Starting phenix.real_space_refine
on Thu Oct 22 18:11:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xgw_66860/10_2026/9xgw_66860.cif"
  }
  resolution = 3.2
  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=   0.034
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      13      5.16       5
     C    2065      2.51       5
     N     547      2.21       5
     O     632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3257
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 978
          Classifications: {'peptide': 127}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "B"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 811
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "E"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1454
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 9, 'TRANS': 172}
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.85, per 1000 atoms: 0.26
  Number of scatterers: 3257
  At special positions: 0
  Unit cell: (81.606, 69.412, 68.474, 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      13     16.00
     O     632      8.00
     N     547      7.00
     C    2065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 87.4 milliseconds
  

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 7 sheets defined
      11.5% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 65
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 4.013A  pdb=" N   THR A  91 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.769A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 372
      removed outlier: 4.228A  pdb=" N   TYR E 369 " --> pdb=" O   TYR E 365 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA E 372 " --> pdb=" O   LEU E 368 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
    Processing helix  chain 'E' and resid 405 through 410
      removed outlier: 4.122A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE E 410 " --> pdb=" O   VAL E 407 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.311A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   MET A  34 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLY A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL A  48 " --> pdb=" O   TYR A  60 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   TYR A  60 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLY A  50 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6
      removed outlier: 3.876A  pdb=" N   ARG B  24 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.977A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA B  35 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   LEU B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR B  50 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 20
    Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'E' and resid 452 through 454

    85 hydrogen bonds defined for protein.
    198 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: 0.35

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1048
        1.34 -     1.46: 871
        1.46 -     1.58: 1405
        1.58 -     1.70: 0
        1.70 -     1.82: 15
  Bond restraints: 3339
  Sorted by residual:
  bond pdb=" C1  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.58e+00
  bond pdb=" C5  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.28e+00
  bond pdb=" C3  NAG E 601 "
       pdb=" O3  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.87e-01
  bond pdb=" C2  NAG E 601 "
       pdb=" N2  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.455 -0.016 2.00e-02 2.50e+03 6.15e-01
  bond pdb=" C   TYR E 396 "
       pdb=" O   TYR E 396 "
    ideal  model  delta    sigma   weight residual
    1.232  1.224  0.008 1.01e-02 9.80e+03 6.13e-01
  ... (remaining 3334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 4387
        1.25 -     2.51: 114
        2.51 -     3.76: 25
        3.76 -     5.02: 2
        5.02 -     6.27: 3
  Bond angle restraints: 4531
  Sorted by residual:
  angle pdb=" N   ASP A 108 "
        pdb=" CA  ASP A 108 "
        pdb=" C   ASP A 108 "
      ideal   model   delta    sigma   weight residual
     112.93  109.48    3.45 1.33e+00 5.65e-01 6.72e+00
  angle pdb=" N   GLN B  91 "
        pdb=" CA  GLN B  91 "
        pdb=" C   GLN B  91 "
      ideal   model   delta    sigma   weight residual
     107.61  111.63   -4.02 1.74e+00 3.30e-01 5.34e+00
  angle pdb=" C   ASN E 394 "
        pdb=" N   VAL E 395 "
        pdb=" CA  VAL E 395 "
      ideal   model   delta    sigma   weight residual
     120.91  118.05    2.86 1.39e+00 5.18e-01 4.23e+00
  angle pdb=" N   VAL E 395 "
        pdb=" CA  VAL E 395 "
        pdb=" C   VAL E 395 "
      ideal   model   delta    sigma   weight residual
     109.58  107.05    2.53 1.29e+00 6.01e-01 3.86e+00
  angle pdb=" N   TYR A 107 "
        pdb=" CA  TYR A 107 "
        pdb=" C   TYR A 107 "
      ideal   model   delta    sigma   weight residual
     113.37  110.69    2.68 1.38e+00 5.25e-01 3.78e+00
  ... (remaining 4526 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.52: 1777
       12.52 -    25.04: 141
       25.04 -    37.56: 33
       37.56 -    50.08: 9
       50.08 -    62.59: 7
  Dihedral angle restraints: 1967
    sinusoidal: 776
      harmonic: 1191
  Sorted by residual:
  dihedral pdb=" CA  SER B  95 "
           pdb=" C   SER B  95 "
           pdb=" N   LEU B  96 "
           pdb=" CA  LEU B  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TYR E 396 "
           pdb=" C   TYR E 396 "
           pdb=" N   ALA E 397 "
           pdb=" CA  ALA E 397 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.27  -15.73     0      5.00e+00 4.00e-02 9.89e+00
  dihedral pdb=" CA  ASP E 420 "
           pdb=" C   ASP E 420 "
           pdb=" N   TYR E 421 "
           pdb=" CA  TYR E 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.34  -15.66     0      5.00e+00 4.00e-02 9.81e+00
  ... (remaining 1964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 265
       0.026 -    0.052: 132
       0.052 -    0.079: 43
       0.079 -    0.105: 24
       0.105 -    0.131: 15
  Chirality restraints: 479
  Sorted by residual:
  chirality pdb=" CA  VAL A  37 "
            pdb=" N   VAL A  37 "
            pdb=" C   VAL A  37 "
            pdb=" CB  VAL A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  ILE B  76 "
            pdb=" N   ILE B  76 "
            pdb=" C   ILE B  76 "
            pdb=" CB  ILE B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  ILE E 358 "
            pdb=" N   ILE E 358 "
            pdb=" C   ILE E 358 "
            pdb=" CB  ILE E 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  ... (remaining 476 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO E 463 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 478 "    0.016 5.00e-02 4.00e+02   2.47e-02 9.77e-01
        pdb=" N   PRO E 479 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO E 479 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 479 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  95 "   -0.005 2.00e-02 2.50e+03   9.61e-03 9.23e-01
        pdb=" C   SER B  95 "    0.017 2.00e-02 2.50e+03
        pdb=" O   SER B  95 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   LEU B  96 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 945
        2.81 -     3.33: 2691
        3.33 -     3.86: 5226
        3.86 -     4.38: 6307
        4.38 -     4.90: 10826
  Nonbonded interactions: 25995
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  37 "
            pdb=" OE1 GLN B  90 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER B   7 "
            pdb=" OG1 THR B 104 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" NE  ARG B  62 "
            pdb=" OD2 ASP B  83 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" O   SER B  32 "
            pdb=" OG  SER B  32 "
     model   vdw
     2.482 3.040
  nonbonded pdb=" NH2 ARG E 355 "
            pdb=" OD2 ASP E 398 "
     model   vdw
     2.488 3.120
  ... (remaining 25990 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.180
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
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      :  0.003   0.025   3345  Z= 0.122
  Angle     :  0.519   6.274   4544  Z= 0.274
  Chirality :  0.041   0.131    479
  Planarity :  0.003   0.026    590
  Dihedral  : 10.594  62.594   1202
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.86 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.02 (0.40), residues: 410
  helix: -1.75 (1.22), residues: 13
  sheet: -0.83 (0.47), residues: 136
  loop : -1.65 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.009   0.001   TYR E 495 
 PHE   0.008   0.001   PHE E 515 
 TRP   0.011   0.001   TRP A 117 
 HIS   0.001   0.000   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 3339)
  covalent geometry    : angle       0.51877 /  0.27 ( 4531)
  SS BOND              : bond        0.00126 /  0.06 (    5)
  SS BOND              : angle       0.59889 /  0.39 (   10)
  hydrogen bonds       : bond        0.11185 /  7.08 (   85)
  hydrogen bonds       : angle       7.76449 /  5.56 (  198)
  link_NAG-ASN         : bond        0.00060 /  0.03 (    1)
  link_NAG-ASN         : angle       0.90288 /  0.51 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.118 
Fit side-chains
REVERT: E  396 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5266 (m-10)
REVERT: E  465 GLU cc_start: 0.7831 (tp30) cc_final: 0.7526 (tp30)
  outliers start: 3
  outliers final: 2
  residues processed: 67
  average time/residue: 0.0874
  time to fit residues: 6.8758
Evaluate side-chains
  50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37]
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0670
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8320

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
E 388 ASN
E 450 ASN
E 474 GLN
E 506 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.186961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.163512 restraints weight = 4023.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.15
r_work: 0.3873 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3345  Z= 0.128
  Angle     :  0.537   8.687   4544  Z= 0.278
  Chirality :  0.043   0.212    479
  Planarity :  0.004   0.030    590
  Dihedral  :  7.239  56.299    491
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  8.86 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.74 (0.41), residues: 410
  helix: -1.24 (1.23), residues: 19
  sheet: -0.66 (0.47), residues: 139
  loop : -1.46 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 454 
 TYR   0.011   0.001   TYR B  92 
 PHE   0.020   0.001   PHE A  29 
 TRP   0.010   0.001   TRP A 117 
 HIS   0.002   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 3339)
  covalent geometry    : angle       0.53334 /  0.28 ( 4531)
  SS BOND              : bond        0.00158 /  0.09 (    5)
  SS BOND              : angle       1.38293 /  1.13 (   10)
  hydrogen bonds       : bond        0.02899 /  2.06 (   85)
  hydrogen bonds       : angle       6.64667 /  4.67 (  198)
  link_NAG-ASN         : bond        0.00205 /  0.11 (    1)
  link_NAG-ASN         : angle       0.58735 /  0.32 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7667 (tptt) cc_final: 0.7200 (mttp)
REVERT: E  394 ASN cc_start: 0.7732 (m-40) cc_final: 0.7203 (p0)
REVERT: E  396 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5469 (m-10)
REVERT: E  465 GLU cc_start: 0.8224 (tp30) cc_final: 0.7750 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0631
  time to fit residues: 4.7328
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [13, 1, 29, 39, 38, 11, 28, 20, 37, 27, 36]
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0870
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.8960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN
E 394 ASN
E 506 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.186037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.162572 restraints weight = 3995.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.14
r_work: 0.3863 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3345  Z= 0.133
  Angle     :  0.519   5.819   4544  Z= 0.271
  Chirality :  0.043   0.160    479
  Planarity :  0.004   0.034    590
  Dihedral  :  6.898  54.933    491
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.71 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.66 (0.42), residues: 410
  helix: -1.15 (1.26), residues: 19
  sheet: -0.50 (0.49), residues: 139
  loop : -1.49 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.010   0.001   TYR B  92 
 PHE   0.015   0.001   PHE A  29 
 TRP   0.009   0.001   TRP A 117 
 HIS   0.002   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 ( 3339)
  covalent geometry    : angle       0.51728 /  0.27 ( 4531)
  SS BOND              : bond        0.00172 /  0.11 (    5)
  SS BOND              : angle       1.09872 /  0.93 (   10)
  hydrogen bonds       : bond        0.02899 /  2.06 (   85)
  hydrogen bonds       : angle       6.52133 /  4.58 (  198)
  link_NAG-ASN         : bond        0.00138 /  0.07 (    1)
  link_NAG-ASN         : angle       0.55368 /  0.31 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7739 (tptt) cc_final: 0.7310 (mttp)
REVERT: E  394 ASN cc_start: 0.7690 (m110) cc_final: 0.7205 (p0)
REVERT: E  396 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.5503 (m-10)
REVERT: E  465 GLU cc_start: 0.8262 (tp30) cc_final: 0.7853 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0725
  time to fit residues: 5.0790
Evaluate side-chains
  55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [6, 29, 1, 30, 22, 16, 27, 11, 2, 33, 10]
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0670
   chunk 27 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0570
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN
E 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.188922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.165530 restraints weight = 3956.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.12
r_work: 0.3897 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3764 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3345  Z= 0.092
  Angle     :  0.485   7.669   4544  Z= 0.249
  Chirality :  0.042   0.191    479
  Planarity :  0.003   0.040    590
  Dihedral  :  6.399  51.010    491
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.43 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.55 (0.41), residues: 410
  helix: -1.40 (1.07), residues: 25
  sheet: -0.38 (0.48), residues: 138
  loop : -1.40 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.011   0.001   TYR B  92 
 PHE   0.009   0.001   PHE A  29 
 TRP   0.008   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.09 ( 3339)
  covalent geometry    : angle       0.48329 /  0.25 ( 4531)
  SS BOND              : bond        0.00106 /  0.06 (    5)
  SS BOND              : angle       0.94216 /  0.78 (   10)
  hydrogen bonds       : bond        0.02661 /  1.88 (   85)
  hydrogen bonds       : angle       6.14265 /  4.32 (  198)
  link_NAG-ASN         : bond        0.00181 /  0.10 (    1)
  link_NAG-ASN         : angle       0.56894 /  0.33 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7717 (tptt) cc_final: 0.7381 (mttp)
REVERT: B   13 LEU cc_start: 0.8232 (pt) cc_final: 0.7737 (mp)
REVERT: E  368 LEU cc_start: 0.6977 (mt) cc_final: 0.6685 (mt)
REVERT: E  394 ASN cc_start: 0.7633 (m110) cc_final: 0.7323 (p0)
REVERT: E  396 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5484 (m-10)
REVERT: E  465 GLU cc_start: 0.8176 (tp30) cc_final: 0.7741 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.0737
  time to fit residues: 5.0103
Evaluate side-chains
  50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [24, 16, 22, 33, 38, 21, 8, 9, 7, 5, 17]
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 388 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.184344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.160834 restraints weight = 3930.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.12
r_work: 0.3852 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3345  Z= 0.156
  Angle     :  0.526   6.543   4544  Z= 0.273
  Chirality :  0.043   0.178    479
  Planarity :  0.004   0.061    590
  Dihedral  :  6.689  55.015    491
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.43 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.50 (0.41), residues: 410
  helix: -1.05 (1.30), residues: 19
  sheet: -0.15 (0.49), residues: 133
  loop : -1.51 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 454 
 TYR   0.011   0.001   TYR B  50 
 PHE   0.011   0.001   PHE B 100 
 TRP   0.009   0.001   TRP A 117 
 HIS   0.002   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 3339)
  covalent geometry    : angle       0.52237 /  0.27 ( 4531)
  SS BOND              : bond        0.00215 /  0.14 (    5)
  SS BOND              : angle       1.41361 /  1.20 (   10)
  hydrogen bonds       : bond        0.02997 /  2.14 (   85)
  hydrogen bonds       : angle       6.39164 /  4.48 (  198)
  link_NAG-ASN         : bond        0.00104 /  0.05 (    1)
  link_NAG-ASN         : angle       0.70987 /  0.41 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7786 (tptt) cc_final: 0.7389 (mttp)
REVERT: B   82 GLU cc_start: 0.7834 (tt0) cc_final: 0.7620 (tt0)
REVERT: E  368 LEU cc_start: 0.7018 (mt) cc_final: 0.6723 (mt)
REVERT: E  394 ASN cc_start: 0.7648 (m110) cc_final: 0.7251 (p0)
REVERT: E  396 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5596 (m-10)
REVERT: E  465 GLU cc_start: 0.8258 (tp30) cc_final: 0.7835 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 52
  average time/residue: 0.0749
  time to fit residues: 4.7307
Evaluate side-chains
  49 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [3, 34, 21, 32, 26, 2, 18, 36, 17, 0, 8]
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.181886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.159493 restraints weight = 3965.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.00
r_work: 0.3828 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3345  Z= 0.182
  Angle     :  0.555   6.407   4544  Z= 0.290
  Chirality :  0.044   0.168    479
  Planarity :  0.004   0.047    590
  Dihedral  :  6.978  58.254    491
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.57 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.61 (0.41), residues: 410
  helix: -1.55 (1.05), residues: 25
  sheet: -0.19 (0.49), residues: 133
  loop : -1.56 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 454 
 TYR   0.013   0.001   TYR B  50 
 PHE   0.013   0.002   PHE B 100 
 TRP   0.010   0.002   TRP A 117 
 HIS   0.002   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.18 ( 3339)
  covalent geometry    : angle       0.55123 /  0.29 ( 4531)
  SS BOND              : bond        0.00287 /  0.17 (    5)
  SS BOND              : angle       1.43666 /  1.26 (   10)
  hydrogen bonds       : bond        0.03275 /  2.35 (   85)
  hydrogen bonds       : angle       6.59968 /  4.61 (  198)
  link_NAG-ASN         : bond        0.00010 /  0.01 (    1)
  link_NAG-ASN         : angle       0.87743 /  0.51 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7696 (tptt) cc_final: 0.7440 (mttp)
REVERT: E  368 LEU cc_start: 0.7048 (mt) cc_final: 0.6743 (mt)
REVERT: E  394 ASN cc_start: 0.7671 (m110) cc_final: 0.7398 (p0)
REVERT: E  396 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5670 (m-10)
REVERT: E  465 GLU cc_start: 0.8294 (tp30) cc_final: 0.7858 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0723
  time to fit residues: 4.8882
Evaluate side-chains
  54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [17, 10, 38, 32, 3, 20, 19, 9, 18, 34, 22]
   chunk 17 optimal weight:    0.0670
   chunk 10 optimal weight:    0.0060
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4734

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.187409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.163821 restraints weight = 3964.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.16
r_work: 0.3890 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3345  Z= 0.094
  Angle     :  0.483   6.738   4544  Z= 0.250
  Chirality :  0.042   0.150    479
  Planarity :  0.003   0.036    590
  Dihedral  :  6.320  52.936    491
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.86 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.46 (0.42), residues: 410
  helix: -1.53 (0.93), residues: 31
  sheet: -0.09 (0.49), residues: 133
  loop : -1.43 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 454 
 TYR   0.014   0.001   TYR E 423 
 PHE   0.007   0.001   PHE A  29 
 TRP   0.006   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.09 ( 3339)
  covalent geometry    : angle       0.47889 /  0.25 ( 4531)
  SS BOND              : bond        0.00113 /  0.06 (    5)
  SS BOND              : angle       1.38675 /  1.19 (   10)
  hydrogen bonds       : bond        0.02845 /  2.02 (   85)
  hydrogen bonds       : angle       5.99885 /  4.20 (  198)
  link_NAG-ASN         : bond        0.00095 /  0.05 (    1)
  link_NAG-ASN         : angle       0.82170 /  0.48 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7731 (tptt) cc_final: 0.7473 (mttp)
REVERT: E  368 LEU cc_start: 0.6929 (mt) cc_final: 0.6630 (mt)
REVERT: E  377 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7310 (t80)
REVERT: E  394 ASN cc_start: 0.7699 (m110) cc_final: 0.7387 (p0)
REVERT: E  396 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5422 (m-10)
REVERT: E  402 ILE cc_start: 0.7488 (pt) cc_final: 0.7253 (pt)
REVERT: E  465 GLU cc_start: 0.8180 (tp30) cc_final: 0.7750 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 54
  average time/residue: 0.0743
  time to fit residues: 4.8450
Evaluate side-chains
  53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  377 PHE
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [37, 30, 27, 36, 35, 6, 26, 17, 39, 11, 25]
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    8.9990
   chunk 36 optimal weight:    0.0870
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    0.3980
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    0.4980
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.3760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.182330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.158318 restraints weight = 4069.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.18
r_work: 0.3817 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3681 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3345  Z= 0.186
  Angle     :  0.556   6.390   4544  Z= 0.289
  Chirality :  0.044   0.155    479
  Planarity :  0.004   0.038    590
  Dihedral  :  6.859  57.401    491
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.43 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.55 (0.42), residues: 410
  helix: -1.54 (0.95), residues: 31
  sheet: -0.11 (0.50), residues: 126
  loop : -1.49 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 454 
 TYR   0.013   0.001   TYR B  50 
 PHE   0.013   0.001   PHE B 100 
 TRP   0.010   0.002   TRP A 117 
 HIS   0.002   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.19 ( 3339)
  covalent geometry    : angle       0.55071 /  0.29 ( 4531)
  SS BOND              : bond        0.00282 /  0.17 (    5)
  SS BOND              : angle       1.60930 /  1.32 (   10)
  hydrogen bonds       : bond        0.03336 /  2.38 (   85)
  hydrogen bonds       : angle       6.48281 /  4.54 (  198)
  link_NAG-ASN         : bond        0.00024 /  0.01 (    1)
  link_NAG-ASN         : angle       0.95233 /  0.55 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7730 (tptt) cc_final: 0.7437 (mttp)
REVERT: E  368 LEU cc_start: 0.6993 (mt) cc_final: 0.6675 (mt)
REVERT: E  394 ASN cc_start: 0.7776 (m110) cc_final: 0.7343 (p0)
REVERT: E  396 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.5579 (m-80)
REVERT: E  465 GLU cc_start: 0.8286 (tp30) cc_final: 0.7838 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 55
  average time/residue: 0.0705
  time to fit residues: 4.7822
Evaluate side-chains
  57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  467 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [24, 38, 28, 29, 12, 37, 14, 11, 2, 21, 7]
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 28 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.185918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.162072 restraints weight = 3979.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3967 rms_B_bonded: 2.19
r_work: 0.3867 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3345  Z= 0.110
  Angle     :  0.516   7.640   4544  Z= 0.262
  Chirality :  0.042   0.148    479
  Planarity :  0.003   0.038    590
  Dihedral  :  6.478  53.327    491
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.43 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.44 (0.42), residues: 410
  helix: -1.61 (0.92), residues: 31
  sheet: -0.08 (0.49), residues: 133
  loop : -1.41 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 454 
 TYR   0.011   0.001   TYR E 423 
 PHE   0.007   0.001   PHE B 100 
 TRP   0.006   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 3339)
  covalent geometry    : angle       0.51111 /  0.26 ( 4531)
  SS BOND              : bond        0.00132 /  0.08 (    5)
  SS BOND              : angle       1.47505 /  1.22 (   10)
  hydrogen bonds       : bond        0.02901 /  2.07 (   85)
  hydrogen bonds       : angle       6.08401 /  4.27 (  198)
  link_NAG-ASN         : bond        0.00082 /  0.04 (    1)
  link_NAG-ASN         : angle       0.89417 /  0.52 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7739 (tptt) cc_final: 0.7462 (mttp)
REVERT: E  368 LEU cc_start: 0.6947 (mt) cc_final: 0.6640 (mt)
REVERT: E  394 ASN cc_start: 0.7665 (m110) cc_final: 0.7411 (p0)
REVERT: E  396 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5409 (m-10)
REVERT: E  402 ILE cc_start: 0.7514 (pt) cc_final: 0.7283 (pt)
REVERT: E  465 GLU cc_start: 0.8169 (tp30) cc_final: 0.7737 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 53
  average time/residue: 0.0680
  time to fit residues: 4.4776
Evaluate side-chains
  55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  467 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [10, 31, 25, 8, 4, 7, 28, 15, 6, 33, 1]
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.185333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.161562 restraints weight = 3952.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 2.17
r_work: 0.3868 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3345  Z= 0.116
  Angle     :  0.527  10.431   4544  Z= 0.264
  Chirality :  0.043   0.144    479
  Planarity :  0.003   0.038    590
  Dihedral  :  6.473  54.013    491
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.71 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.41 (0.42), residues: 410
  helix: -1.58 (0.92), residues: 31
  sheet: -0.07 (0.50), residues: 132
  loop : -1.36 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 454 
 TYR   0.009   0.001   TYR A  95 
 PHE   0.008   0.001   PHE B 100 
 TRP   0.007   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 3339)
  covalent geometry    : angle       0.52262 /  0.26 ( 4531)
  SS BOND              : bond        0.00162 /  0.10 (    5)
  SS BOND              : angle       1.46125 /  1.20 (   10)
  hydrogen bonds       : bond        0.02930 /  2.09 (   85)
  hydrogen bonds       : angle       6.06071 /  4.26 (  198)
  link_NAG-ASN         : bond        0.00094 /  0.05 (    1)
  link_NAG-ASN         : angle       0.93305 /  0.54 (    3)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A   76 LYS cc_start: 0.7680 (tptt) cc_final: 0.7433 (mttp)
REVERT: E  368 LEU cc_start: 0.6946 (mt) cc_final: 0.6628 (mt)
REVERT: E  394 ASN cc_start: 0.7657 (m110) cc_final: 0.7378 (p0)
REVERT: E  396 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5364 (m-80)
REVERT: E  402 ILE cc_start: 0.7435 (pt) cc_final: 0.7213 (pt)
REVERT: E  465 GLU cc_start: 0.8210 (tp30) cc_final: 0.7752 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0731
  time to fit residues: 4.8555
Evaluate side-chains
  56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  396 TYR
Chi-restraints excluded: chain E residue  408 ARG
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  467 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks: [19, 20, 32, 25, 5, 21, 38, 24, 14, 9, 7]
   chunk 19 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.8712 > 50:)
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 5 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0570
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.188806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.165098 restraints weight = 3999.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 2.19
r_work: 0.3900 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3345  Z= 0.087
  Angle     :  0.499  10.034   4544  Z= 0.248
  Chirality :  0.042   0.143    479
  Planarity :  0.003   0.036    590
  Dihedral  :  6.174  55.047    491
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.00 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.29 (0.43), residues: 410
  helix: -1.57 (0.91), residues: 31
  sheet:  0.04 (0.50), residues: 132
  loop : -1.30 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 454 
 TYR   0.010   0.001   TYR E 423 
 PHE   0.008   0.001   PHE A  29 
 TRP   0.006   0.001   TRP A 117 
 HIS   0.003   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00194 /  0.09 ( 3339)
  covalent geometry    : angle       0.49480 /  0.25 ( 4531)
  SS BOND              : bond        0.00101 /  0.06 (    5)
  SS BOND              : angle       1.34675 /  1.11 (   10)
  hydrogen bonds       : bond        0.02682 /  1.90 (   85)
  hydrogen bonds       : angle       5.75980 /  4.04 (  198)
  link_NAG-ASN         : bond        0.00092 /  0.05 (    1)
  link_NAG-ASN         : angle       0.95809 /  0.56 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1071.94 seconds
wall clock time: 19 minutes 2.05 seconds (1142.05 seconds total)