Starting phenix.real_space_refine
on Wed Sep 17 05:40:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nnh_12477/09_2025/7nnh_12477.map"
  }
  resolution = 4.0
  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=  -0.001 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    3332      2.51       5
     N     916      2.21       5
     O    1013      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5299
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "X"
      Number of atoms: 5299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 637, 5299
          Classifications: {'peptide': 637}
          Link IDs: {'CIS': 19, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 598}
  Time building chain proxies: 1.51, per 1000 atoms: 0.28
  Number of scatterers: 5299
  At special positions: 0
  Unit cell: (74.7, 123.67, 98.77, 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      38     16.00
     O    1013      8.00
     N     916      7.00
     C    3332      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS X1993 " - pdb=" SG  CYS X2173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2003 " - pdb=" SG  CYS X2158 " distance=2.02
    Simple disulfide: pdb=" SG  CYS X2012 " - pdb=" SG  CYS X2049 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2210 " - pdb=" SG  CYS X2226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2276 " - pdb=" SG  CYS X2279 " distance=2.04
    Simple disulfide: pdb=" SG  CYS X2333 " - pdb=" SG  CYS X2480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2518 " - pdb=" SG  CYS X2601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2532 " - pdb=" SG  CYS X2547 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X2594 " - pdb=" SG  CYS X2599 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 194.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1222

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      48.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'X' and resid 2000 through 2006
      removed outlier: 4.081A  pdb=" N   ASP X2004 " --> pdb=" O   MET X2000 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2083 through 2089
      removed outlier: 4.261A  pdb=" N   GLU X2087 " --> pdb=" O   ASN X2083 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2090 through 2111
      removed outlier: 4.076A  pdb=" N   ALA X2094 " --> pdb=" O   ASP X2090 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2122 through 2133
    Processing helix  chain 'X' and resid 2139 through 2145
    Processing helix  chain 'X' and resid 2169 through 2174
    Processing helix  chain 'X' and resid 2182 through 2209
      removed outlier: 4.328A  pdb=" N   GLN X2198 " --> pdb=" O   ASN X2194 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2224 through 2250
      removed outlier: 4.023A  pdb=" N   SER X2228 " --> pdb=" O   ASN X2224 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ILE X2230 " --> pdb=" O   CYS X2226 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2267 through 2275
    Processing helix  chain 'X' and resid 2308 through 2315
      removed outlier: 4.494A  pdb=" N   ASP X2315 " --> pdb=" O   ALA X2311 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2331 through 2340
    Processing helix  chain 'X' and resid 2354 through 2358
      removed outlier: 3.645A  pdb=" N   LYS X2357 " --> pdb=" O   ASN X2354 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS X2358 " --> pdb=" O   PHE X2355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'X' and resid 2354 through 2358'
    Processing helix  chain 'X' and resid 2369 through 2374
      removed outlier: 4.336A  pdb=" N   ASN X2374 " --> pdb=" O   PRO X2370 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2390 through 2414
    Processing helix  chain 'X' and resid 2416 through 2437
      removed outlier: 3.646A  pdb=" N   HIS X2422 " --> pdb=" O   ALA X2418 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2444 through 2452
    Processing helix  chain 'X' and resid 2460 through 2487
      removed outlier: 3.611A  pdb=" N   ASP X2468 " --> pdb=" O   LYS X2464 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   MET X2469 " --> pdb=" O   LYS X2465 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   TYR X2472 " --> pdb=" O   ASP X2468 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   HIS X2473 " --> pdb=" O   MET X2469 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLU X2484 " --> pdb=" O   CYS X2480 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   ALA X2485 " --> pdb=" O   GLY X2481 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLU X2486 " --> pdb=" O   TYR X2482 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 2498 through 2502
    Processing helix  chain 'X' and resid 2504 through 2516
    Processing helix  chain 'X' and resid 2519 through 2528
    Processing helix  chain 'X' and resid 2544 through 2576
    Processing helix  chain 'X' and resid 2585 through 2594

    205 hydrogen bonds defined for protein.
    609 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: 0.71

  Time building geometry restraints manager: 0.52 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: 1720
        1.34 -     1.47: 1260
        1.47 -     1.60: 2382
        1.60 -     1.72: 0
        1.72 -     1.85: 52
  Bond restraints: 5414
  Sorted by residual:
  bond pdb=" C   HIS X2322 "
       pdb=" O   HIS X2322 "
    ideal  model  delta    sigma   weight residual
    1.235  1.216  0.019 1.26e-02 6.30e+03 2.38e+00
  bond pdb=" N   GLU X2305 "
       pdb=" CA  GLU X2305 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.019 1.29e-02 6.01e+03 2.20e+00
  bond pdb=" C   TYR X2251 "
       pdb=" N   LYS X2252 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.84e+00
  bond pdb=" CA  PHE X2300 "
       pdb=" C   PHE X2300 "
    ideal  model  delta    sigma   weight residual
    1.524  1.543 -0.019 1.43e-02 4.89e+03 1.76e+00
  bond pdb=" C   LYS X2297 "
       pdb=" N   GLU X2298 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.74e+00
  ... (remaining 5409 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 6980
        2.80 -     5.59: 232
        5.59 -     8.39: 36
        8.39 -    11.18: 14
       11.18 -    13.98: 7
  Bond angle restraints: 7269
  Sorted by residual:
  angle pdb=" N   ASN X2291 "
        pdb=" CA  ASN X2291 "
        pdb=" C   ASN X2291 "
      ideal   model   delta    sigma   weight residual
     110.91  120.42   -9.51 1.17e+00 7.31e-01 6.61e+01
  angle pdb=" N   ASP X2285 "
        pdb=" CA  ASP X2285 "
        pdb=" C   ASP X2285 "
      ideal   model   delta    sigma   weight residual
     113.31   99.33   13.98 2.04e+00 2.40e-01 4.69e+01
  angle pdb=" N   ASP X2519 "
        pdb=" CA  ASP X2519 "
        pdb=" C   ASP X2519 "
      ideal   model   delta    sigma   weight residual
     113.88  106.08    7.80 1.23e+00 6.61e-01 4.02e+01
  angle pdb=" C   GLU X2324 "
        pdb=" N   TYR X2325 "
        pdb=" CA  TYR X2325 "
      ideal   model   delta    sigma   weight residual
     121.70  132.88  -11.18 1.80e+00 3.09e-01 3.86e+01
  angle pdb=" C   CYS X2279 "
        pdb=" N   PRO X2280 "
        pdb=" CD  PRO X2280 "
      ideal   model   delta    sigma   weight residual
     120.60  107.22   13.38 2.20e+00 2.07e-01 3.70e+01
  ... (remaining 7264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.32: 3176
       26.32 -    52.64: 152
       52.64 -    78.96: 20
       78.96 -   105.28: 2
      105.28 -   131.60: 4
  Dihedral angle restraints: 3354
    sinusoidal: 1466
      harmonic: 1888
  Sorted by residual:
  dihedral pdb=" CA  ASN X2290 "
           pdb=" C   ASN X2290 "
           pdb=" N   ASN X2291 "
           pdb=" CA  ASN X2291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -48.40 -131.60     0      5.00e+00 4.00e-02 6.93e+02
  dihedral pdb=" CA  LYS X2304 "
           pdb=" C   LYS X2304 "
           pdb=" N   GLU X2305 "
           pdb=" CA  GLU X2305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   50.07  129.93     0      5.00e+00 4.00e-02 6.75e+02
  dihedral pdb=" CA  LYS X2321 "
           pdb=" C   LYS X2321 "
           pdb=" N   HIS X2322 "
           pdb=" CA  HIS X2322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   61.27  118.73     0      5.00e+00 4.00e-02 5.64e+02
  ... (remaining 3351 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 585
       0.058 -    0.117: 127
       0.117 -    0.175: 17
       0.175 -    0.234: 7
       0.234 -    0.292: 2
  Chirality restraints: 738
  Sorted by residual:
  chirality pdb=" CA  TYR X2325 "
            pdb=" N   TYR X2325 "
            pdb=" C   TYR X2325 "
            pdb=" CB  TYR X2325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  ASP X2326 "
            pdb=" N   ASP X2326 "
            pdb=" C   ASP X2326 "
            pdb=" CB  ASP X2326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  GLU X2305 "
            pdb=" N   GLU X2305 "
            pdb=" C   GLU X2305 "
            pdb=" CB  GLU X2305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 735 not shown)

  Planarity restraints: 938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP X2145 "   -0.021 2.00e-02 2.50e+03   1.78e-02 7.89e+00
        pdb=" CG  TRP X2145 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP X2145 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP X2145 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP X2145 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP X2145 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP X2145 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP X2145 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP X2145 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP X2145 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP X2244 "    0.023 2.00e-02 2.50e+03   1.71e-02 7.34e+00
        pdb=" CG  TRP X2244 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP X2244 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP X2244 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP X2244 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP X2244 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP X2244 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP X2244 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP X2244 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP X2244 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP X2380 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO X2381 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO X2381 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO X2381 "    0.031 5.00e-02 4.00e+02
  ... (remaining 935 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 153
        2.63 -     3.20: 5907
        3.20 -     3.77: 9243
        3.77 -     4.33: 12464
        4.33 -     4.90: 18196
  Nonbonded interactions: 45963
  Sorted by model distance:
  nonbonded pdb=" O   PHE X1994 "
            pdb=" OG1 THR X1998 "
     model   vdw
     2.066 3.040
  nonbonded pdb=" O   GLU X2245 "
            pdb=" OG  SER X2248 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" OD1 ASN X2290 "
            pdb=" ND2 ASN X2292 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" O   SER X2076 "
            pdb=" OH  TYR X2085 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   ASN X2374 "
            pdb=" NH1 ARG X2408 "
     model   vdw
     2.176 3.120
  ... (remaining 45958 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             5.590
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.830
  Find NCS groups from input model:        0.020
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
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      :  0.004   0.055   5423  Z= 0.223
  Angle     :  1.284  13.978   7287  Z= 0.754
  Chirality :  0.052   0.292    738
  Planarity :  0.006   0.056    938
  Dihedral  : 15.824 131.595   2105
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 35.16
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  : 22.99 %
    Favored  : 76.54 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  1.19 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 0.00 %
    Twisted General : 1.62 %

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 aren not related in a simple way.
  whole: -3.61 (0.29), residues: 635
  helix: -0.57 (0.28), residues: 274
  sheet:  None (None), residues: 0
  loop : -4.17 (0.25), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG X2052 
 TYR   0.034   0.002   TYR X2325 
 PHE   0.030   0.002   PHE X2300 
 TRP   0.047   0.004   TRP X2145 
 HIS   0.006   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 5414)
  covalent geometry    : angle       1.28258 ( 7269)
  SS BOND              : bond        0.00407 (    9)
  SS BOND              : angle       1.85612 (   18)
  hydrogen bonds       : bond        0.17474 (  205)
  hydrogen bonds       : angle       7.35255 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2245 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8938 (mm-30)
REVERT: X 2511 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8897 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8774 (t80) cc_final: 0.8249 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0992
  time to fit residues: 8.2585
Evaluate side-chains
  44 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** X2083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.058155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.043719 restraints weight = 39166.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.046643 restraints weight = 36848.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.047315 restraints weight = 21913.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.047512 restraints weight = 18401.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.047775 restraints weight = 17963.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5423  Z= 0.245
  Angle     :  1.090  13.208   7287  Z= 0.579
  Chirality :  0.052   0.261    738
  Planarity :  0.007   0.079    938
  Dihedral  :  9.744  53.464    693
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 32.49
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 20.94 %
    Favored  : 78.43 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 13.58 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 1.62 %

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 aren not related in a simple way.
  whole: -3.20 (0.30), residues: 635
  helix: -0.12 (0.30), residues: 265
  sheet:  None (None), residues: 0
  loop : -3.94 (0.26), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG X2186 
 TYR   0.034   0.002   TYR X2325 
 PHE   0.023   0.002   PHE X2066 
 TRP   0.039   0.004   TRP X2244 
 HIS   0.011   0.002   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 5414)
  covalent geometry    : angle       1.08400 ( 7269)
  SS BOND              : bond        0.00570 (    9)
  SS BOND              : angle       2.47253 (   18)
  hydrogen bonds       : bond        0.06121 (  205)
  hydrogen bonds       : angle       5.97396 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2114 MET cc_start: 0.9138 (mpp) cc_final: 0.8638 (pmm)
REVERT: X 2286 MET cc_start: 0.9164 (mmm) cc_final: 0.8834 (mmm)
REVERT: X 2424 MET cc_start: 0.9558 (mtm) cc_final: 0.9268 (mtp)
REVERT: X 2511 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8983 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8746 (t80) cc_final: 0.8258 (t80)
  outliers start: 6
  outliers final: 2
  residues processed: 53
  average time/residue: 0.0815
  time to fit residues: 5.5336
Evaluate side-chains
  45 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2377 LEU
Chi-restraints excluded: chain X residue 2554 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0370
   chunk 53 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2083 ASN
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2529 ASN
** X2556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2574 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.061345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.046681 restraints weight = 38302.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.048246 restraints weight = 27967.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.049387 restraints weight = 22252.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.050214 restraints weight = 18708.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.050799 restraints weight = 16408.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5423  Z= 0.176
  Angle     :  1.007  12.667   7287  Z= 0.529
  Chirality :  0.049   0.233    738
  Planarity :  0.006   0.058    938
  Dihedral  :  8.800  43.666    693
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 25.13
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 19.84 %
    Favored  : 79.84 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.58 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

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 aren not related in a simple way.
  whole: -2.95 (0.30), residues: 635
  helix:  0.10 (0.30), residues: 265
  sheet:  None (None), residues: 0
  loop : -3.81 (0.26), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X2186 
 TYR   0.020   0.002   TYR X2325 
 PHE   0.020   0.002   PHE X2283 
 TRP   0.036   0.003   TRP X2144 
 HIS   0.004   0.001   HIS X2036 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 5414)
  covalent geometry    : angle       1.00414 ( 7269)
  SS BOND              : bond        0.00445 (    9)
  SS BOND              : angle       1.85464 (   18)
  hydrogen bonds       : bond        0.05484 (  205)
  hydrogen bonds       : angle       5.49834 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2016 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8054 (m)
REVERT: X 2085 TYR cc_start: 0.5397 (OUTLIER) cc_final: 0.5150 (p90)
REVERT: X 2139 LYS cc_start: 0.9823 (pttm) cc_final: 0.9584 (ptmt)
REVERT: X 2245 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8891 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8535 (mm) cc_final: 0.8290 (mm)
REVERT: X 2424 MET cc_start: 0.9597 (mtm) cc_final: 0.9218 (mtp)
REVERT: X 2511 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9016 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8837 (t80) cc_final: 0.8340 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1018
  time to fit residues: 7.8847
Evaluate side-chains
  50 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2002 VAL
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2085 TYR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2377 LEU
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   chunk 15 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0870
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2556 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.062408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.048380 restraints weight = 38308.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.049565 restraints weight = 27683.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.050092 restraints weight = 23552.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.050424 restraints weight = 21452.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.050841 restraints weight = 19728.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5423  Z= 0.165
  Angle     :  0.990  17.499   7287  Z= 0.515
  Chirality :  0.048   0.232    738
  Planarity :  0.005   0.049    938
  Dihedral  :  8.384  43.592    693
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 22.26
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 19.69 %
    Favored  : 80.00 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.32 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

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 aren not related in a simple way.
  whole: -2.99 (0.30), residues: 635
  helix:  0.04 (0.29), residues: 273
  sheet:  None (None), residues: 0
  loop : -3.88 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG X2186 
 TYR   0.020   0.002   TYR X2325 
 PHE   0.018   0.001   PHE X2283 
 TRP   0.037   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5414)
  covalent geometry    : angle       0.98831 ( 7269)
  SS BOND              : bond        0.00414 (    9)
  SS BOND              : angle       1.53836 (   18)
  hydrogen bonds       : bond        0.05131 (  205)
  hydrogen bonds       : angle       5.35932 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2114 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8598 (pmm)
REVERT: X 2245 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8910 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8556 (mm) cc_final: 0.8249 (mm)
REVERT: X 2424 MET cc_start: 0.9514 (mtm) cc_final: 0.9313 (mtp)
REVERT: X 2478 MET cc_start: 0.9592 (mtp) cc_final: 0.8982 (ttm)
REVERT: X 2511 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8960 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8769 (t80) cc_final: 0.8284 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 62
  average time/residue: 0.0914
  time to fit residues: 7.2732
Evaluate side-chains
  54 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2002 VAL
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2114 MET
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2377 LEU
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0000
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
X2075 GLN
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.062468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.047853 restraints weight = 38938.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.049439 restraints weight = 28559.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.050439 restraints weight = 22757.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.051344 restraints weight = 19461.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.051937 restraints weight = 17089.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5423  Z= 0.164
  Angle     :  0.980  16.539   7287  Z= 0.510
  Chirality :  0.048   0.236    738
  Planarity :  0.005   0.049    938
  Dihedral  :  8.217  42.876    693
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 24.17
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 20.63 %
    Favored  : 79.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.02 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

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 aren not related in a simple way.
  whole: -2.92 (0.30), residues: 635
  helix:  0.07 (0.30), residues: 272
  sheet:  None (None), residues: 0
  loop : -3.81 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X2129 
 TYR   0.022   0.001   TYR X2325 
 PHE   0.021   0.002   PHE X2376 
 TRP   0.033   0.003   TRP X2144 
 HIS   0.005   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5414)
  covalent geometry    : angle       0.97822 ( 7269)
  SS BOND              : bond        0.00344 (    9)
  SS BOND              : angle       1.51111 (   18)
  hydrogen bonds       : bond        0.04941 (  205)
  hydrogen bonds       : angle       5.22895 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2065 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8477 (mp0)
REVERT: X 2114 MET cc_start: 0.8917 (pmm) cc_final: 0.8654 (pmm)
REVERT: X 2189 LYS cc_start: 0.9431 (tmmt) cc_final: 0.8623 (mtmm)
REVERT: X 2245 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8910 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8473 (mm) cc_final: 0.8209 (mm)
REVERT: X 2424 MET cc_start: 0.9571 (mtm) cc_final: 0.9359 (mtp)
REVERT: X 2478 MET cc_start: 0.9607 (mtp) cc_final: 0.8990 (ttm)
REVERT: X 2511 GLN cc_start: 0.9382 (tm-30) cc_final: 0.9045 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8810 (t80) cc_final: 0.8303 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 57
  average time/residue: 0.0933
  time to fit residues: 6.8584
Evaluate side-chains
  54 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2377 LEU
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2513 TRP
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
X2047 GLN
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X2284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.062082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.047946 restraints weight = 37797.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.050529 restraints weight = 28453.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.050818 restraints weight = 20578.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.051332 restraints weight = 17681.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.051513 restraints weight = 16627.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5423  Z= 0.163
  Angle     :  0.967  15.839   7287  Z= 0.501
  Chirality :  0.048   0.234    738
  Planarity :  0.005   0.049    938
  Dihedral  :  8.084  42.248    693
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 22.64
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.79 %
    Favored  : 79.06 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.03 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.88 (0.31), residues: 635
  helix:  0.10 (0.30), residues: 272
  sheet:  None (None), residues: 0
  loop : -3.79 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X2129 
 TYR   0.022   0.001   TYR X2325 
 PHE   0.018   0.001   PHE X2066 
 TRP   0.031   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5414)
  covalent geometry    : angle       0.96551 ( 7269)
  SS BOND              : bond        0.00379 (    9)
  SS BOND              : angle       1.48241 (   18)
  hydrogen bonds       : bond        0.04788 (  205)
  hydrogen bonds       : angle       5.16267 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2065 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8445 (mp0)
REVERT: X 2114 MET cc_start: 0.8837 (pmm) cc_final: 0.8573 (pmm)
REVERT: X 2189 LYS cc_start: 0.9424 (tmmt) cc_final: 0.8614 (mtmm)
REVERT: X 2245 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8893 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8471 (mm) cc_final: 0.8152 (mm)
REVERT: X 2300 PHE cc_start: 0.9482 (t80) cc_final: 0.9186 (t80)
REVERT: X 2424 MET cc_start: 0.9521 (mtm) cc_final: 0.9310 (mtp)
REVERT: X 2478 MET cc_start: 0.9575 (mtp) cc_final: 0.8938 (ttm)
REVERT: X 2511 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8997 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8766 (t80) cc_final: 0.8118 (t80)
REVERT: X 2601 CYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5504 (p)
  outliers start: 15
  outliers final: 12
  residues processed: 61
  average time/residue: 0.0989
  time to fit residues: 7.6940
Evaluate side-chains
  59 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2234 GLN
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Chi-restraints excluded: chain X residue 2601 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 4 optimal weight:    0.0010
   chunk 14 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.063610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.049525 restraints weight = 37386.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.051454 restraints weight = 28183.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.052794 restraints weight = 21089.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.052881 restraints weight = 17203.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053056 restraints weight = 16492.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5423  Z= 0.156
  Angle     :  0.959  15.407   7287  Z= 0.497
  Chirality :  0.047   0.233    738
  Planarity :  0.005   0.050    938
  Dihedral  :  7.891  41.611    693
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 20.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 19.69 %
    Favored  : 80.16 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.69 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.83 (0.31), residues: 635
  helix:  0.19 (0.30), residues: 271
  sheet:  None (None), residues: 0
  loop : -3.79 (0.27), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X2129 
 TYR   0.021   0.001   TYR X2325 
 PHE   0.017   0.001   PHE X2066 
 TRP   0.030   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5414)
  covalent geometry    : angle       0.95785 ( 7269)
  SS BOND              : bond        0.00341 (    9)
  SS BOND              : angle       1.41946 (   18)
  hydrogen bonds       : bond        0.04683 (  205)
  hydrogen bonds       : angle       5.06556 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9339 (pm20) cc_final: 0.8738 (tt0)
REVERT: X 2065 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8494 (mp0)
REVERT: X 2114 MET cc_start: 0.8776 (pmm) cc_final: 0.8539 (pmm)
REVERT: X 2189 LYS cc_start: 0.9380 (tmmt) cc_final: 0.8652 (mttt)
REVERT: X 2245 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8937 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8436 (mm) cc_final: 0.8097 (mm)
REVERT: X 2300 PHE cc_start: 0.9518 (t80) cc_final: 0.9222 (t80)
REVERT: X 2461 GLU cc_start: 0.9231 (pm20) cc_final: 0.8656 (pm20)
REVERT: X 2478 MET cc_start: 0.9580 (mtp) cc_final: 0.8953 (ttm)
REVERT: X 2511 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9025 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8795 (t80) cc_final: 0.7904 (t80)
REVERT: X 2521 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8706 (mtm180)
REVERT: X 2601 CYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5495 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 67
  average time/residue: 0.0878
  time to fit residues: 7.5530
Evaluate side-chains
  61 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2178 THR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2234 GLN
Chi-restraints excluded: chain X residue 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2334 ASN
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2549 HIS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Chi-restraints excluded: chain X residue 2601 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 17 optimal weight:    0.0000
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
X1997 GLN
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2292 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.062504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.048137 restraints weight = 37317.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.049853 restraints weight = 27962.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.051191 restraints weight = 21644.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.051277 restraints weight = 17400.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.051648 restraints weight = 16914.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5423  Z= 0.171
  Angle     :  0.992  15.548   7287  Z= 0.517
  Chirality :  0.048   0.237    738
  Planarity :  0.005   0.048    938
  Dihedral  :  7.812  41.143    693
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 24.36
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 20.79 %
    Favored  : 78.90 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.05 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.81 (0.31), residues: 635
  helix:  0.15 (0.30), residues: 271
  sheet:  None (None), residues: 0
  loop : -3.73 (0.28), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG X2129 
 TYR   0.022   0.001   TYR X2325 
 PHE   0.018   0.001   PHE X2066 
 TRP   0.031   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5414)
  covalent geometry    : angle       0.99110 ( 7269)
  SS BOND              : bond        0.00330 (    9)
  SS BOND              : angle       1.40224 (   18)
  hydrogen bonds       : bond        0.04828 (  205)
  hydrogen bonds       : angle       5.16148 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9310 (pm20) cc_final: 0.8778 (tt0)
REVERT: X 2065 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8226 (mp0)
REVERT: X 2114 MET cc_start: 0.8792 (pmm) cc_final: 0.8542 (pmm)
REVERT: X 2139 LYS cc_start: 0.9796 (tmmt) cc_final: 0.9568 (pptt)
REVERT: X 2189 LYS cc_start: 0.9414 (tmmt) cc_final: 0.8574 (mtmm)
REVERT: X 2245 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8886 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8442 (mm) cc_final: 0.8094 (mm)
REVERT: X 2300 PHE cc_start: 0.9510 (t80) cc_final: 0.9212 (t80)
REVERT: X 2424 MET cc_start: 0.9485 (mtp) cc_final: 0.9264 (ttt)
REVERT: X 2478 MET cc_start: 0.9453 (mtp) cc_final: 0.9081 (mtm)
REVERT: X 2511 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9028 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8775 (t80) cc_final: 0.7920 (t80)
REVERT: X 2521 ARG cc_start: 0.9194 (mtm110) cc_final: 0.8784 (mtm180)
REVERT: X 2601 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.4674 (p)
  outliers start: 17
  outliers final: 15
  residues processed: 58
  average time/residue: 0.0896
  time to fit residues: 6.7267
Evaluate side-chains
  60 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2178 THR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2234 GLN
Chi-restraints excluded: chain X residue 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2334 ASN
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Chi-restraints excluded: chain X residue 2601 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 32 optimal weight:    0.5980
   chunk 42 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.063199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.049328 restraints weight = 37465.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.052028 restraints weight = 28534.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.052401 restraints weight = 19825.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.052910 restraints weight = 16941.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.053128 restraints weight = 15990.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5423  Z= 0.164
  Angle     :  0.990  15.374   7287  Z= 0.514
  Chirality :  0.049   0.235    738
  Planarity :  0.005   0.050    938
  Dihedral  :  7.759  40.823    693
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.47 %
    Favored  : 79.37 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 21.05 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.84 (0.31), residues: 635
  helix:  0.10 (0.30), residues: 277
  sheet:  None (None), residues: 0
  loop : -3.78 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X2129 
 TYR   0.023   0.001   TYR X2325 
 PHE   0.021   0.001   PHE X2283 
 TRP   0.032   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5414)
  covalent geometry    : angle       0.98890 ( 7269)
  SS BOND              : bond        0.00374 (    9)
  SS BOND              : angle       1.49587 (   18)
  hydrogen bonds       : bond        0.04770 (  205)
  hydrogen bonds       : angle       5.14149 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9354 (pm20) cc_final: 0.8722 (tt0)
REVERT: X 2065 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8271 (mp0)
REVERT: X 2114 MET cc_start: 0.8806 (pmm) cc_final: 0.8571 (pmm)
REVERT: X 2139 LYS cc_start: 0.9801 (tmmt) cc_final: 0.9582 (pptt)
REVERT: X 2189 LYS cc_start: 0.9394 (tmmt) cc_final: 0.8553 (mtmm)
REVERT: X 2245 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8916 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8438 (mm) cc_final: 0.8096 (mm)
REVERT: X 2300 PHE cc_start: 0.9500 (t80) cc_final: 0.9235 (t80)
REVERT: X 2424 MET cc_start: 0.9482 (mtp) cc_final: 0.9118 (ttm)
REVERT: X 2461 GLU cc_start: 0.9452 (pm20) cc_final: 0.9245 (pm20)
REVERT: X 2511 GLN cc_start: 0.9373 (tm-30) cc_final: 0.9029 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8781 (t80) cc_final: 0.7909 (t80)
REVERT: X 2521 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8736 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9360 (m-30) cc_final: 0.9122 (p0)
REVERT: X 2601 CYS cc_start: 0.5989 (OUTLIER) cc_final: 0.4325 (p)
  outliers start: 17
  outliers final: 15
  residues processed: 62
  average time/residue: 0.1023
  time to fit residues: 7.9747
Evaluate side-chains
  59 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2178 THR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2234 GLN
Chi-restraints excluded: chain X residue 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2334 ASN
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Chi-restraints excluded: chain X residue 2601 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 19 optimal weight:    0.3980
   chunk 23 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.064057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.049636 restraints weight = 39016.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.051813 restraints weight = 29567.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.052900 restraints weight = 21833.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.053065 restraints weight = 18696.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053235 restraints weight = 17568.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5423  Z= 0.166
  Angle     :  1.015  15.330   7287  Z= 0.525
  Chirality :  0.049   0.240    738
  Planarity :  0.005   0.050    938
  Dihedral  :  7.664  40.356    693
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 22.07
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 21.10 %
    Favored  : 78.74 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.05 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.85 (0.31), residues: 635
  helix: -0.03 (0.29), residues: 282
  sheet:  None (None), residues: 0
  loop : -3.73 (0.28), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG X2129 
 TYR   0.022   0.001   TYR X2325 
 PHE   0.030   0.002   PHE X2283 
 TRP   0.026   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 5414)
  covalent geometry    : angle       1.01379 ( 7269)
  SS BOND              : bond        0.00388 (    9)
  SS BOND              : angle       1.48720 (   18)
  hydrogen bonds       : bond        0.04753 (  205)
  hydrogen bonds       : angle       5.15850 (  609)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9360 (pm20) cc_final: 0.8699 (pt0)
REVERT: X 2065 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8210 (mp0)
REVERT: X 2114 MET cc_start: 0.8769 (pmm) cc_final: 0.8560 (pmm)
REVERT: X 2139 LYS cc_start: 0.9792 (tmmt) cc_final: 0.9565 (pptt)
REVERT: X 2189 LYS cc_start: 0.9372 (tmmt) cc_final: 0.8554 (mtmm)
REVERT: X 2201 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8611 (mm-30)
REVERT: X 2245 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8921 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8421 (mm) cc_final: 0.8076 (mm)
REVERT: X 2511 GLN cc_start: 0.9368 (tm-30) cc_final: 0.9018 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8781 (t80) cc_final: 0.7925 (t80)
REVERT: X 2521 ARG cc_start: 0.9202 (mtm110) cc_final: 0.8753 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9398 (m-30) cc_final: 0.9172 (p0)
REVERT: X 2601 CYS cc_start: 0.5941 (OUTLIER) cc_final: 0.4301 (p)
  outliers start: 20
  outliers final: 18
  residues processed: 63
  average time/residue: 0.0929
  time to fit residues: 7.4572
Evaluate side-chains
  65 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2140 LYS
Chi-restraints excluded: chain X residue 2178 THR
Chi-restraints excluded: chain X residue 2205 TYR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2234 GLN
Chi-restraints excluded: chain X residue 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2334 ASN
Chi-restraints excluded: chain X residue 2407 GLU
Chi-restraints excluded: chain X residue 2426 TYR
Chi-restraints excluded: chain X residue 2440 MET
Chi-restraints excluded: chain X residue 2547 CYS
Chi-restraints excluded: chain X residue 2549 HIS
Chi-restraints excluded: chain X residue 2554 TYR
Chi-restraints excluded: chain X residue 2568 GLN
Chi-restraints excluded: chain X residue 2601 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.063404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.048992 restraints weight = 39111.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.050821 restraints weight = 30636.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.052430 restraints weight = 22331.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.052684 restraints weight = 18819.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.052953 restraints weight = 16954.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5423  Z= 0.174
  Angle     :  1.022  15.238   7287  Z= 0.530
  Chirality :  0.049   0.272    738
  Planarity :  0.005   0.049    938
  Dihedral  :  7.699  39.866    693
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 24.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 21.10 %
    Favored  : 78.74 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.22 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

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 aren not related in a simple way.
  whole: -2.80 (0.31), residues: 635
  helix: -0.00 (0.29), residues: 283
  sheet:  None (None), residues: 0
  loop : -3.70 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG X2129 
 TYR   0.023   0.001   TYR X2325 
 PHE   0.043   0.002   PHE X2283 
 TRP   0.023   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5414)
  covalent geometry    : angle       1.02045 ( 7269)
  SS BOND              : bond        0.00484 (    9)
  SS BOND              : angle       1.65381 (   18)
  hydrogen bonds       : bond        0.04735 (  205)
  hydrogen bonds       : angle       5.15054 (  609)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1183.63 seconds
wall clock time: 21 minutes 16.02 seconds (1276.02 seconds total)