# Date 2008-01-16 Time 06:17:58 PST -0800 (1200493078.31 s)
#phil __OFF__

Command line arguments: "../1092.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30973
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1092

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.7567, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.95392
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.93108

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1679
                             d_min =   1.9539

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: (71.655, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.95392
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.93108

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1683 -  4.1829 [2206/2233]  1988   218   9.9%
  bin  2:  4.1829 -  3.3317 [2112/2132]  1899   213  10.1%
  bin  3:  3.3317 -  2.9139 [2096/2115]  1882   214  10.2%
  bin  4:  2.9139 -  2.6490 [2043/2073]  1838   205  10.0%
  bin  5:  2.6490 -  2.4600 [2074/2093]  1873   201   9.7%
  bin  6:  2.4600 -  2.3155 [2044/2069]  1835   209  10.2%
  bin  7:  2.3155 -  2.1999 [2046/2074]  1835   211  10.3%
  bin  8:  2.1999 -  2.1044 [2029/2065]  1837   192   9.5%
  bin  9:  2.1044 -  2.0236 [1983/2066]  1783   200  10.1%
  bin 10:  2.0236 -  1.9539 [ 956/2059]   860    96  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/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:
        1.49 -     2.18: 22
        2.18 -     2.86: 1185
        2.86 -     3.54: 4489
        3.54 -     4.22: 9336
        4.22 -     4.90: 13533
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.494 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.540 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " OG BSER A 216 " - " O   HOH Z 113 "  1.726 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28560 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 =====================


==================== 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/noshake/run_1092/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.75675 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4751   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.288026                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.6664 0.99   1427  162 0.3972 0.4125       6.594       6.627|
|  2:  4.6664 -  3.7219 0.99   1370  152 0.4220 0.4118      6.8359      6.8247|
|  3:  3.7219 -  3.2567 0.99   1351  145 0.4521 0.4339      6.6909      6.6995|
|  4:  3.2567 -  2.9614 0.99   1343  155 0.4700 0.4895      6.5412      6.5171|
|  5:  2.9614 -  2.7504 0.99   1340  146 0.5036 0.5180       6.372      6.3988|
|  6:  2.7504 -  2.5891 0.99   1333  145 0.5095 0.5004       6.283      6.2236|
|  7:  2.5891 -  2.4600 0.99   1316  146 0.5139 0.4938      6.2387      6.1805|
|  8:  2.4600 -  2.3533 0.98   1316  146 0.5177 0.5090      6.1697      6.1975|
|  9:  2.3533 -  2.2631 0.98   1307  152 0.5141 0.5242      6.1228      6.1423|
| 10:  2.2631 -  2.1852 1.00   1293  153 0.5263 0.5007       6.091      6.0632|
| 11:  2.1852 -  2.1171 0.98   1321  131 0.5178 0.5213      6.0186      6.0764|
| 12:  2.1171 -  2.0567 0.98   1302  151 0.5054 0.5209      5.9441      5.9716|
| 13:  2.0567 -  2.0027 0.88   1162  127 0.5297 0.4576      5.8664      5.8118|
| 14:  2.0027 -  1.9539 0.34    449   48 0.5258 0.5110      5.8594      5.7934|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.6664  1427   162  0.68  36.27   0.81     0.75      80554.22|
|  2:  4.6664 -  3.7219  1370   152  0.66  38.38   0.89     0.79     121549.63|
|  3:  3.7219 -  3.2567  1351   145  0.54  49.03   0.90     0.72     132119.99|
|  4:  3.2567 -  2.9614  1343   155  0.41  58.56   0.91     0.60     124676.08|
|  5:  2.9614 -  2.7504  1340   146  0.32  66.09   0.87     0.47      97246.44|
|  6:  2.7504 -  2.5891  1333   145  0.31  67.04   0.88     0.45      82810.76|
|  7:  2.5891 -  2.4600  1316   146  0.33  65.55   0.90     0.47      68747.05|
|  8:  2.4600 -  2.3533  1316   146  0.34  64.45   0.91     0.50      60930.61|
|  9:  2.3533 -  2.2631  1307   152  0.33  65.02   0.92     0.49      55509.31|
| 10:  2.2631 -  2.1852  1293   153  0.31  66.91   0.92     0.47      52046.34|
| 11:  2.1852 -  2.1171  1321   131  0.29  68.09   0.96     0.47      49913.21|
| 12:  2.1171 -  2.0567  1302   151  0.31  66.67   0.95     0.50      44161.22|
| 13:  2.0567 -  2.0027  1162   127  0.34  64.35   0.93     0.57      35530.66|
| 14:  2.0027 -  1.9539   449    48  0.45  56.22   0.99     0.66      25816.79|
|alpha:            min =        0.45 max =            0.79 mean =         0.56|
|beta:             min =    25816.79 max =       132119.99 mean =     76853.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.36|
|phase err.(test): min =        0.00 max =           90.00 mean =        59.51|
|-----------------------------------------------------------------------------|

============================== 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 = 15.085953             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.617   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.220338              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.104   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.494 -  1.835:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.835 -  2.176:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.176 -  2.516:       45 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.516 -  2.857:     1140 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.857 -  3.197:     1971 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.197 -  3.538:     2518 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.538 -  3.878:     4697 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.878 -  4.219:     4639 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.219 -  4.559:     6152 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.559 -  4.900:     7381 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.188 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.494 |       0.579 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4751   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.288026                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4703   r_free= 0.4674   ksol= 0.34   Bsol= 39.99   scale= 0.915   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,1.76,-1.40,0.00,-0.00,-0.00); trace/3= 0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.285302                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.289086             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.672   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.540748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.716   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4703      final r-factor (work) = 0.3892          |
| start r-factor (free) = 0.4674      final r-factor (free) = 0.4297          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.7817 = 12.29 * 0.50 * 6.2809 + 1.00 * 0.1885                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2691 = 12.29 * 0.50 * 6.2070 + 1.00 * 0.1299                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3892      final r-factor (work) = 0.3611          |
| start r-factor (free) = 0.4297      final r-factor (free) = 0.4323          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5698 = 1.54 * 1.00 * 6.2070 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5383 = 1.54 * 1.00 * 6.1417 + 1.00 * 0.0754                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    138.02  17.09    None  None   None       |
|    all(noH): 2823   0      0.00    138.02  17.09    None  None   None       |
|    Sol.    : 438    0      0.00    66.08   35.71    None  None   None       |
|    Mac.    : 2385   0      0.00    138.02  13.67    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 -  13.802: 1322   |   5:    69.010 -  82.812:    0        |
|      1:    13.802 -  27.604:  999   |   6:    82.812 -  96.614:    0        |
|      2:    27.604 -  41.406:  331   |   7:    96.614 - 110.416:    0        |
|      3:    41.406 -  55.208:  141   |   8:   110.416 - 124.218:    0        |
|      4:    55.208 -  69.010:   29   |   9:   124.218 - 138.020:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3611 r_free = 0.4323             target_work(ml) = 6.144         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3606 r_free = 0.4333             target_work(ml) = 6.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3606   r_free= 0.4333   ksol= 0.34   Bsol= 39.99   scale= 0.963   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,1.76,-1.40,0.00,-0.00,-0.00); trace/3= 0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.143154                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3611   r_free= 0.4319   ksol= 0.37   Bsol= 74.66   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.44,0.09,0.00,0.00,0.00); trace/3= 0.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.145572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.589561             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.656  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.829254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.896   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3611      final r-factor (work) = 0.2991          |
| start r-factor (free) = 0.4319      final r-factor (free) = 0.3641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.6629 = 10.59 * 0.50 * 6.1443 + 1.00 * 0.1299                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.3021 = 10.59 * 0.50 * 6.0805 + 1.00 * 0.1074                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2991      final r-factor (work) = 0.2790          |
| start r-factor (free) = 0.3641      final r-factor (free) = 0.3678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1426 = 1.83 * 1.00 * 6.0805 + 1.00 * 0.0199                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9401 = 1.83 * 1.00 * 5.9670 + 1.00 * 0.0250                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.66  19.58    None  None   None       |
|    all(noH): 2823   0      0.00    104.66  19.58    None  None   None       |
|    Sol.    : 438    0      0.00    104.66  40.95    None  None   None       |
|    Mac.    : 2385   0      0.00    88.95   15.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.466: 1053   |   5:    52.331 -  62.797:   70        |
|      1:    10.466 -  20.932:  806   |   6:    62.797 -  73.263:   63        |
|      2:    20.932 -  31.398:  396   |   7:    73.263 -  83.729:   26        |
|      3:    31.398 -  41.865:  251   |   8:    83.729 -  94.195:   10        |
|      4:    41.865 -  52.331:  145   |   9:    94.195 - 104.661:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2790 r_free = 0.3678             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2788 r_free = 0.3680             target_work(ml) = 5.967         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2788   r_free= 0.3680   ksol= 0.37   Bsol= 74.66   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.44,0.09,0.00,0.00,0.00); trace/3= 0.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.967207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2793   r_free= 0.3670   ksol= 0.36   Bsol= 77.49   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,0.77,1.04,0.00,0.00,0.00); trace/3= 0.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.965682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.016919              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306966              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.887  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2793      final r-factor (work) = 0.2293          |
| start r-factor (free) = 0.3670      final r-factor (free) = 0.3021          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0142 = 9.02 * 0.50 * 5.9681 + 1.00 * 0.1074                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6504 = 9.02 * 0.50 * 5.8925 + 1.00 * 0.0844                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2293      final r-factor (work) = 0.2123          |
| start r-factor (free) = 0.3021      final r-factor (free) = 0.2736          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8341 = 0.31 * 1.00 * 5.8925 + 1.00 * 0.0253                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7776 = 0.31 * 1.00 * 5.7588 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.02   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    94.02   17.25    None  None   None       |
|    Sol.    : 438    0      3.34    94.02   39.98    None  None   None       |
|    Mac.    : 2385   0      0.00    83.53   13.08    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 -   9.402: 1012   |   5:    47.009 -  56.411:   90        |
|      1:     9.402 -  18.804: 1029   |   6:    56.411 -  65.812:   58        |
|      2:    18.804 -  28.205:  282   |   7:    65.812 -  75.214:   23        |
|      3:    28.205 -  37.607:  191   |   8:    75.214 -  84.616:    6        |
|      4:    37.607 -  47.009:  130   |   9:    84.616 -  94.018:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2123 r_free = 0.2736             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2118 r_free = 0.2721             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2118   r_free= 0.2721   ksol= 0.36   Bsol= 77.49   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.70,0.77,1.04,0.00,0.00,0.00); trace/3= 0.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.703364                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2109   r_free= 0.2702   ksol= 0.34   Bsol= 62.82   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.85,-0.20,-0.00,-0.00,-0.00); trace/3= -0.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.700531                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.592026              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.409  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.926  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2109      final r-factor (work) = 0.1722          |
| start r-factor (free) = 0.2702      final r-factor (free) = 0.2233          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5513 = 2.59 * 0.50 * 5.7616 + 1.00 * 0.0842                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3312 = 2.59 * 0.50 * 5.6139 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1722      final r-factor (work) = 0.1613          |
| start r-factor (free) = 0.2233      final r-factor (free) = 0.2157          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0464 = 0.36 * 1.00 * 5.6139 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0008 = 0.36 * 1.00 * 5.4857 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.82   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    90.82   17.24    None  None   None       |
|    Sol.    : 438    0      5.91    90.82   42.90    None  None   None       |
|    Mac.    : 2385   0      0.00    84.99   12.53    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 -   9.082: 1001   |   5:    45.410 -  54.492:  101        |
|      1:     9.082 -  18.164: 1052   |   6:    54.492 -  63.574:   88        |
|      2:    18.164 -  27.246:  280   |   7:    63.574 -  72.656:   43        |
|      3:    27.246 -  36.328:  127   |   8:    72.656 -  81.738:    9        |
|      4:    36.328 -  45.410:  118   |   9:    81.738 -  90.820:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1613 r_free = 0.2157             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1611 r_free = 0.2154             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2154   ksol= 0.34   Bsol= 62.82   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,-0.85,-0.20,-0.00,-0.00,-0.00); trace/3= -0.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.468346                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1612   r_free= 0.2151   ksol= 0.33   Bsol= 57.24   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.467111                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.464172              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.304  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.681681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.430  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.2151      final r-factor (free) = 0.1861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3021 = 4.46 * 0.50 * 5.4866 + 1.00 * 0.0556                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0936 = 4.46 * 0.50 * 5.3873 + 1.00 * 0.0686                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6829 = 0.68 * 1.00 * 5.3873 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6090 = 0.68 * 1.00 * 5.2781 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.05   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.05   17.25    None  None   None       |
|    Sol.    : 438    0      5.67    97.83   44.59    None  None   None       |
|    Mac.    : 2385   0      0.00    98.05   12.23    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 -   9.805: 1196   |   5:    49.025 -  58.830:   93        |
|      1:     9.805 -  19.610:  971   |   6:    58.830 -  68.635:   69        |
|      2:    19.610 -  29.415:  222   |   7:    68.635 -  78.440:   41        |
|      3:    29.415 -  39.220:  120   |   8:    78.440 -  88.245:   15        |
|      4:    39.220 -  49.025:   90   |   9:    88.245 -  98.050:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1263 r_free = 0.1794             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1262 r_free = 0.1791             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1791   ksol= 0.33   Bsol= 57.24   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.256426                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.6664 0.99   1427  162 0.0948 0.1430      5.3767      5.6582|
|  2:  4.6664 -  3.7219 0.99   1370  152 0.0866 0.1256       5.495      5.7681|
|  3:  3.7219 -  3.2567 0.99   1351  145 0.1233 0.1683      5.5922      5.9006|
|  4:  3.2567 -  2.9614 0.99   1343  155 0.1432 0.1925      5.5885      5.7487|
|  5:  2.9614 -  2.7504 0.99   1340  146 0.1546 0.2085      5.4487      5.7096|
|  6:  2.7504 -  2.5891 0.99   1333  145 0.1391 0.2034       5.309      5.5301|
|  7:  2.5891 -  2.4600 0.99   1316  146 0.1440 0.1967      5.2631       5.471|
|  8:  2.4600 -  2.3533 0.98   1316  146 0.1397 0.1908      5.1915      5.4167|
|  9:  2.3533 -  2.2631 0.98   1307  152 0.1387 0.1923      5.1528      5.3742|
| 10:  2.2631 -  2.1852 1.00   1293  153 0.1304 0.1912      5.0642      5.2877|
| 11:  2.1852 -  2.1171 0.98   1321  131 0.1280 0.2065      5.0457      5.4213|
| 12:  2.1171 -  2.0567 0.98   1302  151 0.1270 0.2027      4.9803      5.2457|
| 13:  2.0567 -  2.0027 0.88   1162  127 0.1367 0.1795      4.9084      5.1308|
| 14:  2.0027 -  1.9539 0.34    449   48 0.1176 0.1816      4.7598      5.0098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.6664  1427   162  0.93  10.14   0.97     0.95       8118.64|
|  2:  4.6664 -  3.7219  1370   152  0.95   9.13   1.02     1.01      11111.45|
|  3:  3.7219 -  3.2567  1351   145  0.91  13.82   1.04     1.04      13397.15|
|  4:  3.2567 -  2.9614  1343   155  0.89  17.34   1.02     1.00      14265.27|
|  5:  2.9614 -  2.7504  1340   146  0.88  18.09   1.01     0.99      10451.83|
|  6:  2.7504 -  2.5891  1333   145  0.88  18.43   0.99     0.95       8706.71|
|  7:  2.5891 -  2.4600  1316   146  0.88  18.11   1.01     0.98       7669.51|
|  8:  2.4600 -  2.3533  1316   146  0.89  17.86   0.99     0.97       6696.48|
|  9:  2.3533 -  2.2631  1307   152  0.88  18.24   1.01     0.96       6260.76|
| 10:  2.2631 -  2.1852  1293   153  0.88  18.27   1.00     0.97       5544.82|
| 11:  2.1852 -  2.1171  1321   131  0.88  18.87   1.00     0.96       5566.84|
| 12:  2.1171 -  2.0567  1302   151  0.88  18.76   1.00     0.98       5129.74|
| 13:  2.0567 -  2.0027  1162   127  0.87  19.39   1.01     0.99       4307.84|
| 14:  2.0027 -  1.9539   449    48  0.90  16.20   0.98     0.95       3114.18|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3114.18 max =        14265.27 mean =      8188.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.55|
|phase err.(test): min =        0.00 max =           89.75 mean =        15.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1791   ksol= 0.33   Bsol= 57.24   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.257446                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1791   ksol= 0.33   Bsol= 57.24   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.257446                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.6664 0.99   1427  162 0.0962 0.1419      5.3805      5.6528|
|  2:  4.6664 -  3.7219 0.99   1370  152 0.0879 0.1252      5.4989       5.767|
|  3:  3.7219 -  3.2567 0.99   1351  145 0.1239 0.1684      5.5944         5.9|
|  4:  3.2567 -  2.9614 0.99   1343  155 0.1432 0.1930      5.5897      5.7512|
|  5:  2.9614 -  2.7504 0.99   1340  146 0.1547 0.2082      5.4491      5.7078|
|  6:  2.7504 -  2.5891 0.99   1333  145 0.1391 0.2033      5.3098       5.531|
|  7:  2.5891 -  2.4600 0.99   1316  146 0.1441 0.1966      5.2635        5.47|
|  8:  2.4600 -  2.3533 0.98   1316  146 0.1396 0.1908      5.1915      5.4183|
|  9:  2.3533 -  2.2631 0.98   1307  152 0.1387 0.1922      5.1532      5.3744|
| 10:  2.2631 -  2.1852 1.00   1293  153 0.1303 0.1911      5.0642      5.2874|
| 11:  2.1852 -  2.1171 0.98   1321  131 0.1279 0.2064      5.0456      5.4209|
| 12:  2.1171 -  2.0567 0.98   1302  151 0.1270 0.2027      4.9801      5.2459|
| 13:  2.0567 -  2.0027 0.88   1162  127 0.1367 0.1796      4.9085      5.1312|
| 14:  2.0027 -  1.9539 0.34    449   48 0.1176 0.1818        4.76      5.0096|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.6664  1427   162  0.93  10.19   0.97     0.95       8031.11|
|  2:  4.6664 -  3.7219  1370   152  0.95   9.08   1.03     1.01      11026.72|
|  3:  3.7219 -  3.2567  1351   145  0.92  13.76   1.04     1.04      13361.90|
|  4:  3.2567 -  2.9614  1343   155  0.89  17.36   1.02     1.00      14306.85|
|  5:  2.9614 -  2.7504  1340   146  0.88  18.11   1.01     0.99      10467.20|
|  6:  2.7504 -  2.5891  1333   145  0.88  18.44   0.99     0.95       8715.49|
|  7:  2.5891 -  2.4600  1316   146  0.88  18.11   1.00     0.98       7669.17|
|  8:  2.4600 -  2.3533  1316   146  0.88  17.89   0.99     0.97       6710.77|
|  9:  2.3533 -  2.2631  1307   152  0.88  18.25   1.01     0.96       6264.23|
| 10:  2.2631 -  2.1852  1293   153  0.88  18.28   1.00     0.97       5549.82|
| 11:  2.1852 -  2.1171  1321   131  0.88  18.87   1.00     0.96       5564.09|
| 12:  2.1171 -  2.0567  1302   151  0.88  18.76   1.00     0.98       5127.55|
| 13:  2.0567 -  2.0027  1162   127  0.87  19.40   1.01     0.99       4310.03|
| 14:  2.0027 -  1.9539   449    48  0.90  16.21   0.98     0.95       3116.31|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3116.31 max =        14306.85 mean =      8179.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.55|
|phase err.(test): min =        0.00 max =           89.83 mean =        15.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.685)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.05   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    98.05   17.25    None  None   None       |
|    Sol.    : 438    0      5.68    97.83   44.59    None  None   None       |
|    Mac.    : 2385   0      0.00    98.05   12.23    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:     0.003 -   9.808: 1196   |   5:    49.028 -  58.833:   93        |
|      1:     9.808 -  19.613:  971   |   6:    58.833 -  68.638:   69        |
|      2:    19.613 -  29.418:  222   |   7:    68.638 -  78.443:   41        |
|      3:    29.418 -  39.223:  120   |   8:    78.443 -  88.248:   15        |
|      4:    39.223 -  49.028:   90   |   9:    88.248 -  98.053:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 5.635
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 342 from: 344
   mapped sites are within: 0.724 - 5.635

peak=    7.716 closest distance to " O   HOH Z 390 " =    1.255
peak=    6.769 closest distance to " O   HOH Z 120 " =    1.446
peak=    6.312 closest distance to " O   HOH Z 431 " =    1.735
peak=    6.000 closest distance to " O   HOH Z  65 " =    1.669
peak=    5.996 closest distance to " O   HOH Z 385 " =    1.327
peak=    5.875 closest distance to " NE2 GLN A  11 " =    1.421
peak=    5.581 closest distance to " O   HOH Z   7 " =    2.032
peak=    5.535 closest distance to " O   HOH Z 214 " =    2.026
peak=    5.411 closest distance to " O   HOH Z 289 " =    1.362
peak=    5.373 closest distance to " O   HOH Z 403 " =    1.575
peak=    5.362 closest distance to " O   HOH Z 159 " =    0.943
peak=    5.259 closest distance to " O   HOH Z 245 " =    1.301
peak=    5.205 closest distance to " O   HOH Z 222 " =    1.322
peak=    5.185 closest distance to " CB  PRO A  54 " =    1.142
peak=    5.093 closest distance to " O   HOH Z 144 " =    1.680
peak=    5.051 closest distance to " O   HOH Z 416 " =    1.360
peak=    5.039 closest distance to " O   HOH Z  49 " =    1.546
peak=    4.948 closest distance to " O   HOH Z 417 " =    2.160
peak=    4.877 closest distance to " O   HOH Z 139 " =    1.687
peak=    4.856 closest distance to " O   HOH Z 427 " =    1.220
peak=    4.848 closest distance to " O   HOH Z  97 " =    1.421
peak=    4.820 closest distance to " O   HOH Z 363 " =    1.298
peak=    4.817 closest distance to " O   HOH Z 126 " =    2.048
peak=    4.793 closest distance to " CG  PRO A  54 " =    1.326
peak=    4.752 closest distance to " O   HOH Z 427 " =    2.148
peak=    4.737 closest distance to " O   PRO A 198 " =    1.344
peak=    4.714 closest distance to " CB  GLN A 223 " =    1.489
peak=    4.691 closest distance to " O   HOH Z  29 " =    1.115
peak=    4.659 closest distance to " O   HOH Z 232 " =    2.194
peak=    4.635 closest distance to " CA  TYR A  30 " =    1.080
peak=    4.606 closest distance to " CB  SER A 216 " =    1.039
peak=    4.520 closest distance to " NZ  LYS A 117 " =    1.272
peak=    4.509 closest distance to " O   HOH Z 381 " =    1.131
peak=    4.487 closest distance to " O   HOH Z 414 " =    1.452
peak=    4.479 closest distance to " O   HOH Z 182 " =    1.227
peak=    4.475 closest distance to " O   HOH Z   9 " =    1.259
peak=    4.455 closest distance to " N   GLN A 278 " =    1.104
peak=    4.440 closest distance to " O   HOH Z 112 " =    1.166
peak=    4.437 closest distance to " O   HOH Z  78 " =    1.633
peak=    4.400 closest distance to " O   HOH Z 415 " =    1.197
peak=    4.395 closest distance to " CB  ARG A 275 " =    1.055
peak=    4.349 closest distance to " O   HOH Z 158 " =    1.427
peak=    4.346 closest distance to " O   HOH Z 147 " =    1.433
peak=    4.345 closest distance to " O   HOH Z 316 " =    3.071
peak=    4.339 closest distance to " O   HOH Z 130 " =    0.823
peak=    4.298 closest distance to " CE  MET A  93 " =    1.412
peak=    4.296 closest distance to " O   HOH Z 287 " =    2.055
peak=    4.270 closest distance to " O   HOH Z  63 " =    1.764
peak=    4.268 closest distance to " O   HOH Z 193 " =    1.857
peak=    4.261 closest distance to " O   HOH Z 272 " =    1.917
peak=    4.244 closest distance to " NZ BLYS A 290 " =    1.115
peak=    4.239 closest distance to " CB  ASP A 124 " =    0.910
peak=    4.231 closest distance to " O   HOH Z  57 " =    1.216
peak=    4.221 closest distance to " O   HOH Z  61 " =    1.619
peak=    4.177 closest distance to " CB  SER A  63 " =    1.395
peak=    4.174 closest distance to " O   HOH Z 217 " =    2.454
peak=    4.173 closest distance to " O   HOH Z  28 " =    1.515
peak=    4.169 closest distance to " O   HOH Z   4 " =    1.127
peak=    4.168 closest distance to " O   HOH Z 394 " =    1.922
peak=    4.164 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.147 closest distance to " O   HOH Z 298 " =    2.263
peak=    4.143 closest distance to " O   HOH Z 207 " =    2.277
peak=    4.140 closest distance to " O   HOH Z 111 " =    1.650
peak=    4.138 closest distance to " O   HOH Z 145 " =    2.087
peak=    4.137 closest distance to " O   HOH Z 244 " =    1.537
peak=    4.136 closest distance to " CG  PRO A 213 " =    1.262
peak=    4.112 closest distance to " O   HOH Z  88 " =    3.052
peak=    4.093 closest distance to " O   HOH Z   2 " =    1.996
peak=    4.079 closest distance to " CG1BVAL A 121 " =    2.080
peak=    4.069 closest distance to " O   HOH Z 424 " =    1.288
peak=    4.065 closest distance to " O   HOH Z 410 " =    1.524
peak=    4.063 closest distance to " OG BSER A 258 " =    0.982
peak=    4.059 closest distance to " O   HOH Z 126 " =    1.513
peak=    4.052 closest distance to " CB  SER A   3 " =    1.455
peak=    4.050 closest distance to " O   HOH Z 423 " =    1.937
peak=    4.044 closest distance to " CB  GLU A 128 " =    1.050
peak=    4.044 closest distance to " ND2 ASN A 249 " =    1.930
peak=    4.043 closest distance to " O   HOH Z  17 " =    2.149
peak=    4.043 closest distance to " O   HOH Z 134 " =    1.476
peak=    4.039 closest distance to " CG  PRO A  90 " =    1.190
peak=    4.021 closest distance to " O   HOH Z 155 " =    1.936
peak=    4.014 closest distance to " O   HOH Z 135 " =    1.939
peak=    4.001 closest distance to " CG  PRO A 198 " =    1.369
peak=    4.001 closest distance to " O   HOH Z 371 " =    2.026
peak=    3.983 closest distance to " O   HOH Z 311 " =    2.280
peak=    3.970 closest distance to " CD2 TRP A 179 " =    2.001
peak=    3.967 closest distance to " O   HOH Z 380 " =    1.966
peak=    3.967 closest distance to " O   HOH Z  91 " =    2.260
peak=    3.966 closest distance to " CB  TRP A 179 " =    1.515
peak=    3.965 closest distance to " CA  GLU A 152 " =    1.200
peak=    3.957 closest distance to " NE1 TRP A 274 " =    1.083
peak=    3.957 closest distance to " O   HOH Z 239 " =    1.519
peak=    3.948 closest distance to " O   HOH Z 392 " =    1.419
peak=    3.948 closest distance to " O   HOH Z 371 " =    1.905
peak=    3.944 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.943 closest distance to " O   HOH Z 293 " =    1.367
peak=    3.935 closest distance to " CB  GLN A 183 " =    1.148
peak=    3.927 closest distance to " O   HOH Z 313 " =    2.264
peak=    3.921 closest distance to " O   HOH Z 105 " =    1.304
peak=    3.919 closest distance to " O   HOH Z  44 " =    2.713
peak=    3.918 closest distance to " O   HOH Z 261 " =    2.159
peak=    3.916 closest distance to " O   ALA A 165 " =    1.326
peak=    3.914 closest distance to " O   HOH Z 186 " =    1.251
peak=    3.908 closest distance to " CG  GLN A 278 " =    3.795
peak=    3.895 closest distance to " O   HOH Z 258 " =    1.995
peak=    3.881 closest distance to " O   HOH Z 334 " =    2.614
peak=    3.875 closest distance to " O   HOH Z  57 " =    2.477
peak=    3.871 closest distance to " CB  TRP A 266 " =    1.019
peak=    3.870 closest distance to " O   HOH Z 171 " =    2.465
peak=    3.862 closest distance to " O   HOH Z 166 " =    1.379
peak=    3.846 closest distance to " CG  ARG A 159 " =    0.817
peak=    3.845 closest distance to " CB  GLU A 152 " =    1.241
peak=    3.833 closest distance to " O   HOH Z 183 " =    1.569
peak=    3.827 closest distance to " O   HOH Z 358 " =    1.264
peak=    3.817 closest distance to " O   HOH Z 131 " =    1.223
peak=    3.805 closest distance to " CG2 THR A 279 " =    1.025
peak=    3.802 closest distance to " O   HOH Z 281 " =    2.091
peak=    3.793 closest distance to " CB  MET A 105 " =    1.490
peak=    3.793 closest distance to " ND2 ASN A  60 " =    2.962
peak=    3.792 closest distance to " CA  LEU A 282 " =    0.989
peak=    3.792 closest distance to " CG  LEU A 167 " =    1.339
peak=    3.789 closest distance to " O   HOH Z 352 " =    1.573
peak=    3.778 closest distance to " NH1AARG A 145 " =    1.112
peak=    3.753 closest distance to " C   ASN A 209 " =    1.579
peak=    3.751 closest distance to " O   HOH Z 361 " =    1.318
peak=    3.749 closest distance to " O   HOH Z 211 " =    1.327
peak=    3.742 closest distance to " N   TYR A  15 " =    1.100
peak=    3.737 closest distance to " O   HOH Z 236 " =    1.598
peak=    3.736 closest distance to " O   HOH Z  22 " =    1.955
peak=    3.734 closest distance to " CA  GLY A 267 " =    1.379
peak=    3.730 closest distance to " O   HOH Z  51 " =    1.746
peak=    3.717 closest distance to " O   HOH Z  44 " =    1.833
peak=    3.708 closest distance to " CB  MET A  47 " =    1.132
peak=    3.699 closest distance to " NH2 ARG A 219 " =    1.653
peak=    3.697 closest distance to " O   HOH Z 258 " =    1.612
peak=    3.670 closest distance to " CD  GLN A  58 " =    5.635
peak=    3.657 closest distance to " CA  ARG A 195 " =    1.475
peak=    3.657 closest distance to " O   HOH Z 302 " =    1.493
peak=    3.656 closest distance to " OG  SER A 276 " =    0.958
peak=    3.638 closest distance to " O   HOH Z 119 " =    1.443
peak=    3.634 closest distance to " O   HOH Z 417 " =    1.749
peak=    3.631 closest distance to " O   HOH Z 359 " =    1.480
peak=    3.628 closest distance to " O   HOH Z 411 " =    3.109
peak=    3.622 closest distance to " O   HOH Z  59 " =    1.360
peak=    3.619 closest distance to " OD2 ASP A 286 " =    2.719
peak=    3.607 closest distance to " CG2 VAL A 257 " =    0.958
peak=    3.600 closest distance to " N   CYS A 260 " =    0.872
peak=    3.598 closest distance to " O   HOH Z 375 " =    0.947
peak=    3.597 closest distance to " O   HOH Z 418 " =    0.876
peak=    3.594 closest distance to " N   GLU A   2 " =    1.299
peak=    3.587 closest distance to " CB  GLU A 277 " =    3.620
peak=    3.583 closest distance to " O   HOH Z  55 " =    1.893
peak=    3.583 closest distance to " CD BLYS A 290 " =    1.115
peak=    3.580 closest distance to " CB  VAL A 265 " =    1.363
peak=    3.577 closest distance to " O   HOH Z 299 " =    2.972
peak=    3.575 closest distance to " O   HOH Z 104 " =    1.672
peak=    3.574 closest distance to " O   HOH Z 209 " =    2.430
peak=    3.573 closest distance to " CB  SER A 276 " =    1.146
peak=    3.573 closest distance to " NE AARG A 275 " =    1.568
peak=    3.558 closest distance to " O   HOH Z 384 " =    1.241
peak=    3.557 closest distance to " NE2 GLN A  58 " =    3.763
peak=    3.556 closest distance to " CB  ARG A 190 " =    1.507
peak=    3.556 closest distance to " CE3 TRP A 274 " =    1.430
peak=    3.550 closest distance to " O   HOH Z 234 " =    3.843
peak=    3.548 closest distance to " O   HOH Z 189 " =    2.173
peak=    3.547 closest distance to " O   HOH Z 133 " =    2.422
peak=    3.545 closest distance to " OG BSER A  99 " =    2.346
peak=    3.541 closest distance to " CG2 THR A 221 " =    1.161
peak=    3.525 closest distance to " NH2BARG A 102 " =    1.046
peak=    3.525 closest distance to " O   HOH Z   6 " =    1.791
peak=    3.524 closest distance to " O   HOH Z 130 " =    2.125
peak=    3.517 closest distance to " O   HOH Z 115 " =    1.844
peak=    3.517 closest distance to " CA  ASP A  50 " =    1.276
peak=    3.505 closest distance to " O   HOH Z 371 " =    3.292
peak=    3.505 closest distance to " ND1 HIS A  81 " =    1.450
peak=    3.500 closest distance to " O   HOH Z  37 " =    1.278
peak=    3.499 closest distance to " CB  ASN A 187 " =    0.995
peak=    3.496 closest distance to " O   HOH Z 402 " =    1.364
peak=    3.494 closest distance to " O   HOH Z 373 " =    1.463
peak=    3.491 closest distance to " O   HOH Z 171 " =    1.988
peak=    3.489 closest distance to " CB  ALA A  43 " =    0.977
peak=    3.488 closest distance to " CD  LYS A 166 " =    1.641
peak=    3.488 closest distance to " O   THR A 220 " =    1.635
peak=    3.487 closest distance to " O   HOH Z 119 " =    4.220
peak=    3.486 closest distance to " CE3 TRP A 274 " =    2.213
peak=    3.484 closest distance to " O   HOH Z 222 " =    2.057
peak=    3.479 closest distance to " O   HOH Z 411 " =    1.305
peak=    3.476 closest distance to " O   HOH Z  11 " =    1.774
peak=    3.475 closest distance to " O   HOH Z 217 " =    1.696
peak=    3.475 closest distance to " O   HOH Z 284 " =    1.340
peak=    3.473 closest distance to " CA  GLU A  46 " =    0.757
peak=    3.468 closest distance to " O   HOH Z 225 " =    1.444
peak=    3.467 closest distance to " O   HOH Z   9 " =    1.402
peak=    3.462 closest distance to " CB  LYS A 290 " =    0.873
peak=    3.461 closest distance to " O   HOH Z 345 " =    1.913
peak=    3.456 closest distance to " CA  ASN A 127 " =    0.973
peak=    3.456 closest distance to " CG  GLN A  88 " =    1.063
peak=    3.449 closest distance to " O   HOH Z 148 " =    1.548
peak=    3.448 closest distance to " O   HOH Z 288 " =    1.931
peak=    3.447 closest distance to " CA  GLY A 196 " =    0.963
peak=    3.444 closest distance to " O   HOH Z  61 " =    1.608
peak=    3.443 closest distance to " O   HOH Z 233 " =    1.450
peak=    3.442 closest distance to " O   HOH Z 405 " =    1.829
peak=    3.429 closest distance to " ND2 ASN A  60 " =    3.782
peak=    3.427 closest distance to " O   HOH Z 311 " =    1.495
peak=    3.425 closest distance to " CA  ILE A 234 " =    1.103
peak=    3.421 closest distance to " O   HOH Z   9 " =    2.318
peak=    3.417 closest distance to " O   HOH Z 385 " =    3.431
peak=    3.415 closest distance to " O   HOH Z 413 " =    1.586
peak=    3.415 closest distance to " O   HOH Z  11 " =    1.210
peak=    3.412 closest distance to " CA  ARG A  36 " =    1.418
peak=    3.410 closest distance to " O   HOH Z 122 " =    1.821
peak=    3.408 closest distance to " O   HOH Z 409 " =    2.051
peak=    3.402 closest distance to " N   SER A 210 " =    1.156
peak=    3.400 closest distance to " OD1 ASN A 217 " =    1.572
peak=    3.399 closest distance to " CD2 TRP A 179 " =    1.403
peak=    3.399 closest distance to " OE1 GLN A  88 " =    0.916
peak=    3.393 closest distance to " OG BSER A 212 " =    2.846
peak=    3.392 closest distance to " O   HOH Z 152 " =    2.177
peak=    3.391 closest distance to " O   HOH Z 282 " =    1.638
peak=    3.390 closest distance to " CA  TYR A 186 " =    1.562
peak=    3.389 closest distance to " NH2BARG A 190 " =    1.538
peak=    3.388 closest distance to " O   HOH Z 167 " =    1.692
peak=    3.384 closest distance to " O   HOH Z 158 " =    2.432
peak=    3.377 closest distance to " O   HOH Z 431 " =    1.386
peak=    3.376 closest distance to " OE1 GLN A  11 " =    2.150
peak=    3.375 closest distance to " O   HOH Z 368 " =    1.871
peak=    3.371 closest distance to " O   HOH Z 108 " =    1.679
peak=    3.369 closest distance to " O   HOH Z  32 " =    2.288
peak=    3.366 closest distance to " NH1 ARG A  56 " =    1.172
peak=    3.366 closest distance to " O   HOH Z 278 " =    1.101
peak=    3.363 closest distance to " O   HOH Z   7 " =    3.137
peak=    3.360 closest distance to " O   HOH Z 175 " =    3.501
peak=    3.360 closest distance to " OE1 GLN A 240 " =    1.752
peak=    3.359 closest distance to " O   ARG A  56 " =    1.843
peak=    3.359 closest distance to " O   HOH Z  68 " =    1.886
peak=    3.352 closest distance to " O   HOH Z  95 " =    1.894
peak=    3.347 closest distance to " O   HOH Z 276 " =    1.229
peak=    3.345 closest distance to " CA  ALA A  21 " =    1.157
peak=    3.341 closest distance to " CA  MET A 105 " =    0.849
peak=    3.340 closest distance to " CB  LYS A 117 " =    1.171
peak=    3.340 closest distance to " CA  ALA A 160 " =    0.809
peak=    3.336 closest distance to " O   ASN A 301 " =    2.177
peak=    3.333 closest distance to " CD1 ILE A  33 " =    1.727
peak=    3.332 closest distance to " CD  ARG A 159 " =    0.904
peak=    3.328 closest distance to " CD  LYS A 119 " =    1.266
peak=    3.325 closest distance to " CB  LEU A 228 " =    1.133
peak=    3.325 closest distance to " CA  SER A  32 " =    1.725
peak=    3.322 closest distance to " O   HOH Z 412 " =    1.501
peak=    3.320 closest distance to " O   HOH Z 132 " =    1.013
peak=    3.317 closest distance to " CB  GLU A 236 " =    1.488
peak=    3.313 closest distance to " O   HOH Z  47 " =    1.607
peak=    3.307 closest distance to " CG2 ILE A 234 " =    0.976
peak=    3.304 closest distance to " CG  LYS A  76 " =    1.638
peak=    3.294 closest distance to " CA  ALA A  51 " =    1.189
peak=    3.294 closest distance to " CZ  PHE A  38 " =    1.386
peak=    3.291 closest distance to " N   ARG A 156 " =    1.281
peak=    3.290 closest distance to " CB  LEU A 300 " =    0.939
peak=    3.290 closest distance to " OE2 GLU A  53 " =    1.983
peak=    3.289 closest distance to " O   GLY A 302 " =    2.534
peak=    3.286 closest distance to " O   HOH Z 239 " =    1.604
peak=    3.286 closest distance to " O   HOH Z 295 " =    1.630
peak=    3.286 closest distance to " O   HOH Z 271 " =    2.183
peak=    3.279 closest distance to " O   HOH Z 422 " =    2.692
peak=    3.276 closest distance to " O   HOH Z 399 " =    0.879
peak=    3.274 closest distance to " CB  THR A  82 " =    1.170
peak=    3.274 closest distance to " OG  SER A  26 " =    1.480
peak=    3.272 closest distance to " N   PHE A 130 " =    1.253
peak=    3.271 closest distance to " O   HOH Z 117 " =    1.229
peak=    3.270 closest distance to " CB  ALA A  34 " =    1.323
peak=    3.269 closest distance to " N   ASN A 127 " =    1.286
peak=    3.254 closest distance to " O   HOH Z 170 " =    2.098
peak=    3.247 closest distance to " CB  MET A  40 " =    0.884
peak=    3.247 closest distance to " CB  PHE A 225 " =    1.465
peak=    3.246 closest distance to " O   HOH Z 326 " =    3.613
peak=    3.242 closest distance to " O   HOH Z 220 " =    1.223
peak=    3.237 closest distance to " O   HOH Z  10 " =    1.823
peak=    3.237 closest distance to " O   HOH Z 133 " =    1.399
peak=    3.237 closest distance to " O   HOH Z 400 " =    0.726
peak=    3.236 closest distance to " O   HOH Z 344 " =    3.430
peak=    3.233 closest distance to " CB  GLU A 236 " =    1.405
peak=    3.227 closest distance to " O   HOH Z 393 " =    1.376
peak=    3.227 closest distance to " CB  GLU A 277 " =    1.210
peak=    3.226 closest distance to " CA  ASN A 217 " =    1.245
peak=    3.215 closest distance to " CD  ARG A 138 " =    0.803
peak=    3.215 closest distance to " CB  GLU A 152 " =    0.902
peak=    3.209 closest distance to " O   MET A 105 " =    1.724
peak=    3.206 closest distance to " O   HOH Z 128 " =    2.299
peak=    3.204 closest distance to " CZ  PHE A 192 " =    1.004
peak=    3.204 closest distance to " O   HOH Z 411 " =    0.994
peak=    3.203 closest distance to " O   HOH Z  30 " =    1.792
peak=    3.203 closest distance to " CG1 VAL A 202 " =    1.992
peak=    3.202 closest distance to " CB  TYR A 116 " =    1.148
peak=    3.196 closest distance to " N   ALA A   1 " =    2.650
peak=    3.196 closest distance to " O   HOH Z 213 " =    1.814
peak=    3.195 closest distance to " O   HOH Z 108 " =    1.850
peak=    3.194 closest distance to " CB  ASN A 285 " =    0.926
peak=    3.193 closest distance to " O   HOH Z 216 " =    2.485
peak=    3.191 closest distance to " O   HOH Z 284 " =    1.042
peak=    3.189 closest distance to " SD  MET A 188 " =    1.573
peak=    3.187 closest distance to " O   HOH Z  53 " =    1.539
peak=    3.185 closest distance to " O   HOH Z 353 " =    2.423
peak=    3.184 closest distance to " O   HOH Z 425 " =    2.042
peak=    3.183 closest distance to " O   HOH Z 180 " =    2.161
peak=    3.181 closest distance to " O   HOH Z 380 " =    3.088
peak=    3.179 closest distance to " O   HOH Z  40 " =    2.224
peak=    3.179 closest distance to " O   HOH Z 286 " =    2.375
peak=    3.177 closest distance to " CG2 ILE A 151 " =    1.142
peak=    3.169 closest distance to " O   TYR A 116 " =    1.234
peak=    3.165 closest distance to " CA  PRO A 280 " =    1.645
peak=    3.163 closest distance to " CB  PRO A 243 " =    1.105
peak=    3.163 closest distance to " CB  SER A 288 " =    0.726
peak=    3.162 closest distance to " CE3 TRP A  85 " =    0.890
peak=    3.155 closest distance to " O   HOH Z 276 " =    2.131
peak=    3.155 closest distance to " O   HOH Z 435 " =    2.691
peak=    3.152 closest distance to " OD1 ASP A 238 " =    0.930
peak=    3.150 closest distance to " O   HOH Z 368 " =    3.783
peak=    3.149 closest distance to " O   HOH Z 193 " =    2.087
peak=    3.147 closest distance to " O   HOH Z  76 " =    0.986
peak=    3.142 closest distance to " ND2 ASN A 187 " =    1.447
peak=    3.140 closest distance to " CG  GLN A  11 " =    2.185
peak=    3.134 closest distance to " CG1 ILE A 120 " =    1.461
peak=    3.134 closest distance to " O   HOH Z 248 " =    1.987
peak=    3.131 closest distance to " CB  ASN A 170 " =    1.444
peak=    3.130 closest distance to " NZ  LYS A  76 " =    1.519
peak=    3.128 closest distance to " CD  ARG A 195 " =    3.465
peak=    3.127 closest distance to " NH2BARG A 145 " =    2.130
peak=    3.126 closest distance to " O   HOH Z 170 " =    1.186
peak=    3.123 closest distance to " O   HOH Z 216 " =    1.661
peak=    3.121 closest distance to " CA  THR A 264 " =    0.858
peak=    3.120 closest distance to " O   HOH Z   1 " =    1.664
peak=    3.119 closest distance to " O   HOH Z 419 " =    2.152
peak=    3.104 closest distance to " SD  MET A  93 " =    1.049
peak=    3.104 closest distance to " CA  SER A  12 " =    1.439
peak=    3.101 closest distance to " CB  GLN A 103 " =    1.114
peak=    3.097 closest distance to " O   HOH Z 216 " =    1.513
peak=    3.092 closest distance to " CE AMET A  47 " =    1.281
peak=    3.058 closest distance to " CB  ALA A 114 " =    1.068
peak=    3.051 closest distance to " CB  ALA A  84 " =    0.724
peak=    3.037 closest distance to " CG2 VAL A  78 " =    1.019
peak=    3.025 closest distance to " CB  TRP A 274 " =    1.421
peak=    3.007 closest distance to " O   HOH Z 421 " =    2.674

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 5.772
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.718 - 5.772

peak=   -4.610 closest distance to " CG  MET A 105 " =    0.972
peak=   -4.527 closest distance to " CD  ARG A  14 " =    3.158
peak=   -4.225 closest distance to " O   HOH Z  60 " =    1.789
peak=   -4.211 closest distance to " O   HOH Z 290 " =    1.280
peak=   -4.198 closest distance to " CB  PRO A 243 " =    2.430
peak=   -4.194 closest distance to " CG  GLN A  88 " =    0.877
peak=   -4.176 closest distance to " NE1 TRP A 179 " =    1.169
peak=   -4.115 closest distance to " O   HOH Z 407 " =    3.378
peak=   -4.114 closest distance to " O   HOH Z 404 " =    0.946
peak=   -4.068 closest distance to " O   PRO A 198 " =    1.274
peak=   -4.049 closest distance to " OG BSER A 134 " =    1.624
peak=   -4.016 closest distance to " CG  PRO A 163 " =    2.428
peak=   -3.978 closest distance to " CB  ASP A  27 " =    2.489
peak=   -3.974 closest distance to " CB  ALA A 248 " =    1.916
peak=   -3.963 closest distance to " O   HOH Z 166 " =    1.185
peak=   -3.844 closest distance to " O   HOH Z  88 " =    2.057
peak=   -3.829 closest distance to " O   HOH Z 111 " =    2.025
peak=   -3.829 closest distance to " OE1 GLN A  88 " =    0.985
peak=   -3.826 closest distance to " O   HOH Z  43 " =    1.395
peak=   -3.824 closest distance to " O   HOH Z 425 " =    0.898
peak=   -3.818 closest distance to " O   HOH Z 377 " =    1.895
peak=   -3.789 closest distance to " O   ALA A   1 " =    1.064
peak=   -3.787 closest distance to " O   HOH Z 418 " =    1.173
peak=   -3.782 closest distance to " O   HOH Z 417 " =    3.014
peak=   -3.777 closest distance to " O   ASP A 191 " =    1.955
peak=   -3.774 closest distance to " O   HOH Z 385 " =    1.135
peak=   -3.766 closest distance to " N   THR A 157 " =    1.467
peak=   -3.765 closest distance to " CA  GLY A 133 " =    1.990
peak=   -3.722 closest distance to " O   HOH Z 231 " =    0.754
peak=   -3.707 closest distance to " CZ  PHE A  59 " =    1.431
peak=   -3.702 closest distance to " OG  SER A  97 " =    2.083
peak=   -3.700 closest distance to " O   HOH Z   1 " =    3.742
peak=   -3.669 closest distance to " CG  GLU A 152 " =    2.269
peak=   -3.654 closest distance to " O   HOH Z  77 " =    1.707
peak=   -3.653 closest distance to " O   HOH Z 198 " =    2.261
peak=   -3.652 closest distance to " O   HOH Z 411 " =    1.468
peak=   -3.651 closest distance to " CD  ARG A 156 " =    1.893
peak=   -3.643 closest distance to " O   HOH Z 185 " =    2.279
peak=   -3.642 closest distance to " OG  SER A  87 " =    1.345
peak=   -3.617 closest distance to " O   HOH Z 386 " =    3.240
peak=   -3.605 closest distance to " O   HOH Z  51 " =    0.909
peak=   -3.604 closest distance to " CB  SER A  62 " =    2.446
peak=   -3.598 closest distance to " OD1 ASN A  60 " =    0.988
peak=   -3.597 closest distance to " NH2AARG A 275 " =    5.772
peak=   -3.590 closest distance to " CE  MET A 113 " =    2.280
peak=   -3.574 closest distance to " CB  ALA A 100 " =    2.112
peak=   -3.571 closest distance to " NE2 GLN A  55 " =    0.732
peak=   -3.571 closest distance to " CA  GLY A  23 " =    2.786
peak=   -3.571 closest distance to " CD  GLU A 277 " =    2.424
peak=   -3.570 closest distance to " OH  TYR A 214 " =    1.183
peak=   -3.566 closest distance to " O   HOH Z 102 " =    1.755
peak=   -3.560 closest distance to " CB  ALA A 227 " =    2.301
peak=   -3.543 closest distance to " N   ARG A 159 " =    1.899
peak=   -3.542 closest distance to " CB  TYR A  15 " =    2.055
peak=   -3.542 closest distance to " OE1 GLN A  58 " =    2.684
peak=   -3.540 closest distance to " O   HOH Z 415 " =    1.215
peak=   -3.539 closest distance to " O   HOH Z 124 " =    1.174
peak=   -3.538 closest distance to " O   HOH Z 117 " =    0.718
peak=   -3.537 closest distance to " O   HOH Z   4 " =    1.306
peak=   -3.531 closest distance to " NH2 ARG A  79 " =    1.871
peak=   -3.530 closest distance to " O   HOH Z  90 " =    2.720
peak=   -3.521 closest distance to " CA  GLY A 241 " =    2.172
peak=   -3.520 closest distance to " O   HOH Z 163 " =    1.511
peak=   -3.511 closest distance to " CB  ASN A 285 " =    2.150
peak=   -3.510 closest distance to " O   HOH Z 231 " =    1.948
peak=   -3.501 closest distance to " O   HOH Z  28 " =    1.748
peak=   -3.493 closest distance to " O   SER A 216 " =    1.916
peak=   -3.487 closest distance to " O   GLY A  80 " =    2.449
peak=   -3.483 closest distance to " CG2AVAL A  41 " =    2.717
peak=   -3.482 closest distance to " O   HOH Z 174 " =    2.952
peak=   -3.477 closest distance to " CA  ALA A  71 " =    2.138
peak=   -3.468 closest distance to " O   HOH Z   1 " =    1.333
peak=   -3.468 closest distance to " OG ASER A 134 " =    1.187
peak=   -3.467 closest distance to " O   HOH Z 140 " =    4.857
peak=   -3.465 closest distance to " CB  CYS A 201 " =    2.307
peak=   -3.463 closest distance to " O   HOH Z 426 " =    1.726
peak=   -3.450 closest distance to " O   ASN A 301 " =    1.267
peak=   -3.449 closest distance to " CD  LYS A 289 " =    2.507
peak=   -3.444 closest distance to " OG  SER A 245 " =    1.195
peak=   -3.443 closest distance to " O   HOH Z 143 " =    1.210
peak=   -3.441 closest distance to " CD2 TYR A 293 " =    1.881
peak=   -3.440 closest distance to " CD  LYS A 166 " =    2.334
peak=   -3.436 closest distance to " O   HOH Z  97 " =    1.380
peak=   -3.433 closest distance to " O   HOH Z 211 " =    1.678
peak=   -3.432 closest distance to " O   HOH Z 278 " =    1.094
peak=   -3.429 closest distance to " O   HOH Z 359 " =    1.426
peak=   -3.421 closest distance to " CG BLYS A 290 " =    0.919
peak=   -3.407 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.407 closest distance to " O   HOH Z 417 " =    2.068
peak=   -3.406 closest distance to " O   HOH Z 139 " =    2.396
peak=   -3.406 closest distance to " N   SER A  12 " =    1.140
peak=   -3.400 closest distance to " OD1 ASN A 301 " =    2.089
peak=   -3.400 closest distance to " O   SER A 135 " =    1.539
peak=   -3.400 closest distance to " OE2 GLU A 152 " =    2.212
peak=   -3.398 closest distance to " O   HOH Z  52 " =    1.797
peak=   -3.396 closest distance to " OD2 ASP A 298 " =    0.987
peak=   -3.393 closest distance to " CB  ALA A 291 " =    1.900
peak=   -3.390 closest distance to " O   HOH Z 118 " =    1.180
peak=   -3.385 closest distance to " OD2 ASP A 171 " =    2.049
peak=   -3.385 closest distance to " CD  ARG A 219 " =    2.463
peak=   -3.385 closest distance to " CD2 LEU A 237 " =    2.502
peak=   -3.384 closest distance to " N   ALA A  43 " =    2.351
peak=   -3.377 closest distance to " CD  GLN A 223 " =    1.385
peak=   -3.374 closest distance to " O   HOH Z  24 " =    1.348
peak=   -3.370 closest distance to " O   HOH Z 286 " =    1.694
peak=   -3.363 closest distance to " NH2 ARG A 219 " =    1.788
peak=   -3.357 closest distance to " CD1 LEU A 101 " =    2.336
peak=   -3.356 closest distance to " C   VAL A  72 " =    1.002
peak=   -3.355 closest distance to " O   HOH Z 126 " =    1.887
peak=   -3.354 closest distance to " O   HOH Z 297 " =    3.731
peak=   -3.352 closest distance to " OD2 ASP A 132 " =    2.258
peak=   -3.350 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.350 closest distance to " OE1 GLN A 223 " =    2.314
peak=   -3.349 closest distance to " CD  ARG A 139 " =    1.574
peak=   -3.347 closest distance to " O   ILE A  49 " =    1.631
peak=   -3.346 closest distance to " CA  GLY A  98 " =    1.715
peak=   -3.346 closest distance to " CB  ASP A 132 " =    2.369
peak=   -3.344 closest distance to " O   PRO A 243 " =    2.375
peak=   -3.344 closest distance to " O   HOH Z  39 " =    1.449
peak=   -3.339 closest distance to " ND2 ASN A 209 " =    1.804
peak=   -3.326 closest distance to " O   ALA A  10 " =    1.631
peak=   -3.317 closest distance to " O   HOH Z 234 " =    4.806
peak=   -3.314 closest distance to " O   TRP A  70 " =    1.479
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.803
peak=   -3.311 closest distance to " CB  PHE A 208 " =    2.140
peak=   -3.306 closest distance to " O   HOH Z 352 " =    1.954
peak=   -3.306 closest distance to " O   HOH Z  49 " =    1.564
peak=   -3.305 closest distance to " NH2BARG A 275 " =    1.818
peak=   -3.304 closest distance to " O   HOH Z 388 " =    1.885
peak=   -3.293 closest distance to " N   GLN A  58 " =    1.311
peak=   -3.290 closest distance to " OE1 GLN A 278 " =    1.229
peak=   -3.286 closest distance to " CE2 TYR A  30 " =    2.689
peak=   -3.284 closest distance to " O   HOH Z 266 " =    4.563
peak=   -3.279 closest distance to " OG  SER A 206 " =    1.920
peak=   -3.278 closest distance to " O   HOH Z  52 " =    1.285
peak=   -3.275 closest distance to " CA  HIS A  86 " =    2.146
peak=   -3.271 closest distance to " O   HOH Z  71 " =    2.305
peak=   -3.268 closest distance to " CE2 TYR A 186 " =    1.894
peak=   -3.264 closest distance to " N   ASP A 270 " =    1.435
peak=   -3.262 closest distance to " O   ARG A 145 " =    1.229
peak=   -3.259 closest distance to " O   HOH Z 435 " =    3.136
peak=   -3.249 closest distance to " CD  GLN A  58 " =    0.956
peak=   -3.248 closest distance to " OE1 GLN A 223 " =    2.598
peak=   -3.247 closest distance to " CA  GLY A 203 " =    2.249
peak=   -3.245 closest distance to " CB  TYR A  68 " =    1.860
peak=   -3.242 closest distance to " CZ2 TRP A 274 " =    1.032
peak=   -3.239 closest distance to " O   HOH Z 323 " =    1.990
peak=   -3.238 closest distance to " CB  SER A 271 " =    1.097
peak=   -3.238 closest distance to " CB  TRP A  85 " =    2.497
peak=   -3.237 closest distance to " O   HOH Z 209 " =    2.643
peak=   -3.234 closest distance to " O   HOH Z 372 " =    2.612
peak=   -3.227 closest distance to " O   HOH Z 426 " =    2.285
peak=   -3.226 closest distance to " O   HOH Z 393 " =    2.702
peak=   -3.223 closest distance to " O   HOH Z 411 " =    1.264
peak=   -3.223 closest distance to " O   HOH Z 298 " =    1.004
peak=   -3.222 closest distance to " CE  LYS A 166 " =    1.108
peak=   -3.221 closest distance to " O   HOH Z 424 " =    0.945
peak=   -3.218 closest distance to " O   HOH Z 431 " =    1.311
peak=   -3.218 closest distance to " O   HOH Z 196 " =    1.716
peak=   -3.206 closest distance to " N   GLN A  58 " =    1.749
peak=   -3.188 closest distance to " CB  PHE A 192 " =    1.558
peak=   -3.188 closest distance to " CB  ALA A 291 " =    2.141
peak=   -3.183 closest distance to " C   HIS A 108 " =    1.201
peak=   -3.183 closest distance to " CB  ILE A 199 " =    2.739
peak=   -3.181 closest distance to " OE2 GLU A 152 " =    0.999
peak=   -3.174 closest distance to " O   HOH Z 292 " =    1.271
peak=   -3.171 closest distance to " C   GLU A 277 " =    2.281
peak=   -3.171 closest distance to " O   HOH Z 213 " =    1.177
peak=   -3.170 closest distance to " O   TYR A  30 " =    1.830
peak=   -3.163 closest distance to " O   HOH Z  73 " =    2.394
peak=   -3.163 closest distance to " CG2BVAL A  41 " =    2.584
peak=   -3.162 closest distance to " O   HOH Z   2 " =    0.911
peak=   -3.160 closest distance to " O   HOH Z  60 " =    2.267
peak=   -3.159 closest distance to " CE3 TRP A 179 " =    1.404
peak=   -3.156 closest distance to " O   ASN A 301 " =    1.809
peak=   -3.156 closest distance to " O   HOH Z 409 " =    5.619
peak=   -3.150 closest distance to " CG  ARG A 259 " =    2.530
peak=   -3.148 closest distance to " O   HOH Z  76 " =    1.014
peak=   -3.139 closest distance to " CE3 TRP A 150 " =    2.137
peak=   -3.136 closest distance to " CE2 TYR A 116 " =    3.107
peak=   -3.134 closest distance to " CA  ASN A 127 " =    1.469
peak=   -3.132 closest distance to " N   ALA A   1 " =    2.895
peak=   -3.127 closest distance to " CB  ALA A  43 " =    2.161
peak=   -3.126 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.124 closest distance to " CG1BVAL A  41 " =    2.828
peak=   -3.124 closest distance to " CG2 ILE A  20 " =    2.919
peak=   -3.122 closest distance to " ND2 ASN A 187 " =    1.596
peak=   -3.120 closest distance to " O   SER A 146 " =    1.377
peak=   -3.118 closest distance to " O   ARG A  56 " =    1.587
peak=   -3.117 closest distance to " CB  CYS A 254 " =    1.874
peak=   -3.112 closest distance to " O   MET A  47 " =    2.672
peak=   -3.107 closest distance to " O   HOH Z 416 " =    0.826
peak=   -3.103 closest distance to " O   HOH Z 336 " =    5.719
peak=   -3.100 closest distance to " OH  TYR A 247 " =    1.408
peak=   -3.099 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.090 closest distance to " O   HOH Z 218 " =    3.340
peak=   -3.088 closest distance to " O   HOH Z 438 " =    0.861
peak=   -3.086 closest distance to " O   HOH Z 393 " =    4.592
peak=   -3.085 closest distance to " O   HOH Z 381 " =    1.214
peak=   -3.080 closest distance to " CG2 ILE A 151 " =    2.531
peak=   -3.073 closest distance to " O   HOH Z 247 " =    1.315
peak=   -3.053 closest distance to " NH2 ARG A 159 " =    2.487
peak=   -3.048 closest distance to " O   VAL A 125 " =    2.230
peak=   -3.028 closest distance to " OXT GLY A 302 " =    3.208
peak=   -3.020 closest distance to " CB  ARG A  79 " =    2.549

================= 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    :  0.4780 0.4751   6.288026e+00   6.284610e+00
   1_bss:  0.4703 0.4674   6.285302e+00   6.277779e+00
   1_xyz:  0.3892 0.4297   6.177232e+00   6.225729e+00
   1_adp:  0.3611 0.4323   6.144150e+00   6.228304e+00
   1_occ:  0.3606 0.4333   6.143154e+00   6.228112e+00
   2_bss:  0.3611 0.4319   6.145572e+00   6.228471e+00
   2_xyz:  0.2991 0.3641   5.998451e+00   6.126445e+00
   2_adp:  0.2790 0.3678   5.967563e+00   6.127413e+00
   2_occ:  0.2788 0.3680   5.967207e+00   6.127611e+00
   3_bss:  0.2793 0.3670   5.965682e+00   6.125821e+00
   3_xyz:  0.2293 0.3021   5.785793e+00   5.975672e+00
   3_adp:  0.2123 0.2736   5.706013e+00   5.890920e+00
   3_occ:  0.2118 0.2721   5.703364e+00   5.888064e+00
   4_bss:  0.2109 0.2702   5.700531e+00   5.883719e+00
   4_xyz:  0.1722 0.2233   5.515798e+00   5.719199e+00
   4_adp:  0.1613 0.2157   5.469502e+00   5.685699e+00
   4_occ:  0.1611 0.2154   5.468346e+00   5.684431e+00
   5_bss:  0.1612 0.2151   5.467111e+00   5.683142e+00
   5_xyz:  0.1326 0.1861   5.297761e+00   5.541325e+00
   5_adp:  0.1263 0.1794   5.257123e+00   5.506253e+00
   5_occ:  0.1262 0.1791   5.256426e+00   5.505548e+00
   5_bss:  0.1267 0.1791   5.257446e+00   5.505137e+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:  0.345  39.990  -0.030   1.763  -1.396   0.000  -0.000  -0.000
   1_xyz:  0.345  39.990  -0.030   1.763  -1.396   0.000  -0.000  -0.000
   1_adp:  0.345  39.990  -0.030   1.763  -1.396   0.000  -0.000  -0.000
   1_occ:  0.345  39.990  -0.030   1.763  -1.396   0.000  -0.000  -0.000
   2_bss:  0.366  74.664   0.520   1.440   0.088   0.000   0.000   0.000
   2_xyz:  0.366  74.664   0.520   1.440   0.088   0.000   0.000   0.000
   2_adp:  0.366  74.664   0.520   1.440   0.088   0.000   0.000   0.000
   2_occ:  0.366  74.664   0.520   1.440   0.088   0.000   0.000   0.000
   3_bss:  0.361  77.492   0.696   0.769   1.038   0.000   0.000   0.000
   3_xyz:  0.361  77.492   0.696   0.769   1.038   0.000   0.000   0.000
   3_adp:  0.361  77.492   0.696   0.769   1.038   0.000   0.000   0.000
   3_occ:  0.361  77.492   0.696   0.769   1.038   0.000   0.000   0.000
   4_bss:  0.337  62.822  -0.580  -0.851  -0.200  -0.000  -0.000  -0.000
   4_xyz:  0.337  62.822  -0.580  -0.851  -0.200  -0.000  -0.000  -0.000
   4_adp:  0.337  62.822  -0.580  -0.851  -0.200  -0.000  -0.000  -0.000
   4_occ:  0.337  62.822  -0.580  -0.851  -0.200  -0.000  -0.000  -0.000
   5_bss:  0.326  57.239  -0.966  -1.720  -0.547  -0.000  -0.000  -0.000
   5_xyz:  0.326  57.239  -0.966  -1.720  -0.547  -0.000  -0.000  -0.000
   5_adp:  0.326  57.239  -0.966  -1.720  -0.547  -0.000  -0.000  -0.000
   5_occ:  0.326  57.239  -0.966  -1.720  -0.547  -0.000  -0.000  -0.000
   5_bss:  0.326  57.242  -0.969  -1.723  -0.550  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.373 0.4022  0.5600    76850.477
   1_bss:  58.634 0.4105  0.5787    74343.533
   1_xyz:  50.805 0.5095  0.6979    57733.634
   1_adp:  51.176 0.5045  0.6724    58206.318
   1_occ:  51.191 0.5043  0.6716    58176.181
   2_bss:  51.106 0.5053  0.6872    58022.684
   2_xyz:  40.743 0.6327  0.8448    38790.629
   2_adp:  40.543 0.6348  0.8471    39244.118
   2_occ:  40.564 0.6345  0.8463    39201.055
   3_bss:  40.414 0.6360  0.8522    38762.519
   3_xyz:  31.993 0.7343  0.9559    25151.637
   3_adp:  27.626 0.7839  0.9895    20012.238
   3_occ:  27.522 0.7849  0.9898    19826.023
   4_bss:  27.363 0.7863  0.9433    19535.168
   4_xyz:  22.016 0.8411  0.9807    13051.202
   4_adp:  21.026 0.8513  0.9817    12120.585
   4_occ:  20.982 0.8518  0.9815    12072.328
   5_bss:  20.937 0.8521  0.9631    12010.828
   5_xyz:  17.457 0.8849  0.9817     8792.985
   5_adp:  16.504 0.8939  0.9804     8209.416
   5_occ:  16.483 0.8941  0.9804     8189.088
   5_bss:  16.485 0.8940  0.9803     8179.222
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8846e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8846e-01
   1_xyz:   1.557  0.012  0.108 15.994  0.006  4.105   1.2990e-01
   1_adp:   1.557  0.012  0.108 15.994  0.006  4.105   1.2990e-01
   1_occ:   1.557  0.012  0.108 15.994  0.006  4.105   1.2990e-01
   2_bss:   1.557  0.012  0.108 15.994  0.006  4.105   1.2990e-01
   2_xyz:   1.341  0.010  0.089 15.309  0.005  4.105   1.0738e-01
   2_adp:   1.341  0.010  0.089 15.309  0.005  4.105   1.0738e-01
   2_occ:   1.341  0.010  0.089 15.309  0.005  4.105   1.0738e-01
   3_bss:   1.341  0.010  0.089 15.309  0.005  4.105   1.0738e-01
   3_xyz:   1.232  0.009  0.087 14.793  0.004  4.117   8.4449e-02
   3_adp:   1.232  0.009  0.087 14.793  0.004  4.117   8.4449e-02
   3_occ:   1.232  0.009  0.087 14.793  0.004  4.117   8.4449e-02
   4_bss:   1.232  0.009  0.087 14.793  0.004  4.117   8.4449e-02
   4_xyz:   0.958  0.006  0.068 14.120  0.003  4.114   5.5559e-02
   4_adp:   0.958  0.006  0.068 14.120  0.003  4.114   5.5559e-02
   4_occ:   0.958  0.006  0.068 14.120  0.003  4.114   5.5559e-02
   5_bss:   0.958  0.006  0.068 14.120  0.003  4.114   5.5559e-02
   5_xyz:   1.096  0.008  0.075 14.573  0.004  4.108   6.8636e-02
   5_adp:   1.096  0.008  0.075 14.573  0.004  4.108   6.8636e-02
   5_occ:   1.096  0.008  0.075 14.573  0.004  4.108   6.8636e-02
   5_bss:   1.096  0.008  0.075 14.573  0.004  4.108   6.8636e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.494   2.4033e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.494   2.4033e-01
   1_xyz:  10.436  0.108  0.581 87.231  0.031  1.971   9.9806e-02
   1_adp:  10.436  0.108  0.581 87.231  0.031  1.971   9.9806e-02
   1_occ:  10.436  0.108  0.581 87.231  0.031  1.971   9.9806e-02
   2_bss:  10.436  0.108  0.581 87.231  0.031  1.971   9.9806e-02
   2_xyz:   8.293  0.060  0.313 81.615  0.054  1.956   1.7571e-01
   2_adp:   8.293  0.060  0.313 81.615  0.054  1.956   1.7571e-01
   2_occ:   8.293  0.060  0.313 81.615  0.054  1.956   1.7571e-01
   3_bss:   8.293  0.060  0.313 81.615  0.054  1.956   1.7571e-01
   3_xyz:   8.505  0.047  0.437 76.642  0.030  2.150   8.1548e-02
   3_adp:   8.505  0.047  0.437 76.642  0.030  2.150   8.1548e-02
   3_occ:   8.505  0.047  0.437 76.642  0.030  2.150   8.1548e-02
   4_bss:   8.505  0.047  0.437 76.642  0.030  2.150   8.1548e-02
   4_xyz:   7.385  0.040  0.209 76.320  0.032  2.367   6.1308e-02
   4_adp:   7.385  0.040  0.209 76.320  0.032  2.367   6.1308e-02
   4_occ:   7.385  0.040  0.209 76.320  0.032  2.367   6.1308e-02
   5_bss:   7.385  0.040  0.209 76.320  0.032  2.367   6.1308e-02
   5_xyz:   8.637  0.039  0.231 83.147  0.038  2.245   5.5632e-02
   5_adp:   8.637  0.039  0.231 83.147  0.038  2.245   5.5632e-02
   5_occ:   8.637  0.039  0.231 83.147  0.038  2.245   5.5632e-02
   5_bss:   8.637  0.039  0.231 83.147  0.038  2.245   5.5632e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 138.02   0.00  17.09 138.02   0.00  13.67  66.08   0.00  35.71
   1_occ: 138.02   0.00  17.09 138.02   0.00  13.67  66.08   0.00  35.71
   2_bss: 138.02   0.00  17.09 138.02   0.00  13.67  66.08   0.00  35.71
   2_xyz: 138.02   0.00  17.09 138.02   0.00  13.67  66.08   0.00  35.71
   2_adp: 104.66   0.00  19.58  88.95   0.00  15.65 104.66   0.00  40.95
   2_occ: 104.66   0.00  19.58  88.95   0.00  15.65 104.66   0.00  40.95
   3_bss: 104.66   0.00  19.58  88.95   0.00  15.65 104.66   0.00  40.95
   3_xyz: 104.66   0.00  19.58  88.95   0.00  15.65 104.66   0.00  40.95
   3_adp:  94.02   0.00  17.25  83.53   0.00  13.08  94.02   3.34  39.98
   3_occ:  94.02   0.00  17.25  83.53   0.00  13.08  94.02   3.34  39.98
   4_bss:  94.02   0.00  17.25  83.53   0.00  13.08  94.02   3.34  39.98
   4_xyz:  94.02   0.00  17.25  83.53   0.00  13.08  94.02   3.34  39.98
   4_adp:  90.82   0.00  17.24  84.99   0.00  12.53  90.82   5.91  42.90
   4_occ:  90.82   0.00  17.24  84.99   0.00  12.53  90.82   5.91  42.90
   5_bss:  90.82   0.00  17.24  84.99   0.00  12.53  90.82   5.91  42.90
   5_xyz:  90.82   0.00  17.24  84.99   0.00  12.53  90.82   5.91  42.90
   5_adp:  98.05   0.00  17.25  98.05   0.00  12.23  97.83   5.67  44.59
   5_occ:  98.05   0.00  17.25  98.05   0.00  12.23  97.83   5.67  44.59
   5_bss:  98.05   0.00  17.25  98.05   0.00  12.23  97.83   5.68  44.59
------------------------------------------------------------------------
 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:    1.689    0.010    0.322
   1_adp:    1.689    0.010    0.322
   1_occ:    1.689    0.010    0.322
   2_bss:    1.689    0.010    0.322
   2_xyz:    1.450    0.036    0.539
   2_adp:    1.450    0.036    0.539
   2_occ:    1.450    0.036    0.539
   3_bss:    1.450    0.036    0.539
   3_xyz:    1.870    0.056    0.718
   3_adp:    1.870    0.056    0.718
   3_occ:    1.870    0.056    0.718
   4_bss:    1.870    0.056    0.718
   4_xyz:    1.841    0.060    0.786
   4_adp:    1.841    0.060    0.786
   4_occ:    1.841    0.060    0.786
   5_bss:    1.841    0.060    0.786
   5_xyz:    1.861    0.044    0.852
   5_adp:    1.861    0.044    0.852
   5_occ:    1.861    0.044    0.852
   5_bss:    1.861    0.044    0.852
------------------------------------------------------------------------

CPU time actual refinement: 354.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/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/noshake/run_1092/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1092/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.49 
  Macro-tasks:
    bulk solvent and scale       = 44.36  
    individual site refinement   = 144.23 
    weights calculation          = 30.31  
    collect and process          = 6.40   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 225.42 
  Micro-tasks:
    mask                            = 3.08   
    f_calc                          = 115.10 
    alpha_beta                      = 8.63   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 122.24 
    fmodel                         = 7.29   
    r_factors                      = 0.21   
    phase_errors                   = 10.22  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 268.15 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.059 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    636 calls, 114.78 s
gradients_fft:          581 calls, 109.46 s

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

# Date 2008-01-16 Time 06:24:05 PST -0800 (1200493445.61 s)
Start R-work = 0.4780, R-free = 0.4751 (no bulk solvent and anisotropic scale)
Final R-work = 0.1447, R-free = 0.1939 (no bulk solvent and anisotropic scale)

Start R-work = 0.4703, R-free = 0.4674
Final R-work = 0.1267, R-free = 0.1791