Starting phenix.real_space_refine
on Tue Mar  3 11:05:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mji_23874/03_2026/7mji_23874.cif"
  }
  resolution = 2.81
  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=   0.024
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      14      5.16       5
     C    1597      2.51       5
     N     425      2.21       5
     O     486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2522
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1547
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "E"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 961
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 4, 'TRANS': 120}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.68, per 1000 atoms: 0.27
  Number of scatterers: 2522
  At special positions: 0
  Unit cell: (84, 59, 79, 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      14     16.00
     O     486      8.00
     N     425      7.00
     C    1597      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  43 " - pdb=" SG  CYS E 116 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
  Time building additional restraints: 0.19
  Conformation dependent library (CDL) restraints added in 76.1 milliseconds
  

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  582

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 7 sheets defined
      16.6% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 3.648A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.555A  pdb=" N   GLU B 406 " --> pdb=" O   ARG B 403 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL B 407 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.614A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 53
      removed outlier: 4.400A  pdb=" N   ASP E  52 " --> pdb=" O   THR E  49 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR E  53 " --> pdb=" O   PHE E  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 49 through 53'
    Processing helix  chain 'E' and resid 84 through 86
      No H-bonds generated for 'chain 'E' and resid 84 through 86'
    Processing helix  chain 'E' and resid 107 through 111
      removed outlier: 3.511A  pdb=" N   THR E 111 " --> pdb=" O   ALA E 108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.835A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.835A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 28
      removed outlier: 3.644A  pdb=" N   LEU E  99 " --> pdb=" O   CYS E  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 33
      removed outlier: 6.611A  pdb=" N   MET E  55 " --> pdb=" O   ARG E  71 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   ARG E  71 " --> pdb=" O   MET E  55 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   TRP E  57 " --> pdb=" O   ILE E  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 33
      removed outlier: 4.140A  pdb=" N   VAL E 134 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)

    88 hydrogen bonds defined for protein.
    210 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.35

  Time building geometry restraints manager: 0.25 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: 813
        1.34 -     1.46: 685
        1.46 -     1.58: 1070
        1.58 -     1.71: 0
        1.71 -     1.83: 18
  Bond restraints: 2586
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.72e+00
  bond pdb=" CG  LEU E  41 "
       pdb=" CD1 LEU E  41 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.96e+00
  bond pdb=" CB  ASN B 360 "
       pdb=" CG  ASN B 360 "
    ideal  model  delta    sigma   weight residual
    1.516  1.556 -0.040 2.50e-02 1.60e+03 2.52e+00
  bond pdb=" C   TYR B 505 "
       pdb=" N   GLN B 506 "
    ideal  model  delta    sigma   weight residual
    1.340  1.266  0.074 5.87e-02 2.90e+02 1.58e+00
  bond pdb=" CG1 ILE E  69 "
       pdb=" CD1 ILE E  69 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.58e+00
  ... (remaining 2581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 3354
        1.81 -     3.63: 139
        3.63 -     5.44: 18
        5.44 -     7.25: 3
        7.25 -     9.06: 1
  Bond angle restraints: 3515
  Sorted by residual:
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.23   -2.63 1.00e+00 1.00e+00 6.90e+00
  angle pdb=" CA  LEU E  84 "
        pdb=" CB  LEU E  84 "
        pdb=" CG  LEU E  84 "
      ideal   model   delta    sigma   weight residual
     116.30  125.36   -9.06 3.50e+00 8.16e-02 6.71e+00
  angle pdb=" C   LYS E  96 "
        pdb=" N   ASN E  97 "
        pdb=" CA  ASN E  97 "
      ideal   model   delta    sigma   weight residual
     122.36  125.96   -3.60 1.42e+00 4.96e-01 6.41e+00
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.93  126.73   -3.80 1.51e+00 4.39e-01 6.33e+00
  angle pdb=" CB  ARG E  59 "
        pdb=" CG  ARG E  59 "
        pdb=" CD  ARG E  59 "
      ideal   model   delta    sigma   weight residual
     111.30  116.91   -5.61 2.30e+00 1.89e-01 5.95e+00
  ... (remaining 3510 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.39: 1393
       15.39 -    30.77: 110
       30.77 -    46.15: 20
       46.15 -    61.54: 6
       61.54 -    76.92: 5
  Dihedral angle restraints: 1534
    sinusoidal: 610
      harmonic: 924
  Sorted by residual:
  dihedral pdb=" CA  LEU B 517 "
           pdb=" C   LEU B 517 "
           pdb=" N   LEU B 518 "
           pdb=" CA  LEU B 518 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.84   18.16     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  ARG B 403 "
           pdb=" C   ARG B 403 "
           pdb=" N   GLY B 404 "
           pdb=" CA  GLY B 404 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.99  -18.01     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  PHE B 515 "
           pdb=" C   PHE B 515 "
           pdb=" N   GLU B 516 "
           pdb=" CA  GLU B 516 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.13   17.87     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 175
       0.032 -    0.063: 114
       0.063 -    0.095: 52
       0.095 -    0.127: 26
       0.127 -    0.158: 7
  Chirality restraints: 374
  Sorted by residual:
  chirality pdb=" CA  VAL E  58 "
            pdb=" N   VAL E  58 "
            pdb=" C   VAL E  58 "
            pdb=" CB  VAL E  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  ILE B 358 "
            pdb=" N   ILE B 358 "
            pdb=" C   ILE B 358 "
            pdb=" CB  ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.07e-01
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 371 not shown)

  Planarity restraints: 459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET E 103 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.48e+00
        pdb=" C   MET E 103 "    0.040 2.00e-02 2.50e+03
        pdb=" O   MET E 103 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN E 104 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS E  43 "    0.012 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   CYS E  43 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   CYS E  43 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA E  44 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 520 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO B 521 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 521 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 521 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 456 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 917
        2.87 -     3.38: 2025
        3.38 -     3.89: 4248
        3.89 -     4.39: 4808
        4.39 -     4.90: 8495
  Nonbonded interactions: 20493
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 366 "
            pdb=" OD1 ASN B 388 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" NE  ARG E  71 "
            pdb=" OD2 ASP E 119 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" NE2 GLN E  60 "
            pdb=" O   LYS E  64 "
     model   vdw
     2.446 3.120
  nonbonded pdb=" OH  TYR B 489 "
            pdb=" NH2 ARG E 124 "
     model   vdw
     2.474 3.120
  nonbonded pdb=" NE  ARG B 457 "
            pdb=" OD2 ASP B 467 "
     model   vdw
     2.492 3.120
  ... (remaining 20488 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.100
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.006   0.074   2592  Z= 0.258
  Angle     :  0.818   9.063   3528  Z= 0.430
  Chirality :  0.053   0.158    374
  Planarity :  0.008   0.070    458
  Dihedral  : 12.491  76.924    937
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.44), residues: 316
  helix: -4.87 (0.21), residues: 27
  sheet:  0.26 (0.55), residues: 93
  loop : -0.23 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG B 357 
 TYR   0.021   0.002   TYR B 495 
 PHE   0.017   0.002   PHE B 377 
 TRP   0.016   0.002   TRP E  68 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 2586)
  covalent geometry    : angle       0.80814 ( 3515)
  SS BOND              : bond        0.00448 (    5)
  SS BOND              : angle       1.73843 (   10)
  hydrogen bonds       : bond        0.14570 (   78)
  hydrogen bonds       : angle       9.73884 (  210)
  link_NAG-ASN         : bond        0.00920 (    1)
  link_NAG-ASN         : angle       3.50596 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.4531
  time to fit residues: 34.3065
Evaluate side-chains
  63 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0010
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 360 ASN
B 388 ASN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 120 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.095988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084407 restraints weight = 4332.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.69
r_work: 0.3089 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2592  Z= 0.148
  Angle     :  0.526   4.375   3528  Z= 0.273
  Chirality :  0.043   0.129    374
  Planarity :  0.004   0.029    458
  Dihedral  :  5.248  39.730    380
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 10.29 %
    Favored  : 86.03 %
  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: -0.19 (0.46), residues: 316
  helix: -4.14 (0.44), residues: 28
  sheet:  0.67 (0.57), residues: 89
  loop :  0.21 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.013   0.001   TYR B 365 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.010   0.001   TRP E  57 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2586)
  covalent geometry    : angle       0.51717 ( 3515)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       1.40043 (   10)
  hydrogen bonds       : bond        0.04006 (   78)
  hydrogen bonds       : angle       7.34506 (  210)
  link_NAG-ASN         : bond        0.00275 (    1)
  link_NAG-ASN         : angle       2.22755 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.091 
Fit side-chains
REVERT: B  360 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (t0)
REVERT: B  394 ASN cc_start: 0.7349 (m-40) cc_final: 0.7066 (p0)
REVERT: E   42 SER cc_start: 0.8644 (m) cc_final: 0.8389 (p)
REVERT: E   77 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7961 (ptp90)
  outliers start: 10
  outliers final: 4
  residues processed: 78
  average time/residue: 0.4624
  time to fit residues: 36.9720
Evaluate side-chains
  75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain E residue   77 ARG
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 360 ASN
B 370 ASN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.095270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.084184 restraints weight = 4219.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.48
r_work: 0.3055 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   2592  Z= 0.188
  Angle     :  0.532   4.627   3528  Z= 0.275
  Chirality :  0.043   0.130    374
  Planarity :  0.004   0.028    458
  Dihedral  :  5.367  43.019    380
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.07 %
    Favored  : 81.62 %
  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: -0.05 (0.47), residues: 316
  helix: -3.42 (0.73), residues: 28
  sheet:  0.59 (0.56), residues: 89
  loop :  0.30 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.008   0.001   PHE B 377 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 2586)
  covalent geometry    : angle       0.52396 ( 3515)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       1.55126 (   10)
  hydrogen bonds       : bond        0.03544 (   78)
  hydrogen bonds       : angle       7.06303 (  210)
  link_NAG-ASN         : bond        0.00337 (    1)
  link_NAG-ASN         : angle       1.87874 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.101 
Fit side-chains
REVERT: E   42 SER cc_start: 0.8582 (m) cc_final: 0.8307 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 76
  average time/residue: 0.4320
  time to fit residues: 33.7031
Evaluate side-chains
  74 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   91 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 370 ASN
B 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.093844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.082727 restraints weight = 4423.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.65
r_work: 0.3057 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2592  Z= 0.165
  Angle     :  0.529   5.061   3528  Z= 0.274
  Chirality :  0.044   0.160    374
  Planarity :  0.003   0.029    458
  Dihedral  :  5.238  42.012    380
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.44 %
    Favored  : 81.62 %
  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: -0.09 (0.46), residues: 316
  helix: -3.13 (0.87), residues: 28
  sheet:  0.07 (0.55), residues: 84
  loop :  0.48 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 357 
 TYR   0.012   0.001   TYR B 495 
 PHE   0.012   0.001   PHE B 392 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 2586)
  covalent geometry    : angle       0.52147 ( 3515)
  SS BOND              : bond        0.00377 (    5)
  SS BOND              : angle       1.41569 (   10)
  hydrogen bonds       : bond        0.03180 (   78)
  hydrogen bonds       : angle       6.90575 (  210)
  link_NAG-ASN         : bond        0.00289 (    1)
  link_NAG-ASN         : angle       1.87627 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.099 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.4523
  time to fit residues: 34.3650
Evaluate side-chains
  76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   91 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 14 optimal weight:    0.0060
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.094369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.083238 restraints weight = 4407.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.67
r_work: 0.3062 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2592  Z= 0.142
  Angle     :  0.514   5.229   3528  Z= 0.266
  Chirality :  0.043   0.137    374
  Planarity :  0.003   0.026    458
  Dihedral  :  5.166  41.170    380
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.44 %
    Favored  : 82.35 %
  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: -0.08 (0.47), residues: 316
  helix: -2.92 (0.93), residues: 28
  sheet: -0.05 (0.54), residues: 84
  loop :  0.53 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.010   0.001   TYR B 495 
 PHE   0.012   0.001   PHE B 392 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 2586)
  covalent geometry    : angle       0.50745 ( 3515)
  SS BOND              : bond        0.00258 (    5)
  SS BOND              : angle       1.26949 (   10)
  hydrogen bonds       : bond        0.03106 (   78)
  hydrogen bonds       : angle       6.71448 (  210)
  link_NAG-ASN         : bond        0.00262 (    1)
  link_NAG-ASN         : angle       1.88201 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.063 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.4224
  time to fit residues: 30.7857
Evaluate side-chains
  73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   91 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.093680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.082609 restraints weight = 4424.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.65
r_work: 0.3052 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2592  Z= 0.165
  Angle     :  0.523   6.233   3528  Z= 0.269
  Chirality :  0.043   0.140    374
  Planarity :  0.003   0.026    458
  Dihedral  :  5.296  43.184    380
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.54 %
    Favored  : 80.51 %
  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: -0.21 (0.46), residues: 316
  helix: -3.18 (1.11), residues: 21
  sheet: -0.22 (0.55), residues: 82
  loop :  0.35 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.011   0.001   TYR B 495 
 PHE   0.009   0.001   PHE B 392 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 2586)
  covalent geometry    : angle       0.51645 ( 3515)
  SS BOND              : bond        0.00351 (    5)
  SS BOND              : angle       1.34029 (   10)
  hydrogen bonds       : bond        0.03004 (   78)
  hydrogen bonds       : angle       6.73478 (  210)
  link_NAG-ASN         : bond        0.00217 (    1)
  link_NAG-ASN         : angle       1.91844 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.091 
Fit side-chains
REVERT: B  360 ASN cc_start: 0.8929 (t0) cc_final: 0.8610 (t0)
REVERT: E   77 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7887 (ptp90)
  outliers start: 8
  outliers final: 5
  residues processed: 75
  average time/residue: 0.4490
  time to fit residues: 34.5627
Evaluate side-chains
  76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   77 ARG
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.094276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.083310 restraints weight = 4268.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.59
r_work: 0.3070 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2592  Z= 0.144
  Angle     :  0.514   6.393   3528  Z= 0.264
  Chirality :  0.043   0.140    374
  Planarity :  0.003   0.027    458
  Dihedral  :  5.173  41.680    380
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.91 %
    Favored  : 79.41 %
  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: -0.17 (0.46), residues: 316
  helix: -3.23 (1.06), residues: 21
  sheet: -0.19 (0.54), residues: 84
  loop :  0.40 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 357 
 TYR   0.010   0.001   TYR B 495 
 PHE   0.008   0.001   PHE B 392 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2586)
  covalent geometry    : angle       0.50676 ( 3515)
  SS BOND              : bond        0.00342 (    5)
  SS BOND              : angle       1.37539 (   10)
  hydrogen bonds       : bond        0.02872 (   78)
  hydrogen bonds       : angle       6.70578 (  210)
  link_NAG-ASN         : bond        0.00225 (    1)
  link_NAG-ASN         : angle       1.95640 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B  360 ASN cc_start: 0.8950 (t0) cc_final: 0.8600 (t0)
REVERT: E   77 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7929 (ptp90)
  outliers start: 10
  outliers final: 5
  residues processed: 76
  average time/residue: 0.4216
  time to fit residues: 32.9368
Evaluate side-chains
  75 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   77 ARG
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   91 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0470
   chunk 2 optimal weight:    0.0030
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.3488

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
B 414 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.095585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.084508 restraints weight = 4383.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.66
r_work: 0.3085 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   2592  Z= 0.106
  Angle     :  0.496   6.954   3528  Z= 0.254
  Chirality :  0.042   0.140    374
  Planarity :  0.003   0.027    458
  Dihedral  :  4.868  38.565    380
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.18 %
    Favored  : 80.51 %
  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: -0.01 (0.47), residues: 316
  helix: -3.22 (1.04), residues: 21
  sheet: -0.05 (0.55), residues: 82
  loop :  0.50 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 357 
 TYR   0.012   0.001   TYR B 365 
 PHE   0.008   0.001   PHE B 392 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2586)
  covalent geometry    : angle       0.48964 ( 3515)
  SS BOND              : bond        0.00296 (    5)
  SS BOND              : angle       1.24677 (   10)
  hydrogen bonds       : bond        0.02759 (   78)
  hydrogen bonds       : angle       6.61236 (  210)
  link_NAG-ASN         : bond        0.00256 (    1)
  link_NAG-ASN         : angle       1.92537 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.098 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9154 (ttt90) cc_final: 0.8863 (ptm160)
REVERT: B  360 ASN cc_start: 0.8957 (t0) cc_final: 0.8598 (t0)
REVERT: B  424 LYS cc_start: 0.9034 (tptp) cc_final: 0.8617 (tppp)
REVERT: E   77 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7836 (ptp90)
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.4473
  time to fit residues: 33.9535
Evaluate side-chains
  78 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 MET
Chi-restraints excluded: chain E residue   77 ARG
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  139 THR
Chi-restraints excluded: chain E residue  144 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0370
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.094795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.083561 restraints weight = 4434.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.67
r_work: 0.3072 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2592  Z= 0.135
  Angle     :  0.527   7.269   3528  Z= 0.270
  Chirality :  0.043   0.141    374
  Planarity :  0.003   0.026    458
  Dihedral  :  5.094  40.537    380
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.91 %
    Favored  : 80.15 %
  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: -0.03 (0.47), residues: 316
  helix: -3.12 (1.07), residues: 21
  sheet:  0.02 (0.55), residues: 82
  loop :  0.43 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.011   0.001   TYR E  80 
 PHE   0.007   0.001   PHE B 392 
 TRP   0.007   0.001   TRP E  68 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 2586)
  covalent geometry    : angle       0.52097 ( 3515)
  SS BOND              : bond        0.00325 (    5)
  SS BOND              : angle       1.27374 (   10)
  hydrogen bonds       : bond        0.02947 (   78)
  hydrogen bonds       : angle       6.54200 (  210)
  link_NAG-ASN         : bond        0.00249 (    1)
  link_NAG-ASN         : angle       1.88850 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.087 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9196 (ttt90) cc_final: 0.8869 (ptm160)
REVERT: B  360 ASN cc_start: 0.8990 (t0) cc_final: 0.8624 (t0)
REVERT: B  418 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8566 (mp)
REVERT: B  424 LYS cc_start: 0.9030 (tptp) cc_final: 0.8614 (tppp)
REVERT: E   85 LYS cc_start: 0.7774 (tttm) cc_final: 0.7396 (mtpm)
REVERT: E  119 ASP cc_start: 0.8575 (m-30) cc_final: 0.8310 (m-30)
REVERT: E  132 MET cc_start: 0.8738 (mmt) cc_final: 0.7846 (mmt)
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.4627
  time to fit residues: 32.2743
Evaluate side-chains
  70 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   87 LEU
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  144 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0670
   chunk 12 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.3318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.096040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.084861 restraints weight = 4419.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.65
r_work: 0.3097 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2592  Z= 0.106
  Angle     :  0.515   7.219   3528  Z= 0.264
  Chirality :  0.043   0.140    374
  Planarity :  0.003   0.026    458
  Dihedral  :  4.868  37.995    380
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.28 %
    Favored  : 80.51 %
  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:  0.01 (0.47), residues: 316
  helix: -3.19 (1.03), residues: 21
  sheet:  0.04 (0.56), residues: 82
  loop :  0.47 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.013   0.001   TYR B 365 
 PHE   0.008   0.001   PHE B 392 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2586)
  covalent geometry    : angle       0.50826 ( 3515)
  SS BOND              : bond        0.00256 (    5)
  SS BOND              : angle       1.28229 (   10)
  hydrogen bonds       : bond        0.02897 (   78)
  hydrogen bonds       : angle       6.46935 (  210)
  link_NAG-ASN         : bond        0.00264 (    1)
  link_NAG-ASN         : angle       1.91113 (    3)

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

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

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  632 Ramachandran restraints generated.
    316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.098 
Fit side-chains
REVERT: B  357 ARG cc_start: 0.9191 (ttt90) cc_final: 0.8882 (ptm160)
REVERT: B  360 ASN cc_start: 0.8981 (t0) cc_final: 0.8617 (t0)
REVERT: B  418 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8483 (mp)
REVERT: B  424 LYS cc_start: 0.9028 (tptp) cc_final: 0.8601 (tppp)
REVERT: E   85 LYS cc_start: 0.7801 (tttm) cc_final: 0.7430 (mtpm)
  outliers start: 6
  outliers final: 4
  residues processed: 73
  average time/residue: 0.4226
  time to fit residues: 31.6895
Evaluate side-chains
  69 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  515 PHE
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  144 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 31
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0050
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0040
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.7008

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.082500 restraints weight = 4370.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.59
r_work: 0.3030 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2592  Z= 0.162
  Angle     :  0.546   7.396   3528  Z= 0.279
  Chirality :  0.044   0.141    374
  Planarity :  0.003   0.026    458
  Dihedral  :  5.238  42.441    380
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.75 %
    Favored  : 79.41 %
  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: -0.03 (0.47), residues: 316
  helix: -3.09 (1.09), residues: 21
  sheet:  0.03 (0.57), residues: 82
  loop :  0.42 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.010   0.001   TYR B 495 
 PHE   0.008   0.001   PHE B 515 
 TRP   0.007   0.001   TRP E  68 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 2586)
  covalent geometry    : angle       0.53939 ( 3515)
  SS BOND              : bond        0.00303 (    5)
  SS BOND              : angle       1.37749 (   10)
  hydrogen bonds       : bond        0.02947 (   78)
  hydrogen bonds       : angle       6.66921 (  210)
  link_NAG-ASN         : bond        0.00196 (    1)
  link_NAG-ASN         : angle       1.95068 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1313.13 seconds
wall clock time: 22 minutes 58.42 seconds (1378.42 seconds total)