Starting phenix.real_space_refine
on Tue Feb 11 11:09:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nnh_12477/02_2025/7nnh_12477.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nnh_12477/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nnh_12477/02_2025/7nnh_12477.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nnh_12477/02_2025/7nnh_12477.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nnh_12477/02_2025/7nnh_12477.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nnh_12477/02_2025/7nnh_12477.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.02, per 1000 atoms: 0.95
  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: 1.29
  Conformation dependent library (CDL) restraints added in 589.9 milliseconds
  

  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: 0.44
  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: 1.17

  Time building geometry restraints manager: 1.53 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:             4.840
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.250
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.400
-------------------------------------------------------------------------------
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   5414  Z= 0.265
  Angle     :  1.283  13.978   7269  Z= 0.753
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.047   0.004   TRP X2145 
 HIS   0.006   0.001   HIS X2322 
 PHE   0.030   0.002   PHE X2300 
 TYR   0.034   0.002   TYR X2325 
 ARG   0.007   0.001   ARG X2052 

*********************** 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  : 0.543 
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: 0.2180
  time to fit residues: 18.1490
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  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6962

-------------------------------------------------------------------------------
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**
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2529 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.061946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.046770 restraints weight = 37240.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.049737 restraints weight = 34610.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.050537 restraints weight = 21887.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   5414  Z= 0.245
  Angle     :  1.059  13.697   7269  Z= 0.557
  Chirality :  0.051   0.262    738
  Planarity :  0.006   0.078    938
  Dihedral  :  9.410  54.264    693
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 24.75
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 19.37 %
    Favored  : 80.00 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 11.54 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 1.46 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.30), residues: 635
  helix:  0.10 (0.30), residues: 264
  sheet:  None (None), residues: 0
  loop : -3.85 (0.27), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP X2244 
 HIS   0.009   0.002   HIS X2322 
 PHE   0.023   0.002   PHE X2066 
 TYR   0.031   0.002   TYR X2325 
 ARG   0.006   0.001   ARG X2186 

*********************** 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
  61 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2114 MET cc_start: 0.9077 (mpp) cc_final: 0.8556 (pmm)
REVERT: X 2286 MET cc_start: 0.8791 (mmm) cc_final: 0.8568 (mmm)
REVERT: X 2424 MET cc_start: 0.9566 (mtm) cc_final: 0.9326 (mtp)
REVERT: X 2438 ASP cc_start: 0.9103 (m-30) cc_final: 0.8345 (p0)
REVERT: X 2511 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8966 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8753 (t80) cc_final: 0.8241 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 58
  average time/residue: 0.2323
  time to fit residues: 16.9111
Evaluate side-chains
  47 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2002 VAL
Chi-restraints excluded: chain X residue 2230 ILE
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 25 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X2574 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.062612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.047274 restraints weight = 37238.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.050182 restraints weight = 34699.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.051175 restraints weight = 21830.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5414  Z= 0.219
  Angle     :  1.001  12.677   7269  Z= 0.525
  Chirality :  0.049   0.234    738
  Planarity :  0.006   0.056    938
  Dihedral  :  8.632  44.076    693
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 24.17
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 19.21 %
    Favored  : 80.47 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.30), residues: 635
  helix:  0.13 (0.30), residues: 266
  sheet:  None (None), residues: 0
  loop : -3.81 (0.26), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP X2144 
 HIS   0.004   0.001   HIS X2036 
 PHE   0.020   0.002   PHE X2066 
 TYR   0.022   0.002   TYR X2325 
 ARG   0.010   0.001   ARG X2129 

*********************** 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
  63 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2016 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8190 (m)
REVERT: X 2139 LYS cc_start: 0.9804 (pttm) cc_final: 0.9587 (ptmt)
REVERT: X 2245 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8882 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8529 (mm) cc_final: 0.8254 (mm)
REVERT: X 2424 MET cc_start: 0.9573 (mtm) cc_final: 0.9206 (mtp)
REVERT: X 2511 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8928 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8751 (t80) cc_final: 0.8266 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 60
  average time/residue: 0.1985
  time to fit residues: 15.4082
Evaluate side-chains
  56 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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 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 46 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0170
   chunk 30 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.0022

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

Flipped N/Q/H residues before XYZ refinement:
X2047 GLN
X2083 ASN
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2556 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.061353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.047328 restraints weight = 38653.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.049058 restraints weight = 28639.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.050176 restraints weight = 22292.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5414  Z= 0.221
  Angle     :  0.987  17.519   7269  Z= 0.512
  Chirality :  0.048   0.235    738
  Planarity :  0.005   0.048    938
  Dihedral  :  8.435  43.391    693
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 25.89
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 20.63 %
    Favored  : 79.06 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.47 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.30), residues: 635
  helix:  0.05 (0.30), residues: 278
  sheet:  None (None), residues: 0
  loop : -4.00 (0.26), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP X2144 
 HIS   0.003   0.001   HIS X2322 
 PHE   0.018   0.002   PHE X2066 
 TYR   0.022   0.002   TYR X2325 
 ARG   0.007   0.001   ARG X2186 

*********************** 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: 21
    poor density    : 44
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2114 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (pmm)
REVERT: X 2139 LYS cc_start: 0.9832 (pttm) cc_final: 0.9608 (ptmt)
REVERT: X 2245 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8910 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8515 (mm) cc_final: 0.8246 (mm)
REVERT: X 2424 MET cc_start: 0.9584 (mtm) cc_final: 0.9371 (mtp)
REVERT: X 2478 MET cc_start: 0.9623 (mtp) cc_final: 0.8973 (ttm)
REVERT: X 2511 GLN cc_start: 0.9368 (tm-30) cc_final: 0.9016 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8727 (t80) cc_final: 0.8282 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 61
  average time/residue: 0.1895
  time to fit residues: 15.3248
Evaluate side-chains
  55 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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 2041 ILE
Chi-restraints excluded: chain X residue 2066 PHE
Chi-restraints excluded: chain X residue 2083 ASN
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 26 optimal weight:    0.0570
   chunk 56 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0270
   chunk 1 optimal weight:    0.4980
   chunk 0 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
X2047 GLN
** X2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.063598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.049435 restraints weight = 38013.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.051502 restraints weight = 28181.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.052910 restraints weight = 20744.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5414  Z= 0.199
  Angle     :  0.969  15.979   7269  Z= 0.504
  Chirality :  0.047   0.232    738
  Planarity :  0.005   0.050    938
  Dihedral  :  8.174  42.906    693
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 19.84 %
    Favored  : 79.84 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.85 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.31), residues: 635
  helix:  0.15 (0.30), residues: 272
  sheet:  None (None), residues: 0
  loop : -3.84 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 
 PHE   0.020   0.001   PHE X2376 
 TYR   0.021   0.002   TYR X2325 
 ARG   0.008   0.001   ARG X2371 

*********************** 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: 12
    poor density    : 48
  time to evaluate  : 0.636 
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: 0.8876 (mm-30) cc_final: 0.8458 (mp0)
REVERT: X 2114 MET cc_start: 0.8907 (pmm) cc_final: 0.8619 (pmm)
REVERT: X 2245 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8905 (mm-30)
REVERT: X 2478 MET cc_start: 0.9583 (mtp) cc_final: 0.8945 (ttm)
REVERT: X 2511 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8758 (t80) cc_final: 0.8293 (t80)
  outliers start: 12
  outliers final: 11
  residues processed: 57
  average time/residue: 0.2144
  time to fit residues: 15.8896
Evaluate side-chains
  54 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue 2016 THR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2236 TRP
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 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 23 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
X2047 GLN
X2083 ASN
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.060451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.046116 restraints weight = 39286.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.047608 restraints weight = 28771.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.048662 restraints weight = 23116.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5414  Z= 0.245
  Angle     :  0.984  15.120   7269  Z= 0.515
  Chirality :  0.048   0.241    738
  Planarity :  0.005   0.048    938
  Dihedral  :  8.210  42.424    693
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 28.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 22.05 %
    Favored  : 77.80 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.19 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.81 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.31), residues: 635
  helix:  0.17 (0.30), residues: 271
  sheet:  None (None), residues: 0
  loop : -3.80 (0.27), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP X2144 
 HIS   0.003   0.001   HIS X2036 
 PHE   0.017   0.002   PHE X2066 
 TYR   0.024   0.002   TYR X2325 
 ARG   0.003   0.001   ARG X2129 

*********************** 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
  63 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2114 MET cc_start: 0.8964 (pmm) cc_final: 0.8657 (pmm)
REVERT: X 2245 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8925 (mm-30)
REVERT: X 2424 MET cc_start: 0.9507 (mtp) cc_final: 0.9136 (ttt)
REVERT: X 2478 MET cc_start: 0.9492 (mtp) cc_final: 0.8506 (mtp)
REVERT: X 2511 GLN cc_start: 0.9383 (tm-30) cc_final: 0.9061 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8791 (t80) cc_final: 0.8199 (t80)
REVERT: X 2601 CYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5560 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 58
  average time/residue: 0.1710
  time to fit residues: 13.3808
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  : 0.640 
-------------------------------------------------------------------------------
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 2205 TYR
Chi-restraints excluded: chain X residue 2226 CYS
Chi-restraints excluded: chain X residue 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2285 ASP
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 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 41 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0670
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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**
X2284 ASN
X2334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.062672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.048201 restraints weight = 38267.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.049775 restraints weight = 27839.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.050880 restraints weight = 22104.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5414  Z= 0.201
  Angle     :  0.969  14.301   7269  Z= 0.504
  Chirality :  0.047   0.232    738
  Planarity :  0.005   0.050    938
  Dihedral  :  8.042  42.140    693
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 23.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.00 %
    Favored  : 79.84 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.54 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.31), residues: 635
  helix:  0.18 (0.30), residues: 272
  sheet:  None (None), residues: 0
  loop : -3.74 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 
 PHE   0.017   0.001   PHE X2066 
 TYR   0.021   0.001   TYR X2325 
 ARG   0.004   0.000   ARG X2129 

*********************** 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
  67 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9508 (pm20) cc_final: 0.8687 (tt0)
REVERT: X 2065 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8656 (mp0)
REVERT: X 2114 MET cc_start: 0.8884 (pmm) cc_final: 0.8607 (pmm)
REVERT: X 2245 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8939 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8437 (mm) cc_final: 0.8096 (mm)
REVERT: X 2300 PHE cc_start: 0.9511 (t80) cc_final: 0.9195 (t80)
REVERT: X 2424 MET cc_start: 0.9485 (mtp) cc_final: 0.9125 (ttm)
REVERT: X 2511 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9060 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8833 (t80) cc_final: 0.7990 (t80)
REVERT: X 2521 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8791 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9446 (m-30) cc_final: 0.9225 (p0)
REVERT: X 2601 CYS cc_start: 0.6066 (OUTLIER) cc_final: 0.4639 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 62
  average time/residue: 0.2008
  time to fit residues: 16.4316
Evaluate side-chains
  56 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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 2236 TRP
Chi-restraints excluded: chain X residue 2263 VAL
Chi-restraints excluded: chain X residue 2283 PHE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 51 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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**
** X2291 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 = 0.3685 r_free = 0.3685 target = 0.061383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.046955 restraints weight = 37316.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.048479 restraints weight = 27017.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.049590 restraints weight = 21474.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5414  Z= 0.218
  Angle     :  0.984  14.520   7269  Z= 0.514
  Chirality :  0.048   0.237    738
  Planarity :  0.005   0.050    938
  Dihedral  :  7.983  41.298    693
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 25.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 21.26 %
    Favored  : 78.58 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.88 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.31), residues: 635
  helix:  0.19 (0.30), residues: 270
  sheet:  None (None), residues: 0
  loop : -3.73 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 
 PHE   0.018   0.001   PHE X2066 
 TYR   0.022   0.001   TYR X2325 
 ARG   0.003   0.000   ARG X2129 

*********************** 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
  65 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 46
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9528 (pm20) cc_final: 0.8704 (tt0)
REVERT: X 2065 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8366 (mp0)
REVERT: X 2114 MET cc_start: 0.8913 (pmm) cc_final: 0.8639 (pmm)
REVERT: X 2245 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8944 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8454 (mm) cc_final: 0.8117 (mm)
REVERT: X 2300 PHE cc_start: 0.9499 (t80) cc_final: 0.9203 (t80)
REVERT: X 2511 GLN cc_start: 0.9413 (tm-30) cc_final: 0.9088 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8850 (t80) cc_final: 0.8021 (t80)
REVERT: X 2521 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8819 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9434 (m-30) cc_final: 0.9209 (p0)
REVERT: X 2601 CYS cc_start: 0.6106 (OUTLIER) cc_final: 0.4638 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 60
  average time/residue: 0.2027
  time to fit residues: 15.9008
Evaluate side-chains
  59 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
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 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 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 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0370
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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**
X2292 ASN
** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.063474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.049902 restraints weight = 38087.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.050985 restraints weight = 27536.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.051357 restraints weight = 24463.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5414  Z= 0.202
  Angle     :  1.004  14.277   7269  Z= 0.521
  Chirality :  0.049   0.233    738
  Planarity :  0.005   0.055    938
  Dihedral  :  7.921  41.069    693
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 21.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.47 %
    Favored  : 79.37 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.05 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.31), residues: 635
  helix:  0.16 (0.30), residues: 270
  sheet:  None (None), residues: 0
  loop : -3.72 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 
 PHE   0.017   0.001   PHE X2066 
 TYR   0.022   0.001   TYR X2085 
 ARG   0.009   0.001   ARG X2371 

*********************** 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
  64 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 45
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X 2020 GLU cc_start: 0.9534 (pm20) cc_final: 0.8720 (tt0)
REVERT: X 2065 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8332 (mp0)
REVERT: X 2114 MET cc_start: 0.8798 (pmm) cc_final: 0.8544 (pmm)
REVERT: X 2199 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8791 (mtpt)
REVERT: X 2245 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8948 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8419 (mm) cc_final: 0.8080 (mm)
REVERT: X 2300 PHE cc_start: 0.9573 (t80) cc_final: 0.9320 (t80)
REVERT: X 2511 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9014 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8813 (t80) cc_final: 0.7944 (t80)
REVERT: X 2521 ARG cc_start: 0.9189 (mtm110) cc_final: 0.8724 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9436 (m-30) cc_final: 0.9216 (p0)
REVERT: X 2601 CYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5182 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 59
  average time/residue: 0.2141
  time to fit residues: 16.3568
Evaluate side-chains
  63 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
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 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 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 1 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0270
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3752 r_free = 0.3752 target = 0.064622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.050231 restraints weight = 38019.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.052181 restraints weight = 28826.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.053291 restraints weight = 22090.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5414  Z= 0.203
  Angle     :  1.005  14.002   7269  Z= 0.521
  Chirality :  0.049   0.243    738
  Planarity :  0.005   0.053    938
  Dihedral  :  7.757  40.391    693
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 21.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.94 %
    Favored  : 78.90 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.05 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 2.59 %
    Twisted Proline : 5.26 %
    Twisted General : 0.65 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.31), residues: 635
  helix:  0.07 (0.30), residues: 277
  sheet:  None (None), residues: 0
  loop : -3.69 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP X2144 
 HIS   0.005   0.001   HIS X2322 
 PHE   0.021   0.001   PHE X2283 
 TYR   0.020   0.001   TYR X2325 
 ARG   0.009   0.001   ARG X2371 

********************** 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
  64 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.597 
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: 0.9525 (pm20) cc_final: 0.8659 (pt0)
REVERT: X 2065 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8213 (mp0)
REVERT: X 2114 MET cc_start: 0.8801 (pmm) cc_final: 0.8564 (pmm)
REVERT: X 2201 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8492 (mm-30)
REVERT: X 2245 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8917 (mm-30)
REVERT: X 2247 ILE cc_start: 0.8367 (mm) cc_final: 0.8013 (mm)
REVERT: X 2511 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9012 (tm-30)
REVERT: X 2517 PHE cc_start: 0.8818 (t80) cc_final: 0.7945 (t80)
REVERT: X 2521 ARG cc_start: 0.9185 (mtm110) cc_final: 0.8683 (mtm180)
REVERT: X 2526 ASP cc_start: 0.9413 (m-30) cc_final: 0.9178 (p0)
REVERT: X 2601 CYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5272 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 60
  average time/residue: 0.2120
  time to fit residues: 16.5441
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  : 0.623 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
X1997 GLN
** X2202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** X2291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X2292 ASN
** X2582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.063263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.048829 restraints weight = 38438.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.050671 restraints weight = 30952.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.052283 restraints weight = 22502.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5414  Z= 0.216
  Angle     :  1.033  15.414   7269  Z= 0.532
  Chirality :  0.050   0.290    738
  Planarity :  0.005   0.053    938
  Dihedral  :  7.818  40.172    693
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 24.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 20.16 %
    Favored  : 79.69 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.76 (0.31), residues: 635
  helix:  0.09 (0.30), residues: 276
  sheet:  None (None), residues: 0
  loop : -3.66 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP X2144 
 HIS   0.004   0.001   HIS X2322 
 PHE   0.038   0.002   PHE X2283 
 TYR   0.022   0.001   TYR X2325 
 ARG   0.007   0.001   ARG X2371 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2062.47 seconds
wall clock time: 37 minutes 51.69 seconds (2271.69 seconds total)