Starting phenix.real_space_refine
on Tue Mar  3 11:39:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp5_32669/03_2026/7wp5_32669.map"
  }
  resolution = 3.9
  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=   0.008
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      15      5.16       5
     C    2118      2.51       5
     N     563      2.21       5
     O     644      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3340
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 811
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1017
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "F"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1484
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 10, 'TRANS': 172}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.76, per 1000 atoms: 0.23
  Number of scatterers: 3340
  At special positions: 0
  Unit cell: (77.022, 80.912, 81.69, 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      15     16.00
     O     644      8.00
     N     563      7.00
     C    2118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 106.1 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 7 sheets defined
      2.4% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'F' and resid 336 through 340
      removed outlier: 3.688A  pdb=" N   ASP F 339 " --> pdb=" O   CYS F 336 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLU F 340 " --> pdb=" O   PRO F 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 336 through 340'
    Processing helix  chain 'F' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23
      removed outlier: 3.750A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50
      removed outlier: 5.740A  pdb=" N   LEU L  48 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   GLN L  39 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.600A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.618A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 126 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR H 125 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104
      removed outlier: 3.606A  pdb=" N   TYR H 103 " --> pdb=" O   ASN H 111 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN H 111 " --> pdb=" O   TYR H 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 358 through 359
      removed outlier: 3.735A  pdb=" N   VAL F 395 " --> pdb=" O   ILE F 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 376 through 379
      removed outlier: 3.527A  pdb=" N   THR F 376 " --> pdb=" O   ALA F 435 " (cutoff:3.500A)

    63 hydrogen bonds defined for protein.
    153 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: 0.43

  Time building geometry restraints manager: 0.28 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: 1052
        1.34 -     1.46: 852
        1.46 -     1.58: 1503
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 3426
  Sorted by residual:
  bond pdb=" CA  SER F 446 "
       pdb=" C   SER F 446 "
    ideal  model  delta    sigma   weight residual
    1.522  1.544 -0.022 1.37e-02 5.33e+03 2.59e+00
  bond pdb=" CA  CYS F 336 "
       pdb=" C   CYS F 336 "
    ideal  model  delta    sigma   weight residual
    1.525  1.557 -0.032 2.10e-02 2.27e+03 2.31e+00
  bond pdb=" C3  NAG A   1 "
       pdb=" O3  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C3  NAG A   2 "
       pdb=" O3  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.431 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C4  NAG A   1 "
       pdb=" O4  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.435 -0.026 2.00e-02 2.50e+03 1.75e+00
  ... (remaining 3421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 4522
        2.60 -     5.21: 110
        5.21 -     7.81: 17
        7.81 -    10.41: 1
       10.41 -    13.01: 4
  Bond angle restraints: 4654
  Sorted by residual:
  angle pdb=" C   ASN F 477 "
        pdb=" N   LYS F 478 "
        pdb=" CA  LYS F 478 "
      ideal   model   delta    sigma   weight residual
     121.80  132.91  -11.11 2.44e+00 1.68e-01 2.07e+01
  angle pdb=" C   GLY L  52 "
        pdb=" N   ASN L  53 "
        pdb=" CA  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     121.54  130.03   -8.49 1.91e+00 2.74e-01 1.98e+01
  angle pdb=" C   TYR F 369 "
        pdb=" N   ASN F 370 "
        pdb=" CA  ASN F 370 "
      ideal   model   delta    sigma   weight residual
     122.19  128.42   -6.23 1.41e+00 5.03e-01 1.95e+01
  angle pdb=" C   SER F 359 "
        pdb=" N   ASN F 360 "
        pdb=" CA  ASN F 360 "
      ideal   model   delta    sigma   weight residual
     122.46  128.68   -6.22 1.41e+00 5.03e-01 1.95e+01
  angle pdb=" CA  LEU F 371 "
        pdb=" CB  LEU F 371 "
        pdb=" CG  LEU F 371 "
      ideal   model   delta    sigma   weight residual
     116.30  129.31  -13.01 3.50e+00 8.16e-02 1.38e+01
  ... (remaining 4649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 1729
       14.85 -    29.70: 224
       29.70 -    44.55: 56
       44.55 -    59.41: 6
       59.41 -    74.26: 5
  Dihedral angle restraints: 2020
    sinusoidal: 800
      harmonic: 1220
  Sorted by residual:
  dihedral pdb=" CA  ASN F 460 "
           pdb=" C   ASN F 460 "
           pdb=" N   LEU F 461 "
           pdb=" CA  LEU F 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.27  -32.73     0      5.00e+00 4.00e-02 4.29e+01
  dihedral pdb=" CA  ASN F 477 "
           pdb=" C   ASN F 477 "
           pdb=" N   LYS F 478 "
           pdb=" CA  LYS F 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.90  -24.10     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ASN H 115 "
           pdb=" C   ASN H 115 "
           pdb=" N   TYR H 116 "
           pdb=" CA  TYR H 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.61  -20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 2017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 392
       0.066 -    0.132: 80
       0.132 -    0.198: 21
       0.198 -    0.264: 1
       0.264 -    0.329: 1
  Chirality restraints: 495
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN F 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.11e+00
  chirality pdb=" CB  THR H  91 "
            pdb=" CA  THR H  91 "
            pdb=" OG1 THR H  91 "
            pdb=" CG2 THR H  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.87e-01
  ... (remaining 492 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.278 2.00e-02 2.50e+03   2.38e-01 7.10e+02
        pdb=" C7  NAG A   1 "    0.061 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "    0.016 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.402 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.202 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "    0.028 2.00e-02 2.50e+03   2.34e-02 6.84e+00
        pdb=" C7  NAG A   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "   -0.037 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 411 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO F 412 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F 412 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 412 "    0.029 5.00e-02 4.00e+02
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 935
        2.80 -     3.33: 2725
        3.33 -     3.85: 5189
        3.85 -     4.38: 5630
        4.38 -     4.90: 9998
  Nonbonded interactions: 24477
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F 442 "
            pdb=" OH  TYR F 451 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD2 ASP F 398 "
            pdb=" OH  TYR F 423 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NE2 HIS L  36 "
            pdb=" O   ASN H 115 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" NE2 GLN L  39 "
            pdb=" OD1 ASP L  84 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OG  SER H 130 "
            pdb=" N   SER H 131 "
     model   vdw
     2.373 3.120
  ... (remaining 24472 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=0.00 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:             17.210
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.330
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
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      :  0.005   0.039   3431  Z= 0.250
  Angle     :  1.027  13.015   4666  Z= 0.561
  Chirality :  0.060   0.329    495
  Planarity :  0.012   0.238    603
  Dihedral  : 13.947  74.258   1245
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.07 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.64 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -4.27 (0.34), residues: 419
  helix: -5.34 (0.29), residues: 11
  sheet: -1.85 (0.43), residues: 135
  loop : -3.47 (0.29), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  56 
 TYR   0.018   0.002   TYR F 508 
 PHE   0.017   0.003   PHE F 515 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.005   0.002   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 3426)
  covalent geometry    : angle       1.02540 ( 4654)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       0.69593 (    6)
  hydrogen bonds       : bond        0.30171 (   63)
  hydrogen bonds       : angle      11.42120 (  153)
  link_BETA1-4         : bond        0.00664 (    1)
  link_BETA1-4         : angle       1.18892 (    3)
  link_NAG-ASN         : bond        0.00320 (    1)
  link_NAG-ASN         : angle       2.42326 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8612 (tp) cc_final: 0.8355 (tt)
REVERT: H   51 MET cc_start: 0.8021 (ttp) cc_final: 0.7744 (ttm)
REVERT: F  339 ASP cc_start: 0.7344 (t70) cc_final: 0.6809 (t70)
REVERT: F  368 LEU cc_start: 0.8505 (mt) cc_final: 0.8287 (mt)
REVERT: F  406 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7871 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 113
  average time/residue: 0.0752
  time to fit residues: 10.0418
Evaluate side-chains
  84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  497 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
L  81 GLN
H 115 ASN
F 417 ASN
F 448 ASN
F 450 ASN
F 474 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.170508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154481 restraints weight = 6528.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.158984 restraints weight = 4900.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.161055 restraints weight = 2272.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.162379 restraints weight = 1606.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.162642 restraints weight = 1346.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3923 r_free = 0.3923    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3922 r_free = 0.3922    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3431  Z= 0.157
  Angle     :  0.743   8.629   4666  Z= 0.377
  Chirality :  0.047   0.197    495
  Planarity :  0.005   0.035    603
  Dihedral  :  6.630  37.944    522
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.55 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.49 %
    Favored  : 77.59 %
  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: -3.71 (0.37), residues: 419
  helix: -4.06 (1.04), residues: 13
  sheet: -1.50 (0.42), residues: 143
  loop : -3.12 (0.33), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 457 
 TYR   0.023   0.001   TYR F 369 
 PHE   0.012   0.002   PHE F 338 
 TRP   0.008   0.001   TRP L 100 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3426)
  covalent geometry    : angle       0.73859 ( 4654)
  SS BOND              : bond        0.00458 (    3)
  SS BOND              : angle       1.92377 (    6)
  hydrogen bonds       : bond        0.04573 (   63)
  hydrogen bonds       : angle       7.78946 (  153)
  link_BETA1-4         : bond        0.00431 (    1)
  link_BETA1-4         : angle       1.19628 (    3)
  link_NAG-ASN         : bond        0.01014 (    1)
  link_NAG-ASN         : angle       2.06495 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8540 (tp) cc_final: 0.8234 (tt)
REVERT: H   38 ARG cc_start: 0.8228 (ptt180) cc_final: 0.7958 (ptm-80)
REVERT: H   51 MET cc_start: 0.7670 (ttp) cc_final: 0.7330 (ttm)
REVERT: H  116 TYR cc_start: 0.8546 (m-80) cc_final: 0.8253 (m-80)
REVERT: F  365 TYR cc_start: 0.8080 (m-10) cc_final: 0.7860 (m-10)
REVERT: F  406 GLU cc_start: 0.8707 (mm-30) cc_final: 0.7657 (mm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0537
  time to fit residues: 6.0272
Evaluate side-chains
  92 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  497 PHE
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 115 ASN
F 370 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 448 ASN
F 506 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.166309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.151491 restraints weight = 6610.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.155658 restraints weight = 5209.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.157313 restraints weight = 2398.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157520 restraints weight = 1935.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.157980 restraints weight = 1679.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3860 r_free = 0.3860    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3431  Z= 0.229
  Angle     :  0.774   8.081   4666  Z= 0.391
  Chirality :  0.048   0.191    495
  Planarity :  0.005   0.043    603
  Dihedral  :  6.766  30.478    522
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.69 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 19.33 %
    Favored  : 73.67 %
  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: -3.68 (0.36), residues: 419
  helix: -4.36 (0.83), residues: 13
  sheet: -1.39 (0.43), residues: 138
  loop : -3.11 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 457 
 TYR   0.017   0.002   TYR F 369 
 PHE   0.016   0.002   PHE F 515 
 TRP   0.011   0.002   TRP L 100 
 HIS   0.004   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 3426)
  covalent geometry    : angle       0.77074 ( 4654)
  SS BOND              : bond        0.00603 (    3)
  SS BOND              : angle       1.73453 (    6)
  hydrogen bonds       : bond        0.04288 (   63)
  hydrogen bonds       : angle       6.97865 (  153)
  link_BETA1-4         : bond        0.00424 (    1)
  link_BETA1-4         : angle       1.37524 (    3)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       1.12068 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8591 (tp) cc_final: 0.8239 (tt)
REVERT: H   51 MET cc_start: 0.7778 (ttp) cc_final: 0.7463 (ttm)
REVERT: H  116 TYR cc_start: 0.8574 (m-80) cc_final: 0.8363 (m-80)
REVERT: F  365 TYR cc_start: 0.8098 (m-10) cc_final: 0.7882 (m-10)
REVERT: F  406 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8565 (mm-30)
REVERT: F  425 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (mp)
  outliers start: 25
  outliers final: 16
  residues processed: 97
  average time/residue: 0.0522
  time to fit residues: 6.3418
Evaluate side-chains
  99 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  127 VAL
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
H 115 ASN
** F 409 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 = 0.3986 r_free = 0.3986 target = 0.167667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.152811 restraints weight = 6661.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157154 restraints weight = 5204.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.158679 restraints weight = 2307.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.160382 restraints weight = 1737.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.160630 restraints weight = 1394.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3894 r_free = 0.3894    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3895 r_free = 0.3895    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3431  Z= 0.157
  Angle     :  0.695   7.624   4666  Z= 0.355
  Chirality :  0.046   0.171    495
  Planarity :  0.004   0.039    603
  Dihedral  :  6.098  25.420    520
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.07 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 22.13 %
    Favored  : 71.71 %
  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: -3.38 (0.38), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -1.12 (0.44), residues: 136
  loop : -2.97 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 355 
 TYR   0.016   0.001   TYR F 369 
 PHE   0.010   0.002   PHE F 338 
 TRP   0.008   0.001   TRP L  37 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3426)
  covalent geometry    : angle       0.69291 ( 4654)
  SS BOND              : bond        0.00377 (    3)
  SS BOND              : angle       1.23686 (    6)
  hydrogen bonds       : bond        0.03565 (   63)
  hydrogen bonds       : angle       6.55278 (  153)
  link_BETA1-4         : bond        0.00406 (    1)
  link_BETA1-4         : angle       1.38984 (    3)
  link_NAG-ASN         : bond        0.00285 (    1)
  link_NAG-ASN         : angle       1.23165 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8514 (tp) cc_final: 0.8207 (tt)
REVERT: H   51 MET cc_start: 0.7644 (ttp) cc_final: 0.7383 (ttm)
REVERT: H   90 ASP cc_start: 0.7408 (m-30) cc_final: 0.6999 (m-30)
REVERT: F  406 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8283 (mm-30)
REVERT: F  425 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8275 (mp)
REVERT: F  495 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.6222 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0547
  time to fit residues: 6.6892
Evaluate side-chains
  95 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0060
   chunk 15 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 1 optimal weight:    0.0020
   overall best weight:    0.1962

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

Flipped N/Q/H residues before XYZ refinement:
H 115 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 ASN
F 448 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.170255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.153849 restraints weight = 6440.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.159262 restraints weight = 3869.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.160736 restraints weight = 1994.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.162210 restraints weight = 1386.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.162558 restraints weight = 1264.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3431  Z= 0.114
  Angle     :  0.665   7.430   4666  Z= 0.333
  Chirality :  0.044   0.138    495
  Planarity :  0.004   0.041    603
  Dihedral  :  6.551  47.308    520
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.59 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 24.09 %
    Favored  : 69.75 %
  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: -3.15 (0.38), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -0.92 (0.44), residues: 138
  loop : -2.83 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 457 
 TYR   0.014   0.001   TYR F 369 
 PHE   0.012   0.001   PHE H  29 
 TRP   0.008   0.001   TRP F 436 
 HIS   0.002   0.001   HIS L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 3426)
  covalent geometry    : angle       0.65987 ( 4654)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       0.94019 (    6)
  hydrogen bonds       : bond        0.03049 (   63)
  hydrogen bonds       : angle       6.24125 (  153)
  link_BETA1-4         : bond        0.01297 (    1)
  link_BETA1-4         : angle       1.76654 (    3)
  link_NAG-ASN         : bond        0.00232 (    1)
  link_NAG-ASN         : angle       2.74919 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8501 (tp) cc_final: 0.8216 (tt)
REVERT: H   12 VAL cc_start: 0.6002 (t) cc_final: 0.5746 (p)
REVERT: H   46 GLU cc_start: 0.7668 (pt0) cc_final: 0.7413 (pt0)
REVERT: H   51 MET cc_start: 0.7602 (ttp) cc_final: 0.7315 (ttm)
REVERT: F  365 TYR cc_start: 0.8099 (m-10) cc_final: 0.7822 (m-10)
REVERT: F  425 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8196 (mp)
  outliers start: 22
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0500
  time to fit residues: 6.2197
Evaluate side-chains
  96 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  420 ASP
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 38 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 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 = 0.3997 r_free = 0.3997 target = 0.168429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.152127 restraints weight = 6653.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157497 restraints weight = 4094.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.158539 restraints weight = 2178.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.159807 restraints weight = 1536.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.160047 restraints weight = 1534.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3431  Z= 0.168
  Angle     :  0.721   7.806   4666  Z= 0.357
  Chirality :  0.045   0.142    495
  Planarity :  0.004   0.033    603
  Dihedral  :  6.428  39.784    520
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.79 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 23.81 %
    Favored  : 70.31 %
  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: -3.09 (0.39), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -0.86 (0.45), residues: 138
  loop : -2.81 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 457 
 TYR   0.013   0.001   TYR F 369 
 PHE   0.022   0.002   PHE H  27 
 TRP   0.007   0.001   TRP L 100 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3426)
  covalent geometry    : angle       0.71673 ( 4654)
  SS BOND              : bond        0.00384 (    3)
  SS BOND              : angle       1.13885 (    6)
  hydrogen bonds       : bond        0.03322 (   63)
  hydrogen bonds       : angle       6.09266 (  153)
  link_BETA1-4         : bond        0.00776 (    1)
  link_BETA1-4         : angle       1.35916 (    3)
  link_NAG-ASN         : bond        0.00738 (    1)
  link_NAG-ASN         : angle       2.56580 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8527 (tp) cc_final: 0.8214 (tt)
REVERT: H   12 VAL cc_start: 0.6235 (t) cc_final: 0.6029 (m)
REVERT: H   51 MET cc_start: 0.7490 (ttp) cc_final: 0.6904 (ttm)
REVERT: F  365 TYR cc_start: 0.8102 (m-10) cc_final: 0.7821 (m-10)
REVERT: F  406 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8570 (mm-30)
REVERT: F  425 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8221 (mp)
  outliers start: 21
  outliers final: 18
  residues processed: 92
  average time/residue: 0.0490
  time to fit residues: 5.8623
Evaluate side-chains
  97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0670
   chunk 12 optimal weight:    0.0770
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 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 = 0.4028 r_free = 0.4028 target = 0.170550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154069 restraints weight = 6565.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.159120 restraints weight = 4087.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.160630 restraints weight = 2266.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.161312 restraints weight = 1580.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.161871 restraints weight = 1523.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3431  Z= 0.121
  Angle     :  0.666   7.354   4666  Z= 0.333
  Chirality :  0.044   0.135    495
  Planarity :  0.004   0.031    603
  Dihedral  :  5.985  30.172    520
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.88 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.65 %
    Favored  : 70.59 %
  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: -2.91 (0.39), residues: 419
  helix: -5.85 (0.26), residues: 5
  sheet: -0.76 (0.45), residues: 138
  loop : -2.66 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 457 
 TYR   0.012   0.001   TYR F 369 
 PHE   0.022   0.001   PHE H  27 
 TRP   0.009   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3426)
  covalent geometry    : angle       0.66150 ( 4654)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       0.88859 (    6)
  hydrogen bonds       : bond        0.02897 (   63)
  hydrogen bonds       : angle       5.97538 (  153)
  link_BETA1-4         : bond        0.00580 (    1)
  link_BETA1-4         : angle       1.37655 (    3)
  link_NAG-ASN         : bond        0.00345 (    1)
  link_NAG-ASN         : angle       2.87476 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.124 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8486 (tp) cc_final: 0.8215 (tt)
REVERT: H   28 THR cc_start: 0.8229 (m) cc_final: 0.7953 (p)
REVERT: H   51 MET cc_start: 0.7309 (ttp) cc_final: 0.6984 (ttm)
REVERT: F  365 TYR cc_start: 0.8044 (m-10) cc_final: 0.7796 (m-10)
REVERT: F  406 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: F  425 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8203 (mp)
  outliers start: 17
  outliers final: 15
  residues processed: 90
  average time/residue: 0.0526
  time to fit residues: 6.0619
Evaluate side-chains
  93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 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 = 0.3992 r_free = 0.3992 target = 0.167469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.151916 restraints weight = 6709.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.156201 restraints weight = 5242.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.157999 restraints weight = 2434.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.159335 restraints weight = 1765.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.159537 restraints weight = 1520.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3431  Z= 0.168
  Angle     :  0.698   7.538   4666  Z= 0.353
  Chirality :  0.045   0.146    495
  Planarity :  0.004   0.031    603
  Dihedral  :  6.051  25.562    520
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.26 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 23.53 %
    Favored  : 70.59 %
  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: -2.90 (0.39), residues: 419
  helix: -5.64 (0.19), residues: 11
  sheet: -0.83 (0.45), residues: 139
  loop : -2.52 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 457 
 TYR   0.012   0.001   TYR F 369 
 PHE   0.024   0.002   PHE H  27 
 TRP   0.009   0.001   TRP L  37 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3426)
  covalent geometry    : angle       0.69287 ( 4654)
  SS BOND              : bond        0.00391 (    3)
  SS BOND              : angle       1.13699 (    6)
  hydrogen bonds       : bond        0.03258 (   63)
  hydrogen bonds       : angle       5.89165 (  153)
  link_BETA1-4         : bond        0.00791 (    1)
  link_BETA1-4         : angle       1.35821 (    3)
  link_NAG-ASN         : bond        0.00451 (    1)
  link_NAG-ASN         : angle       3.01655 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.078 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8536 (tp) cc_final: 0.8216 (tt)
REVERT: H   28 THR cc_start: 0.8216 (m) cc_final: 0.7948 (p)
REVERT: H   51 MET cc_start: 0.7448 (ttp) cc_final: 0.7242 (ttp)
REVERT: F  365 TYR cc_start: 0.8014 (m-10) cc_final: 0.7768 (m-10)
REVERT: F  406 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8521 (mm-30)
REVERT: F  425 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8233 (mp)
  outliers start: 21
  outliers final: 18
  residues processed: 89
  average time/residue: 0.0492
  time to fit residues: 5.5716
Evaluate side-chains
  93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0060
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** F 409 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 = 0.4002 r_free = 0.4002 target = 0.168706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.153002 restraints weight = 6556.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.157597 restraints weight = 5030.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.159779 restraints weight = 2252.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.161072 restraints weight = 1542.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.161269 restraints weight = 1330.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3431  Z= 0.132
  Angle     :  0.667   7.405   4666  Z= 0.337
  Chirality :  0.044   0.140    495
  Planarity :  0.004   0.031    603
  Dihedral  :  5.756  24.818    520
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.64 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 24.37 %
    Favored  : 70.03 %
  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: -2.83 (0.39), residues: 419
  helix: -5.84 (0.26), residues: 5
  sheet: -0.83 (0.45), residues: 139
  loop : -2.52 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 457 
 TYR   0.013   0.001   TYR F 369 
 PHE   0.024   0.002   PHE H  27 
 TRP   0.009   0.001   TRP L  37 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3426)
  covalent geometry    : angle       0.66097 ( 4654)
  SS BOND              : bond        0.00264 (    3)
  SS BOND              : angle       0.92728 (    6)
  hydrogen bonds       : bond        0.02915 (   63)
  hydrogen bonds       : angle       5.77323 (  153)
  link_BETA1-4         : bond        0.00717 (    1)
  link_BETA1-4         : angle       1.39028 (    3)
  link_NAG-ASN         : bond        0.00347 (    1)
  link_NAG-ASN         : angle       3.18552 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.076 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8500 (tp) cc_final: 0.8218 (tt)
REVERT: H   28 THR cc_start: 0.8262 (m) cc_final: 0.7984 (p)
REVERT: H   51 MET cc_start: 0.7346 (ttp) cc_final: 0.7092 (ttm)
REVERT: F  406 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8494 (mm-30)
REVERT: F  425 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8194 (mp)
  outliers start: 20
  outliers final: 17
  residues processed: 84
  average time/residue: 0.0442
  time to fit residues: 4.8273
Evaluate side-chains
  91 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0670
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 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 = 0.4012 r_free = 0.4012 target = 0.169413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.154060 restraints weight = 6554.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.158218 restraints weight = 4962.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.160304 restraints weight = 2341.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.161278 restraints weight = 1623.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.161467 restraints weight = 1429.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3431  Z= 0.129
  Angle     :  0.656   7.421   4666  Z= 0.333
  Chirality :  0.044   0.144    495
  Planarity :  0.004   0.029    603
  Dihedral  :  5.621  24.999    520
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.07 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 25.49 %
    Favored  : 69.19 %
  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: -2.78 (0.39), residues: 419
  helix: -5.84 (0.26), residues: 5
  sheet: -0.81 (0.44), residues: 139
  loop : -2.48 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 457 
 TYR   0.012   0.001   TYR F 369 
 PHE   0.023   0.001   PHE H  27 
 TRP   0.009   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3426)
  covalent geometry    : angle       0.64974 ( 4654)
  SS BOND              : bond        0.00258 (    3)
  SS BOND              : angle       0.97998 (    6)
  hydrogen bonds       : bond        0.02913 (   63)
  hydrogen bonds       : angle       5.66181 (  153)
  link_BETA1-4         : bond        0.00757 (    1)
  link_BETA1-4         : angle       1.34579 (    3)
  link_NAG-ASN         : bond        0.00343 (    1)
  link_NAG-ASN         : angle       3.19261 (    3)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.101 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8414 (tp) cc_final: 0.8122 (tt)
REVERT: H   28 THR cc_start: 0.8286 (m) cc_final: 0.8026 (p)
REVERT: F  406 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8518 (mm-30)
REVERT: F  425 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8206 (mp)
  outliers start: 19
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0368
  time to fit residues: 4.1151
Evaluate side-chains
  89 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  371 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 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 = 0.3993 r_free = 0.3993 target = 0.167772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152284 restraints weight = 6707.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.156470 restraints weight = 5174.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.158438 restraints weight = 2390.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.159325 restraints weight = 1704.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.159616 restraints weight = 1520.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3431  Z= 0.161
  Angle     :  0.688   7.535   4666  Z= 0.348
  Chirality :  0.045   0.151    495
  Planarity :  0.004   0.029    603
  Dihedral  :  5.801  24.762    520
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.31 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 25.49 %
    Favored  : 69.19 %
  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: -2.73 (0.39), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -0.73 (0.45), residues: 139
  loop : -2.48 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 457 
 TYR   0.018   0.001   TYR F 365 
 PHE   0.025   0.002   PHE H  27 
 TRP   0.009   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3426)
  covalent geometry    : angle       0.68145 ( 4654)
  SS BOND              : bond        0.00378 (    3)
  SS BOND              : angle       1.19887 (    6)
  hydrogen bonds       : bond        0.03152 (   63)
  hydrogen bonds       : angle       5.70962 (  153)
  link_BETA1-4         : bond        0.00806 (    1)
  link_BETA1-4         : angle       1.32468 (    3)
  link_NAG-ASN         : bond        0.00373 (    1)
  link_NAG-ASN         : angle       3.26036 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 987.16 seconds
wall clock time: 17 minutes 42.50 seconds (1062.50 seconds total)