# Date 2008-01-16 Time 05:51:18 PST -0800 (1200491478.59 s)
#phil __OFF__

Command line arguments: "../904.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30643
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 904

-------------------------------------------------------------------------------
  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: (70.9525, 46.93, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97117
Completeness in resolution range: 0.949401
Completeness with d_max=infinity: 0.946557

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0395
                             d_min =   1.9712

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0395 1.97117
Completeness in resolution range: 0.949401
Completeness with d_max=infinity: 0.946557

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0399 -  4.2185 [2168/2197]  1954   214   9.9%
  bin  2:  4.2185 -  3.3606 [2073/2089]  1863   210  10.1%
  bin  3:  3.3606 -  2.9394 [2049/2068]  1843   206  10.1%
  bin  4:  2.9394 -  2.6723 [2046/2076]  1848   198   9.7%
  bin  5:  2.6723 -  2.4817 [2036/2055]  1832   204  10.0%
  bin  6:  2.4817 -  2.3359 [2014/2050]  1806   208  10.3%
  bin  7:  2.3359 -  2.2193 [1984/2017]  1783   201  10.1%
  bin  8:  2.2193 -  2.1230 [2004/2038]  1808   196   9.8%
  bin  9:  2.1230 -  2.0415 [1980/2008]  1781   199  10.1%
  bin 10:  2.0415 -  1.9712 [1235/2035]  1112   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/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: 21
        2.42 -     3.04: 2205
        3.04 -     3.66: 4703
        3.66 -     4.28: 9032
        4.28 -     4.90: 12410
  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 113 " - " O   HOH Z 350 "  1.958 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.969 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.149 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.191 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28366 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_904/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/model_refine_001.geo

CPU time processing inputs: 9.41


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.93 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 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3097   r_free= 0.3163   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.007644                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7053 0.99   1402  157 0.2772 0.2741      6.3328       6.309|
|  2:  4.7053 -  3.7539 0.99   1359  145 0.2389 0.2304      6.3712      6.3449|
|  3:  3.7539 -  3.2850 0.99   1322  154 0.2670 0.2541      6.2742      6.3719|
|  4:  3.2850 -  2.9872 0.99   1331  147 0.2735 0.3044      6.1592      6.1805|
|  5:  2.9872 -  2.7745 0.99   1313  143 0.3098 0.3063      6.0492      6.0689|
|  6:  2.7745 -  2.6119 0.99   1298  145 0.3363 0.3467      6.0128      6.0168|
|  7:  2.6119 -  2.4817 0.99   1315  141 0.3222 0.3084      5.9834      5.9323|
|  8:  2.4817 -  2.3741 0.98   1274  150 0.3439 0.3380      5.9287      5.9361|
|  9:  2.3741 -  2.2830 0.98   1298  148 0.3406 0.3500       5.886      5.8494|
| 10:  2.2830 -  2.2045 0.98   1281  134 0.3512 0.4376      5.8741       6.035|
| 11:  2.2045 -  2.1357 1.00   1281  142 0.3553 0.3846      5.8322       5.896|
| 12:  2.1357 -  2.0748 0.97   1261  139 0.3666 0.3905      5.7806       5.854|
| 13:  2.0748 -  2.0204 0.98   1285  143 0.3636 0.3621       5.688      5.6207|
| 14:  2.0204 -  1.9712 0.47    610   71 0.3973 0.4343      5.7091      5.6875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7053  1402   157  0.80  24.78   0.87     0.81      39103.33|
|  2:  4.7053 -  3.7539  1359   145  0.85  21.47   0.98     0.92      42558.38|
|  3:  3.7539 -  3.2850  1322   154  0.81  25.60   1.00     0.96      42069.51|
|  4:  3.2850 -  2.9872  1331   147  0.79  27.85   1.01     0.95      37646.77|
|  5:  2.9872 -  2.7745  1313   143  0.73  33.17   0.99     0.91      32089.76|
|  6:  2.7745 -  2.6119  1298   145  0.72  33.86   1.01     0.91      27835.74|
|  7:  2.6119 -  2.4817  1315   141  0.74  32.57   1.01     0.93      24810.86|
|  8:  2.4817 -  2.3741  1274   150  0.72  34.29   1.00     0.94      23380.26|
|  9:  2.3741 -  2.2830  1298   148  0.71  35.30   1.05     0.93      22646.63|
| 10:  2.2830 -  2.2045  1281   134  0.67  38.43   1.05     0.91      24065.98|
| 11:  2.2045 -  2.1357  1281   142  0.65  39.71   1.06     0.90      23123.76|
| 12:  2.1357 -  2.0748  1261   139  0.65  40.31   1.05     0.93      22000.82|
| 13:  2.0748 -  2.0204  1285   143  0.64  41.16   1.04     0.89      18638.14|
| 14:  2.0204 -  1.9712   610    71  0.62  43.07   1.04     0.80      16615.57|
|alpha:            min =        0.80 max =            0.96 mean =         0.91|
|beta:             min =    16615.57 max =        42558.38 mean =     28969.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.73|
|phase err.(work): min =        0.00 max =           89.94 mean =        33.17|
|phase err.(test): min =        0.00 max =           89.99 mean =        33.32|
|-----------------------------------------------------------------------------|

============================== 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 = 5.376610              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.077   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.096   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      190 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2015 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1853 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2850 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4644 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4388 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5665 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6745 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.190 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    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 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3097   r_free= 0.3163   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.007644                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2944   r_free= 0.3024   ksol= 0.31   Bsol= 35.16   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-2.94,1.14,-0.00,0.00,0.00); trace/3= -1.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.987026                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.586328              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.279   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.905   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2944      final r-factor (work) = 0.1638          |
| start r-factor (free) = 0.3024      final r-factor (free) = 0.1869          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9066 = 4.59 * 0.50 * 5.9933 + 1.00 * 0.1629                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1362 = 4.59 * 0.50 * 5.7006 + 1.00 * 0.0639                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1638      final r-factor (work) = 0.1515          |
| start r-factor (free) = 0.1869      final r-factor (free) = 0.1918          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8792 = 0.33 * 1.00 * 5.7006 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7902 = 0.33 * 1.00 * 5.3767 + 1.00 * 0.0237                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.67   16.67    None  None   None       |
|    all(noH): 2823   0      0.00    62.67   16.67    None  None   None       |
|    Sol.    : 438    0      6.89    62.67   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    55.55   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.267:  204   |   5:    31.334 -  37.601:   95        |
|      1:     6.267 -  12.534: 1212   |   6:    37.601 -  43.867:  115        |
|      2:    12.534 -  18.800:  711   |   7:    43.867 -  50.134:   74        |
|      3:    18.800 -  25.067:  218   |   8:    50.134 -  56.401:   63        |
|      4:    25.067 -  31.334:  108   |   9:    56.401 -  62.668:   23        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1515 r_free = 0.1918             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1510 r_free = 0.1916             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1510   r_free= 0.1916   ksol= 0.31   Bsol= 35.16   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-2.94,1.14,-0.00,0.00,0.00); trace/3= -1.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.387610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1493   r_free= 0.1882   ksol= 0.32   Bsol= 47.73   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-3.06,-1.33,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.377487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.198788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.261  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207746              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.343   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1882      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9910 = 2.20 * 0.50 * 5.3912 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8732 = 2.20 * 0.50 * 5.2913 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1288 = 0.21 * 1.00 * 5.2913 + 1.00 * 0.0296                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0839 = 0.21 * 1.00 * 5.1824 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.86    71.19   16.84    None  None   None       |
|    all(noH): 2823   0      1.86    71.19   16.84    None  None   None       |
|    Sol.    : 438    0      5.91    68.23   37.93    None  None   None       |
|    Mac.    : 2385   0      1.86    71.19   12.97    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:     1.859 -   8.792:  642   |   5:    36.522 -  43.455:  101        |
|      1:     8.792 -  15.724: 1269   |   6:    43.455 -  50.388:   98        |
|      2:    15.724 -  22.657:  369   |   7:    50.388 -  57.320:   67        |
|      3:    22.657 -  29.590:  136   |   8:    57.320 -  64.253:   28        |
|      4:    29.590 -  36.522:  107   |   9:    64.253 -  71.186:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1563             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1562             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1562   ksol= 0.32   Bsol= 47.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-3.06,-1.33,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1561   ksol= 0.32   Bsol= 45.39   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.70,-1.71,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.164141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.160597              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.067  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.032  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6532 = 2.16 * 0.50 * 5.1812 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6114 = 2.16 * 0.50 * 5.1389 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1532      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6343 = 0.32 * 1.00 * 5.1389 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6300 = 0.32 * 1.00 * 5.1241 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    72.90   16.79    None  None   None       |
|    all(noH): 2823   0      1.61    72.90   16.79    None  None   None       |
|    Sol.    : 438    0      6.30    68.64   38.03    None  None   None       |
|    Mac.    : 2385   0      1.61    72.90   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:     1.610 -   8.738:  655   |   5:    37.253 -  44.382:  105        |
|      1:     8.738 -  15.867: 1275   |   6:    44.382 -  51.511:   99        |
|      2:    15.867 -  22.996:  360   |   7:    51.511 -  58.640:   60        |
|      3:    22.996 -  30.125:  131   |   8:    58.640 -  65.768:   24        |
|      4:    30.125 -  37.253:  108   |   9:    65.768 -  72.897:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1534             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1093 r_free = 0.1535             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1535   ksol= 0.32   Bsol= 45.39   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-2.70,-1.71,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1534   ksol= 0.32   Bsol= 45.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.48,-1.72,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125214                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.842835              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.496  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.227111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.286  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1093      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7813 = 1.84 * 0.50 * 5.1242 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7776 = 1.84 * 0.50 * 5.1251 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4218 = 2.23 * 1.00 * 5.1251 + 1.00 * 0.0076                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4223 = 2.23 * 1.00 * 5.1246 + 1.00 * 0.0093                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    82.21   17.06    None  None   None       |
|    all(noH): 2823   0      0.43    82.21   17.06    None  None   None       |
|    Sol.    : 438    0      6.59    73.25   39.55    None  None   None       |
|    Mac.    : 2385   0      0.43    82.21   12.93    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:     0.434 -   8.611:  690   |   5:    41.319 -  49.496:  115        |
|      1:     8.611 -  16.788: 1301   |   6:    49.496 -  57.674:   83        |
|      2:    16.788 -  24.965:  330   |   7:    57.674 -  65.851:   44        |
|      3:    24.965 -  33.142:  132   |   8:    65.851 -  74.028:   19        |
|      4:    33.142 -  41.319:  104   |   9:    74.028 -  82.205:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1566             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1567             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1567   ksol= 0.32   Bsol= 45.39   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.48,-1.72,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1567   ksol= 0.32   Bsol= 46.95   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.24,-1.57,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132233                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.464066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.825  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.674596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.664  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1081      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8070 = 1.46 * 0.50 * 5.1252 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8104 = 1.46 * 0.50 * 5.1360 + 1.00 * 0.0506                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4740 = 0.67 * 1.00 * 5.1360 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4768 = 0.67 * 1.00 * 5.1404 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.38    85.20   16.88    None  None   None       |
|    all(noH): 2823   0      0.38    85.20   16.88    None  None   None       |
|    Sol.    : 438    0      6.31    74.51   39.23    None  None   None       |
|    Mac.    : 2385   0      0.38    85.20   12.77    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:     0.377 -   8.859:  784   |   5:    42.789 -  51.271:  111        |
|      1:     8.859 -  17.342: 1267   |   6:    51.271 -  59.753:   74        |
|      2:    17.342 -  25.824:  293   |   7:    59.753 -  68.236:   35        |
|      3:    25.824 -  34.306:  132   |   8:    68.236 -  76.718:   12        |
|      4:    34.306 -  42.789:  110   |   9:    76.718 -  85.200:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1576             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1577             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1577   ksol= 0.32   Bsol= 46.95   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.24,-1.57,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.139901                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7053 0.99   1402  157 0.0974 0.1278      5.3683      5.5313|
|  2:  4.7053 -  3.7539 0.99   1359  145 0.0833 0.1052      5.4152      5.5901|
|  3:  3.7539 -  3.2850 0.99   1322  154 0.1036 0.1557      5.4532      5.8713|
|  4:  3.2850 -  2.9872 0.99   1331  147 0.1166 0.1492      5.4414      5.5777|
|  5:  2.9872 -  2.7745 0.99   1313  143 0.1292 0.1788      5.3159      5.5323|
|  6:  2.7745 -  2.6119 0.99   1298  145 0.1197 0.1786      5.2009      5.4568|
|  7:  2.6119 -  2.4817 0.99   1315  141 0.1205 0.1641      5.1461      5.3635|
|  8:  2.4817 -  2.3741 0.98   1274  150 0.1129 0.1734      5.0443       5.306|
|  9:  2.3741 -  2.2830 0.98   1298  148 0.1130 0.1877      5.0168      5.3413|
| 10:  2.2830 -  2.2045 0.98   1281  134 0.1103 0.1688      4.9624      5.2103|
| 11:  2.2045 -  2.1357 1.00   1281  142 0.1145 0.1783      4.9549      5.2888|
| 12:  2.1357 -  2.0748 0.97   1261  139 0.1077 0.1627      4.8764      5.1159|
| 13:  2.0748 -  2.0204 0.98   1285  143 0.1166 0.1786      4.7934      5.0547|
| 14:  2.0204 -  1.9712 0.47    610   71 0.0998 0.1705      4.6401      4.9597|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7053  1402   157  0.94   8.74   0.98     0.95       6762.27|
|  2:  4.7053 -  3.7539  1359   145  0.95   7.76   1.01     1.00       8596.43|
|  3:  3.7539 -  3.2850  1322   154  0.93  11.22   1.03     1.02      10069.17|
|  4:  3.2850 -  2.9872  1331   147  0.92  13.68   1.01     0.99      10455.96|
|  5:  2.9872 -  2.7745  1313   143  0.90  16.16   0.99     0.97       8360.38|
|  6:  2.7745 -  2.6119  1298   145  0.90  15.97   0.99     0.96       7097.68|
|  7:  2.6119 -  2.4817  1315   141  0.91  15.11   0.99     0.96       6064.04|
|  8:  2.4817 -  2.3741  1274   150  0.91  15.27   0.99     0.97       5206.84|
|  9:  2.3741 -  2.2830  1298   148  0.91  15.16   1.00     0.97       4970.80|
| 10:  2.2830 -  2.2045  1281   134  0.90  15.94   0.98     0.94       4470.10|
| 11:  2.2045 -  2.1357  1281   142  0.90  16.60   0.99     0.95       4542.63|
| 12:  2.1357 -  2.0748  1261   139  0.91  15.33   1.00     0.98       4108.22|
| 13:  2.0748 -  2.0204  1285   143  0.90  16.58   0.99     0.98       3397.46|
| 14:  2.0204 -  1.9712   610    71  0.91  14.62   0.97     0.94       2499.14|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2499.14 max =        10455.96 mean =      6367.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.07|
|phase err.(test): min =        0.00 max =           89.49 mean =        13.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1577   ksol= 0.32   Bsol= 46.94   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.05,-1.40,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140000                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1091   r_free= 0.1577   ksol= 0.32   Bsol= 46.94   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.05,-1.40,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140000                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0399 -  4.7053 0.99   1402  157 0.0974 0.1279      5.3692      5.5325|
|  2:  4.7053 -  3.7539 0.99   1359  145 0.0834 0.1052      5.4155        5.59|
|  3:  3.7539 -  3.2850 0.99   1322  154 0.1036 0.1557      5.4531      5.8711|
|  4:  3.2850 -  2.9872 0.99   1331  147 0.1166 0.1493      5.4413      5.5777|
|  5:  2.9872 -  2.7745 0.99   1313  143 0.1292 0.1788      5.3159      5.5321|
|  6:  2.7745 -  2.6119 0.99   1298  145 0.1197 0.1786      5.2009       5.457|
|  7:  2.6119 -  2.4817 0.99   1315  141 0.1205 0.1641      5.1463      5.3636|
|  8:  2.4817 -  2.3741 0.98   1274  150 0.1129 0.1735      5.0444       5.306|
|  9:  2.3741 -  2.2830 0.98   1298  148 0.1130 0.1877      5.0169      5.3413|
| 10:  2.2830 -  2.2045 0.98   1281  134 0.1103 0.1688      4.9625      5.2102|
| 11:  2.2045 -  2.1357 1.00   1281  142 0.1145 0.1783       4.955      5.2889|
| 12:  2.1357 -  2.0748 0.97   1261  139 0.1077 0.1627      4.8763       5.116|
| 13:  2.0748 -  2.0204 0.98   1285  143 0.1166 0.1785      4.7933      5.0543|
| 14:  2.0204 -  1.9712 0.47    610   71 0.0998 0.1705      4.6403        4.96|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0399 -  4.7053  1402   157  0.94   8.75   0.98     0.95       6774.92|
|  2:  4.7053 -  3.7539  1359   145  0.95   7.77   1.02     1.00       8603.80|
|  3:  3.7539 -  3.2850  1322   154  0.93  11.22   1.03     1.02      10067.35|
|  4:  3.2850 -  2.9872  1331   147  0.92  13.68   1.01     0.99      10454.43|
|  5:  2.9872 -  2.7745  1313   143  0.90  16.17   1.00     0.97       8360.33|
|  6:  2.7745 -  2.6119  1298   145  0.90  15.97   0.99     0.96       7098.30|
|  7:  2.6119 -  2.4817  1315   141  0.91  15.11   0.99     0.96       6064.66|
|  8:  2.4817 -  2.3741  1274   150  0.91  15.27   1.00     0.97       5207.24|
|  9:  2.3741 -  2.2830  1298   148  0.91  15.16   1.00     0.98       4970.65|
| 10:  2.2830 -  2.2045  1281   134  0.90  15.94   0.99     0.95       4470.30|
| 11:  2.2045 -  2.1357  1281   142  0.90  16.60   1.00     0.96       4541.97|
| 12:  2.1357 -  2.0748  1261   139  0.91  15.33   1.01     0.99       4107.11|
| 13:  2.0748 -  2.0204  1285   143  0.90  16.58   1.00     0.99       3397.13|
| 14:  2.0204 -  1.9712   610    71  0.91  14.63   0.98     0.95       2499.95|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2499.95 max =        10454.43 mean =      6368.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.07|
|phase err.(test): min =        0.00 max =           89.49 mean =        13.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.875)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    85.19   16.87    None  None   None       |
|    all(noH): 2823   0      0.37    85.19   16.87    None  None   None       |
|    Sol.    : 438    0      6.30    74.50   39.22    None  None   None       |
|    Mac.    : 2385   0      0.37    85.19   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:     0.366 -   8.848:  784   |   5:    42.777 -  51.260:  111        |
|      1:     8.848 -  17.330: 1267   |   6:    51.260 -  59.742:   74        |
|      2:    17.330 -  25.813:  293   |   7:    59.742 -  68.224:   35        |
|      3:    25.813 -  34.295:  132   |   8:    68.224 -  76.707:   12        |
|      4:    34.295 -  42.777:  110   |   9:    76.707 -  85.189:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.640 - 5.567
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 303
   mapped sites are within: 0.750 - 5.567

peak=    5.877 closest distance to " CG  PRO A  54 " =    1.259
peak=    5.545 closest distance to " CB  GLN A 223 " =    1.442
peak=    5.339 closest distance to " NH2 ARG A  56 " =    2.180
peak=    5.318 closest distance to " CG  PRO A  90 " =    1.124
peak=    5.197 closest distance to " O   HOH Z 126 " =    1.890
peak=    5.135 closest distance to " CB  SER A  63 " =    1.229
peak=    5.075 closest distance to " CB  ARG A 275 " =    0.906
peak=    5.013 closest distance to " O   HOH Z 232 " =    2.270
peak=    4.970 closest distance to " CB  PRO A  54 " =    0.950
peak=    4.801 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.777 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.764 closest distance to " NE2 GLN A  11 " =    1.090
peak=    4.736 closest distance to " C   PRO A 198 " =    1.569
peak=    4.640 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.637 closest distance to " CB  GLU A 128 " =    1.059
peak=    4.605 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.573 closest distance to " O   HOH Z 142 " =    1.718
peak=    4.530 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.523 closest distance to " O   HOH Z 298 " =    1.856
peak=    4.507 closest distance to " OD1 ASN A  69 " =    2.576
peak=    4.487 closest distance to " O   HOH Z  15 " =    2.198
peak=    4.443 closest distance to " CB  TYR A 169 " =    0.750
peak=    4.407 closest distance to " CB  ASN A 148 " =    1.347
peak=    4.376 closest distance to " O   HOH Z 236 " =    2.010
peak=    4.365 closest distance to " O   HOH Z 193 " =    1.875
peak=    4.357 closest distance to " O   HOH Z 427 " =    2.948
peak=    4.320 closest distance to " CG  PRO A 243 " =    1.125
peak=    4.219 closest distance to " CB  SER A   3 " =    1.375
peak=    4.207 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.206 closest distance to " ND2 ASN A 187 " =    1.489
peak=    4.169 closest distance to " OD2 ASP A 286 " =    2.872
peak=    4.145 closest distance to " CA  ALA A  21 " =    1.179
peak=    4.140 closest distance to " O   HOH Z 234 " =    3.756
peak=    4.140 closest distance to " CB  TRP A 179 " =    1.326
peak=    4.110 closest distance to " CG2 VAL A 257 " =    0.945
peak=    4.109 closest distance to " CB  VAL A 265 " =    1.201
peak=    4.061 closest distance to " O   HOH Z 344 " =    3.102
peak=    4.057 closest distance to " CG1 ILE A  33 " =    1.302
peak=    4.048 closest distance to " O   HOH Z 316 " =    3.090
peak=    3.968 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.967 closest distance to " CB  TRP A 266 " =    0.966
peak=    3.955 closest distance to " O   HOH Z 389 " =    1.927
peak=    3.939 closest distance to " O   HOH Z 261 " =    2.272
peak=    3.907 closest distance to " CA  ASN A 215 " =    1.178
peak=    3.905 closest distance to " O   HOH Z 369 " =    2.006
peak=    3.901 closest distance to " O   HOH Z 135 " =    1.654
peak=    3.898 closest distance to " CA  THR A 264 " =    0.848
peak=    3.897 closest distance to " CB  ARG A 190 " =    1.685
peak=    3.890 closest distance to " O   HOH Z 303 " =    2.018
peak=    3.889 closest distance to " CA  THR A 221 " =    0.993
peak=    3.881 closest distance to " O   HOH Z 352 " =    1.891
peak=    3.872 closest distance to " O   HOH Z 368 " =    1.964
peak=    3.852 closest distance to " CD  ARG A 159 " =    0.780
peak=    3.842 closest distance to " CB  SER A 216 " =    0.828
peak=    3.832 closest distance to " O   HOH Z 272 " =    1.849
peak=    3.825 closest distance to " NH2 ARG A 156 " =    1.175
peak=    3.815 closest distance to " O   HOH Z 132 " =    2.519
peak=    3.811 closest distance to " O   HOH Z 108 " =    2.220
peak=    3.804 closest distance to " O   HOH Z 214 " =    2.029
peak=    3.802 closest distance to " CE  LYS A  76 " =    0.885
peak=    3.796 closest distance to " O   HOH Z 346 " =    1.628
peak=    3.796 closest distance to " CB  ARG A  79 " =    1.368
peak=    3.791 closest distance to " NH1AARG A 145 " =    1.147
peak=    3.782 closest distance to " O   HOH Z 158 " =    2.981
peak=    3.776 closest distance to " CZ  PHE A 218 " =    1.056
peak=    3.772 closest distance to " O   HOH Z  40 " =    1.604
peak=    3.772 closest distance to " CB  VAL A 202 " =    1.632
peak=    3.770 closest distance to " O   HOH Z  10 " =    1.874
peak=    3.764 closest distance to " CB  GLU A 277 " =    3.600
peak=    3.759 closest distance to " N   ARG A 156 " =    1.340
peak=    3.754 closest distance to " CD  ARG A 269 " =    0.952
peak=    3.745 closest distance to " O   HOH Z 189 " =    2.267
peak=    3.741 closest distance to " NZ  LYS A 117 " =    3.313
peak=    3.739 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.738 closest distance to " CB  LEU A 143 " =    1.121
peak=    3.738 closest distance to " O   HOH Z 426 " =    1.568
peak=    3.737 closest distance to " O   HOH Z 371 " =    3.178
peak=    3.736 closest distance to " O   HOH Z  21 " =    1.682
peak=    3.728 closest distance to " O   MET A 105 " =    1.838
peak=    3.720 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.714 closest distance to " O   HOH Z  49 " =    2.160
peak=    3.711 closest distance to " CD  ARG A  66 " =    2.428
peak=    3.709 closest distance to " O   HOH Z 250 " =    1.405
peak=    3.682 closest distance to " CG2 THR A 221 " =    1.064
peak=    3.682 closest distance to " O   HOH Z 368 " =    3.647
peak=    3.678 closest distance to " O   HOH Z  59 " =    2.066
peak=    3.677 closest distance to " ND2 ASN A 110 " =    1.873
peak=    3.670 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.647 closest distance to " O   HOH Z 133 " =    1.628
peak=    3.645 closest distance to " CB  SER A 212 " =    1.105
peak=    3.643 closest distance to " CD2 LEU A 297 " =    0.913
peak=    3.642 closest distance to " CA  ASP A 140 " =    1.158
peak=    3.637 closest distance to " CG2 ILE A 120 " =    1.237
peak=    3.636 closest distance to " O   HOH Z 180 " =    2.164
peak=    3.634 closest distance to " CD BLYS A 290 " =    1.109
peak=    3.631 closest distance to " O   HOH Z 295 " =    1.484
peak=    3.625 closest distance to " O   HOH Z  66 " =    2.036
peak=    3.623 closest distance to " CA  MET A  40 " =    1.095
peak=    3.622 closest distance to " NH2BARG A 145 " =    2.106
peak=    3.609 closest distance to " O   HOH Z 193 " =    1.714
peak=    3.608 closest distance to " CB  MET A  47 " =    0.981
peak=    3.602 closest distance to " CD1 ILE A 106 " =    0.837
peak=    3.602 closest distance to " ND1 HIS A  86 " =    1.738
peak=    3.600 closest distance to " CG1BVAL A  72 " =    1.560
peak=    3.597 closest distance to " O   HOH Z 411 " =    3.849
peak=    3.591 closest distance to " CG  LEU A 167 " =    1.194
peak=    3.580 closest distance to " O   HOH Z   6 " =    2.215
peak=    3.575 closest distance to " O   HOH Z 402 " =    1.435
peak=    3.572 closest distance to " CD2 LEU A 255 " =    1.416
peak=    3.568 closest distance to " O   HOH Z 273 " =    2.692
peak=    3.566 closest distance to " O   HOH Z   9 " =    2.060
peak=    3.562 closest distance to " CB  ALA A 291 " =    1.384
peak=    3.560 closest distance to " O   HOH Z  97 " =    1.933
peak=    3.554 closest distance to " O   HOH Z  54 " =    1.662
peak=    3.549 closest distance to " O   HOH Z 403 " =    1.689
peak=    3.546 closest distance to " N   ASN A 127 " =    1.245
peak=    3.540 closest distance to " O   HOH Z 134 " =    1.326
peak=    3.540 closest distance to " O   HOH Z 197 " =    3.164
peak=    3.536 closest distance to " O   HOH Z  43 " =    1.862
peak=    3.536 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.532 closest distance to " O   HOH Z 172 " =    3.532
peak=    3.528 closest distance to " O   HOH Z 219 " =    1.978
peak=    3.524 closest distance to " O   HOH Z 245 " =    1.300
peak=    3.524 closest distance to " O   HOH Z 329 " =    3.652
peak=    3.519 closest distance to " O   TRP A 274 " =    1.831
peak=    3.518 closest distance to " O   HOH Z   1 " =    1.880
peak=    3.499 closest distance to " O   SER A  87 " =    2.309
peak=    3.490 closest distance to " CA  ALA A 291 " =    0.884
peak=    3.490 closest distance to " CG1 ILE A 151 " =    0.959
peak=    3.487 closest distance to " CB  LEU A 255 " =    0.759
peak=    3.470 closest distance to " CB  SER A  62 " =    1.251
peak=    3.470 closest distance to " OG BSER A 164 " =    2.331
peak=    3.469 closest distance to " CA  ARG A 195 " =    1.252
peak=    3.467 closest distance to " O   HOH Z  64 " =    2.188
peak=    3.461 closest distance to " O   HOH Z 280 " =    3.016
peak=    3.459 closest distance to " O   HOH Z 147 " =    1.719
peak=    3.456 closest distance to " CB  PRO A 198 " =    0.975
peak=    3.455 closest distance to " CB  TRP A 179 " =    1.447
peak=    3.454 closest distance to " O   HOH Z  44 " =    1.776
peak=    3.446 closest distance to " O   HOH Z  88 " =    3.495
peak=    3.446 closest distance to " CB  GLN A  88 " =    1.243
peak=    3.440 closest distance to " CB  ASP A 140 " =    0.927
peak=    3.435 closest distance to " O   ALA A 165 " =    1.391
peak=    3.430 closest distance to " CB  ASN A  39 " =    0.939
peak=    3.429 closest distance to " CG2BVAL A  41 " =    0.850
peak=    3.428 closest distance to " CD  LYS A 119 " =    1.147
peak=    3.426 closest distance to " O   HOH Z 211 " =    2.714
peak=    3.416 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.405 closest distance to " CD  LYS A 166 " =    1.264
peak=    3.402 closest distance to " ND1 HIS A  81 " =    1.584
peak=    3.392 closest distance to " O   THR A 220 " =    1.322
peak=    3.386 closest distance to " OD1 ASN A 217 " =    1.619
peak=    3.384 closest distance to " CB  SER A 141 " =    1.056
peak=    3.383 closest distance to " O   HOH Z  93 " =    2.572
peak=    3.383 closest distance to " N   VAL A 126 " =    1.276
peak=    3.379 closest distance to " O   HOH Z 345 " =    3.460
peak=    3.378 closest distance to " CE1 TYR A 186 " =    1.325
peak=    3.377 closest distance to " CD  ARG A  66 " =    2.461
peak=    3.375 closest distance to " O   HOH Z 327 " =    1.823
peak=    3.373 closest distance to " CB  MET A  40 " =    0.827
peak=    3.371 closest distance to " O   HOH Z 406 " =    1.608
peak=    3.371 closest distance to " O   HOH Z  19 " =    2.531
peak=    3.368 closest distance to " CA  ALA A 154 " =    1.051
peak=    3.368 closest distance to " CG  MET A 185 " =    1.165
peak=    3.367 closest distance to " O   HOH Z 133 " =    2.449
peak=    3.366 closest distance to " O   HOH Z 271 " =    2.364
peak=    3.365 closest distance to " CB  ARG A 139 " =    0.893
peak=    3.364 closest distance to " CG  GLU A 277 " =    2.089
peak=    3.364 closest distance to " O   HOH Z 173 " =    1.815
peak=    3.362 closest distance to " O   HOH Z 128 " =    2.273
peak=    3.360 closest distance to " O   HOH Z 163 " =    1.695
peak=    3.357 closest distance to " CA  LYS A 117 " =    1.214
peak=    3.354 closest distance to " O   HOH Z 193 " =    2.098
peak=    3.354 closest distance to " CA  GLY A 267 " =    1.175
peak=    3.354 closest distance to " O   HOH Z 391 " =    2.938
peak=    3.353 closest distance to " CA  ALA A 248 " =    1.252
peak=    3.348 closest distance to " O   HOH Z 353 " =    2.754
peak=    3.346 closest distance to " N   ASN A  39 " =    1.292
peak=    3.343 closest distance to " O   HOH Z 291 " =    1.501
peak=    3.340 closest distance to " O   HOH Z 407 " =    2.594
peak=    3.333 closest distance to " N   GLN A 278 " =    1.047
peak=    3.331 closest distance to " OG  SER A  22 " =    2.711
peak=    3.328 closest distance to " CA  GLY A  80 " =    1.100
peak=    3.326 closest distance to " N   SER A 134 " =    1.384
peak=    3.324 closest distance to " O   HOH Z 411 " =    1.788
peak=    3.324 closest distance to " O   THR A 251 " =    1.154
peak=    3.322 closest distance to " OG  SER A  97 " =    3.508
peak=    3.320 closest distance to " CB  ALA A 248 " =    1.370
peak=    3.317 closest distance to " CD2 HIS A  81 " =    1.231
peak=    3.316 closest distance to " O   HOH Z 281 " =    4.578
peak=    3.313 closest distance to " O   HOH Z 227 " =    1.627
peak=    3.301 closest distance to " O   HOH Z 305 " =    3.630
peak=    3.301 closest distance to " O   HOH Z 366 " =    3.205
peak=    3.300 closest distance to " O   HOH Z 227 " =    1.635
peak=    3.296 closest distance to " CB  ARG A  79 " =    0.868
peak=    3.294 closest distance to " CG  MET A 185 " =    1.056
peak=    3.294 closest distance to " O   HOH Z 423 " =    1.815
peak=    3.293 closest distance to " CA  SER A  87 " =    1.031
peak=    3.292 closest distance to " CB  ASN A 215 " =    1.118
peak=    3.292 closest distance to " CB  ASN A 142 " =    0.999
peak=    3.292 closest distance to " CG  MET A 113 " =    1.254
peak=    3.291 closest distance to " CA  ASN A 217 " =    1.255
peak=    3.290 closest distance to " CA  ASN A 176 " =    1.215
peak=    3.279 closest distance to " CB  GLU A 152 " =    1.473
peak=    3.277 closest distance to " O   THR A  31 " =    1.518
peak=    3.273 closest distance to " O   ALA A   1 " =    1.487
peak=    3.266 closest distance to " O   HOH Z 185 " =    1.739
peak=    3.263 closest distance to " O   HOH Z 374 " =    2.597
peak=    3.263 closest distance to " N   ASN A 252 " =    1.389
peak=    3.259 closest distance to " CB  PHE A  16 " =    0.998
peak=    3.258 closest distance to " O   HOH Z 425 " =    1.264
peak=    3.257 closest distance to " O   HOH Z 437 " =    1.520
peak=    3.256 closest distance to " CD1 LEU A  96 " =    0.790
peak=    3.255 closest distance to " CG  LYS A  76 " =    1.033
peak=    3.253 closest distance to " CA  ARG A 102 " =    1.174
peak=    3.252 closest distance to " O   HOH Z 287 " =    1.826
peak=    3.252 closest distance to " NH1BARG A 145 " =    1.156
peak=    3.246 closest distance to " O   HOH Z  49 " =    2.497
peak=    3.245 closest distance to " O   HOH Z  40 " =    1.916
peak=    3.239 closest distance to " CB  TYR A 116 " =    0.831
peak=    3.238 closest distance to " N   SER A 135 " =    1.316
peak=    3.238 closest distance to " CB  ALA A  34 " =    1.014
peak=    3.235 closest distance to " O   HOH Z  66 " =    2.033
peak=    3.235 closest distance to " CD2 TRP A 179 " =    1.376
peak=    3.233 closest distance to " O   HOH Z 409 " =    3.036
peak=    3.233 closest distance to " O   HOH Z 279 " =    2.178
peak=    3.233 closest distance to " O   HOH Z 213 " =    1.782
peak=    3.232 closest distance to " CD  ARG A 219 " =    0.982
peak=    3.232 closest distance to " CG1 VAL A 202 " =    1.995
peak=    3.229 closest distance to " OD1BASN A 224 " =    2.326
peak=    3.228 closest distance to " O   HOH Z 227 " =    2.180
peak=    3.227 closest distance to " O   HOH Z 126 " =    2.118
peak=    3.227 closest distance to " O   HOH Z 383 " =    1.727
peak=    3.223 closest distance to " O   GLY A  57 " =    2.565
peak=    3.216 closest distance to " CZ  PHE A 192 " =    0.858
peak=    3.215 closest distance to " CZ2 TRP A 179 " =    1.634
peak=    3.212 closest distance to " CB  THR A 157 " =    1.053
peak=    3.211 closest distance to " CA  ALA A 233 " =    1.411
peak=    3.210 closest distance to " CA  ILE A 234 " =    0.942
peak=    3.208 closest distance to " O   HOH Z 234 " =    1.734
peak=    3.205 closest distance to " CB  ILE A 120 " =    1.268
peak=    3.202 closest distance to " O   HOH Z 125 " =    2.335
peak=    3.202 closest distance to " O   HOH Z   3 " =    1.624
peak=    3.197 closest distance to " CB  LYS A 193 " =    0.952
peak=    3.197 closest distance to " OD1 ASP A 238 " =    0.917
peak=    3.196 closest distance to " O   HOH Z 359 " =    3.821
peak=    3.192 closest distance to " CG1 ILE A 120 " =    1.113
peak=    3.192 closest distance to " O   HOH Z   1 " =    1.652
peak=    3.191 closest distance to " CA  ALA A 160 " =    0.866
peak=    3.189 closest distance to " C   SER A  32 " =    1.060
peak=    3.188 closest distance to " O   HOH Z 403 " =    1.337
peak=    3.187 closest distance to " O   ALA A 158 " =    1.282
peak=    3.187 closest distance to " C   TYR A 214 " =    1.509
peak=    3.186 closest distance to " NZ  LYS A  76 " =    1.289
peak=    3.181 closest distance to " O   HOH Z  20 " =    1.531
peak=    3.181 closest distance to " N   ALA A 154 " =    0.964
peak=    3.180 closest distance to " N   TYR A  15 " =    0.785
peak=    3.176 closest distance to " O   HOH Z  44 " =    3.366
peak=    3.176 closest distance to " O   HOH Z  68 " =    1.504
peak=    3.176 closest distance to " CD  PRO A 243 " =    1.603
peak=    3.171 closest distance to " NH2AARG A 190 " =    1.291
peak=    3.170 closest distance to " OG  SER A 206 " =    1.257
peak=    3.168 closest distance to " CB  ALA A  71 " =    1.364
peak=    3.164 closest distance to " O   HOH Z 423 " =    2.940
peak=    3.163 closest distance to " O   HOH Z 334 " =    1.488
peak=    3.162 closest distance to " O   HOH Z 128 " =    2.103
peak=    3.159 closest distance to " O   HOH Z  96 " =    2.039
peak=    3.156 closest distance to " CG2 ILE A 106 " =    1.131
peak=    3.146 closest distance to " O   HOH Z   4 " =    1.869
peak=    3.145 closest distance to " O   HOH Z  54 " =    2.382
peak=    3.143 closest distance to " OD2 ASP A 200 " =    1.279
peak=    3.140 closest distance to " CA  ALA A  43 " =    1.236
peak=    3.131 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.127 closest distance to " N   TYR A 116 " =    1.759
peak=    3.127 closest distance to " CG  PRO A 213 " =    1.024
peak=    3.126 closest distance to " O   HOH Z 261 " =    2.066
peak=    3.124 closest distance to " CA  ALA A 158 " =    1.152
peak=    3.115 closest distance to " NZ ALYS A 290 " =    1.145
peak=    3.115 closest distance to " CD2 TYR A  30 " =    0.886
peak=    3.113 closest distance to " O   HOH Z 337 " =    3.776
peak=    3.112 closest distance to " OD1 ASP A 171 " =    1.260
peak=    3.109 closest distance to " CA  LEU A 282 " =    1.109
peak=    3.108 closest distance to " O   HOH Z 430 " =    5.567
peak=    3.104 closest distance to " O   HOH Z 359 " =    1.371
peak=    3.101 closest distance to " CA  ASP A 191 " =    0.759
peak=    3.099 closest distance to " NZ  LYS A 166 " =    2.988
peak=    3.095 closest distance to " NH2AARG A 190 " =    1.458
peak=    3.093 closest distance to " O   ALA A   1 " =    1.613
peak=    3.092 closest distance to " O   HOH Z 144 " =    1.742
peak=    3.077 closest distance to " O   HOH Z 166 " =    3.776
peak=    3.072 closest distance to " O   HOH Z 302 " =    1.932
peak=    3.070 closest distance to " CA  VAL A  41 " =    0.934
peak=    3.069 closest distance to " CB  VAL A 126 " =    1.172
peak=    3.067 closest distance to " CA  ALA A  84 " =    1.401
peak=    3.066 closest distance to " O   HOH Z 387 " =    3.219
peak=    3.064 closest distance to " CG2 VAL A  67 " =    1.061
peak=    3.042 closest distance to " CA  MET A 105 " =    1.012
peak=    3.027 closest distance to " CB  ARG A 138 " =    0.968
peak=    3.001 closest distance to " O   HOH Z  88 " =    2.933

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.815 - 5.581
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 199
   mapped sites are within: 0.815 - 5.581

peak=   -4.737 closest distance to " O   HOH Z 266 " =    4.550
peak=   -4.564 closest distance to " CB  PRO A 243 " =    2.607
peak=   -4.301 closest distance to " CD  ARG A 156 " =    1.995
peak=   -4.247 closest distance to " CG  GLN A 223 " =    1.945
peak=   -4.246 closest distance to " O   HOH Z 377 " =    1.975
peak=   -4.214 closest distance to " O   HOH Z 198 " =    2.111
peak=   -4.187 closest distance to " O   HOH Z 372 " =    2.436
peak=   -4.162 closest distance to " CB  ALA A 161 " =    2.569
peak=   -4.103 closest distance to " O   HOH Z 290 " =    1.109
peak=   -4.095 closest distance to " N   ALA A  43 " =    2.506
peak=   -4.050 closest distance to " O   VAL A  67 " =    2.726
peak=   -3.993 closest distance to " O   HOH Z  43 " =    1.602
peak=   -3.990 closest distance to " O   HOH Z 126 " =    1.923
peak=   -3.989 closest distance to " SG  CYS A 254 " =    3.261
peak=   -3.982 closest distance to " O   HOH Z 118 " =    3.032
peak=   -3.980 closest distance to " O   HOH Z 353 " =    2.228
peak=   -3.975 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.962 closest distance to " O   HOH Z 231 " =    2.145
peak=   -3.950 closest distance to " CE2 TYR A  30 " =    2.774
peak=   -3.937 closest distance to " O   HOH Z  10 " =    1.504
peak=   -3.905 closest distance to " CG  PHE A 283 " =    2.755
peak=   -3.892 closest distance to " CG1 VAL A 112 " =    2.843
peak=   -3.892 closest distance to " O   HOH Z 185 " =    2.297
peak=   -3.887 closest distance to " ND2 ASN A  45 " =    0.949
peak=   -3.873 closest distance to " O   HOH Z  52 " =    1.378
peak=   -3.869 closest distance to " C   HIS A 108 " =    1.046
peak=   -3.849 closest distance to " O   HOH Z 389 " =    1.832
peak=   -3.836 closest distance to " OG BSER A 134 " =    1.169
peak=   -3.824 closest distance to " CD  ARG A 139 " =    1.536
peak=   -3.821 closest distance to " ND2 ASN A  45 " =    1.200
peak=   -3.811 closest distance to " CZ3 TRP A 179 " =    1.167
peak=   -3.788 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.779 closest distance to " CD1 PHE A  59 " =    1.844
peak=   -3.768 closest distance to " CG  ASP A 231 " =    0.830
peak=   -3.764 closest distance to " O   PRO A 163 " =    2.030
peak=   -3.763 closest distance to " CE  MET A 105 " =    2.219
peak=   -3.753 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.752 closest distance to " CD1 LEU A 228 " =    2.293
peak=   -3.731 closest distance to " CB  ASN A  39 " =    2.204
peak=   -3.725 closest distance to " CA  GLY A 203 " =    2.267
peak=   -3.713 closest distance to " N   SER A 212 " =    2.001
peak=   -3.699 closest distance to " CZ  TYR A 169 " =    1.720
peak=   -3.686 closest distance to " CB  ALA A 291 " =    2.218
peak=   -3.675 closest distance to " CZ  PHE A  59 " =    1.630
peak=   -3.639 closest distance to " OXT GLY A 302 " =    2.840
peak=   -3.635 closest distance to " NH2AARG A 275 " =    5.417
peak=   -3.627 closest distance to " CE2 PHE A 218 " =    2.504
peak=   -3.619 closest distance to " OE1 GLN A  88 " =    1.142
peak=   -3.611 closest distance to " CD  GLN A  58 " =    1.118
peak=   -3.607 closest distance to " CD2 LEU A 300 " =    2.923
peak=   -3.606 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.603 closest distance to " CD2 LEU A 143 " =    2.676
peak=   -3.588 closest distance to " O   HOH Z  98 " =    2.245
peak=   -3.588 closest distance to " O   HOH Z 435 " =    2.739
peak=   -3.584 closest distance to " O   HOH Z 417 " =    2.503
peak=   -3.582 closest distance to " O   HOH Z 292 " =    4.508
peak=   -3.572 closest distance to " O   HOH Z 407 " =    3.155
peak=   -3.557 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.557 closest distance to " O   GLY A 196 " =    1.053
peak=   -3.554 closest distance to " CG  ARG A 269 " =    2.579
peak=   -3.549 closest distance to " O   HOH Z 311 " =    3.589
peak=   -3.547 closest distance to " OD1 ASP A 191 " =    1.645
peak=   -3.528 closest distance to " CG1 VAL A 250 " =    2.603
peak=   -3.528 closest distance to " C   ASN A 285 " =    2.527
peak=   -3.526 closest distance to " CB  TYR A  15 " =    2.197
peak=   -3.521 closest distance to " N   GLN A  58 " =    1.750
peak=   -3.518 closest distance to " CA  GLY A  98 " =    2.004
peak=   -3.513 closest distance to " O   HOH Z  93 " =    1.981
peak=   -3.511 closest distance to " O   HOH Z  13 " =    1.585
peak=   -3.506 closest distance to " O   HOH Z  11 " =    1.789
peak=   -3.504 closest distance to " O   HOH Z 313 " =    2.012
peak=   -3.497 closest distance to " O   HOH Z 351 " =    1.491
peak=   -3.479 closest distance to " O   HOH Z 222 " =    1.242
peak=   -3.477 closest distance to " OG BSER A 134 " =    1.762
peak=   -3.476 closest distance to " OG  SER A  62 " =    1.674
peak=   -3.476 closest distance to " O   SER A 135 " =    1.495
peak=   -3.475 closest distance to " CD1 LEU A 101 " =    2.440
peak=   -3.474 closest distance to " O   VAL A 153 " =    2.356
peak=   -3.472 closest distance to " O   HOH Z 211 " =    1.673
peak=   -3.471 closest distance to " CB  ALA A 248 " =    1.985
peak=   -3.467 closest distance to " O   HOH Z 196 " =    2.152
peak=   -3.463 closest distance to " CD1 ILE A 239 " =    2.076
peak=   -3.452 closest distance to " CD  LYS A 289 " =    2.479
peak=   -3.440 closest distance to " NE2 GLN A  88 " =    1.921
peak=   -3.436 closest distance to " CB  CYS A 201 " =    2.653
peak=   -3.430 closest distance to " CB  ALA A 131 " =    2.068
peak=   -3.428 closest distance to " O   HOH Z  38 " =    1.536
peak=   -3.427 closest distance to " CD  GLU A 236 " =    1.053
peak=   -3.419 closest distance to " O   GLY A 211 " =    1.473
peak=   -3.417 closest distance to " O   HOH Z 275 " =    1.523
peak=   -3.415 closest distance to " CG  MET A 105 " =    0.965
peak=   -3.411 closest distance to " CB  PHE A 192 " =    2.034
peak=   -3.411 closest distance to " N   ALA A 248 " =    1.578
peak=   -3.408 closest distance to " SG ACYS A 201 " =    2.070
peak=   -3.406 closest distance to " CB  ALA A 291 " =    2.387
peak=   -3.402 closest distance to " CD  ARG A 195 " =    5.205
peak=   -3.398 closest distance to " O   HOH Z 198 " =    1.486
peak=   -3.397 closest distance to " OD1 ASN A 148 " =    1.652
peak=   -3.382 closest distance to " CA  ASP A 298 " =    1.029
peak=   -3.377 closest distance to " OD2 ASP A 171 " =    1.789
peak=   -3.374 closest distance to " O   MET A  40 " =    2.721
peak=   -3.374 closest distance to " O   VAL A  67 " =    2.654
peak=   -3.373 closest distance to " O   HOH Z 388 " =    1.976
peak=   -3.370 closest distance to " CD2 LEU A 300 " =    2.880
peak=   -3.369 closest distance to " C   LEU A 143 " =    1.190
peak=   -3.364 closest distance to " CE  MET A  93 " =    1.301
peak=   -3.359 closest distance to " CA  GLY A 241 " =    3.038
peak=   -3.358 closest distance to " O   HOH Z  11 " =    2.047
peak=   -3.348 closest distance to " CE3 TRP A 274 " =    2.405
peak=   -3.348 closest distance to " O   ALA A 161 " =    1.628
peak=   -3.345 closest distance to " ND2 ASN A 249 " =    2.332
peak=   -3.344 closest distance to " O   VAL A 174 " =    2.038
peak=   -3.338 closest distance to " CG  GLU A   2 " =    1.907
peak=   -3.336 closest distance to " O   HOH Z 317 " =    2.430
peak=   -3.324 closest distance to " CA  ASP A  27 " =    2.483
peak=   -3.324 closest distance to " N   THR A 157 " =    1.557
peak=   -3.324 closest distance to " CB  PRO A 163 " =    2.542
peak=   -3.323 closest distance to " O   HOH Z 385 " =    2.054
peak=   -3.321 closest distance to " CB  TRP A  85 " =    2.497
peak=   -3.320 closest distance to " CD2 TYR A 293 " =    2.008
peak=   -3.315 closest distance to " O   HOH Z 298 " =    1.229
peak=   -3.309 closest distance to " O   HOH Z 166 " =    1.844
peak=   -3.309 closest distance to " OH  TYR A 169 " =    1.022
peak=   -3.302 closest distance to " N   THR A 235 " =    1.313
peak=   -3.301 closest distance to " O   HOH Z 102 " =    1.623
peak=   -3.299 closest distance to " O   HOH Z  47 " =    1.492
peak=   -3.294 closest distance to " O   HOH Z 166 " =    1.498
peak=   -3.289 closest distance to " O   HOH Z  76 " =    1.872
peak=   -3.288 closest distance to " N   SER A 276 " =    1.233
peak=   -3.285 closest distance to " NH2 ARG A  66 " =    2.116
peak=   -3.279 closest distance to " CD1 ILE A 239 " =    2.473
peak=   -3.278 closest distance to " CG  GLU A 277 " =    1.171
peak=   -3.274 closest distance to " OD1 ASP A 191 " =    1.550
peak=   -3.273 closest distance to " CG  ARG A  66 " =    2.371
peak=   -3.265 closest distance to " O   HOH Z 168 " =    1.846
peak=   -3.265 closest distance to " O   HOH Z 322 " =    1.540
peak=   -3.260 closest distance to " O   HOH Z 191 " =    5.581
peak=   -3.257 closest distance to " O   HOH Z 385 " =    1.982
peak=   -3.257 closest distance to " C   MET A 188 " =    1.498
peak=   -3.255 closest distance to " CA  GLY A 133 " =    1.986
peak=   -3.250 closest distance to " O   HOH Z 148 " =    3.657
peak=   -3.249 closest distance to " O   ALA A  34 " =    2.626
peak=   -3.248 closest distance to " OG ASER A 134 " =    1.154
peak=   -3.248 closest distance to " NH2 ARG A  79 " =    1.903
peak=   -3.245 closest distance to " CG1 VAL A 197 " =    2.265
peak=   -3.237 closest distance to " O   HOH Z 252 " =    4.301
peak=   -3.232 closest distance to " CG1 VAL A 125 " =    2.033
peak=   -3.229 closest distance to " CB  ASP A 286 " =    2.234
peak=   -3.229 closest distance to " C   LEU A 222 " =    0.815
peak=   -3.228 closest distance to " CG2 VAL A 189 " =    1.999
peak=   -3.228 closest distance to " O   HOH Z 266 " =    4.902
peak=   -3.226 closest distance to " O   HOH Z 111 " =    2.333
peak=   -3.222 closest distance to " OD1 ASN A 187 " =    1.565
peak=   -3.221 closest distance to " O   HOH Z  73 " =    2.291
peak=   -3.220 closest distance to " O   VAL A 189 " =    2.533
peak=   -3.220 closest distance to " CE3 TRP A 150 " =    2.014
peak=   -3.215 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.212 closest distance to " O   HOH Z 298 " =    2.658
peak=   -3.211 closest distance to " CG  PRO A 163 " =    2.477
peak=   -3.210 closest distance to " O   HOH Z 128 " =    2.472
peak=   -3.206 closest distance to " OG BSER A 210 " =    2.082
peak=   -3.202 closest distance to " CD2 PHE A  61 " =    2.504
peak=   -3.201 closest distance to " CG  ASN A 301 " =    1.945
peak=   -3.198 closest distance to " O   LEU A 167 " =    1.438
peak=   -3.195 closest distance to " O   HOH Z  88 " =    2.216
peak=   -3.195 closest distance to " CB  CYS A 254 " =    2.282
peak=   -3.194 closest distance to " O   HOH Z  24 " =    1.585
peak=   -3.191 closest distance to " O   PRO A 243 " =    1.838
peak=   -3.191 closest distance to " N   ALA A 226 " =    2.088
peak=   -3.188 closest distance to " O   PHE A 218 " =    1.523
peak=   -3.188 closest distance to " CB  PHE A 208 " =    2.238
peak=   -3.187 closest distance to " CD2 LEU A 237 " =    2.698
peak=   -3.171 closest distance to " CG  TRP A 266 " =    1.841
peak=   -3.160 closest distance to " O   ASN A 249 " =    1.531
peak=   -3.160 closest distance to " O   HOH Z 324 " =    2.132
peak=   -3.157 closest distance to " O   ALA A 180 " =    1.338
peak=   -3.154 closest distance to " CD1 LEU A 297 " =    2.442
peak=   -3.153 closest distance to " OD1 ASP A 200 " =    1.359
peak=   -3.150 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.148 closest distance to " O   ALA A  51 " =    1.371
peak=   -3.141 closest distance to " O   HOH Z 393 " =    1.422
peak=   -3.132 closest distance to " O   TRP A  70 " =    1.536
peak=   -3.126 closest distance to " NH2BARG A 275 " =    1.972
peak=   -3.125 closest distance to " NH2 ARG A  79 " =    1.583
peak=   -3.118 closest distance to " O   HOH Z   6 " =    1.580
peak=   -3.109 closest distance to " O   HOH Z 357 " =    2.065
peak=   -3.106 closest distance to " CG  PHE A  59 " =    2.176
peak=   -3.101 closest distance to " CE  LYS A  76 " =    2.682
peak=   -3.084 closest distance to " CB  ASP A 132 " =    2.291
peak=   -3.068 closest distance to " O   HOH Z 137 " =    1.492
peak=   -3.065 closest distance to " ND2 ASN A  60 " =    1.524
peak=   -3.061 closest distance to " CB  ASP A 132 " =    2.325
peak=   -3.059 closest distance to " O   HOH Z 210 " =    1.137
peak=   -3.049 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.046 closest distance to " O   HOH Z 244 " =    2.053
peak=   -3.035 closest distance to " O   HOH Z 234 " =    4.189
peak=   -3.028 closest distance to " O   HOH Z 108 " =    2.147
peak=   -3.014 closest distance to " O   HOH Z 377 " =    0.926

================= 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    :  0.3097 0.3163   6.007644e+00   6.023673e+00
   1_bss:  0.2944 0.3024   5.987026e+00   5.993030e+00
   1_xyz:  0.1638 0.1869   5.433000e+00   5.556958e+00
   1_adp:  0.1515 0.1918   5.389772e+00   5.587059e+00
   1_occ:  0.1510 0.1916   5.387610e+00   5.585216e+00
   2_bss:  0.1493 0.1882   5.377487e+00   5.571871e+00
   2_xyz:  0.1224 0.1601   5.203903e+00   5.419097e+00
   2_adp:  0.1169 0.1563   5.164852e+00   5.384847e+00
   2_occ:  0.1168 0.1562   5.164464e+00   5.384642e+00
   3_bss:  0.1168 0.1561   5.164141e+00   5.384855e+00
   3_xyz:  0.1104 0.1532   5.128635e+00   5.365685e+00
   3_adp:  0.1094 0.1534   5.125216e+00   5.366464e+00
   3_occ:  0.1093 0.1535   5.125308e+00   5.366806e+00
   4_bss:  0.1093 0.1534   5.125214e+00   5.366750e+00
   4_xyz:  0.1091 0.1544   5.129413e+00   5.374760e+00
   4_adp:  0.1082 0.1566   5.132152e+00   5.384560e+00
   4_occ:  0.1082 0.1567   5.132394e+00   5.385039e+00
   5_bss:  0.1081 0.1567   5.132233e+00   5.384861e+00
   5_xyz:  0.1092 0.1580   5.141302e+00   5.393488e+00
   5_adp:  0.1092 0.1576   5.139727e+00   5.391877e+00
   5_occ:  0.1092 0.1577   5.139901e+00   5.392231e+00
   5_bss:  0.1091 0.1577   5.140000e+00   5.392308e+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:  0.309  35.164  -1.478  -2.941   1.138  -0.000   0.000   0.000
   1_xyz:  0.309  35.164  -1.478  -2.941   1.138  -0.000   0.000   0.000
   1_adp:  0.309  35.164  -1.478  -2.941   1.138  -0.000   0.000   0.000
   1_occ:  0.309  35.164  -1.478  -2.941   1.138  -0.000   0.000   0.000
   2_bss:  0.317  47.731  -2.455  -3.065  -1.325  -0.000  -0.000  -0.000
   2_xyz:  0.317  47.731  -2.455  -3.065  -1.325  -0.000  -0.000  -0.000
   2_adp:  0.317  47.731  -2.455  -3.065  -1.325  -0.000  -0.000  -0.000
   2_occ:  0.317  47.731  -2.455  -3.065  -1.325  -0.000  -0.000  -0.000
   3_bss:  0.322  45.392  -2.497  -2.701  -1.707  -0.000  -0.000  -0.000
   3_xyz:  0.322  45.392  -2.497  -2.701  -1.707  -0.000  -0.000  -0.000
   3_adp:  0.322  45.392  -2.497  -2.701  -1.707  -0.000  -0.000  -0.000
   3_occ:  0.322  45.392  -2.497  -2.701  -1.707  -0.000  -0.000  -0.000
   4_bss:  0.322  45.392  -2.398  -2.480  -1.717  -0.000  -0.000  -0.000
   4_xyz:  0.322  45.392  -2.398  -2.480  -1.717  -0.000  -0.000  -0.000
   4_adp:  0.322  45.392  -2.398  -2.480  -1.717  -0.000  -0.000  -0.000
   4_occ:  0.322  45.392  -2.398  -2.480  -1.717  -0.000  -0.000  -0.000
   5_bss:  0.321  46.947  -2.206  -2.242  -1.570  -0.000  -0.000  -0.000
   5_xyz:  0.321  46.947  -2.206  -2.242  -1.570  -0.000  -0.000  -0.000
   5_adp:  0.321  46.947  -2.206  -2.242  -1.570  -0.000  -0.000  -0.000
   5_occ:  0.321  46.947  -2.206  -2.242  -1.570  -0.000  -0.000  -0.000
   5_bss:  0.321  46.936  -2.028  -2.052  -1.400  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.183 0.7249  0.9099    28967.854
   1_bss:  31.729 0.7388  0.8956    25555.697
   1_xyz:  17.351 0.8878  1.0078     9122.881
   1_adp:  18.194 0.8796  1.0044     9631.456
   1_occ:  18.164 0.8797  1.0042     9573.486
   2_bss:  17.792 0.8832  0.9649     9286.731
   2_xyz:  14.615 0.9099  0.9787     6735.359
   2_adp:  13.933 0.9156  0.9794     6305.543
   2_occ:  13.930 0.9156  0.9793     6302.030
   3_bss:  13.942 0.9155  0.9782     6320.943
   3_xyz:  13.571 0.9184  0.9789     6066.347
   3_adp:  13.552 0.9187  0.9747     6075.049
   3_occ:  13.555 0.9187  0.9746     6078.735
   4_bss:  13.556 0.9187  0.9781     6078.646
   4_xyz:  13.677 0.9178  0.9771     6164.345
   4_adp:  13.895 0.9161  0.9712     6265.129
   4_occ:  13.905 0.9160  0.9711     6270.921
   5_bss:  13.904 0.9160  0.9779     6268.602
   5_xyz:  14.053 0.9148  0.9769     6381.109
   5_adp:  14.024 0.9150  0.9715     6364.598
   5_occ:  14.030 0.9150  0.9714     6367.246
   5_bss:  14.033 0.9149  0.9773     6368.564
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6292e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6292e-01
   1_xyz:   1.039  0.008  0.072 15.074  0.004  4.113   6.3907e-02
   1_adp:   1.039  0.008  0.072 15.074  0.004  4.113   6.3907e-02
   1_occ:   1.039  0.008  0.072 15.074  0.004  4.113   6.3907e-02
   2_bss:   1.039  0.008  0.072 15.074  0.004  4.113   6.3907e-02
   2_xyz:   0.968  0.006  0.071 14.767  0.004  4.119   5.5955e-02
   2_adp:   0.968  0.006  0.071 14.767  0.004  4.119   5.5955e-02
   2_occ:   0.968  0.006  0.071 14.767  0.004  4.119   5.5955e-02
   3_bss:   0.968  0.006  0.071 14.767  0.004  4.119   5.5955e-02
   3_xyz:   0.992  0.007  0.074 14.948  0.004  4.121   5.9824e-02
   3_adp:   0.992  0.007  0.074 14.948  0.004  4.121   5.9824e-02
   3_occ:   0.992  0.007  0.074 14.948  0.004  4.121   5.9824e-02
   4_bss:   0.992  0.007  0.074 14.948  0.004  4.121   5.9824e-02
   4_xyz:   0.947  0.006  0.072 14.791  0.004  4.121   5.5177e-02
   4_adp:   0.947  0.006  0.072 14.791  0.004  4.121   5.5177e-02
   4_occ:   0.947  0.006  0.072 14.791  0.004  4.121   5.5177e-02
   5_bss:   0.947  0.006  0.072 14.791  0.004  4.121   5.5177e-02
   5_xyz:   0.901  0.006  0.068 14.678  0.003  4.121   5.0620e-02
   5_adp:   0.901  0.006  0.068 14.678  0.003  4.121   5.0620e-02
   5_occ:   0.901  0.006  0.068 14.678  0.003  4.121   5.0620e-02
   5_bss:   0.901  0.006  0.068 14.678  0.003  4.121   5.0620e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4047e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4047e-01
   1_xyz:   8.040  0.049  0.322 82.649  0.038  2.308   6.5656e-02
   1_adp:   8.040  0.049  0.322 82.649  0.038  2.308   6.5656e-02
   1_occ:   8.040  0.049  0.322 82.649  0.038  2.308   6.5656e-02
   2_bss:   8.040  0.049  0.322 82.649  0.038  2.308   6.5656e-02
   2_xyz:   7.248  0.032  0.221 84.837  0.033  2.344   3.9458e-02
   2_adp:   7.248  0.032  0.221 84.837  0.033  2.344   3.9458e-02
   2_occ:   7.248  0.032  0.221 84.837  0.033  2.344   3.9458e-02
   3_bss:   7.248  0.032  0.221 84.837  0.033  2.344   3.9458e-02
   3_xyz:   7.052  0.036  0.235 83.589  0.036  2.317   4.3092e-02
   3_adp:   7.052  0.036  0.235 83.589  0.036  2.317   4.3092e-02
   3_occ:   7.052  0.036  0.235 83.589  0.036  2.317   4.3092e-02
   4_bss:   7.052  0.036  0.235 83.589  0.036  2.317   4.3092e-02
   4_xyz:   6.924  0.037  0.221 83.595  0.035  2.356   3.6625e-02
   4_adp:   6.924  0.037  0.221 83.595  0.035  2.356   3.6625e-02
   4_occ:   6.924  0.037  0.221 83.595  0.035  2.356   3.6625e-02
   5_bss:   6.924  0.037  0.221 83.595  0.035  2.356   3.6625e-02
   5_xyz:   7.021  0.036  0.209 83.272  0.034  2.364   2.9390e-02
   5_adp:   7.021  0.036  0.209 83.272  0.034  2.364   2.9390e-02
   5_occ:   7.021  0.036  0.209 83.272  0.034  2.364   2.9390e-02
   5_bss:   7.021  0.036  0.209 83.272  0.034  2.364   2.9390e-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:  62.67   0.00  16.67  55.55   0.00  12.81  62.67   6.89  37.66
   1_occ:  62.67   0.00  16.67  55.55   0.00  12.81  62.67   6.89  37.66
   2_bss:  62.67   0.00  16.67  55.55   0.00  12.81  62.67   6.89  37.66
   2_xyz:  62.67   0.00  16.67  55.55   0.00  12.81  62.67   6.89  37.66
   2_adp:  71.19   1.86  16.84  71.19   1.86  12.97  68.23   5.91  37.93
   2_occ:  71.19   1.86  16.84  71.19   1.86  12.97  68.23   5.91  37.93
   3_bss:  71.19   1.86  16.84  71.19   1.86  12.97  68.23   5.91  37.93
   3_xyz:  71.19   1.86  16.84  71.19   1.86  12.97  68.23   5.91  37.93
   3_adp:  72.90   1.61  16.79  72.90   1.61  12.89  68.64   6.30  38.03
   3_occ:  72.90   1.61  16.79  72.90   1.61  12.89  68.64   6.30  38.03
   4_bss:  72.90   1.61  16.79  72.90   1.61  12.89  68.64   6.30  38.03
   4_xyz:  72.90   1.61  16.79  72.90   1.61  12.89  68.64   6.30  38.03
   4_adp:  82.21   0.43  17.06  82.21   0.43  12.93  73.25   6.59  39.55
   4_occ:  82.21   0.43  17.06  82.21   0.43  12.93  73.25   6.59  39.55
   5_bss:  82.21   0.43  17.06  82.21   0.43  12.93  73.25   6.59  39.55
   5_xyz:  82.21   0.43  17.06  82.21   0.43  12.93  73.25   6.59  39.55
   5_adp:  85.20   0.38  16.88  85.20   0.38  12.77  74.51   6.31  39.23
   5_occ:  85.20   0.38  16.88  85.20   0.38  12.77  74.51   6.31  39.23
   5_bss:  85.19   0.37  16.87  85.19   0.37  12.76  74.50   6.30  39.22
------------------------------------------------------------------------
 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:    1.133    0.021    0.292
   1_adp:    1.133    0.021    0.292
   1_occ:    1.133    0.021    0.292
   2_bss:    1.133    0.021    0.292
   2_xyz:    0.772    0.015    0.330
   2_adp:    0.772    0.015    0.330
   2_occ:    0.772    0.015    0.330
   3_bss:    0.772    0.015    0.330
   3_xyz:    0.920    0.027    0.351
   3_adp:    0.920    0.027    0.351
   3_occ:    0.920    0.027    0.351
   4_bss:    0.920    0.027    0.351
   4_xyz:    0.999    0.032    0.362
   4_adp:    0.999    0.032    0.362
   4_occ:    0.999    0.032    0.362
   5_bss:    0.999    0.032    0.362
   5_xyz:    1.014    0.026    0.366
   5_adp:    1.014    0.026    0.366
   5_occ:    1.014    0.026    0.366
   5_bss:    1.014    0.026    0.366
------------------------------------------------------------------------

CPU time actual refinement: 321.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/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_904/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_904/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.83 
  Macro-tasks:
    bulk solvent and scale       = 37.47  
    individual site refinement   = 136.42 
    weights calculation          = 28.79  
    collect and process          = 6.52   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 209.31 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 101.95 
    alpha_beta                      = 8.19   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.28 
    fmodel                         = 6.28   
    r_factors                      = 0.17   
    phase_errors                   = 10.89  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 242.35 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.516 micro seconds
Total CPU time: 5.59 minutes
from_scatterers_fft:    648 calls, 101.71 s
gradients_fft:          593 calls,  98.18 s

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

# Date 2008-01-16 Time 05:56:52 PST -0800 (1200491812.56 s)
Start R-work = 0.3097, R-free = 0.3163 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.2944, R-free = 0.3024
Final R-work = 0.1091, R-free = 0.1577