# Date 2008-01-16 Time 00:33:46 PST -0800 (1200472426.79 s)
#phil __OFF__

Command line arguments: "../78.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29896
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 78

-------------------------------------------------------------------------------
  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: (68.4938, 47.3993, 84.6622, 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: 3.29, per 1000 atoms: 1.17


================================== 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: (68.4938, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8023 1.95062
Completeness in resolution range: 0.949079
Completeness with d_max=infinity: 0.946191

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8023
                             d_min =   1.9506

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: (68.4938, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8023 1.95062
Completeness in resolution range: 0.949079
Completeness with d_max=infinity: 0.946191

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8027 -  4.1740 [2171/2200]  1953   218  10.0%
  bin  2:  4.1740 -  3.3254 [2080/2103]  1875   205   9.9%
  bin  3:  3.3254 -  2.9087 [2061/2086]  1849   212  10.3%
  bin  4:  2.9087 -  2.6444 [2025/2041]  1830   195   9.6%
  bin  5:  2.6444 -  2.4558 [2005/2049]  1795   210  10.5%
  bin  6:  2.4558 -  2.3115 [2027/2055]  1836   191   9.4%
  bin  7:  2.3115 -  2.1962 [2002/2038]  1796   206  10.3%
  bin  8:  2.1962 -  2.1008 [1982/2024]  1790   192   9.7%
  bin  9:  2.1008 -  2.0202 [1981/2027]  1780   201  10.1%
  bin 10:  2.0202 -  1.9506 [1255/2017]  1126   129  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/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: 0.14 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:
        1.12 -     1.88: 18
        1.88 -     2.63: 121
        2.63 -     3.39: 4385
        3.39 -     4.14: 9568
        4.14 -     4.90: 14793
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.122 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.218 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.298 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.427 3.270 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.506 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 28880 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_78/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/model_refine_001.geo

CPU time processing inputs: 9.34


============================ 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 = 68.49375 47.3993 84.6622 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: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5015   r_free= 0.4940   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.298468                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6556 0.99   1405  158 0.4143 0.4039      6.6257       6.662|
|  2:  4.6556 -  3.7145 0.99   1350  151 0.4310 0.4138      6.8224       6.829|
|  3:  3.7145 -  3.2506 0.99   1332  147 0.4665 0.4570       6.706      6.7706|
|  4:  3.2506 -  2.9560 0.99   1323  138 0.4845 0.4815      6.5331      6.5112|
|  5:  2.9560 -  2.7456 0.98   1308  148 0.5296 0.5376      6.3955      6.4066|
|  6:  2.7456 -  2.5846 0.99   1304  147 0.5238 0.5375      6.2809      6.2029|
|  7:  2.5846 -  2.4558 0.98   1280  151 0.5469 0.4798      6.2822      6.1855|
|  8:  2.4558 -  2.3493 0.99   1311  133 0.5369 0.5286      6.1895      6.1751|
|  9:  2.3493 -  2.2592 0.99   1298  149 0.5477 0.5513      6.1257      6.1787|
| 10:  2.2592 -  2.1815 0.98   1283  142 0.5400 0.5417      6.1205      6.1328|
| 11:  2.1815 -  2.1135 0.97   1275  149 0.5481 0.6104      6.0357      6.0474|
| 12:  2.1135 -  2.0532 0.99   1276  141 0.5402 0.5555      5.9698      6.0078|
| 13:  2.0532 -  1.9993 0.94   1253  129 0.5696 0.5233      5.8984      5.8852|
| 14:  1.9993 -  1.9506 0.50    632   76 0.5439 0.4833      5.8989      5.6841|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6556  1405   158  0.65  38.47   0.79     0.66      83456.73|
|  2:  4.6556 -  3.7145  1350   151  0.64  40.37   0.87     0.71     128616.36|
|  3:  3.7145 -  3.2506  1332   147  0.53  49.27   0.84     0.66     138343.18|
|  4:  3.2506 -  2.9560  1323   138  0.44  56.79   0.80     0.55     117868.97|
|  5:  2.9560 -  2.7456  1308   148  0.36  63.24   0.73     0.45      94690.56|
|  6:  2.7456 -  2.5846  1304   147  0.34  64.78   0.71     0.40      76448.52|
|  7:  2.5846 -  2.4558  1280   151  0.34  64.42   0.73     0.39      68483.39|
|  8:  2.4558 -  2.3493  1311   133  0.34  64.41   0.73     0.40      59627.98|
|  9:  2.3493 -  2.2592  1298   149  0.29  68.45   0.72     0.36      59082.40|
| 10:  2.2592 -  2.1815  1283   142  0.23  72.49   0.78     0.29      55432.43|
| 11:  2.1815 -  2.1135  1275   149  0.15  79.03   0.73     0.19      55735.09|
| 12:  2.1135 -  2.0532  1276   141  0.15  78.66   0.75     0.20      50951.88|
| 13:  2.0532 -  1.9993  1253   129  0.23  72.56   0.73     0.31      40222.12|
| 14:  1.9993 -  1.9506   632    76  0.47  54.54   0.72     0.52      23874.02|
|alpha:            min =        0.19 max =            0.71 mean =         0.44|
|beta:             min =    23874.02 max =       138343.18 mean =     77699.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.93|
|phase err.(test): min =        0.00 max =           90.00 mean =        62.26|
|-----------------------------------------------------------------------------|

============================== 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 = 23.281339             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.453   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.563870              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.952   (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 |  0.952 -  1.347:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.347 -  1.742:       13 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.742 -  2.136:      105 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.136 -  2.531:      482 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.531 -  2.926:     1280 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.926 -  3.321:     2458 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.321 -  3.716:     4015 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.716 -  4.110:     5285 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.110 -  4.505:     6956 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.505 -  4.900:     8333 |
|-----------------------------------------------------------------------------|
|-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 |       52.928 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.952 |       3.384 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    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 = 11.400)------------------------------------------|
|    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: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5055   r_free= 0.5014   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.298958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4932   r_free= 0.4855   ksol= 0.38   Bsol= 14.01   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.54,8.46,8.33,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.294428                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.759930             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.573745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.386   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4932      final r-factor (work) = 0.4118          |
| start r-factor (free) = 0.4855      final r-factor (free) = 0.4389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 115.1471 = 19.76 * 0.50 * 6.2975 + 1.00 * 52.9282                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.6236 = 19.76 * 0.50 * 6.2169 + 1.00 * 0.2011                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4118      final r-factor (work) = 0.3698          |
| start r-factor (free) = 0.4389      final r-factor (free) = 0.4253          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7981 = 1.57 * 1.00 * 6.2169 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6995 = 1.57 * 1.00 * 6.1510 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.91   13.98    None  None   None       |
|    all(noH): 2823   0      0.00    78.91   13.98    None  None   None       |
|    Sol.    : 438    0      0.00    78.91   26.10    None  None   None       |
|    Mac.    : 2385   0      0.00    69.32   11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.891: 1137   |   5:    39.454 -  47.345:   67        |
|      1:     7.891 -  15.782:  723   |   6:    47.345 -  55.236:   34        |
|      2:    15.782 -  23.673:  427   |   7:    55.236 -  63.127:   17        |
|      3:    23.673 -  31.563:  257   |   8:    63.127 -  71.017:   12        |
|      4:    31.563 -  39.454:  143   |   9:    71.017 -  78.908:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3698 r_free = 0.4253             target_work(ml) = 6.132         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3690 r_free = 0.4256             target_work(ml) = 6.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3690   r_free= 0.4256   ksol= 0.38   Bsol= 14.01   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.54,8.46,8.33,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.130020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3674   r_free= 0.4197   ksol= 0.34   Bsol= 29.47   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.56,5.31,5.89,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.129274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.835578              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.646   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664595              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.851  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3674      final r-factor (work) = 0.2841          |
| start r-factor (free) = 0.4197      final r-factor (free) = 0.3389          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3569 = 8.84 * 0.50 * 6.1469 + 1.00 * 0.2011                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7525 = 8.84 * 0.50 * 6.0336 + 1.00 * 0.0972                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2841      final r-factor (work) = 0.2595          |
| start r-factor (free) = 0.3389      final r-factor (free) = 0.3192          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0298 = 0.66 * 1.00 * 6.0336 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9269 = 0.66 * 1.00 * 5.8858 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.40   14.05    None  None   None       |
|    all(noH): 2823   0      0.00    85.40   14.05    None  None   None       |
|    Sol.    : 438    0      1.75    85.40   32.21    None  None   None       |
|    Mac.    : 2385   0      0.00    72.47   10.72    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 -   8.540: 1314   |   5:    42.702 -  51.242:   87        |
|      1:     8.540 -  17.081:  707   |   6:    51.242 -  59.782:   48        |
|      2:    17.081 -  25.621:  337   |   7:    59.782 -  68.323:   16        |
|      3:    25.621 -  34.161:  195   |   8:    68.323 -  76.863:    6        |
|      4:    34.161 -  42.702:  109   |   9:    76.863 -  85.403:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2595 r_free = 0.3192             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2593 r_free = 0.3189             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2593   r_free= 0.3189   ksol= 0.34   Bsol= 29.47   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.56,5.31,5.89,0.00,0.00,0.00); trace/3= 5.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.855153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2567   r_free= 0.3165   ksol= 0.33   Bsol= 36.51   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.27,3.57,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.851609                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.735226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.015  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.275  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2567      final r-factor (work) = 0.1909          |
| start r-factor (free) = 0.3165      final r-factor (free) = 0.2464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0940 = 3.74 * 0.50 * 5.8882 + 1.00 * 0.0972                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7892 = 3.74 * 0.50 * 5.7411 + 1.00 * 0.0671                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1909      final r-factor (work) = 0.1768          |
| start r-factor (free) = 0.2464      final r-factor (free) = 0.2241          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2969 = 0.22 * 1.00 * 5.7411 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2611 = 0.22 * 1.00 * 5.5737 + 1.00 * 0.0175                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.99  13.56    None  None   None       |
|    all(noH): 2823   0      0.00    105.99  13.56    None  None   None       |
|    Sol.    : 438    0      2.93    84.72   33.99    None  None   None       |
|    Mac.    : 2385   0      0.00    105.99  9.81     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 -  10.599: 1714   |   5:    52.994 -  63.593:   31        |
|      1:    10.599 -  21.198:  572   |   6:    63.593 -  74.192:   14        |
|      2:    21.198 -  31.797:  202   |   7:    74.192 -  84.791:    2        |
|      3:    31.797 -  42.395:  181   |   8:    84.791 -  95.389:    0        |
|      4:    42.395 -  52.994:  106   |   9:    95.389 - 105.988:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1768 r_free = 0.2241             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1764 r_free = 0.2243             target_work(ml) = 5.524         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1764   r_free= 0.2243   ksol= 0.33   Bsol= 36.51   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.10,3.27,3.57,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.524265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1752   r_free= 0.2220   ksol= 0.32   Bsol= 32.20   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,2.11,2.17,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.522010                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.966370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.867  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.337277              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.431   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1752      final r-factor (work) = 0.1454          |
| start r-factor (free) = 0.2220      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5535 = 1.97 * 0.50 * 5.5803 + 1.00 * 0.0670                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4059 = 1.97 * 0.50 * 5.4395 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1454      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.1879      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8450 = 0.34 * 1.00 * 5.4395 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8074 = 0.34 * 1.00 * 5.3289 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.34   13.81    None  None   None       |
|    all(noH): 2823   0      0.00    86.34   13.81    None  None   None       |
|    Sol.    : 438    0      2.96    86.34   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    77.27   9.59     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 -   8.634: 1482   |   5:    43.170 -  51.804:   98        |
|      1:     8.634 -  17.268:  714   |   6:    51.804 -  60.438:   62        |
|      2:    17.268 -  25.902:  186   |   7:    60.438 -  69.071:   25        |
|      3:    25.902 -  34.536:  120   |   8:    69.071 -  77.705:    6        |
|      4:    34.536 -  43.170:  129   |   9:    77.705 -  86.339:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1827             target_work(ml) = 5.312         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1827             target_work(ml) = 5.311         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1827   ksol= 0.32   Bsol= 32.20   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.73,2.11,2.17,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.311017                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1827   ksol= 0.31   Bsol= 35.51   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.42,1.81,1.86,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.310996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.500469              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.775  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.503118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.383  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1384      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7219 = 2.50 * 0.50 * 5.3301 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6392 = 2.50 * 0.50 * 5.2574 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6552 = 0.50 * 1.00 * 5.2574 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6306 = 0.50 * 1.00 * 5.2077 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.44   13.76    None  None   None       |
|    all(noH): 2823   0      0.00    86.44   13.76    None  None   None       |
|    Sol.    : 438    0      2.77    86.44   37.11    None  None   None       |
|    Mac.    : 2385   0      0.00    78.47   9.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.644: 1514   |   5:    43.221 -  51.866:   97        |
|      1:     8.644 -  17.289:  699   |   6:    51.866 -  60.510:   65        |
|      2:    17.289 -  25.933:  172   |   7:    60.510 -  69.154:   26        |
|      3:    25.933 -  34.577:  124   |   8:    69.154 -  77.799:    7        |
|      4:    34.577 -  43.221:  117   |   9:    77.799 -  86.443:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1672             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1200 r_free = 0.1671             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1671   ksol= 0.31   Bsol= 35.51   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.42,1.81,1.86,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205625                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6556 0.99   1405  158 0.1031 0.1343       5.431      5.5985|
|  2:  4.6556 -  3.7145 0.99   1350  151 0.0919 0.1236      5.5099      5.7581|
|  3:  3.7145 -  3.2506 0.99   1332  147 0.1134 0.1626      5.5448      5.8911|
|  4:  3.2506 -  2.9560 0.99   1323  138 0.1330 0.1595      5.5118      5.6769|
|  5:  2.9560 -  2.7456 0.98   1308  148 0.1438 0.1672      5.3826        5.51|
|  6:  2.7456 -  2.5846 0.99   1304  147 0.1372 0.2202      5.2823      5.5716|
|  7:  2.5846 -  2.4558 0.98   1280  151 0.1232 0.1627      5.1882      5.3727|
|  8:  2.4558 -  2.3493 0.99   1311  133 0.1244 0.1779      5.1366      5.3808|
|  9:  2.3493 -  2.2592 0.99   1298  149 0.1258 0.1801      5.0714      5.3339|
| 10:  2.2592 -  2.1815 0.98   1283  142 0.1229 0.1893      5.0451      5.2837|
| 11:  2.1815 -  2.1135 0.97   1275  149 0.1198 0.1842      4.9638      5.2671|
| 12:  2.1135 -  2.0532 0.99   1276  141 0.1183 0.1845      4.9054      5.1918|
| 13:  2.0532 -  1.9993 0.94   1253  129 0.1246 0.1842      4.8498      5.0858|
| 14:  1.9993 -  1.9506 0.50    632   76 0.1144 0.1881      4.7539      4.9814|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6556  1405   158  0.94   9.79   0.98     0.97       8310.47|
|  2:  4.6556 -  3.7145  1350   151  0.94   9.29   1.03     1.01      10780.38|
|  3:  3.7145 -  3.2506  1332   147  0.93  12.49   1.04     1.03      12186.41|
|  4:  3.2506 -  2.9560  1323   138  0.91  14.74   1.02     1.02      11407.15|
|  5:  2.9560 -  2.7456  1308   148  0.89  16.85   1.00     0.97       9041.09|
|  6:  2.7456 -  2.5846  1304   147  0.89  17.31   0.98     0.95       7972.45|
|  7:  2.5846 -  2.4558  1280   151  0.90  16.09   0.99     0.94       6583.23|
|  8:  2.4558 -  2.3493  1311   133  0.90  16.47   1.02     1.00       6241.05|
|  9:  2.3493 -  2.2592  1298   149  0.89  16.91   1.01     0.99       5560.50|
| 10:  2.2592 -  2.1815  1283   142  0.89  16.73   1.01     0.98       5246.09|
| 11:  2.1815 -  2.1135  1275   149  0.89  17.17   1.01     0.99       4721.58|
| 12:  2.1135 -  2.0532  1276   141  0.90  16.21   1.01     0.98       4166.43|
| 13:  2.0532 -  1.9993  1253   129  0.89  17.32   1.01     1.01       3745.02|
| 14:  1.9993 -  1.9506   632    76  0.90  16.31   1.00     0.96       3076.88|
|alpha:            min =        0.94 max =            1.03 mean =         0.99|
|beta:             min =     3076.88 max =        12186.41 mean =      7277.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.16|
|phase err.(test): min =        0.00 max =           87.89 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1670   ksol= 0.32   Bsol= 36.87   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,0.40,0.51,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205861                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1670   ksol= 0.32   Bsol= 36.87   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,0.40,0.51,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205861                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8027 -  4.6556 0.99   1405  158 0.1033 0.1346       5.434      5.6014|
|  2:  4.6556 -  3.7145 0.99   1350  151 0.0917 0.1234      5.5097      5.7563|
|  3:  3.7145 -  3.2506 0.99   1332  147 0.1133 0.1627      5.5443      5.8913|
|  4:  3.2506 -  2.9560 0.99   1323  138 0.1329 0.1595      5.5117      5.6768|
|  5:  2.9560 -  2.7456 0.98   1308  148 0.1438 0.1672      5.3826      5.5097|
|  6:  2.7456 -  2.5846 0.99   1304  147 0.1372 0.2201      5.2822      5.5716|
|  7:  2.5846 -  2.4558 0.98   1280  151 0.1232 0.1628      5.1882      5.3729|
|  8:  2.4558 -  2.3493 0.99   1311  133 0.1244 0.1778      5.1368      5.3811|
|  9:  2.3493 -  2.2592 0.99   1298  149 0.1257 0.1801      5.0716      5.3342|
| 10:  2.2592 -  2.1815 0.98   1283  142 0.1229 0.1894      5.0453      5.2843|
| 11:  2.1815 -  2.1135 0.97   1275  149 0.1198 0.1841      4.9639      5.2669|
| 12:  2.1135 -  2.0532 0.99   1276  141 0.1184 0.1846      4.9054      5.1919|
| 13:  2.0532 -  1.9993 0.94   1253  129 0.1246 0.1841      4.8499      5.0855|
| 14:  1.9993 -  1.9506 0.50    632   76 0.1143 0.1880      4.7538      4.9811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8027 -  4.6556  1405   158  0.94   9.83   0.98     0.97       8384.23|
|  2:  4.6556 -  3.7145  1350   151  0.94   9.30   1.03     1.01      10800.69|
|  3:  3.7145 -  3.2506  1332   147  0.93  12.48   1.04     1.03      12169.89|
|  4:  3.2506 -  2.9560  1323   138  0.91  14.73   1.02     1.02      11406.89|
|  5:  2.9560 -  2.7456  1308   148  0.89  16.85   1.00     0.97       9039.07|
|  6:  2.7456 -  2.5846  1304   147  0.89  17.30   0.98     0.95       7970.68|
|  7:  2.5846 -  2.4558  1280   151  0.90  16.09   0.99     0.94       6583.96|
|  8:  2.4558 -  2.3493  1311   133  0.90  16.48   1.02     1.00       6245.10|
|  9:  2.3493 -  2.2592  1298   149  0.89  16.92   1.01     0.99       5565.74|
| 10:  2.2592 -  2.1815  1283   142  0.89  16.74   1.01     0.98       5248.58|
| 11:  2.1815 -  2.1135  1275   149  0.89  17.17   1.01     0.99       4723.60|
| 12:  2.1135 -  2.0532  1276   141  0.90  16.21   1.01     0.98       4166.97|
| 13:  2.0532 -  1.9993  1253   129  0.89  17.32   1.01     1.01       3743.63|
| 14:  1.9993 -  1.9506   632    76  0.90  16.31   1.00     0.96       3074.09|
|alpha:            min =        0.94 max =            1.03 mean =         0.99|
|beta:             min =     3074.09 max =        12169.89 mean =      7284.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.16|
|phase err.(test): min =        0.00 max =           87.95 mean =        14.64|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.400)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.36    87.80   15.12    None  None   None       |
|    all(noH): 2823   0      1.36    87.80   15.12    None  None   None       |
|    Sol.    : 438    0      4.13    87.80   38.48    None  None   None       |
|    Mac.    : 2385   0      1.36    79.83   10.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.362 -  10.006: 1514   |   5:    44.583 -  53.228:   97        |
|      1:    10.006 -  18.651:  699   |   6:    53.228 -  61.872:   65        |
|      2:    18.651 -  27.295:  172   |   7:    61.872 -  70.516:   26        |
|      3:    27.295 -  35.939:  124   |   8:    70.516 -  79.161:    7        |
|      4:    35.939 -  44.583:  117   |   9:    79.161 -  87.805:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.252 - 5.973
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.740 - 5.973

peak=   11.610 closest distance to " O   HOH Z 178 " =    1.977
peak=   10.925 closest distance to " CB  VAL A 230 " =    1.414
peak=    7.290 closest distance to " O   HOH Z 120 " =    1.311
peak=    6.437 closest distance to " O   HOH Z 138 " =    0.923
peak=    6.014 closest distance to " CB  VAL A 296 " =    1.149
peak=    5.927 closest distance to " O   HOH Z 279 " =    1.168
peak=    5.804 closest distance to " CD1AILE A 234 " =    1.092
peak=    5.764 closest distance to " O   HOH Z 102 " =    1.434
peak=    5.734 closest distance to " O   HOH Z 137 " =    1.087
peak=    5.687 closest distance to " O   HOH Z 278 " =    1.713
peak=    5.571 closest distance to " CG1 VAL A 296 " =    1.173
peak=    5.559 closest distance to " O   HOH Z 236 " =    1.655
peak=    5.468 closest distance to " O   HOH Z 193 " =    1.850
peak=    5.289 closest distance to " CG  LEU A   5 " =    1.297
peak=    5.252 closest distance to " O   HOH Z 124 " =    1.664
peak=    5.196 closest distance to " O   HOH Z 249 " =    1.334
peak=    5.195 closest distance to " O   HOH Z 406 " =    1.424
peak=    5.154 closest distance to " O   HOH Z 142 " =    1.708
peak=    5.062 closest distance to " CD2 LEU A   5 " =    1.253
peak=    4.917 closest distance to " O   HOH Z 199 " =    1.085
peak=    4.907 closest distance to " CB  ARG A 275 " =    0.964
peak=    4.893 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.891 closest distance to " O   SER A  87 " =    2.287
peak=    4.830 closest distance to " O   HOH Z  80 " =    1.874
peak=    4.791 closest distance to " O   HOH Z 402 " =    1.560
peak=    4.773 closest distance to " CB  ASN A 187 " =    2.061
peak=    4.763 closest distance to " CG AARG A 275 " =    1.142
peak=    4.752 closest distance to " O   HOH Z 247 " =    1.331
peak=    4.670 closest distance to " CB  GLN A 223 " =    1.425
peak=    4.666 closest distance to " O   HOH Z 272 " =    1.931
peak=    4.592 closest distance to " O   HOH Z 316 " =    2.386
peak=    4.528 closest distance to " NE2 GLN A  11 " =    1.032
peak=    4.515 closest distance to " O   HOH Z  85 " =    1.759
peak=    4.511 closest distance to " O   HOH Z 394 " =    1.479
peak=    4.496 closest distance to " NH2 ARG A  56 " =    2.086
peak=    4.483 closest distance to " C   PRO A 198 " =    1.478
peak=    4.474 closest distance to " O   HOH Z  43 " =    1.487
peak=    4.453 closest distance to " O   HOH Z 411 " =    3.614
peak=    4.394 closest distance to " O   HOH Z 178 " =    1.421
peak=    4.387 closest distance to " CA  TYR A  30 " =    1.037
peak=    4.341 closest distance to " CD2 LEU A 228 " =    1.272
peak=    4.328 closest distance to " O   HOH Z 155 " =    1.835
peak=    4.326 closest distance to " O   HOH Z 132 " =    1.196
peak=    4.318 closest distance to " O   HOH Z  97 " =    1.932
peak=    4.317 closest distance to " NZ  LYS A 117 " =    3.192
peak=    4.281 closest distance to " O   HOH Z 327 " =    1.857
peak=    4.279 closest distance to " CG  ARG A  66 " =    1.211
peak=    4.246 closest distance to " O   HOH Z 203 " =    1.556
peak=    4.239 closest distance to " O   HOH Z 414 " =    1.674
peak=    4.234 closest distance to " O   HOH Z  48 " =    2.026
peak=    4.229 closest distance to " O   HOH Z 234 " =    3.677
peak=    4.223 closest distance to " O   HOH Z  47 " =    1.793
peak=    4.207 closest distance to " O   HOH Z 345 " =    1.933
peak=    4.199 closest distance to " O   HOH Z 346 " =    1.402
peak=    4.196 closest distance to " O   HOH Z 368 " =    2.041
peak=    4.181 closest distance to " O   HOH Z 345 " =    2.374
peak=    4.171 closest distance to " CB  SER A  63 " =    1.118
peak=    4.167 closest distance to " CD2 TRP A 179 " =    1.367
peak=    4.166 closest distance to " NE BARG A 275 " =    1.319
peak=    4.163 closest distance to " CG2 VAL A 296 " =    1.025
peak=    4.161 closest distance to " CG  LEU A 228 " =    1.186
peak=    4.160 closest distance to " O   HOH Z 188 " =    1.174
peak=    4.153 closest distance to " CA  VAL A  41 " =    0.831
peak=    4.151 closest distance to " O   HOH Z 232 " =    2.008
peak=    4.144 closest distance to " CB  SER A  26 " =    1.690
peak=    4.137 closest distance to " O   HOH Z 303 " =    2.141
peak=    4.137 closest distance to " O   HOH Z 156 " =    3.144
peak=    4.132 closest distance to " O   HOH Z 134 " =    1.779
peak=    4.101 closest distance to " CA  ALA A  21 " =    1.223
peak=    4.096 closest distance to " CB  GLU A 152 " =    1.058
peak=    4.070 closest distance to " O   HOH Z  63 " =    2.512
peak=    4.027 closest distance to " CB  VAL A 230 " =    1.165
peak=    4.021 closest distance to " O   GLY A  91 " =    1.540
peak=    4.016 closest distance to " CB  SER A   3 " =    1.235
peak=    4.015 closest distance to " O   HOH Z 192 " =    1.712
peak=    4.013 closest distance to " OE1 GLU A   2 " =    2.070
peak=    4.000 closest distance to " O   HOH Z 128 " =    1.941
peak=    3.995 closest distance to " CB  GLN A 183 " =    1.338
peak=    3.993 closest distance to " O   HOH Z  97 " =    2.239
peak=    3.979 closest distance to " O   HOH Z 191 " =    1.387
peak=    3.974 closest distance to " CD  ARG A 269 " =    1.140
peak=    3.960 closest distance to " O   HOH Z 357 " =    1.842
peak=    3.956 closest distance to " O   HOH Z 128 " =    1.770
peak=    3.955 closest distance to " O   HOH Z 245 " =    1.440
peak=    3.952 closest distance to " N   ASN A  39 " =    1.343
peak=    3.952 closest distance to " O   HOH Z 426 " =    1.425
peak=    3.951 closest distance to " O   HOH Z  68 " =    2.626
peak=    3.943 closest distance to " O   HOH Z 154 " =    1.565
peak=    3.943 closest distance to " O   HOH Z 403 " =    1.207
peak=    3.878 closest distance to " CG  PRO A 198 " =    1.146
peak=    3.877 closest distance to " O   HOH Z 108 " =    1.078
peak=    3.859 closest distance to " CB  ALA A   9 " =    1.553
peak=    3.859 closest distance to " O   HOH Z  59 " =    2.161
peak=    3.859 closest distance to " CE BMET A  47 " =    1.191
peak=    3.849 closest distance to " O   HOH Z 248 " =    1.559
peak=    3.848 closest distance to " O   HOH Z 423 " =    1.828
peak=    3.840 closest distance to " O   HOH Z 189 " =    2.171
peak=    3.831 closest distance to " O   HOH Z 421 " =    1.938
peak=    3.829 closest distance to " CB  TRP A 179 " =    1.072
peak=    3.826 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.822 closest distance to " OD1 ASN A  60 " =    1.421
peak=    3.820 closest distance to " NH1AARG A 275 " =    1.158
peak=    3.818 closest distance to " O   HOH Z 284 " =    2.844
peak=    3.816 closest distance to " O   HOH Z 326 " =    1.486
peak=    3.815 closest distance to " O   HOH Z 361 " =    2.982
peak=    3.815 closest distance to " CB  VAL A 265 " =    1.285
peak=    3.809 closest distance to " CG2 ILE A 234 " =    0.999
peak=    3.807 closest distance to " O   HOH Z  54 " =    1.478
peak=    3.781 closest distance to " CA  ASN A 176 " =    0.971
peak=    3.780 closest distance to " O   HOH Z 214 " =    2.752
peak=    3.771 closest distance to " CG  GLN A  77 " =    2.183
peak=    3.763 closest distance to " O   HOH Z 136 " =    1.233
peak=    3.745 closest distance to " O   HOH Z 261 " =    1.833
peak=    3.737 closest distance to " O   HOH Z 260 " =    1.545
peak=    3.732 closest distance to " O   HOH Z 214 " =    1.295
peak=    3.732 closest distance to " O   HOH Z 322 " =    1.730
peak=    3.718 closest distance to " O   HOH Z 344 " =    1.300
peak=    3.712 closest distance to " CB  SER A  62 " =    1.255
peak=    3.707 closest distance to " O   HOH Z  20 " =    1.693
peak=    3.707 closest distance to " O   HOH Z 241 " =    1.597
peak=    3.698 closest distance to " O   HOH Z 420 " =    2.073
peak=    3.695 closest distance to " O   HOH Z 253 " =    1.804
peak=    3.693 closest distance to " O   HOH Z 369 " =    1.937
peak=    3.692 closest distance to " O   HOH Z 408 " =    1.864
peak=    3.688 closest distance to " O   HOH Z  48 " =    2.233
peak=    3.681 closest distance to " CB  MET A  47 " =    1.485
peak=    3.680 closest distance to " CB  ASN A 148 " =    1.323
peak=    3.670 closest distance to " O   HOH Z 113 " =    2.015
peak=    3.670 closest distance to " O   HOH Z 389 " =    1.644
peak=    3.666 closest distance to " O   HOH Z 126 " =    2.355
peak=    3.661 closest distance to " O   HOH Z 250 " =    1.390
peak=    3.650 closest distance to " CG2 THR A 221 " =    1.143
peak=    3.649 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.647 closest distance to " O   HOH Z 334 " =    1.563
peak=    3.646 closest distance to " O   HOH Z  40 " =    1.674
peak=    3.645 closest distance to " CA  ALA A  51 " =    1.185
peak=    3.635 closest distance to " O   HOH Z  78 " =    1.581
peak=    3.619 closest distance to " O   HOH Z 365 " =    2.822
peak=    3.617 closest distance to " O   HOH Z  59 " =    1.972
peak=    3.607 closest distance to " O   HOH Z 128 " =    1.598
peak=    3.605 closest distance to " O   HOH Z 255 " =    1.357
peak=    3.604 closest distance to " CG2AVAL A 121 " =    2.148
peak=    3.604 closest distance to " O   HOH Z 280 " =    2.367
peak=    3.600 closest distance to " O   HOH Z 227 " =    1.546
peak=    3.599 closest distance to " CB  ARG A 139 " =    0.977
peak=    3.599 closest distance to " CB  ALA A 100 " =    1.175
peak=    3.591 closest distance to " NZ  LYS A 119 " =    1.515
peak=    3.586 closest distance to " CZ AARG A 102 " =    1.615
peak=    3.581 closest distance to " CG1BVAL A  72 " =    1.646
peak=    3.579 closest distance to " O   HOH Z   4 " =    1.442
peak=    3.577 closest distance to " O   HOH Z 215 " =    1.512
peak=    3.576 closest distance to " O   HOH Z 425 " =    2.174
peak=    3.575 closest distance to " O   HOH Z 402 " =    2.845
peak=    3.573 closest distance to " O   HOH Z 315 " =    1.803
peak=    3.571 closest distance to " O   HOH Z 113 " =    1.548
peak=    3.571 closest distance to " CG2 ILE A 120 " =    1.333
peak=    3.569 closest distance to " CE  LYS A 119 " =    0.969
peak=    3.568 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.568 closest distance to " CD  GLN A  58 " =    5.973
peak=    3.568 closest distance to " CB BVAL A  41 " =    1.043
peak=    3.563 closest distance to " O   HOH Z 109 " =    2.024
peak=    3.550 closest distance to " O   HOH Z 118 " =    1.666
peak=    3.546 closest distance to " O   HOH Z  19 " =    2.108
peak=    3.541 closest distance to " O   HOH Z 313 " =    1.582
peak=    3.540 closest distance to " O   HOH Z 265 " =    2.401
peak=    3.538 closest distance to " O   HOH Z  92 " =    1.032
peak=    3.537 closest distance to " O   HOH Z 209 " =    2.415
peak=    3.533 closest distance to " O   HOH Z 344 " =    2.463
peak=    3.529 closest distance to " O   HOH Z 427 " =    2.567
peak=    3.518 closest distance to " NH1 ARG A  14 " =    1.079
peak=    3.514 closest distance to " CG  PRO A  54 " =    1.497
peak=    3.513 closest distance to " O   HOH Z 422 " =    2.544
peak=    3.512 closest distance to " CH2 TRP A 274 " =    2.236
peak=    3.506 closest distance to " O   HOH Z 261 " =    1.950
peak=    3.504 closest distance to " O   HOH Z  44 " =    1.963
peak=    3.504 closest distance to " O   HOH Z 404 " =    1.353
peak=    3.501 closest distance to " O   HOH Z 425 " =    1.386
peak=    3.500 closest distance to " CB  ASN A  39 " =    0.749
peak=    3.493 closest distance to " O   HOH Z 415 " =    3.292
peak=    3.488 closest distance to " O   HOH Z 298 " =    1.978
peak=    3.486 closest distance to " O   HOH Z 130 " =    2.715
peak=    3.484 closest distance to " O   HOH Z 163 " =    1.393
peak=    3.482 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.480 closest distance to " O   HOH Z 353 " =    2.803
peak=    3.471 closest distance to " O   HOH Z 381 " =    1.429
peak=    3.469 closest distance to " O   HOH Z 192 " =    1.243
peak=    3.465 closest distance to " CG  ARG A 138 " =    1.037
peak=    3.461 closest distance to " NE1 TRP A 274 " =    0.905
peak=    3.460 closest distance to " O   HOH Z 367 " =    3.507
peak=    3.449 closest distance to " O   HOH Z 118 " =    1.814
peak=    3.438 closest distance to " CB  TYR A 169 " =    0.750
peak=    3.435 closest distance to " O   HOH Z 263 " =    1.400
peak=    3.427 closest distance to " O   HOH Z 169 " =    0.789
peak=    3.426 closest distance to " O   HOH Z 303 " =    1.469
peak=    3.419 closest distance to " O   HOH Z  35 " =    2.273
peak=    3.418 closest distance to " NH1 ARG A 138 " =    1.273
peak=    3.415 closest distance to " O   HOH Z  88 " =    3.857
peak=    3.406 closest distance to " CD2 HIS A  81 " =    1.391
peak=    3.403 closest distance to " O   HOH Z 194 " =    2.148
peak=    3.402 closest distance to " O   HOH Z 166 " =    1.389
peak=    3.397 closest distance to " O   HOH Z 374 " =    2.498
peak=    3.391 closest distance to " CB  ARG A  79 " =    1.352
peak=    3.391 closest distance to " O   HOH Z 112 " =    1.609
peak=    3.388 closest distance to " O   HOH Z 380 " =    1.992
peak=    3.377 closest distance to " O   HOH Z  66 " =    2.146
peak=    3.373 closest distance to " O   HOH Z 409 " =    1.865
peak=    3.373 closest distance to " ND1 HIS A  81 " =    1.292
peak=    3.371 closest distance to " O   HOH Z 383 " =    1.819
peak=    3.369 closest distance to " CB  GLU A 128 " =    1.197
peak=    3.369 closest distance to " O   HOH Z 155 " =    2.479
peak=    3.366 closest distance to " O   HOH Z 108 " =    2.390
peak=    3.364 closest distance to " O   HOH Z 380 " =    1.936
peak=    3.363 closest distance to " O   HOH Z 214 " =    2.280
peak=    3.363 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.363 closest distance to " O   HOH Z 162 " =    1.702
peak=    3.359 closest distance to " O   HOH Z 392 " =    2.473
peak=    3.357 closest distance to " NH2AARG A 145 " =    2.175
peak=    3.355 closest distance to " O   HOH Z 148 " =    2.960
peak=    3.354 closest distance to " OG  SER A  62 " =    2.886
peak=    3.352 closest distance to " O   HOH Z 435 " =    1.881
peak=    3.351 closest distance to " CD BLYS A 290 " =    1.045
peak=    3.350 closest distance to " O   HOH Z  68 " =    1.720
peak=    3.349 closest distance to " O   HOH Z 284 " =    1.420
peak=    3.349 closest distance to " CA  VAL A 126 " =    0.965
peak=    3.346 closest distance to " NH2BARG A 145 " =    1.689
peak=    3.343 closest distance to " OD1 ASP A 286 " =    1.581
peak=    3.341 closest distance to " CB  TRP A 266 " =    1.222
peak=    3.341 closest distance to " CA  ARG A 195 " =    1.147
peak=    3.327 closest distance to " O   HOH Z 111 " =    3.383
peak=    3.327 closest distance to " CB  PRO A 213 " =    1.843
peak=    3.326 closest distance to " CD  LYS A  76 " =    1.739
peak=    3.323 closest distance to " O   THR A  82 " =    1.892
peak=    3.320 closest distance to " O   HOH Z  37 " =    1.285
peak=    3.318 closest distance to " O   HOH Z 207 " =    1.629
peak=    3.312 closest distance to " O   HOH Z 227 " =    1.722
peak=    3.309 closest distance to " O   HOH Z 273 " =    2.718
peak=    3.307 closest distance to " OD2 ASP A 286 " =    2.523
peak=    3.307 closest distance to " O   HOH Z  61 " =    1.588
peak=    3.304 closest distance to " CB  THR A  31 " =    1.503
peak=    3.299 closest distance to " CB  LEU A 237 " =    0.868
peak=    3.290 closest distance to " CG  ARG A 269 " =    0.983
peak=    3.289 closest distance to " O   HOH Z 279 " =    2.080
peak=    3.280 closest distance to " O   HOH Z 379 " =    1.460
peak=    3.279 closest distance to " CA  ARG A  36 " =    0.892
peak=    3.278 closest distance to " CB  GLN A  89 " =    1.208
peak=    3.277 closest distance to " OD2 ASP A 298 " =    3.999
peak=    3.276 closest distance to " O   HOH Z  50 " =    1.685
peak=    3.274 closest distance to " O   HOH Z 428 " =    3.854
peak=    3.272 closest distance to " O   HOH Z  89 " =    1.687
peak=    3.267 closest distance to " CA  LYS A 117 " =    1.319
peak=    3.257 closest distance to " O   TRP A 274 " =    1.781
peak=    3.256 closest distance to " N   ASP A 162 " =    1.257
peak=    3.251 closest distance to " CA  ARG A  66 " =    0.940
peak=    3.243 closest distance to " OG BSER A 164 " =    2.352
peak=    3.235 closest distance to " O   HOH Z  85 " =    1.711
peak=    3.233 closest distance to " CD1BILE A 234 " =    0.907
peak=    3.232 closest distance to " CG2 ILE A  20 " =    1.404
peak=    3.224 closest distance to " O   HOH Z 145 " =    2.481
peak=    3.222 closest distance to " ND2 ASN A 187 " =    1.548
peak=    3.220 closest distance to " CB  TYR A  30 " =    1.628
peak=    3.214 closest distance to " O   ASN A 301 " =    2.791
peak=    3.211 closest distance to " CB  ARG A 259 " =    1.893
peak=    3.208 closest distance to " CB  ASN A 110 " =    1.035
peak=    3.206 closest distance to " O   HOH Z 392 " =    1.802
peak=    3.203 closest distance to " CB  ASP A 107 " =    1.156
peak=    3.203 closest distance to " CB  GLN A  73 " =    1.576
peak=    3.202 closest distance to " O   HOH Z 276 " =    1.278
peak=    3.200 closest distance to " NZ  LYS A 119 " =    2.866
peak=    3.200 closest distance to " O   HOH Z 359 " =    1.424
peak=    3.197 closest distance to " CA  THR A 221 " =    0.928
peak=    3.195 closest distance to " CB  ASN A  45 " =    1.047
peak=    3.192 closest distance to " CG  MET A  93 " =    1.061
peak=    3.188 closest distance to " CD  GLN A 194 " =    1.588
peak=    3.187 closest distance to " O   HOH Z   1 " =    2.078
peak=    3.186 closest distance to " N   TYR A  15 " =    0.994
peak=    3.179 closest distance to " CB  SER A 141 " =    1.034
peak=    3.177 closest distance to " CA  SER A  12 " =    1.532
peak=    3.174 closest distance to " CD AARG A 190 " =    1.610
peak=    3.168 closest distance to " NE  ARG A  14 " =    1.282
peak=    3.164 closest distance to " CB  ALA A   1 " =    1.245
peak=    3.163 closest distance to " OG  SER A 245 " =    1.359
peak=    3.163 closest distance to " CA  ASN A 217 " =    1.296
peak=    3.157 closest distance to " CD  LYS A 166 " =    1.330
peak=    3.157 closest distance to " NH2 ARG A 156 " =    1.013
peak=    3.156 closest distance to " O   HOH Z  59 " =    1.705
peak=    3.151 closest distance to " CD2 LEU A 255 " =    1.128
peak=    3.144 closest distance to " O   HOH Z 343 " =    2.295
peak=    3.142 closest distance to " O   HOH Z 429 " =    2.126
peak=    3.135 closest distance to " O   HOH Z 438 " =    1.691
peak=    3.134 closest distance to " O   HOH Z 173 " =    1.733
peak=    3.134 closest distance to " O   HOH Z 337 " =    3.545
peak=    3.120 closest distance to " CB  VAL A 268 " =    0.853
peak=    3.113 closest distance to " O   HOH Z 214 " =    2.123
peak=    3.113 closest distance to " N   SER A 135 " =    1.244
peak=    3.113 closest distance to " O   HOH Z  59 " =    2.117
peak=    3.107 closest distance to " CB  ASN A 215 " =    1.033
peak=    3.099 closest distance to " OH  TYR A 116 " =    1.065
peak=    3.097 closest distance to " CG2 THR A  42 " =    0.852
peak=    3.096 closest distance to " CB  GLN A 278 " =    0.848
peak=    3.094 closest distance to " CE  MET A  93 " =    1.379
peak=    3.091 closest distance to " O   HOH Z 279 " =    2.477
peak=    3.084 closest distance to " CG2 ILE A 106 " =    0.868
peak=    3.084 closest distance to " O   HOH Z 130 " =    2.586
peak=    3.081 closest distance to " CA  LEU A 101 " =    1.274
peak=    3.078 closest distance to " CG2 ILE A 234 " =    1.939
peak=    3.071 closest distance to " CD  LYS A 119 " =    1.812
peak=    3.070 closest distance to " CE BLYS A 290 " =    0.953
peak=    3.069 closest distance to " CD1 LEU A 228 " =    1.415
peak=    3.067 closest distance to " CA  ALA A 299 " =    0.952
peak=    3.063 closest distance to " O   HOH Z 183 " =    1.883
peak=    3.063 closest distance to " CE  MET A  40 " =    1.140
peak=    3.055 closest distance to " O   HOH Z  63 " =    1.923
peak=    3.048 closest distance to " O   HOH Z  96 " =    1.772
peak=    3.028 closest distance to " CE  LYS A 119 " =    1.592

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.352 - 5.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 205
   mapped sites are within: 0.741 - 5.564

peak=   -5.258 closest distance to " CG2 VAL A 230 " =    0.741
peak=   -4.324 closest distance to " OXT GLY A 302 " =    2.802
peak=   -4.252 closest distance to " O   HOH Z 423 " =    2.356
peak=   -4.164 closest distance to " C   HIS A 108 " =    1.205
peak=   -4.099 closest distance to " O   HOH Z 290 " =    0.877
peak=   -4.075 closest distance to " O   PRO A 163 " =    2.064
peak=   -4.072 closest distance to " CG  ARG A 219 " =    2.267
peak=   -4.065 closest distance to " O   HOH Z  13 " =    1.434
peak=   -4.065 closest distance to " O   HOH Z 362 " =    5.564
peak=   -4.060 closest distance to " CG2BVAL A  41 " =    2.636
peak=   -4.016 closest distance to " O   HOH Z 166 " =    1.995
peak=   -4.014 closest distance to " CD2 LEU A 300 " =    2.813
peak=   -4.003 closest distance to " CD  ARG A  14 " =    3.196
peak=   -3.990 closest distance to " C   GLY A  80 " =    2.195
peak=   -3.980 closest distance to " O   HOH Z 103 " =    1.876
peak=   -3.965 closest distance to " CD1 LEU A 101 " =    2.465
peak=   -3.963 closest distance to " O   SER A 273 " =    1.226
peak=   -3.933 closest distance to " O   VAL A  67 " =    2.582
peak=   -3.918 closest distance to " CB  PRO A 163 " =    2.798
peak=   -3.899 closest distance to " CE2 TYR A  30 " =    2.817
peak=   -3.883 closest distance to " O   ASN A  45 " =    1.805
peak=   -3.883 closest distance to " O   ALA A  51 " =    1.319
peak=   -3.858 closest distance to " OG BSER A 134 " =    1.390
peak=   -3.842 closest distance to " CG1 VAL A 296 " =    0.932
peak=   -3.842 closest distance to " O   HOH Z 407 " =    2.516
peak=   -3.839 closest distance to " CD  ARG A 156 " =    2.059
peak=   -3.832 closest distance to " CB  ALA A 248 " =    1.970
peak=   -3.826 closest distance to " NH2 ARG A  79 " =    1.936
peak=   -3.804 closest distance to " O   HOH Z 266 " =    4.400
peak=   -3.801 closest distance to " O   MET A  40 " =    2.785
peak=   -3.767 closest distance to " ND2 ASN A 187 " =    1.443
peak=   -3.755 closest distance to " N   ALA A 226 " =    1.911
peak=   -3.740 closest distance to " O   HOH Z  56 " =    1.951
peak=   -3.727 closest distance to " CD1 TYR A 247 " =    2.338
peak=   -3.709 closest distance to " O   HOH Z 139 " =    5.039
peak=   -3.698 closest distance to " C   GLY A  91 " =    1.326
peak=   -3.697 closest distance to " O   ASN A 187 " =    1.461
peak=   -3.693 closest distance to " CG  GLN A  58 " =    1.381
peak=   -3.686 closest distance to " O   VAL A 197 " =    1.258
peak=   -3.663 closest distance to " O   HOH Z 250 " =    1.408
peak=   -3.659 closest distance to " O   HOH Z  11 " =    1.707
peak=   -3.650 closest distance to " O   GLY A  80 " =    2.654
peak=   -3.639 closest distance to " O   HOH Z 431 " =    1.790
peak=   -3.637 closest distance to " C   THR A 279 " =    1.181
peak=   -3.634 closest distance to " OG ASER A 134 " =    1.329
peak=   -3.625 closest distance to " O   HOH Z 313 " =    1.255
peak=   -3.622 closest distance to " OG1 THR A  82 " =    1.277
peak=   -3.621 closest distance to " CB  ALA A 161 " =    2.387
peak=   -3.612 closest distance to " N   GLN A 122 " =    1.481
peak=   -3.609 closest distance to " O   HOH Z 166 " =    2.062
peak=   -3.608 closest distance to " OG  SER A  97 " =    2.100
peak=   -3.589 closest distance to " N   ALA A 248 " =    1.812
peak=   -3.585 closest distance to " O   HOH Z  60 " =    1.672
peak=   -3.580 closest distance to " CB  PHE A 208 " =    2.254
peak=   -3.569 closest distance to " NH2 ARG A  66 " =    1.489
peak=   -3.568 closest distance to " N   SER A 276 " =    1.345
peak=   -3.551 closest distance to " O   HOH Z 234 " =    4.125
peak=   -3.549 closest distance to " O   SER A 146 " =    0.874
peak=   -3.548 closest distance to " O   HOH Z 137 " =    1.755
peak=   -3.547 closest distance to " OD2 ASP A  50 " =    1.452
peak=   -3.547 closest distance to " CD  LYS A 289 " =    2.607
peak=   -3.544 closest distance to " O   HOH Z  11 " =    1.802
peak=   -3.543 closest distance to " CB  GLN A  11 " =    1.888
peak=   -3.532 closest distance to " O   HOH Z  92 " =    1.770
peak=   -3.528 closest distance to " O   HOH Z 310 " =    3.587
peak=   -3.527 closest distance to " ND2 ASN A  45 " =    1.107
peak=   -3.513 closest distance to " O   HOH Z 388 " =    2.100
peak=   -3.513 closest distance to " N   THR A  52 " =    1.679
peak=   -3.500 closest distance to " N   GLN A  58 " =    1.871
peak=   -3.498 closest distance to " CA  GLY A  23 " =    1.755
peak=   -3.496 closest distance to " CD  ARG A 139 " =    1.563
peak=   -3.491 closest distance to " CD1 PHE A  59 " =    1.877
peak=   -3.490 closest distance to " O   TRP A  92 " =    1.949
peak=   -3.488 closest distance to " O   HOH Z 183 " =    1.508
peak=   -3.472 closest distance to " CG2 THR A 221 " =    2.285
peak=   -3.461 closest distance to " O   HOH Z 377 " =    2.170
peak=   -3.452 closest distance to " CD  GLN A 103 " =    1.306
peak=   -3.452 closest distance to " O   HOH Z 174 " =    2.350
peak=   -3.447 closest distance to " O   HOH Z 165 " =    1.943
peak=   -3.446 closest distance to " O   HOH Z  34 " =    1.906
peak=   -3.441 closest distance to " CG  ARG A 219 " =    2.796
peak=   -3.439 closest distance to " O   LEU A 228 " =    2.206
peak=   -3.439 closest distance to " C   ALA A 158 " =    1.121
peak=   -3.438 closest distance to " OG  SER A   3 " =    1.220
peak=   -3.437 closest distance to " N   GLY A  17 " =    1.428
peak=   -3.433 closest distance to " OG  SER A  62 " =    1.213
peak=   -3.424 closest distance to " CB  ALA A 291 " =    2.116
peak=   -3.395 closest distance to " C   ASN A 285 " =    2.115
peak=   -3.387 closest distance to " O   GLY A 118 " =    2.184
peak=   -3.384 closest distance to " O   HOH Z 138 " =    1.026
peak=   -3.384 closest distance to " O   HOH Z 346 " =    1.972
peak=   -3.383 closest distance to " O   PRO A 198 " =    1.310
peak=   -3.372 closest distance to " O   HOH Z 427 " =    1.502
peak=   -3.369 closest distance to " O   LEU A 143 " =    1.555
peak=   -3.367 closest distance to " OG BSER A 134 " =    1.573
peak=   -3.365 closest distance to " NZ  LYS A 119 " =    3.254
peak=   -3.364 closest distance to " CG  GLU A   2 " =    1.868
peak=   -3.363 closest distance to " O   HOH Z 424 " =    2.999
peak=   -3.363 closest distance to " N   THR A 235 " =    1.332
peak=   -3.359 closest distance to " CB  ALA A 291 " =    2.373
peak=   -3.358 closest distance to " CA  GLY A 133 " =    1.890
peak=   -3.353 closest distance to " OD2 ASP A 191 " =    1.523
peak=   -3.350 closest distance to " N   THR A 157 " =    1.544
peak=   -3.350 closest distance to " OG  SER A 206 " =    1.388
peak=   -3.347 closest distance to " CG  GLN A  88 " =    1.229
peak=   -3.347 closest distance to " O   VAL A 174 " =    1.882
peak=   -3.343 closest distance to " O   HOH Z 351 " =    1.411
peak=   -3.336 closest distance to " O   HOH Z  63 " =    0.915
peak=   -3.336 closest distance to " O   HOH Z 208 " =    1.045
peak=   -3.334 closest distance to " CA  GLY A 241 " =    2.380
peak=   -3.332 closest distance to " NH2AARG A 275 " =    4.496
peak=   -3.331 closest distance to " OG1 THR A 251 " =    2.775
peak=   -3.329 closest distance to " O   HOH Z 435 " =    2.626
peak=   -3.327 closest distance to " OG  SER A  63 " =    1.154
peak=   -3.325 closest distance to " N   ARG A  66 " =    1.813
peak=   -3.324 closest distance to " O   HOH Z  97 " =    1.235
peak=   -3.324 closest distance to " N   SER A 206 " =    1.783
peak=   -3.323 closest distance to " CB  ALA A  43 " =    2.287
peak=   -3.321 closest distance to " O   HOH Z 111 " =    4.115
peak=   -3.317 closest distance to " O   HOH Z 281 " =    2.907
peak=   -3.316 closest distance to " O   HOH Z  98 " =    1.496
peak=   -3.313 closest distance to " O   HOH Z 120 " =    1.153
peak=   -3.312 closest distance to " N   HIS A 115 " =    2.005
peak=   -3.301 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.292 closest distance to " CD1 PHE A  59 " =    2.341
peak=   -3.292 closest distance to " O   ALA A 160 " =    1.348
peak=   -3.287 closest distance to " CG2 VAL A 296 " =    1.391
peak=   -3.286 closest distance to " OG BSER A 210 " =    1.458
peak=   -3.282 closest distance to " CG  ARG A 269 " =    2.137
peak=   -3.276 closest distance to " CG2 ILE A 263 " =    2.231
peak=   -3.266 closest distance to " NE2 GLN A  88 " =    1.802
peak=   -3.261 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.260 closest distance to " ND2 ASN A  69 " =    1.735
peak=   -3.252 closest distance to " CB  ALA A 100 " =    1.621
peak=   -3.250 closest distance to " CD1 LEU A  96 " =    2.093
peak=   -3.250 closest distance to " O   HOH Z 172 " =    4.905
peak=   -3.247 closest distance to " NH2 ARG A  79 " =    1.766
peak=   -3.246 closest distance to " O   HOH Z 227 " =    1.120
peak=   -3.241 closest distance to " O   HOH Z 215 " =    3.545
peak=   -3.239 closest distance to " OD1 ASP A 200 " =    1.233
peak=   -3.237 closest distance to " CE  LYS A 166 " =    3.001
peak=   -3.231 closest distance to " O   ALA A 161 " =    1.370
peak=   -3.230 closest distance to " CE  MET A 105 " =    1.870
peak=   -3.228 closest distance to " O   HOH Z  71 " =    1.395
peak=   -3.225 closest distance to " CB  ASP A 162 " =    2.484
peak=   -3.223 closest distance to " ND2 ASN A 142 " =    1.886
peak=   -3.222 closest distance to " O   HOH Z  52 " =    1.829
peak=   -3.215 closest distance to " O   HOH Z 174 " =    4.322
peak=   -3.211 closest distance to " ND2 ASN A  39 " =    1.064
peak=   -3.210 closest distance to " O   HOH Z 265 " =    2.095
peak=   -3.208 closest distance to " O   HOH Z 177 " =    1.621
peak=   -3.200 closest distance to " CG BARG A 275 " =    0.950
peak=   -3.199 closest distance to " OD2 ASP A 286 " =    2.256
peak=   -3.199 closest distance to " CD1 LEU A  83 " =    2.273
peak=   -3.198 closest distance to " CG1 ILE A 199 " =    1.848
peak=   -3.194 closest distance to " OE1 GLN A 223 " =    4.944
peak=   -3.193 closest distance to " CE BMET A  47 " =    1.399
peak=   -3.191 closest distance to " CD2 TYR A 293 " =    2.015
peak=   -3.186 closest distance to " O   HOH Z 151 " =    1.690
peak=   -3.184 closest distance to " O   HOH Z 169 " =    1.174
peak=   -3.184 closest distance to " O   HOH Z  17 " =    1.049
peak=   -3.176 closest distance to " CA  VAL A 296 " =    1.059
peak=   -3.175 closest distance to " N   ALA A  43 " =    2.533
peak=   -3.174 closest distance to " CG  LYS A 193 " =    2.108
peak=   -3.172 closest distance to " CD1 LEU A 228 " =    2.155
peak=   -3.169 closest distance to " O   GLY A  75 " =    1.441
peak=   -3.163 closest distance to " CG  ASP A 132 " =    2.198
peak=   -3.163 closest distance to " O   HOH Z 191 " =    5.149
peak=   -3.157 closest distance to " CD2 LEU A 167 " =    1.717
peak=   -3.145 closest distance to " O   HOH Z 426 " =    1.771
peak=   -3.145 closest distance to " O   HOH Z 198 " =    1.919
peak=   -3.142 closest distance to " O   HOH Z 249 " =    1.328
peak=   -3.140 closest distance to " O   PHE A 218 " =    1.663
peak=   -3.133 closest distance to " C   ASP A 270 " =    1.477
peak=   -3.133 closest distance to " CE3 TRP A 150 " =    2.168
peak=   -3.131 closest distance to " CD  GLN A  11 " =    0.773
peak=   -3.128 closest distance to " O   HOH Z 250 " =    1.422
peak=   -3.126 closest distance to " N   SER A 210 " =    1.339
peak=   -3.125 closest distance to " N   SER A 245 " =    2.396
peak=   -3.121 closest distance to " OG  SER A  26 " =    1.394
peak=   -3.120 closest distance to " O   GLY A 196 " =    1.194
peak=   -3.116 closest distance to " CG1 VAL A 112 " =    2.835
peak=   -3.111 closest distance to " OD1 ASN A  39 " =    2.180
peak=   -3.105 closest distance to " O   HOH Z 422 " =    1.604
peak=   -3.102 closest distance to " O   HOH Z   1 " =    4.024
peak=   -3.099 closest distance to " O   HOH Z 385 " =    3.345
peak=   -3.098 closest distance to " O   HOH Z  55 " =    2.456
peak=   -3.092 closest distance to " OG1 THR A 246 " =    1.371
peak=   -3.089 closest distance to " O   SER A 210 " =    1.893
peak=   -3.087 closest distance to " CB  ALA A 248 " =    2.138
peak=   -3.087 closest distance to " O   HOH Z 313 " =    1.289
peak=   -3.086 closest distance to " O   LEU A 222 " =    1.295
peak=   -3.084 closest distance to " CD2 TRP A 274 " =    0.997
peak=   -3.078 closest distance to " CD2 TYR A  15 " =    2.331
peak=   -3.075 closest distance to " O   PHE A  59 " =    2.150
peak=   -3.067 closest distance to " O   HOH Z 135 " =    1.911
peak=   -3.049 closest distance to " O   HOH Z 218 " =    1.182
peak=   -3.047 closest distance to " OD1 ASP A 171 " =    1.611
peak=   -3.045 closest distance to " O   HOH Z 310 " =    1.425
peak=   -3.035 closest distance to " O   HOH Z 139 " =    3.091
peak=   -3.024 closest distance to " O   HOH Z 193 " =    1.675

================= 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    :  0.5015 0.4940   6.298468e+00   6.290822e+00
   1_bss:  0.4932 0.4855   6.294428e+00   6.283638e+00
   1_xyz:  0.4118 0.4389   6.193688e+00   6.236739e+00
   1_adp:  0.3698 0.4253   6.131513e+00   6.214843e+00
   1_occ:  0.3690 0.4256   6.130020e+00   6.213956e+00
   2_bss:  0.3674 0.4197   6.129274e+00   6.212166e+00
   2_xyz:  0.2841 0.3389   5.925701e+00   6.060577e+00
   2_adp:  0.2595 0.3192   5.855684e+00   6.008678e+00
   2_occ:  0.2593 0.3189   5.855153e+00   6.008237e+00
   3_bss:  0.2567 0.3165   5.851609e+00   6.005908e+00
   3_xyz:  0.1909 0.2464   5.607997e+00   5.805917e+00
   3_adp:  0.1768 0.2241   5.524694e+00   5.711452e+00
   3_occ:  0.1764 0.2243   5.524265e+00   5.712044e+00
   4_bss:  0.1752 0.2220   5.522010e+00   5.707978e+00
   4_xyz:  0.1454 0.1879   5.354624e+00   5.552543e+00
   4_adp:  0.1381 0.1827   5.311636e+00   5.518342e+00
   4_occ:  0.1380 0.1827   5.311017e+00   5.517846e+00
   5_bss:  0.1384 0.1827   5.310996e+00   5.517402e+00
   5_xyz:  0.1226 0.1680   5.217221e+00   5.446943e+00
   5_adp:  0.1201 0.1672   5.205993e+00   5.442523e+00
   5_occ:  0.1200 0.1671   5.205625e+00   5.442263e+00
   5_bss:  0.1200 0.1670   5.205861e+00   5.442417e+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:  0.375  14.014   7.536   8.461   8.329   0.000   0.000   0.000
   1_xyz:  0.375  14.014   7.536   8.461   8.329   0.000   0.000   0.000
   1_adp:  0.375  14.014   7.536   8.461   8.329   0.000   0.000   0.000
   1_occ:  0.375  14.014   7.536   8.461   8.329   0.000   0.000   0.000
   2_bss:  0.344  29.473   4.562   5.311   5.888   0.000   0.000   0.000
   2_xyz:  0.344  29.473   4.562   5.311   5.888   0.000   0.000   0.000
   2_adp:  0.344  29.473   4.562   5.311   5.888   0.000   0.000   0.000
   2_occ:  0.344  29.473   4.562   5.311   5.888   0.000   0.000   0.000
   3_bss:  0.329  36.512   2.104   3.267   3.569   0.000   0.000   0.000
   3_xyz:  0.329  36.512   2.104   3.267   3.569   0.000   0.000   0.000
   3_adp:  0.329  36.512   2.104   3.267   3.569   0.000   0.000   0.000
   3_occ:  0.329  36.512   2.104   3.267   3.569   0.000   0.000   0.000
   4_bss:  0.322  32.202   0.729   2.108   2.169   0.000   0.000   0.000
   4_xyz:  0.322  32.202   0.729   2.108   2.169   0.000   0.000   0.000
   4_adp:  0.322  32.202   0.729   2.108   2.169   0.000   0.000   0.000
   4_occ:  0.322  32.202   0.729   2.108   2.169   0.000   0.000   0.000
   5_bss:  0.313  35.507   0.422   1.813   1.865   0.000   0.000   0.000
   5_xyz:  0.313  35.507   0.422   1.813   1.865   0.000   0.000   0.000
   5_adp:  0.313  35.507   0.422   1.813   1.865   0.000   0.000   0.000
   5_occ:  0.313  35.507   0.422   1.813   1.865   0.000   0.000   0.000
   5_bss:  0.318  36.869  -0.918   0.404   0.514   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.961 0.3685  0.4363    77683.891
   1_bss:  61.628 0.3709  0.5529    74791.813
   1_xyz:  54.026 0.4675  0.6888    59216.312
   1_adp:  49.278 0.5285  0.8331    53626.632
   1_occ:  49.155 0.5300  0.8338    53376.464
   2_bss:  48.738 0.5350  0.7626    52536.790
   2_xyz:  36.758 0.6798  0.9463    31698.439
   2_adp:  33.417 0.7188  0.9926    27018.947
   2_occ:  33.389 0.7192  0.9930    26988.833
   3_bss:  33.153 0.7216  0.9157    26577.837
   3_xyz:  24.679 0.8142  0.9980    15882.670
   3_adp:  21.570 0.8470  1.0224    13016.014
   3_occ:  21.576 0.8470  1.0222    13026.174
   4_bss:  21.448 0.8480  0.9735    12828.672
   4_xyz:  17.616 0.8845  0.9909     9095.678
   4_adp:  16.796 0.8920  0.9927     8546.776
   4_occ:  16.776 0.8922  0.9927     8532.457
   5_bss:  16.756 0.8924  0.9820     8528.141
   5_xyz:  15.247 0.9051  0.9879     7318.016
   5_adp:  15.115 0.9064  0.9854     7280.760
   5_occ:  15.104 0.9065  0.9854     7275.912
   5_bss:  15.108 0.9065  0.9853     7282.713
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2928e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2928e+01
   1_xyz:   2.046  0.017  0.125 18.806  0.008  4.105   2.0105e-01
   1_adp:   2.046  0.017  0.125 18.806  0.008  4.105   2.0105e-01
   1_occ:   2.046  0.017  0.125 18.806  0.008  4.105   2.0105e-01
   2_bss:   2.046  0.017  0.125 18.806  0.008  4.105   2.0105e-01
   2_xyz:   1.272  0.009  0.086 17.102  0.006  4.104   9.7239e-02
   2_adp:   1.272  0.009  0.086 17.102  0.006  4.104   9.7239e-02
   2_occ:   1.272  0.009  0.086 17.102  0.006  4.104   9.7239e-02
   3_bss:   1.272  0.009  0.086 17.102  0.006  4.104   9.7239e-02
   3_xyz:   1.044  0.007  0.073 16.014  0.004  4.120   6.7116e-02
   3_adp:   1.044  0.007  0.073 16.014  0.004  4.120   6.7116e-02
   3_occ:   1.044  0.007  0.073 16.014  0.004  4.120   6.7116e-02
   4_bss:   1.044  0.007  0.073 16.014  0.004  4.120   6.7116e-02
   4_xyz:   0.965  0.005  0.070 15.832  0.004  4.113   5.7937e-02
   4_adp:   0.965  0.005  0.070 15.832  0.004  4.113   5.7937e-02
   4_occ:   0.965  0.005  0.070 15.832  0.004  4.113   5.7937e-02
   5_bss:   0.965  0.005  0.070 15.832  0.004  4.113   5.7937e-02
   5_xyz:   1.075  0.007  0.078 15.841  0.004  4.115   6.6255e-02
   5_adp:   1.075  0.007  0.078 15.841  0.004  4.115   6.6255e-02
   5_occ:   1.075  0.007  0.078 15.841  0.004  4.115   6.6255e-02
   5_bss:   1.075  0.007  0.078 15.841  0.004  4.115   6.6255e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.952   6.8495e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.952   6.8495e+00
   1_xyz:  18.097  0.232  0.641 87.206  0.053  2.039   1.2976e-01
   1_adp:  18.097  0.232  0.641 87.206  0.053  2.039   1.2976e-01
   1_occ:  18.097  0.232  0.641 87.206  0.053  2.039   1.2976e-01
   2_bss:  18.097  0.232  0.641 87.206  0.053  2.039   1.2976e-01
   2_xyz:   8.497  0.117  0.428 83.590  0.059  2.233   7.6253e-02
   2_adp:   8.497  0.117  0.428 83.590  0.059  2.233   7.6253e-02
   2_occ:   8.497  0.117  0.428 83.590  0.059  2.233   7.6253e-02
   3_bss:   8.497  0.117  0.428 83.590  0.059  2.233   7.6253e-02
   3_xyz:   7.398  0.047  0.261 82.502  0.035  2.338   4.9678e-02
   3_adp:   7.398  0.047  0.261 82.502  0.035  2.338   4.9678e-02
   3_occ:   7.398  0.047  0.261 82.502  0.035  2.338   4.9678e-02
   4_bss:   7.398  0.047  0.261 82.502  0.035  2.338   4.9678e-02
   4_xyz:   6.966  0.033  0.266 81.461  0.029  2.317   3.4708e-02
   4_adp:   6.966  0.033  0.266 81.461  0.029  2.317   3.4708e-02
   4_occ:   6.966  0.033  0.266 81.461  0.029  2.317   3.4708e-02
   5_bss:   6.966  0.033  0.266 81.461  0.029  2.317   3.4708e-02
   5_xyz:   7.012  0.041  0.440 82.444  0.031  2.289   4.3334e-02
   5_adp:   7.012  0.041  0.440 82.444  0.031  2.289   4.3334e-02
   5_occ:   7.012  0.041  0.440 82.444  0.031  2.289   4.3334e-02
   5_bss:   7.012  0.041  0.440 82.444  0.031  2.289   4.3334e-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:  78.91   0.00  13.98  69.32   0.00  11.76  78.91   0.00  26.10
   1_occ:  78.91   0.00  13.98  69.32   0.00  11.76  78.91   0.00  26.10
   2_bss:  78.91   0.00  13.98  69.32   0.00  11.76  78.91   0.00  26.10
   2_xyz:  78.91   0.00  13.98  69.32   0.00  11.76  78.91   0.00  26.10
   2_adp:  85.40   0.00  14.05  72.47   0.00  10.72  85.40   1.75  32.21
   2_occ:  85.40   0.00  14.05  72.47   0.00  10.72  85.40   1.75  32.21
   3_bss:  85.40   0.00  14.05  72.47   0.00  10.72  85.40   1.75  32.21
   3_xyz:  85.40   0.00  14.05  72.47   0.00  10.72  85.40   1.75  32.21
   3_adp: 105.99   0.00  13.56 105.99   0.00   9.81  84.72   2.93  33.99
   3_occ: 105.99   0.00  13.56 105.99   0.00   9.81  84.72   2.93  33.99
   4_bss: 105.99   0.00  13.56 105.99   0.00   9.81  84.72   2.93  33.99
   4_xyz: 105.99   0.00  13.56 105.99   0.00   9.81  84.72   2.93  33.99
   4_adp:  86.34   0.00  13.81  77.27   0.00   9.59  86.34   2.96  36.83
   4_occ:  86.34   0.00  13.81  77.27   0.00   9.59  86.34   2.96  36.83
   5_bss:  86.34   0.00  13.81  77.27   0.00   9.59  86.34   2.96  36.83
   5_xyz:  86.34   0.00  13.81  77.27   0.00   9.59  86.34   2.96  36.83
   5_adp:  86.44   0.00  13.76  78.47   0.00   9.47  86.44   2.77  37.11
   5_occ:  86.44   0.00  13.76  78.47   0.00   9.47  86.44   2.77  37.11
   5_bss:  87.80   1.36  15.12  79.83   1.36  10.83  87.80   4.13  38.48
------------------------------------------------------------------------
 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:    1.269    0.025    0.449
   1_adp:    1.269    0.025    0.449
   1_occ:    1.269    0.025    0.449
   2_bss:    1.269    0.025    0.449
   2_xyz:    1.767    0.022    0.630
   2_adp:    1.767    0.022    0.630
   2_occ:    1.767    0.022    0.630
   3_bss:    1.767    0.022    0.630
   3_xyz:    1.860    0.052    0.728
   3_adp:    1.860    0.052    0.728
   3_occ:    1.860    0.052    0.728
   4_bss:    1.860    0.052    0.728
   4_xyz:    1.876    0.022    0.778
   4_adp:    1.876    0.022    0.778
   4_occ:    1.876    0.022    0.778
   5_bss:    1.876    0.022    0.778
   5_xyz:    1.866    0.066    0.810
   5_adp:    1.866    0.066    0.810
   5_occ:    1.866    0.066    0.810
   5_bss:    1.866    0.066    0.810
------------------------------------------------------------------------

CPU time actual refinement: 351.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/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_78/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_78/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.00 
  Macro-tasks:
    bulk solvent and scale       = 40.57  
    individual site refinement   = 154.81 
    weights calculation          = 32.05  
    collect and process          = 6.43   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 233.97 
  Micro-tasks:
    mask                            = 2.53   
    f_calc                          = 110.89 
    alpha_beta                      = 8.32   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.77 
    fmodel                         = 6.91   
    r_factors                      = 0.25   
    phase_errors                   = 10.12  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 264.20 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.846 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    661 calls, 110.58 s
gradients_fft:          605 calls, 109.48 s

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

# Date 2008-01-16 Time 00:39:51 PST -0800 (1200472791.82 s)
Start R-work = 0.5015, R-free = 0.4940 (no bulk solvent and anisotropic scale)
Final R-work = 0.1375, R-free = 0.1827 (no bulk solvent and anisotropic scale)

Start R-work = 0.4932, R-free = 0.4855
Final R-work = 0.1200, R-free = 0.1670