# Date 2008-01-16 Time 02:22:05 PST -0800 (1200478925.27 s)
#phil __OFF__

Command line arguments: "../802.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4202
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 802

-------------------------------------------------------------------------------
  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: (70.6012, 47.1647, 88.5498, 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: 3.30, 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: (70.6012, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01033
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964405

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0103

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: (70.6012, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01033
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964405

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.3012 [2138/2162]  1920   218  10.2%
  bin  2:  4.3012 -  3.4270 [2036/2056]  1838   198   9.7%
  bin  3:  3.4270 -  2.9976 [2019/2038]  1816   203  10.1%
  bin  4:  2.9976 -  2.7253 [1980/2010]  1776   204  10.3%
  bin  5:  2.7253 -  2.5309 [2002/2021]  1806   196   9.8%
  bin  6:  2.5309 -  2.3823 [1977/2002]  1778   199  10.1%
  bin  7:  2.3823 -  2.2634 [1960/1988]  1766   194   9.9%
  bin  8:  2.2634 -  2.1651 [1962/1998]  1766   196  10.0%
  bin  9:  2.1651 -  2.0820 [1946/1988]  1754   192   9.9%
  bin 10:  2.0820 -  2.0103 [1569/1986]  1410   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/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:
        1.54 -     2.21: 7
        2.21 -     2.88: 1252
        2.88 -     3.56: 4351
        3.56 -     4.23: 9046
        4.23 -     4.90: 13156
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.540 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.713 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.802 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27807 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_802/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 70.60125 47.16465 88.54975 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: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4698   r_free= 0.4618   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.271705                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.3878 0.3557      6.5964      6.4832|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.3796 0.4226      6.7616       6.906|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.4279 0.4108      6.6667      6.6509|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.4620 0.4084      6.5258      6.4249|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.4913 0.4747      6.3671      6.3872|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.4870 0.5498       6.274      6.2001|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.5108 0.4878      6.2365      6.1804|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.5244 0.4472       6.187      6.1415|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.5030 0.5545      6.1093      6.1573|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.5232 0.4743      6.1253      6.0772|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.5097 0.5317      6.0251      6.0931|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.5243 0.4918      5.9723      6.0235|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.5181 0.5281      5.8919      5.8475|
| 14:  2.0605 -  2.0103 0.71    904  106 0.5283 0.4979      5.8716      5.7512|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7971  1388   152  0.73  32.03   0.79     0.75      62346.10|
|  2:  4.7971 -  3.8278  1319   152  0.73  32.77   0.87     0.78      96063.12|
|  3:  3.8278 -  3.3499  1300   142  0.64  40.67   0.83     0.73     102147.12|
|  4:  3.3499 -  3.0464  1308   142  0.54  48.46   0.79     0.61      92352.60|
|  5:  3.0464 -  2.8295  1278   144  0.45  56.12   0.75     0.51      77291.99|
|  6:  2.8295 -  2.6636  1286   143  0.41  59.09   0.71     0.45      70713.20|
|  7:  2.6636 -  2.5309  1277   144  0.40  59.54   0.73     0.45      62229.38|
|  8:  2.5309 -  2.4212  1270   138  0.43  57.97   0.72     0.49      53382.97|
|  9:  2.4212 -  2.3283  1266   143  0.43  57.87   0.72     0.49      49699.79|
| 10:  2.3283 -  2.2482  1276   142  0.40  59.92   0.74     0.46      46397.02|
| 11:  2.2482 -  2.1781  1249   134  0.36  63.00   0.74     0.43      45855.52|
| 12:  2.1781 -  2.1161  1244   141  0.36  63.35   0.74     0.44      41627.43|
| 13:  2.1161 -  2.0605  1265   136  0.35  63.76   0.72     0.42      35864.22|
| 14:  2.0605 -  2.0103   904   106  0.37  62.14   0.72     0.38      28102.61|
|alpha:            min =        0.38 max =            0.78 mean =         0.53|
|beta:             min =    28102.61 max =       102147.12 mean =     62720.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.93 mean =        53.62|
|phase err.(test): min =        0.00 max =           89.74 mean =        53.92|
|-----------------------------------------------------------------------------|

============================== 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 = 12.770935             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.623   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.111579              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.811   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1484 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2570 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3840 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4986 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6505 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7568 |
|-----------------------------------------------------------------------------|
|-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 |       54.498 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.760 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    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 = 12.269)------------------------------------------|
|    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: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4749   r_free= 0.4590   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.275343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4602   r_free= 0.4463   ksol= 0.32   Bsol= 23.94   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.51,7.27,12.20,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.265661                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.351805             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.388   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.041141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.542   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4602      final r-factor (work) = 0.3700          |
| start r-factor (free) = 0.4463      final r-factor (free) = 0.3977          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.1032 = 11.35 * 0.50 * 6.2730 + 1.00 * 54.4980                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.1177 = 11.35 * 0.50 * 6.1622 + 1.00 * 0.1417                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3700      final r-factor (work) = 0.3222          |
| start r-factor (free) = 0.3977      final r-factor (free) = 0.3726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4301 = 1.04 * 1.00 * 6.1622 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3272 = 1.04 * 1.00 * 6.0620 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.53   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    67.53   12.77    None  None   None       |
|    Sol.    : 438    0      0.00    67.53   27.17    None  None   None       |
|    Mac.    : 2385   0      0.00    64.99   10.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.753: 1084   |   5:    33.767 -  40.520:   74        |
|      1:     6.753 -  13.507:  758   |   6:    40.520 -  47.274:   57        |
|      2:    13.507 -  20.260:  403   |   7:    47.274 -  54.027:   39        |
|      3:    20.260 -  27.014:  232   |   8:    54.027 -  60.781:   16        |
|      4:    27.014 -  33.767:  152   |   9:    60.781 -  67.534:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3222 r_free = 0.3726             target_work(ml) = 6.033         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3217 r_free = 0.3734             target_work(ml) = 6.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3217   r_free= 0.3734   ksol= 0.32   Bsol= 23.94   scale= 1.084   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.51,7.27,12.20,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.032642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3197   r_free= 0.3702   ksol= 0.33   Bsol= 61.22   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,4.11,8.41,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.034051                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.569157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.137   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.378  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3197      final r-factor (work) = 0.2348          |
| start r-factor (free) = 0.3702      final r-factor (free) = 0.2933          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0656 = 7.57 * 0.50 * 6.0572 + 1.00 * 0.1417                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4241 = 7.57 * 0.50 * 5.9016 + 1.00 * 0.0889                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2348      final r-factor (work) = 0.2112          |
| start r-factor (free) = 0.2933      final r-factor (free) = 0.2675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8675 = 0.48 * 1.00 * 5.9016 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7816 = 0.48 * 1.00 * 5.7242 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.93   12.54    None  None   None       |
|    all(noH): 2823   0      0.00    75.93   12.54    None  None   None       |
|    Sol.    : 438    0      0.00    68.39   32.48    None  None   None       |
|    Mac.    : 2385   0      0.00    75.93   8.88     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 -   7.593: 1396   |   5:    37.965 -  45.558:  100        |
|      1:     7.593 -  15.186:  683   |   6:    45.558 -  53.151:   64        |
|      2:    15.186 -  22.779:  277   |   7:    53.151 -  60.745:   23        |
|      3:    22.779 -  30.372:  147   |   8:    60.745 -  68.338:    6        |
|      4:    30.372 -  37.965:  125   |   9:    68.338 -  75.931:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2112 r_free = 0.2675             target_work(ml) = 5.688         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2110 r_free = 0.2674             target_work(ml) = 5.689         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2110   r_free= 0.2674   ksol= 0.33   Bsol= 61.22   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.34,4.11,8.41,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.688510                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2097   r_free= 0.2672   ksol= 0.33   Bsol= 61.22   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,3.03,5.51,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.689618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.203189              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.018  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.055862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.613  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2097      final r-factor (work) = 0.1552          |
| start r-factor (free) = 0.2672      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9919 = 5.20 * 0.50 * 5.7283 + 1.00 * 0.0892                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5783 = 5.20 * 0.50 * 5.5717 + 1.00 * 0.0830                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1552      final r-factor (work) = 0.1391          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1902          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4700 = 2.06 * 1.00 * 5.5717 + 1.00 * 0.0153                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0536 = 2.06 * 1.00 * 5.3689 + 1.00 * 0.0160                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.72   13.27    None  None   None       |
|    all(noH): 2823   0      0.00    87.72   13.27    None  None   None       |
|    Sol.    : 438    0      0.51    87.72   38.79    None  None   None       |
|    Mac.    : 2385   0      0.00    73.49   8.58     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 -   8.772: 1610   |   5:    43.859 -  52.630:  109        |
|      1:     8.772 -  17.544:  610   |   6:    52.630 -  61.402:   68        |
|      2:    17.544 -  26.315:  177   |   7:    61.402 -  70.174:   39        |
|      3:    26.315 -  35.087:  110   |   8:    70.174 -  78.946:    8        |
|      4:    35.087 -  43.859:   87   |   9:    78.946 -  87.717:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1391 r_free = 0.1902             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1388 r_free = 0.1899             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1388   r_free= 0.1899   ksol= 0.33   Bsol= 61.22   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,3.03,5.51,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.330229                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1387   r_free= 0.1893   ksol= 0.34   Bsol= 72.57   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.61,4.52,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.327489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.650715              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.247952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.079  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1893      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2016 = 2.65 * 0.50 * 5.3706 + 1.00 * 0.0837                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0853 = 2.65 * 0.50 * 5.2911 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1262      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6189 = 1.25 * 1.00 * 5.2911 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5594 = 1.25 * 1.00 * 5.2413 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.38   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    97.38   13.13    None  None   None       |
|    Sol.    : 438    0      0.37    97.38   38.88    None  None   None       |
|    Mac.    : 2385   0      0.00    82.37   8.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.739: 1767   |   5:    48.692 -  58.431:   94        |
|      1:     9.739 -  19.477:  523   |   6:    58.431 -  68.169:   48        |
|      2:    19.477 -  29.215:  150   |   7:    68.169 -  77.908:   25        |
|      3:    29.215 -  38.954:  123   |   8:    77.908 -  87.646:    7        |
|      4:    38.954 -  48.692:   83   |   9:    87.646 -  97.385:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1725             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1723             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1723   ksol= 0.34   Bsol= 72.57   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.61,4.52,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232657                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1722   ksol= 0.34   Bsol= 72.57   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.68,4.43,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.232652                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.773253              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.161  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330318              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.335   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9610 = 3.77 * 0.50 * 5.2413 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9128 = 3.77 * 0.50 * 5.2068 + 1.00 * 0.0895                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7371 = 0.33 * 1.00 * 5.2068 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7391 = 0.33 * 1.00 * 5.1954 + 1.00 * 0.0229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.61   12.90    None  None   None       |
|    all(noH): 2823   0      0.00    96.61   12.90    None  None   None       |
|    Sol.    : 438    0      0.90    96.61   37.93    None  None   None       |
|    Mac.    : 2385   0      0.00    84.16   8.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.661: 1814   |   5:    48.303 -  57.964:   87        |
|      1:     9.661 -  19.321:  484   |   6:    57.964 -  67.624:   44        |
|      2:    19.321 -  28.982:  146   |   7:    67.624 -  77.285:   22        |
|      3:    28.982 -  38.642:  121   |   8:    77.285 -  86.945:   10        |
|      4:    38.642 -  48.303:   92   |   9:    86.945 -  96.606:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1652             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1653             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1653   ksol= 0.34   Bsol= 72.57   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.33,2.68,4.43,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.184187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.1015 0.1395      5.4291      5.5863|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.0843 0.1164      5.4561      5.6942|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.1061 0.1496      5.4941      5.8465|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.1231 0.1699      5.4692      5.6465|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.1383 0.1696      5.3702      5.5677|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.1265 0.2258      5.2608      5.5929|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.1343 0.1700      5.2336      5.3839|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.1239 0.1705      5.1404      5.3968|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.1226 0.1948      5.0891      5.3569|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.1195 0.1736      5.0109      5.2348|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.1194 0.1781      4.9855      5.2589|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.1201 0.1889      4.9192      5.3034|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1174 0.1758      4.8266      5.0491|
| 14:  2.0605 -  2.0103 0.71    904  106 0.1071 0.1696      4.6903      4.9506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7971  1388   152  0.93   9.98   0.97     0.94       8403.40|
|  2:  4.7971 -  3.8278  1319   152  0.95   8.65   1.00     0.99       9998.12|
|  3:  3.8278 -  3.3499  1300   142  0.93  11.50   1.02     1.02      10991.25|
|  4:  3.3499 -  3.0464  1308   142  0.92  13.82   1.00     0.99      10649.35|
|  5:  3.0464 -  2.8295  1278   144  0.90  16.37   1.00     0.97       8895.03|
|  6:  2.8295 -  2.6636  1286   143  0.89  17.19   0.98     0.95       7987.52|
|  7:  2.6636 -  2.5309  1277   144  0.90  16.81   0.99     0.95       7103.04|
|  8:  2.5309 -  2.4212  1270   138  0.90  16.51   0.99     0.96       6171.78|
|  9:  2.4212 -  2.3283  1266   143  0.90  16.44   1.01     0.97       5783.68|
| 10:  2.3283 -  2.2482  1276   142  0.89  16.79   1.00     0.95       4797.22|
| 11:  2.2482 -  2.1781  1249   134  0.90  16.83   1.00     0.96       4847.03|
| 12:  2.1781 -  2.1161  1244   141  0.90  16.73   1.00     0.99       4305.79|
| 13:  2.1161 -  2.0605  1265   136  0.90  16.46   0.99     0.97       3576.53|
| 14:  2.0605 -  2.0103   904   106  0.92  14.32   0.97     0.94       2573.70|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2573.70 max =        10991.25 mean =      6995.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.84|
|phase err.(test): min =        0.00 max =           89.41 mean =        14.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1652   ksol= 0.32   Bsol= 68.33   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,-0.47,1.28,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1652   ksol= 0.32   Bsol= 68.33   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,-0.47,1.28,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183879                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7971 0.99   1388  152 0.1010 0.1393      5.4226       5.582|
|  2:  4.7971 -  3.8278 0.99   1319  152 0.0840 0.1160      5.4533      5.6902|
|  3:  3.8278 -  3.3499 0.99   1300  142 0.1060 0.1497      5.4926      5.8465|
|  4:  3.3499 -  3.0464 0.99   1308  142 0.1233 0.1699      5.4703      5.6468|
|  5:  3.0464 -  2.8295 0.99   1278  144 0.1385 0.1698      5.3718      5.5695|
|  6:  2.8295 -  2.6636 0.99   1286  143 0.1266 0.2263      5.2622      5.5947|
|  7:  2.6636 -  2.5309 0.99   1277  144 0.1345 0.1701      5.2348      5.3849|
|  8:  2.5309 -  2.4212 0.98   1270  138 0.1239 0.1705      5.1409      5.3966|
|  9:  2.4212 -  2.3283 0.98   1266  143 0.1227 0.1948      5.0893      5.3571|
| 10:  2.3283 -  2.2482 1.00   1276  142 0.1195 0.1736      5.0113      5.2352|
| 11:  2.2482 -  2.1781 0.97   1249  134 0.1194 0.1781      4.9858      5.2593|
| 12:  2.1781 -  2.1161 0.98   1244  141 0.1201 0.1890      4.9194      5.3036|
| 13:  2.1161 -  2.0605 1.00   1265  136 0.1174 0.1759      4.8268      5.0493|
| 14:  2.0605 -  2.0103 0.71    904  106 0.1072 0.1697      4.6906      4.9509|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7971  1388   152  0.93   9.94   0.97     0.94       8315.11|
|  2:  4.7971 -  3.8278  1319   152  0.95   8.59   1.00     0.99       9934.54|
|  3:  3.8278 -  3.3499  1300   142  0.93  11.47   1.02     1.02      10954.16|
|  4:  3.3499 -  3.0464  1308   142  0.92  13.83   1.00     0.99      10659.57|
|  5:  3.0464 -  2.8295  1278   144  0.90  16.38   1.00     0.97       8919.94|
|  6:  2.8295 -  2.6636  1286   143  0.89  17.22   0.98     0.95       8011.31|
|  7:  2.6636 -  2.5309  1277   144  0.90  16.83   0.99     0.95       7121.21|
|  8:  2.5309 -  2.4212  1270   138  0.90  16.52   0.99     0.96       6176.66|
|  9:  2.4212 -  2.3283  1266   143  0.90  16.44   1.01     0.97       5787.94|
| 10:  2.3283 -  2.2482  1276   142  0.89  16.79   1.00     0.95       4799.88|
| 11:  2.2482 -  2.1781  1249   134  0.90  16.84   0.99     0.96       4850.83|
| 12:  2.1781 -  2.1161  1244   141  0.90  16.74   1.00     0.99       4308.80|
| 13:  2.1161 -  2.0605  1265   136  0.90  16.47   0.99     0.97       3578.58|
| 14:  2.0605 -  2.0103   904   106  0.92  14.32   0.97     0.94       2575.26|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2575.26 max =        10954.16 mean =      6987.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.84|
|phase err.(test): min =        0.00 max =           89.25 mean =        14.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.269)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.15    99.75   16.04    None  None   None       |
|    all(noH): 2823   0      3.15    99.75   16.04    None  None   None       |
|    Sol.    : 438    0      4.04    99.75   41.07    None  None   None       |
|    Mac.    : 2385   0      3.15    87.30   11.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.147 -  12.807: 1814   |   5:    51.450 -  61.110:   87        |
|      1:    12.807 -  22.468:  484   |   6:    61.110 -  70.771:   44        |
|      2:    22.468 -  32.129:  146   |   7:    70.771 -  80.431:   22        |
|      3:    32.129 -  41.789:  121   |   8:    80.431 -  90.092:   10        |
|      4:    41.789 -  51.450:   92   |   9:    90.092 -  99.753:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.221 - 4.948
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 323
   mapped sites are within: 0.729 - 4.948

peak=   10.716 closest distance to " CB  VAL A 230 " =    1.453
peak=    6.028 closest distance to " CG  LEU A   5 " =    1.258
peak=    5.634 closest distance to " NH2 ARG A  56 " =    2.146
peak=    5.417 closest distance to " CG  LEU A 228 " =    1.214
peak=    5.405 closest distance to " CB  GLN A 223 " =    1.539
peak=    5.287 closest distance to " NE2 GLN A  11 " =    1.096
peak=    5.129 closest distance to " CB  VAL A 296 " =    1.078
peak=    4.919 closest distance to " O   HOH Z 142 " =    1.822
peak=    4.828 closest distance to " CG2 VAL A 296 " =    1.032
peak=    4.827 closest distance to " CD2 LEU A   5 " =    1.121
peak=    4.805 closest distance to " O   HOH Z 232 " =    2.262
peak=    4.734 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.635 closest distance to " CB  ASN A 142 " =    1.149
peak=    4.610 closest distance to " CG  PRO A  54 " =    1.266
peak=    4.518 closest distance to " O   HOH Z 425 " =    1.546
peak=    4.511 closest distance to " O   HOH Z 265 " =    2.051
peak=    4.497 closest distance to " CB  ARG A 190 " =    1.442
peak=    4.477 closest distance to " O   HOH Z 126 " =    1.643
peak=    4.428 closest distance to " O   HOH Z 248 " =    1.510
peak=    4.419 closest distance to " O   HOH Z 369 " =    2.182
peak=    4.400 closest distance to " O   HOH Z 427 " =    3.091
peak=    4.390 closest distance to " CB  SER A  63 " =    1.174
peak=    4.386 closest distance to " O   HOH Z 303 " =    2.152
peak=    4.361 closest distance to " O   SER A  87 " =    2.361
peak=    4.336 closest distance to " CZ  PHE A 218 " =    1.172
peak=    4.310 closest distance to " CA  ALA A  51 " =    0.974
peak=    4.258 closest distance to " CB  ASP A 124 " =    0.733
peak=    4.240 closest distance to " CB  PRO A  54 " =    0.949
peak=    4.238 closest distance to " O   HOH Z   9 " =    1.486
peak=    4.225 closest distance to " O   HOH Z 411 " =    3.875
peak=    4.209 closest distance to " O   HOH Z 368 " =    2.371
peak=    4.196 closest distance to " CG  PRO A 243 " =    1.121
peak=    4.194 closest distance to " O  BHOH Z 338 " =    2.333
peak=    4.188 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    4.181 closest distance to " CB  ASN A 148 " =    1.442
peak=    4.170 closest distance to " O   HOH Z 188 " =    2.907
peak=    4.144 closest distance to " CB  ARG A 275 " =    0.970
peak=    4.140 closest distance to " O   HOH Z 251 " =    1.657
peak=    4.129 closest distance to " ND2 ASN A 187 " =    1.596
peak=    4.113 closest distance to " O   HOH Z 359 " =    1.785
peak=    4.076 closest distance to " O   HOH Z 313 " =    1.844
peak=    4.065 closest distance to " CB  VAL A 265 " =    1.355
peak=    4.064 closest distance to " CB  ARG A  79 " =    1.507
peak=    4.062 closest distance to " CB  GLU A 277 " =    3.745
peak=    4.057 closest distance to " CB  GLU A 152 " =    1.206
peak=    4.044 closest distance to " CG  MET A 185 " =    1.217
peak=    4.035 closest distance to " O   PRO A 198 " =    1.540
peak=    4.033 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.014 closest distance to " O   HOH Z 126 " =    1.919
peak=    3.979 closest distance to " O   HOH Z 290 " =    1.119
peak=    3.949 closest distance to " O   HOH Z 346 " =    1.556
peak=    3.948 closest distance to " O   HOH Z  19 " =    2.309
peak=    3.943 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.940 closest distance to " O   HOH Z 353 " =    2.584
peak=    3.934 closest distance to " O   HOH Z 287 " =    1.993
peak=    3.931 closest distance to " CG1 ILE A  49 " =    1.561
peak=    3.922 closest distance to " CD  LYS A 166 " =    1.353
peak=    3.899 closest distance to " O   HOH Z  61 " =    1.740
peak=    3.879 closest distance to " CB  ASP A 140 " =    0.995
peak=    3.862 closest distance to " CG  PRO A 213 " =    1.157
peak=    3.856 closest distance to " O   HOH Z  76 " =    1.158
peak=    3.844 closest distance to " CD2 LEU A 228 " =    1.228
peak=    3.841 closest distance to " CG  LEU A 167 " =    1.202
peak=    3.839 closest distance to " O   HOH Z  78 " =    1.623
peak=    3.810 closest distance to " CE  LYS A  76 " =    0.897
peak=    3.807 closest distance to " O   HOH Z 298 " =    1.878
peak=    3.803 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.801 closest distance to " CA  ARG A 195 " =    1.269
peak=    3.797 closest distance to " CG  PRO A 198 " =    1.338
peak=    3.793 closest distance to " CD2 TRP A 179 " =    1.268
peak=    3.791 closest distance to " CA  ALA A 295 " =    1.110
peak=    3.788 closest distance to " CB  VAL A 202 " =    1.574
peak=    3.784 closest distance to " O   HOH Z 214 " =    1.210
peak=    3.777 closest distance to " O   HOH Z 158 " =    3.178
peak=    3.770 closest distance to " N   ASN A  39 " =    1.246
peak=    3.746 closest distance to " O   HOH Z 273 " =    2.920
peak=    3.746 closest distance to " O   HOH Z 422 " =    2.627
peak=    3.745 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.740 closest distance to " O   HOH Z 128 " =    0.995
peak=    3.730 closest distance to " O   HOH Z 234 " =    3.608
peak=    3.728 closest distance to " CB  TRP A 266 " =    1.037
peak=    3.723 closest distance to " CB  ALA A   9 " =    1.658
peak=    3.708 closest distance to " O   HOH Z 406 " =    1.573
peak=    3.698 closest distance to " O   HOH Z  59 " =    2.253
peak=    3.693 closest distance to " O   HOH Z 423 " =    1.808
peak=    3.677 closest distance to " O   HOH Z 214 " =    2.287
peak=    3.669 closest distance to " CG AARG A 102 " =    1.092
peak=    3.666 closest distance to " CA  ASP A 162 " =    0.859
peak=    3.665 closest distance to " NH1AARG A 145 " =    1.271
peak=    3.655 closest distance to " CA  ALA A 158 " =    1.216
peak=    3.651 closest distance to " CA  ALA A 160 " =    1.045
peak=    3.649 closest distance to " CB  PRO A  90 " =    1.246
peak=    3.635 closest distance to " ND2 ASN A 249 " =    1.929
peak=    3.631 closest distance to " CA  TYR A 116 " =    1.434
peak=    3.627 closest distance to " O   HOH Z  80 " =    1.786
peak=    3.627 closest distance to " CD  PRO A  54 " =    0.970
peak=    3.624 closest distance to " CG1 VAL A 296 " =    1.213
peak=    3.618 closest distance to " CB  GLN A  89 " =    1.195
peak=    3.616 closest distance to " CB  THR A  31 " =    1.585
peak=    3.614 closest distance to " OD1 ASN A  69 " =    2.495
peak=    3.609 closest distance to " O   ASN A 284 " =    1.739
peak=    3.609 closest distance to " O   HOH Z  43 " =    2.079
peak=    3.604 closest distance to " O   HOH Z 299 " =    4.309
peak=    3.600 closest distance to " O   ALA A 158 " =    1.305
peak=    3.599 closest distance to " CA  MET A 105 " =    0.983
peak=    3.595 closest distance to " CA  THR A 264 " =    0.831
peak=    3.592 closest distance to " O   HOH Z 227 " =    1.762
peak=    3.587 closest distance to " CG  PHE A 204 " =    0.945
peak=    3.587 closest distance to " O   HOH Z 272 " =    1.847
peak=    3.586 closest distance to " O   ASP A 124 " =    1.198
peak=    3.586 closest distance to " CB  ASP A 298 " =    1.159
peak=    3.585 closest distance to " O   HOH Z  97 " =    2.043
peak=    3.579 closest distance to " OE2 GLU A  53 " =    2.047
peak=    3.565 closest distance to " CG AARG A 275 " =    1.354
peak=    3.564 closest distance to " CB  GLN A 205 " =    1.111
peak=    3.564 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.562 closest distance to " CB  GLU A 128 " =    1.003
peak=    3.562 closest distance to " NE2 GLN A  77 " =    3.347
peak=    3.556 closest distance to " CB AVAL A  41 " =    1.294
peak=    3.555 closest distance to " CB  ASN A  39 " =    0.892
peak=    3.554 closest distance to " OG BSER A 164 " =    2.280
peak=    3.551 closest distance to " O   HOH Z  49 " =    1.063
peak=    3.548 closest distance to " O   HOH Z 154 " =    1.390
peak=    3.546 closest distance to " CD1 ILE A  33 " =    1.771
peak=    3.545 closest distance to " CB  ARG A  79 " =    0.946
peak=    3.545 closest distance to " O   HOH Z 171 " =    4.047
peak=    3.543 closest distance to " CD1 LEU A  96 " =    0.815
peak=    3.538 closest distance to " CB  LEU A 143 " =    1.232
peak=    3.536 closest distance to " CD1 ILE A 199 " =    1.154
peak=    3.535 closest distance to " O   HOH Z 371 " =    2.750
peak=    3.531 closest distance to " O   HOH Z 197 " =    2.908
peak=    3.530 closest distance to " CB  TRP A 179 " =    1.392
peak=    3.526 closest distance to " CB  VAL A 230 " =    1.212
peak=    3.524 closest distance to " CG  MET A 185 " =    1.038
peak=    3.521 closest distance to " CA  VAL A 125 " =    1.181
peak=    3.519 closest distance to " CD  ARG A  66 " =    2.550
peak=    3.518 closest distance to " O   HOH Z 313 " =    1.405
peak=    3.513 closest distance to " CA  SER A  87 " =    0.952
peak=    3.508 closest distance to " O   GLN A  88 " =    1.681
peak=    3.507 closest distance to " NZ  LYS A  48 " =    1.242
peak=    3.504 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.503 closest distance to " CG  GLU A  37 " =    1.037
peak=    3.497 closest distance to " CA  ALA A 291 " =    0.879
peak=    3.493 closest distance to " CA  LEU A 282 " =    1.152
peak=    3.491 closest distance to " O   HOH Z 368 " =    3.391
peak=    3.487 closest distance to " O   HOH Z 261 " =    2.109
peak=    3.485 closest distance to " CA  ASP A 191 " =    1.206
peak=    3.485 closest distance to " CG2 THR A 221 " =    1.109
peak=    3.483 closest distance to " CG2 VAL A 257 " =    0.837
peak=    3.480 closest distance to " CB  ASN A 148 " =    2.002
peak=    3.473 closest distance to " O   HOH Z  63 " =    1.818
peak=    3.470 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.468 closest distance to " CB  THR A  82 " =    1.257
peak=    3.465 closest distance to " CB  TRP A 150 " =    1.387
peak=    3.459 closest distance to " CG2AVAL A 121 " =    2.293
peak=    3.454 closest distance to " N   PHE A 130 " =    1.288
peak=    3.442 closest distance to " O   MET A 105 " =    1.763
peak=    3.437 closest distance to " NH2AARG A 145 " =    1.189
peak=    3.428 closest distance to " O   HOH Z 285 " =    2.081
peak=    3.426 closest distance to " CB  GLN A  88 " =    1.183
peak=    3.425 closest distance to " O   HOH Z 357 " =    2.723
peak=    3.422 closest distance to " O   HOH Z   3 " =    1.751
peak=    3.422 closest distance to " O   HOH Z  10 " =    1.768
peak=    3.420 closest distance to " OG  SER A 245 " =    1.617
peak=    3.419 closest distance to " CA  ILE A 106 " =    0.768
peak=    3.416 closest distance to " CZ  PHE A  38 " =    1.145
peak=    3.415 closest distance to " O   HOH Z 258 " =    2.040
peak=    3.409 closest distance to " CB  ALA A 104 " =    0.729
peak=    3.405 closest distance to " OE1 GLN A  55 " =    1.538
peak=    3.404 closest distance to " O   HOH Z 145 " =    2.145
peak=    3.404 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.403 closest distance to " CB  ASN A 215 " =    1.223
peak=    3.399 closest distance to " ND2 ASN A 249 " =    0.876
peak=    3.397 closest distance to " NZ  LYS A 117 " =    3.217
peak=    3.395 closest distance to " O   HOH Z 316 " =    3.142
peak=    3.392 closest distance to " NH2AARG A 275 " =    3.363
peak=    3.387 closest distance to " CA  ALA A  21 " =    1.084
peak=    3.385 closest distance to " CB  VAL A 257 " =    0.747
peak=    3.384 closest distance to " O   HOH Z 365 " =    2.852
peak=    3.377 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.369 closest distance to " OD2 ASP A 298 " =    3.983
peak=    3.366 closest distance to " CG1 VAL A 153 " =    0.976
peak=    3.365 closest distance to " O   HOH Z 361 " =    3.749
peak=    3.363 closest distance to " CA  GLU A 152 " =    0.933
peak=    3.357 closest distance to " O   HOH Z 148 " =    3.365
peak=    3.356 closest distance to " CB  ASN A 173 " =    1.008
peak=    3.348 closest distance to " CB  SER A 212 " =    1.310
peak=    3.345 closest distance to " CB  ALA A 248 " =    1.123
peak=    3.337 closest distance to " O   HOH Z  44 " =    2.214
peak=    3.337 closest distance to " CA  ALA A 100 " =    0.892
peak=    3.336 closest distance to " NE2 HIS A 207 " =    1.209
peak=    3.335 closest distance to " O   HOH Z 203 " =    1.633
peak=    3.332 closest distance to " O   HOH Z  88 " =    3.301
peak=    3.324 closest distance to " ND1 HIS A  81 " =    1.733
peak=    3.323 closest distance to " CA  ASN A 127 " =    1.014
peak=    3.321 closest distance to " CG2AVAL A  72 " =    1.824
peak=    3.317 closest distance to " NH2 ARG A 156 " =    1.100
peak=    3.312 closest distance to " O   HOH Z 403 " =    1.654
peak=    3.311 closest distance to " CA  LYS A 117 " =    1.268
peak=    3.310 closest distance to " CD1 LEU A 300 " =    1.103
peak=    3.310 closest distance to " O   PHE A 192 " =    1.472
peak=    3.308 closest distance to " O   HOH Z 261 " =    1.594
peak=    3.299 closest distance to " CD  LYS A 119 " =    2.013
peak=    3.299 closest distance to " CG2 ILE A 234 " =    1.118
peak=    3.299 closest distance to " O   HOH Z 213 " =    1.913
peak=    3.295 closest distance to " O   HOH Z 417 " =    3.320
peak=    3.293 closest distance to " CB  SER A  26 " =    1.865
peak=    3.291 closest distance to " CB  ALA A 227 " =    1.090
peak=    3.291 closest distance to " CB  ASN A 110 " =    1.142
peak=    3.291 closest distance to " CA  TYR A  30 " =    1.068
peak=    3.288 closest distance to " O   HOH Z 211 " =    1.057
peak=    3.287 closest distance to " O   HOH Z 166 " =    3.799
peak=    3.285 closest distance to " OG  SER A  22 " =    2.818
peak=    3.284 closest distance to " O   HOH Z 238 " =    2.232
peak=    3.283 closest distance to " CB  THR A  52 " =    0.928
peak=    3.282 closest distance to " CA  GLN A  94 " =    0.754
peak=    3.279 closest distance to " O   HOH Z  30 " =    1.294
peak=    3.273 closest distance to " CG1 ILE A  20 " =    1.343
peak=    3.270 closest distance to " CB  PHE A 204 " =    0.967
peak=    3.269 closest distance to " CE3 TRP A 150 " =    1.061
peak=    3.267 closest distance to " O   HOH Z  40 " =    1.739
peak=    3.266 closest distance to " CD ALYS A 290 " =    1.066
peak=    3.262 closest distance to " O   HOH Z  88 " =    3.035
peak=    3.256 closest distance to " O   ASN A  74 " =    1.464
peak=    3.255 closest distance to " CA  GLY A 267 " =    0.801
peak=    3.255 closest distance to " O   HOH Z  68 " =    2.142
peak=    3.252 closest distance to " O   HOH Z 193 " =    1.938
peak=    3.252 closest distance to " N   ASP A 162 " =    1.252
peak=    3.246 closest distance to " O   HOH Z  78 " =    1.841
peak=    3.241 closest distance to " O   HOH Z 185 " =    2.437
peak=    3.240 closest distance to " O   HOH Z 215 " =    3.028
peak=    3.238 closest distance to " O   HOH Z 394 " =    3.839
peak=    3.235 closest distance to " CA  ARG A 139 " =    1.165
peak=    3.235 closest distance to " CB  PRO A 243 " =    1.810
peak=    3.233 closest distance to " OG1 THR A 279 " =    1.444
peak=    3.230 closest distance to " CZ3 TRP A 274 " =    4.548
peak=    3.230 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.230 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.229 closest distance to " O   HOH Z 430 " =    1.559
peak=    3.229 closest distance to " OG  SER A  62 " =    2.941
peak=    3.223 closest distance to " CB  ARG A 138 " =    1.028
peak=    3.222 closest distance to " CE  MET A 113 " =    1.813
peak=    3.222 closest distance to " CG BARG A 275 " =    1.382
peak=    3.220 closest distance to " CB  SER A 288 " =    1.449
peak=    3.211 closest distance to " O   HOH Z 199 " =    1.616
peak=    3.209 closest distance to " CB  LYS A 117 " =    1.192
peak=    3.208 closest distance to " CB  ASN A 187 " =    1.136
peak=    3.207 closest distance to " O   TYR A 116 " =    1.265
peak=    3.206 closest distance to " O   HOH Z 390 " =    2.700
peak=    3.206 closest distance to " O   HOH Z 298 " =    2.444
peak=    3.203 closest distance to " O   HOH Z 162 " =    3.841
peak=    3.203 closest distance to " O   HOH Z 402 " =    1.354
peak=    3.202 closest distance to " CG2 ILE A  20 " =    1.476
peak=    3.200 closest distance to " CG BARG A 102 " =    1.828
peak=    3.200 closest distance to " O   HOH Z 327 " =    2.421
peak=    3.200 closest distance to " CA  ALA A 129 " =    1.458
peak=    3.199 closest distance to " CA  ARG A  24 " =    0.803
peak=    3.199 closest distance to " CB  SER A   3 " =    1.416
peak=    3.197 closest distance to " OD1 ASN A 217 " =    1.570
peak=    3.195 closest distance to " O   HOH Z 141 " =    1.626
peak=    3.193 closest distance to " CA  GLY A 211 " =    1.427
peak=    3.190 closest distance to " N   ALA A 256 " =    1.153
peak=    3.190 closest distance to " CG2 ILE A 120 " =    1.263
peak=    3.188 closest distance to " C   ALA A 299 " =    0.894
peak=    3.184 closest distance to " CB  TYR A 116 " =    0.928
peak=    3.184 closest distance to " OG BSER A  99 " =    2.265
peak=    3.183 closest distance to " OD2 ASP A  65 " =    2.904
peak=    3.181 closest distance to " OG  SER A  62 " =    2.943
peak=    3.179 closest distance to " O   HOH Z  48 " =    1.594
peak=    3.179 closest distance to " CB  SER A  62 " =    1.093
peak=    3.176 closest distance to " CB  LEU A 300 " =    0.898
peak=    3.171 closest distance to " CB  ALA A   1 " =    4.948
peak=    3.169 closest distance to " CB  LEU A  96 " =    1.342
peak=    3.169 closest distance to " O   ILE A  49 " =    1.089
peak=    3.166 closest distance to " CB  ASN A 285 " =    0.979
peak=    3.164 closest distance to " CD  LYS A  76 " =    1.859
peak=    3.164 closest distance to " O   HOH Z 409 " =    3.146
peak=    3.161 closest distance to " CB  ALA A  43 " =    0.893
peak=    3.159 closest distance to " O   HOH Z 193 " =    1.625
peak=    3.150 closest distance to " CA  ALA A 154 " =    1.084
peak=    3.148 closest distance to " O   HOH Z 148 " =    2.093
peak=    3.147 closest distance to " O   HOH Z 305 " =    3.546
peak=    3.129 closest distance to " CD1 ILE A 263 " =    1.171
peak=    3.128 closest distance to " CB  ALA A 248 " =    1.437
peak=    3.125 closest distance to " N   CYS A 260 " =    0.759
peak=    3.125 closest distance to " O   GLU A   2 " =    1.738
peak=    3.124 closest distance to " O   HOH Z 116 " =    1.829
peak=    3.124 closest distance to " O   HOH Z 393 " =    3.090
peak=    3.124 closest distance to " O   THR A 220 " =    1.280
peak=    3.119 closest distance to " CB  LEU A 228 " =    1.243
peak=    3.114 closest distance to " CA  ASP A 149 " =    1.170
peak=    3.111 closest distance to " CG1 VAL A 174 " =    1.113
peak=    3.102 closest distance to " O   HOH Z 329 " =    4.210
peak=    3.101 closest distance to " CZ3 TRP A  92 " =    1.455
peak=    3.099 closest distance to " O   HOH Z 238 " =    3.630
peak=    3.098 closest distance to " O   PRO A 213 " =    1.492
peak=    3.095 closest distance to " CB  ALA A 242 " =    0.761
peak=    3.094 closest distance to " CB  VAL A 268 " =    0.873
peak=    3.092 closest distance to " O   THR A 182 " =    1.415
peak=    3.089 closest distance to " O   ASP A 200 " =    1.558
peak=    3.088 closest distance to " O   HOH Z 185 " =    1.990
peak=    3.086 closest distance to " CG  GLN A  88 " =    1.119
peak=    3.081 closest distance to " CB  SER A  97 " =    1.158
peak=    3.078 closest distance to " CZ3 TRP A  85 " =    1.136
peak=    3.077 closest distance to " CB  SER A 216 " =    0.831
peak=    3.066 closest distance to " CB  GLU A  37 " =    0.976
peak=    3.063 closest distance to " O   HOH Z 256 " =    2.313
peak=    3.063 closest distance to " O   HOH Z 201 " =    2.966
peak=    3.055 closest distance to " O   HOH Z 258 " =    1.506
peak=    3.053 closest distance to " CG  GLN A  55 " =    2.492
peak=    3.048 closest distance to " CB  ASP A 171 " =    1.171
peak=    3.044 closest distance to " O   HOH Z 171 " =    4.407
peak=    3.043 closest distance to " CA  ALA A 184 " =    1.110
peak=    3.035 closest distance to " CD  ARG A  66 " =    2.340
peak=    3.032 closest distance to " O   HOH Z 263 " =    1.651
peak=    3.026 closest distance to " CG2BVAL A 121 " =    0.784

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 220         
Filter by distance & map next to the model:
   mapped sites are within: 0.741 - 5.670
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 220
   mapped sites are within: 0.741 - 5.670

peak=   -4.769 closest distance to " CG2 VAL A 230 " =    0.741
peak=   -4.754 closest distance to " O   HOH Z 211 " =    0.863
peak=   -4.616 closest distance to " CD  ARG A  14 " =    3.255
peak=   -4.590 closest distance to " CB  PRO A 243 " =    2.720
peak=   -4.581 closest distance to " CG1 VAL A 250 " =    2.808
peak=   -4.433 closest distance to " CG1 VAL A 112 " =    2.663
peak=   -4.317 closest distance to " O   HOH Z 193 " =    1.179
peak=   -4.247 closest distance to " CD  GLN A  58 " =    1.017
peak=   -4.240 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.180 closest distance to " O   VAL A  67 " =    2.700
peak=   -4.112 closest distance to " O   HOH Z 411 " =    5.607
peak=   -4.082 closest distance to " CD1 LEU A 101 " =    2.425
peak=   -4.071 closest distance to " CA  ASP A 298 " =    1.110
peak=   -4.063 closest distance to " O   HOH Z 196 " =    2.211
peak=   -4.054 closest distance to " O   HOH Z 394 " =    1.578
peak=   -4.050 closest distance to " CG  GLN A 223 " =    2.281
peak=   -3.941 closest distance to " O   HOH Z 166 " =    1.826
peak=   -3.938 closest distance to " O   HOH Z 283 " =    2.511
peak=   -3.905 closest distance to " C   HIS A 108 " =    1.228
peak=   -3.878 closest distance to " OG  SER A  97 " =    2.387
peak=   -3.867 closest distance to " OG BSER A 134 " =    1.333
peak=   -3.825 closest distance to " O   HOH Z 231 " =    2.206
peak=   -3.818 closest distance to " CB  PHE A 192 " =    1.995
peak=   -3.808 closest distance to " CB  ALA A 161 " =    2.587
peak=   -3.805 closest distance to " CE2 TRP A  70 " =    2.176
peak=   -3.799 closest distance to " CE BMET A  47 " =    1.673
peak=   -3.798 closest distance to " CZ2 TRP A  92 " =    2.841
peak=   -3.770 closest distance to " CE3 TRP A 150 " =    2.260
peak=   -3.765 closest distance to " O   PRO A 163 " =    2.172
peak=   -3.762 closest distance to " CA  VAL A  67 " =    2.881
peak=   -3.747 closest distance to " O   SER A 271 " =    2.102
peak=   -3.743 closest distance to " O   HOH Z 351 " =    1.641
peak=   -3.731 closest distance to " CE2 TYR A  30 " =    2.645
peak=   -3.716 closest distance to " O   HOH Z 290 " =    1.316
peak=   -3.696 closest distance to " CG1 VAL A 112 " =    2.713
peak=   -3.693 closest distance to " CE3 TRP A  70 " =    1.756
peak=   -3.692 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.691 closest distance to " CZ3 TRP A 179 " =    1.216
peak=   -3.683 closest distance to " CA  GLY A 241 " =    3.256
peak=   -3.682 closest distance to " CD2 TYR A 293 " =    2.025
peak=   -3.679 closest distance to " O   HOH Z 133 " =    1.170
peak=   -3.660 closest distance to " CA  GLY A 241 " =    2.428
peak=   -3.659 closest distance to " O   HOH Z 198 " =    2.077
peak=   -3.652 closest distance to " O   HOH Z  38 " =    1.736
peak=   -3.650 closest distance to " CB  VAL A 230 " =    1.106
peak=   -3.645 closest distance to " O   HOH Z 128 " =    2.501
peak=   -3.637 closest distance to " CB  ALA A 248 " =    2.175
peak=   -3.632 closest distance to " CB  ALA A 248 " =    2.333
peak=   -3.631 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.630 closest distance to " O   HOH Z  10 " =    1.486
peak=   -3.629 closest distance to " N   ALA A  43 " =    2.731
peak=   -3.620 closest distance to " CG  LYS A 193 " =    2.713
peak=   -3.606 closest distance to " CE2 PHE A  61 " =    2.638
peak=   -3.605 closest distance to " CD1 ILE A 151 " =    2.465
peak=   -3.596 closest distance to " O   HOH Z 295 " =    1.612
peak=   -3.592 closest distance to " OD1 ASN A 148 " =    1.467
peak=   -3.591 closest distance to " O   HOH Z 103 " =    1.847
peak=   -3.587 closest distance to " CD2 PHE A  61 " =    2.068
peak=   -3.586 closest distance to " O   HOH Z 377 " =    2.075
peak=   -3.586 closest distance to " O   HOH Z 359 " =    2.870
peak=   -3.585 closest distance to " C   ALA A 158 " =    1.350
peak=   -3.572 closest distance to " CG1 VAL A 296 " =    1.271
peak=   -3.568 closest distance to " CD1 PHE A  59 " =    2.090
peak=   -3.567 closest distance to " O   HOH Z 136 " =    2.607
peak=   -3.561 closest distance to " O   HOH Z 145 " =    1.271
peak=   -3.547 closest distance to " O   HOH Z 285 " =    2.153
peak=   -3.546 closest distance to " OG  SER A  87 " =    1.500
peak=   -3.541 closest distance to " NE2 GLN A 194 " =    1.921
peak=   -3.534 closest distance to " O   HOH Z 177 " =    1.833
peak=   -3.530 closest distance to " O   HOH Z 216 " =    0.993
peak=   -3.530 closest distance to " N   THR A  52 " =    1.634
peak=   -3.522 closest distance to " O   HOH Z 251 " =    5.086
peak=   -3.521 closest distance to " OG  SER A  62 " =    4.355
peak=   -3.516 closest distance to " O   HOH Z  44 " =    2.493
peak=   -3.508 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.505 closest distance to " CG2AVAL A  41 " =    2.887
peak=   -3.498 closest distance to " CG2 VAL A 296 " =    1.168
peak=   -3.485 closest distance to " O   HOH Z 232 " =    1.835
peak=   -3.481 closest distance to " O   HOH Z 357 " =    2.093
peak=   -3.478 closest distance to " OE1 GLN A  88 " =    1.083
peak=   -3.472 closest distance to " NH2AARG A 275 " =    5.211
peak=   -3.457 closest distance to " O   HOH Z 275 " =    1.583
peak=   -3.454 closest distance to " OXT GLY A 302 " =    3.061
peak=   -3.450 closest distance to " CG1 VAL A 125 " =    1.867
peak=   -3.444 closest distance to " CG  GLU A 277 " =    1.266
peak=   -3.442 closest distance to " N   ALA A 226 " =    2.097
peak=   -3.442 closest distance to " CG1 VAL A 112 " =    2.778
peak=   -3.438 closest distance to " CB  HIS A  86 " =    1.194
peak=   -3.436 closest distance to " ND2 ASN A  45 " =    2.057
peak=   -3.427 closest distance to " O   ALA A 227 " =    1.406
peak=   -3.424 closest distance to " O   HOH Z 185 " =    2.447
peak=   -3.418 closest distance to " O   HOH Z 252 " =    3.693
peak=   -3.417 closest distance to " O   HOH Z  52 " =    1.622
peak=   -3.411 closest distance to " CG2 VAL A 202 " =    2.765
peak=   -3.409 closest distance to " CG2BVAL A  41 " =    1.829
peak=   -3.402 closest distance to " O   SER A 210 " =    1.884
peak=   -3.401 closest distance to " CG2 VAL A 189 " =    2.024
peak=   -3.394 closest distance to " CD  GLN A 223 " =    1.366
peak=   -3.392 closest distance to " O   HOH Z 102 " =    1.652
peak=   -3.392 closest distance to " CG  PRO A 163 " =    2.170
peak=   -3.386 closest distance to " O   HOH Z 149 " =    2.193
peak=   -3.384 closest distance to " OH  TYR A 172 " =    1.726
peak=   -3.383 closest distance to " C   LEU A 143 " =    1.060
peak=   -3.382 closest distance to " O   HOH Z  68 " =    1.436
peak=   -3.382 closest distance to " ND2 ASN A 249 " =    2.428
peak=   -3.378 closest distance to " O   HOH Z 411 " =    1.519
peak=   -3.364 closest distance to " O   HOH Z 106 " =    1.957
peak=   -3.358 closest distance to " O   HOH Z 174 " =    2.356
peak=   -3.352 closest distance to " OD1 ASP A 171 " =    1.644
peak=   -3.348 closest distance to " CA  GLY A  98 " =    2.039
peak=   -3.346 closest distance to " CG  GLU A  53 " =    1.755
peak=   -3.344 closest distance to " O   HOH Z  78 " =    1.988
peak=   -3.344 closest distance to " CB  ALA A  10 " =    2.318
peak=   -3.327 closest distance to " O   HOH Z 434 " =    1.614
peak=   -3.325 closest distance to " O   HOH Z 407 " =    3.049
peak=   -3.325 closest distance to " CD  PRO A 213 " =    2.113
peak=   -3.325 closest distance to " CD1 LEU A   5 " =    2.445
peak=   -3.322 closest distance to " O   TYR A 186 " =    1.855
peak=   -3.321 closest distance to " N   PHE A  59 " =    2.017
peak=   -3.317 closest distance to " NH2 ARG A 159 " =    2.411
peak=   -3.315 closest distance to " O   HOH Z 426 " =    1.729
peak=   -3.313 closest distance to " CA  GLY A 203 " =    2.564
peak=   -3.311 closest distance to " NE2 GLN A  88 " =    1.069
peak=   -3.309 closest distance to " CD  PRO A 243 " =    1.969
peak=   -3.309 closest distance to " CG  TRP A 266 " =    1.781
peak=   -3.299 closest distance to " O   HOH Z 131 " =    4.055
peak=   -3.299 closest distance to " C   MET A 188 " =    1.425
peak=   -3.298 closest distance to " CD1 LEU A 228 " =    2.316
peak=   -3.293 closest distance to " CZ  PHE A  38 " =    2.458
peak=   -3.293 closest distance to " O   HOH Z 100 " =    1.228
peak=   -3.293 closest distance to " O   HOH Z 123 " =    2.420
peak=   -3.285 closest distance to " CA  GLY A 133 " =    2.309
peak=   -3.278 closest distance to " O   HOH Z 166 " =    1.819
peak=   -3.277 closest distance to " O   HOH Z 140 " =    1.548
peak=   -3.275 closest distance to " N   TRP A 274 " =    1.156
peak=   -3.274 closest distance to " ND2BASN A 224 " =    1.875
peak=   -3.270 closest distance to " O   HOH Z 238 " =    1.053
peak=   -3.267 closest distance to " CG2 ILE A 263 " =    2.400
peak=   -3.266 closest distance to " N   SER A 276 " =    1.482
peak=   -3.263 closest distance to " CD  LYS A 289 " =    2.396
peak=   -3.263 closest distance to " CD1 ILE A  33 " =    2.496
peak=   -3.261 closest distance to " O   GLY A  17 " =    1.256
peak=   -3.261 closest distance to " CB  ALA A 291 " =    2.323
peak=   -3.260 closest distance to " CB  TYR A  15 " =    2.182
peak=   -3.256 closest distance to " O   HOH Z 435 " =    2.806
peak=   -3.254 closest distance to " OD2 ASP A  50 " =    2.214
peak=   -3.253 closest distance to " O   HOH Z 236 " =    1.427
peak=   -3.251 closest distance to " O   HOH Z 228 " =    1.741
peak=   -3.250 closest distance to " CB  PRO A 163 " =    2.469
peak=   -3.247 closest distance to " N   ALA A 248 " =    2.466
peak=   -3.247 closest distance to " O   HOH Z 421 " =    3.228
peak=   -3.246 closest distance to " CG1BVAL A  72 " =    2.531
peak=   -3.246 closest distance to " CG  LEU A   5 " =    1.568
peak=   -3.242 closest distance to " O   ALA A  34 " =    2.695
peak=   -3.235 closest distance to " O   GLN A 240 " =    2.502
peak=   -3.235 closest distance to " CB  TRP A  85 " =    2.694
peak=   -3.232 closest distance to " NE2 GLN A  11 " =    1.673
peak=   -3.231 closest distance to " OG  SER A 141 " =    1.763
peak=   -3.224 closest distance to " NE2 GLN A 103 " =    1.711
peak=   -3.221 closest distance to " CG  GLN A 103 " =    2.504
peak=   -3.220 closest distance to " O   HOH Z 111 " =    1.612
peak=   -3.219 closest distance to " CZ  TYR A 169 " =    1.833
peak=   -3.209 closest distance to " O   HOH Z 265 " =    1.814
peak=   -3.207 closest distance to " O   SER A 276 " =    1.675
peak=   -3.204 closest distance to " O   HOH Z 431 " =    1.942
peak=   -3.200 closest distance to " CG  ARG A 219 " =    2.887
peak=   -3.200 closest distance to " CB  ASP A 171 " =    2.301
peak=   -3.194 closest distance to " CD1 ILE A 199 " =    2.504
peak=   -3.192 closest distance to " O   HOH Z  60 " =    1.717
peak=   -3.188 closest distance to " O   PHE A 218 " =    1.505
peak=   -3.188 closest distance to " CB  PRO A 163 " =    2.437
peak=   -3.186 closest distance to " SG BCYS A 201 " =    2.378
peak=   -3.184 closest distance to " O   HOH Z 119 " =    2.758
peak=   -3.178 closest distance to " O   HOH Z  44 " =    0.938
peak=   -3.170 closest distance to " CD1 TYR A 247 " =    2.324
peak=   -3.170 closest distance to " CD2 LEU A 167 " =    1.870
peak=   -3.169 closest distance to " OH  TYR A 214 " =    1.242
peak=   -3.169 closest distance to " ND2 ASN A  69 " =    1.927
peak=   -3.168 closest distance to " O   HOH Z  43 " =    1.607
peak=   -3.168 closest distance to " O   ASP A  27 " =    1.999
peak=   -3.165 closest distance to " N   ASP A 171 " =    2.391
peak=   -3.161 closest distance to " O   LYS A 117 " =    1.860
peak=   -3.161 closest distance to " CG1 VAL A 197 " =    2.272
peak=   -3.161 closest distance to " O   HOH Z 365 " =    1.508
peak=   -3.161 closest distance to " O   ALA A 161 " =    1.862
peak=   -3.155 closest distance to " O   HOH Z 189 " =    2.286
peak=   -3.153 closest distance to " NH2 ARG A  79 " =    1.564
peak=   -3.150 closest distance to " CD2 LEU A 237 " =    2.753
peak=   -3.148 closest distance to " O   HOH Z 304 " =    1.472
peak=   -3.148 closest distance to " O   HOH Z  13 " =    1.949
peak=   -3.146 closest distance to " C   ARG A  79 " =    2.603
peak=   -3.142 closest distance to " CG  ASP A 231 " =    0.812
peak=   -3.139 closest distance to " O   HOH Z 396 " =    2.216
peak=   -3.132 closest distance to " OG BSER A 210 " =    1.620
peak=   -3.126 closest distance to " CG  PRO A 163 " =    2.338
peak=   -3.123 closest distance to " O   HOH Z 380 " =    1.439
peak=   -3.122 closest distance to " CG1 VAL A 125 " =    2.418
peak=   -3.122 closest distance to " O   HOH Z 110 " =    1.316
peak=   -3.120 closest distance to " O   HOH Z 100 " =    1.128
peak=   -3.116 closest distance to " CA  SER A  62 " =    2.522
peak=   -3.116 closest distance to " O   HOH Z 191 " =    5.670
peak=   -3.114 closest distance to " CD2 PHE A 225 " =    1.178
peak=   -3.113 closest distance to " N   ALA A 248 " =    1.991
peak=   -3.109 closest distance to " O   HOH Z 378 " =    1.448
peak=   -3.108 closest distance to " O   HOH Z  11 " =    1.888
peak=   -3.100 closest distance to " O   HOH Z  64 " =    1.651
peak=   -3.098 closest distance to " NH2 ARG A  36 " =    2.487
peak=   -3.093 closest distance to " CE1 TYR A 247 " =    2.647
peak=   -3.077 closest distance to " CB  PHE A  16 " =    2.449
peak=   -3.065 closest distance to " CA  GLY A 241 " =    2.901
peak=   -3.055 closest distance to " O   GLY A  80 " =    2.629
peak=   -3.052 closest distance to " CG  ARG A 259 " =    2.397
peak=   -3.050 closest distance to " O   HOH Z 259 " =    2.141
peak=   -3.044 closest distance to " O   HOH Z 177 " =    1.423
peak=   -3.028 closest distance to " OG BSER A 134 " =    1.904
peak=   -3.015 closest distance to " O   HOH Z  60 " =    2.230
peak=   -3.008 closest distance to " CD1 TRP A  70 " =    1.099
peak=   -3.002 closest distance to " O   HOH Z 261 " =    1.535
peak=   -3.001 closest distance to " ND2 ASN A 249 " =    2.231

================= 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    :  0.4698 0.4618   6.271705e+00   6.253156e+00
   1_bss:  0.4602 0.4463   6.265661e+00   6.241004e+00
   1_xyz:  0.3700 0.3977   6.134001e+00   6.168274e+00
   1_adp:  0.3222 0.3726   6.033348e+00   6.122841e+00
   1_occ:  0.3217 0.3734   6.032642e+00   6.124640e+00
   2_bss:  0.3197 0.3702   6.034051e+00   6.123779e+00
   2_xyz:  0.2348 0.2933   5.772686e+00   5.930802e+00
   2_adp:  0.2112 0.2675   5.688372e+00   5.866886e+00
   2_occ:  0.2110 0.2674   5.688510e+00   5.867823e+00
   3_bss:  0.2097 0.2672   5.689618e+00   5.868789e+00
   3_xyz:  0.1552 0.2057   5.417743e+00   5.631446e+00
   3_adp:  0.1391 0.1902   5.331194e+00   5.565105e+00
   3_occ:  0.1388 0.1899   5.330229e+00   5.564329e+00
   4_bss:  0.1387 0.1893   5.327489e+00   5.560212e+00
   4_xyz:  0.1262 0.1754   5.251352e+00   5.488263e+00
   4_adp:  0.1233 0.1725   5.233420e+00   5.471300e+00
   4_occ:  0.1232 0.1723   5.232657e+00   5.470553e+00
   5_bss:  0.1231 0.1722   5.232652e+00   5.470754e+00
   5_xyz:  0.1157 0.1677   5.192223e+00   5.446783e+00
   5_adp:  0.1160 0.1652   5.186045e+00   5.433198e+00
   5_occ:  0.1156 0.1653   5.184187e+00   5.432107e+00
   5_bss:  0.1156 0.1652   5.183879e+00   5.431922e+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:  0.320  23.938   6.507   7.269  12.196   0.000   0.000   0.000
   1_xyz:  0.320  23.938   6.507   7.269  12.196   0.000   0.000   0.000
   1_adp:  0.320  23.938   6.507   7.269  12.196   0.000   0.000   0.000
   1_occ:  0.320  23.938   6.507   7.269  12.196   0.000   0.000   0.000
   2_bss:  0.334  61.216   3.338   4.113   8.410   0.000   0.000   0.000
   2_xyz:  0.334  61.216   3.338   4.113   8.410   0.000   0.000   0.000
   2_adp:  0.334  61.216   3.338   4.113   8.410   0.000   0.000   0.000
   2_occ:  0.334  61.216   3.338   4.113   8.410   0.000   0.000   0.000
   3_bss:  0.328  61.216   2.324   3.026   5.505   0.000   0.000   0.000
   3_xyz:  0.328  61.216   2.324   3.026   5.505   0.000   0.000   0.000
   3_adp:  0.328  61.216   2.324   3.026   5.505   0.000   0.000   0.000
   3_occ:  0.328  61.216   2.324   3.026   5.505   0.000   0.000   0.000
   4_bss:  0.338  72.574   2.092   2.610   4.520   0.000   0.000   0.000
   4_xyz:  0.338  72.574   2.092   2.610   4.520   0.000   0.000   0.000
   4_adp:  0.338  72.574   2.092   2.610   4.520   0.000   0.000   0.000
   4_occ:  0.338  72.574   2.092   2.610   4.520   0.000   0.000   0.000
   5_bss:  0.338  72.574   2.327   2.682   4.431   0.000   0.000   0.000
   5_xyz:  0.338  72.574   2.327   2.682   4.431   0.000   0.000   0.000
   5_adp:  0.338  72.574   2.327   2.682   4.431   0.000   0.000   0.000
   5_occ:  0.338  72.574   2.327   2.682   4.431   0.000   0.000   0.000
   5_bss:  0.324  68.333  -0.819  -0.465   1.284   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.651 0.4754  0.5334    62718.790
   1_bss:  52.101 0.4945  0.7200    60413.635
   1_xyz:  44.738 0.5848  0.8265    45022.334
   1_adp:  40.272 0.6395  0.9274    38561.100
   1_occ:  40.337 0.6387  0.9260    38723.848
   2_bss:  40.140 0.6411  0.8268    38525.798
   2_xyz:  29.855 0.7590  0.9581    22339.435
   2_adp:  26.808 0.7928  0.9844    18870.040
   2_occ:  26.879 0.7920  0.9833    18913.723
   3_bss:  26.802 0.7930  0.9280    18955.711
   3_xyz:  19.707 0.8643  0.9773    10772.911
   3_adp:  17.889 0.8815  0.9764     9300.370
   3_occ:  17.865 0.8818  0.9765     9279.440
   4_bss:  17.749 0.8827  0.9584     9152.063
   4_xyz:  16.049 0.8981  0.9656     7830.055
   4_adp:  15.657 0.9017  0.9603     7594.277
   4_occ:  15.638 0.9018  0.9603     7576.214
   5_bss:  15.639 0.9018  0.9630     7580.999
   5_xyz:  15.126 0.9061  0.9665     7194.416
   5_adp:  14.786 0.9091  0.9674     7015.467
   5_occ:  14.771 0.9092  0.9672     6994.455
   5_bss:  14.772 0.9092  0.9670     6987.186
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4498e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4498e+01
   1_xyz:   1.694  0.014  0.108 18.293  0.006  4.114   1.4173e-01
   1_adp:   1.694  0.014  0.108 18.293  0.006  4.114   1.4173e-01
   1_occ:   1.694  0.014  0.108 18.293  0.006  4.114   1.4173e-01
   2_bss:   1.694  0.014  0.108 18.293  0.006  4.114   1.4173e-01
   2_xyz:   1.241  0.010  0.084 16.663  0.005  4.134   8.8891e-02
   2_adp:   1.241  0.010  0.084 16.663  0.005  4.134   8.8891e-02
   2_occ:   1.241  0.010  0.084 16.663  0.005  4.134   8.8891e-02
   3_bss:   1.241  0.010  0.084 16.663  0.005  4.134   8.8891e-02
   3_xyz:   1.175  0.010  0.089 16.366  0.004  4.139   8.2982e-02
   3_adp:   1.175  0.010  0.089 16.366  0.004  4.139   8.2982e-02
   3_occ:   1.175  0.010  0.089 16.366  0.004  4.139   8.2982e-02
   4_bss:   1.175  0.010  0.089 16.366  0.004  4.139   8.2982e-02
   4_xyz:   1.081  0.009  0.084 15.833  0.004  4.127   7.2688e-02
   4_adp:   1.081  0.009  0.084 15.833  0.004  4.127   7.2688e-02
   4_occ:   1.081  0.009  0.084 15.833  0.004  4.127   7.2688e-02
   5_bss:   1.081  0.009  0.084 15.833  0.004  4.127   7.2688e-02
   5_xyz:   1.216  0.012  0.095 15.681  0.004  4.133   8.9473e-02
   5_adp:   1.216  0.012  0.095 15.681  0.004  4.133   8.9473e-02
   5_occ:   1.216  0.012  0.095 15.681  0.004  4.133   8.9473e-02
   5_bss:   1.216  0.012  0.095 15.681  0.004  4.133   8.9473e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0654e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0654e+00
   1_xyz:  14.204  0.161  0.432 89.377  0.035  2.160   1.0612e-01
   1_adp:  14.204  0.161  0.432 89.377  0.035  2.160   1.0612e-01
   1_occ:  14.204  0.161  0.432 89.377  0.035  2.160   1.0612e-01
   2_bss:  14.204  0.161  0.432 89.377  0.035  2.160   1.0612e-01
   2_xyz:   7.577  0.079  0.282 85.303  0.030  2.213   7.1436e-02
   2_adp:   7.577  0.079  0.282 85.303  0.030  2.213   7.1436e-02
   2_occ:   7.577  0.079  0.282 85.303  0.030  2.213   7.1436e-02
   3_bss:   7.577  0.079  0.282 85.303  0.030  2.213   7.1436e-02
   3_xyz:   6.756  0.057  0.380 86.972  0.040  2.276   7.4045e-02
   3_adp:   6.756  0.057  0.380 86.972  0.040  2.276   7.4045e-02
   3_occ:   6.756  0.057  0.380 86.972  0.040  2.276   7.4045e-02
   4_bss:   6.756  0.057  0.380 86.972  0.040  2.276   7.4045e-02
   4_xyz:   7.143  0.049  0.403 85.515  0.041  2.375   7.9974e-02
   4_adp:   7.143  0.049  0.403 85.515  0.041  2.375   7.9974e-02
   4_occ:   7.143  0.049  0.403 85.515  0.041  2.375   7.9974e-02
   5_bss:   7.143  0.049  0.403 85.515  0.041  2.375   7.9974e-02
   5_xyz:   7.861  0.063  0.569 83.082  0.041  2.290   6.0877e-02
   5_adp:   7.861  0.063  0.569 83.082  0.041  2.290   6.0877e-02
   5_occ:   7.861  0.063  0.569 83.082  0.041  2.290   6.0877e-02
   5_bss:   7.861  0.063  0.569 83.082  0.041  2.290   6.0877e-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:  67.53   0.00  12.77  64.99   0.00  10.13  67.53   0.00  27.17
   1_occ:  67.53   0.00  12.77  64.99   0.00  10.13  67.53   0.00  27.17
   2_bss:  67.53   0.00  12.77  64.99   0.00  10.13  67.53   0.00  27.17
   2_xyz:  67.53   0.00  12.77  64.99   0.00  10.13  67.53   0.00  27.17
   2_adp:  75.93   0.00  12.54  75.93   0.00   8.88  68.39   0.00  32.48
   2_occ:  75.93   0.00  12.54  75.93   0.00   8.88  68.39   0.00  32.48
   3_bss:  75.93   0.00  12.54  75.93   0.00   8.88  68.39   0.00  32.48
   3_xyz:  75.93   0.00  12.54  75.93   0.00   8.88  68.39   0.00  32.48
   3_adp:  87.72   0.00  13.27  73.49   0.00   8.58  87.72   0.51  38.79
   3_occ:  87.72   0.00  13.27  73.49   0.00   8.58  87.72   0.51  38.79
   4_bss:  87.72   0.00  13.27  73.49   0.00   8.58  87.72   0.51  38.79
   4_xyz:  87.72   0.00  13.27  73.49   0.00   8.58  87.72   0.51  38.79
   4_adp:  97.38   0.00  13.13  82.37   0.00   8.40  97.38   0.37  38.88
   4_occ:  97.38   0.00  13.13  82.37   0.00   8.40  97.38   0.37  38.88
   5_bss:  97.38   0.00  13.13  82.37   0.00   8.40  97.38   0.37  38.88
   5_xyz:  97.38   0.00  13.13  82.37   0.00   8.40  97.38   0.37  38.88
   5_adp:  96.61   0.00  12.90  84.16   0.00   8.30  96.61   0.90  37.93
   5_occ:  96.61   0.00  12.90  84.16   0.00   8.30  96.61   0.90  37.93
   5_bss:  99.75   3.15  16.04  87.30   3.15  11.45  99.75   4.04  41.07
------------------------------------------------------------------------
 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:    1.265    0.016    0.413
   1_adp:    1.265    0.016    0.413
   1_occ:    1.265    0.016    0.413
   2_bss:    1.265    0.016    0.413
   2_xyz:    1.846    0.035    0.577
   2_adp:    1.846    0.035    0.577
   2_occ:    1.846    0.035    0.577
   3_bss:    1.846    0.035    0.577
   3_xyz:    1.841    0.030    0.661
   3_adp:    1.841    0.030    0.661
   3_occ:    1.841    0.030    0.661
   4_bss:    1.841    0.030    0.661
   4_xyz:    2.046    0.022    0.685
   4_adp:    2.046    0.022    0.685
   4_occ:    2.046    0.022    0.685
   5_bss:    2.046    0.022    0.685
   5_xyz:    2.047    0.067    0.696
   5_adp:    2.047    0.067    0.696
   5_occ:    2.047    0.067    0.696
   5_bss:    2.047    0.067    0.696
------------------------------------------------------------------------

CPU time actual refinement: 328.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/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_802/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_802/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.20 
  Macro-tasks:
    bulk solvent and scale       = 40.74  
    individual site refinement   = 131.60 
    weights calculation          = 31.92  
    collect and process          = 6.49   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.87 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 101.09 
    alpha_beta                      = 8.33   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.90 
    fmodel                         = 7.15   
    r_factors                      = 0.13   
    phase_errors                   = 10.70  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 241.45 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.671 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    652 calls, 100.72 s
gradients_fft:          597 calls,  98.08 s

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

# Date 2008-01-16 Time 02:27:45 PST -0800 (1200479265.83 s)
Start R-work = 0.4698, R-free = 0.4618 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1802 (no bulk solvent and anisotropic scale)

Start R-work = 0.4602, R-free = 0.4463
Final R-work = 0.1156, R-free = 0.1652