Starting phenix.real_space_refine
on Tue Mar  3 11:37:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wrj_32728/03_2026/7wrj_32728.cif"
  }
  resolution = 4.08
  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=   0.014
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    2091      2.51       5
     N     557      2.21       5
     O     627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 3289
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1504
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 973
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 7, 'TRANS': 117}
    Chain: "B"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 784
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 7, 'TRANS': 98}
    Chain: "C"
      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: 0.74, per 1000 atoms: 0.22
  Number of scatterers: 3289
  At special positions: 0
  Unit cell: (73.83, 75.97, 85.6, 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     627      8.00
     N     557      7.00
     C    2091      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  89 " distance=2.04

  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 C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN R 343 "
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 97.0 milliseconds
  

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 9 sheets defined
      7.7% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'R' and resid 364 through 368
    Processing helix  chain 'R' and resid 403 through 407
      removed outlier: 3.704A  pdb=" N   VAL R 407 " --> pdb=" O   GLY R 404 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'R' and resid 502 through 506
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 3.954A  pdb=" N   ASP B  83 " --> pdb=" O   GLN B  80 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLU B  84 " --> pdb=" O   SER B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 80 through 84'
    Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.628A  pdb=" N   VAL R 395 " --> pdb=" O   ILE R 358 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL R 512 " --> pdb=" O   ASP R 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.510A  pdb=" N   THR A  83 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.589A  pdb=" N   ALA A  98 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   LEU A  52 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A  52 " --> pdb=" O   ARG A  60 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG A  60 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.868A  pdb=" N   MET A 115 " --> pdb=" O   HIS A  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10
    Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19
    Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23
    Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49
      removed outlier: 5.736A  pdb=" N   LEU B  47 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   GLN B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU B  90 " --> pdb=" O   ASN B  35 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLY B  98 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    174 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: 0.42

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 997
        1.33 -     1.46: 912
        1.46 -     1.59: 1448
        1.59 -     1.72: 1
        1.72 -     1.85: 15
  Bond restraints: 3373
  Sorted by residual:
  bond pdb=" CB  CYS R 336 "
       pdb=" SG  CYS R 336 "
    ideal  model  delta    sigma   weight residual
    1.808  1.716  0.092 3.30e-02 9.18e+02 7.73e+00
  bond pdb=" CG1 ILE R 418 "
       pdb=" CD1 ILE R 418 "
    ideal  model  delta    sigma   weight residual
    1.513  1.408  0.105 3.90e-02 6.57e+02 7.27e+00
  bond pdb=" C   PRO R 373 "
       pdb=" O   PRO R 373 "
    ideal  model  delta    sigma   weight residual
    1.235  1.206  0.029 1.30e-02 5.92e+03 5.12e+00
  bond pdb=" CA  CYS R 525 "
       pdb=" C   CYS R 525 "
    ideal  model  delta    sigma   weight residual
    1.527  1.548 -0.021 9.80e-03 1.04e+04 4.56e+00
  bond pdb=" N   LEU R 371 "
       pdb=" CA  LEU R 371 "
    ideal  model  delta    sigma   weight residual
    1.464  1.489 -0.025 1.20e-02 6.94e+03 4.33e+00
  ... (remaining 3368 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 4250
        2.26 -     4.52: 276
        4.52 -     6.78: 51
        6.78 -     9.04: 10
        9.04 -    11.30: 6
  Bond angle restraints: 4593
  Sorted by residual:
  angle pdb=" N   PRO R 373 "
        pdb=" CA  PRO R 373 "
        pdb=" CB  PRO R 373 "
      ideal   model   delta    sigma   weight residual
     103.25   96.66    6.59 1.05e+00 9.07e-01 3.94e+01
  angle pdb=" N   ASN R 370 "
        pdb=" CA  ASN R 370 "
        pdb=" C   ASN R 370 "
      ideal   model   delta    sigma   weight residual
     113.16  106.83    6.33 1.24e+00 6.50e-01 2.61e+01
  angle pdb=" C   ASP R 364 "
        pdb=" N   TYR R 365 "
        pdb=" CA  TYR R 365 "
      ideal   model   delta    sigma   weight residual
     120.28  127.60   -7.32 1.44e+00 4.82e-01 2.58e+01
  angle pdb=" C   TYR B  50 "
        pdb=" N   HIS B  51 "
        pdb=" CA  HIS B  51 "
      ideal   model   delta    sigma   weight residual
     121.54  130.77   -9.23 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" CB  GLN R 409 "
        pdb=" CG  GLN R 409 "
        pdb=" CD  GLN R 409 "
      ideal   model   delta    sigma   weight residual
     112.60  119.86   -7.26 1.70e+00 3.46e-01 1.82e+01
  ... (remaining 4588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.56: 1701
       14.56 -    29.12: 247
       29.12 -    43.68: 52
       43.68 -    58.24: 10
       58.24 -    72.80: 5
  Dihedral angle restraints: 2015
    sinusoidal: 811
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" CA  LEU R 461 "
           pdb=" C   LEU R 461 "
           pdb=" N   LYS R 462 "
           pdb=" CA  LYS R 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.97   31.03     0      5.00e+00 4.00e-02 3.85e+01
  dihedral pdb=" CA  GLN B  80 "
           pdb=" C   GLN B  80 "
           pdb=" N   SER B  81 "
           pdb=" CA  SER B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.63  -27.37     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CB  CYS R 336 "
           pdb=" SG  CYS R 336 "
           pdb=" SG  CYS R 361 "
           pdb=" CB  CYS R 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.11   45.11     1      1.00e+01 1.00e-02 2.82e+01
  ... (remaining 2012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 320
       0.059 -    0.118: 145
       0.118 -    0.177: 39
       0.177 -    0.235: 6
       0.235 -    0.294: 2
  Chirality restraints: 512
  Sorted by residual:
  chirality pdb=" CB  ILE R 468 "
            pdb=" CA  ILE R 468 "
            pdb=" CG1 ILE R 468 "
            pdb=" CG2 ILE R 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.94   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CG  LEU B  96 "
            pdb=" CB  LEU B  96 "
            pdb=" CD1 LEU B  96 "
            pdb=" CD2 LEU B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CG  LEU B  48 "
            pdb=" CB  LEU B  48 "
            pdb=" CD1 LEU B  48 "
            pdb=" CD2 LEU B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 509 not shown)

  Planarity restraints: 589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 365 "    0.013 2.00e-02 2.50e+03   2.82e-02 1.59e+01
        pdb=" CG  TYR R 365 "   -0.066 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 365 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 365 "    0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 365 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 365 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 365 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 365 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 369 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.31e+00
        pdb=" C   TYR R 369 "    0.053 2.00e-02 2.50e+03
        pdb=" O   TYR R 369 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASN R 370 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.017 2.00e-02 2.50e+03   2.05e-02 8.38e+00
        pdb=" CG  TYR B  88 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 586 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 824
        2.78 -     3.31: 3092
        3.31 -     3.84: 5780
        3.84 -     4.37: 6424
        4.37 -     4.90: 10952
  Nonbonded interactions: 27072
  Sorted by model distance:
  nonbonded pdb=" OG  SER R 438 "
            pdb=" O   LYS R 440 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR B  13 "
            pdb=" OE1 GLN B  16 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   PRO B   7 "
            pdb=" OG1 THR B 105 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OD2 ASP R 398 "
            pdb=" OH  TYR R 423 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   TYR R 396 "
            pdb=" OG  SER R 514 "
     model   vdw
     2.307 3.040
  ... (remaining 27067 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.710
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.740
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
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      :  0.009   0.105   3380  Z= 0.400
  Angle     :  1.325  11.297   4609  Z= 0.713
  Chirality :  0.069   0.294    512
  Planarity :  0.009   0.067    588
  Dihedral  : 14.006  72.801   1232
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  : 11.46 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  1.38 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -2.57 (0.39), residues: 410
  helix: -4.65 (0.52), residues: 21
  sheet: -0.77 (0.43), residues: 142
  loop : -2.08 (0.37), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG R 408 
 TYR   0.066   0.005   TYR R 365 
 PHE   0.034   0.004   PHE A  96 
 TRP   0.020   0.004   TRP A  55 
 HIS   0.011   0.003   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00895 ( 3373)
  covalent geometry    : angle       1.31559 ( 4593)
  SS BOND              : bond        0.00546 (    5)
  SS BOND              : angle       3.26513 (   10)
  hydrogen bonds       : bond        0.28264 (   77)
  hydrogen bonds       : angle      11.83711 (  174)
  link_BETA1-4         : bond        0.00189 (    1)
  link_BETA1-4         : angle       3.48057 (    3)
  link_NAG-ASN         : bond        0.00592 (    1)
  link_NAG-ASN         : angle       1.14195 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  353 TRP cc_start: 0.8506 (p-90) cc_final: 0.7034 (p-90)
REVERT: R  387 LEU cc_start: 0.8124 (mp) cc_final: 0.7595 (mp)
REVERT: R  396 TYR cc_start: 0.6913 (m-80) cc_final: 0.6704 (m-80)
REVERT: R  410 ILE cc_start: 0.8475 (mm) cc_final: 0.8253 (mm)
REVERT: R  453 TYR cc_start: 0.7520 (p90) cc_final: 0.7298 (p90)
REVERT: R  496 SER cc_start: 0.8448 (t) cc_final: 0.8172 (p)
REVERT: A    4 LEU cc_start: 0.8974 (mm) cc_final: 0.8681 (mm)
REVERT: A    7 SER cc_start: 0.9348 (p) cc_final: 0.8989 (m)
REVERT: A   69 LEU cc_start: 0.8035 (mm) cc_final: 0.7822 (mm)
REVERT: A  115 MET cc_start: 0.8302 (tpt) cc_final: 0.7835 (tpp)
REVERT: A  121 MET cc_start: 0.6637 (ptt) cc_final: 0.6412 (ppp)
REVERT: B   36 TRP cc_start: 0.8302 (m100) cc_final: 0.8069 (m100)
REVERT: B   37 TYR cc_start: 0.7704 (m-80) cc_final: 0.7321 (m-80)
REVERT: B   90 GLU cc_start: 0.8174 (pt0) cc_final: 0.6756 (pt0)
REVERT: B   91 THR cc_start: 0.8922 (m) cc_final: 0.8605 (p)
REVERT: B  101 PHE cc_start: 0.8501 (m-80) cc_final: 0.8252 (m-10)
REVERT: B  109 VAL cc_start: 0.3809 (p) cc_final: 0.3385 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0742
  time to fit residues: 14.6001
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  38 GLN
B  39 HIS
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.133672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.115999 restraints weight = 8640.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.119226 restraints weight = 5166.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.121483 restraints weight = 3510.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.123088 restraints weight = 2607.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.124251 restraints weight = 2072.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3380  Z= 0.187
  Angle     :  0.824   9.453   4609  Z= 0.424
  Chirality :  0.049   0.194    512
  Planarity :  0.008   0.124    588
  Dihedral  :  7.361  31.166    498
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.78 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.46 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -2.75 (0.38), residues: 410
  helix: -4.52 (0.95), residues: 12
  sheet: -1.20 (0.42), residues: 125
  loop : -2.11 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 457 
 TYR   0.015   0.002   TYR R 421 
 PHE   0.016   0.002   PHE R 377 
 TRP   0.021   0.003   TRP A  49 
 HIS   0.005   0.002   HIS R 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3373)
  covalent geometry    : angle       0.82128 ( 4593)
  SS BOND              : bond        0.00381 (    5)
  SS BOND              : angle       1.34973 (   10)
  hydrogen bonds       : bond        0.04964 (   77)
  hydrogen bonds       : angle       8.60213 (  174)
  link_BETA1-4         : bond        0.00188 (    1)
  link_BETA1-4         : angle       2.11609 (    3)
  link_NAG-ASN         : bond        0.00137 (    1)
  link_NAG-ASN         : angle       0.73140 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  365 TYR cc_start: 0.7578 (m-80) cc_final: 0.7287 (m-80)
REVERT: R  428 ASP cc_start: 0.7732 (t0) cc_final: 0.7200 (t0)
REVERT: R  496 SER cc_start: 0.8449 (t) cc_final: 0.7833 (p)
REVERT: A    7 SER cc_start: 0.9338 (p) cc_final: 0.9013 (m)
REVERT: A   38 TRP cc_start: 0.8791 (m100) cc_final: 0.8262 (m100)
REVERT: A   61 TYR cc_start: 0.6475 (m-80) cc_final: 0.6124 (m-80)
REVERT: A   62 ASN cc_start: 0.9088 (t0) cc_final: 0.8664 (t0)
REVERT: A   87 VAL cc_start: 0.8497 (t) cc_final: 0.8296 (p)
REVERT: A  111 ASP cc_start: 0.9103 (t0) cc_final: 0.8828 (t0)
REVERT: A  115 MET cc_start: 0.8194 (tpt) cc_final: 0.7970 (tpp)
REVERT: B   37 TYR cc_start: 0.7775 (m-80) cc_final: 0.7231 (m-80)
REVERT: B   90 GLU cc_start: 0.7847 (pt0) cc_final: 0.6696 (pt0)
REVERT: B   91 THR cc_start: 0.8829 (m) cc_final: 0.8351 (p)
REVERT: B   99 VAL cc_start: 0.9114 (t) cc_final: 0.8732 (t)
  outliers start: 2
  outliers final: 2
  residues processed: 127
  average time/residue: 0.0672
  time to fit residues: 10.2605
Evaluate side-chains
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
R 334 ASN
R 474 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
B  52 ASN
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.133488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.115806 restraints weight = 8773.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.118884 restraints weight = 5352.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.121090 restraints weight = 3703.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.122690 restraints weight = 2766.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.123666 restraints weight = 2197.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3380  Z= 0.156
  Angle     :  0.730   7.091   4609  Z= 0.380
  Chirality :  0.047   0.174    512
  Planarity :  0.007   0.106    588
  Dihedral  :  6.731  29.362    498
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  : 10.00 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  4.97 %
    Favored  : 94.48 %
  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: -2.47 (0.40), residues: 410
  helix: -4.76 (0.67), residues: 14
  sheet: -1.19 (0.42), residues: 132
  loop : -1.76 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 454 
 TYR   0.019   0.002   TYR R 421 
 PHE   0.017   0.002   PHE R 377 
 TRP   0.021   0.003   TRP A  49 
 HIS   0.005   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3373)
  covalent geometry    : angle       0.72690 ( 4593)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       1.10050 (   10)
  hydrogen bonds       : bond        0.04053 (   77)
  hydrogen bonds       : angle       7.88945 (  174)
  link_BETA1-4         : bond        0.00122 (    1)
  link_BETA1-4         : angle       2.00640 (    3)
  link_NAG-ASN         : bond        0.00182 (    1)
  link_NAG-ASN         : angle       1.06414 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: R  365 TYR cc_start: 0.7563 (m-80) cc_final: 0.7291 (m-80)
REVERT: R  387 LEU cc_start: 0.7953 (mp) cc_final: 0.7753 (mp)
REVERT: R  428 ASP cc_start: 0.7888 (t0) cc_final: 0.7242 (t0)
REVERT: R  474 GLN cc_start: 0.6046 (OUTLIER) cc_final: 0.5499 (tm-30)
REVERT: A    4 LEU cc_start: 0.9087 (mm) cc_final: 0.8885 (mm)
REVERT: A    7 SER cc_start: 0.9306 (p) cc_final: 0.9094 (m)
REVERT: A   61 TYR cc_start: 0.6423 (m-80) cc_final: 0.5682 (m-80)
REVERT: A   62 ASN cc_start: 0.9069 (t0) cc_final: 0.8553 (t0)
REVERT: A  111 ASP cc_start: 0.9059 (t0) cc_final: 0.8682 (t0)
REVERT: B    4 LEU cc_start: 0.5241 (mt) cc_final: 0.4846 (mt)
REVERT: B   37 TYR cc_start: 0.7684 (m-80) cc_final: 0.7326 (m-10)
REVERT: B   90 GLU cc_start: 0.7952 (pt0) cc_final: 0.7087 (pt0)
REVERT: B   99 VAL cc_start: 0.9103 (t) cc_final: 0.8681 (t)
REVERT: B  106 ARG cc_start: 0.8773 (mtm110) cc_final: 0.8519 (mtm-85)
  outliers start: 2
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0575
  time to fit residues: 8.4281
Evaluate side-chains
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 36 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R 417 ASN
B   6 GLN
B  38 GLN
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.133390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.115551 restraints weight = 8309.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.118701 restraints weight = 5033.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.120785 restraints weight = 3453.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.122505 restraints weight = 2592.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.123637 restraints weight = 2044.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3380  Z= 0.159
  Angle     :  0.747   8.144   4609  Z= 0.375
  Chirality :  0.046   0.195    512
  Planarity :  0.007   0.113    588
  Dihedral  :  6.658  31.814    498
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.78 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  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: -2.23 (0.41), residues: 410
  helix: -4.86 (0.60), residues: 14
  sheet: -1.03 (0.44), residues: 131
  loop : -1.57 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.016   0.002   PHE R 377 
 TRP   0.028   0.003   TRP B  36 
 HIS   0.005   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3373)
  covalent geometry    : angle       0.73839 ( 4593)
  SS BOND              : bond        0.00832 (    5)
  SS BOND              : angle       2.30643 (   10)
  hydrogen bonds       : bond        0.03537 (   77)
  hydrogen bonds       : angle       7.22596 (  174)
  link_BETA1-4         : bond        0.00444 (    1)
  link_BETA1-4         : angle       1.94388 (    3)
  link_NAG-ASN         : bond        0.00364 (    1)
  link_NAG-ASN         : angle       1.20244 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  386 LYS cc_start: 0.7893 (pttt) cc_final: 0.7610 (pttp)
REVERT: R  428 ASP cc_start: 0.7915 (t0) cc_final: 0.7247 (t0)
REVERT: R  500 THR cc_start: 0.8823 (p) cc_final: 0.8529 (p)
REVERT: A    7 SER cc_start: 0.9363 (p) cc_final: 0.9135 (m)
REVERT: A   61 TYR cc_start: 0.6834 (m-80) cc_final: 0.6174 (m-80)
REVERT: A   62 ASN cc_start: 0.9011 (t0) cc_final: 0.8540 (t0)
REVERT: A  111 ASP cc_start: 0.9104 (t0) cc_final: 0.8709 (t0)
REVERT: B   49 ILE cc_start: 0.8159 (tp) cc_final: 0.7914 (tp)
REVERT: B   99 VAL cc_start: 0.9169 (t) cc_final: 0.8542 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0568
  time to fit residues: 8.8781
Evaluate side-chains
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 417 ASN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  38 GLN
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.131602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.114048 restraints weight = 8453.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.117190 restraints weight = 5098.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.119365 restraints weight = 3477.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.121049 restraints weight = 2608.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.122264 restraints weight = 2055.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.5231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3380  Z= 0.164
  Angle     :  0.747   6.726   4609  Z= 0.378
  Chirality :  0.047   0.179    512
  Planarity :  0.006   0.093    588
  Dihedral  :  6.583  32.884    498
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.76 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.42), residues: 410
  helix: -3.63 (0.91), residues: 20
  sheet: -0.92 (0.45), residues: 128
  loop : -1.39 (0.40), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 106 
 TYR   0.016   0.002   TYR R 421 
 PHE   0.018   0.002   PHE R 377 
 TRP   0.028   0.003   TRP B  36 
 HIS   0.004   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3373)
  covalent geometry    : angle       0.73776 ( 4593)
  SS BOND              : bond        0.00374 (    5)
  SS BOND              : angle       2.26160 (   10)
  hydrogen bonds       : bond        0.03387 (   77)
  hydrogen bonds       : angle       7.02479 (  174)
  link_BETA1-4         : bond        0.00079 (    1)
  link_BETA1-4         : angle       2.00895 (    3)
  link_NAG-ASN         : bond        0.00479 (    1)
  link_NAG-ASN         : angle       1.66812 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  386 LYS cc_start: 0.7935 (pttt) cc_final: 0.7696 (pttp)
REVERT: R  402 ILE cc_start: 0.8788 (tt) cc_final: 0.8559 (tt)
REVERT: R  428 ASP cc_start: 0.7967 (t0) cc_final: 0.7380 (t70)
REVERT: R  500 THR cc_start: 0.8633 (p) cc_final: 0.8143 (t)
REVERT: A    7 SER cc_start: 0.9345 (p) cc_final: 0.9039 (m)
REVERT: A   13 LYS cc_start: 0.4354 (mmtt) cc_final: 0.3916 (mmmt)
REVERT: A   61 TYR cc_start: 0.6825 (m-80) cc_final: 0.6593 (m-80)
REVERT: B   49 ILE cc_start: 0.8161 (tp) cc_final: 0.7470 (tt)
REVERT: B   90 GLU cc_start: 0.7893 (pt0) cc_final: 0.7158 (pt0)
REVERT: B  106 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8187 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0553
  time to fit residues: 8.2188
Evaluate side-chains
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0970
   chunk 9 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0030
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.2906

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  80 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 = 0.3900 r_free = 0.3900 target = 0.135648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.118189 restraints weight = 8463.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121404 restraints weight = 5113.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.123702 restraints weight = 3507.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.125381 restraints weight = 2604.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.126593 restraints weight = 2042.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3380  Z= 0.124
  Angle     :  0.712   8.849   4609  Z= 0.355
  Chirality :  0.046   0.185    512
  Planarity :  0.007   0.116    588
  Dihedral  :  6.279  33.687    498
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.56 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  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: -1.92 (0.43), residues: 410
  helix: -3.59 (0.88), residues: 20
  sheet: -0.92 (0.45), residues: 139
  loop : -1.28 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.016   0.002   TYR R 365 
 PHE   0.014   0.001   PHE R 377 
 TRP   0.033   0.003   TRP B  36 
 HIS   0.004   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3373)
  covalent geometry    : angle       0.70622 ( 4593)
  SS BOND              : bond        0.00134 (    5)
  SS BOND              : angle       1.74404 (   10)
  hydrogen bonds       : bond        0.03239 (   77)
  hydrogen bonds       : angle       6.76856 (  174)
  link_BETA1-4         : bond        0.00281 (    1)
  link_BETA1-4         : angle       1.77313 (    3)
  link_NAG-ASN         : bond        0.00308 (    1)
  link_NAG-ASN         : angle       1.37561 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  386 LYS cc_start: 0.7616 (pttt) cc_final: 0.7345 (pttp)
REVERT: R  428 ASP cc_start: 0.7896 (t0) cc_final: 0.7383 (t70)
REVERT: R  498 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7944 (ptp-170)
REVERT: R  500 THR cc_start: 0.8607 (p) cc_final: 0.8229 (t)
REVERT: A    7 SER cc_start: 0.9304 (p) cc_final: 0.8965 (m)
REVERT: A   13 LYS cc_start: 0.4792 (mmtt) cc_final: 0.4338 (mmmt)
REVERT: A   48 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6828 (mm-30)
REVERT: A   61 TYR cc_start: 0.6864 (m-80) cc_final: 0.6512 (m-80)
REVERT: A   87 VAL cc_start: 0.8409 (t) cc_final: 0.8010 (p)
REVERT: B   37 TYR cc_start: 0.7502 (m-10) cc_final: 0.6099 (m-10)
REVERT: B   90 GLU cc_start: 0.7900 (pt0) cc_final: 0.7305 (pt0)
REVERT: B   93 ASP cc_start: 0.7129 (t0) cc_final: 0.6531 (t0)
REVERT: B  106 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8401 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0580
  time to fit residues: 9.1346
Evaluate side-chains
  97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0070
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  80 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.134580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.117032 restraints weight = 8396.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.120214 restraints weight = 4990.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.122440 restraints weight = 3387.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.123872 restraints weight = 2510.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.125152 restraints weight = 2009.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.5625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3380  Z= 0.132
  Angle     :  0.702   6.868   4609  Z= 0.355
  Chirality :  0.046   0.186    512
  Planarity :  0.007   0.099    588
  Dihedral  :  6.411  34.636    498
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.78 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  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: -2.06 (0.42), residues: 410
  helix: -3.77 (0.81), residues: 20
  sheet: -1.08 (0.45), residues: 140
  loop : -1.32 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.028   0.002   TYR R 453 
 PHE   0.025   0.001   PHE R 377 
 TRP   0.018   0.002   TRP A  49 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3373)
  covalent geometry    : angle       0.69922 ( 4593)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       1.04266 (   10)
  hydrogen bonds       : bond        0.03239 (   77)
  hydrogen bonds       : angle       6.80011 (  174)
  link_BETA1-4         : bond        0.00226 (    1)
  link_BETA1-4         : angle       1.71091 (    3)
  link_NAG-ASN         : bond        0.00379 (    1)
  link_NAG-ASN         : angle       1.34565 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  386 LYS cc_start: 0.7782 (pttt) cc_final: 0.7551 (pttp)
REVERT: R  428 ASP cc_start: 0.7859 (t0) cc_final: 0.7287 (t70)
REVERT: R  500 THR cc_start: 0.8638 (p) cc_final: 0.8140 (t)
REVERT: A    7 SER cc_start: 0.9312 (p) cc_final: 0.8983 (m)
REVERT: A   15 LYS cc_start: 0.8465 (tppt) cc_final: 0.7686 (tmmt)
REVERT: A   61 TYR cc_start: 0.6760 (m-80) cc_final: 0.6177 (m-80)
REVERT: A   62 ASN cc_start: 0.8818 (t0) cc_final: 0.8413 (t0)
REVERT: A   86 ASN cc_start: 0.7988 (m-40) cc_final: 0.7565 (m-40)
REVERT: B   93 ASP cc_start: 0.7093 (t0) cc_final: 0.6632 (t0)
REVERT: B   99 VAL cc_start: 0.9147 (t) cc_final: 0.8643 (t)
REVERT: B  106 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8385 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0608
  time to fit residues: 9.4199
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0050
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0050
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4208

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
B  38 GLN
** B  80 GLN ** 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 = 0.3885 r_free = 0.3885 target = 0.134929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.116945 restraints weight = 8464.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.120150 restraints weight = 5049.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.122414 restraints weight = 3432.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.124080 restraints weight = 2539.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.125253 restraints weight = 1993.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3380  Z= 0.132
  Angle     :  0.718   7.053   4609  Z= 0.361
  Chirality :  0.046   0.184    512
  Planarity :  0.006   0.090    588
  Dihedral  :  6.342  35.535    498
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.05 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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: -2.11 (0.42), residues: 410
  helix: -3.71 (0.86), residues: 20
  sheet: -1.08 (0.45), residues: 139
  loop : -1.38 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.023   0.002   TYR R 453 
 PHE   0.024   0.001   PHE R 377 
 TRP   0.018   0.002   TRP B  36 
 HIS   0.005   0.002   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3373)
  covalent geometry    : angle       0.71414 ( 4593)
  SS BOND              : bond        0.00200 (    5)
  SS BOND              : angle       1.37224 (   10)
  hydrogen bonds       : bond        0.03273 (   77)
  hydrogen bonds       : angle       6.71388 (  174)
  link_BETA1-4         : bond        0.00250 (    1)
  link_BETA1-4         : angle       1.72668 (    3)
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       1.28371 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.129 
Fit side-chains
REVERT: R  386 LYS cc_start: 0.7821 (pttt) cc_final: 0.7571 (pttp)
REVERT: R  428 ASP cc_start: 0.7907 (t0) cc_final: 0.7266 (t70)
REVERT: R  500 THR cc_start: 0.8627 (p) cc_final: 0.8123 (t)
REVERT: A    7 SER cc_start: 0.9309 (p) cc_final: 0.8970 (m)
REVERT: A   13 LYS cc_start: 0.4655 (mmtt) cc_final: 0.4345 (mmmt)
REVERT: A   47 LEU cc_start: 0.8626 (mp) cc_final: 0.8073 (mp)
REVERT: A   48 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7428 (mt-10)
REVERT: A   96 PHE cc_start: 0.9226 (m-80) cc_final: 0.8984 (m-10)
REVERT: B   90 GLU cc_start: 0.8148 (pt0) cc_final: 0.7839 (pt0)
REVERT: B   93 ASP cc_start: 0.7056 (t0) cc_final: 0.6679 (t0)
REVERT: B  106 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8377 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0535
  time to fit residues: 8.5880
Evaluate side-chains
  103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 15 optimal weight:    0.0050
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4774

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  80 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 = 0.3885 r_free = 0.3885 target = 0.134682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.116665 restraints weight = 8498.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.120088 restraints weight = 4984.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.122428 restraints weight = 3340.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.123948 restraints weight = 2450.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.125287 restraints weight = 1953.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.6077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3380  Z= 0.146
  Angle     :  0.764   7.861   4609  Z= 0.382
  Chirality :  0.047   0.177    512
  Planarity :  0.006   0.086    588
  Dihedral  :  6.735  37.654    498
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.51 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -2.25 (0.41), residues: 410
  helix: -3.77 (0.83), residues: 20
  sheet: -1.16 (0.44), residues: 142
  loop : -1.50 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  40 
 TYR   0.018   0.002   TYR R 453 
 PHE   0.024   0.002   PHE R 377 
 TRP   0.045   0.003   TRP B  36 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3373)
  covalent geometry    : angle       0.75285 ( 4593)
  SS BOND              : bond        0.00704 (    5)
  SS BOND              : angle       2.67515 (   10)
  hydrogen bonds       : bond        0.03322 (   77)
  hydrogen bonds       : angle       6.74693 (  174)
  link_BETA1-4         : bond        0.00206 (    1)
  link_BETA1-4         : angle       1.73097 (    3)
  link_NAG-ASN         : bond        0.00325 (    1)
  link_NAG-ASN         : angle       1.20738 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
REVERT: R  428 ASP cc_start: 0.7976 (t0) cc_final: 0.7361 (t70)
REVERT: R  500 THR cc_start: 0.8737 (p) cc_final: 0.8234 (t)
REVERT: A    7 SER cc_start: 0.9319 (p) cc_final: 0.8953 (m)
REVERT: A   13 LYS cc_start: 0.4775 (mmtt) cc_final: 0.4104 (mmmt)
REVERT: A   15 LYS cc_start: 0.8496 (tppt) cc_final: 0.7732 (tmmt)
REVERT: A   40 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7908 (ttm-80)
REVERT: A   48 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7409 (mt-10)
REVERT: A   86 ASN cc_start: 0.8183 (m-40) cc_final: 0.7787 (m-40)
REVERT: A   96 PHE cc_start: 0.9261 (m-80) cc_final: 0.9019 (m-10)
REVERT: B   84 GLU cc_start: 0.7685 (mp0) cc_final: 0.7308 (mp0)
REVERT: B   93 ASP cc_start: 0.7164 (t0) cc_final: 0.6786 (t0)
REVERT: B  106 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8385 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0540
  time to fit residues: 8.4983
Evaluate side-chains
  103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0470
   chunk 7 optimal weight:    0.7980
   chunk 10 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0040
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.3290

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

Flipped N/Q/H residues before XYZ refinement:
** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  80 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 = 0.3912 r_free = 0.3912 target = 0.136631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.118620 restraints weight = 8566.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.121978 restraints weight = 5122.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.124319 restraints weight = 3490.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.125992 restraints weight = 2603.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.127177 restraints weight = 2062.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3380  Z= 0.138
  Angle     :  0.773  10.583   4609  Z= 0.388
  Chirality :  0.047   0.181    512
  Planarity :  0.006   0.083    588
  Dihedral  :  6.676  36.334    498
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.05 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.51 %

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: -2.18 (0.41), residues: 410
  helix: -3.84 (0.79), residues: 20
  sheet: -0.94 (0.45), residues: 126
  loop : -1.55 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  40 
 TYR   0.027   0.002   TYR B  50 
 PHE   0.014   0.001   PHE R 377 
 TRP   0.025   0.003   TRP B  36 
 HIS   0.005   0.001   HIS A  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3373)
  covalent geometry    : angle       0.76148 ( 4593)
  SS BOND              : bond        0.00963 (    5)
  SS BOND              : angle       2.74468 (   10)
  hydrogen bonds       : bond        0.03403 (   77)
  hydrogen bonds       : angle       6.46699 (  174)
  link_BETA1-4         : bond        0.00346 (    1)
  link_BETA1-4         : angle       1.65702 (    3)
  link_NAG-ASN         : bond        0.00343 (    1)
  link_NAG-ASN         : angle       1.24957 (    3)

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

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: R  428 ASP cc_start: 0.7944 (t0) cc_final: 0.7319 (t70)
REVERT: R  452 LEU cc_start: 0.8952 (mt) cc_final: 0.8744 (mt)
REVERT: R  500 THR cc_start: 0.8760 (p) cc_final: 0.8254 (t)
REVERT: A    7 SER cc_start: 0.9305 (p) cc_final: 0.8913 (m)
REVERT: A   13 LYS cc_start: 0.4735 (mmtt) cc_final: 0.4043 (mmmt)
REVERT: A   40 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7610 (ttm-80)
REVERT: A   48 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7421 (mt-10)
REVERT: A   49 TRP cc_start: 0.8319 (t60) cc_final: 0.7826 (t60)
REVERT: A   62 ASN cc_start: 0.8787 (t0) cc_final: 0.7901 (t0)
REVERT: A   96 PHE cc_start: 0.9208 (m-80) cc_final: 0.8978 (m-10)
REVERT: B   84 GLU cc_start: 0.7754 (mp0) cc_final: 0.7475 (mp0)
REVERT: B   90 GLU cc_start: 0.8124 (pt0) cc_final: 0.7802 (pt0)
REVERT: B   99 VAL cc_start: 0.9208 (t) cc_final: 0.8865 (t)
REVERT: B  106 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8207 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0529
  time to fit residues: 8.5185
Evaluate side-chains
  103 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0770
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  80 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 = 0.3903 r_free = 0.3903 target = 0.135857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.117640 restraints weight = 8604.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.121105 restraints weight = 5069.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.123461 restraints weight = 3426.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.125121 restraints weight = 2527.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.126158 restraints weight = 1985.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.6465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   3380  Z= 0.150
  Angle     :  0.778   8.489   4609  Z= 0.391
  Chirality :  0.047   0.175    512
  Planarity :  0.006   0.082    588
  Dihedral  :  6.662  37.067    498
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.76 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -2.18 (0.41), residues: 410
  helix: -3.80 (0.78), residues: 20
  sheet: -1.06 (0.45), residues: 131
  loop : -1.48 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  40 
 TYR   0.017   0.002   TYR R 453 
 PHE   0.022   0.001   PHE R 377 
 TRP   0.060   0.003   TRP B  36 
 HIS   0.005   0.002   HIS B  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3373)
  covalent geometry    : angle       0.76599 ( 4593)
  SS BOND              : bond        0.00688 (    5)
  SS BOND              : angle       2.90015 (   10)
  hydrogen bonds       : bond        0.03257 (   77)
  hydrogen bonds       : angle       6.42737 (  174)
  link_BETA1-4         : bond        0.00222 (    1)
  link_BETA1-4         : angle       1.66257 (    3)
  link_NAG-ASN         : bond        0.00380 (    1)
  link_NAG-ASN         : angle       1.12861 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 867.67 seconds
wall clock time: 15 minutes 36.39 seconds (936.39 seconds total)