.586   7245  Z= 0.339
  Chirality :  0.045   0.231    780
  Planarity :  0.005   0.041    927
  Dihedral  :  4.788  19.490    738
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.88 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.77 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.73 (0.33), residues: 659
  helix: -3.98 (0.50), residues: 33
  sheet:  0.49 (0.32), residues: 242
  loop :  1.12 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.024   0.002   TYR H  99 
 PHE   0.023   0.002   PHE H  67 
 TRP   0.016   0.002   TRP B  96 
 HIS   0.002   0.001   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.17 ( 5327)
  covalent geometry    : angle       0.61827 /  0.34 ( 7228)
  SS BOND              : bond        0.01357 /  0.68 (    7)
  SS BOND              : angle       1.77231 /  0.82 (   14)
  hydrogen bonds       : bond        0.04087 /  2.76 (  189)
  hydrogen bonds       : angle       6.12186 /  4.25 (  456)
  link_NAG-ASN         : bond        0.00030 /  0.02 (    1)
  link_NAG-ASN         : angle       1.58381 /  0.92 (    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
  151 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8071 (mmm) cc_final: 0.7657 (mmm)
REVERT: H   39 GLN cc_start: 0.7784 (pp30) cc_final: 0.7101 (pp30)
REVERT: H   67 PHE cc_start: 0.5891 (m-80) cc_final: 0.5376 (m-80)
REVERT: L    3 VAL cc_start: 0.8147 (t) cc_final: 0.7941 (m)
REVERT: L   30 LEU cc_start: 0.8537 (tp) cc_final: 0.8175 (tp)
REVERT: L   30 TYR cc_start: 0.8093 (t80) cc_final: 0.7513 (t80)
REVERT: L   48 MET cc_start: 0.7574 (tpp) cc_final: 0.6824 (mmm)
REVERT: L   58 VAL cc_start: 0.8145 (p) cc_final: 0.7942 (p)
REVERT: A  355 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7227 (ttp-170)
REVERT: B   17 GLU cc_start: 0.8609 (mp0) cc_final: 0.8345 (mp0)
REVERT: B   46 LEU cc_start: 0.8513 (tp) cc_final: 0.8298 (tp)
REVERT: C   36 TRP cc_start: 0.9042 (m100) cc_final: 0.8812 (m100)
REVERT: C   46 GLU cc_start: 0.8160 (tt0) cc_final: 0.7853 (tt0)
REVERT: C   56 ASN cc_start: 0.7680 (m110) cc_final: 0.7358 (m-40)
REVERT: C   57 THR cc_start: 0.8742 (p) cc_final: 0.8538 (p)
REVERT: C   71 ARG cc_start: 0.7751 (pmt-80) cc_final: 0.7117 (pmt-80)
REVERT: C   72 ASP cc_start: 0.8617 (t0) cc_final: 0.7583 (t70)
REVERT: C   73 MET cc_start: 0.7067 (pmm) cc_final: 0.6561 (pmm)
REVERT: C   82 LEU cc_start: 0.8054 (tp) cc_final: 0.7822 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0671
  time to fit residues: 13.2271
Evaluate side-chains
  108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0870
   overall best weight:    3.4164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.088418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.075180 restraints weight = 18207.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.077393 restraints weight = 10555.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.078911 restraints weight = 7236.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079949 restraints weight = 5504.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.080684 restraints weight = 4499.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   5335  Z= 0.236
  Angle     :  0.691   8.739   7245  Z= 0.377
  Chirality :  0.049   0.298    780
  Planarity :  0.005   0.042    927
  Dihedral  :  5.157  20.362    738
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.01 %
    Favored  : 96.81 %
  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:  0.13 (0.33), residues: 659
  helix: -3.96 (0.59), residues: 33
  sheet:  0.31 (0.32), residues: 245
  loop :  0.47 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 357 
 TYR   0.040   0.003   TYR H  99 
 PHE   0.024   0.002   PHE A 515 
 TRP   0.026   0.003   TRP A 353 
 HIS   0.003   0.001   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.24 ( 5327)
  covalent geometry    : angle       0.68496 /  0.37 ( 7228)
  SS BOND              : bond        0.01348 /  0.68 (    7)
  SS BOND              : angle       2.07403 /  0.95 (   14)
  hydrogen bonds       : bond        0.04189 /  2.90 (  189)
  hydrogen bonds       : angle       6.02208 /  4.24 (  456)
  link_NAG-ASN         : bond        0.00070 /  0.04 (    1)
  link_NAG-ASN         : angle       2.05094 /  1.10 (    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
  146 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8137 (tt0) cc_final: 0.7627 (tt0)
REVERT: H   67 PHE cc_start: 0.6395 (m-80) cc_final: 0.6053 (m-80)
REVERT: L    4 MET cc_start: 0.7662 (tpt) cc_final: 0.7398 (tpt)
REVERT: L  103 LYS cc_start: 0.8434 (tttt) cc_final: 0.7884 (tptm)
REVERT: A  355 ARG cc_start: 0.7632 (ttt90) cc_final: 0.7205 (ttp-170)
REVERT: A  455 LEU cc_start: 0.8600 (tp) cc_final: 0.8351 (tp)
REVERT: A  464 PHE cc_start: 0.8344 (m-80) cc_final: 0.8085 (m-80)
REVERT: B   46 LEU cc_start: 0.8481 (tp) cc_final: 0.8241 (tp)
REVERT: C   46 GLU cc_start: 0.8091 (tt0) cc_final: 0.7555 (tt0)
REVERT: C   72 ASP cc_start: 0.8600 (t0) cc_final: 0.7418 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0585
  time to fit residues: 11.2964
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 50 optimal weight:    8.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    2.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.089007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075788 restraints weight = 18661.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077982 restraints weight = 10910.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.079512 restraints weight = 7502.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.080527 restraints weight = 5702.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.081282 restraints weight = 4670.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.5520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5335  Z= 0.200
  Angle     :  0.659  12.783   7245  Z= 0.358
  Chirality :  0.047   0.304    780
  Planarity :  0.005   0.054    927
  Dihedral  :  5.144  19.786    738
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  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:  0.03 (0.32), residues: 659
  helix: -3.95 (0.59), residues: 27
  sheet:  0.30 (0.33), residues: 239
  loop :  0.27 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.033   0.002   TYR H  99 
 PHE   0.017   0.002   PHE A 374 
 TRP   0.012   0.002   TRP H 115 
 HIS   0.001   0.001   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.20 ( 5327)
  covalent geometry    : angle       0.65070 /  0.35 ( 7228)
  SS BOND              : bond        0.01278 /  0.64 (    7)
  SS BOND              : angle       2.38653 /  1.08 (   14)
  hydrogen bonds       : bond        0.03889 /  2.64 (  189)
  hydrogen bonds       : angle       6.02987 /  4.27 (  456)
  link_NAG-ASN         : bond        0.00003 /  0.00 (    1)
  link_NAG-ASN         : angle       1.88769 /  1.01 (    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
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.243 
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: 0.8211 (mmm) cc_final: 0.7878 (mmm)
REVERT: H   46 GLU cc_start: 0.8138 (tt0) cc_final: 0.7630 (tt0)
REVERT: H   67 PHE cc_start: 0.6352 (m-80) cc_final: 0.6066 (m-80)
REVERT: A  355 ARG cc_start: 0.7597 (ttt90) cc_final: 0.7212 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8867 (pt) cc_final: 0.8599 (pt)
REVERT: A  455 LEU cc_start: 0.8621 (tp) cc_final: 0.8265 (tp)
REVERT: A  464 PHE cc_start: 0.8284 (m-80) cc_final: 0.8014 (m-80)
REVERT: C   29 PHE cc_start: 0.8484 (t80) cc_final: 0.8225 (t80)
REVERT: C   46 GLU cc_start: 0.8104 (tt0) cc_final: 0.7640 (tt0)
REVERT: C   72 ASP cc_start: 0.8614 (t0) cc_final: 0.7419 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0710
  time to fit residues: 12.1183
Evaluate side-chains
  94 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
** L  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 = 0.3491 r_free = 0.3491 target = 0.088893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.075811 restraints weight = 18576.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.078024 restraints weight = 10821.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.079544 restraints weight = 7407.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.080592 restraints weight = 5618.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.081346 restraints weight = 4574.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.5768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5335  Z= 0.182
  Angle     :  0.631   9.110   7245  Z= 0.342
  Chirality :  0.046   0.225    780
  Planarity :  0.004   0.041    927
  Dihedral  :  5.093  22.798    738
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.21 (0.32), residues: 659
  helix: -3.91 (0.61), residues: 27
  sheet:  0.21 (0.32), residues: 242
  loop :  0.03 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 357 
 TYR   0.030   0.002   TYR H  99 
 PHE   0.013   0.002   PHE A 374 
 TRP   0.024   0.002   TRP C  50 
 HIS   0.004   0.002   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 ( 5327)
  covalent geometry    : angle       0.62890 /  0.34 ( 7228)
  SS BOND              : bond        0.00724 /  0.36 (    7)
  SS BOND              : angle       0.90628 /  0.47 (   14)
  hydrogen bonds       : bond        0.03764 /  2.57 (  189)
  hydrogen bonds       : angle       6.10465 /  4.31 (  456)
  link_NAG-ASN         : bond        0.00061 /  0.03 (    1)
  link_NAG-ASN         : angle       1.94302 /  1.05 (    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
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.211 
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: 0.8104 (mmm) cc_final: 0.7741 (mmm)
REVERT: H   46 GLU cc_start: 0.8061 (tt0) cc_final: 0.7520 (tt0)
REVERT: L   85 ILE cc_start: 0.8697 (mm) cc_final: 0.7979 (tp)
REVERT: A  355 ARG cc_start: 0.7509 (ttt90) cc_final: 0.7215 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8972 (pt) cc_final: 0.8701 (pt)
REVERT: A  455 LEU cc_start: 0.8605 (tp) cc_final: 0.8308 (tp)
REVERT: A  464 PHE cc_start: 0.8285 (m-80) cc_final: 0.8009 (m-80)
REVERT: A  468 ILE cc_start: 0.9068 (pt) cc_final: 0.8520 (mm)
REVERT: C   10 GLU cc_start: 0.7528 (pp20) cc_final: 0.6878 (pp20)
REVERT: C   46 GLU cc_start: 0.8187 (tt0) cc_final: 0.7600 (tt0)
REVERT: C   72 ASP cc_start: 0.8797 (t0) cc_final: 0.7651 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0736
  time to fit residues: 12.4610
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  : 0.200 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0060
   chunk 42 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 19 optimal weight:    0.4980
   chunk 52 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.2598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
L  89 GLN
A 481 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.090243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.076864 restraints weight = 18718.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.079129 restraints weight = 10896.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.080690 restraints weight = 7476.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.081771 restraints weight = 5690.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.082567 restraints weight = 4647.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5335  Z= 0.130
  Angle     :  0.597   7.285   7245  Z= 0.324
  Chirality :  0.046   0.244    780
  Planarity :  0.004   0.041    927
  Dihedral  :  4.875  20.513    738
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.21 (0.32), residues: 659
  helix: -3.89 (0.65), residues: 27
  sheet:  0.28 (0.33), residues: 240
  loop : -0.04 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.042   0.002   PHE H  67 
 TRP   0.026   0.002   TRP A 353 
 HIS   0.002   0.001   HIS B  90 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 5327)
  covalent geometry    : angle       0.59568 /  0.32 ( 7228)
  SS BOND              : bond        0.00634 /  0.31 (    7)
  SS BOND              : angle       0.72466 /  0.39 (   14)
  hydrogen bonds       : bond        0.03586 /  2.40 (  189)
  hydrogen bonds       : angle       5.88206 /  4.16 (  456)
  link_NAG-ASN         : bond        0.00039 /  0.02 (    1)
  link_NAG-ASN         : angle       1.69129 /  0.92 (    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
  134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.246 
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: 0.8091 (mmm) cc_final: 0.7745 (mpp)
REVERT: H   46 GLU cc_start: 0.7894 (tt0) cc_final: 0.7345 (tt0)
REVERT: H  120 LEU cc_start: 0.8898 (tp) cc_final: 0.7974 (pp)
REVERT: L   85 ILE cc_start: 0.8694 (mm) cc_final: 0.8046 (tp)
REVERT: A  355 ARG cc_start: 0.7514 (ttt90) cc_final: 0.7287 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8904 (pt) cc_final: 0.8640 (pt)
REVERT: A  409 GLN cc_start: 0.8446 (mp10) cc_final: 0.8005 (mp10)
REVERT: A  455 LEU cc_start: 0.8616 (tp) cc_final: 0.8323 (tp)
REVERT: A  464 PHE cc_start: 0.8269 (m-80) cc_final: 0.8058 (m-80)
REVERT: B   71 PHE cc_start: 0.7626 (m-10) cc_final: 0.7215 (m-80)
REVERT: C   36 TRP cc_start: 0.9272 (m100) cc_final: 0.8682 (m100)
REVERT: C   46 GLU cc_start: 0.8134 (tt0) cc_final: 0.7543 (tt0)
REVERT: C   72 ASP cc_start: 0.8596 (t0) cc_final: 0.7464 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.0568
  time to fit residues: 10.1151
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.089606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.076041 restraints weight = 18569.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.078248 restraints weight = 10931.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.079776 restraints weight = 7583.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.080871 restraints weight = 5793.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.081634 restraints weight = 4749.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.6155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5335  Z= 0.161
  Angle     :  0.618   6.235   7245  Z= 0.334
  Chirality :  0.045   0.156    780
  Planarity :  0.004   0.041    927
  Dihedral  :  4.978  21.625    738
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  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: -0.27 (0.32), residues: 659
  helix: -3.84 (0.69), residues: 27
  sheet:  0.25 (0.33), residues: 235
  loop : -0.08 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.025   0.002   TYR H  99 
 PHE   0.030   0.002   PHE H  67 
 TRP   0.023   0.002   TRP C  50 
 HIS   0.001   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 ( 5327)
  covalent geometry    : angle       0.61670 /  0.33 ( 7228)
  SS BOND              : bond        0.00577 /  0.29 (    7)
  SS BOND              : angle       0.78701 /  0.43 (   14)
  hydrogen bonds       : bond        0.03610 /  2.45 (  189)
  hydrogen bonds       : angle       5.87762 /  4.14 (  456)
  link_NAG-ASN         : bond        0.00026 /  0.01 (    1)
  link_NAG-ASN         : angle       1.75922 /  0.96 (    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
  124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.152 
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: symmetry clash
REVERT: H   34 MET cc_start: 0.8089 (mmm) cc_final: 0.7711 (mmm)
REVERT: H   46 GLU cc_start: 0.7844 (tt0) cc_final: 0.7201 (tt0)
REVERT: H   67 PHE cc_start: 0.6367 (m-80) cc_final: 0.5313 (m-80)
REVERT: H  120 LEU cc_start: 0.8892 (tp) cc_final: 0.7975 (pp)
REVERT: A  355 ARG cc_start: 0.7418 (ttt90) cc_final: 0.7176 (ttp-170)
REVERT: A  455 LEU cc_start: 0.8725 (tp) cc_final: 0.8449 (tp)
REVERT: B   67 SER cc_start: 0.8412 (m) cc_final: 0.7915 (p)
REVERT: C   10 GLU cc_start: 0.7874 (pp20) cc_final: 0.7465 (pp20)
REVERT: C   46 GLU cc_start: 0.7975 (tt0) cc_final: 0.7287 (tt0)
REVERT: C   72 ASP cc_start: 0.8597 (t0) cc_final: 0.7520 (t70)
REVERT: C   85 GLU cc_start: 0.8364 (pm20) cc_final: 0.8021 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0673
  time to fit residues: 10.9342
Evaluate side-chains
  90 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
A 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.090725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.077225 restraints weight = 18668.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.079488 restraints weight = 11033.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.081036 restraints weight = 7588.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.082106 restraints weight = 5790.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.082893 restraints weight = 4762.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5335  Z= 0.133
  Angle     :  0.603   6.883   7245  Z= 0.328
  Chirality :  0.045   0.161    780
  Planarity :  0.004   0.042    927
  Dihedral  :  4.907  23.990    738
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.53 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.29 (0.33), residues: 659
  helix: -3.89 (0.68), residues: 27
  sheet:  0.31 (0.33), residues: 235
  loop : -0.15 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 357 
 TYR   0.023   0.001   TYR H  99 
 PHE   0.025   0.001   PHE H  67 
 TRP   0.019   0.002   TRP C  50 
 HIS   0.001   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 5327)
  covalent geometry    : angle       0.60200 /  0.33 ( 7228)
  SS BOND              : bond        0.00599 /  0.30 (    7)
  SS BOND              : angle       0.85682 /  0.45 (   14)
  hydrogen bonds       : bond        0.03450 /  2.29 (  189)
  hydrogen bonds       : angle       5.92725 /  4.15 (  456)
  link_NAG-ASN         : bond        0.00038 /  0.02 (    1)
  link_NAG-ASN         : angle       1.63220 /  0.89 (    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
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.201 
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: 0.8152 (mmm) cc_final: 0.7768 (mmm)
REVERT: H   46 GLU cc_start: 0.7839 (tt0) cc_final: 0.7229 (tt0)
REVERT: H   63 VAL cc_start: 0.8371 (m) cc_final: 0.7987 (m)
REVERT: H   67 PHE cc_start: 0.6237 (m-80) cc_final: 0.5427 (m-80)
REVERT: H  120 LEU cc_start: 0.8857 (tp) cc_final: 0.7957 (pp)
REVERT: L   70 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8154 (mm-30)
REVERT: L   85 ILE cc_start: 0.8627 (mm) cc_final: 0.7974 (tp)
REVERT: A  455 LEU cc_start: 0.8726 (tp) cc_final: 0.8394 (tp)
REVERT: A  464 PHE cc_start: 0.8269 (m-80) cc_final: 0.8036 (m-80)
REVERT: C   36 TRP cc_start: 0.9236 (m100) cc_final: 0.8742 (m100)
REVERT: C   46 GLU cc_start: 0.7988 (tt0) cc_final: 0.7237 (tt0)
REVERT: C   58 ASN cc_start: 0.7125 (m-40) cc_final: 0.6557 (t0)
REVERT: C   72 ASP cc_start: 0.8639 (t0) cc_final: 0.7623 (t70)
REVERT: C   85 GLU cc_start: 0.8190 (pm20) cc_final: 0.7911 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0729
  time to fit residues: 12.6309
Evaluate side-chains
  103 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 42 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  30EASN
B  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.090002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.076544 restraints weight = 18784.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.078725 restraints weight = 11234.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.080234 restraints weight = 7862.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.081256 restraints weight = 6070.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.081987 restraints weight = 5030.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.6412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5335  Z= 0.140
  Angle     :  0.613   6.123   7245  Z= 0.331
  Chirality :  0.045   0.150    780
  Planarity :  0.005   0.057    927
  Dihedral  :  4.865  24.384    738
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.40 (0.33), residues: 659
  helix: -3.88 (0.69), residues: 27
  sheet:  0.26 (0.33), residues: 241
  loop : -0.25 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 357 
 TYR   0.020   0.002   TYR H  99 
 PHE   0.022   0.002   PHE H  67 
 TRP   0.022   0.002   TRP A 353 
 HIS   0.001   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 5327)
  covalent geometry    : angle       0.61162 /  0.33 ( 7228)
  SS BOND              : bond        0.00542 /  0.27 (    7)
  SS BOND              : angle       0.73715 /  0.40 (   14)
  hydrogen bonds       : bond        0.03511 /  2.34 (  189)
  hydrogen bonds       : angle       5.80873 /  4.05 (  456)
  link_NAG-ASN         : bond        0.00020 /  0.01 (    1)
  link_NAG-ASN         : angle       1.61527 /  0.88 (    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
  129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.199 
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: 0.8155 (mmm) cc_final: 0.7789 (mmm)
REVERT: H   46 GLU cc_start: 0.7855 (tt0) cc_final: 0.7583 (tt0)
REVERT: H   63 VAL cc_start: 0.8349 (m) cc_final: 0.7990 (m)
REVERT: H   67 PHE cc_start: 0.6348 (m-80) cc_final: 0.5589 (m-80)
REVERT: H  120 LEU cc_start: 0.8849 (tp) cc_final: 0.7954 (pp)
REVERT: L   85 ILE cc_start: 0.8631 (mm) cc_final: 0.7849 (tt)
REVERT: A  455 LEU cc_start: 0.8722 (tp) cc_final: 0.8407 (tp)
REVERT: C   36 TRP cc_start: 0.9232 (m100) cc_final: 0.8749 (m100)
REVERT: C   46 GLU cc_start: 0.7971 (tt0) cc_final: 0.7254 (tt0)
REVERT: C   72 ASP cc_start: 0.8526 (t0) cc_final: 0.7586 (t70)
REVERT: C   85 GLU cc_start: 0.8177 (pm20) cc_final: 0.7866 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0684
  time to fit residues: 11.4389
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  : 0.200 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 55 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.4384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 117 GLN
L  30EASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.088874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.075449 restraints weight = 18882.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.077625 restraints weight = 11316.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.079094 restraints weight = 7938.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.080125 restraints weight = 6152.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.080833 restraints weight = 5096.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.6549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5335  Z= 0.176
  Angle     :  0.629   5.652   7245  Z= 0.343
  Chirality :  0.045   0.145    780
  Planarity :  0.005   0.062    927
  Dihedral  :  5.024  25.100    738
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.50 (0.33), residues: 659
  helix: -3.92 (0.66), residues: 27
  sheet:  0.24 (0.34), residues: 234
  loop : -0.37 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 357 
 TYR   0.022   0.002   TYR H  99 
 PHE   0.022   0.002   PHE H  67 
 TRP   0.025   0.002   TRP C  50 
 HIS   0.001   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.18 ( 5327)
  covalent geometry    : angle       0.62741 /  0.34 ( 7228)
  SS BOND              : bond        0.00518 /  0.26 (    7)
  SS BOND              : angle       0.80648 /  0.45 (   14)
  hydrogen bonds       : bond        0.03630 /  2.45 (  189)
  hydrogen bonds       : angle       5.97515 /  4.16 (  456)
  link_NAG-ASN         : bond        0.00044 /  0.02 (    1)
  link_NAG-ASN         : angle       1.75562 /  0.94 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1169.19 seconds
wall clock time: 21 minutes 0.10 seconds (1260.10 seconds total)