# Date 2008-01-16 Time 01:28:07 PST -0800 (1200475687.24 s)
#phil __OFF__

Command line arguments: "../436.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31525
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 436

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.1647, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.9807
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.95083

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9236
                             d_min =   1.9807

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9236 1.9807
Completeness in resolution range: 0.953793
Completeness with d_max=infinity: 0.95083

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9240 -  4.2378 [2167/2194]  1948   219  10.1%
  bin  2:  4.2378 -  3.3765 [2061/2077]  1858   203   9.8%
  bin  3:  3.3765 -  2.9534 [2053/2072]  1847   206  10.0%
  bin  4:  2.9534 -  2.6851 [2023/2053]  1823   200   9.9%
  bin  5:  2.6851 -  2.4936 [2005/2024]  1800   205  10.2%
  bin  6:  2.4936 -  2.3472 [2015/2051]  1814   201  10.0%
  bin  7:  2.3472 -  2.2300 [1987/2020]  1793   194   9.8%
  bin  8:  2.2300 -  2.1332 [1988/2023]  1784   204  10.3%
  bin  9:  2.1332 -  2.0513 [1976/2003]  1782   194   9.8%
  bin 10:  2.0513 -  1.9807 [1314/2021]  1181   133  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2198
        3.04 -     3.66: 4636
        3.66 -     4.28: 9031
        4.28 -     4.90: 12348
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.864 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.979 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.045 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  2.083 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28227 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001.geo

CPU time processing inputs: 9.05


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4368   r_free= 0.4212   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.231538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.3556 0.3423      6.5151      6.4813|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.3277 0.3514      6.6322      6.7134|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.3830 0.3472      6.5679      6.5367|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.4166 0.3946      6.4483      6.3954|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.4558 0.4485      6.3182      6.3396|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.4617 0.5292      6.2332      6.1916|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.4762 0.4607      6.1961      6.1222|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.4858 0.4255      6.1601      6.1173|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.4979 0.4621       6.092      6.0949|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.5064 0.4328      6.1222      5.9969|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.5009 0.4550      6.0224      6.0273|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.5064 0.4904      5.9467      5.9775|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.4963 0.4977      5.8721      5.8134|
| 14:  2.0301 -  1.9807 0.53    683   77 0.5130 0.4312       5.879      5.7093|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.73  31.20   0.82     0.75      59250.01|
|  2:  4.7264 -  3.7714  1350   153  0.77  29.26   0.91     0.81      76566.24|
|  3:  3.7714 -  3.3005  1317   146  0.70  35.26   0.87     0.78      79336.34|
|  4:  3.3005 -  3.0015  1309   137  0.63  40.90   0.82     0.70      70111.48|
|  5:  3.0015 -  2.7878  1309   152  0.54  48.69   0.77     0.61      63361.98|
|  6:  2.7878 -  2.6244  1302   144  0.50  51.91   0.75     0.56      58331.00|
|  7:  2.6244 -  2.4936  1287   146  0.49  53.06   0.77     0.56      53423.75|
|  8:  2.4936 -  2.3855  1303   141  0.51  51.05   0.75     0.58      44946.15|
|  9:  2.3855 -  2.2940  1283   145  0.54  49.14   0.74     0.62      38981.42|
| 10:  2.2940 -  2.2151  1270   138  0.55  48.53   0.75     0.62      35167.53|
| 11:  2.2151 -  2.1460  1281   145  0.51  51.54   0.76     0.60      35028.73|
| 12:  2.1460 -  2.0849  1276   137  0.46  55.09   0.79     0.57      34244.04|
| 13:  2.0849 -  2.0301  1258   143  0.46  55.44   0.75     0.55      30076.89|
| 14:  2.0301 -  1.9807   683    77  0.51  51.76   0.74     0.53      22845.39|
|alpha:            min =        0.53 max =            0.81 mean =         0.64|
|beta:             min =    22845.39 max =        79336.34 mean =     51366.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.25|
|phase err.(test): min =        0.00 max =           89.89 mean =        46.47|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.477346              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.490   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.617757              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.253   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      698 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1484 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2636 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3905 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5061 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6576 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7701 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.831 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.780 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4443   r_free= 0.4221   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.238403                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4090   ksol= 0.34   Bsol= 20.03   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,8.41,9.62,0.00,0.00,0.00); trace/3= 8.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.224683                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.001020              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.153   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.578624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 73.961   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4275      final r-factor (work) = 0.3162          |
| start r-factor (free) = 0.4090      final r-factor (free) = 0.3345          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.6882 = 7.00 * 0.50 * 6.2440 + 1.00 * 53.8312                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3424 = 7.00 * 0.50 * 6.0627 + 1.00 * 0.1200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3162      final r-factor (work) = 0.2537          |
| start r-factor (free) = 0.3345      final r-factor (free) = 0.2875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5224 = 0.58 * 1.00 * 6.0627 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4114 = 0.58 * 1.00 * 5.8750 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.66   10.87    None  None   None       |
|    all(noH): 2823   0      0.00    58.66   10.87    None  None   None       |
|    Sol.    : 438    0      0.00    57.02   27.44    None  None   None       |
|    Mac.    : 2385   0      0.00    58.66   7.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.866: 1185   |   5:    29.329 -  35.195:  100        |
|      1:     5.866 -  11.732:  784   |   6:    35.195 -  41.061:   71        |
|      2:    11.732 -  17.597:  327   |   7:    41.061 -  46.926:   47        |
|      3:    17.597 -  23.463:  147   |   8:    46.926 -  52.792:   26        |
|      4:    23.463 -  29.329:  127   |   9:    52.792 -  58.658:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2537 r_free = 0.2875             target_work(ml) = 5.813         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2531 r_free = 0.2886             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2531   r_free= 0.2886   ksol= 0.34   Bsol= 20.03   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,8.41,9.62,0.00,0.00,0.00); trace/3= 8.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.811921                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2475   r_free= 0.2833   ksol= 0.32   Bsol= 38.05   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.47,5.82,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.812225                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.464551              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.566   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.911  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2475      final r-factor (work) = 0.1593          |
| start r-factor (free) = 0.2833      final r-factor (free) = 0.1975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2703 = 4.46 * 0.50 * 5.8910 + 1.00 * 0.1200                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6142 = 4.46 * 0.50 * 5.6202 + 1.00 * 0.0684                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1593      final r-factor (work) = 0.1429          |
| start r-factor (free) = 0.1975      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7823 = 0.31 * 1.00 * 5.6202 + 1.00 * 0.0242                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7751 = 0.31 * 1.00 * 5.3687 + 1.00 * 0.0957                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.54   11.28    None  None   None       |
|    all(noH): 2823   0      0.00    68.54   11.28    None  None   None       |
|    Sol.    : 438    0      1.02    61.45   32.03    None  None   None       |
|    Mac.    : 2385   0      0.00    68.54   7.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.854: 1501   |   5:    34.271 -  41.125:  100        |
|      1:     6.854 -  13.708:  673   |   6:    41.125 -  47.979:  105        |
|      2:    13.708 -  20.562:  182   |   7:    47.979 -  54.833:   37        |
|      3:    20.562 -  27.417:  103   |   8:    54.833 -  61.687:   12        |
|      4:    27.417 -  34.271:  106   |   9:    61.687 -  68.541:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1429 r_free = 0.1821             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1428 r_free = 0.1822             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1428   r_free= 0.1822   ksol= 0.32   Bsol= 38.05   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.68,4.47,5.82,0.00,0.00,0.00); trace/3= 4.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.329814                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1825   ksol= 0.33   Bsol= 50.56   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.57,4.71,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330023                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.574851              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.966  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210999              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.489   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1420      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1825      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9881 = 2.57 * 0.50 * 5.3749 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8385 = 2.57 * 0.50 * 5.2606 + 1.00 * 0.0658                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3920 = 1.21 * 1.00 * 5.2606 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2867 = 1.21 * 1.00 * 5.1803 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.45   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    75.45   11.73    None  None   None       |
|    Sol.    : 438    0      0.00    69.20   34.73    None  None   None       |
|    Mac.    : 2385   0      0.00    75.45   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.546: 1635   |   5:    37.727 -  45.273:   84        |
|      1:     7.546 -  15.091:  565   |   6:    45.273 -  52.818:   89        |
|      2:    15.091 -  22.636:  173   |   7:    52.818 -  60.364:   49        |
|      3:    22.636 -  30.182:   99   |   8:    60.364 -  67.909:   14        |
|      4:    30.182 -  37.727:  111   |   9:    67.909 -  75.454:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1588             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1588             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1588   ksol= 0.33   Bsol= 50.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.57,4.71,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176754                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1588   ksol= 0.33   Bsol= 50.56   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.57,4.71,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.176754                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.222283              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.323  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.266604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.553  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8219 = 2.22 * 0.50 * 5.1800 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8029 = 2.22 * 0.50 * 5.1648 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3903 = 0.27 * 1.00 * 5.1648 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3916 = 0.27 * 1.00 * 5.1625 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.84   11.48    None  None   None       |
|    all(noH): 2823   0      0.00    75.84   11.48    None  None   None       |
|    Sol.    : 438    0      0.70    68.00   33.49    None  None   None       |
|    Mac.    : 2385   0      0.00    75.84   7.43     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.584: 1658   |   5:    37.921 -  45.506:   87        |
|      1:     7.584 -  15.169:  564   |   6:    45.506 -  53.090:   74        |
|      2:    15.169 -  22.753:  165   |   7:    53.090 -  60.674:   38        |
|      3:    22.753 -  30.337:  109   |   8:    60.674 -  68.258:   14        |
|      4:    30.337 -  37.921:  111   |   9:    68.258 -  75.842:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1569             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1570             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1570   ksol= 0.33   Bsol= 50.56   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.57,4.71,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158482                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1569   ksol= 0.33   Bsol= 50.56   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.33,4.52,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158578                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.952850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.683  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.026   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6848 = 2.95 * 0.50 * 5.1616 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6691 = 2.95 * 0.50 * 5.1433 + 1.00 * 0.0754                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6290 = 0.31 * 1.00 * 5.1433 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6485 = 0.31 * 1.00 * 5.1366 + 1.00 * 0.0354                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.53   11.25    None  None   None       |
|    all(noH): 2823   0      0.00    76.53   11.25    None  None   None       |
|    Sol.    : 438    0      0.91    67.27   32.58    None  None   None       |
|    Mac.    : 2385   0      0.00    76.53   7.33     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.653: 1681   |   5:    38.265 -  45.918:   86        |
|      1:     7.653 -  15.306:  556   |   6:    45.918 -  53.571:   64        |
|      2:    15.306 -  22.959:  158   |   7:    53.571 -  61.225:   32        |
|      3:    22.959 -  30.612:  115   |   8:    61.225 -  68.878:    9        |
|      4:    30.612 -  38.265:  119   |   9:    68.878 -  76.531:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1098 r_free = 0.1556             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1098 r_free = 0.1557             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1557   ksol= 0.33   Bsol= 50.56   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.33,4.52,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135741                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.1004 0.1300      5.3949      5.5399|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.0863 0.1107      5.4463      5.6403|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.1046 0.1513      5.4606      5.8466|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.1166 0.1512      5.4184      5.5734|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.1285 0.1594      5.2994      5.4862|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.1201 0.2021      5.1907      5.4943|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.1218 0.1607      5.1552       5.333|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.1107 0.1704       5.055      5.3401|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.1183 0.1923      5.0324      5.3391|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.1114 0.1510      4.9577      5.1239|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.1111 0.1759      4.9275      5.2754|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.1104 0.1674      4.8637       5.171|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.1086 0.1715      4.7616      4.9925|
| 14:  2.0301 -  1.9807 0.53    683   77 0.0990 0.1701      4.6339      4.9328|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.94   9.34   0.98     0.95       7393.85|
|  2:  4.7264 -  3.7714  1350   153  0.95   8.06   1.01     1.00       9189.58|
|  3:  3.7714 -  3.3005  1317   146  0.94  11.13   1.02     1.01      10194.44|
|  4:  3.3005 -  3.0015  1309   137  0.93  12.92   1.00     0.99       9777.92|
|  5:  3.0015 -  2.7878  1309   152  0.90  15.35   0.99     0.96       7815.09|
|  6:  2.7878 -  2.6244  1302   144  0.90  16.02   0.98     0.95       6810.67|
|  7:  2.6244 -  2.4936  1287   146  0.91  15.25   0.98     0.94       6005.95|
|  8:  2.4936 -  2.3855  1303   141  0.91  14.85   0.99     0.97       5307.57|
|  9:  2.3855 -  2.2940  1283   145  0.90  15.92   1.00     0.97       5101.48|
| 10:  2.2940 -  2.2151  1270   138  0.90  16.13   1.00     0.96       4476.45|
| 11:  2.2151 -  2.1460  1281   145  0.90  16.00   0.99     0.95       4340.51|
| 12:  2.1460 -  2.0849  1276   137  0.91  15.37   1.01     1.00       3873.87|
| 13:  2.0849 -  2.0301  1258   143  0.91  15.55   1.00     0.99       3194.97|
| 14:  2.0301 -  1.9807   683    77  0.92  13.65   0.97     0.93       2342.77|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2342.77 max =        10194.44 mean =      6301.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.54 mean =        13.46|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1557   ksol= 0.32   Bsol= 48.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,-0.15,1.07,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135826                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1098   r_free= 0.1557   ksol= 0.32   Bsol= 48.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,-0.15,1.07,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135826                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9240 -  4.7264 0.99   1402  155 0.1001 0.1295      5.3914      5.5362|
|  2:  4.7264 -  3.7714 0.99   1350  153 0.0859 0.1103      5.4427      5.6363|
|  3:  3.7714 -  3.3005 0.99   1317  146 0.1044 0.1513       5.459      5.8472|
|  4:  3.3005 -  3.0015 0.99   1309  137 0.1168 0.1515      5.4194      5.5748|
|  5:  3.0015 -  2.7878 0.99   1309  152 0.1288 0.1598      5.3015      5.4881|
|  6:  2.7878 -  2.6244 0.99   1302  144 0.1204 0.2025      5.1926      5.4963|
|  7:  2.6244 -  2.4936 0.99   1287  146 0.1219 0.1611       5.157       5.335|
|  8:  2.4936 -  2.3855 0.98   1303  141 0.1108 0.1704      5.0559      5.3405|
|  9:  2.3855 -  2.2940 0.98   1283  145 0.1183 0.1922      5.0331      5.3394|
| 10:  2.2940 -  2.2151 0.98   1270  138 0.1114 0.1511      4.9582      5.1249|
| 11:  2.2151 -  2.1460 1.00   1281  145 0.1112 0.1761       4.928      5.2758|
| 12:  2.1460 -  2.0849 0.97   1276  137 0.1104 0.1675      4.8639      5.1711|
| 13:  2.0849 -  2.0301 0.98   1258  143 0.1086 0.1715      4.7619      4.9927|
| 14:  2.0301 -  1.9807 0.53    683   77 0.0991 0.1702      4.6347      4.9339|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9240 -  4.7264  1402   155  0.94   9.30   0.98     0.95       7330.30|
|  2:  4.7264 -  3.7714  1350   153  0.95   8.03   1.01     1.00       9128.09|
|  3:  3.7714 -  3.3005  1317   146  0.94  11.11   1.02     1.01      10161.44|
|  4:  3.3005 -  3.0015  1309   137  0.93  12.94   1.00     0.99       9802.71|
|  5:  3.0015 -  2.7878  1309   152  0.90  15.37   0.99     0.96       7846.51|
|  6:  2.7878 -  2.6244  1302   144  0.90  16.06   0.98     0.95       6836.70|
|  7:  2.6244 -  2.4936  1287   146  0.91  15.28   0.98     0.94       6027.27|
|  8:  2.4936 -  2.3855  1303   141  0.91  14.87   1.00     0.97       5318.51|
|  9:  2.3855 -  2.2940  1283   145  0.90  15.93   1.01     0.97       5110.10|
| 10:  2.2940 -  2.2151  1270   138  0.90  16.14   1.00     0.96       4480.73|
| 11:  2.2151 -  2.1460  1281   145  0.90  16.01   0.99     0.96       4346.26|
| 12:  2.1460 -  2.0849  1276   137  0.91  15.38   1.01     1.00       3878.24|
| 13:  2.0849 -  2.0301  1258   143  0.91  15.56   1.00     0.99       3198.93|
| 14:  2.0301 -  1.9807   683    77  0.92  13.66   0.97     0.94       2347.02|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2347.02 max =        10161.44 mean =      6299.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.44 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.924)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.53    80.06   14.77    None  None   None       |
|    all(noH): 2823   0      3.53    80.06   14.77    None  None   None       |
|    Sol.    : 438    0      4.43    70.79   36.11    None  None   None       |
|    Mac.    : 2385   0      3.53    80.06   10.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.528 -  11.181: 1681   |   5:    41.793 -  49.446:   86        |
|      1:    11.181 -  18.834:  556   |   6:    49.446 -  57.099:   64        |
|      2:    18.834 -  26.487:  158   |   7:    57.099 -  64.752:   32        |
|      3:    26.487 -  34.140:  115   |   8:    64.752 -  72.405:    9        |
|      4:    34.140 -  41.793:  119   |   9:    72.405 -  80.058:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.245 - 5.919
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 302
   mapped sites are within: 0.722 - 5.919

peak=   11.237 closest distance to " CB  VAL A 230 " =    1.505
peak=    6.487 closest distance to " CG  LEU A   5 " =    1.238
peak=    6.119 closest distance to " NH2 ARG A  56 " =    2.221
peak=    5.952 closest distance to " CB  VAL A 296 " =    1.159
peak=    5.633 closest distance to " CG  LEU A 228 " =    1.192
peak=    5.322 closest distance to " CG  PRO A  54 " =    1.274
peak=    5.209 closest distance to " O   HOH Z 142 " =    1.728
peak=    5.138 closest distance to " NE2 GLN A  11 " =    1.139
peak=    5.085 closest distance to " CB  ARG A 275 " =    0.903
peak=    4.974 closest distance to " CB  GLN A 223 " =    1.490
peak=    4.924 closest distance to " CD2 LEU A   5 " =    1.167
peak=    4.886 closest distance to " CG2 VAL A 296 " =    0.990
peak=    4.872 closest distance to " CB  GLN A 183 " =    1.277
peak=    4.737 closest distance to " CB  SER A  63 " =    1.188
peak=    4.714 closest distance to " O   HOH Z 209 " =    2.280
peak=    4.653 closest distance to " O   HOH Z 126 " =    1.897
peak=    4.649 closest distance to " CB  VAL A 230 " =    1.176
peak=    4.597 closest distance to " C   PRO A 198 " =    1.492
peak=    4.559 closest distance to " O   SER A  87 " =    2.227
peak=    4.533 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.526 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.503 closest distance to " CB  GLU A 152 " =    1.190
peak=    4.488 closest distance to " O   HOH Z  61 " =    1.662
peak=    4.407 closest distance to " CB  ARG A  79 " =    1.477
peak=    4.398 closest distance to " CZ  PHE A 218 " =    1.170
peak=    4.369 closest distance to " CB  PRO A  54 " =    0.917
peak=    4.333 closest distance to " O   HOH Z 423 " =    1.878
peak=    4.304 closest distance to " O   HOH Z 346 " =    1.568
peak=    4.291 closest distance to " O   HOH Z 126 " =    2.102
peak=    4.286 closest distance to " O   HOH Z 369 " =    2.198
peak=    4.279 closest distance to " CG1 VAL A 296 " =    1.128
peak=    4.262 closest distance to " O   HOH Z 402 " =    1.462
peak=    4.259 closest distance to " O   HOH Z 248 " =    1.569
peak=    4.229 closest distance to " O   HOH Z 193 " =    1.804
peak=    4.227 closest distance to " O   HOH Z 236 " =    2.019
peak=    4.206 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.200 closest distance to " CA  TYR A  30 " =    0.893
peak=    4.197 closest distance to " ND2 ASN A 187 " =    1.544
peak=    4.174 closest distance to " CB  ASN A 148 " =    1.435
peak=    4.144 closest distance to " O   HOH Z 368 " =    2.202
peak=    4.130 closest distance to " CB  ARG A 190 " =    1.691
peak=    4.120 closest distance to " O   HOH Z  43 " =    2.016
peak=    4.119 closest distance to " O   HOH Z 234 " =    3.658
peak=    4.106 closest distance to " CG  PRO A 243 " =    1.104
peak=    4.078 closest distance to " O   HOH Z 427 " =    2.962
peak=    4.077 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.074 closest distance to " O   HOH Z 280 " =    2.955
peak=    4.040 closest distance to " CB  VAL A 265 " =    1.311
peak=    4.034 closest distance to " O   HOH Z 158 " =    3.171
peak=    4.019 closest distance to " CD2 TRP A 179 " =    1.349
peak=    4.009 closest distance to " O   HOH Z 214 " =    2.165
peak=    4.007 closest distance to " OG ASER A 258 " =    3.073
peak=    4.007 closest distance to " CB  TRP A 266 " =    0.957
peak=    3.972 closest distance to " OD1 ASN A  69 " =    2.568
peak=    3.961 closest distance to " O   HOH Z 313 " =    1.837
peak=    3.947 closest distance to " CB  ASN A 187 " =    1.414
peak=    3.943 closest distance to " O   HOH Z  78 " =    1.618
peak=    3.930 closest distance to " O   HOH Z 265 " =    2.137
peak=    3.921 closest distance to " O   HOH Z 189 " =    2.802
peak=    3.919 closest distance to " CB  VAL A 202 " =    1.470
peak=    3.917 closest distance to " CB  GLU A 277 " =    3.573
peak=    3.908 closest distance to " O   HOH Z 403 " =    1.683
peak=    3.896 closest distance to " O   HOH Z 250 " =    1.351
peak=    3.888 closest distance to " O   HOH Z  97 " =    2.396
peak=    3.887 closest distance to " O   HOH Z 407 " =    2.514
peak=    3.881 closest distance to " CD2 LEU A 228 " =    1.231
peak=    3.879 closest distance to " O   HOH Z  59 " =    2.188
peak=    3.873 closest distance to " CB  ASN A 142 " =    1.085
peak=    3.855 closest distance to " CG1 ILE A  49 " =    1.508
peak=    3.855 closest distance to " O   HOH Z 298 " =    1.767
peak=    3.853 closest distance to " CB  ASN A  39 " =    0.839
peak=    3.843 closest distance to " O   HOH Z  15 " =    2.067
peak=    3.838 closest distance to " O   HOH Z 197 " =    3.000
peak=    3.832 closest distance to " CB  SER A  26 " =    1.781
peak=    3.812 closest distance to " CB  ASP A 140 " =    1.051
peak=    3.802 closest distance to " O   HOH Z  68 " =    2.212
peak=    3.797 closest distance to " O   HOH Z  85 " =    1.371
peak=    3.771 closest distance to " OG BSER A 164 " =    2.248
peak=    3.769 closest distance to " CB  ALA A   9 " =    1.641
peak=    3.753 closest distance to " O   HOH Z 128 " =    2.022
peak=    3.752 closest distance to " CB  TRP A 179 " =    1.438
peak=    3.751 closest distance to " O   HOH Z  40 " =    1.652
peak=    3.743 closest distance to " O   HOH Z  80 " =    1.751
peak=    3.741 closest distance to " CG2AVAL A  72 " =    1.692
peak=    3.731 closest distance to " O   HOH Z 261 " =    1.968
peak=    3.728 closest distance to " CA  ALA A  51 " =    0.907
peak=    3.724 closest distance to " N   ASN A  39 " =    1.234
peak=    3.720 closest distance to " CG2 ILE A  20 " =    1.434
peak=    3.717 closest distance to " O   HOH Z 180 " =    2.123
peak=    3.715 closest distance to " CB  GLU A  46 " =    1.027
peak=    3.714 closest distance to " O   HOH Z 203 " =    1.652
peak=    3.711 closest distance to " O   HOH Z 411 " =    3.860
peak=    3.710 closest distance to " CB  THR A  31 " =    1.507
peak=    3.710 closest distance to " CD  LYS A 166 " =    1.283
peak=    3.692 closest distance to " O   HOH Z 147 " =    1.829
peak=    3.687 closest distance to " CA  ASN A 215 " =    1.034
peak=    3.686 closest distance to " CB  SER A   3 " =    1.234
peak=    3.675 closest distance to " O   HOH Z  21 " =    1.805
peak=    3.674 closest distance to " O   HOH Z  19 " =    2.084
peak=    3.659 closest distance to " O   HOH Z 273 " =    2.862
peak=    3.648 closest distance to " CB  GLN A  88 " =    1.154
peak=    3.647 closest distance to " CB AVAL A  41 " =    1.060
peak=    3.643 closest distance to " CB  ARG A  79 " =    0.908
peak=    3.642 closest distance to " O   HOH Z  97 " =    1.982
peak=    3.629 closest distance to " O   HOH Z 145 " =    2.391
peak=    3.628 closest distance to " O   HOH Z 365 " =    2.859
peak=    3.628 closest distance to " O   HOH Z 371 " =    3.096
peak=    3.622 closest distance to " CA  ARG A  36 " =    1.034
peak=    3.614 closest distance to " O   HOH Z 389 " =    1.859
peak=    3.608 closest distance to " O   HOH Z 251 " =    1.500
peak=    3.602 closest distance to " CB  ARG A 139 " =    0.996
peak=    3.598 closest distance to " CD  ARG A 159 " =    0.722
peak=    3.598 closest distance to " O   HOH Z 417 " =    3.200
peak=    3.597 closest distance to " CG  MET A 185 " =    1.114
peak=    3.594 closest distance to " O   HOH Z 193 " =    1.969
peak=    3.577 closest distance to " CG  LEU A 167 " =    1.267
peak=    3.568 closest distance to " N   ASP A 162 " =    1.219
peak=    3.565 closest distance to " O   HOH Z 299 " =    4.196
peak=    3.565 closest distance to " O   HOH Z 128 " =    2.229
peak=    3.564 closest distance to " O   HOH Z 422 " =    2.614
peak=    3.554 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.547 closest distance to " O   HOH Z 322 " =    2.075
peak=    3.543 closest distance to " O  BHOH Z 338 " =    2.389
peak=    3.542 closest distance to " NE2 GLN A  77 " =    3.336
peak=    3.540 closest distance to " O   TRP A 274 " =    1.870
peak=    3.535 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.527 closest distance to " CB  ASN A 110 " =    1.102
peak=    3.524 closest distance to " OE1 GLU A   2 " =    2.160
peak=    3.520 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.513 closest distance to " O   HOH Z  54 " =    1.575
peak=    3.505 closest distance to " CA  ALA A  21 " =    1.097
peak=    3.497 closest distance to " CG  PRO A 198 " =    1.262
peak=    3.491 closest distance to " CA  ARG A 195 " =    1.210
peak=    3.490 closest distance to " CB  GLU A 128 " =    1.024
peak=    3.487 closest distance to " O   HOH Z 359 " =    1.431
peak=    3.484 closest distance to " O   HOH Z 187 " =    2.307
peak=    3.470 closest distance to " O   ARG A  56 " =    2.926
peak=    3.469 closest distance to " O   HOH Z 380 " =    1.903
peak=    3.464 closest distance to " O   HOH Z 285 " =    2.724
peak=    3.463 closest distance to " NZ  LYS A  48 " =    1.251
peak=    3.461 closest distance to " CB  GLN A 278 " =    0.830
peak=    3.455 closest distance to " CB  ALA A 248 " =    1.361
peak=    3.454 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.449 closest distance to " CA  ASP A 162 " =    1.024
peak=    3.438 closest distance to " CB  THR A  52 " =    0.962
peak=    3.438 closest distance to " O   HOH Z 337 " =    3.488
peak=    3.436 closest distance to " O   HOH Z 294 " =    1.545
peak=    3.431 closest distance to " N   PHE A 130 " =    1.252
peak=    3.430 closest distance to " CA  THR A 264 " =    0.808
peak=    3.422 closest distance to " CB  SER A 212 " =    1.160
peak=    3.420 closest distance to " CG  ARG A  66 " =    2.661
peak=    3.420 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.407 closest distance to " O   HOH Z 344 " =    2.926
peak=    3.402 closest distance to " CG  GLN A  77 " =    2.160
peak=    3.401 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.400 closest distance to " O   HOH Z 166 " =    3.887
peak=    3.399 closest distance to " O   HOH Z 325 " =    2.270
peak=    3.397 closest distance to " CB  PRO A  90 " =    1.136
peak=    3.394 closest distance to " CG2 VAL A 257 " =    0.839
peak=    3.393 closest distance to " O   HOH Z 112 " =    1.666
peak=    3.390 closest distance to " O   HOH Z 234 " =    1.886
peak=    3.390 closest distance to " O   HOH Z 353 " =    2.642
peak=    3.380 closest distance to " N   SER A 135 " =    1.435
peak=    3.376 closest distance to " CD2 LEU A 297 " =    0.939
peak=    3.374 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.368 closest distance to " CA  PHE A 283 " =    1.156
peak=    3.364 closest distance to " CA  ALA A 291 " =    0.824
peak=    3.362 closest distance to " CZ3 TRP A  85 " =    0.966
peak=    3.362 closest distance to " O   ASN A  74 " =    1.511
peak=    3.348 closest distance to " NH2 ARG A 156 " =    1.068
peak=    3.347 closest distance to " NZ  LYS A 117 " =    3.186
peak=    3.346 closest distance to " CG2 THR A 221 " =    1.215
peak=    3.344 closest distance to " O   HOH Z 291 " =    1.568
peak=    3.344 closest distance to " O   HOH Z 141 " =    1.617
peak=    3.342 closest distance to " O   HOH Z 383 " =    1.898
peak=    3.342 closest distance to " CB  TRP A 150 " =    1.481
peak=    3.338 closest distance to " O   HOH Z  88 " =    3.006
peak=    3.329 closest distance to " O   HOH Z 148 " =    3.327
peak=    3.322 closest distance to " CB  ALA A 295 " =    1.153
peak=    3.321 closest distance to " CB  ALA A 291 " =    1.325
peak=    3.320 closest distance to " O   HOH Z 172 " =    3.688
peak=    3.315 closest distance to " O   HOH Z 305 " =    3.632
peak=    3.309 closest distance to " O   HOH Z 258 " =    2.249
peak=    3.309 closest distance to " O   SER A 164 " =    1.149
peak=    3.300 closest distance to " O   ASP A 124 " =    1.254
peak=    3.298 closest distance to " CB  ASN A 215 " =    1.215
peak=    3.297 closest distance to " O   HOH Z 435 " =    1.944
peak=    3.297 closest distance to " CB  PHE A 204 " =    0.778
peak=    3.295 closest distance to " O   LYS A 290 " =    2.401
peak=    3.292 closest distance to " CB  GLN A 205 " =    1.163
peak=    3.291 closest distance to " OE2 GLU A  53 " =    1.989
peak=    3.289 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.287 closest distance to " CA  ASN A 217 " =    1.247
peak=    3.286 closest distance to " O   HOH Z 368 " =    3.589
peak=    3.285 closest distance to " CD  LYS A 119 " =    1.815
peak=    3.284 closest distance to " O   HOH Z 102 " =    1.275
peak=    3.282 closest distance to " OD1BASN A 224 " =    2.275
peak=    3.279 closest distance to " O   HOH Z 213 " =    1.730
peak=    3.275 closest distance to " O   HOH Z 425 " =    1.990
peak=    3.275 closest distance to " O   HOH Z   9 " =    2.082
peak=    3.273 closest distance to " CA  ALA A 248 " =    1.257
peak=    3.273 closest distance to " O   HOH Z 171 " =    3.847
peak=    3.269 closest distance to " O   HOH Z 437 " =    1.763
peak=    3.268 closest distance to " CA  VAL A  41 " =    0.812
peak=    3.268 closest distance to " CG1 ILE A  33 " =    1.265
peak=    3.266 closest distance to " O   HOH Z 421 " =    1.680
peak=    3.264 closest distance to " N   VAL A 126 " =    1.415
peak=    3.264 closest distance to " CA  ILE A 106 " =    0.743
peak=    3.261 closest distance to " O   HOH Z 406 " =    1.632
peak=    3.260 closest distance to " O   LEU A 228 " =    1.836
peak=    3.259 closest distance to " O   HOH Z 345 " =    3.192
peak=    3.258 closest distance to " NH2 ARG A  79 " =    1.301
peak=    3.256 closest distance to " CD BLYS A 290 " =    1.120
peak=    3.255 closest distance to " O   HOH Z   1 " =    2.094
peak=    3.254 closest distance to " CG  MET A 185 " =    0.984
peak=    3.252 closest distance to " CG  LYS A  76 " =    0.929
peak=    3.250 closest distance to " O   HOH Z 227 " =    1.613
peak=    3.249 closest distance to " O   HOH Z  62 " =    2.326
peak=    3.247 closest distance to " CB  HIS A 108 " =    0.806
peak=    3.246 closest distance to " CB  ALA A 248 " =    0.990
peak=    3.246 closest distance to " OG  SER A  22 " =    2.684
peak=    3.245 closest distance to " CG2AVAL A 121 " =    2.294
peak=    3.245 closest distance to " O   HOH Z  88 " =    2.499
peak=    3.244 closest distance to " CD  ARG A  79 " =    1.874
peak=    3.243 closest distance to " O   HOH Z 216 " =    2.938
peak=    3.242 closest distance to " CG2 ILE A 120 " =    1.140
peak=    3.240 closest distance to " O   HOH Z 185 " =    1.716
peak=    3.237 closest distance to " CB  LYS A 290 " =    0.926
peak=    3.237 closest distance to " O   HOH Z 329 " =    4.041
peak=    3.236 closest distance to " CA  ASN A 176 " =    1.107
peak=    3.227 closest distance to " CD1 LEU A   5 " =    1.361
peak=    3.227 closest distance to " O   MET A 105 " =    1.835
peak=    3.223 closest distance to " CZ  PHE A  38 " =    1.159
peak=    3.221 closest distance to " CD1 ILE A  33 " =    1.700
peak=    3.220 closest distance to " O   HOH Z 403 " =    1.368
peak=    3.216 closest distance to " CB  ALA A 114 " =    1.305
peak=    3.211 closest distance to " O   HOH Z  94 " =    2.192
peak=    3.210 closest distance to " O   HOH Z 171 " =    2.295
peak=    3.207 closest distance to " CA  ALA A  84 " =    1.331
peak=    3.206 closest distance to " N   SER A  12 " =    1.622
peak=    3.204 closest distance to " CD1 ILE A 106 " =    1.087
peak=    3.202 closest distance to " O   HOH Z 426 " =    1.575
peak=    3.202 closest distance to " O   HOH Z 245 " =    1.412
peak=    3.199 closest distance to " O   HOH Z 154 " =    1.445
peak=    3.198 closest distance to " CB  THR A 157 " =    1.131
peak=    3.194 closest distance to " O   HOH Z 263 " =    1.670
peak=    3.193 closest distance to " CB  ALA A 242 " =    0.866
peak=    3.190 closest distance to " CA  ASP A 191 " =    1.096
peak=    3.188 closest distance to " CG BARG A 275 " =    1.309
peak=    3.183 closest distance to " CD2 TYR A 186 " =    1.063
peak=    3.178 closest distance to " N   GLU A  44 " =    2.103
peak=    3.177 closest distance to " O   HOH Z 261 " =    1.842
peak=    3.176 closest distance to " O   HOH Z 116 " =    1.743
peak=    3.173 closest distance to " CG BARG A 102 " =    1.696
peak=    3.173 closest distance to " CB  ALA A 100 " =    1.186
peak=    3.169 closest distance to " CD1 ILE A 199 " =    0.950
peak=    3.167 closest distance to " OG1 THR A 294 " =    1.719
peak=    3.161 closest distance to " CA  LEU A 282 " =    1.098
peak=    3.152 closest distance to " OG  SER A 245 " =    1.583
peak=    3.148 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.145 closest distance to " CD  LYS A  76 " =    1.817
peak=    3.137 closest distance to " CB  SER A 273 " =    0.853
peak=    3.135 closest distance to " CA  ASN A 127 " =    1.031
peak=    3.134 closest distance to " O   HOH Z 357 " =    1.904
peak=    3.127 closest distance to " CB  LEU A 228 " =    1.224
peak=    3.126 closest distance to " O   ALA A   1 " =    1.744
peak=    3.123 closest distance to " O   ASN A 284 " =    1.713
peak=    3.122 closest distance to " CD  ARG A  66 " =    2.741
peak=    3.117 closest distance to " O   HOH Z  10 " =    1.772
peak=    3.116 closest distance to " O   HOH Z  90 " =    3.330
peak=    3.114 closest distance to " O   HOH Z 319 " =    2.373
peak=    3.112 closest distance to " O   HOH Z 183 " =    1.787
peak=    3.112 closest distance to " CB  ILE A 120 " =    1.350
peak=    3.104 closest distance to " CB  MET A  47 " =    1.109
peak=    3.104 closest distance to " CD1 LEU A 228 " =    1.964
peak=    3.101 closest distance to " CG2 THR A  18 " =    1.460
peak=    3.099 closest distance to " O   HOH Z 123 " =    2.269
peak=    3.099 closest distance to " O   HOH Z 109 " =    2.528
peak=    3.094 closest distance to " O   HOH Z  83 " =    1.544
peak=    3.091 closest distance to " CE AMET A  47 " =    1.400
peak=    3.090 closest distance to " N   ASN A 127 " =    1.257
peak=    3.090 closest distance to " CA  SER A  87 " =    0.993
peak=    3.087 closest distance to " NE2 HIS A 207 " =    1.238
peak=    3.087 closest distance to " CA  SER A 146 " =    1.787
peak=    3.081 closest distance to " O   ALA A 158 " =    1.342
peak=    3.069 closest distance to " CB  GLN A 103 " =    0.944
peak=    3.068 closest distance to " O   GLN A 278 " =    1.487
peak=    3.065 closest distance to " O   HOH Z 293 " =    1.738
peak=    3.059 closest distance to " O   HOH Z 417 " =    2.244
peak=    3.056 closest distance to " CB  ASN A 224 " =    0.986
peak=    3.054 closest distance to " O   HOH Z 420 " =    5.919
peak=    3.048 closest distance to " CA  LYS A 290 " =    1.208
peak=    3.036 closest distance to " C   ALA A 299 " =    0.949

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.709 - 5.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 201
   mapped sites are within: 0.709 - 5.551

peak=   -5.694 closest distance to " CG2 VAL A 230 " =    0.709
peak=   -4.911 closest distance to " SG  CYS A 254 " =    3.325
peak=   -4.649 closest distance to " CD  GLN A  58 " =    1.032
peak=   -4.436 closest distance to " CD  ARG A 156 " =    2.006
peak=   -4.382 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.305 closest distance to " CG  GLN A 223 " =    2.055
peak=   -4.245 closest distance to " O   HOH Z 266 " =    5.286
peak=   -4.210 closest distance to " O   HOH Z 196 " =    2.017
peak=   -4.182 closest distance to " O   VAL A  67 " =    2.669
peak=   -4.137 closest distance to " C   HIS A 108 " =    1.235
peak=   -4.132 closest distance to " OG BSER A 134 " =    1.233
peak=   -4.037 closest distance to " O   HOH Z 290 " =    1.149
peak=   -3.978 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.974 closest distance to " CA  VAL A  67 " =    2.889
peak=   -3.962 closest distance to " O   HOH Z 231 " =    2.175
peak=   -3.935 closest distance to " O   HOH Z 114 " =    3.143
peak=   -3.927 closest distance to " OXT GLY A 302 " =    2.766
peak=   -3.917 closest distance to " O   HOH Z 166 " =    1.906
peak=   -3.914 closest distance to " CZ3 TRP A 179 " =    1.251
peak=   -3.900 closest distance to " ND2 ASN A 187 " =    1.560
peak=   -3.894 closest distance to " O   PRO A 163 " =    2.163
peak=   -3.867 closest distance to " OG  SER A  97 " =    2.317
peak=   -3.867 closest distance to " CA  ASP A 298 " =    1.100
peak=   -3.859 closest distance to " CB  ALA A 248 " =    2.346
peak=   -3.851 closest distance to " CD1 LEU A 255 " =    2.779
peak=   -3.846 closest distance to " CB  ALA A 161 " =    2.533
peak=   -3.802 closest distance to " CD1 LEU A 101 " =    2.325
peak=   -3.793 closest distance to " CB  PHE A 192 " =    2.035
peak=   -3.790 closest distance to " CG1 VAL A 112 " =    2.704
peak=   -3.790 closest distance to " O   PRO A 198 " =    1.200
peak=   -3.750 closest distance to " CG1 VAL A 250 " =    2.792
peak=   -3.746 closest distance to " CE2 TYR A  30 " =    2.757
peak=   -3.719 closest distance to " ND2 ASN A  45 " =    1.173
peak=   -3.715 closest distance to " CB  PRO A 163 " =    2.501
peak=   -3.705 closest distance to " O   HOH Z  37 " =    1.870
peak=   -3.703 closest distance to " O   HOH Z 394 " =    1.496
peak=   -3.694 closest distance to " O   HOH Z  11 " =    1.872
peak=   -3.687 closest distance to " O   HOH Z 211 " =    1.633
peak=   -3.687 closest distance to " O   SER A 210 " =    1.948
peak=   -3.686 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.675 closest distance to " CB  ALA A 248 " =    2.201
peak=   -3.667 closest distance to " O   HOH Z  44 " =    2.253
peak=   -3.657 closest distance to " NE2 GLN A  88 " =    1.900
peak=   -3.649 closest distance to " OD2 ASP A 171 " =    2.325
peak=   -3.648 closest distance to " CG2 ILE A  49 " =    2.800
peak=   -3.638 closest distance to " CD1 PHE A  59 " =    2.027
peak=   -3.630 closest distance to " N   ALA A 248 " =    1.805
peak=   -3.629 closest distance to " CG2 ILE A 263 " =    2.285
peak=   -3.627 closest distance to " CB  ALA A 291 " =    2.235
peak=   -3.605 closest distance to " CB  ALA A  43 " =    2.368
peak=   -3.600 closest distance to " CG2 VAL A 296 " =    1.389
peak=   -3.588 closest distance to " CD  ARG A 139 " =    1.646
peak=   -3.569 closest distance to " CG1 VAL A 296 " =    1.151
peak=   -3.565 closest distance to " CE  MET A 105 " =    2.234
peak=   -3.563 closest distance to " C   ILE A 239 " =    2.024
peak=   -3.563 closest distance to " CD  LYS A 289 " =    2.485
peak=   -3.561 closest distance to " O   HOH Z 185 " =    2.516
peak=   -3.555 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.553 closest distance to " CG1 VAL A 230 " =    1.898
peak=   -3.552 closest distance to " O   HOH Z  73 " =    2.289
peak=   -3.552 closest distance to " CZ  TYR A 169 " =    1.761
peak=   -3.549 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.548 closest distance to " N   GLN A  58 " =    1.669
peak=   -3.529 closest distance to " CE3 TRP A 150 " =    2.200
peak=   -3.508 closest distance to " C   ASP A 231 " =    2.457
peak=   -3.502 closest distance to " CD2 LEU A 300 " =    2.613
peak=   -3.489 closest distance to " O   HOH Z  60 " =    2.066
peak=   -3.484 closest distance to " NH2AARG A 275 " =    5.079
peak=   -3.480 closest distance to " CG1 VAL A 112 " =    2.853
peak=   -3.477 closest distance to " N   ALA A 226 " =    2.008
peak=   -3.477 closest distance to " O   HOH Z  13 " =    1.705
peak=   -3.473 closest distance to " CG  GLU A 277 " =    1.226
peak=   -3.471 closest distance to " CG1 VAL A 112 " =    2.638
peak=   -3.465 closest distance to " O   HOH Z 359 " =    3.067
peak=   -3.462 closest distance to " O   HOH Z 131 " =    4.061
peak=   -3.460 closest distance to " O   HOH Z 407 " =    3.074
peak=   -3.455 closest distance to " NE2 GLN A 194 " =    1.843
peak=   -3.450 closest distance to " O   VAL A 189 " =    2.656
peak=   -3.449 closest distance to " O   GLY A 196 " =    1.234
peak=   -3.445 closest distance to " O   HOH Z 389 " =    1.971
peak=   -3.440 closest distance to " CG  TRP A 266 " =    1.883
peak=   -3.434 closest distance to " CA  GLY A 241 " =    3.093
peak=   -3.433 closest distance to " N   THR A 157 " =    1.528
peak=   -3.432 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.423 closest distance to " ND2 ASN A  45 " =    1.820
peak=   -3.419 closest distance to " OH  TYR A 247 " =    2.015
peak=   -3.414 closest distance to " OD1 ASN A 148 " =    1.496
peak=   -3.412 closest distance to " N   ALA A 248 " =    2.261
peak=   -3.405 closest distance to " NE2 GLN A  88 " =    1.013
peak=   -3.397 closest distance to " O   HOH Z 174 " =    4.094
peak=   -3.396 closest distance to " NE2 GLN A 278 " =    1.905
peak=   -3.395 closest distance to " OG BSER A 134 " =    1.862
peak=   -3.394 closest distance to " OD2 ASP A  50 " =    2.160
peak=   -3.391 closest distance to " NH2 ARG A  79 " =    1.662
peak=   -3.370 closest distance to " CD1 ILE A 199 " =    2.419
peak=   -3.368 closest distance to " O   HOH Z 102 " =    1.608
peak=   -3.366 closest distance to " O   HOH Z  19 " =    2.312
peak=   -3.365 closest distance to " O   ALA A  10 " =    1.736
peak=   -3.365 closest distance to " C   MET A 188 " =    1.380
peak=   -3.363 closest distance to " CB  ASP A 132 " =    2.386
peak=   -3.359 closest distance to " CA  GLY A 241 " =    2.408
peak=   -3.359 closest distance to " CD  GLN A 223 " =    0.717
peak=   -3.359 closest distance to " N   ALA A  43 " =    2.620
peak=   -3.351 closest distance to " CB  VAL A 296 " =    1.010
peak=   -3.348 closest distance to " CB  ASN A  69 " =    1.233
peak=   -3.340 closest distance to " N   ASP A 171 " =    2.234
peak=   -3.331 closest distance to " O   PHE A 218 " =    1.709
peak=   -3.330 closest distance to " O   HOH Z 353 " =    2.148
peak=   -3.321 closest distance to " O   HOH Z 174 " =    2.377
peak=   -3.316 closest distance to " NE2 GLN A 103 " =    1.691
peak=   -3.315 closest distance to " ND2 ASN A 249 " =    2.375
peak=   -3.314 closest distance to " N   SER A 276 " =    1.379
peak=   -3.308 closest distance to " O   HOH Z 198 " =    2.246
peak=   -3.306 closest distance to " CD2 LEU A 167 " =    1.848
peak=   -3.304 closest distance to " O   HOH Z 313 " =    1.749
peak=   -3.301 closest distance to " O   HOH Z 193 " =    1.700
peak=   -3.298 closest distance to " C   ALA A 158 " =    1.338
peak=   -3.297 closest distance to " CG1 VAL A  67 " =    3.084
peak=   -3.296 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.287 closest distance to " O   HOH Z 134 " =    3.082
peak=   -3.285 closest distance to " O   HOH Z  38 " =    1.661
peak=   -3.283 closest distance to " O   HOH Z  88 " =    4.409
peak=   -3.283 closest distance to " O   HOH Z  52 " =    1.589
peak=   -3.278 closest distance to " OXT GLY A 302 " =    3.471
peak=   -3.277 closest distance to " O   HOH Z 191 " =    5.551
peak=   -3.276 closest distance to " N   PHE A  59 " =    2.200
peak=   -3.273 closest distance to " O   ALA A 161 " =    1.744
peak=   -3.271 closest distance to " O   ALA A  51 " =    1.339
peak=   -3.270 closest distance to " O   HOH Z 311 " =    3.670
peak=   -3.270 closest distance to " CA  GLY A 133 " =    2.302
peak=   -3.262 closest distance to " N   THR A  52 " =    1.735
peak=   -3.256 closest distance to " CD2 TYR A 247 " =    2.336
peak=   -3.255 closest distance to " O   ARG A  24 " =    1.997
peak=   -3.253 closest distance to " O   GLN A 240 " =    2.103
peak=   -3.248 closest distance to " O   HOH Z 165 " =    1.962
peak=   -3.246 closest distance to " O   MET A  40 " =    2.823
peak=   -3.245 closest distance to " N   GLY A  23 " =    2.352
peak=   -3.245 closest distance to " O   HOH Z 166 " =    1.490
peak=   -3.245 closest distance to " CG  PHE A 283 " =    2.673
peak=   -3.243 closest distance to " O   ASN A 187 " =    1.596
peak=   -3.243 closest distance to " CA  GLY A  98 " =    1.846
peak=   -3.242 closest distance to " N   MET A 188 " =    1.919
peak=   -3.239 closest distance to " CG  ARG A 269 " =    2.308
peak=   -3.237 closest distance to " O   HOH Z 313 " =    1.135
peak=   -3.235 closest distance to " CD2 PHE A  61 " =    2.543
peak=   -3.229 closest distance to " CG1 VAL A 197 " =    2.165
peak=   -3.228 closest distance to " CE BMET A  47 " =    1.651
peak=   -3.216 closest distance to " OG  SER A 206 " =    1.655
peak=   -3.213 closest distance to " O   HOH Z  10 " =    1.446
peak=   -3.212 closest distance to " O   HOH Z 372 " =    2.384
peak=   -3.212 closest distance to " C   SER A 206 " =    1.489
peak=   -3.211 closest distance to " C   ASP A 270 " =    1.226
peak=   -3.210 closest distance to " O   HOH Z 200 " =    4.659
peak=   -3.202 closest distance to " O   HOH Z 339 " =    1.752
peak=   -3.200 closest distance to " O   HOH Z 123 " =    2.275
peak=   -3.197 closest distance to " ND2 ASN A  60 " =    1.282
peak=   -3.195 closest distance to " C   ILE A 234 " =    1.361
peak=   -3.195 closest distance to " CD  PRO A 213 " =    2.158
peak=   -3.192 closest distance to " O   HOH Z 434 " =    1.712
peak=   -3.187 closest distance to " CG  LEU A 228 " =    0.944
peak=   -3.185 closest distance to " ND2 ASN A  39 " =    1.166
peak=   -3.184 closest distance to " OD1 ASN A 301 " =    1.922
peak=   -3.182 closest distance to " O   HOH Z 139 " =    3.159
peak=   -3.179 closest distance to " CA  GLY A 133 " =    1.900
peak=   -3.175 closest distance to " OG ASER A 134 " =    1.376
peak=   -3.172 closest distance to " CB  TRP A  85 " =    2.629
peak=   -3.164 closest distance to " OD1 ASP A 171 " =    1.656
peak=   -3.163 closest distance to " CG2 ILE A  20 " =    2.785
peak=   -3.158 closest distance to " O   SER A 271 " =    2.169
peak=   -3.153 closest distance to " O   HOH Z   6 " =    1.585
peak=   -3.153 closest distance to " O   HOH Z 154 " =    1.721
peak=   -3.152 closest distance to " O   HOH Z 216 " =    1.568
peak=   -3.152 closest distance to " CD1 LEU A 101 " =    2.913
peak=   -3.151 closest distance to " OG  SER A   3 " =    1.728
peak=   -3.150 closest distance to " O   VAL A 174 " =    2.147
peak=   -3.148 closest distance to " O   HOH Z 262 " =    2.885
peak=   -3.147 closest distance to " O   SER A 276 " =    1.577
peak=   -3.146 closest distance to " O   HOH Z 234 " =    4.072
peak=   -3.143 closest distance to " CB  ASN A  39 " =    2.237
peak=   -3.143 closest distance to " O   ASN A  45 " =    1.905
peak=   -3.135 closest distance to " N   SER A   3 " =    2.056
peak=   -3.134 closest distance to " O   HOH Z 139 " =    5.141
peak=   -3.133 closest distance to " O   HOH Z 369 " =    2.262
peak=   -3.130 closest distance to " O   HOH Z 431 " =    1.949
peak=   -3.128 closest distance to " CG  GLU A  53 " =    1.622
peak=   -3.127 closest distance to " O   ALA A   1 " =    1.698
peak=   -3.115 closest distance to " O   HOH Z 421 " =    3.287
peak=   -3.109 closest distance to " O   ALA A   8 " =    1.915
peak=   -3.101 closest distance to " OG  SER A  62 " =    1.532
peak=   -3.098 closest distance to " O   ASN A 301 " =    1.479
peak=   -3.096 closest distance to " O   HOH Z 422 " =    1.593
peak=   -3.093 closest distance to " C   ASN A 285 " =    2.233
peak=   -3.090 closest distance to " O   HOH Z 389 " =    4.910
peak=   -3.087 closest distance to " CE1 TYR A 247 " =    2.726
peak=   -3.086 closest distance to " OD1 ASN A  39 " =    2.192
peak=   -3.070 closest distance to " O   HOH Z 298 " =    2.688
peak=   -3.063 closest distance to " CA  SER A  62 " =    2.602
peak=   -3.056 closest distance to " CE1 HIS A  81 " =    1.426
peak=   -3.049 closest distance to " O   HOH Z 426 " =    1.692
peak=   -3.042 closest distance to " CG  PRO A 163 " =    2.731

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4368 0.4212   6.231538e+00   6.201637e+00
   1_bss:  0.4275 0.4090   6.224683e+00   6.188523e+00
   1_xyz:  0.3162 0.3345   6.005610e+00   6.040774e+00
   1_adp:  0.2537 0.2875   5.812897e+00   5.916748e+00
   1_occ:  0.2531 0.2886   5.811921e+00   5.918957e+00
   2_bss:  0.2475 0.2833   5.812225e+00   5.916212e+00
   2_xyz:  0.1593 0.1975   5.422645e+00   5.602501e+00
   2_adp:  0.1429 0.1821   5.330397e+00   5.523515e+00
   2_occ:  0.1428 0.1822   5.329814e+00   5.523485e+00
   3_bss:  0.1420 0.1825   5.330023e+00   5.523162e+00
   3_xyz:  0.1211 0.1606   5.198028e+00   5.414894e+00
   3_adp:  0.1166 0.1588   5.176944e+00   5.406775e+00
   3_occ:  0.1165 0.1588   5.176754e+00   5.406647e+00
   4_bss:  0.1165 0.1588   5.176754e+00   5.406647e+00
   4_xyz:  0.1134 0.1575   5.159634e+00   5.399413e+00
   4_adp:  0.1138 0.1569   5.158557e+00   5.393674e+00
   4_occ:  0.1138 0.1570   5.158482e+00   5.393996e+00
   5_bss:  0.1137 0.1569   5.158578e+00   5.392792e+00
   5_xyz:  0.1099 0.1556   5.137316e+00   5.383890e+00
   5_adp:  0.1098 0.1556   5.135616e+00   5.381946e+00
   5_occ:  0.1098 0.1557   5.135741e+00   5.382264e+00
   5_bss:  0.1098 0.1557   5.135826e+00   5.382460e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.340  20.026   7.389   8.414   9.624   0.000   0.000   0.000
   1_xyz:  0.340  20.026   7.389   8.414   9.624   0.000   0.000   0.000
   1_adp:  0.340  20.026   7.389   8.414   9.624   0.000   0.000   0.000
   1_occ:  0.340  20.026   7.389   8.414   9.624   0.000   0.000   0.000
   2_bss:  0.317  38.047   3.677   4.473   5.824   0.000   0.000   0.000
   2_xyz:  0.317  38.047   3.677   4.473   5.824   0.000   0.000   0.000
   2_adp:  0.317  38.047   3.677   4.473   5.824   0.000   0.000   0.000
   2_occ:  0.317  38.047   3.677   4.473   5.824   0.000   0.000   0.000
   3_bss:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   3_xyz:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   3_adp:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   3_occ:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   4_bss:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   4_xyz:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   4_adp:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   4_occ:  0.330  50.563   2.697   3.569   4.709   0.000   0.000   0.000
   5_bss:  0.330  50.563   2.524   3.326   4.515   0.000   0.000   0.000
   5_xyz:  0.330  50.563   2.524   3.326   4.515   0.000   0.000   0.000
   5_adp:  0.330  50.563   2.524   3.326   4.515   0.000   0.000   0.000
   5_occ:  0.330  50.563   2.524   3.326   4.515   0.000   0.000   0.000
   5_bss:  0.323  48.700  -0.915  -0.153   1.068  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.276 0.5688  0.6369    51364.434
   1_bss:  45.511 0.5766  0.8356    48517.284
   1_xyz:  35.479 0.6951  0.9708    29816.301
   1_adp:  28.711 0.7723  1.0553    21031.664
   1_occ:  28.805 0.7713  1.0533    21144.071
   2_bss:  28.635 0.7731  0.9206    20986.529
   2_xyz:  19.122 0.8696  0.9974     9949.579
   2_adp:  17.154 0.8881  1.0086     8543.032
   2_occ:  17.159 0.8880  1.0086     8537.967
   3_bss:  17.134 0.8883  0.9726     8546.068
   3_xyz:  14.705 0.9091  0.9807     6761.806
   3_adp:  14.478 0.9113  0.9784     6641.858
   3_occ:  14.477 0.9113  0.9782     6638.547
   4_bss:  14.477 0.9113  0.9782     6638.547
   4_xyz:  14.225 0.9135  0.9796     6518.373
   4_adp:  14.071 0.9148  0.9801     6443.352
   4_occ:  14.075 0.9148  0.9800     6448.015
   5_bss:  14.085 0.9147  0.9726     6443.299
   5_xyz:  13.933 0.9158  0.9733     6333.135
   5_adp:  13.867 0.9163  0.9707     6296.874
   5_occ:  13.872 0.9163  0.9706     6300.576
   5_bss:  13.878 0.9162  0.9730     6298.922
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3831e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3831e+01
   1_xyz:   1.547  0.012  0.103 17.735  0.006  4.112   1.1997e-01
   1_adp:   1.547  0.012  0.103 17.735  0.006  4.112   1.1997e-01
   1_occ:   1.547  0.012  0.103 17.735  0.006  4.112   1.1997e-01
   2_bss:   1.547  0.012  0.103 17.735  0.006  4.112   1.1997e-01
   2_xyz:   1.064  0.008  0.077 15.938  0.004  4.126   6.8357e-02
   2_adp:   1.064  0.008  0.077 15.938  0.004  4.126   6.8357e-02
   2_occ:   1.064  0.008  0.077 15.938  0.004  4.126   6.8357e-02
   3_bss:   1.064  0.008  0.077 15.938  0.004  4.126   6.8357e-02
   3_xyz:   1.049  0.008  0.082 15.725  0.004  4.128   6.5846e-02
   3_adp:   1.049  0.008  0.082 15.725  0.004  4.128   6.5846e-02
   3_occ:   1.049  0.008  0.082 15.725  0.004  4.128   6.5846e-02
   4_bss:   1.049  0.008  0.082 15.725  0.004  4.128   6.5846e-02
   4_xyz:   1.024  0.008  0.083 15.492  0.004  4.119   6.4083e-02
   4_adp:   1.024  0.008  0.083 15.492  0.004  4.119   6.4083e-02
   4_occ:   1.024  0.008  0.083 15.492  0.004  4.119   6.4083e-02
   5_bss:   1.024  0.008  0.083 15.492  0.004  4.119   6.4083e-02
   5_xyz:   1.120  0.010  0.091 15.635  0.004  4.122   7.5411e-02
   5_adp:   1.120  0.010  0.091 15.635  0.004  4.122   7.5411e-02
   5_occ:   1.120  0.010  0.091 15.635  0.004  4.122   7.5411e-02
   5_bss:   1.120  0.010  0.091 15.635  0.004  4.122   7.5411e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9789e+00
   1_xyz:  13.480  0.139  0.429 86.485  0.036  2.282   9.0486e-02
   1_adp:  13.480  0.139  0.429 86.485  0.036  2.282   9.0486e-02
   1_occ:  13.480  0.139  0.429 86.485  0.036  2.282   9.0486e-02
   2_bss:  13.480  0.139  0.429 86.485  0.036  2.282   9.0486e-02
   2_xyz:   6.760  0.084  0.307 82.427  0.033  2.314   5.6321e-02
   2_adp:   6.760  0.084  0.307 82.427  0.033  2.314   5.6321e-02
   2_occ:   6.760  0.084  0.307 82.427  0.033  2.314   5.6321e-02
   3_bss:   6.760  0.084  0.307 82.427  0.033  2.314   5.6321e-02
   3_xyz:   6.967  0.050  0.479 83.112  0.040  2.336   5.8925e-02
   3_adp:   6.967  0.050  0.479 83.112  0.040  2.336   5.8925e-02
   3_occ:   6.967  0.050  0.479 83.112  0.040  2.336   5.8925e-02
   4_bss:   6.967  0.050  0.479 83.112  0.040  2.336   5.8925e-02
   4_xyz:   7.087  0.048  0.480 81.944  0.036  2.346   4.1129e-02
   4_adp:   7.087  0.048  0.480 81.944  0.036  2.346   4.1129e-02
   4_occ:   7.087  0.048  0.480 81.944  0.036  2.346   4.1129e-02
   5_bss:   7.087  0.048  0.480 81.944  0.036  2.346   4.1129e-02
   5_xyz:   7.610  0.058  0.576 82.847  0.038  2.292   5.6272e-02
   5_adp:   7.610  0.058  0.576 82.847  0.038  2.292   5.6272e-02
   5_occ:   7.610  0.058  0.576 82.847  0.038  2.292   5.6272e-02
   5_bss:   7.610  0.058  0.576 82.847  0.038  2.292   5.6272e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  58.66   0.00  10.87  58.66   0.00   7.83  57.02   0.00  27.44
   1_occ:  58.66   0.00  10.87  58.66   0.00   7.83  57.02   0.00  27.44
   2_bss:  58.66   0.00  10.87  58.66   0.00   7.83  57.02   0.00  27.44
   2_xyz:  58.66   0.00  10.87  58.66   0.00   7.83  57.02   0.00  27.44
   2_adp:  68.54   0.00  11.28  68.54   0.00   7.47  61.45   1.02  32.03
   2_occ:  68.54   0.00  11.28  68.54   0.00   7.47  61.45   1.02  32.03
   3_bss:  68.54   0.00  11.28  68.54   0.00   7.47  61.45   1.02  32.03
   3_xyz:  68.54   0.00  11.28  68.54   0.00   7.47  61.45   1.02  32.03
   3_adp:  75.45   0.00  11.73  75.45   0.00   7.51  69.20   0.00  34.73
   3_occ:  75.45   0.00  11.73  75.45   0.00   7.51  69.20   0.00  34.73
   4_bss:  75.45   0.00  11.73  75.45   0.00   7.51  69.20   0.00  34.73
   4_xyz:  75.45   0.00  11.73  75.45   0.00   7.51  69.20   0.00  34.73
   4_adp:  75.84   0.00  11.48  75.84   0.00   7.43  68.00   0.70  33.49
   4_occ:  75.84   0.00  11.48  75.84   0.00   7.43  68.00   0.70  33.49
   5_bss:  75.84   0.00  11.48  75.84   0.00   7.43  68.00   0.70  33.49
   5_xyz:  75.84   0.00  11.48  75.84   0.00   7.43  68.00   0.70  33.49
   5_adp:  76.53   0.00  11.25  76.53   0.00   7.33  67.27   0.91  32.58
   5_occ:  76.53   0.00  11.25  76.53   0.00   7.33  67.27   0.91  32.58
   5_bss:  80.06   3.53  14.77  80.06   3.53  10.85  70.79   4.43  36.11
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.229    0.016    0.405
   1_adp:    1.229    0.016    0.405
   1_occ:    1.229    0.016    0.405
   2_bss:    1.229    0.016    0.405
   2_xyz:    1.514    0.029    0.512
   2_adp:    1.514    0.029    0.512
   2_occ:    1.514    0.029    0.512
   3_bss:    1.514    0.029    0.512
   3_xyz:    1.507    0.019    0.544
   3_adp:    1.507    0.019    0.544
   3_occ:    1.507    0.019    0.544
   4_bss:    1.507    0.019    0.544
   4_xyz:    1.675    0.039    0.557
   4_adp:    1.675    0.039    0.557
   4_occ:    1.675    0.039    0.557
   5_bss:    1.675    0.039    0.557
   5_xyz:    1.676    0.043    0.567
   5_adp:    1.676    0.043    0.567
   5_occ:    1.676    0.043    0.567
   5_bss:    1.676    0.043    0.567
------------------------------------------------------------------------

CPU time actual refinement: 341.59


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_436/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 341.44 
  Macro-tasks:
    bulk solvent and scale       = 42.84  
    individual site refinement   = 148.84 
    weights calculation          = 32.23  
    collect and process          = 6.53   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 230.59 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 104.25 
    alpha_beta                      = 8.17   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 117.62 
    fmodel                         = 7.14   
    r_factors                      = 0.26   
    phase_errors                   = 10.98  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 251.62 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.686 micro seconds
Total CPU time: 5.91 minutes
from_scatterers_fft:    663 calls, 103.94 s
gradients_fft:          608 calls, 102.84 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 01:34:02 PST -0800 (1200476042.36 s)
Start R-work = 0.4368, R-free = 0.4212 (no bulk solvent and anisotropic scale)
Final R-work = 0.1280, R-free = 0.1721 (no bulk solvent and anisotropic scale)

Start R-work = 0.4275, R-free = 0.4090
Final R-work = 0.1098, R-free = 0.1557