# Date 2008-01-16 Time 03:27:06 PST -0800 (1200482826.39 s)
#phil __OFF__

Command line arguments: "../1246.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 = 1311
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1246

-------------------------------------------------------------------------------
  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: (72.0062, 46.4607, 85.5261, 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: 3.26, 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: (72.0062, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98037
Completeness in resolution range: 0.952263
Completeness with d_max=infinity: 0.949447

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9804

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: (72.0062, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98037
Completeness in resolution range: 0.952263
Completeness with d_max=infinity: 0.949447

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2388 [2152/2178]  1940   212   9.9%
  bin  2:  4.2388 -  3.3765 [2084/2104]  1874   210  10.1%
  bin  3:  3.3765 -  2.9532 [2034/2053]  1828   206  10.1%
  bin  4:  2.9532 -  2.6848 [2021/2051]  1824   197   9.7%
  bin  5:  2.6848 -  2.4933 [2042/2061]  1841   201   9.8%
  bin  6:  2.4933 -  2.3468 [2007/2032]  1795   212  10.6%
  bin  7:  2.3468 -  2.2297 [1997/2025]  1797   200  10.0%
  bin  8:  2.2297 -  2.1329 [1971/2007]  1780   191   9.7%
  bin  9:  2.1329 -  2.0510 [1992/2034]  1795   197   9.9%
  bin 10:  2.0510 -  1.9804 [1289/2026]  1156   133  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/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:
        1.78 -     2.41: 21
        2.41 -     3.03: 2111
        3.03 -     3.65: 4664
        3.65 -     4.28: 9106
        4.28 -     4.90: 12389
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.785 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.881 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.036 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  2.075 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28286 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_1246/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 72.00625 46.4607 85.5261 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 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4806   r_free= 0.4657   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.280027                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7283 0.99   1405  158 0.3978 0.4181       6.586      6.5918|
|  2:  4.7283 -  3.7718 0.99   1348  146 0.3988 0.4121      6.7984      6.8098|
|  3:  3.7718 -  3.3005 0.99   1307  144 0.4451 0.4045      6.6574      6.6779|
|  4:  3.3005 -  3.0013 0.99   1328  155 0.4595 0.4441       6.532      6.4964|
|  5:  3.0013 -  2.7876 0.99   1314  140 0.5028 0.5245      6.3689      6.3651|
|  6:  2.7876 -  2.6241 0.99   1285  149 0.5037 0.4920       6.283      6.2616|
|  7:  2.6241 -  2.4933 0.99   1320  134 0.5358 0.4804      6.2615      6.2146|
|  8:  2.4933 -  2.3852 0.98   1256  151 0.5343 0.4626      6.1715      6.1444|
|  9:  2.3852 -  2.2937 0.98   1290  146 0.5091 0.5076      6.1303      6.1271|
| 10:  2.2937 -  2.2148 1.00   1290  143 0.5240 0.4809      6.0965      6.0789|
| 11:  2.2148 -  2.1457 0.98   1286  135 0.5248 0.4971      6.0473      6.0431|
| 12:  2.1457 -  2.0845 0.98   1256  147 0.5120 0.5531       5.965      6.0195|
| 13:  2.0845 -  2.0298 0.96   1242  138 0.5527 0.5038      5.8905      5.8075|
| 14:  2.0298 -  1.9804 0.53    703   73 0.5517 0.4812      5.8419      5.8197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7283  1405   158  0.67  36.56   0.79     0.73      80208.14|
|  2:  4.7283 -  3.7718  1348   146  0.70  35.49   0.88     0.77     109288.64|
|  3:  3.7718 -  3.3005  1307   144  0.59  44.41   0.84     0.72     115179.60|
|  4:  3.3005 -  3.0013  1328   155  0.51  50.99   0.80     0.62     104770.47|
|  5:  3.0013 -  2.7876  1314   140  0.41  59.29   0.73     0.48      84680.79|
|  6:  2.7876 -  2.6241  1285   149  0.39  60.77   0.74     0.46      73940.96|
|  7:  2.6241 -  2.4933  1320   134  0.39  60.91   0.72     0.44      63199.47|
|  8:  2.4933 -  2.3852  1256   151  0.40  59.63   0.70     0.48      55518.88|
|  9:  2.3852 -  2.2937  1290   146  0.43  57.50   0.74     0.49      47964.53|
| 10:  2.2937 -  2.2148  1290   143  0.42  58.58   0.74     0.49      44722.16|
| 11:  2.2148 -  2.1457  1286   135  0.37  62.37   0.76     0.45      44725.72|
| 12:  2.1457 -  2.0845  1256   147  0.32  66.03   0.75     0.39      43276.31|
| 13:  2.0845 -  2.0298  1242   138  0.28  69.29   0.72     0.36      38583.45|
| 14:  2.0298 -  1.9804   703    73  0.32  66.20   0.69     0.36      31570.81|
|alpha:            min =        0.36 max =            0.77 mean =         0.53|
|beta:             min =    31570.81 max =       115179.60 mean =     68671.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.68|
|phase err.(test): min =        0.00 max =           89.98 mean =        55.75|
|-----------------------------------------------------------------------------|

============================== 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 = 14.369210             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.438   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.196218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.977   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2637 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3940 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5049 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6562 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7710 |
|-----------------------------------------------------------------------------|
|-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 |       53.766 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.732 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    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 = 11.950)------------------------------------------|
|    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 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4845   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.281542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4719   r_free= 0.4565   ksol= 0.30   Bsol= 20.00   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.17,7.29,6.44,0.00,0.00,0.00); trace/3= 7.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.275640                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.822675             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.804   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.030650              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.622   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4719      final r-factor (work) = 0.3895          |
| start r-factor (free) = 0.4565      final r-factor (free) = 0.4135          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 94.0082 = 12.82 * 0.50 * 6.2767 + 1.00 * 53.7661                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.8254 = 12.82 * 0.50 * 6.1891 + 1.00 * 0.1451                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3895      final r-factor (work) = 0.3423          |
| start r-factor (free) = 0.4135      final r-factor (free) = 0.3894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3932 = 1.03 * 1.00 * 6.1891 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3047 = 1.03 * 1.00 * 6.1026 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.01   13.09    None  None   None       |
|    all(noH): 2823   0      0.00    85.01   13.09    None  None   None       |
|    Sol.    : 438    0      0.00    73.03   27.18    None  None   None       |
|    Mac.    : 2385   0      0.00    85.01   10.50    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 -   8.501: 1284   |   5:    42.505 -  51.005:   57        |
|      1:     8.501 -  17.002:  781   |   6:    51.005 -  59.506:   24        |
|      2:    17.002 -  25.503:  364   |   7:    59.506 -  68.007:   13        |
|      3:    25.503 -  34.004:  186   |   8:    68.007 -  76.508:    4        |
|      4:    34.004 -  42.505:  109   |   9:    76.508 -  85.009:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3423 r_free = 0.3894             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3416 r_free = 0.3907             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3416   r_free= 0.3907   ksol= 0.30   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.17,7.29,6.44,0.00,0.00,0.00); trace/3= 7.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.078422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3401   r_free= 0.3874   ksol= 0.33   Bsol= 42.63   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.09,4.27,4.53,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.079000                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.605682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.327   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3401      final r-factor (work) = 0.2587          |
| start r-factor (free) = 0.3874      final r-factor (free) = 0.3143          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1874 = 4.61 * 0.50 * 6.0978 + 1.00 * 0.1451                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8209 = 4.61 * 0.50 * 5.9682 + 1.00 * 0.0771                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2587      final r-factor (work) = 0.2432          |
| start r-factor (free) = 0.3143      final r-factor (free) = 0.3062          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8372 = 0.47 * 1.00 * 5.9682 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7748 = 0.47 * 1.00 * 5.8361 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.73   13.24    None  None   None       |
|    all(noH): 2823   0      0.00    84.73   13.24    None  None   None       |
|    Sol.    : 438    0      0.00    73.51   29.84    None  None   None       |
|    Mac.    : 2385   0      0.00    84.73   10.19    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 -   8.473: 1270   |   5:    42.367 -  50.840:   54        |
|      1:     8.473 -  16.947:  809   |   6:    50.840 -  59.313:   23        |
|      2:    16.947 -  25.420:  335   |   7:    59.313 -  67.786:   15        |
|      3:    25.420 -  33.893:  205   |   8:    67.786 -  76.260:    3        |
|      4:    33.893 -  42.367:  108   |   9:    76.260 -  84.733:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2432 r_free = 0.3062             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2429 r_free = 0.3064             target_work(ml) = 5.821         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2429   r_free= 0.3064   ksol= 0.33   Bsol= 42.63   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.09,4.27,4.53,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.821124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2419   r_free= 0.3052   ksol= 0.34   Bsol= 52.12   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,2.33,3.33,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.821813                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.898656              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.089   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316100              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.145  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2419      final r-factor (work) = 0.1827          |
| start r-factor (free) = 0.3052      final r-factor (free) = 0.2401          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4567 = 3.90 * 0.50 * 5.8377 + 1.00 * 0.0772                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1962 = 3.90 * 0.50 * 5.7081 + 1.00 * 0.0692                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1827      final r-factor (work) = 0.1633          |
| start r-factor (free) = 0.2401      final r-factor (free) = 0.2148          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8176 = 0.32 * 1.00 * 5.7081 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7546 = 0.32 * 1.00 * 5.5203 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.56   13.17    None  None   None       |
|    all(noH): 2823   0      0.00    82.56   13.17    None  None   None       |
|    Sol.    : 438    0      1.77    76.46   34.14    None  None   None       |
|    Mac.    : 2385   0      0.00    82.56   9.32     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 -   8.256: 1401   |   5:    41.281 -  49.537:  116        |
|      1:     8.256 -  16.513:  772   |   6:    49.537 -  57.794:   34        |
|      2:    16.513 -  24.769:  213   |   7:    57.794 -  66.050:   13        |
|      3:    24.769 -  33.025:  129   |   8:    66.050 -  74.306:    4        |
|      4:    33.025 -  41.281:  139   |   9:    74.306 -  82.562:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1633 r_free = 0.2148             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1633 r_free = 0.2144             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1633   r_free= 0.2144   ksol= 0.34   Bsol= 52.12   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.78,2.33,3.33,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.463885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2134   ksol= 0.34   Bsol= 55.33   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.36,1.33,2.34,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.464166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.094807              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.505  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.873055              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.153  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1630      final r-factor (work) = 0.1397          |
| start r-factor (free) = 0.2134      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8586 = 2.09 * 0.50 * 5.5274 + 1.00 * 0.0692                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7101 = 2.09 * 0.50 * 5.3974 + 1.00 * 0.0568                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.1866      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7218 = 0.87 * 1.00 * 5.3974 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6397 = 0.87 * 1.00 * 5.2999 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.26   13.93    None  None   None       |
|    all(noH): 2823   0      0.00    88.26   13.93    None  None   None       |
|    Sol.    : 438    0      2.59    83.49   38.56    None  None   None       |
|    Mac.    : 2385   0      0.00    88.26   9.41     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 -   8.826: 1513   |   5:    44.131 -  52.957:   96        |
|      1:     8.826 -  17.652:  699   |   6:    52.957 -  61.783:   72        |
|      2:    17.652 -  26.478:  187   |   7:    61.783 -  70.609:   27        |
|      3:    26.478 -  35.305:  110   |   8:    70.609 -  79.435:   11        |
|      4:    35.305 -  44.131:  104   |   9:    79.435 -  88.261:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1321 r_free = 0.1821             target_work(ml) = 5.287         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1319 r_free = 0.1819             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1819   ksol= 0.34   Bsol= 55.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.36,1.33,2.34,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285936                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1814   ksol= 0.33   Bsol= 55.33   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,1.08,2.11,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.285368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.893812              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.973  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.597301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.488  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0757 = 1.89 * 0.50 * 5.3004 + 1.00 * 0.0568                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0344 = 1.89 * 0.50 * 5.2533 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1688          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1503 = 0.60 * 1.00 * 5.2533 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1420 = 0.60 * 1.00 * 5.2205 + 1.00 * 0.0238                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.21   13.84    None  None   None       |
|    all(noH): 2823   0      0.00    92.21   13.84    None  None   None       |
|    Sol.    : 438    0      2.61    89.95   38.18    None  None   None       |
|    Mac.    : 2385   0      0.00    92.21   9.36     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 -   9.221: 1588   |   5:    46.104 -  55.325:   93        |
|      1:     9.221 -  18.442:  657   |   6:    55.325 -  64.546:   55        |
|      2:    18.442 -  27.663:  167   |   7:    64.546 -  73.767:   23        |
|      3:    27.663 -  36.883:  128   |   8:    73.767 -  82.987:    9        |
|      4:    36.883 -  46.104:   98   |   9:    82.987 -  92.208:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1688             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1687             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1687   ksol= 0.33   Bsol= 55.33   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,1.08,2.11,0.00,0.00,0.00); trace/3= 1.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.211480                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7283 0.99   1405  158 0.1011 0.1392      5.4055      5.5975|
|  2:  4.7283 -  3.7718 0.99   1348  146 0.0906 0.1123      5.4783      5.6429|
|  3:  3.7718 -  3.3005 0.99   1307  144 0.1124 0.1607      5.5278      5.8836|
|  4:  3.3005 -  3.0013 0.99   1328  155 0.1320 0.1686      5.5278      5.6587|
|  5:  3.0013 -  2.7876 0.99   1314  140 0.1414 0.1937      5.3741      5.6292|
|  6:  2.7876 -  2.6241 0.99   1285  149 0.1299 0.1932       5.264      5.5258|
|  7:  2.6241 -  2.4933 0.99   1320  134 0.1359 0.1694      5.2293      5.3814|
|  8:  2.4933 -  2.3852 0.98   1256  151 0.1281 0.2006      5.1377      5.4542|
|  9:  2.3852 -  2.2937 0.98   1290  146 0.1307 0.1913        5.13      5.3835|
| 10:  2.2937 -  2.2148 1.00   1290  143 0.1247 0.1885      5.0322      5.2788|
| 11:  2.2148 -  2.1457 0.98   1286  135 0.1277 0.1944       5.034      5.3745|
| 12:  2.1457 -  2.0845 0.98   1256  147 0.1200 0.1692      4.9286      5.1388|
| 13:  2.0845 -  2.0298 0.96   1242  138 0.1280 0.1894      4.8746      5.1308|
| 14:  2.0298 -  1.9804 0.53    703   73 0.1111 0.1708      4.7289      4.9702|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7283  1405   158  0.94   9.57   0.97     0.96       7892.86|
|  2:  4.7283 -  3.7718  1348   146  0.95   8.57   1.01     1.00       9718.31|
|  3:  3.7718 -  3.3005  1307   144  0.93  11.78   1.03     1.03      11383.26|
|  4:  3.3005 -  3.0013  1328   155  0.91  15.04   1.01     0.98      11780.76|
|  5:  3.0013 -  2.7876  1314   140  0.89  16.60   1.00     0.98       8914.93|
|  6:  2.7876 -  2.6241  1285   149  0.90  16.70   0.99     0.96       7813.85|
|  7:  2.6241 -  2.4933  1320   134  0.90  16.68   0.99     0.97       6997.37|
|  8:  2.4933 -  2.3852  1256   151  0.89  17.40   0.98     0.95       6168.79|
|  9:  2.3852 -  2.2937  1290   146  0.89  17.17   1.00     0.97       6098.25|
| 10:  2.2937 -  2.2148  1290   143  0.90  16.69   1.00     0.96       5034.95|
| 11:  2.2148 -  2.1457  1286   135  0.89  17.81   0.99     0.94       5140.07|
| 12:  2.1457 -  2.0845  1256   147  0.90  16.26   1.01     1.00       4369.04|
| 13:  2.0845 -  2.0298  1242   138  0.89  17.47   1.00     0.98       3907.77|
| 14:  2.0298 -  1.9804   703    73  0.90  16.78   0.98     0.95       3109.69|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3109.69 max =        11780.76 mean =      7200.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.88 mean =        14.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1687   ksol= 0.33   Bsol= 53.15   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.57,0.41,-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: 5.211404                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1687   ksol= 0.33   Bsol= 53.15   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.57,0.41,-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: 5.211404                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7283 0.99   1405  158 0.1009 0.1389      5.4025      5.5951|
|  2:  4.7283 -  3.7718 0.99   1348  146 0.0904 0.1119      5.4759      5.6397|
|  3:  3.7718 -  3.3005 0.99   1307  144 0.1123 0.1605      5.5265      5.8827|
|  4:  3.3005 -  3.0013 0.99   1328  155 0.1321 0.1686       5.528       5.659|
|  5:  3.0013 -  2.7876 0.99   1314  140 0.1416 0.1937       5.375      5.6297|
|  6:  2.7876 -  2.6241 0.99   1285  149 0.1302 0.1935      5.2651       5.527|
|  7:  2.6241 -  2.4933 0.99   1320  134 0.1359 0.1693        5.23      5.3816|
|  8:  2.4933 -  2.3852 0.98   1256  151 0.1282 0.2007      5.1383      5.4553|
|  9:  2.3852 -  2.2937 0.98   1290  146 0.1307 0.1913      5.1306      5.3839|
| 10:  2.2937 -  2.2148 1.00   1290  143 0.1248 0.1885      5.0325      5.2785|
| 11:  2.2148 -  2.1457 0.98   1286  135 0.1277 0.1946      5.0344      5.3752|
| 12:  2.1457 -  2.0845 0.98   1256  147 0.1200 0.1692       4.929       5.139|
| 13:  2.0845 -  2.0298 0.96   1242  138 0.1280 0.1895       4.875      5.1311|
| 14:  2.0298 -  1.9804 0.53    703   73 0.1111 0.1710      4.7294       4.971|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.7283  1405   158  0.94   9.53   0.97     0.96       7842.25|
|  2:  4.7283 -  3.7718  1348   146  0.95   8.53   1.01     1.00       9664.88|
|  3:  3.7718 -  3.3005  1307   144  0.93  11.75   1.03     1.03      11336.44|
|  4:  3.3005 -  3.0013  1328   155  0.91  15.04   1.01     0.98      11779.14|
|  5:  3.0013 -  2.7876  1314   140  0.89  16.62   1.00     0.98       8929.33|
|  6:  2.7876 -  2.6241  1285   149  0.89  16.72   0.99     0.96       7830.68|
|  7:  2.6241 -  2.4933  1320   134  0.90  16.70   0.99     0.97       7013.71|
|  8:  2.4933 -  2.3852  1256   151  0.89  17.41   0.98     0.95       6179.59|
|  9:  2.3852 -  2.2937  1290   146  0.89  17.19   1.00     0.97       6105.47|
| 10:  2.2937 -  2.2148  1290   143  0.90  16.70   1.00     0.97       5038.13|
| 11:  2.2148 -  2.1457  1286   135  0.89  17.81   0.99     0.94       5142.03|
| 12:  2.1457 -  2.0845  1256   147  0.90  16.27   1.01     1.00       4374.01|
| 13:  2.0845 -  2.0298  1242   138  0.89  17.49   1.00     0.99       3912.15|
| 14:  2.0298 -  1.9804   703    73  0.89  16.80   0.99     0.96       3114.98|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3114.98 max =        11779.14 mean =      7195.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.75 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.69 mean =        14.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.950)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    93.95   15.57    None  None   None       |
|    all(noH): 2823   0      1.74    93.95   15.57    None  None   None       |
|    Sol.    : 438    0      4.35    91.69   39.92    None  None   None       |
|    Mac.    : 2385   0      1.74    93.95   11.10    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:     1.740 -  10.960: 1588   |   5:    47.844 -  57.064:   93        |
|      1:    10.960 -  20.181:  657   |   6:    57.064 -  66.285:   55        |
|      2:    20.181 -  29.402:  167   |   7:    66.285 -  75.506:   23        |
|      3:    29.402 -  38.623:  128   |   8:    75.506 -  84.727:    9        |
|      4:    38.623 -  47.844:   98   |   9:    84.727 -  93.948:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.425 - 5.601
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 318 from: 322
   mapped sites are within: 0.709 - 5.601

peak=   10.441 closest distance to " CB  VAL A 230 " =    1.440
peak=    9.407 closest distance to " CG2 VAL A 296 " =    1.372
peak=    7.473 closest distance to " CG  ARG A 138 " =    1.256
peak=    6.475 closest distance to " CD2 LEU A   5 " =    1.221
peak=    5.855 closest distance to " CD1AILE A 234 " =    1.123
peak=    5.525 closest distance to " O   HOH Z 111 " =    2.172
peak=    5.411 closest distance to " NH1 ARG A 138 " =    1.028
peak=    5.245 closest distance to " NE2 GLN A  11 " =    1.140
peak=    5.144 closest distance to " CD  ARG A 138 " =    1.086
peak=    5.135 closest distance to " CB  GLN A 223 " =    1.400
peak=    5.115 closest distance to " CG  LEU A   5 " =    1.235
peak=    5.104 closest distance to " CG  PRO A 213 " =    1.306
peak=    5.072 closest distance to " NH1AARG A 145 " =    1.197
peak=    5.057 closest distance to " O   HOH Z 102 " =    0.911
peak=    5.017 closest distance to " CG  PRO A 198 " =    1.248
peak=    4.950 closest distance to " O   HOH Z 144 " =    1.756
peak=    4.947 closest distance to " O   HOH Z 183 " =    1.515
peak=    4.883 closest distance to " O   HOH Z 186 " =    1.495
peak=    4.860 closest distance to " CG  LEU A 228 " =    1.208
peak=    4.855 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.818 closest distance to " CB  ASN A 148 " =    1.311
peak=    4.813 closest distance to " O   HOH Z 232 " =    2.236
peak=    4.809 closest distance to " O   PRO A 198 " =    1.553
peak=    4.789 closest distance to " O   HOH Z 298 " =    1.914
peak=    4.761 closest distance to " CD2 LEU A 228 " =    1.234
peak=    4.716 closest distance to " O   HOH Z 193 " =    1.826
peak=    4.657 closest distance to " O   HOH Z 196 " =    3.171
peak=    4.531 closest distance to " CB  SER A  63 " =    1.310
peak=    4.524 closest distance to " CB  VAL A 230 " =    1.194
peak=    4.513 closest distance to " O   HOH Z 316 " =    3.093
peak=    4.498 closest distance to " O   HOH Z 112 " =    1.568
peak=    4.442 closest distance to " CB  SER A   3 " =    1.528
peak=    4.441 closest distance to " O   HOH Z 410 " =    1.530
peak=    4.435 closest distance to " O   HOH Z 425 " =    1.560
peak=    4.420 closest distance to " NH1 ARG A  56 " =    1.064
peak=    4.375 closest distance to " O   HOH Z 369 " =    1.980
peak=    4.364 closest distance to " OD2 ASP A 286 " =    2.889
peak=    4.360 closest distance to " CG  PRO A 280 " =    0.923
peak=    4.358 closest distance to " CG  PRO A 243 " =    1.171
peak=    4.347 closest distance to " O   HOH Z   7 " =    1.294
peak=    4.284 closest distance to " O   HOH Z 236 " =    1.932
peak=    4.256 closest distance to " CB  ASP A 124 " =    0.763
peak=    4.227 closest distance to " O   HOH Z 411 " =    3.486
peak=    4.200 closest distance to " CB  TRP A 266 " =    0.971
peak=    4.159 closest distance to " O   HOH Z 217 " =    2.886
peak=    4.158 closest distance to " O   HOH Z 368 " =    2.058
peak=    4.149 closest distance to " O   HOH Z 437 " =    2.086
peak=    4.116 closest distance to " CB  LEU A 228 " =    1.313
peak=    4.081 closest distance to " O   HOH Z   2 " =    1.852
peak=    4.062 closest distance to " CG  GLN A  88 " =    1.098
peak=    4.051 closest distance to " O   HOH Z 126 " =    1.928
peak=    4.024 closest distance to " O   HOH Z  48 " =    1.598
peak=    4.013 closest distance to " CG2 THR A 221 " =    1.123
peak=    4.004 closest distance to " NH2BARG A 102 " =    1.031
peak=    3.998 closest distance to " O   HOH Z  37 " =    1.236
peak=    3.987 closest distance to " O   HOH Z 247 " =    1.390
peak=    3.986 closest distance to " CD1 LEU A 300 " =    1.320
peak=    3.980 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.977 closest distance to " CB  ARG A 275 " =    0.921
peak=    3.977 closest distance to " O   HOH Z 303 " =    2.318
peak=    3.973 closest distance to " O   HOH Z   9 " =    2.078
peak=    3.968 closest distance to " CB  ARG A  79 " =    1.521
peak=    3.958 closest distance to " CB  MET A  40 " =    0.841
peak=    3.941 closest distance to " CB  ASN A 187 " =    1.151
peak=    3.936 closest distance to " O   HOH Z 132 " =    2.443
peak=    3.933 closest distance to " O   HOH Z  78 " =    2.415
peak=    3.929 closest distance to " CB  GLU A 152 " =    1.380
peak=    3.921 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.920 closest distance to " CD ALYS A 290 " =    1.043
peak=    3.904 closest distance to " O   HOH Z 184 " =    1.539
peak=    3.904 closest distance to " CA  LEU A 282 " =    1.070
peak=    3.892 closest distance to " CA  ILE A 234 " =    1.043
peak=    3.877 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.872 closest distance to " ND2 ASN A 187 " =    1.517
peak=    3.864 closest distance to " O   HOH Z 222 " =    2.279
peak=    3.860 closest distance to " O   HOH Z 271 " =    2.112
peak=    3.846 closest distance to " CB  PRO A  54 " =    0.786
peak=    3.844 closest distance to " CG1 ILE A  33 " =    1.288
peak=    3.844 closest distance to " O   HOH Z 179 " =    0.875
peak=    3.842 closest distance to " O   ASP A 132 " =    3.815
peak=    3.838 closest distance to " CA  ALA A 299 " =    0.980
peak=    3.834 closest distance to " CD1 ILE A  33 " =    1.719
peak=    3.818 closest distance to " CB  LEU A 237 " =    0.921
peak=    3.817 closest distance to " NE AARG A 275 " =    1.373
peak=    3.815 closest distance to " O   HOH Z 193 " =    2.049
peak=    3.804 closest distance to " ND1 HIS A  86 " =    1.778
peak=    3.784 closest distance to " O   HOH Z 281 " =    4.539
peak=    3.776 closest distance to " CB  TYR A 169 " =    0.718
peak=    3.766 closest distance to " CB  SER A 216 " =    0.980
peak=    3.750 closest distance to " CD  ARG A 159 " =    0.789
peak=    3.749 closest distance to " O   HOH Z  55 " =    2.321
peak=    3.748 closest distance to " CB  VAL A 265 " =    1.261
peak=    3.744 closest distance to " O   HOH Z 334 " =    1.722
peak=    3.742 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.739 closest distance to " O   SER A  87 " =    2.401
peak=    3.735 closest distance to " CA  TYR A  30 " =    0.972
peak=    3.735 closest distance to " CD  ARG A 269 " =    0.950
peak=    3.719 closest distance to " O   HOH Z 345 " =    3.438
peak=    3.715 closest distance to " O   MET A 105 " =    1.757
peak=    3.713 closest distance to " O   HOH Z 158 " =    2.828
peak=    3.708 closest distance to " O   HOH Z 170 " =    1.142
peak=    3.707 closest distance to " CB  TRP A 179 " =    1.462
peak=    3.688 closest distance to " O   HOH Z  80 " =    1.602
peak=    3.687 closest distance to " O   HOH Z 371 " =    2.879
peak=    3.686 closest distance to " O   HOH Z 227 " =    1.666
peak=    3.685 closest distance to " O   HOH Z 302 " =    1.769
peak=    3.682 closest distance to " OD1 ASN A  69 " =    2.744
peak=    3.672 closest distance to " CA  ALA A  51 " =    1.108
peak=    3.666 closest distance to " O   HOH Z 222 " =    2.268
peak=    3.661 closest distance to " CB  SER A 212 " =    1.208
peak=    3.659 closest distance to " O   HOH Z  88 " =    2.991
peak=    3.649 closest distance to " O   HOH Z 189 " =    2.904
peak=    3.643 closest distance to " CB  ASP A 140 " =    0.841
peak=    3.640 closest distance to " O   HOH Z 117 " =    1.863
peak=    3.636 closest distance to " O   HOH Z   3 " =    1.891
peak=    3.634 closest distance to " O   HOH Z  78 " =    1.645
peak=    3.633 closest distance to " CA  ALA A  21 " =    1.185
peak=    3.628 closest distance to " CD  GLN A 240 " =    1.620
peak=    3.627 closest distance to " O   HOH Z 371 " =    1.600
peak=    3.625 closest distance to " OD1 ASN A 217 " =    1.619
peak=    3.622 closest distance to " O   HOH Z  20 " =    2.088
peak=    3.621 closest distance to " O   HOH Z  57 " =    1.390
peak=    3.618 closest distance to " CD2 LEU A 255 " =    1.609
peak=    3.615 closest distance to " CA  SER A  87 " =    0.942
peak=    3.610 closest distance to " CA  GLY A 267 " =    1.190
peak=    3.610 closest distance to " O   HOH Z 133 " =    2.463
peak=    3.608 closest distance to " CB  ASN A 142 " =    0.963
peak=    3.601 closest distance to " O   HOH Z 134 " =    1.480
peak=    3.590 closest distance to " O   HOH Z 180 " =    2.094
peak=    3.581 closest distance to " CG2 VAL A 257 " =    0.999
peak=    3.581 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.578 closest distance to " O   HOH Z 282 " =    1.980
peak=    3.573 closest distance to " N   PHE A 130 " =    1.356
peak=    3.573 closest distance to " O   HOH Z 359 " =    3.846
peak=    3.572 closest distance to " O   HOH Z 280 " =    2.997
peak=    3.568 closest distance to " O   HOH Z 409 " =    2.727
peak=    3.567 closest distance to " CB  LEU A 143 " =    1.158
peak=    3.565 closest distance to " CB  ALA A 161 " =    0.978
peak=    3.559 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.552 closest distance to " CE  LYS A  76 " =    0.908
peak=    3.551 closest distance to " CA  ALA A 154 " =    1.133
peak=    3.547 closest distance to " O   HOH Z 255 " =    1.778
peak=    3.546 closest distance to " CZ  PHE A 192 " =    1.012
peak=    3.534 closest distance to " CA  MET A  40 " =    1.049
peak=    3.522 closest distance to " O   HOH Z 423 " =    1.501
peak=    3.520 closest distance to " OG BSER A 134 " =    2.861
peak=    3.507 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.505 closest distance to " CB  THR A  82 " =    1.242
peak=    3.499 closest distance to " O   HOH Z 222 " =    1.291
peak=    3.497 closest distance to " CD  ARG A  14 " =    1.214
peak=    3.489 closest distance to " O   HOH Z 350 " =    1.490
peak=    3.487 closest distance to " CB  ALA A 248 " =    1.315
peak=    3.487 closest distance to " CA  ASN A 215 " =    1.270
peak=    3.485 closest distance to " CG BARG A 275 " =    1.587
peak=    3.483 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.482 closest distance to " CG1 VAL A 153 " =    0.951
peak=    3.477 closest distance to " O   HOH Z 407 " =    2.028
peak=    3.476 closest distance to " CB  ASN A  39 " =    0.946
peak=    3.473 closest distance to " NH1 ARG A  14 " =    0.982
peak=    3.472 closest distance to " CB  SER A 273 " =    0.915
peak=    3.468 closest distance to " C   GLU A 277 " =    1.406
peak=    3.467 closest distance to " O   HOH Z 115 " =    1.923
peak=    3.467 closest distance to " CA  TYR A 186 " =    1.568
peak=    3.464 closest distance to " O   HOH Z  58 " =    1.955
peak=    3.464 closest distance to " CB  GLU A 236 " =    1.305
peak=    3.461 closest distance to " O   HOH Z  44 " =    2.357
peak=    3.461 closest distance to " O   PRO A 198 " =    1.204
peak=    3.449 closest distance to " O   HOH Z  68 " =    1.949
peak=    3.444 closest distance to " O   HOH Z 236 " =    1.636
peak=    3.440 closest distance to " O   HOH Z 175 " =    2.213
peak=    3.438 closest distance to " O   ALA A 291 " =    1.596
peak=    3.437 closest distance to " CG1 ILE A 151 " =    1.111
peak=    3.434 closest distance to " CZ  PHE A 192 " =    0.709
peak=    3.433 closest distance to " CB  TYR A 116 " =    1.036
peak=    3.432 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.429 closest distance to " CE  MET A  93 " =    1.524
peak=    3.428 closest distance to " OH  TYR A 186 " =    1.097
peak=    3.422 closest distance to " CE3 TRP A 274 " =    1.254
peak=    3.422 closest distance to " CB  ALA A 104 " =    0.817
peak=    3.417 closest distance to " CG  ARG A 159 " =    0.991
peak=    3.406 closest distance to " O   HOH Z  59 " =    2.065
peak=    3.402 closest distance to " CA  ASN A 127 " =    1.102
peak=    3.401 closest distance to " O   HOH Z 332 " =    1.625
peak=    3.400 closest distance to " CB  GLU A 152 " =    0.945
peak=    3.399 closest distance to " O   HOH Z 109 " =    2.602
peak=    3.397 closest distance to " O   GLY A  57 " =    2.604
peak=    3.393 closest distance to " O   HOH Z  53 " =    2.597
peak=    3.392 closest distance to " O   HOH Z 175 " =    3.669
peak=    3.390 closest distance to " CA  ALA A 160 " =    0.919
peak=    3.389 closest distance to " O   HOH Z  22 " =    2.119
peak=    3.388 closest distance to " OG  SER A  62 " =    2.936
peak=    3.387 closest distance to " CB BVAL A  41 " =    1.297
peak=    3.386 closest distance to " NH2BARG A 145 " =    2.061
peak=    3.386 closest distance to " CB  GLN A  89 " =    1.269
peak=    3.382 closest distance to " CA  LYS A 117 " =    1.194
peak=    3.379 closest distance to " CB  ARG A 138 " =    1.578
peak=    3.376 closest distance to " O   HOH Z 392 " =    1.221
peak=    3.376 closest distance to " CB  SER A 210 " =    0.885
peak=    3.371 closest distance to " NZ ALYS A 290 " =    1.129
peak=    3.368 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.364 closest distance to " O   HOH Z 263 " =    1.560
peak=    3.357 closest distance to " O   HOH Z 295 " =    1.552
peak=    3.357 closest distance to " CG1BVAL A  72 " =    1.543
peak=    3.354 closest distance to " O   HOH Z 392 " =    2.036
peak=    3.354 closest distance to " CA  GLU A 152 " =    0.849
peak=    3.352 closest distance to " O   HOH Z 156 " =    2.838
peak=    3.350 closest distance to " CA  LEU A 101 " =    1.494
peak=    3.349 closest distance to " O   HOH Z  68 " =    1.504
peak=    3.347 closest distance to " CD1 LEU A 101 " =    1.144
peak=    3.346 closest distance to " O   HOH Z  40 " =    2.447
peak=    3.343 closest distance to " O   HOH Z 346 " =    1.595
peak=    3.342 closest distance to " CB  GLN A  88 " =    1.326
peak=    3.341 closest distance to " O   HOH Z  40 " =    2.256
peak=    3.336 closest distance to " O   HOH Z 305 " =    3.436
peak=    3.335 closest distance to " O   HOH Z 281 " =    1.734
peak=    3.335 closest distance to " O   HOH Z 276 " =    1.263
peak=    3.331 closest distance to " O   HOH Z  64 " =    2.284
peak=    3.329 closest distance to " O   HOH Z 271 " =    2.381
peak=    3.328 closest distance to " CA  ALA A 295 " =    1.149
peak=    3.327 closest distance to " O   HOH Z 216 " =    2.623
peak=    3.323 closest distance to " CG2 VAL A 112 " =    1.094
peak=    3.322 closest distance to " CH2 TRP A 150 " =    1.001
peak=    3.322 closest distance to " O   HOH Z 116 " =    1.726
peak=    3.311 closest distance to " O   HOH Z 130 " =    2.187
peak=    3.309 closest distance to " CA  TYR A 116 " =    1.599
peak=    3.306 closest distance to " O   TYR A 116 " =    1.182
peak=    3.305 closest distance to " O   ALA A 165 " =    1.351
peak=    3.305 closest distance to " O   HOH Z 133 " =    1.773
peak=    3.300 closest distance to " CB  LEU A 255 " =    0.907
peak=    3.298 closest distance to " O   HOH Z 290 " =    1.262
peak=    3.297 closest distance to " CB  TRP A 150 " =    1.454
peak=    3.296 closest distance to " CB  THR A 157 " =    1.091
peak=    3.295 closest distance to " OE1 GLN A 278 " =    1.037
peak=    3.295 closest distance to " O   HOH Z 126 " =    1.651
peak=    3.292 closest distance to " OD1BASN A 224 " =    2.299
peak=    3.291 closest distance to " CB  GLU A 277 " =    3.600
peak=    3.287 closest distance to " N   SER A 134 " =    1.381
peak=    3.287 closest distance to " CB  ALA A 291 " =    1.510
peak=    3.286 closest distance to " O   HOH Z 148 " =    1.588
peak=    3.280 closest distance to " CZ  PHE A 218 " =    1.079
peak=    3.278 closest distance to " N   TYR A  15 " =    0.889
peak=    3.277 closest distance to " CG1BVAL A 121 " =    1.083
peak=    3.277 closest distance to " CD1 TRP A 266 " =    1.206
peak=    3.277 closest distance to " O   HOH Z  59 " =    1.769
peak=    3.269 closest distance to " O   HOH Z   1 " =    1.986
peak=    3.266 closest distance to " O   HOH Z 344 " =    2.937
peak=    3.265 closest distance to " N   GLU A   2 " =    1.608
peak=    3.261 closest distance to " O   HOH Z 329 " =    3.830
peak=    3.258 closest distance to " O   HOH Z 227 " =    2.059
peak=    3.258 closest distance to " OH  TYR A 214 " =    1.286
peak=    3.254 closest distance to " O   HOH Z 273 " =    2.703
peak=    3.248 closest distance to " O   HOH Z 280 " =    1.773
peak=    3.243 closest distance to " CB  ALA A 137 " =    0.917
peak=    3.241 closest distance to " CA  THR A 221 " =    0.898
peak=    3.239 closest distance to " OG  SER A  22 " =    3.028
peak=    3.233 closest distance to " OG  SER A 206 " =    1.222
peak=    3.230 closest distance to " O   HOH Z 153 " =    1.765
peak=    3.228 closest distance to " O   HOH Z  99 " =    2.559
peak=    3.225 closest distance to " CA  ALA A 158 " =    1.173
peak=    3.214 closest distance to " CB  SER A 276 " =    1.151
peak=    3.213 closest distance to " CA  THR A  42 " =    0.923
peak=    3.210 closest distance to " CA  LYS A  48 " =    1.426
peak=    3.205 closest distance to " NH2 ARG A 219 " =    1.788
peak=    3.202 closest distance to " CA  VAL A  41 " =    0.996
peak=    3.201 closest distance to " O   HOH Z 340 " =    2.295
peak=    3.200 closest distance to " CB  VAL A 268 " =    0.890
peak=    3.200 closest distance to " CA  ARG A 195 " =    1.273
peak=    3.198 closest distance to " O   HOH Z 296 " =    1.610
peak=    3.195 closest distance to " OD1 ASN A  45 " =    1.524
peak=    3.194 closest distance to " O   ALA A 233 " =    1.956
peak=    3.193 closest distance to " CG BARG A 102 " =    1.882
peak=    3.192 closest distance to " O   HOH Z 130 " =    3.869
peak=    3.192 closest distance to " ND2 ASN A  60 " =    3.051
peak=    3.189 closest distance to " N   ARG A 156 " =    1.371
peak=    3.188 closest distance to " NE2 GLN A  58 " =    5.589
peak=    3.183 closest distance to " CD  ARG A 195 " =    3.412
peak=    3.178 closest distance to " O   HOH Z 119 " =    1.551
peak=    3.177 closest distance to " O   HOH Z 327 " =    2.300
peak=    3.176 closest distance to " CA  ALA A 291 " =    0.961
peak=    3.171 closest distance to " N   GLN A 278 " =    0.932
peak=    3.167 closest distance to " NE  ARG A  56 " =    3.559
peak=    3.165 closest distance to " O   HOH Z 245 " =    1.199
peak=    3.164 closest distance to " O   HOH Z 357 " =    2.074
peak=    3.163 closest distance to " CG2 ILE A 109 " =    0.923
peak=    3.161 closest distance to " O   HOH Z 145 " =    3.429
peak=    3.160 closest distance to " O   HOH Z 128 " =    1.637
peak=    3.159 closest distance to " O   HOH Z 148 " =    3.848
peak=    3.157 closest distance to " OE1 GLN A  11 " =    1.832
peak=    3.155 closest distance to " O   HOH Z 412 " =    5.601
peak=    3.153 closest distance to " CB  ASN A 110 " =    1.272
peak=    3.148 closest distance to " CD  LYS A 119 " =    1.236
peak=    3.143 closest distance to " CA  VAL A 126 " =    1.143
peak=    3.140 closest distance to " O   HOH Z 196 " =    1.184
peak=    3.135 closest distance to " O   HOH Z  61 " =    1.594
peak=    3.133 closest distance to " CA  ILE A  33 " =    1.654
peak=    3.133 closest distance to " O   HOH Z 172 " =    3.325
peak=    3.129 closest distance to " CB  ILE A 120 " =    1.363
peak=    3.128 closest distance to " O   HOH Z 193 " =    1.731
peak=    3.125 closest distance to " O   HOH Z   4 " =    1.538
peak=    3.120 closest distance to " O   HOH Z 258 " =    2.084
peak=    3.119 closest distance to " O   HOH Z 122 " =    1.688
peak=    3.119 closest distance to " CB  TYR A  30 " =    1.418
peak=    3.117 closest distance to " O   HOH Z 298 " =    2.660
peak=    3.116 closest distance to " CB  ARG A 139 " =    0.937
peak=    3.103 closest distance to " CE1 PHE A 208 " =    1.095
peak=    3.103 closest distance to " O   HOH Z 368 " =    3.593
peak=    3.102 closest distance to " N   ASN A  39 " =    1.124
peak=    3.102 closest distance to " CG  MET A 188 " =    1.454
peak=    3.095 closest distance to " CG  GLN A 278 " =    1.143
peak=    3.076 closest distance to " CE2 TYR A 293 " =    1.041
peak=    3.071 closest distance to " O   HOH Z 288 " =    1.975
peak=    3.068 closest distance to " CA  ARG A  56 " =    2.072
peak=    3.068 closest distance to " O   HOH Z  21 " =    1.698
peak=    3.051 closest distance to " O   HOH Z 305 " =    1.801
peak=    3.047 closest distance to " O   HOH Z 128 " =    1.937
peak=    3.045 closest distance to " O   HOH Z  88 " =    2.805
peak=    3.021 closest distance to " O   HOH Z 148 " =    2.465
peak=    3.008 closest distance to " O   HOH Z 225 " =    1.879

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.719 - 5.586
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.719 - 5.586

peak=   -5.338 closest distance to " CD  ARG A 138 " =    1.023
peak=   -5.312 closest distance to " CG2 VAL A 230 " =    0.863
peak=   -4.999 closest distance to " O   HOH Z 102 " =    1.128
peak=   -4.389 closest distance to " OE1 GLN A  88 " =    0.970
peak=   -4.356 closest distance to " O   HOH Z 377 " =    1.376
peak=   -4.347 closest distance to " CB  ASP A  27 " =    2.446
peak=   -4.254 closest distance to " O   HOH Z 231 " =    1.456
peak=   -4.223 closest distance to " CD  ARG A 156 " =    1.944
peak=   -4.146 closest distance to " CG  ARG A 138 " =    0.806
peak=   -4.091 closest distance to " O   HOH Z 388 " =    2.053
peak=   -4.013 closest distance to " CD  ARG A  14 " =    3.176
peak=   -4.006 closest distance to " CD1 TYR A 247 " =    2.859
peak=   -3.996 closest distance to " CD2 LEU A 143 " =    2.589
peak=   -3.933 closest distance to " N   THR A 157 " =    1.534
peak=   -3.893 closest distance to " O   HOH Z 290 " =    1.115
peak=   -3.886 closest distance to " OG  SER A  87 " =    1.380
peak=   -3.871 closest distance to " C   ALA A 158 " =    1.239
peak=   -3.870 closest distance to " OE1 GLN A 223 " =    2.319
peak=   -3.855 closest distance to " O   HOH Z  52 " =    1.714
peak=   -3.855 closest distance to " O   HOH Z  43 " =    1.747
peak=   -3.815 closest distance to " CG  GLN A  88 " =    0.841
peak=   -3.812 closest distance to " CG1 VAL A 250 " =    2.659
peak=   -3.811 closest distance to " CB  PRO A 243 " =    2.564
peak=   -3.808 closest distance to " OG ASER A 134 " =    1.088
peak=   -3.782 closest distance to " O   PRO A 163 " =    1.926
peak=   -3.781 closest distance to " O   GLY A  80 " =    2.465
peak=   -3.773 closest distance to " O   PRO A 198 " =    1.296
peak=   -3.772 closest distance to " OG BSER A 134 " =    1.393
peak=   -3.730 closest distance to " O   HOH Z 166 " =    1.288
peak=   -3.727 closest distance to " CG  MET A 105 " =    0.990
peak=   -3.726 closest distance to " C   ASN A 285 " =    2.521
peak=   -3.710 closest distance to " CD1 LEU A 101 " =    2.614
peak=   -3.688 closest distance to " O   HOH Z 389 " =    1.831
peak=   -3.688 closest distance to " O   HOH Z 407 " =    3.321
peak=   -3.686 closest distance to " CG  PRO A 163 " =    2.419
peak=   -3.682 closest distance to " O   SER A  62 " =    2.321
peak=   -3.676 closest distance to " O   HOH Z 231 " =    0.793
peak=   -3.651 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.651 closest distance to " CE2 TYR A  30 " =    2.883
peak=   -3.642 closest distance to " CA  SER A 271 " =    2.401
peak=   -3.638 closest distance to " O   HOH Z 211 " =    1.495
peak=   -3.621 closest distance to " O   ILE A 109 " =    2.654
peak=   -3.620 closest distance to " O   HOH Z  65 " =    1.250
peak=   -3.620 closest distance to " CG2 VAL A 296 " =    1.745
peak=   -3.619 closest distance to " O   HOH Z  71 " =    1.063
peak=   -3.619 closest distance to " CD2 LEU A   5 " =    1.033
peak=   -3.615 closest distance to " O   HOH Z 350 " =    1.747
peak=   -3.614 closest distance to " O   HOH Z 266 " =    4.896
peak=   -3.609 closest distance to " CB  ALA A  43 " =    2.476
peak=   -3.609 closest distance to " O   HOH Z 353 " =    2.262
peak=   -3.579 closest distance to " CB  PRO A  54 " =    2.362
peak=   -3.565 closest distance to " CD1 LEU A   5 " =    2.610
peak=   -3.556 closest distance to " OG  SER A 206 " =    1.609
peak=   -3.555 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.553 closest distance to " O   HOH Z  44 " =    2.183
peak=   -3.553 closest distance to " O   HOH Z 275 " =    1.596
peak=   -3.542 closest distance to " CE1 TYR A 169 " =    2.608
peak=   -3.537 closest distance to " CD1 LEU A 228 " =    2.424
peak=   -3.527 closest distance to " NH2AARG A 275 " =    5.586
peak=   -3.518 closest distance to " O   GLY A 203 " =    2.405
peak=   -3.517 closest distance to " CB  PRO A 163 " =    2.524
peak=   -3.514 closest distance to " CD1 PHE A  59 " =    1.874
peak=   -3.513 closest distance to " CB  CYS A 254 " =    1.778
peak=   -3.509 closest distance to " CD2 LEU A 167 " =    1.784
peak=   -3.503 closest distance to " CB  TYR A  15 " =    2.187
peak=   -3.499 closest distance to " CB  TRP A  85 " =    2.386
peak=   -3.496 closest distance to " N   ALA A  43 " =    2.256
peak=   -3.496 closest distance to " CZ3 TRP A 179 " =    1.194
peak=   -3.496 closest distance to " O   HOH Z  60 " =    2.081
peak=   -3.485 closest distance to " NH1 ARG A  56 " =    2.343
peak=   -3.478 closest distance to " OH  TYR A 214 " =    1.099
peak=   -3.477 closest distance to " O   HOH Z 274 " =    2.892
peak=   -3.470 closest distance to " CE  MET A 105 " =    2.199
peak=   -3.468 closest distance to " CB  ALA A   9 " =    2.579
peak=   -3.446 closest distance to " SD BMET A  47 " =    0.871
peak=   -3.446 closest distance to " CG  TRP A 266 " =    1.657
peak=   -3.435 closest distance to " O   HOH Z 128 " =    2.512
peak=   -3.432 closest distance to " O   HOH Z 184 " =    1.920
peak=   -3.432 closest distance to " CB  SER A  63 " =    3.370
peak=   -3.429 closest distance to " O   SER A 135 " =    1.476
peak=   -3.424 closest distance to " CA  GLY A 241 " =    2.226
peak=   -3.410 closest distance to " CD1 ILE A 199 " =    2.582
peak=   -3.403 closest distance to " O   HOH Z 351 " =    1.352
peak=   -3.399 closest distance to " N   GLN A  58 " =    1.667
peak=   -3.387 closest distance to " O   HOH Z 281 " =    2.888
peak=   -3.382 closest distance to " O   HOH Z  38 " =    1.723
peak=   -3.381 closest distance to " OG  SER A  97 " =    2.231
peak=   -3.381 closest distance to " C   HIS A 108 " =    1.070
peak=   -3.372 closest distance to " O   HOH Z 359 " =    1.685
peak=   -3.371 closest distance to " OG1 THR A 178 " =    1.203
peak=   -3.369 closest distance to " O   GLY A 211 " =    1.352
peak=   -3.367 closest distance to " NH1 ARG A 139 " =    2.440
peak=   -3.364 closest distance to " C   LEU A 143 " =    1.373
peak=   -3.356 closest distance to " N   VAL A 125 " =    0.886
peak=   -3.356 closest distance to " CB  ALA A 248 " =    2.473
peak=   -3.351 closest distance to " C   ASN A 187 " =    1.568
peak=   -3.351 closest distance to " ND2 ASN A  45 " =    1.051
peak=   -3.350 closest distance to " CB  VAL A 230 " =    1.066
peak=   -3.349 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.346 closest distance to " CD1 TRP A 179 " =    0.971
peak=   -3.340 closest distance to " NH2 ARG A  79 " =    1.870
peak=   -3.330 closest distance to " CD2 PHE A  61 " =    1.850
peak=   -3.326 closest distance to " O   HOH Z 281 " =    5.140
peak=   -3.325 closest distance to " O   HOH Z 111 " =    4.517
peak=   -3.325 closest distance to " CG1 VAL A 296 " =    1.400
peak=   -3.322 closest distance to " C   GLN A 240 " =    2.379
peak=   -3.320 closest distance to " C   LEU A 222 " =    0.719
peak=   -3.313 closest distance to " CD1 ILE A 239 " =    2.060
peak=   -3.313 closest distance to " O   HOH Z 190 " =    2.052
peak=   -3.307 closest distance to " C   MET A 188 " =    1.587
peak=   -3.307 closest distance to " O   VAL A 197 " =    1.665
peak=   -3.296 closest distance to " CB  ASN A  39 " =    1.997
peak=   -3.294 closest distance to " CZ BARG A 275 " =    1.720
peak=   -3.294 closest distance to " CD  GLN A  88 " =    2.281
peak=   -3.292 closest distance to " O   HOH Z  90 " =    3.138
peak=   -3.291 closest distance to " CB  ALA A 227 " =    2.418
peak=   -3.287 closest distance to " O   HOH Z 359 " =    3.458
peak=   -3.283 closest distance to " O   GLN A 194 " =    1.329
peak=   -3.282 closest distance to " CB  TYR A 172 " =    2.425
peak=   -3.282 closest distance to " O   HOH Z 298 " =    1.223
peak=   -3.281 closest distance to " CG  GLN A 278 " =    2.366
peak=   -3.281 closest distance to " CG2 VAL A 202 " =    2.713
peak=   -3.281 closest distance to " CE2 PHE A 283 " =    2.448
peak=   -3.280 closest distance to " CE3 TRP A 150 " =    2.185
peak=   -3.279 closest distance to " O   HOH Z 295 " =    1.384
peak=   -3.279 closest distance to " CD  ARG A 139 " =    1.650
peak=   -3.272 closest distance to " O   ASP A 270 " =    1.515
peak=   -3.262 closest distance to " SG  CYS A 254 " =    2.912
peak=   -3.261 closest distance to " CZ  PHE A 130 " =    1.005
peak=   -3.261 closest distance to " CG2 VAL A 112 " =    2.588
peak=   -3.258 closest distance to " CB  ARG A  79 " =    2.540
peak=   -3.255 closest distance to " OD2 ASP A  50 " =    1.766
peak=   -3.252 closest distance to " CG  ASN A  45 " =    1.856
peak=   -3.251 closest distance to " CE2 TYR A 116 " =    3.087
peak=   -3.250 closest distance to " ND2BASN A 224 " =    1.435
peak=   -3.249 closest distance to " O   SER A  22 " =    2.489
peak=   -3.247 closest distance to " O   TYR A  30 " =    2.793
peak=   -3.246 closest distance to " CB  ALA A 248 " =    1.911
peak=   -3.242 closest distance to " O   HOH Z  76 " =    1.607
peak=   -3.239 closest distance to " N   SER A 276 " =    1.321
peak=   -3.239 closest distance to " OG  SER A  26 " =    1.242
peak=   -3.231 closest distance to " O   HOH Z 426 " =    2.263
peak=   -3.229 closest distance to " O   HOH Z 435 " =    2.177
peak=   -3.227 closest distance to " CG  GLU A 152 " =    2.056
peak=   -3.227 closest distance to " C   PHE A  59 " =    1.220
peak=   -3.222 closest distance to " C   ASP A  50 " =    1.046
peak=   -3.220 closest distance to " O   HOH Z  13 " =    1.415
peak=   -3.218 closest distance to " C   LEU A 101 " =    1.067
peak=   -3.217 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.216 closest distance to " O   HOH Z  98 " =    2.087
peak=   -3.206 closest distance to " OD2 ASP A 171 " =    1.773
peak=   -3.204 closest distance to " OE1 GLU A 277 " =    2.089
peak=   -3.198 closest distance to " O   HOH Z 345 " =    2.033
peak=   -3.198 closest distance to " O   HOH Z 198 " =    1.634
peak=   -3.194 closest distance to " O   HOH Z 435 " =    2.844
peak=   -3.192 closest distance to " CE  LYS A  76 " =    2.681
peak=   -3.191 closest distance to " O   HOH Z 423 " =    1.117
peak=   -3.191 closest distance to " N   MET A 105 " =    2.589
peak=   -3.190 closest distance to " CG2AVAL A  41 " =    2.812
peak=   -3.186 closest distance to " CG  LEU A 282 " =    2.491
peak=   -3.179 closest distance to " O   HOH Z  38 " =    4.738
peak=   -3.172 closest distance to " NH1 ARG A 138 " =    1.060
peak=   -3.170 closest distance to " CZ2 TRP A 274 " =    0.889
peak=   -3.165 closest distance to " CE2 PHE A 218 " =    2.550
peak=   -3.158 closest distance to " O   HOH Z 317 " =    2.117
peak=   -3.155 closest distance to " CB  ALA A   8 " =    2.658
peak=   -3.153 closest distance to " N   ALA A  84 " =    1.730
peak=   -3.153 closest distance to " O   HOH Z 108 " =    1.742
peak=   -3.151 closest distance to " O   HOH Z 147 " =    1.541
peak=   -3.149 closest distance to " O   HOH Z 111 " =    1.162
peak=   -3.149 closest distance to " CG2 THR A   4 " =    2.053
peak=   -3.142 closest distance to " O   HOH Z  98 " =    2.275
peak=   -3.139 closest distance to " SG BCYS A 201 " =    2.226
peak=   -3.123 closest distance to " O   HOH Z 166 " =    1.872
peak=   -3.122 closest distance to " O   HOH Z 399 " =    2.096
peak=   -3.121 closest distance to " O   HOH Z  98 " =    1.674
peak=   -3.119 closest distance to " O   SER A 164 " =    1.975
peak=   -3.117 closest distance to " CE BMET A  47 " =    1.596
peak=   -3.116 closest distance to " OD1 ASN A 148 " =    1.483
peak=   -3.113 closest distance to " O   HOH Z 436 " =    1.294
peak=   -3.108 closest distance to " CA  GLY A 133 " =    1.962
peak=   -3.107 closest distance to " ND2 ASN A 209 " =    1.998
peak=   -3.100 closest distance to " OG  SER A   3 " =    1.697
peak=   -3.099 closest distance to " OG1 THR A 246 " =    1.369
peak=   -3.098 closest distance to " CG  PHE A 283 " =    2.594
peak=   -3.093 closest distance to " CE  MET A 105 " =    2.223
peak=   -3.082 closest distance to " O   HOH Z 309 " =    2.319
peak=   -3.072 closest distance to " CB  ALA A 291 " =    2.010
peak=   -3.059 closest distance to " CG2 VAL A 296 " =    1.246
peak=   -3.047 closest distance to " O   HOH Z 396 " =    1.658
peak=   -3.021 closest distance to " C   LEU A 222 " =    0.787
peak=   -3.018 closest distance to " CB  ALA A 100 " =    2.372

================= 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    :  0.4806 0.4657   6.280027e+00   6.268374e+00
   1_bss:  0.4719 0.4565   6.275640e+00   6.262908e+00
   1_xyz:  0.3895 0.4135   6.162563e+00   6.199607e+00
   1_adp:  0.3423 0.3894   6.078698e+00   6.166930e+00
   1_occ:  0.3416 0.3907   6.078422e+00   6.167878e+00
   2_bss:  0.3401 0.3874   6.079000e+00   6.166792e+00
   2_xyz:  0.2587 0.3143   5.863292e+00   6.013578e+00
   2_adp:  0.2432 0.3062   5.821224e+00   5.986318e+00
   2_occ:  0.2429 0.3064   5.821124e+00   5.986442e+00
   3_bss:  0.2419 0.3052   5.821813e+00   5.986269e+00
   3_xyz:  0.1827 0.2401   5.569995e+00   5.775381e+00
   3_adp:  0.1633 0.2148   5.465048e+00   5.673609e+00
   3_occ:  0.1633 0.2144   5.463885e+00   5.672190e+00
   4_bss:  0.1630 0.2134   5.464166e+00   5.671169e+00
   4_xyz:  0.1397 0.1866   5.325139e+00   5.546297e+00
   4_adp:  0.1321 0.1821   5.286652e+00   5.520469e+00
   4_occ:  0.1319 0.1819   5.285936e+00   5.519520e+00
   5_bss:  0.1319 0.1814   5.285368e+00   5.517868e+00
   5_xyz:  0.1225 0.1715   5.226024e+00   5.467120e+00
   5_adp:  0.1207 0.1688   5.211780e+00   5.452852e+00
   5_occ:  0.1206 0.1687   5.211480e+00   5.452474e+00
   5_bss:  0.1205 0.1687   5.211404e+00   5.452375e+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:  0.300  20.000   9.172   7.289   6.444   0.000   0.000   0.000
   1_xyz:  0.300  20.000   9.172   7.289   6.444   0.000   0.000   0.000
   1_adp:  0.300  20.000   9.172   7.289   6.444   0.000   0.000   0.000
   1_occ:  0.300  20.000   9.172   7.289   6.444   0.000   0.000   0.000
   2_bss:  0.334  42.627   6.090   4.274   4.535   0.000   0.000   0.000
   2_xyz:  0.334  42.627   6.090   4.274   4.535   0.000   0.000   0.000
   2_adp:  0.334  42.627   6.090   4.274   4.535   0.000   0.000   0.000
   2_occ:  0.334  42.627   6.090   4.274   4.535   0.000   0.000   0.000
   3_bss:  0.343  52.115   3.779   2.326   3.330   0.000   0.000   0.000
   3_xyz:  0.343  52.115   3.779   2.326   3.330   0.000   0.000   0.000
   3_adp:  0.343  52.115   3.779   2.326   3.330   0.000   0.000   0.000
   3_occ:  0.343  52.115   3.779   2.326   3.330   0.000   0.000   0.000
   4_bss:  0.340  55.331   2.360   1.334   2.345   0.000   0.000   0.000
   4_xyz:  0.340  55.331   2.360   1.334   2.345   0.000   0.000   0.000
   4_adp:  0.340  55.331   2.360   1.334   2.345   0.000   0.000   0.000
   4_occ:  0.340  55.331   2.360   1.334   2.345   0.000   0.000   0.000
   5_bss:  0.332  55.331   1.903   1.080   2.112   0.000   0.000   0.000
   5_xyz:  0.332  55.331   1.903   1.080   2.112   0.000   0.000   0.000
   5_adp:  0.332  55.331   1.903   1.080   2.112   0.000   0.000   0.000
   5_occ:  0.332  55.331   1.903   1.080   2.112   0.000   0.000   0.000
   5_bss:  0.325  53.151   0.162  -0.575   0.413  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.692 0.4499  0.5253    68675.633
   1_bss:  55.964 0.4448  0.6446    66496.327
   1_xyz:  47.791 0.5469  0.7755    50833.100
   1_adp:  43.269 0.6033  0.8955    44581.819
   1_occ:  43.483 0.6005  0.8901    44851.134
   2_bss:  43.291 0.6028  0.8150    44588.880
   2_xyz:  33.401 0.7188  0.9420    27333.423
   2_adp:  31.843 0.7369  0.9689    25595.789
   2_occ:  31.880 0.7364  0.9684    25612.168
   3_bss:  31.786 0.7375  0.9087    25549.431
   3_xyz:  23.600 0.8256  0.9861    14874.846
   3_adp:  20.512 0.8570  1.0059    11839.693
   3_occ:  20.469 0.8574  1.0061    11790.814
   4_bss:  20.419 0.8579  0.9662    11736.261
   4_xyz:  17.223 0.8878  0.9815     8833.167
   4_adp:  16.600 0.8935  0.9819     8313.684
   4_occ:  16.581 0.8936  0.9818     8298.212
   5_bss:  16.567 0.8937  0.9709     8265.688
   5_xyz:  15.545 0.9024  0.9754     7420.184
   5_adp:  15.163 0.9058  0.9745     7210.787
   5_occ:  15.157 0.9059  0.9745     7201.825
   5_bss:  15.159 0.9059  0.9758     7196.185
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3766e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3766e+01
   1_xyz:   1.714  0.014  0.109 18.370  0.006  4.110   1.4511e-01
   1_adp:   1.714  0.014  0.109 18.370  0.006  4.110   1.4511e-01
   1_occ:   1.714  0.014  0.109 18.370  0.006  4.110   1.4511e-01
   2_bss:   1.714  0.014  0.109 18.370  0.006  4.110   1.4511e-01
   2_xyz:   1.134  0.008  0.074 16.402  0.005  4.125   7.7083e-02
   2_adp:   1.134  0.008  0.074 16.402  0.005  4.125   7.7083e-02
   2_occ:   1.134  0.008  0.074 16.402  0.005  4.125   7.7083e-02
   3_bss:   1.134  0.008  0.074 16.402  0.005  4.125   7.7083e-02
   3_xyz:   1.080  0.007  0.080 15.783  0.004  4.122   6.9173e-02
   3_adp:   1.080  0.007  0.080 15.783  0.004  4.122   6.9173e-02
   3_occ:   1.080  0.007  0.080 15.783  0.004  4.122   6.9173e-02
   4_bss:   1.080  0.007  0.080 15.783  0.004  4.122   6.9173e-02
   4_xyz:   0.928  0.006  0.071 15.412  0.003  4.130   5.6798e-02
   4_adp:   0.928  0.006  0.071 15.412  0.003  4.130   5.6798e-02
   4_occ:   0.928  0.006  0.071 15.412  0.003  4.130   5.6798e-02
   5_bss:   0.928  0.006  0.071 15.412  0.003  4.130   5.6798e-02
   5_xyz:   0.991  0.007  0.075 15.477  0.003  4.111   6.0065e-02
   5_adp:   0.991  0.007  0.075 15.477  0.003  4.111   6.0065e-02
   5_occ:   0.991  0.007  0.075 15.477  0.003  4.111   6.0065e-02
   5_bss:   0.991  0.007  0.075 15.477  0.003  4.111   6.0065e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9709e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9709e+00
   1_xyz:  14.209  0.169  0.480 87.722  0.042  2.177   1.0551e-01
   1_adp:  14.209  0.169  0.480 87.722  0.042  2.177   1.0551e-01
   1_occ:  14.209  0.169  0.480 87.722  0.042  2.177   1.0551e-01
   2_bss:  14.209  0.169  0.480 87.722  0.042  2.177   1.0551e-01
   2_xyz:   8.181  0.086  0.269 84.686  0.045  2.315   7.1363e-02
   2_adp:   8.181  0.086  0.269 84.686  0.045  2.315   7.1363e-02
   2_occ:   8.181  0.086  0.269 84.686  0.045  2.315   7.1363e-02
   3_bss:   8.181  0.086  0.269 84.686  0.045  2.315   7.1363e-02
   3_xyz:   9.366  0.089  0.354 87.841  0.044  2.337   5.2719e-02
   3_adp:   9.366  0.089  0.354 87.841  0.044  2.337   5.2719e-02
   3_occ:   9.366  0.089  0.354 87.841  0.044  2.337   5.2719e-02
   4_bss:   9.366  0.089  0.354 87.841  0.044  2.337   5.2719e-02
   4_xyz:   8.389  0.054  0.301 81.100  0.032  2.297   4.2839e-02
   4_adp:   8.389  0.054  0.301 81.100  0.032  2.297   4.2839e-02
   4_occ:   8.389  0.054  0.301 81.100  0.032  2.297   4.2839e-02
   5_bss:   8.389  0.054  0.301 81.100  0.032  2.297   4.2839e-02
   5_xyz:   8.469  0.061  0.360 85.808  0.033  2.341   3.4252e-02
   5_adp:   8.469  0.061  0.360 85.808  0.033  2.341   3.4252e-02
   5_occ:   8.469  0.061  0.360 85.808  0.033  2.341   3.4252e-02
   5_bss:   8.469  0.061  0.360 85.808  0.033  2.341   3.4252e-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:  85.01   0.00  13.09  85.01   0.00  10.50  73.03   0.00  27.18
   1_occ:  85.01   0.00  13.09  85.01   0.00  10.50  73.03   0.00  27.18
   2_bss:  85.01   0.00  13.09  85.01   0.00  10.50  73.03   0.00  27.18
   2_xyz:  85.01   0.00  13.09  85.01   0.00  10.50  73.03   0.00  27.18
   2_adp:  84.73   0.00  13.24  84.73   0.00  10.19  73.51   0.00  29.84
   2_occ:  84.73   0.00  13.24  84.73   0.00  10.19  73.51   0.00  29.84
   3_bss:  84.73   0.00  13.24  84.73   0.00  10.19  73.51   0.00  29.84
   3_xyz:  84.73   0.00  13.24  84.73   0.00  10.19  73.51   0.00  29.84
   3_adp:  82.56   0.00  13.17  82.56   0.00   9.32  76.46   1.77  34.14
   3_occ:  82.56   0.00  13.17  82.56   0.00   9.32  76.46   1.77  34.14
   4_bss:  82.56   0.00  13.17  82.56   0.00   9.32  76.46   1.77  34.14
   4_xyz:  82.56   0.00  13.17  82.56   0.00   9.32  76.46   1.77  34.14
   4_adp:  88.26   0.00  13.93  88.26   0.00   9.41  83.49   2.59  38.56
   4_occ:  88.26   0.00  13.93  88.26   0.00   9.41  83.49   2.59  38.56
   5_bss:  88.26   0.00  13.93  88.26   0.00   9.41  83.49   2.59  38.56
   5_xyz:  88.26   0.00  13.93  88.26   0.00   9.41  83.49   2.59  38.56
   5_adp:  92.21   0.00  13.84  92.21   0.00   9.36  89.95   2.61  38.18
   5_occ:  92.21   0.00  13.84  92.21   0.00   9.36  89.95   2.61  38.18
   5_bss:  93.95   1.74  15.57  93.95   1.74  11.10  91.69   4.35  39.92
------------------------------------------------------------------------
 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:    1.223    0.027    0.414
   1_adp:    1.223    0.027    0.414
   1_occ:    1.223    0.027    0.414
   2_bss:    1.223    0.027    0.414
   2_xyz:    1.535    0.019    0.558
   2_adp:    1.535    0.019    0.558
   2_occ:    1.535    0.019    0.558
   3_bss:    1.535    0.019    0.558
   3_xyz:    1.546    0.027    0.651
   3_adp:    1.546    0.027    0.651
   3_occ:    1.546    0.027    0.651
   4_bss:    1.546    0.027    0.651
   4_xyz:    1.901    0.051    0.702
   4_adp:    1.901    0.051    0.702
   4_occ:    1.901    0.051    0.702
   5_bss:    1.901    0.051    0.702
   5_xyz:    2.036    0.027    0.726
   5_adp:    2.036    0.027    0.726
   5_occ:    2.036    0.027    0.726
   5_bss:    2.036    0.027    0.726
------------------------------------------------------------------------

CPU time actual refinement: 367.96


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/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_1246/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1246/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.82 
  Macro-tasks:
    bulk solvent and scale       = 42.37  
    individual site refinement   = 157.25 
    weights calculation          = 33.60  
    collect and process          = 6.61   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 239.94 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 118.34 
    alpha_beta                      = 8.33   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 128.49 
    fmodel                         = 7.58   
    r_factors                      = 0.32   
    phase_errors                   = 10.64  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 277.55 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.108 micro seconds
Total CPU time: 6.36 minutes
from_scatterers_fft:    654 calls, 118.00 s
gradients_fft:          598 calls, 114.74 s

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

# Date 2008-01-16 Time 03:33:28 PST -0800 (1200483208.12 s)
Start R-work = 0.4806, R-free = 0.4657 (no bulk solvent and anisotropic scale)
Final R-work = 0.1370, R-free = 0.1861 (no bulk solvent and anisotropic scale)

Start R-work = 0.4719, R-free = 0.4565
Final R-work = 0.1205, R-free = 0.1687