# Date 2008-01-16 Time 04:54:06 PST -0800 (1200488046.07 s)
#phil __OFF__

Command line arguments: "../508.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 944
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 508

-------------------------------------------------------------------------------
  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: (69.8988, 46.2261, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97037
Completeness in resolution range: 0.976374
Completeness with d_max=infinity: 0.973366

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8779
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97037
Completeness in resolution range: 0.976374
Completeness with d_max=infinity: 0.973366

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8783 -  4.2159 [2099/2124]  1889   210  10.0%
  bin  2:  4.2159 -  3.3589 [2031/2051]  1828   203  10.0%
  bin  3:  3.3589 -  2.9380 [1998/2017]  1796   202  10.1%
  bin  4:  2.9380 -  2.6711 [1973/2003]  1779   194   9.8%
  bin  5:  2.6711 -  2.4806 [1978/1997]  1781   197  10.0%
  bin  6:  2.4806 -  2.3349 [1957/1982]  1762   195  10.0%
  bin  7:  2.3349 -  2.2184 [1943/1971]  1743   200  10.3%
  bin  8:  2.2184 -  2.1221 [1950/1986]  1756   194   9.9%
  bin  9:  2.1221 -  2.0406 [1929/1971]  1742   187   9.7%
  bin 10:  2.0406 -  1.9704 [1731/1961]  1554   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/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:
        1.81 -     2.42: 47
        2.42 -     3.04: 2226
        3.04 -     3.66: 4817
        3.66 -     4.28: 9173
        4.28 -     4.90: 12550
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.844 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.873 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.893 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.013 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28808 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_508/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/model_refine_001.geo

CPU time processing inputs: 9.82


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.22605 85.09415 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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4015   r_free= 0.3990   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.193821                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7020 0.99   1372  152 0.3268 0.3217      6.4537      6.4222|
|  2:  4.7020 -  3.7518 0.99   1316  146 0.3318 0.3104      6.6517      6.5954|
|  3:  3.7518 -  3.2834 0.99   1286  144 0.3546 0.3495      6.5502      6.6425|
|  4:  3.2834 -  2.9858 0.99   1279  144 0.3699 0.4000      6.4142      6.4283|
|  5:  2.9858 -  2.7733 0.99   1279  141 0.4176 0.3898      6.2855      6.2264|
|  6:  2.7733 -  2.6107 0.99   1271  139 0.4219 0.4587      6.2111      6.2013|
|  7:  2.6107 -  2.4806 0.99   1270  140 0.4313 0.4122      6.1577      6.1215|
|  8:  2.4806 -  2.3731 0.98   1255  143 0.4429 0.4444      6.1347      6.1447|
|  9:  2.3731 -  2.2820 0.98   1244  134 0.4487 0.4545      6.0726      6.0818|
| 10:  2.2820 -  2.2036 1.00   1247  144 0.4425 0.4264      6.0396      6.0274|
| 11:  2.2036 -  2.1349 0.97   1259  136 0.4647 0.4694      5.9904      6.0434|
| 12:  2.1349 -  2.0740 0.98   1233  139 0.4599 0.4565      5.9527      5.9576|
| 13:  2.0740 -  2.0195 0.99   1246  141 0.4553 0.4404       5.847      5.8162|
| 14:  2.0195 -  1.9704 0.84   1073  116 0.4887 0.4449      5.8305      5.7227|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7020  1372   152  0.75  29.62   0.85     0.79      54334.62|
|  2:  4.7020 -  3.7518  1316   146  0.78  28.05   0.95     0.89      72321.83|
|  3:  3.7518 -  3.2834  1286   144  0.72  34.08   0.98     0.91      77316.05|
|  4:  3.2834 -  2.9858  1279   144  0.65  39.70   0.98     0.85      71211.19|
|  5:  2.9858 -  2.7733  1279   141  0.58  45.13   0.94     0.79      58187.49|
|  6:  2.7733 -  2.6107  1271   139  0.57  46.44   0.96     0.77      51200.50|
|  7:  2.6107 -  2.4806  1270   140  0.56  47.40   0.95     0.77      46481.55|
|  8:  2.4806 -  2.3731  1255   143  0.54  48.68   0.98     0.76      43112.61|
|  9:  2.3731 -  2.2820  1244   134  0.55  48.38   0.96     0.75      38911.31|
| 10:  2.2820 -  2.2036  1247   144  0.53  49.55   1.00     0.75      36529.63|
| 11:  2.2036 -  2.1349  1259   136  0.51  51.61   1.02     0.76      35042.01|
| 12:  2.1349 -  2.0740  1233   139  0.52  50.65   1.02     0.77      31687.47|
| 13:  2.0740 -  2.0195  1246   141  0.52  51.07   1.00     0.76      26663.93|
| 14:  2.0195 -  1.9704  1073   116  0.54  49.00   1.00     0.74      20896.75|
|alpha:            min =        0.74 max =            0.91 mean =         0.79|
|beta:             min =    20896.75 max =        77316.05 mean =     47966.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.01|
|phase err.(test): min =        0.00 max =           89.90 mean =        44.04|
|-----------------------------------------------------------------------------|

============================== 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 = 5.346248              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.708   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.363708              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.334   (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 |  1.806 -  2.115:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       39 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      212 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2014 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1939 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2878 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4696 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4477 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5715 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6835 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.308 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4015   r_free= 0.3990   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.193821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3884   r_free= 0.3840   ksol= 0.33   Bsol= 22.92   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,1.79,0.68,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.182273                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.414324              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.628   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.714703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.240   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3884      final r-factor (work) = 0.2585          |
| start r-factor (free) = 0.3840      final r-factor (free) = 0.2864          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8071 = 4.41 * 0.50 * 6.1790 + 1.00 * 0.1689                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2683 = 4.41 * 0.50 * 5.9698 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2585      final r-factor (work) = 0.2355          |
| start r-factor (free) = 0.2864      final r-factor (free) = 0.2980          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2726 = 0.71 * 1.00 * 5.9698 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1466 = 0.71 * 1.00 * 5.7833 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.69   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    83.69   17.89    None  None   None       |
|    Sol.    : 438    0      3.51    80.89   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    83.69   13.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.369:  707   |   5:    41.845 -  50.215:  116        |
|      1:     8.369 -  16.738: 1083   |   6:    50.215 -  58.584:   85        |
|      2:    16.738 -  25.107:  444   |   7:    58.584 -  66.953:   38        |
|      3:    25.107 -  33.476:  189   |   8:    66.953 -  75.322:   14        |
|      4:    33.476 -  41.845:  143   |   9:    75.322 -  83.691:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2355 r_free = 0.2980             target_work(ml) = 5.796         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2351 r_free = 0.2981             target_work(ml) = 5.795         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2351   r_free= 0.2981   ksol= 0.33   Bsol= 22.92   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,1.79,0.68,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.795349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2333   r_free= 0.2957   ksol= 0.33   Bsol= 37.51   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-0.82,-0.93,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.791314                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.046889              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.448   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205174              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.154  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2333      final r-factor (work) = 0.1658          |
| start r-factor (free) = 0.2957      final r-factor (free) = 0.2148          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7996 = 4.05 * 0.50 * 5.7860 + 1.00 * 0.0919                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4923 = 4.05 * 0.50 * 5.6489 + 1.00 * 0.0620                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1658      final r-factor (work) = 0.1497          |
| start r-factor (free) = 0.2148      final r-factor (free) = 0.1953          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1722 = 0.21 * 1.00 * 5.6489 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1217 = 0.21 * 1.00 * 5.4296 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    82.87   17.09    None  None   None       |
|    all(noH): 2823   0      1.52    82.87   17.09    None  None   None       |
|    Sol.    : 438    0      5.56    75.73   39.04    None  None   None       |
|    Mac.    : 2385   0      1.52    82.87   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.522 -   9.657:  904   |   5:    42.196 -  50.331:  118        |
|      1:     9.657 -  17.792: 1142   |   6:    50.331 -  58.466:   73        |
|      2:    17.792 -  25.927:  278   |   7:    58.466 -  66.601:   32        |
|      3:    25.927 -  34.062:  125   |   8:    66.601 -  74.736:    7        |
|      4:    34.062 -  42.196:  141   |   9:    74.736 -  82.870:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1497 r_free = 0.1953             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1494 r_free = 0.1951             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1951   ksol= 0.33   Bsol= 37.51   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-0.82,-0.93,-0.00,-0.00,-0.00); trace/3= -1.48                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.383349                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1950   ksol= 0.32   Bsol= 38.04   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.89,-1.15,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.379934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.860000              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.001  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.160685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.656  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1950      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8250 = 2.86 * 0.50 * 5.4287 + 1.00 * 0.0620                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6188 = 2.86 * 0.50 * 5.2880 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1454 = 1.16 * 1.00 * 5.2880 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0090 = 1.16 * 1.00 * 5.1691 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.20   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    91.20   17.30    None  None   None       |
|    Sol.    : 438    0      2.18    81.83   41.33    None  None   None       |
|    Mac.    : 2385   0      0.00    91.20   12.89    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 -   9.120:  829   |   5:    45.601 -  54.722:  113        |
|      1:     9.120 -  18.241: 1260   |   6:    54.722 -  63.842:   65        |
|      2:    18.241 -  27.361:  265   |   7:    63.842 -  72.962:   36        |
|      3:    27.361 -  36.481:  125   |   8:    72.962 -  82.082:   12        |
|      4:    36.481 -  45.601:  116   |   9:    82.082 -  91.203:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1603             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1602             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1602   ksol= 0.32   Bsol= 38.04   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-1.89,-1.15,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152852                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1601   ksol= 0.32   Bsol= 41.09   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.29,-1.45,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.408396              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.206  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572385              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.322  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2831 = 2.41 * 0.50 * 5.1704 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2340 = 2.41 * 0.50 * 5.1287 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9449 = 0.57 * 1.00 * 5.1287 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9347 = 0.57 * 1.00 * 5.1114 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    93.66   17.05    None  None   None       |
|    all(noH): 2823   0      0.45    93.66   17.05    None  None   None       |
|    Sol.    : 438    0      3.59    82.76   40.44    None  None   None       |
|    Mac.    : 2385   0      0.45    93.66   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.450 -   9.771: 1020   |   5:    47.056 -  56.377:   99        |
|      1:     9.771 -  19.092: 1133   |   6:    56.377 -  65.698:   53        |
|      2:    19.092 -  28.413:  223   |   7:    65.698 -  75.019:   29        |
|      3:    28.413 -  37.735:  135   |   8:    75.019 -  84.341:    8        |
|      4:    37.735 -  47.056:  121   |   9:    84.341 -  93.662:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1548             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1547             target_work(ml) = 5.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1547   ksol= 0.32   Bsol= 41.09   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.29,-1.45,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1547   ksol= 0.32   Bsol= 41.22   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.24,-1.32,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107763                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.233866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.342  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.485652              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1078      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7667 = 2.23 * 0.50 * 5.1116 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7549 = 2.23 * 0.50 * 5.1017 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6901 = 2.49 * 1.00 * 5.1017 + 1.00 * 0.0091                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6804 = 2.49 * 1.00 * 5.0975 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.02  16.96    None  None   None       |
|    all(noH): 2823   0      0.00    100.02  16.96    None  None   None       |
|    Sol.    : 438    0      5.22    87.85   40.30    None  None   None       |
|    Mac.    : 2385   0      0.00    100.02  12.67    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 -  10.002: 1092   |   5:    50.012 -  60.015:   85        |
|      1:    10.002 -  20.005: 1106   |   6:    60.015 -  70.017:   40        |
|      2:    20.005 -  30.007:  203   |   7:    70.017 -  80.019:   16        |
|      3:    30.007 -  40.010:  146   |   8:    80.019 -  90.022:    9        |
|      4:    40.010 -  50.012:  124   |   9:    90.022 - 100.024:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1551             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1057 r_free = 0.1550             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1550   ksol= 0.32   Bsol= 41.22   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.24,-1.32,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101009                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7020 0.99   1372  152 0.0947 0.1238       5.347      5.4964|
|  2:  4.7020 -  3.7518 0.99   1316  146 0.0814 0.1139       5.408      5.6307|
|  3:  3.7518 -  3.2834 0.99   1286  144 0.1017 0.1528      5.4556      5.8522|
|  4:  3.2834 -  2.9858 0.99   1279  144 0.1175 0.1547      5.4375      5.5808|
|  5:  2.9858 -  2.7733 0.99   1279  141 0.1219 0.1756      5.2791       5.533|
|  6:  2.7733 -  2.6107 0.99   1271  139 0.1094 0.1657      5.1595      5.3587|
|  7:  2.6107 -  2.4806 0.99   1270  140 0.1198 0.1578      5.1154      5.3726|
|  8:  2.4806 -  2.3731 0.98   1255  143 0.1091 0.1685      5.0215      5.3208|
|  9:  2.3731 -  2.2820 0.98   1244  134 0.1097 0.1586      4.9921      5.2062|
| 10:  2.2820 -  2.2036 1.00   1247  144 0.1029 0.1833      4.9149      5.2603|
| 11:  2.2036 -  2.1349 0.97   1259  136 0.1076 0.1642      4.9103      5.2266|
| 12:  2.1349 -  2.0740 0.98   1233  139 0.1057 0.1720      4.8419      5.2119|
| 13:  2.0740 -  2.0195 0.99   1246  141 0.1046 0.1696      4.7634      5.0437|
| 14:  2.0195 -  1.9704 0.84   1073  116 0.1001 0.1674      4.6342      4.8923|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7020  1372   152  0.94   8.70   0.98     0.96       6662.84|
|  2:  4.7020 -  3.7518  1316   146  0.95   7.85   1.03     1.02       8839.29|
|  3:  3.7518 -  3.2834  1286   144  0.94  10.91   1.04     1.03      10149.73|
|  4:  3.2834 -  2.9858  1279   144  0.92  13.14   1.02     1.01      10102.24|
|  5:  2.9858 -  2.7733  1279   141  0.91  15.06   1.00     0.97       7730.62|
|  6:  2.7733 -  2.6107  1271   139  0.91  14.88   0.99     0.97       6578.91|
|  7:  2.6107 -  2.4806  1270   140  0.91  15.23   0.99     0.96       5731.65|
|  8:  2.4806 -  2.3731  1255   143  0.91  14.25   1.00     0.97       4802.67|
|  9:  2.3731 -  2.2820  1244   134  0.92  14.31   1.01     0.98       4634.78|
| 10:  2.2820 -  2.2036  1247   144  0.91  14.28   1.00     0.97       4000.65|
| 11:  2.2036 -  2.1349  1259   136  0.90  16.20   1.00     0.97       4245.31|
| 12:  2.1349 -  2.0740  1233   139  0.92  14.46   1.01     0.99       3687.77|
| 13:  2.0740 -  2.0195  1246   141  0.91  15.00   1.01     1.00       3212.04|
| 14:  2.0195 -  1.9704  1073   116  0.92  14.05   0.99     0.96       2440.41|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2440.41 max =        10149.73 mean =      5988.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.39|
|phase err.(test): min =        0.00 max =           89.15 mean =        13.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1551   ksol= 0.32   Bsol= 41.22   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.11,-1.15,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101105                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1551   ksol= 0.32   Bsol= 41.22   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.11,-1.15,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101105                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7020 0.99   1372  152 0.0947 0.1240      5.3485      5.4981|
|  2:  4.7020 -  3.7518 0.99   1316  146 0.0814 0.1139      5.4086      5.6306|
|  3:  3.7518 -  3.2834 0.99   1286  144 0.1017 0.1529      5.4558      5.8526|
|  4:  3.2834 -  2.9858 0.99   1279  144 0.1175 0.1547      5.4374      5.5809|
|  5:  2.9858 -  2.7733 0.99   1279  141 0.1219 0.1755      5.2789      5.5325|
|  6:  2.7733 -  2.6107 0.99   1271  139 0.1093 0.1657      5.1593      5.3583|
|  7:  2.6107 -  2.4806 0.99   1270  140 0.1198 0.1579      5.1155      5.3733|
|  8:  2.4806 -  2.3731 0.98   1255  143 0.1092 0.1684      5.0216      5.3204|
|  9:  2.3731 -  2.2820 0.98   1244  134 0.1098 0.1587      4.9921       5.206|
| 10:  2.2820 -  2.2036 1.00   1247  144 0.1029 0.1835       4.915      5.2612|
| 11:  2.2036 -  2.1349 0.97   1259  136 0.1077 0.1641      4.9104      5.2264|
| 12:  2.1349 -  2.0740 0.98   1233  139 0.1057 0.1720      4.8416      5.2118|
| 13:  2.0740 -  2.0195 0.99   1246  141 0.1046 0.1695      4.7631       5.043|
| 14:  2.0195 -  1.9704 0.84   1073  116 0.1002 0.1673      4.6339      4.8916|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7020  1372   152  0.94   8.72   0.99     0.96       6687.18|
|  2:  4.7020 -  3.7518  1316   146  0.95   7.86   1.03     1.02       8856.53|
|  3:  3.7518 -  3.2834  1286   144  0.94  10.91   1.04     1.03      10154.41|
|  4:  3.2834 -  2.9858  1279   144  0.92  13.14   1.02     1.01      10099.63|
|  5:  2.9858 -  2.7733  1279   141  0.91  15.06   1.01     0.98       7726.29|
|  6:  2.7733 -  2.6107  1271   139  0.91  14.88   1.00     0.97       6576.05|
|  7:  2.6107 -  2.4806  1270   140  0.91  15.23   1.00     0.96       5731.94|
|  8:  2.4806 -  2.3731  1255   143  0.91  14.25   1.00     0.98       4801.87|
|  9:  2.3731 -  2.2820  1244   134  0.92  14.31   1.02     0.99       4636.80|
| 10:  2.2820 -  2.2036  1247   144  0.91  14.28   1.01     0.97       4000.50|
| 11:  2.2036 -  2.1349  1259   136  0.90  16.21   1.01     0.98       4246.45|
| 12:  2.1349 -  2.0740  1233   139  0.92  14.45   1.02     1.00       3685.59|
| 13:  2.0740 -  2.0195  1246   141  0.91  14.99   1.02     1.01       3209.24|
| 14:  2.0195 -  1.9704  1073   116  0.92  14.04   1.00     0.97       2437.47|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2437.47 max =        10154.41 mean =      5990.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.39|
|phase err.(test): min =        0.00 max =           89.17 mean =        13.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.507)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.03  16.96    None  None   None       |
|    all(noH): 2823   0      0.00    100.03  16.96    None  None   None       |
|    Sol.    : 438    0      5.22    87.85   40.30    None  None   None       |
|    Mac.    : 2385   0      0.00    100.03  12.67    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:     0.003 -  10.005: 1092   |   5:    50.015 -  60.017:   85        |
|      1:    10.005 -  20.008: 1106   |   6:    60.017 -  70.020:   40        |
|      2:    20.008 -  30.010:  203   |   7:    70.020 -  80.022:   16        |
|      3:    30.010 -  40.013:  146   |   8:    80.022 -  90.025:    9        |
|      4:    40.013 -  50.015:  124   |   9:    90.025 - 100.027:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.415 - 4.553
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 274 from: 278
   mapped sites are within: 0.743 - 4.553

peak=    6.262 closest distance to " NE2 GLN A  11 " =    1.216
peak=    5.877 closest distance to " O   HOH Z 126 " =    1.891
peak=    5.607 closest distance to " O   HOH Z 144 " =    1.703
peak=    5.454 closest distance to " CG  PRO A  54 " =    1.216
peak=    5.428 closest distance to " NH2 ARG A  56 " =    2.160
peak=    5.174 closest distance to " CG  PRO A 213 " =    1.246
peak=    4.960 closest distance to " CB  SER A  63 " =    1.194
peak=    4.907 closest distance to " O   HOH Z 232 " =    2.321
peak=    4.900 closest distance to " CB  GLN A 223 " =    1.524
peak=    4.877 closest distance to " CB  ARG A 275 " =    0.894
peak=    4.793 closest distance to " O   HOH Z 427 " =    2.701
peak=    4.734 closest distance to " O   HOH Z  78 " =    1.819
peak=    4.722 closest distance to " O   HOH Z 193 " =    1.783
peak=    4.690 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.633 closest distance to " O   HOH Z 209 " =    2.195
peak=    4.588 closest distance to " O   HOH Z 287 " =    2.126
peak=    4.554 closest distance to " C   PRO A 198 " =    1.463
peak=    4.440 closest distance to " O   HOH Z   9 " =    2.291
peak=    4.436 closest distance to " CG  ARG A  66 " =    2.427
peak=    4.422 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.409 closest distance to " O   HOH Z 371 " =    1.822
peak=    4.388 closest distance to " O   HOH Z 369 " =    2.137
peak=    4.357 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.354 closest distance to " O   HOH Z   1 " =    1.872
peak=    4.351 closest distance to " CB  ARG A  79 " =    1.451
peak=    4.324 closest distance to " O   HOH Z 303 " =    2.211
peak=    4.319 closest distance to " O   HOH Z 272 " =    1.789
peak=    4.319 closest distance to " O   HOH Z 298 " =    1.795
peak=    4.281 closest distance to " ND2 ASN A 187 " =    1.394
peak=    4.274 closest distance to " CG2 VAL A 257 " =    0.847
peak=    4.267 closest distance to " NZ  LYS A 117 " =    3.142
peak=    4.246 closest distance to " OG BSER A 164 " =    2.303
peak=    4.232 closest distance to " O   HOH Z 203 " =    1.797
peak=    4.225 closest distance to " CB  SER A   3 " =    1.295
peak=    4.201 closest distance to " O   HOH Z 316 " =    2.993
peak=    4.176 closest distance to " CB  GLU A 128 " =    1.084
peak=    4.174 closest distance to " O   HOH Z 234 " =    3.560
peak=    4.172 closest distance to " CB  VAL A 265 " =    1.352
peak=    4.144 closest distance to " O   HOH Z 425 " =    2.050
peak=    4.136 closest distance to " O   HOH Z  63 " =    1.446
peak=    4.125 closest distance to " CG  PRO A 198 " =    1.200
peak=    4.108 closest distance to " CG  PRO A  90 " =    1.062
peak=    4.096 closest distance to " O   HOH Z 261 " =    2.271
peak=    4.066 closest distance to " CG1 ILE A  33 " =    1.250
peak=    4.065 closest distance to " CB  GLU A 152 " =    1.248
peak=    4.060 closest distance to " O   HOH Z 368 " =    3.579
peak=    4.059 closest distance to " CA  TYR A  30 " =    0.918
peak=    4.008 closest distance to " O   HOH Z 419 " =    2.123
peak=    4.004 closest distance to " O   HOH Z 344 " =    3.135
peak=    3.997 closest distance to " CB  ARG A 139 " =    0.971
peak=    3.984 closest distance to " O   HOH Z  61 " =    1.716
peak=    3.967 closest distance to " O   HOH Z 132 " =    2.252
peak=    3.956 closest distance to " O   HOH Z  44 " =    1.761
peak=    3.954 closest distance to " CB  LEU A 228 " =    1.082
peak=    3.951 closest distance to " OD1 ASN A  69 " =    2.710
peak=    3.948 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.936 closest distance to " O   HOH Z 158 " =    3.042
peak=    3.913 closest distance to " O   HOH Z  40 " =    1.997
peak=    3.909 closest distance to " O   HOH Z 289 " =    1.677
peak=    3.905 closest distance to " ND1 HIS A  86 " =    1.786
peak=    3.874 closest distance to " O   SER A  87 " =    2.152
peak=    3.874 closest distance to " O   HOH Z   3 " =    1.948
peak=    3.865 closest distance to " O   HOH Z 189 " =    1.769
peak=    3.853 closest distance to " CB  SER A  26 " =    1.624
peak=    3.852 closest distance to " CB  TRP A 179 " =    1.323
peak=    3.844 closest distance to " CD BLYS A 290 " =    1.234
peak=    3.839 closest distance to " O   HOH Z  66 " =    2.110
peak=    3.839 closest distance to " O   HOH Z   1 " =    1.684
peak=    3.830 closest distance to " CG  PRO A 243 " =    1.087
peak=    3.820 closest distance to " O   HOH Z 147 " =    1.762
peak=    3.816 closest distance to " O   HOH Z  61 " =    1.523
peak=    3.811 closest distance to " O   HOH Z 368 " =    1.878
peak=    3.809 closest distance to " CB  ARG A 190 " =    1.589
peak=    3.802 closest distance to " O   HOH Z 327 " =    1.625
peak=    3.790 closest distance to " CB  TYR A 169 " =    0.766
peak=    3.785 closest distance to " O   HOH Z 389 " =    1.770
peak=    3.782 closest distance to " O   HOH Z 207 " =    1.681
peak=    3.773 closest distance to " O   HOH Z 245 " =    1.280
peak=    3.773 closest distance to " O   HOH Z 425 " =    1.282
peak=    3.771 closest distance to " O   HOH Z 403 " =    1.673
peak=    3.762 closest distance to " OD2 ASP A 286 " =    2.734
peak=    3.756 closest distance to " O   HOH Z 263 " =    2.318
peak=    3.754 closest distance to " O   HOH Z 236 " =    1.437
peak=    3.748 closest distance to " CD2 TRP A 179 " =    1.376
peak=    3.741 closest distance to " CA  ASN A 215 " =    1.247
peak=    3.732 closest distance to " O   HOH Z 407 " =    2.235
peak=    3.724 closest distance to " O   HOH Z 180 " =    2.153
peak=    3.723 closest distance to " NH2BARG A 145 " =    2.097
peak=    3.722 closest distance to " O   HOH Z 124 " =    1.349
peak=    3.712 closest distance to " O   HOH Z 214 " =    2.116
peak=    3.710 closest distance to " O   HOH Z 353 " =    2.563
peak=    3.707 closest distance to " O   HOH Z 392 " =    3.108
peak=    3.704 closest distance to " O   HOH Z 405 " =    1.149
peak=    3.699 closest distance to " O   HOH Z 423 " =    2.487
peak=    3.693 closest distance to " CA  ALA A  21 " =    1.130
peak=    3.688 closest distance to " O   HOH Z  93 " =    2.070
peak=    3.678 closest distance to " CB  GLU A 277 " =    3.489
peak=    3.668 closest distance to " O   HOH Z 426 " =    1.632
peak=    3.658 closest distance to " O   HOH Z 380 " =    1.578
peak=    3.644 closest distance to " NH1BARG A 145 " =    1.327
peak=    3.631 closest distance to " O   HOH Z 286 " =    2.285
peak=    3.631 closest distance to " O   HOH Z 250 " =    1.463
peak=    3.630 closest distance to " CB  SER A 216 " =    0.780
peak=    3.625 closest distance to " OD1BASN A 224 " =    2.194
peak=    3.624 closest distance to " CB  THR A 157 " =    1.056
peak=    3.620 closest distance to " O   HOH Z  10 " =    1.770
peak=    3.608 closest distance to " O   HOH Z 423 " =    1.392
peak=    3.607 closest distance to " N   PHE A 130 " =    1.219
peak=    3.605 closest distance to " NH1AARG A 145 " =    1.146
peak=    3.587 closest distance to " O   HOH Z 371 " =    2.941
peak=    3.580 closest distance to " CE  LYS A  76 " =    0.874
peak=    3.580 closest distance to " O   HOH Z 227 " =    1.771
peak=    3.578 closest distance to " CB  ALA A  34 " =    1.046
peak=    3.577 closest distance to " O   HOH Z  59 " =    1.541
peak=    3.571 closest distance to " OG  SER A  62 " =    2.874
peak=    3.570 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.560 closest distance to " O   HOH Z 336 " =    2.067
peak=    3.557 closest distance to " O   HOH Z 357 " =    1.856
peak=    3.552 closest distance to " O   HOH Z  40 " =    1.912
peak=    3.551 closest distance to " O   HOH Z 108 " =    1.228
peak=    3.551 closest distance to " CG2 THR A 221 " =    1.166
peak=    3.544 closest distance to " O   HOH Z 284 " =    2.874
peak=    3.543 closest distance to " CA  THR A 264 " =    0.833
peak=    3.523 closest distance to " O   HOH Z 345 " =    3.310
peak=    3.517 closest distance to " O   HOH Z 227 " =    2.155
peak=    3.515 closest distance to " CG  GLN A  77 " =    2.356
peak=    3.514 closest distance to " O   HOH Z  71 " =    1.920
peak=    3.509 closest distance to " O   HOH Z  43 " =    1.824
peak=    3.500 closest distance to " O   HOH Z 411 " =    3.705
peak=    3.496 closest distance to " O   HOH Z 234 " =    3.683
peak=    3.491 closest distance to " CD2 LEU A 297 " =    0.948
peak=    3.486 closest distance to " O   HOH Z 402 " =    1.395
peak=    3.485 closest distance to " O   HOH Z 290 " =    0.925
peak=    3.483 closest distance to " O   HOH Z 365 " =    2.765
peak=    3.481 closest distance to " O   HOH Z   6 " =    2.089
peak=    3.479 closest distance to " O   HOH Z 193 " =    1.773
peak=    3.474 closest distance to " O   HOH Z 298 " =    2.611
peak=    3.468 closest distance to " CA  ALA A 158 " =    1.153
peak=    3.467 closest distance to " O   HOH Z  21 " =    1.693
peak=    3.462 closest distance to " O   HOH Z 128 " =    2.030
peak=    3.458 closest distance to " O   HOH Z 283 " =    2.319
peak=    3.458 closest distance to " CA  PHE A 283 " =    1.322
peak=    3.450 closest distance to " CG2 ILE A 120 " =    1.167
peak=    3.448 closest distance to " CB  LYS A 117 " =    1.164
peak=    3.442 closest distance to " O   HOH Z  88 " =    2.725
peak=    3.439 closest distance to " O   HOH Z 437 " =    1.647
peak=    3.438 closest distance to " CB  TRP A 266 " =    1.044
peak=    3.438 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.430 closest distance to " CA  LYS A 290 " =    1.348
peak=    3.427 closest distance to " CA  MET A  40 " =    1.068
peak=    3.418 closest distance to " O   HOH Z  49 " =    2.041
peak=    3.418 closest distance to " OG BSER A  99 " =    2.263
peak=    3.416 closest distance to " O   HOH Z 258 " =    2.261
peak=    3.410 closest distance to " CG1 ILE A 151 " =    0.941
peak=    3.405 closest distance to " CB  SER A  62 " =    1.276
peak=    3.402 closest distance to " CE AMET A  47 " =    1.387
peak=    3.400 closest distance to " O   HOH Z 261 " =    2.220
peak=    3.394 closest distance to " CD  PRO A 243 " =    1.532
peak=    3.393 closest distance to " O   HOH Z 417 " =    3.336
peak=    3.387 closest distance to " O   HOH Z 305 " =    3.526
peak=    3.385 closest distance to " O   HOH Z 172 " =    3.148
peak=    3.382 closest distance to " O   HOH Z 126 " =    1.494
peak=    3.380 closest distance to " CB  ALA A 291 " =    1.499
peak=    3.376 closest distance to " O   HOH Z 146 " =    1.709
peak=    3.372 closest distance to " CZ  PHE A 218 " =    0.975
peak=    3.368 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.367 closest distance to " CB  ALA A  21 " =    1.884
peak=    3.366 closest distance to " O  BHOH Z  74 " =    1.424
peak=    3.364 closest distance to " O   HOH Z  97 " =    1.970
peak=    3.363 closest distance to " O   HOH Z  55 " =    2.220
peak=    3.363 closest distance to " O   HOH Z 108 " =    2.048
peak=    3.363 closest distance to " O   MET A 105 " =    1.814
peak=    3.359 closest distance to " CB  SER A 212 " =    0.979
peak=    3.358 closest distance to " OG  SER A  22 " =    2.742
peak=    3.358 closest distance to " CB  ALA A   1 " =    4.553
peak=    3.357 closest distance to " CE1 TYR A 186 " =    1.302
peak=    3.353 closest distance to " CB  MET A  47 " =    1.259
peak=    3.349 closest distance to " O   HOH Z 337 " =    3.601
peak=    3.345 closest distance to " O   HOH Z 266 " =    3.124
peak=    3.345 closest distance to " O   HOH Z 128 " =    2.065
peak=    3.342 closest distance to " O   HOH Z 433 " =    1.776
peak=    3.336 closest distance to " N   ASN A 127 " =    1.283
peak=    3.335 closest distance to " CB  ILE A 120 " =    1.326
peak=    3.335 closest distance to " O   HOH Z 211 " =    2.704
peak=    3.332 closest distance to " CA  ASP A 162 " =    1.087
peak=    3.327 closest distance to " CB  THR A  31 " =    1.767
peak=    3.325 closest distance to " OE2 GLU A  53 " =    2.100
peak=    3.324 closest distance to " CG2BVAL A  41 " =    0.894
peak=    3.322 closest distance to " O   HOH Z 286 " =    2.376
peak=    3.315 closest distance to " O  BHOH Z 338 " =    2.364
peak=    3.315 closest distance to " O   HOH Z 141 " =    1.618
peak=    3.314 closest distance to " O   HOH Z 153 " =    1.627
peak=    3.307 closest distance to " CD  LYS A 166 " =    1.269
peak=    3.302 closest distance to " O   HOH Z 213 " =    1.972
peak=    3.296 closest distance to " N   ARG A 156 " =    1.266
peak=    3.291 closest distance to " N   GLN A 278 " =    1.091
peak=    3.287 closest distance to " CG  GLN A  89 " =    1.463
peak=    3.284 closest distance to " O   HOH Z 432 " =    1.730
peak=    3.282 closest distance to " O   HOH Z 391 " =    2.965
peak=    3.282 closest distance to " O   HOH Z 175 " =    2.187
peak=    3.279 closest distance to " CG1BVAL A  72 " =    1.363
peak=    3.277 closest distance to " CG BARG A 102 " =    1.811
peak=    3.275 closest distance to " CA  ALA A 233 " =    0.991
peak=    3.272 closest distance to " CB  ASN A  39 " =    0.833
peak=    3.266 closest distance to " CB  ASP A 140 " =    0.916
peak=    3.265 closest distance to " O   HOH Z 112 " =    2.518
peak=    3.258 closest distance to " O   HOH Z 213 " =    1.865
peak=    3.251 closest distance to " NH2 ARG A 219 " =    1.900
peak=    3.250 closest distance to " CG  MET A 185 " =    1.272
peak=    3.248 closest distance to " O   ARG A 145 " =    1.765
peak=    3.244 closest distance to " CB  LEU A 143 " =    1.121
peak=    3.242 closest distance to " O   HOH Z 291 " =    1.818
peak=    3.242 closest distance to " O   HOH Z 135 " =    1.700
peak=    3.242 closest distance to " CG  GLU A 277 " =    2.028
peak=    3.240 closest distance to " CG AARG A 275 " =    1.030
peak=    3.240 closest distance to " CB  ALA A 233 " =    1.367
peak=    3.235 closest distance to " ND1 HIS A  81 " =    1.573
peak=    3.235 closest distance to " O   HOH Z  64 " =    2.021
peak=    3.233 closest distance to " OH  TYR A 116 " =    1.030
peak=    3.232 closest distance to " CG  MET A 113 " =    1.112
peak=    3.229 closest distance to " CA  ALA A  84 " =    1.424
peak=    3.228 closest distance to " CA  ALA A 299 " =    0.900
peak=    3.226 closest distance to " O   HOH Z 271 " =    2.185
peak=    3.226 closest distance to " O   HOH Z 244 " =    1.711
peak=    3.225 closest distance to " CD2 LEU A 255 " =    1.375
peak=    3.225 closest distance to " O   HOH Z 359 " =    1.331
peak=    3.223 closest distance to " CA  SER A  32 " =    1.647
peak=    3.219 closest distance to " CB  ALA A 114 " =    1.442
peak=    3.218 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.215 closest distance to " O   HOH Z 148 " =    3.298
peak=    3.213 closest distance to " O   HOH Z  47 " =    1.808
peak=    3.211 closest distance to " CB  SER A 273 " =    0.782
peak=    3.210 closest distance to " O   HOH Z 409 " =    2.498
peak=    3.209 closest distance to " CB  LEU A 255 " =    0.756
peak=    3.206 closest distance to " CB  LYS A 290 " =    1.156
peak=    3.205 closest distance to " NH2AARG A 190 " =    1.860
peak=    3.204 closest distance to " CB  THR A 279 " =    1.779
peak=    3.200 closest distance to " NH1 ARG A  14 " =    1.121
peak=    3.198 closest distance to " N   ALA A   1 " =    1.887
peak=    3.194 closest distance to " NE2 GLN A  73 " =    3.564
peak=    3.191 closest distance to " CD2 HIS A  81 " =    1.099
peak=    3.189 closest distance to " O   HOH Z 291 " =    1.532
peak=    3.189 closest distance to " N   ASN A  39 " =    1.197
peak=    3.184 closest distance to " O   HOH Z 217 " =    1.490
peak=    3.177 closest distance to " CB  VAL A 126 " =    1.127
peak=    3.174 closest distance to " O   HOH Z 152 " =    2.598
peak=    3.172 closest distance to " CG1 ILE A 120 " =    1.185
peak=    3.172 closest distance to " CG  LEU A 167 " =    1.201
peak=    3.172 closest distance to " O   HOH Z 189 " =    2.056
peak=    3.172 closest distance to " O   HOH Z 346 " =    1.425
peak=    3.168 closest distance to " NH1 ARG A 138 " =    1.200
peak=    3.162 closest distance to " CB  TYR A 116 " =    0.830
peak=    3.162 closest distance to " O   HOH Z 248 " =    1.510
peak=    3.155 closest distance to " O   HOH Z 438 " =    1.936
peak=    3.154 closest distance to " O   HOH Z  40 " =    2.741
peak=    3.145 closest distance to " O   HOH Z  44 " =    3.166
peak=    3.134 closest distance to " CA  MET A 105 " =    0.914
peak=    3.133 closest distance to " O   HOH Z  88 " =    3.198
peak=    3.131 closest distance to " O   HOH Z 218 " =    2.116
peak=    3.117 closest distance to " O   HOH Z 189 " =    1.253
peak=    3.114 closest distance to " CB  ALA A 248 " =    0.926
peak=    3.103 closest distance to " O   HOH Z 133 " =    1.387
peak=    3.100 closest distance to " CA  LEU A 300 " =    1.069
peak=    3.099 closest distance to " O   HOH Z  59 " =    1.904
peak=    3.097 closest distance to " CG1BVAL A  72 " =    1.472
peak=    3.091 closest distance to " O   ALA A   1 " =    1.673
peak=    3.087 closest distance to " CB  ASN A 110 " =    1.110
peak=    3.079 closest distance to " CB  GLN A  88 " =    1.254
peak=    3.076 closest distance to " O   HOH Z 380 " =    1.854
peak=    3.067 closest distance to " O   HOH Z  66 " =    1.924
peak=    3.067 closest distance to " CA  ALA A  51 " =    0.936
peak=    3.052 closest distance to " O   HOH Z 110 " =    1.679
peak=    3.029 closest distance to " O   HOH Z 409 " =    3.244
peak=    3.024 closest distance to " O   HOH Z 367 " =    3.542

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.769 - 5.981
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.769 - 5.981

peak=   -4.871 closest distance to " O   HOH Z 377 " =    2.036
peak=   -4.731 closest distance to " CB  PRO A 243 " =    2.561
peak=   -4.652 closest distance to " C   HIS A 108 " =    1.100
peak=   -4.534 closest distance to " O   HOH Z 266 " =    4.553
peak=   -4.504 closest distance to " CD  ARG A 156 " =    2.007
peak=   -4.391 closest distance to " CG  GLN A 223 " =    1.938
peak=   -4.269 closest distance to " SG  CYS A 254 " =    3.311
peak=   -4.203 closest distance to " N   GLN A  58 " =    1.584
peak=   -4.184 closest distance to " CE2 PHE A 218 " =    2.481
peak=   -4.156 closest distance to " OG BSER A 134 " =    1.250
peak=   -4.133 closest distance to " CZ  PHE A  59 " =    1.479
peak=   -4.127 closest distance to " CG1 VAL A 112 " =    2.895
peak=   -4.094 closest distance to " O   VAL A  67 " =    2.670
peak=   -4.061 closest distance to " O   HOH Z 372 " =    2.494
peak=   -4.039 closest distance to " O   HOH Z 290 " =    1.200
peak=   -4.034 closest distance to " CB  TYR A  15 " =    2.154
peak=   -4.034 closest distance to " O   HOH Z 435 " =    2.872
peak=   -4.028 closest distance to " O   HOH Z 231 " =    2.196
peak=   -4.024 closest distance to " O   VAL A  67 " =    2.747
peak=   -3.999 closest distance to " O   PRO A 198 " =    1.315
peak=   -3.972 closest distance to " O   ARG A 145 " =    1.532
peak=   -3.919 closest distance to " O   HOH Z 313 " =    1.870
peak=   -3.912 closest distance to " O   HOH Z  13 " =    1.449
peak=   -3.911 closest distance to " CG  PHE A 283 " =    2.670
peak=   -3.908 closest distance to " CA  GLY A  98 " =    1.857
peak=   -3.898 closest distance to " O   HOH Z 198 " =    2.036
peak=   -3.886 closest distance to " CB  ALA A 291 " =    2.110
peak=   -3.880 closest distance to " ND2 ASN A  45 " =    0.993
peak=   -3.861 closest distance to " CZ  TYR A 169 " =    1.635
peak=   -3.858 closest distance to " O   HOH Z 351 " =    1.563
peak=   -3.858 closest distance to " O   HOH Z 389 " =    1.830
peak=   -3.857 closest distance to " O   HOH Z 185 " =    2.036
peak=   -3.838 closest distance to " OD1 ASN A 187 " =    1.574
peak=   -3.821 closest distance to " CB  ASN A  39 " =    2.232
peak=   -3.813 closest distance to " O   HOH Z 407 " =    3.090
peak=   -3.793 closest distance to " N   ASP A 286 " =    2.406
peak=   -3.787 closest distance to " O   ALA A 161 " =    1.586
peak=   -3.777 closest distance to " O   SER A 135 " =    1.474
peak=   -3.773 closest distance to " OD2 ASP A 191 " =    1.431
peak=   -3.771 closest distance to " OD1 ASP A 191 " =    1.873
peak=   -3.760 closest distance to " CE  MET A 105 " =    2.233
peak=   -3.758 closest distance to " O   PRO A 243 " =    2.536
peak=   -3.758 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.743 closest distance to " CD1 PHE A  59 " =    1.926
peak=   -3.729 closest distance to " CG  ASP A 231 " =    0.769
peak=   -3.728 closest distance to " O   HOH Z 102 " =    1.579
peak=   -3.727 closest distance to " O   HOH Z  43 " =    1.737
peak=   -3.726 closest distance to " O   HOH Z 263 " =    2.865
peak=   -3.701 closest distance to " O   HOH Z 126 " =    1.849
peak=   -3.684 closest distance to " CA  GLY A 203 " =    2.122
peak=   -3.683 closest distance to " ND2 ASN A  45 " =    1.600
peak=   -3.681 closest distance to " CB  ALA A 291 " =    2.357
peak=   -3.678 closest distance to " N   ALA A 248 " =    1.545
peak=   -3.662 closest distance to " O   PRO A 163 " =    1.956
peak=   -3.658 closest distance to " O   HOH Z 388 " =    2.012
peak=   -3.655 closest distance to " CE2 TYR A  30 " =    2.773
peak=   -3.630 closest distance to " O   VAL A 153 " =    2.351
peak=   -3.627 closest distance to " CD1 LEU A 228 " =    2.121
peak=   -3.625 closest distance to " O   HOH Z 385 " =    1.807
peak=   -3.618 closest distance to " O   HOH Z  52 " =    1.513
peak=   -3.613 closest distance to " OXT GLY A 302 " =    2.805
peak=   -3.612 closest distance to " CD  ARG A 139 " =    1.523
peak=   -3.610 closest distance to " NE  ARG A  36 " =    1.889
peak=   -3.609 closest distance to " CA  GLY A 133 " =    1.978
peak=   -3.599 closest distance to " OD1 ASN A 148 " =    1.602
peak=   -3.597 closest distance to " O   PHE A 218 " =    1.556
peak=   -3.596 closest distance to " OD1 ASP A 171 " =    1.538
peak=   -3.595 closest distance to " NH1 ARG A 195 " =    2.615
peak=   -3.589 closest distance to " OD2 ASP A 171 " =    2.134
peak=   -3.578 closest distance to " O   HOH Z 198 " =    1.546
peak=   -3.577 closest distance to " O   ILE A 109 " =    2.530
peak=   -3.570 closest distance to " O   HOH Z  11 " =    1.846
peak=   -3.561 closest distance to " O   HOH Z  24 " =    1.286
peak=   -3.538 closest distance to " C   LEU A 143 " =    1.126
peak=   -3.520 closest distance to " OD1 ASP A 191 " =    1.439
peak=   -3.518 closest distance to " O   HOH Z 250 " =    1.449
peak=   -3.502 closest distance to " C   ALA A 158 " =    1.271
peak=   -3.499 closest distance to " NH2BARG A 275 " =    1.816
peak=   -3.497 closest distance to " NH2 ARG A  79 " =    1.933
peak=   -3.493 closest distance to " CB  CYS A 254 " =    2.220
peak=   -3.490 closest distance to " CD1 LEU A 101 " =    2.289
peak=   -3.485 closest distance to " O   HOH Z 131 " =    4.106
peak=   -3.473 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.466 closest distance to " CZ3 TRP A 179 " =    1.238
peak=   -3.464 closest distance to " O   HOH Z  60 " =    2.306
peak=   -3.455 closest distance to " CB  PRO A 163 " =    2.452
peak=   -3.451 closest distance to " O   HOH Z 103 " =    1.733
peak=   -3.450 closest distance to " O   MET A  40 " =    2.701
peak=   -3.445 closest distance to " O   HOH Z 211 " =    1.578
peak=   -3.438 closest distance to " O   HOH Z 266 " =    4.322
peak=   -3.435 closest distance to " O   HOH Z 152 " =    5.100
peak=   -3.432 closest distance to " O   HOH Z 111 " =    2.501
peak=   -3.426 closest distance to " O   SER A  95 " =    1.420
peak=   -3.425 closest distance to " CB  ALA A   7 " =    2.048
peak=   -3.421 closest distance to " N   HIS A 115 " =    2.302
peak=   -3.419 closest distance to " O   HOH Z 298 " =    1.285
peak=   -3.414 closest distance to " CG2 VAL A 189 " =    1.969
peak=   -3.412 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.412 closest distance to " CE3 TRP A 123 " =    1.303
peak=   -3.407 closest distance to " O   HOH Z 409 " =    5.981
peak=   -3.405 closest distance to " O   TRP A  70 " =    1.505
peak=   -3.399 closest distance to " CE3 TRP A 274 " =    2.305
peak=   -3.394 closest distance to " O   ALA A  51 " =    1.315
peak=   -3.394 closest distance to " ND2 ASN A 187 " =    1.534
peak=   -3.393 closest distance to " O   HOH Z  90 " =    2.379
peak=   -3.388 closest distance to " N   THR A 157 " =    1.464
peak=   -3.388 closest distance to " CD  LYS A 289 " =    2.347
peak=   -3.387 closest distance to " O   HOH Z 166 " =    1.282
peak=   -3.386 closest distance to " CB  PHE A 192 " =    1.800
peak=   -3.382 closest distance to " O   HOH Z  93 " =    1.868
peak=   -3.380 closest distance to " CB  ILE A  33 " =    2.829
peak=   -3.379 closest distance to " CD  GLN A  88 " =    0.852
peak=   -3.377 closest distance to " C   PRO A  90 " =    1.527
peak=   -3.362 closest distance to " CG1 VAL A 230 " =    1.923
peak=   -3.362 closest distance to " CB  ALA A 248 " =    1.959
peak=   -3.360 closest distance to " CB  ALA A 248 " =    2.295
peak=   -3.359 closest distance to " C   LYS A  76 " =    1.646
peak=   -3.355 closest distance to " O   HOH Z  63 " =    1.876
peak=   -3.344 closest distance to " CG2 THR A 178 " =    2.161
peak=   -3.343 closest distance to " O   HOH Z 140 " =    1.930
peak=   -3.334 closest distance to " O   HOH Z 359 " =    3.325
peak=   -3.325 closest distance to " O   HOH Z 326 " =    1.650
peak=   -3.324 closest distance to " CA  ASP A  27 " =    2.362
peak=   -3.324 closest distance to " CE  LYS A  76 " =    2.927
peak=   -3.320 closest distance to " OXT GLY A 302 " =    3.534
peak=   -3.313 closest distance to " O   SER A  22 " =    2.365
peak=   -3.310 closest distance to " N   SER A 212 " =    1.914
peak=   -3.309 closest distance to " O   VAL A 189 " =    2.486
peak=   -3.305 closest distance to " O   SER A 146 " =    1.034
peak=   -3.302 closest distance to " CE1 TYR A 169 " =    2.438
peak=   -3.300 closest distance to " OG  SER A  97 " =    2.035
peak=   -3.298 closest distance to " OG  SER A 245 " =    1.242
peak=   -3.298 closest distance to " NZ  LYS A 119 " =    3.348
peak=   -3.295 closest distance to " O   ASN A 249 " =    1.442
peak=   -3.292 closest distance to " CD1 ILE A 151 " =    2.188
peak=   -3.290 closest distance to " CD2 LEU A 237 " =    2.719
peak=   -3.290 closest distance to " O   HOH Z 165 " =    2.145
peak=   -3.289 closest distance to " O   VAL A 174 " =    2.137
peak=   -3.289 closest distance to " C   ASP A 231 " =    2.394
peak=   -3.283 closest distance to " CB  ASP A 286 " =    2.198
peak=   -3.282 closest distance to " O   HOH Z 351 " =    1.683
peak=   -3.281 closest distance to " OG  SER A  87 " =    1.284
peak=   -3.280 closest distance to " O   HOH Z 137 " =    1.418
peak=   -3.274 closest distance to " NH2AARG A 275 " =    5.188
peak=   -3.270 closest distance to " O   HOH Z 348 " =    1.811
peak=   -3.267 closest distance to " O   HOH Z 213 " =    1.351
peak=   -3.267 closest distance to " CG  GLN A  58 " =    1.175
peak=   -3.267 closest distance to " CB  ASP A 132 " =    2.201
peak=   -3.267 closest distance to " NE2 GLN A 278 " =    1.714
peak=   -3.266 closest distance to " O   GLN A 144 " =    1.369
peak=   -3.265 closest distance to " ND2 ASN A  69 " =    1.469
peak=   -3.260 closest distance to " CB  TRP A  85 " =    2.448
peak=   -3.254 closest distance to " NH1AARG A 275 " =    1.756
peak=   -3.254 closest distance to " O   ALA A  10 " =    1.704
peak=   -3.253 closest distance to " OD1 ASN A 176 " =    1.253
peak=   -3.252 closest distance to " O   HOH Z 114 " =    2.879
peak=   -3.252 closest distance to " O   HOH Z 438 " =    1.081
peak=   -3.247 closest distance to " O   HOH Z 234 " =    3.888
peak=   -3.246 closest distance to " N   PRO A 163 " =    1.576
peak=   -3.241 closest distance to " CG  GLU A   2 " =    2.047
peak=   -3.230 closest distance to " O   ALA A  34 " =    2.508
peak=   -3.229 closest distance to " OD2 ASP A  50 " =    1.439
peak=   -3.227 closest distance to " OE1 GLN A 223 " =    1.956
peak=   -3.224 closest distance to " O   HOH Z  60 " =    1.963
peak=   -3.224 closest distance to " O   HOH Z 405 " =    2.949
peak=   -3.222 closest distance to " CG  PRO A 243 " =    1.597
peak=   -3.221 closest distance to " N   THR A 235 " =    1.316
peak=   -3.219 closest distance to " CE  MET A  93 " =    1.135
peak=   -3.219 closest distance to " O   HOH Z 191 " =    5.566
peak=   -3.210 closest distance to " O   HOH Z 137 " =    1.452
peak=   -3.210 closest distance to " CB  PHE A 208 " =    2.162
peak=   -3.208 closest distance to " CB  ASP A 286 " =    1.754
peak=   -3.208 closest distance to " O   ALA A 292 " =    1.970
peak=   -3.201 closest distance to " OG ASER A 134 " =    1.021
peak=   -3.199 closest distance to " CB  ALA A  51 " =    1.850
peak=   -3.184 closest distance to " O   HOH Z 423 " =    1.214
peak=   -3.183 closest distance to " O   HOH Z 324 " =    2.153
peak=   -3.181 closest distance to " ND2 ASN A  39 " =    1.462
peak=   -3.178 closest distance to " OH  TYR A 214 " =    1.259
peak=   -3.170 closest distance to " O   HOH Z  38 " =    1.746
peak=   -3.170 closest distance to " CD2 PHE A 225 " =    1.120
peak=   -3.168 closest distance to " CA  GLY A  57 " =    2.067
peak=   -3.159 closest distance to " O   HOH Z 134 " =    3.032
peak=   -3.159 closest distance to " CZ3 TRP A 123 " =    1.785
peak=   -3.155 closest distance to " N   ALA A  43 " =    2.545
peak=   -3.155 closest distance to " O   ASN A 127 " =    2.163
peak=   -3.151 closest distance to " CG1 VAL A 197 " =    2.143
peak=   -3.145 closest distance to " OE2 GLU A 152 " =    1.097
peak=   -3.144 closest distance to " O   HOH Z 394 " =    1.462
peak=   -3.132 closest distance to " CD2 LEU A 300 " =    2.822
peak=   -3.127 closest distance to " O   HOH Z 111 " =    4.599
peak=   -3.126 closest distance to " O   HOH Z 281 " =    2.780
peak=   -3.125 closest distance to " O   HOH Z 236 " =    1.967
peak=   -3.120 closest distance to " CD2 PHE A  61 " =    2.270
peak=   -3.117 closest distance to " O   HOH Z 414 " =    1.880
peak=   -3.115 closest distance to " O   THR A 220 " =    1.847
peak=   -3.113 closest distance to " O   ASP A 162 " =    2.176
peak=   -3.112 closest distance to " CG  PRO A 163 " =    2.631
peak=   -3.108 closest distance to " CD  PRO A 198 " =    1.566
peak=   -3.102 closest distance to " CG  GLU A 152 " =    1.191
peak=   -3.101 closest distance to " CB  ALA A 244 " =    1.997
peak=   -3.097 closest distance to " O   HOH Z 193 " =    2.050
peak=   -3.096 closest distance to " O   HOH Z 244 " =    1.959
peak=   -3.092 closest distance to " OE1 GLN A  77 " =    1.701
peak=   -3.086 closest distance to " O   GLY A  80 " =    2.436
peak=   -3.081 closest distance to " O   HOH Z  51 " =    1.212
peak=   -3.081 closest distance to " CZ2 TRP A 274 " =    0.977
peak=   -3.075 closest distance to " OG1 THR A 246 " =    1.438
peak=   -3.073 closest distance to " O   HOH Z 298 " =    2.450
peak=   -3.070 closest distance to " CD2 TYR A 293 " =    1.955
peak=   -3.060 closest distance to " CG  GLU A 277 " =    1.265
peak=   -3.059 closest distance to " OG  SER A 206 " =    1.732
peak=   -3.050 closest distance to " SG ACYS A 201 " =    1.853
peak=   -3.034 closest distance to " CD  GLN A 223 " =    1.404

================= 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    :  0.4015 0.3990   6.193821e+00   6.183620e+00
   1_bss:  0.3884 0.3840   6.182273e+00   6.158891e+00
   1_xyz:  0.2585 0.2864   5.849378e+00   5.925702e+00
   1_adp:  0.2355 0.2980   5.796153e+00   5.954837e+00
   1_occ:  0.2351 0.2981   5.795349e+00   5.954603e+00
   2_bss:  0.2333 0.2957   5.791314e+00   5.949642e+00
   2_xyz:  0.1658 0.2148   5.474245e+00   5.676596e+00
   2_adp:  0.1497 0.1953   5.384703e+00   5.590797e+00
   2_occ:  0.1494 0.1951   5.383349e+00   5.589080e+00
   3_bss:  0.1494 0.1950   5.379934e+00   5.585452e+00
   3_xyz:  0.1215 0.1646   5.195020e+00   5.423658e+00
   3_adp:  0.1152 0.1603   5.153080e+00   5.394134e+00
   3_occ:  0.1151 0.1602   5.152852e+00   5.393959e+00
   4_bss:  0.1152 0.1601   5.153132e+00   5.393984e+00
   4_xyz:  0.1088 0.1560   5.115197e+00   5.368375e+00
   4_adp:  0.1079 0.1548   5.107934e+00   5.362071e+00
   4_occ:  0.1079 0.1547   5.107775e+00   5.361908e+00
   5_bss:  0.1078 0.1547   5.107763e+00   5.361898e+00
   5_xyz:  0.1062 0.1543   5.100430e+00   5.360768e+00
   5_adp:  0.1058 0.1551   5.101101e+00   5.365555e+00
   5_occ:  0.1057 0.1550   5.101009e+00   5.365481e+00
   5_bss:  0.1057 0.1551   5.101105e+00   5.365552e+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:  0.332  22.917  -3.093   1.792   0.681   0.000   0.000   0.000
   1_xyz:  0.332  22.917  -3.093   1.792   0.681   0.000   0.000   0.000
   1_adp:  0.332  22.917  -3.093   1.792   0.681   0.000   0.000   0.000
   1_occ:  0.332  22.917  -3.093   1.792   0.681   0.000   0.000   0.000
   2_bss:  0.327  37.511  -2.683  -0.818  -0.927  -0.000  -0.000  -0.000
   2_xyz:  0.327  37.511  -2.683  -0.818  -0.927  -0.000  -0.000  -0.000
   2_adp:  0.327  37.511  -2.683  -0.818  -0.927  -0.000  -0.000  -0.000
   2_occ:  0.327  37.511  -2.683  -0.818  -0.927  -0.000  -0.000  -0.000
   3_bss:  0.321  38.041  -2.430  -1.887  -1.155  -0.000  -0.000  -0.000
   3_xyz:  0.321  38.041  -2.430  -1.887  -1.155  -0.000  -0.000  -0.000
   3_adp:  0.321  38.041  -2.430  -1.887  -1.155  -0.000  -0.000  -0.000
   3_occ:  0.321  38.041  -2.430  -1.887  -1.155  -0.000  -0.000  -0.000
   4_bss:  0.318  41.093  -2.558  -2.287  -1.447  -0.000  -0.000  -0.000
   4_xyz:  0.318  41.093  -2.558  -2.287  -1.447  -0.000  -0.000  -0.000
   4_adp:  0.318  41.093  -2.558  -2.287  -1.447  -0.000  -0.000  -0.000
   4_occ:  0.318  41.093  -2.558  -2.287  -1.447  -0.000  -0.000  -0.000
   5_bss:  0.319  41.220  -2.379  -2.236  -1.320  -0.000  -0.000  -0.000
   5_xyz:  0.319  41.220  -2.379  -2.236  -1.320  -0.000  -0.000  -0.000
   5_adp:  0.319  41.220  -2.379  -2.236  -1.320  -0.000  -0.000  -0.000
   5_occ:  0.319  41.220  -2.379  -2.236  -1.320  -0.000  -0.000  -0.000
   5_bss:  0.320  41.223  -2.179  -2.105  -1.149  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.009 0.5967  0.7907    47970.072
   1_bss:  42.436 0.6136  0.8039    43397.501
   1_xyz:  28.226 0.7790  0.9704    21426.203
   1_adp:  29.598 0.7630  0.9549    22988.334
   1_occ:  29.608 0.7628  0.9542    22985.147
   2_bss:  29.282 0.7662  0.9183    22541.135
   2_xyz:  20.745 0.8539  0.9902    11499.675
   2_adp:  18.251 0.8787  1.0003     9616.366
   2_occ:  18.214 0.8790  1.0001     9568.597
   3_bss:  18.098 0.8800  0.9886     9459.088
   3_xyz:  14.699 0.9086  1.0015     6679.774
   3_adp:  14.011 0.9146  0.9986     6336.502
   3_occ:  14.006 0.9146  0.9985     6328.429
   4_bss:  14.007 0.9146  0.9887     6339.345
   4_xyz:  13.500 0.9187  0.9898     5984.461
   4_adp:  13.334 0.9202  0.9853     5924.423
   4_occ:  13.330 0.9202  0.9852     5918.280
   5_bss:  13.330 0.9202  0.9896     5920.218
   5_xyz:  13.277 0.9208  0.9892     5942.508
   5_adp:  13.353 0.9203  0.9826     5990.007
   5_occ:  13.353 0.9203  0.9825     5988.387
   5_bss:  13.354 0.9203  0.9888     5990.848
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6891e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6891e-01
   1_xyz:   1.293  0.010  0.082 15.045  0.005  4.104   9.1935e-02
   1_adp:   1.293  0.010  0.082 15.045  0.005  4.104   9.1935e-02
   1_occ:   1.293  0.010  0.082 15.045  0.005  4.104   9.1935e-02
   2_bss:   1.293  0.010  0.082 15.045  0.005  4.104   9.1935e-02
   2_xyz:   1.068  0.006  0.071 14.325  0.004  4.109   6.1958e-02
   2_adp:   1.068  0.006  0.071 14.325  0.004  4.109   6.1958e-02
   2_occ:   1.068  0.006  0.071 14.325  0.004  4.109   6.1958e-02
   3_bss:   1.068  0.006  0.071 14.325  0.004  4.109   6.1958e-02
   3_xyz:   0.968  0.006  0.071 14.606  0.004  4.105   5.6904e-02
   3_adp:   0.968  0.006  0.071 14.606  0.004  4.105   5.6904e-02
   3_occ:   0.968  0.006  0.071 14.606  0.004  4.105   5.6904e-02
   4_bss:   0.968  0.006  0.071 14.606  0.004  4.105   5.6904e-02
   4_xyz:   0.985  0.006  0.072 14.650  0.004  4.105   5.8081e-02
   4_adp:   0.985  0.006  0.072 14.650  0.004  4.105   5.8081e-02
   4_occ:   0.985  0.006  0.072 14.650  0.004  4.105   5.8081e-02
   5_bss:   0.985  0.006  0.072 14.650  0.004  4.105   5.8081e-02
   5_xyz:   0.978  0.006  0.072 14.539  0.004  4.112   5.6656e-02
   5_adp:   0.978  0.006  0.072 14.539  0.004  4.112   5.6656e-02
   5_occ:   0.978  0.006  0.072 14.539  0.004  4.112   5.6656e-02
   5_bss:   0.978  0.006  0.072 14.539  0.004  4.112   5.6656e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3766e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3766e-01
   1_xyz:   9.194  0.056  0.344 87.458  0.036  2.138   9.1281e-02
   1_adp:   9.194  0.056  0.344 87.458  0.036  2.138   9.1281e-02
   1_occ:   9.194  0.056  0.344 87.458  0.036  2.138   9.1281e-02
   2_bss:   9.194  0.056  0.344 87.458  0.036  2.138   9.1281e-02
   2_xyz:   6.839  0.034  0.237 83.066  0.038  2.311   6.4418e-02
   2_adp:   6.839  0.034  0.237 83.066  0.038  2.311   6.4418e-02
   2_occ:   6.839  0.034  0.237 83.066  0.038  2.311   6.4418e-02
   3_bss:   6.839  0.034  0.237 83.066  0.038  2.311   6.4418e-02
   3_xyz:   6.630  0.045  0.220 85.480  0.034  2.321   4.8619e-02
   3_adp:   6.630  0.045  0.220 85.480  0.034  2.321   4.8619e-02
   3_occ:   6.630  0.045  0.220 85.480  0.034  2.321   4.8619e-02
   4_bss:   6.630  0.045  0.220 85.480  0.034  2.321   4.8619e-02
   4_xyz:   6.166  0.039  0.225 84.124  0.041  2.279   4.3707e-02
   4_adp:   6.166  0.039  0.225 84.124  0.041  2.279   4.3707e-02
   4_occ:   6.166  0.039  0.225 84.124  0.041  2.279   4.3707e-02
   5_bss:   6.166  0.039  0.225 84.124  0.041  2.279   4.3707e-02
   5_xyz:   6.398  0.035  0.230 84.207  0.039  2.289   4.2073e-02
   5_adp:   6.398  0.035  0.230 84.207  0.039  2.289   4.2073e-02
   5_occ:   6.398  0.035  0.230 84.207  0.039  2.289   4.2073e-02
   5_bss:   6.398  0.035  0.230 84.207  0.039  2.289   4.2073e-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:  83.69   0.00  17.89  83.69   0.00  13.88  80.89   3.51  39.73
   1_occ:  83.69   0.00  17.89  83.69   0.00  13.88  80.89   3.51  39.73
   2_bss:  83.69   0.00  17.89  83.69   0.00  13.88  80.89   3.51  39.73
   2_xyz:  83.69   0.00  17.89  83.69   0.00  13.88  80.89   3.51  39.73
   2_adp:  82.87   1.52  17.09  82.87   1.52  13.06  75.73   5.56  39.04
   2_occ:  82.87   1.52  17.09  82.87   1.52  13.06  75.73   5.56  39.04
   3_bss:  82.87   1.52  17.09  82.87   1.52  13.06  75.73   5.56  39.04
   3_xyz:  82.87   1.52  17.09  82.87   1.52  13.06  75.73   5.56  39.04
   3_adp:  91.20   0.00  17.30  91.20   0.00  12.89  81.83   2.18  41.33
   3_occ:  91.20   0.00  17.30  91.20   0.00  12.89  81.83   2.18  41.33
   4_bss:  91.20   0.00  17.30  91.20   0.00  12.89  81.83   2.18  41.33
   4_xyz:  91.20   0.00  17.30  91.20   0.00  12.89  81.83   2.18  41.33
   4_adp:  93.66   0.45  17.05  93.66   0.45  12.76  82.76   3.59  40.44
   4_occ:  93.66   0.45  17.05  93.66   0.45  12.76  82.76   3.59  40.44
   5_bss:  93.66   0.45  17.05  93.66   0.45  12.76  82.76   3.59  40.44
   5_xyz:  93.66   0.45  17.05  93.66   0.45  12.76  82.76   3.59  40.44
   5_adp: 100.02   0.00  16.96 100.02   0.00  12.67  87.85   5.22  40.30
   5_occ: 100.02   0.00  16.96 100.02   0.00  12.67  87.85   5.22  40.30
   5_bss: 100.03   0.00  16.96 100.03   0.00  12.67  87.85   5.22  40.30
------------------------------------------------------------------------
 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:    1.692    0.022    0.323
   1_adp:    1.692    0.022    0.323
   1_occ:    1.692    0.022    0.323
   2_bss:    1.692    0.022    0.323
   2_xyz:    1.048    0.047    0.474
   2_adp:    1.048    0.047    0.474
   2_occ:    1.048    0.047    0.474
   3_bss:    1.048    0.047    0.474
   3_xyz:    1.026    0.038    0.545
   3_adp:    1.026    0.038    0.545
   3_occ:    1.026    0.038    0.545
   4_bss:    1.026    0.038    0.545
   4_xyz:    1.069    0.068    0.565
   4_adp:    1.069    0.068    0.565
   4_occ:    1.069    0.068    0.565
   5_bss:    1.069    0.068    0.565
   5_xyz:    1.179    0.038    0.579
   5_adp:    1.179    0.038    0.579
   5_occ:    1.179    0.038    0.579
   5_bss:    1.179    0.038    0.579
------------------------------------------------------------------------

CPU time actual refinement: 346.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/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_508/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_508/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.62 
  Macro-tasks:
    bulk solvent and scale       = 44.58  
    individual site refinement   = 144.54 
    weights calculation          = 30.54  
    collect and process          = 6.67   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 226.44 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 109.23 
    alpha_beta                      = 8.30   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 119.16 
    fmodel                         = 7.41   
    r_factors                      = 0.33   
    phase_errors                   = 10.57  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 258.30 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.842 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    659 calls, 108.87 s
gradients_fft:          604 calls, 104.98 s

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

# Date 2008-01-16 Time 05:00:05 PST -0800 (1200488405.41 s)
Start R-work = 0.4015, R-free = 0.3990 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1737 (no bulk solvent and anisotropic scale)

Start R-work = 0.3884, R-free = 0.3840
Final R-work = 0.1057, R-free = 0.1551