# Date 2008-01-16 Time 04:03:50 PST -0800 (1200485030.21 s)
#phil __OFF__

Command line arguments: "../163.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22351
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 163

-------------------------------------------------------------------------------
  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: (68.845, 46.4607, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8628 1.96086
Completeness in resolution range: 0.93925
Completeness with d_max=infinity: 0.936377

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8628
                             d_min =   1.9609

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8628 1.96086
Completeness in resolution range: 0.93925
Completeness with d_max=infinity: 0.936377

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8632 -  4.1958 [2193/2220]  1971   222  10.1%
  bin  2:  4.1958 -  3.3428 [2103/2119]  1891   212  10.1%
  bin  3:  3.3428 -  2.9239 [2085/2104]  1883   202   9.7%
  bin  4:  2.9239 -  2.6582 [2055/2085]  1842   213  10.4%
  bin  5:  2.6582 -  2.4686 [2027/2046]  1828   199   9.8%
  bin  6:  2.4686 -  2.3237 [2038/2063]  1831   207  10.2%
  bin  7:  2.3237 -  2.2077 [2015/2049]  1823   192   9.5%
  bin  8:  2.2077 -  2.1119 [2042/2072]  1831   211  10.3%
  bin  9:  2.1119 -  2.0308 [1982/2033]  1786   196   9.9%
  bin 10:  2.0308 -  1.9609 [1049/2065]   944   105  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/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:
        1.27 -     1.99: 13
        1.99 -     2.72: 215
        2.72 -     3.45: 4625
        3.45 -     4.17: 9450
        4.17 -     4.90: 14282
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.266 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.271 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.325 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.669 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.706 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28580 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_163/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.4607 88.1178 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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4383   r_free= 0.4330   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.239993                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8632 -  4.6798 0.99   1424  157 0.3314 0.3246      6.4873      6.4315|
|  2:  4.6798 -  3.7339 0.99   1365  153 0.3528 0.3774      6.6777      6.7348|
|  3:  3.7339 -  3.2676 0.99   1340  149 0.4077 0.3870        6.61       6.615|
|  4:  3.2676 -  2.9715 0.99   1340  144 0.4320 0.4633      6.4698      6.5266|
|  5:  2.9715 -  2.7599 0.99   1318  150 0.4531 0.4170      6.2984      6.2921|
|  6:  2.7599 -  2.5981 0.99   1325  149 0.4692 0.4958      6.2252      6.1634|
|  7:  2.5981 -  2.4686 0.99   1303  146 0.4750 0.3975      6.2074      6.0605|
|  8:  2.4686 -  2.3616 0.98   1316  145 0.4894 0.4813      6.1549      6.1773|
|  9:  2.3616 -  2.2710 0.98   1299  144 0.5100 0.5110      6.1074      6.1539|
| 10:  2.2710 -  2.1929 0.99   1317  139 0.5046 0.4587      6.0814      6.0344|
| 11:  2.1929 -  2.1245 0.99   1278  154 0.5097 0.4573      6.0148      5.9893|
| 12:  2.1245 -  2.0640 0.97   1307  134 0.5044 0.5072      5.9584      5.9854|
| 13:  2.0640 -  2.0098 0.92   1197  134 0.5046 0.5400      5.8789      5.8217|
| 14:  2.0098 -  1.9609 0.38    501   61 0.4916 0.4706      5.8665       5.724|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8632 -  4.6798  1424   157  0.76  28.81   0.84     0.79      53009.84|
|  2:  4.6798 -  3.7339  1365   153  0.75  30.81   0.95     0.85      84760.86|
|  3:  3.7339 -  3.2676  1340   149  0.65  39.33   0.94     0.84      93089.09|
|  4:  3.2676 -  2.9715  1340   144  0.57  45.90   0.92     0.77      85543.73|
|  5:  2.9715 -  2.7599  1318   150  0.52  50.38   0.93     0.72      64597.67|
|  6:  2.7599 -  2.5981  1325   149  0.51  51.24   0.91     0.70      54688.82|
|  7:  2.5981 -  2.4686  1303   146  0.52  50.13   0.94     0.70      48233.37|
|  8:  2.4686 -  2.3616  1316   145  0.48  53.34   0.94     0.67      45555.02|
|  9:  2.3616 -  2.2710  1299   144  0.48  54.06   0.92     0.68      43658.98|
| 10:  2.2710 -  2.1929  1317   139  0.47  54.84   0.95     0.67      39842.33|
| 11:  2.1929 -  2.1245  1278   154  0.45  55.81   0.93     0.72      40208.86|
| 12:  2.1245 -  2.0640  1307   134  0.44  57.09   0.96     0.68      36573.89|
| 13:  2.0640 -  2.0098  1197   134  0.39  60.67   0.95     0.62      33821.93|
| 14:  2.0098 -  1.9609   501    61  0.37  62.10   1.01     0.50      28309.82|
|alpha:            min =        0.50 max =            0.85 mean =         0.72|
|beta:             min =    28309.82 max =        93089.09 mean =     55246.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.95 mean =        48.74|
|phase err.(test): min =        0.00 max =           89.97 mean =        48.61|
|-----------------------------------------------------------------------------|

============================== 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 = 11.419781             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.050   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.428271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.389   (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 |  1.266 -  1.629:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.629 -  1.993:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.993 -  2.356:       25 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.356 -  2.719:      190 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.719 -  3.083:     2310 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.083 -  3.446:     2315 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.446 -  3.810:     4194 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.810 -  4.173:     5256 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.173 -  4.537:     6431 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.537 -  4.900:     7851 |
|-----------------------------------------------------------------------------|
|-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 |        0.195 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.266 |       0.683 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    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: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4383   r_free= 0.4330   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.239993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4293   r_free= 0.4229   ksol= 0.32   Bsol= 24.80   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-0.59,3.36,-0.00,0.00,0.00); trace/3= 0.74                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.231167                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.289187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.739   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.794925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.029   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4293      final r-factor (work) = 0.2571          |
| start r-factor (free) = 0.4229      final r-factor (free) = 0.2925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1198 = 9.29 * 0.50 * 6.2275 + 1.00 * 0.1954                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0403 = 9.29 * 0.50 * 6.0123 + 1.00 * 0.1159                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2571      final r-factor (work) = 0.2326          |
| start r-factor (free) = 0.2925      final r-factor (free) = 0.3006          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7854 = 0.79 * 1.00 * 6.0123 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5933 = 0.79 * 1.00 * 5.7609 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.71   18.04    None  None   None       |
|    all(noH): 2823   0      0.00    89.71   18.04    None  None   None       |
|    Sol.    : 438    0      3.90    89.71   41.58    None  None   None       |
|    Mac.    : 2385   0      0.00    78.61   13.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.972:  811   |   5:    44.857 -  53.829:  112        |
|      1:     8.972 -  17.943: 1088   |   6:    53.829 -  62.800:   61        |
|      2:    17.943 -  26.914:  374   |   7:    62.800 -  71.772:   36        |
|      3:    26.914 -  35.886:  193   |   8:    71.772 -  80.743:   16        |
|      4:    35.886 -  44.857:  129   |   9:    80.743 -  89.715:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2326 r_free = 0.3006             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2324 r_free = 0.3007             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2324   r_free= 0.3007   ksol= 0.32   Bsol= 24.80   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-0.59,3.36,-0.00,0.00,0.00); trace/3= 0.74                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.775819                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2290   r_free= 0.2981   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.94,0.66,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.769497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.756456              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.579   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.503  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.1740          |
| start r-factor (free) = 0.2981      final r-factor (free) = 0.2305          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0720 = 2.76 * 0.50 * 5.7728 + 1.00 * 0.1157                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8723 = 2.76 * 0.50 * 5.6715 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1740      final r-factor (work) = 0.1638          |
| start r-factor (free) = 0.2305      final r-factor (free) = 0.2160          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4482 = 0.25 * 1.00 * 5.6715 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3999 = 0.25 * 1.00 * 5.4990 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.24   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    86.24   17.49    None  None   None       |
|    Sol.    : 438    0      5.72    86.24   40.92    None  None   None       |
|    Mac.    : 2385   0      0.00    79.09   13.19    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:     0.000 -   8.624:  711   |   5:    43.120 -  51.744:  119        |
|      1:     8.624 -  17.248: 1259   |   6:    51.744 -  60.369:   69        |
|      2:    17.248 -  25.872:  340   |   7:    60.369 -  68.993:   36        |
|      3:    25.872 -  34.496:  137   |   8:    68.993 -  77.617:   13        |
|      4:    34.496 -  43.120:  135   |   9:    77.617 -  86.241:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1638 r_free = 0.2160             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1636 r_free = 0.2157             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1636   r_free= 0.2157   ksol= 0.33   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.94,0.66,-0.00,0.00,0.00); trace/3= -1.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464220                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1636   r_free= 0.2155   ksol= 0.33   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.12,0.09,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.462985                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.371390              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.265  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.337158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.410  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1636      final r-factor (work) = 0.1321          |
| start r-factor (free) = 0.2155      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5756 = 2.37 * 0.50 * 5.4989 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4262 = 2.37 * 0.50 * 5.3728 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1321      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5661 = 2.34 * 1.00 * 5.3728 + 1.00 * 0.0090                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2830 = 2.34 * 1.00 * 5.2506 + 1.00 * 0.0115                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    92.94   17.99    None  None   None       |
|    all(noH): 2823   0      0.54    92.94   17.99    None  None   None       |
|    Sol.    : 438    0      6.06    92.80   44.38    None  None   None       |
|    Mac.    : 2385   0      0.54    92.94   13.15    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:     0.537 -   9.777:  987   |   5:    46.737 -  55.977:  104        |
|      1:     9.777 -  19.017: 1134   |   6:    55.977 -  65.217:   75        |
|      2:    19.017 -  28.257:  230   |   7:    65.217 -  74.457:   47        |
|      3:    28.257 -  37.497:  118   |   8:    74.457 -  83.697:   22        |
|      4:    37.497 -  46.737:   99   |   9:    83.697 -  92.937:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1719             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1721             target_work(ml) = 5.239         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1721   ksol= 0.33   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.12,0.09,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1721   ksol= 0.33   Bsol= 55.20   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.12,0.09,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.873238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.452  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.142392              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.857  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9737 = 1.87 * 0.50 * 5.2508 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9393 = 1.87 * 0.50 * 5.2173 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7544 = 0.14 * 1.00 * 5.2173 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7485 = 0.14 * 1.00 * 5.1997 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.78    90.77   16.92    None  None   None       |
|    all(noH): 2823   0      1.78    90.77   16.92    None  None   None       |
|    Sol.    : 438    0      5.97    83.88   39.69    None  None   None       |
|    Mac.    : 2385   0      1.78    90.77   12.74    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:     1.783 -  10.682: 1204   |   5:    46.278 -  55.177:   95        |
|      1:    10.682 -  19.581:  981   |   6:    55.177 -  64.076:   56        |
|      2:    19.581 -  28.480:  211   |   7:    64.076 -  72.975:   23        |
|      3:    28.480 -  37.379:  131   |   8:    72.975 -  81.874:   10        |
|      4:    37.379 -  46.278:  109   |   9:    81.874 -  90.773:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1619             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1619             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1619   ksol= 0.33   Bsol= 55.20   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.12,0.09,-0.00,0.00,0.00); trace/3= -1.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1620   ksol= 0.32   Bsol= 48.62   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.22,-0.21,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.189764                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.627362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.214  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.771053              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.988  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2831 = 1.63 * 0.50 * 5.1992 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2656 = 1.63 * 0.50 * 5.1776 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0002 = 0.77 * 1.00 * 5.1776 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9916 = 0.77 * 1.00 * 5.1644 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    95.98   17.04    None  None   None       |
|    all(noH): 2823   0      1.08    95.98   17.04    None  None   None       |
|    Sol.    : 438    0      5.75    87.29   40.83    None  None   None       |
|    Mac.    : 2385   0      1.08    95.98   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.076 -  10.566: 1231   |   5:    48.525 -  58.015:   99        |
|      1:    10.566 -  20.056:  966   |   6:    58.015 -  67.505:   48        |
|      2:    20.056 -  29.546:  210   |   7:    67.505 -  76.995:   26        |
|      3:    29.546 -  39.036:  121   |   8:    76.995 -  86.485:    9        |
|      4:    39.036 -  48.525:  110   |   9:    86.485 -  95.975:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1595             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1596             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1596   ksol= 0.32   Bsol= 48.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.22,-0.21,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167784                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8632 -  4.6798 0.99   1424  157 0.0997 0.1295      5.3979      5.5658|
|  2:  4.6798 -  3.7339 0.99   1365  153 0.0871 0.1106      5.4477      5.6275|
|  3:  3.7339 -  3.2676 0.99   1340  149 0.1094 0.1557       5.491      5.8737|
|  4:  3.2676 -  2.9715 0.99   1340  144 0.1252 0.1608      5.4647      5.6025|
|  5:  2.9715 -  2.7599 0.99   1318  150 0.1334 0.1593      5.3492      5.5257|
|  6:  2.7599 -  2.5981 0.99   1325  149 0.1270 0.2030      5.2255      5.5191|
|  7:  2.5981 -  2.4686 0.99   1303  146 0.1321 0.1632       5.203      5.3465|
|  8:  2.4686 -  2.3616 0.98   1316  145 0.1194 0.1693      5.0957      5.3131|
|  9:  2.3616 -  2.2710 0.98   1299  144 0.1183 0.1900      5.0382      5.3915|
| 10:  2.2710 -  2.1929 0.99   1317  139 0.1162 0.1667      4.9711      5.1665|
| 11:  2.1929 -  2.1245 0.99   1278  154 0.1165 0.1928       4.944      5.3246|
| 12:  2.1245 -  2.0640 0.97   1307  134 0.1209 0.1586      4.9286      5.1371|
| 13:  2.0640 -  2.0098 0.92   1197  134 0.1051 0.1784      4.7541       5.027|
| 14:  2.0098 -  1.9609 0.38    501   61 0.0920 0.1721      4.5965      4.9098|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8632 -  4.6798  1424   157  0.94   9.24   0.98     0.95       7276.63|
|  2:  4.6798 -  3.7339  1365   153  0.95   7.96   1.02     1.01       9212.22|
|  3:  3.7339 -  3.2676  1340   149  0.93  11.62   1.03     1.02      10549.49|
|  4:  3.2676 -  2.9715  1340   144  0.92  13.72   1.01     1.00      10430.75|
|  5:  2.9715 -  2.7599  1318   150  0.90  16.47   1.00     0.98       8944.36|
|  6:  2.7599 -  2.5981  1325   149  0.89  16.82   0.98     0.94       7193.88|
|  7:  2.5981 -  2.4686  1303   146  0.90  16.30   0.99     0.95       6575.73|
|  8:  2.4686 -  2.3616  1316   145  0.90  15.72   1.00     0.97       5667.67|
|  9:  2.3616 -  2.2710  1299   144  0.90  15.88   0.99     0.95       5066.62|
| 10:  2.2710 -  2.1929  1317   139  0.90  16.37   1.00     0.97       4607.97|
| 11:  2.1929 -  2.1245  1278   154  0.90  16.86   0.99     0.95       4538.92|
| 12:  2.1245 -  2.0640  1307   134  0.90  16.72   1.01     1.00       4377.88|
| 13:  2.0640 -  2.0098  1197   134  0.90  15.96   0.99     0.96       3236.64|
| 14:  2.0098 -  1.9609   501    61  0.93  12.29   0.98     0.94       2181.58|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2181.58 max =        10549.49 mean =      6666.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.45|
|phase err.(test): min =        0.00 max =           89.66 mean =        13.96|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1595   ksol= 0.32   Bsol= 50.45   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.06,-0.10,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1595   ksol= 0.32   Bsol= 50.45   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.70,-2.06,-0.10,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.167620                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8632 -  4.6798 0.99   1424  157 0.0997 0.1296      5.3976      5.5666|
|  2:  4.6798 -  3.7339 0.99   1365  153 0.0874 0.1106      5.4489       5.628|
|  3:  3.7339 -  3.2676 0.99   1340  149 0.1095 0.1556      5.4918      5.8737|
|  4:  3.2676 -  2.9715 0.99   1340  144 0.1252 0.1606      5.4642       5.602|
|  5:  2.9715 -  2.7599 0.99   1318  150 0.1333 0.1590      5.3484      5.5246|
|  6:  2.7599 -  2.5981 0.99   1325  149 0.1269 0.2029      5.2247      5.5186|
|  7:  2.5981 -  2.4686 0.99   1303  146 0.1321 0.1631      5.2024      5.3456|
|  8:  2.4686 -  2.3616 0.98   1316  145 0.1193 0.1691      5.0955      5.3127|
|  9:  2.3616 -  2.2710 0.98   1299  144 0.1182 0.1901       5.038      5.3917|
| 10:  2.2710 -  2.1929 0.99   1317  139 0.1162 0.1665      4.9709      5.1662|
| 11:  2.1929 -  2.1245 0.99   1278  154 0.1165 0.1926      4.9436       5.324|
| 12:  2.1245 -  2.0640 0.97   1307  134 0.1209 0.1586      4.9285      5.1371|
| 13:  2.0640 -  2.0098 0.92   1197  134 0.1051 0.1785      4.7539      5.0273|
| 14:  2.0098 -  1.9609 0.38    501   61 0.0920 0.1719      4.5964      4.9085|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8632 -  4.6798  1424   157  0.94   9.24   0.98     0.95       7271.29|
|  2:  4.6798 -  3.7339  1365   153  0.95   7.97   1.02     1.01       9217.49|
|  3:  3.7339 -  3.2676  1340   149  0.93  11.64   1.03     1.02      10563.79|
|  4:  3.2676 -  2.9715  1340   144  0.92  13.72   1.02     1.00      10420.15|
|  5:  2.9715 -  2.7599  1318   150  0.90  16.46   1.00     0.98       8933.71|
|  6:  2.7599 -  2.5981  1325   149  0.89  16.81   0.98     0.95       7179.93|
|  7:  2.5981 -  2.4686  1303   146  0.90  16.28   0.99     0.95       6564.70|
|  8:  2.4686 -  2.3616  1316   145  0.90  15.72   1.00     0.98       5663.70|
|  9:  2.3616 -  2.2710  1299   144  0.90  15.88   1.00     0.95       5064.35|
| 10:  2.2710 -  2.1929  1317   139  0.90  16.36   1.01     0.98       4605.48|
| 11:  2.1929 -  2.1245  1278   154  0.90  16.85   1.00     0.96       4532.25|
| 12:  2.1245 -  2.0640  1307   134  0.90  16.72   1.01     1.01       4377.66|
| 13:  2.0640 -  2.0098  1197   134  0.90  15.95   1.00     0.97       3233.57|
| 14:  2.0098 -  1.9609   501    61  0.93  12.28   0.99     0.95       2176.71|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2176.71 max =        10563.79 mean =      6663.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.44|
|phase err.(test): min =        0.00 max =           89.69 mean =        13.96|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.647)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.04    95.94   17.00    None  None   None       |
|    all(noH): 2823   0      1.04    95.94   17.00    None  None   None       |
|    Sol.    : 438    0      5.71    87.25   40.79    None  None   None       |
|    Mac.    : 2385   0      1.04    95.94   12.63    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:     1.038 -  10.528: 1231   |   5:    48.488 -  57.978:   99        |
|      1:    10.528 -  20.018:  966   |   6:    57.978 -  67.468:   48        |
|      2:    20.018 -  29.508:  210   |   7:    67.468 -  76.958:   26        |
|      3:    29.508 -  38.998:  121   |   8:    76.958 -  86.448:    9        |
|      4:    38.998 -  48.488:  110   |   9:    86.448 -  95.938:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.483 - 4.455
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 288 from: 294
   mapped sites are within: 0.707 - 4.455

peak=    7.467 closest distance to " O   HOH Z 403 " =    1.242
peak=    5.666 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.646 closest distance to " O   HOH Z 403 " =    2.085
peak=    5.627 closest distance to " O   HOH Z 142 " =    1.801
peak=    5.483 closest distance to " NE2 GLN A  11 " =    1.143
peak=    5.381 closest distance to " CG  PRO A  54 " =    1.345
peak=    5.105 closest distance to " O   HOH Z 126 " =    1.969
peak=    5.054 closest distance to " O   HOH Z 417 " =    1.493
peak=    5.015 closest distance to " CG  PRO A 280 " =    0.922
peak=    5.005 closest distance to " NH2 ARG A  56 " =    2.069
peak=    4.961 closest distance to " CB  GLN A 223 " =    1.446
peak=    4.841 closest distance to " CB  PRO A  54 " =    0.989
peak=    4.784 closest distance to " O   HOH Z 112 " =    1.249
peak=    4.690 closest distance to " O   HOH Z 287 " =    1.842
peak=    4.636 closest distance to " O   HOH Z 427 " =    2.917
peak=    4.621 closest distance to " O   HOH Z 232 " =    2.378
peak=    4.605 closest distance to " O   HOH Z 369 " =    2.173
peak=    4.600 closest distance to " CG2 VAL A 257 " =    0.882
peak=    4.579 closest distance to " O   HOH Z 403 " =    2.317
peak=    4.574 closest distance to " CZ  PHE A 218 " =    1.112
peak=    4.565 closest distance to " O   HOH Z 375 " =    1.101
peak=    4.544 closest distance to " CG  PRO A 213 " =    1.221
peak=    4.489 closest distance to " CG  PRO A 243 " =    1.069
peak=    4.480 closest distance to " O   SER A  87 " =    2.208
peak=    4.445 closest distance to " CG  PRO A  90 " =    1.239
peak=    4.443 closest distance to " O   HOH Z 402 " =    1.401
peak=    4.364 closest distance to " O   HOH Z 298 " =    1.934
peak=    4.310 closest distance to " O   HOH Z 371 " =    1.931
peak=    4.285 closest distance to " ND2 ASN A 187 " =    1.522
peak=    4.276 closest distance to " O   HOH Z  63 " =    2.114
peak=    4.262 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.239 closest distance to " CG  TRP A 179 " =    2.108
peak=    4.224 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.190 closest distance to " CB  GLN A 183 " =    1.191
peak=    4.180 closest distance to " O   HOH Z  78 " =    1.659
peak=    4.170 closest distance to " CB  ASN A 148 " =    1.448
peak=    4.170 closest distance to " O   HOH Z 188 " =    2.714
peak=    4.160 closest distance to " CB  ARG A  79 " =    1.464
peak=    4.152 closest distance to " CD2 TRP A 179 " =    1.295
peak=    4.146 closest distance to " O   HOH Z  40 " =    1.866
peak=    4.142 closest distance to " C   PRO A 198 " =    1.570
peak=    4.111 closest distance to " CB  VAL A 265 " =    1.319
peak=    4.085 closest distance to " CB  ASN A  39 " =    0.888
peak=    4.082 closest distance to " O   HOH Z 419 " =    2.341
peak=    4.079 closest distance to " CB  GLU A  46 " =    1.174
peak=    4.077 closest distance to " OG ASER A 258 " =    2.974
peak=    4.076 closest distance to " O   HOH Z 327 " =    1.590
peak=    4.075 closest distance to " O   HOH Z 188 " =    1.486
peak=    4.054 closest distance to " NZ  LYS A 117 " =    3.015
peak=    4.035 closest distance to " CB  GLU A 152 " =    1.196
peak=    4.031 closest distance to " CB  ASN A 110 " =    1.089
peak=    4.016 closest distance to " CB  VAL A 202 " =    1.616
peak=    4.014 closest distance to " CB  THR A  31 " =    1.558
peak=    3.982 closest distance to " CE  LYS A  76 " =    0.910
peak=    3.980 closest distance to " CB  SER A  63 " =    1.171
peak=    3.977 closest distance to " O   HOH Z 368 " =    3.487
peak=    3.966 closest distance to " CA  ARG A 195 " =    1.268
peak=    3.966 closest distance to " O   HOH Z 250 " =    1.492
peak=    3.960 closest distance to " O   HOH Z 272 " =    1.837
peak=    3.955 closest distance to " OG BSER A 164 " =    2.333
peak=    3.954 closest distance to " ND2 ASN A 249 " =    0.820
peak=    3.950 closest distance to " O   HOH Z 248 " =    1.526
peak=    3.931 closest distance to " O   HOH Z 406 " =    1.605
peak=    3.928 closest distance to " O   HOH Z 353 " =    2.645
peak=    3.925 closest distance to " CB  ASN A 142 " =    1.061
peak=    3.909 closest distance to " O   HOH Z   3 " =    2.101
peak=    3.905 closest distance to " N   TYR A 116 " =    1.512
peak=    3.904 closest distance to " CA  ASN A 215 " =    0.996
peak=    3.886 closest distance to " CB  PRO A  90 " =    1.044
peak=    3.881 closest distance to " O   HOH Z 236 " =    1.388
peak=    3.878 closest distance to " CB  ARG A 190 " =    1.649
peak=    3.876 closest distance to " O   HOH Z 346 " =    1.668
peak=    3.851 closest distance to " NH2AARG A 190 " =    2.031
peak=    3.848 closest distance to " O   HOH Z 365 " =    2.631
peak=    3.848 closest distance to " CZ3 TRP A 266 " =    1.035
peak=    3.822 closest distance to " CB  ILE A 120 " =    1.380
peak=    3.816 closest distance to " O   HOH Z 234 " =    3.571
peak=    3.808 closest distance to " CB  TRP A 266 " =    1.171
peak=    3.805 closest distance to " O   HOH Z 132 " =    2.640
peak=    3.801 closest distance to " CB  GLU A 277 " =    3.590
peak=    3.798 closest distance to " O   HOH Z 394 " =    3.731
peak=    3.794 closest distance to " O   HOH Z 425 " =    1.308
peak=    3.790 closest distance to " N   ASN A  39 " =    1.216
peak=    3.780 closest distance to " CA  ARG A  36 " =    0.932
peak=    3.777 closest distance to " O   HOH Z 394 " =    1.698
peak=    3.764 closest distance to " N   GLN A 278 " =    1.459
peak=    3.760 closest distance to " O   HOH Z  44 " =    1.869
peak=    3.758 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.757 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.755 closest distance to " O   HOH Z 261 " =    1.939
peak=    3.754 closest distance to " CG  GLN A  58 " =    1.008
peak=    3.730 closest distance to " O   THR A 220 " =    1.215
peak=    3.722 closest distance to " O   HOH Z   9 " =    2.170
peak=    3.703 closest distance to " O   HOH Z 158 " =    3.116
peak=    3.698 closest distance to " CG AARG A 275 " =    1.132
peak=    3.698 closest distance to " CD  LYS A  76 " =    2.055
peak=    3.697 closest distance to " CB  ALA A 114 " =    0.878
peak=    3.687 closest distance to " O   ASN A  74 " =    1.359
peak=    3.684 closest distance to " CB  SER A  62 " =    0.831
peak=    3.683 closest distance to " CB  TYR A 169 " =    0.707
peak=    3.679 closest distance to " O   HOH Z  92 " =    2.406
peak=    3.677 closest distance to " CG2AVAL A 121 " =    2.421
peak=    3.675 closest distance to " O   HOH Z 209 " =    2.248
peak=    3.662 closest distance to " O   HOH Z 213 " =    2.202
peak=    3.659 closest distance to " CB  SER A 273 " =    0.909
peak=    3.657 closest distance to " O   HOH Z 425 " =    1.962
peak=    3.651 closest distance to " CB  GLN A  88 " =    1.257
peak=    3.650 closest distance to " CA  ASN A 127 " =    1.128
peak=    3.649 closest distance to " O   HOH Z 233 " =    1.662
peak=    3.645 closest distance to " O   HOH Z   1 " =    1.939
peak=    3.640 closest distance to " O   HOH Z 132 " =    0.956
peak=    3.638 closest distance to " N   PHE A 130 " =    1.263
peak=    3.634 closest distance to " OD1 ASN A  69 " =    2.502
peak=    3.631 closest distance to " O   HOH Z 126 " =    1.534
peak=    3.630 closest distance to " CB  SER A  26 " =    1.777
peak=    3.630 closest distance to " O   HOH Z  97 " =    2.302
peak=    3.629 closest distance to " CG  ARG A  66 " =    2.538
peak=    3.621 closest distance to " O   HOH Z 173 " =    1.914
peak=    3.614 closest distance to " CB  GLU A 128 " =    0.944
peak=    3.598 closest distance to " CG2 ILE A 120 " =    1.209
peak=    3.594 closest distance to " CG2 ILE A 239 " =    0.715
peak=    3.592 closest distance to " O   HOH Z  61 " =    1.673
peak=    3.588 closest distance to " NE2 HIS A 207 " =    1.142
peak=    3.583 closest distance to " CE  LYS A 119 " =    1.221
peak=    3.580 closest distance to " CA  ALA A 129 " =    1.533
peak=    3.572 closest distance to " CA  ASN A 217 " =    1.135
peak=    3.568 closest distance to " O   HOH Z   1 " =    1.592
peak=    3.546 closest distance to " CZ  PHE A  38 " =    1.210
peak=    3.543 closest distance to " O   HOH Z 193 " =    1.558
peak=    3.538 closest distance to " CB  SER A 212 " =    1.293
peak=    3.537 closest distance to " N   ASP A 162 " =    1.125
peak=    3.535 closest distance to " O   HOH Z 258 " =    2.123
peak=    3.525 closest distance to " O   HOH Z  61 " =    1.480
peak=    3.524 closest distance to " CD1 ILE A 199 " =    1.188
peak=    3.521 closest distance to " CB  PHE A 204 " =    0.783
peak=    3.519 closest distance to " CA  GLU A  46 " =    1.057
peak=    3.518 closest distance to " CB  LEU A 228 " =    1.082
peak=    3.512 closest distance to " O   HOH Z 124 " =    1.955
peak=    3.512 closest distance to " O   HOH Z 141 " =    1.655
peak=    3.509 closest distance to " O   HOH Z  49 " =    0.961
peak=    3.503 closest distance to " O   HOH Z 203 " =    1.678
peak=    3.501 closest distance to " O   HOH Z  21 " =    1.783
peak=    3.496 closest distance to " CB  LEU A 300 " =    0.957
peak=    3.490 closest distance to " O   HOH Z 411 " =    3.935
peak=    3.479 closest distance to " CB  LEU A  83 " =    0.757
peak=    3.479 closest distance to " O   HOH Z  10 " =    1.765
peak=    3.477 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.474 closest distance to " CA  ASP A 162 " =    1.077
peak=    3.465 closest distance to " O   HOH Z 337 " =    3.552
peak=    3.457 closest distance to " O   HOH Z 132 " =    2.188
peak=    3.451 closest distance to " CB  SER A   3 " =    1.215
peak=    3.440 closest distance to " O   HOH Z 359 " =    1.627
peak=    3.439 closest distance to " O   HOH Z 357 " =    1.929
peak=    3.438 closest distance to " NH1AARG A 145 " =    1.267
peak=    3.437 closest distance to " CG  GLU A  37 " =    0.982
peak=    3.434 closest distance to " O   HOH Z 128 " =    1.947
peak=    3.429 closest distance to " O   HOH Z  88 " =    2.520
peak=    3.422 closest distance to " O   HOH Z 405 " =    1.280
peak=    3.422 closest distance to " O   HOH Z  59 " =    1.739
peak=    3.419 closest distance to " O  BHOH Z  74 " =    1.243
peak=    3.406 closest distance to " CA  THR A 264 " =    0.916
peak=    3.406 closest distance to " O   HOH Z 371 " =    2.962
peak=    3.405 closest distance to " CB  THR A  52 " =    0.756
peak=    3.405 closest distance to " O   GLN A 194 " =    1.493
peak=    3.401 closest distance to " O   HOH Z  85 " =    1.312
peak=    3.400 closest distance to " C   PHE A  59 " =    0.921
peak=    3.397 closest distance to " O   HOH Z 117 " =    2.194
peak=    3.396 closest distance to " O   HOH Z 345 " =    1.726
peak=    3.395 closest distance to " O   HOH Z 294 " =    1.508
peak=    3.390 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.386 closest distance to " O   HOH Z 325 " =    2.381
peak=    3.385 closest distance to " O   HOH Z 214 " =    2.354
peak=    3.383 closest distance to " O   HOH Z 117 " =    1.950
peak=    3.378 closest distance to " CB  ALA A 291 " =    1.104
peak=    3.377 closest distance to " O   HOH Z  40 " =    1.369
peak=    3.376 closest distance to " O   HOH Z 415 " =    3.656
peak=    3.376 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.375 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.372 closest distance to " CA  VAL A 125 " =    1.146
peak=    3.370 closest distance to " CB  PRO A 198 " =    1.162
peak=    3.369 closest distance to " O   HOH Z 291 " =    1.452
peak=    3.369 closest distance to " CA  ASP A 149 " =    1.212
peak=    3.369 closest distance to " O   THR A 182 " =    1.499
peak=    3.362 closest distance to " CA  ALA A  84 " =    1.258
peak=    3.361 closest distance to " O   HOH Z 193 " =    1.859
peak=    3.356 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.352 closest distance to " CA  ARG A 159 " =    1.232
peak=    3.351 closest distance to " O   HOH Z 421 " =    2.063
peak=    3.350 closest distance to " NH1BARG A 145 " =    1.308
peak=    3.346 closest distance to " O   HOH Z  85 " =    2.354
peak=    3.345 closest distance to " CG  LEU A 167 " =    1.362
peak=    3.342 closest distance to " CA  THR A 221 " =    1.027
peak=    3.339 closest distance to " CB  GLN A  89 " =    1.396
peak=    3.337 closest distance to " O   HOH Z 435 " =    1.922
peak=    3.330 closest distance to " CB  SER A  62 " =    1.125
peak=    3.327 closest distance to " O   HOH Z  48 " =    1.569
peak=    3.325 closest distance to " OG BSER A  99 " =    2.366
peak=    3.325 closest distance to " N   GLU A   2 " =    1.487
peak=    3.322 closest distance to " O   HOH Z 128 " =    1.996
peak=    3.318 closest distance to " O   HOH Z 290 " =    0.989
peak=    3.318 closest distance to " O   HOH Z 265 " =    2.163
peak=    3.315 closest distance to " O   HOH Z 368 " =    2.138
peak=    3.315 closest distance to " O   HOH Z  88 " =    2.460
peak=    3.313 closest distance to " CB  ARG A 156 " =    1.072
peak=    3.310 closest distance to " NE2 GLN A  77 " =    3.025
peak=    3.310 closest distance to " NH2BARG A 145 " =    1.997
peak=    3.308 closest distance to " OG BSER A 134 " =    2.946
peak=    3.300 closest distance to " CG  MET A 185 " =    1.246
peak=    3.299 closest distance to " O   HOH Z 153 " =    3.872
peak=    3.299 closest distance to " CE BMET A  47 " =    0.886
peak=    3.289 closest distance to " CB  PHE A 130 " =    0.926
peak=    3.287 closest distance to " O   HOH Z 299 " =    4.455
peak=    3.286 closest distance to " O   HOH Z 148 " =    3.483
peak=    3.285 closest distance to " CB  ALA A 114 " =    0.937
peak=    3.278 closest distance to " CB  ASN A 215 " =    1.128
peak=    3.277 closest distance to " CG  LYS A 119 " =    1.105
peak=    3.277 closest distance to " N   CYS A 260 " =    0.909
peak=    3.276 closest distance to " CG2 THR A 221 " =    1.129
peak=    3.272 closest distance to " O   HOH Z 423 " =    1.796
peak=    3.272 closest distance to " CG2 VAL A 197 " =    1.020
peak=    3.272 closest distance to " CB  ASN A 285 " =    0.980
peak=    3.270 closest distance to " CA  ALA A 233 " =    1.224
peak=    3.266 closest distance to " CB  ASP A 124 " =    0.727
peak=    3.261 closest distance to " O   HOH Z 380 " =    1.666
peak=    3.257 closest distance to " CA  TYR A 116 " =    1.351
peak=    3.254 closest distance to " O   HOH Z 117 " =    1.201
peak=    3.254 closest distance to " O   HOH Z  28 " =    1.903
peak=    3.244 closest distance to " O   HOH Z 389 " =    1.628
peak=    3.243 closest distance to " CB  SER A 210 " =    0.738
peak=    3.239 closest distance to " CB  PRO A 243 " =    1.223
peak=    3.238 closest distance to " CA  MET A 105 " =    1.018
peak=    3.236 closest distance to " CG2 THR A 220 " =    0.870
peak=    3.235 closest distance to " CB  ASP A 191 " =    1.200
peak=    3.232 closest distance to " CB  ALA A 248 " =    1.387
peak=    3.229 closest distance to " CB  LYS A 117 " =    1.209
peak=    3.228 closest distance to " ND1 HIS A  86 " =    1.753
peak=    3.228 closest distance to " O   HOH Z 280 " =    3.015
peak=    3.224 closest distance to " CG1BVAL A  72 " =    1.530
peak=    3.214 closest distance to " CE AMET A  47 " =    1.440
peak=    3.208 closest distance to " OG1 THR A 221 " =    1.236
peak=    3.205 closest distance to " O   HOH Z 285 " =    2.177
peak=    3.203 closest distance to " O   HOH Z 145 " =    2.769
peak=    3.202 closest distance to " CG  MET A 113 " =    1.000
peak=    3.201 closest distance to " CB  ARG A 139 " =    1.085
peak=    3.198 closest distance to " O   HOH Z 119 " =    4.301
peak=    3.191 closest distance to " O   HOH Z 380 " =    1.927
peak=    3.186 closest distance to " CD  ARG A 269 " =    0.922
peak=    3.185 closest distance to " OG  SER A  62 " =    2.801
peak=    3.184 closest distance to " O   HOH Z 392 " =    2.999
peak=    3.184 closest distance to " CB  ASP A 140 " =    0.999
peak=    3.180 closest distance to " CA  ALA A 160 " =    1.043
peak=    3.179 closest distance to " CA  SER A  87 " =    0.998
peak=    3.179 closest distance to " OG1 THR A 264 " =    0.759
peak=    3.178 closest distance to " O   HOH Z 194 " =    2.312
peak=    3.178 closest distance to " O   HOH Z 438 " =    2.912
peak=    3.175 closest distance to " O   HOH Z 218 " =    1.561
peak=    3.168 closest distance to " CG2 ILE A  20 " =    1.545
peak=    3.166 closest distance to " O   HOH Z 172 " =    3.245
peak=    3.166 closest distance to " CB  TYR A 116 " =    0.842
peak=    3.166 closest distance to " O   HOH Z 421 " =    2.919
peak=    3.162 closest distance to " O   HOH Z 130 " =    2.222
peak=    3.161 closest distance to " CA  ALA A 100 " =    0.952
peak=    3.154 closest distance to " OD2 ASP A 286 " =    3.182
peak=    3.150 closest distance to " CD2 LEU A   5 " =    1.125
peak=    3.150 closest distance to " CB  ASP A 200 " =    0.901
peak=    3.144 closest distance to " CA  ALA A 299 " =    0.965
peak=    3.138 closest distance to " CG2BVAL A  41 " =    0.863
peak=    3.137 closest distance to " CG2 ILE A 234 " =    0.842
peak=    3.124 closest distance to " O   ARG A 145 " =    1.857
peak=    3.120 closest distance to " CD2 TYR A 186 " =    1.039
peak=    3.119 closest distance to " O   HOH Z 329 " =    4.147
peak=    3.113 closest distance to " O  BHOH Z 338 " =    2.296
peak=    3.113 closest distance to " O   HOH Z 251 " =    1.661
peak=    3.112 closest distance to " CB  TRP A 179 " =    1.419
peak=    3.112 closest distance to " O   PHE A 192 " =    1.380
peak=    3.111 closest distance to " O   HOH Z 343 " =    3.245
peak=    3.105 closest distance to " O   HOH Z 234 " =    2.257
peak=    3.105 closest distance to " NH1 ARG A  66 " =    1.258
peak=    3.102 closest distance to " CB  SER A  99 " =    0.841
peak=    3.095 closest distance to " O   HOH Z 213 " =    1.795
peak=    3.093 closest distance to " O   HOH Z 371 " =    3.068
peak=    3.088 closest distance to " CB  SER A 216 " =    0.901
peak=    3.073 closest distance to " O   HOH Z   7 " =    1.431
peak=    3.070 closest distance to " O   HOH Z  30 " =    1.545
peak=    3.069 closest distance to " O   HOH Z 344 " =    3.175
peak=    3.053 closest distance to " O   HOH Z 245 " =    1.372
peak=    3.021 closest distance to " CB  VAL A 265 " =    2.309
peak=    3.014 closest distance to " CA  ARG A 102 " =    1.081

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.941 - 5.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 194
   mapped sites are within: 0.941 - 5.819

peak=   -4.743 closest distance to " CD  ARG A  14 " =    3.288
peak=   -4.740 closest distance to " OG BSER A 134 " =    1.246
peak=   -4.508 closest distance to " CG  GLN A  58 " =    1.009
peak=   -4.330 closest distance to " C   HIS A 108 " =    1.111
peak=   -4.318 closest distance to " CB  PHE A 192 " =    2.011
peak=   -4.312 closest distance to " O   PRO A 198 " =    1.230
peak=   -4.237 closest distance to " O   HOH Z 377 " =    2.081
peak=   -4.119 closest distance to " CG1 VAL A 112 " =    2.926
peak=   -4.085 closest distance to " CA  VAL A  67 " =    2.988
peak=   -4.079 closest distance to " CG  GLN A 223 " =    2.007
peak=   -4.023 closest distance to " OD1 ASP A 171 " =    1.574
peak=   -4.017 closest distance to " CE  MET A 105 " =    2.556
peak=   -3.998 closest distance to " O   HOH Z 351 " =    1.417
peak=   -3.997 closest distance to " O   HOH Z 387 " =    2.603
peak=   -3.966 closest distance to " O   PRO A 163 " =    1.874
peak=   -3.957 closest distance to " O   HOH Z 198 " =    1.283
peak=   -3.921 closest distance to " ND2 ASN A 249 " =    2.228
peak=   -3.913 closest distance to " O   HOH Z 372 " =    2.319
peak=   -3.903 closest distance to " CB  ASN A  39 " =    2.291
peak=   -3.885 closest distance to " O   HOH Z 211 " =    1.235
peak=   -3.878 closest distance to " CG2 THR A  18 " =    2.780
peak=   -3.869 closest distance to " CD1 PHE A  59 " =    2.185
peak=   -3.868 closest distance to " O   HOH Z 231 " =    2.221
peak=   -3.858 closest distance to " CD  ARG A 156 " =    2.049
peak=   -3.856 closest distance to " O   HOH Z 266 " =    5.457
peak=   -3.833 closest distance to " OD2 ASP A 191 " =    1.353
peak=   -3.822 closest distance to " O   HOH Z 119 " =    2.367
peak=   -3.820 closest distance to " O   HOH Z 193 " =    1.118
peak=   -3.786 closest distance to " CE BMET A  47 " =    1.137
peak=   -3.784 closest distance to " O   HOH Z 131 " =    4.019
peak=   -3.773 closest distance to " CD1 LEU A 255 " =    2.734
peak=   -3.765 closest distance to " O   VAL A  67 " =    2.572
peak=   -3.759 closest distance to " O   HOH Z 165 " =    2.276
peak=   -3.752 closest distance to " CD2 LEU A 237 " =    2.864
peak=   -3.722 closest distance to " O   HOH Z 102 " =    1.551
peak=   -3.697 closest distance to " OXT GLY A 302 " =    2.960
peak=   -3.693 closest distance to " O   ALA A  10 " =    1.594
peak=   -3.690 closest distance to " ND2 ASN A  45 " =    1.886
peak=   -3.688 closest distance to " CG2 ILE A  49 " =    2.819
peak=   -3.685 closest distance to " CB  ALA A  43 " =    2.445
peak=   -3.681 closest distance to " CZ  TYR A 169 " =    1.723
peak=   -3.666 closest distance to " O   HOH Z  63 " =    1.707
peak=   -3.652 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.651 closest distance to " OE1 GLN A 183 " =    1.566
peak=   -3.632 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.623 closest distance to " NE2 GLN A  55 " =    1.121
peak=   -3.601 closest distance to " O   HOH Z 290 " =    1.104
peak=   -3.596 closest distance to " N   ALA A  43 " =    2.563
peak=   -3.588 closest distance to " CD1 LEU A 101 " =    2.284
peak=   -3.575 closest distance to " O   HOH Z 185 " =    2.259
peak=   -3.570 closest distance to " O   HOH Z 429 " =    1.832
peak=   -3.565 closest distance to " CG  GLU A 277 " =    1.425
peak=   -3.558 closest distance to " O   HOH Z 139 " =    5.111
peak=   -3.554 closest distance to " OH  TYR A 172 " =    1.827
peak=   -3.549 closest distance to " CE2 TYR A  30 " =    2.737
peak=   -3.546 closest distance to " O   SER A 210 " =    2.008
peak=   -3.545 closest distance to " CD2 TYR A 293 " =    1.942
peak=   -3.542 closest distance to " O   HOH Z 313 " =    1.716
peak=   -3.527 closest distance to " CG1 VAL A 265 " =    2.571
peak=   -3.526 closest distance to " O   SER A  95 " =    1.515
peak=   -3.503 closest distance to " O   GLU A 152 " =    1.348
peak=   -3.500 closest distance to " CB  SER A 210 " =    1.131
peak=   -3.495 closest distance to " O   HOH Z 187 " =    1.595
peak=   -3.493 closest distance to " CD1 ILE A 239 " =    2.464
peak=   -3.487 closest distance to " CB  GLN A  11 " =    1.817
peak=   -3.486 closest distance to " O   HOH Z 359 " =    3.144
peak=   -3.483 closest distance to " O   ALA A 161 " =    1.697
peak=   -3.482 closest distance to " OD1 ASN A 148 " =    1.407
peak=   -3.479 closest distance to " O   TRP A  70 " =    1.421
peak=   -3.475 closest distance to " O   HOH Z 407 " =    2.677
peak=   -3.474 closest distance to " O   HOH Z  49 " =    1.199
peak=   -3.466 closest distance to " O   HOH Z 394 " =    1.471
peak=   -3.466 closest distance to " O   HOH Z 123 " =    2.533
peak=   -3.451 closest distance to " O   HOH Z 362 " =    5.819
peak=   -3.450 closest distance to " CZ3 TRP A 179 " =    1.263
peak=   -3.444 closest distance to " O   HOH Z 298 " =    2.460
peak=   -3.438 closest distance to " CG  LEU A  83 " =    2.028
peak=   -3.431 closest distance to " CE2 PHE A 218 " =    2.435
peak=   -3.430 closest distance to " CD2 PHE A 225 " =    1.148
peak=   -3.429 closest distance to " O   HOH Z 421 " =    3.071
peak=   -3.427 closest distance to " CZ  ARG A 259 " =    0.980
peak=   -3.425 closest distance to " O   PRO A 163 " =    1.278
peak=   -3.422 closest distance to " O   VAL A 189 " =    2.667
peak=   -3.421 closest distance to " OD1 ASP A 191 " =    1.734
peak=   -3.418 closest distance to " CB  ALA A   7 " =    2.069
peak=   -3.413 closest distance to " O   HOH Z  11 " =    1.730
peak=   -3.407 closest distance to " O   ILE A 109 " =    2.489
peak=   -3.403 closest distance to " CA  ASN A 127 " =    1.335
peak=   -3.402 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.399 closest distance to " CG  PHE A 283 " =    2.628
peak=   -3.394 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.392 closest distance to " O   HOH Z  38 " =    2.119
peak=   -3.387 closest distance to " O   HOH Z 369 " =    2.169
peak=   -3.385 closest distance to " CG2 VAL A 296 " =    1.997
peak=   -3.383 closest distance to " CG2 THR A 178 " =    2.330
peak=   -3.377 closest distance to " NE2 GLN A 278 " =    1.579
peak=   -3.372 closest distance to " CB  GLN A  55 " =    1.275
peak=   -3.370 closest distance to " O   LYS A  76 " =    1.970
peak=   -3.364 closest distance to " O   HOH Z 137 " =    1.422
peak=   -3.363 closest distance to " CE2 PHE A  61 " =    2.638
peak=   -3.360 closest distance to " O   PHE A 218 " =    1.537
peak=   -3.359 closest distance to " O   ALA A  34 " =    2.309
peak=   -3.356 closest distance to " OE2 GLU A 152 " =    1.283
peak=   -3.356 closest distance to " CE3 TRP A 274 " =    2.306
peak=   -3.355 closest distance to " O   HOH Z  60 " =    1.695
peak=   -3.352 closest distance to " O   SER A  22 " =    2.425
peak=   -3.352 closest distance to " O   HOH Z 281 " =    2.827
peak=   -3.352 closest distance to " N   THR A  52 " =    1.724
peak=   -3.350 closest distance to " CA  GLY A  57 " =    2.133
peak=   -3.349 closest distance to " CA  GLY A 133 " =    1.993
peak=   -3.348 closest distance to " CG2 ILE A 263 " =    2.255
peak=   -3.344 closest distance to " CA  GLY A 241 " =    3.296
peak=   -3.342 closest distance to " NE  ARG A 156 " =    1.927
peak=   -3.341 closest distance to " CB  ALA A 248 " =    2.326
peak=   -3.339 closest distance to " N   ALA A 226 " =    1.877
peak=   -3.335 closest distance to " O   HOH Z 348 " =    2.194
peak=   -3.327 closest distance to " O   HOH Z 166 " =    2.099
peak=   -3.323 closest distance to " O   HOH Z   9 " =    1.639
peak=   -3.317 closest distance to " CB  ASP A 132 " =    2.414
peak=   -3.314 closest distance to " O   SER A   3 " =    0.990
peak=   -3.314 closest distance to " ND2 ASN A 187 " =    1.503
peak=   -3.313 closest distance to " CB  ASP A  27 " =    2.360
peak=   -3.309 closest distance to " O   SER A 135 " =    1.457
peak=   -3.298 closest distance to " CB  ASP A 171 " =    2.393
peak=   -3.294 closest distance to " CD1 ILE A 199 " =    2.405
peak=   -3.290 closest distance to " OG  SER A   3 " =    1.733
peak=   -3.289 closest distance to " O   HOH Z 140 " =    1.396
peak=   -3.288 closest distance to " N   GLN A  58 " =    1.882
peak=   -3.287 closest distance to " CB  ASP A 132 " =    2.247
peak=   -3.287 closest distance to " NZ  LYS A 166 " =    1.249
peak=   -3.286 closest distance to " O   VAL A 174 " =    2.186
peak=   -3.284 closest distance to " O   HOH Z 174 " =    2.521
peak=   -3.284 closest distance to " O   HOH Z 286 " =    1.744
peak=   -3.282 closest distance to " O   ASN A 252 " =    1.309
peak=   -3.277 closest distance to " O   ALA A 180 " =    1.031
peak=   -3.277 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.267 closest distance to " OD1 ASN A 301 " =    1.716
peak=   -3.265 closest distance to " O   GLN A  77 " =    1.783
peak=   -3.260 closest distance to " N   SER A 276 " =    1.311
peak=   -3.259 closest distance to " C   LEU A   5 " =    1.018
peak=   -3.256 closest distance to " O   ALA A 227 " =    1.460
peak=   -3.248 closest distance to " ND2 ASN A  60 " =    4.076
peak=   -3.248 closest distance to " CA  GLY A 203 " =    2.460
peak=   -3.241 closest distance to " N   ALA A 248 " =    1.607
peak=   -3.237 closest distance to " CB  TRP A  85 " =    2.514
peak=   -3.237 closest distance to " CZ2 TRP A 274 " =    0.951
peak=   -3.237 closest distance to " CB  ALA A 244 " =    2.116
peak=   -3.233 closest distance to " O   ARG A  24 " =    1.742
peak=   -3.231 closest distance to " O   HOH Z 389 " =    2.012
peak=   -3.229 closest distance to " NE2 GLN A 194 " =    1.846
peak=   -3.228 closest distance to " O   HOH Z 236 " =    1.687
peak=   -3.218 closest distance to " CG2 THR A  42 " =    1.835
peak=   -3.210 closest distance to " CE3 TRP A 150 " =    2.308
peak=   -3.207 closest distance to " OD2 ASP A  50 " =    1.565
peak=   -3.206 closest distance to " CG  GLN A  88 " =    0.941
peak=   -3.204 closest distance to " O   HOH Z 177 " =    1.632
peak=   -3.204 closest distance to " O   HOH Z 108 " =    1.451
peak=   -3.200 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.200 closest distance to " O   HOH Z 348 " =    1.850
peak=   -3.198 closest distance to " N   THR A 157 " =    1.570
peak=   -3.194 closest distance to " O   GLN A 240 " =    2.066
peak=   -3.194 closest distance to " C   ARG A 195 " =    1.667
peak=   -3.189 closest distance to " CG  ARG A  66 " =    2.389
peak=   -3.185 closest distance to " C   LEU A 143 " =    0.976
peak=   -3.178 closest distance to " O   HOH Z 390 " =    2.398
peak=   -3.178 closest distance to " NH1 ARG A  66 " =    3.533
peak=   -3.177 closest distance to " O   HOH Z 171 " =    1.273
peak=   -3.173 closest distance to " CD  ARG A  79 " =    1.206
peak=   -3.169 closest distance to " O   HOH Z 275 " =    1.405
peak=   -3.168 closest distance to " O   HOH Z 397 " =    1.171
peak=   -3.164 closest distance to " CB  PRO A 163 " =    2.524
peak=   -3.160 closest distance to " CB  ASN A  45 " =    2.046
peak=   -3.158 closest distance to " O   HOH Z 201 " =    2.016
peak=   -3.155 closest distance to " C   ALA A 114 " =    2.261
peak=   -3.150 closest distance to " O   HOH Z 253 " =    3.609
peak=   -3.148 closest distance to " NH1 ARG A 195 " =    2.677
peak=   -3.147 closest distance to " CB  TYR A  15 " =    2.278
peak=   -3.142 closest distance to " CA  TRP A 274 " =    1.285
peak=   -3.139 closest distance to " O   HOH Z 389 " =    1.389
peak=   -3.129 closest distance to " CD  PRO A 213 " =    2.116
peak=   -3.125 closest distance to " CG1 VAL A 250 " =    2.583
peak=   -3.113 closest distance to " O   HOH Z 418 " =    1.572
peak=   -3.109 closest distance to " C   ASN A 285 " =    2.139
peak=   -3.105 closest distance to " O   HOH Z 219 " =    4.576
peak=   -3.092 closest distance to " O   HOH Z 110 " =    1.442
peak=   -3.090 closest distance to " O   VAL A 125 " =    2.197
peak=   -3.089 closest distance to " CG  GLN A 103 " =    2.452
peak=   -3.079 closest distance to " O   HOH Z  60 " =    2.070
peak=   -3.076 closest distance to " CG1 VAL A  78 " =    2.672
peak=   -3.058 closest distance to " O   ALA A  34 " =    1.581
peak=   -3.028 closest distance to " O   SER A 276 " =    1.747
peak=   -3.023 closest distance to " CD  GLN A 183 " =    1.765
peak=   -3.018 closest distance to " CB  ASP A 286 " =    2.162
peak=   -3.002 closest distance to " CB  ASN A  39 " =    2.116

================= 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    :  0.4383 0.4330   6.239993e+00   6.221004e+00
   1_bss:  0.4293 0.4229   6.231167e+00   6.207197e+00
   1_xyz:  0.2571 0.2925   5.825952e+00   5.920390e+00
   1_adp:  0.2326 0.3006   5.775676e+00   5.951644e+00
   1_occ:  0.2324 0.3007   5.775819e+00   5.952541e+00
   2_bss:  0.2290 0.2981   5.769497e+00   5.948829e+00
   2_xyz:  0.1740 0.2305   5.525579e+00   5.727686e+00
   2_adp:  0.1638 0.2160   5.465106e+00   5.662422e+00
   2_occ:  0.1636 0.2157   5.464220e+00   5.661939e+00
   3_bss:  0.1636 0.2155   5.462985e+00   5.660549e+00
   3_xyz:  0.1321 0.1772   5.277082e+00   5.491735e+00
   3_adp:  0.1252 0.1719   5.239380e+00   5.469253e+00
   3_occ:  0.1251 0.1721   5.239323e+00   5.469412e+00
   4_bss:  0.1253 0.1721   5.239442e+00   5.468675e+00
   4_xyz:  0.1186 0.1657   5.194833e+00   5.433387e+00
   4_adp:  0.1190 0.1619   5.189847e+00   5.414213e+00
   4_occ:  0.1189 0.1619   5.189706e+00   5.414385e+00
   5_bss:  0.1189 0.1620   5.189764e+00   5.414928e+00
   5_xyz:  0.1158 0.1590   5.171183e+00   5.403058e+00
   5_adp:  0.1143 0.1595   5.167813e+00   5.408254e+00
   5_occ:  0.1143 0.1596   5.167784e+00   5.408342e+00
   5_bss:  0.1142 0.1595   5.167620e+00   5.408134e+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:  0.316  24.798  -0.553  -0.594   3.364  -0.000   0.000   0.000
   1_xyz:  0.316  24.798  -0.553  -0.594   3.364  -0.000   0.000   0.000
   1_adp:  0.316  24.798  -0.553  -0.594   3.364  -0.000   0.000   0.000
   1_occ:  0.316  24.798  -0.553  -0.594   3.364  -0.000   0.000   0.000
   2_bss:  0.327  50.000  -2.501  -1.938   0.662  -0.000   0.000   0.000
   2_xyz:  0.327  50.000  -2.501  -1.938   0.662  -0.000   0.000   0.000
   2_adp:  0.327  50.000  -2.501  -1.938   0.662  -0.000   0.000   0.000
   2_occ:  0.327  50.000  -2.501  -1.938   0.662  -0.000   0.000   0.000
   3_bss:  0.327  50.000  -2.876  -2.125   0.087  -0.000   0.000   0.000
   3_xyz:  0.327  50.000  -2.876  -2.125   0.087  -0.000   0.000   0.000
   3_adp:  0.327  50.000  -2.876  -2.125   0.087  -0.000   0.000   0.000
   3_occ:  0.327  50.000  -2.876  -2.125   0.087  -0.000   0.000   0.000
   4_bss:  0.325  55.202  -2.876  -2.125   0.087  -0.000   0.000   0.000
   4_xyz:  0.325  55.202  -2.876  -2.125   0.087  -0.000   0.000   0.000
   4_adp:  0.325  55.202  -2.876  -2.125   0.087  -0.000   0.000   0.000
   4_occ:  0.325  55.202  -2.876  -2.125   0.087  -0.000   0.000   0.000
   5_bss:  0.322  48.621  -2.904  -2.223  -0.210  -0.000  -0.000  -0.000
   5_xyz:  0.322  48.621  -2.904  -2.223  -0.210  -0.000  -0.000  -0.000
   5_adp:  0.322  48.621  -2.904  -2.223  -0.210  -0.000  -0.000  -0.000
   5_occ:  0.322  48.621  -2.904  -2.223  -0.210  -0.000  -0.000  -0.000
   5_bss:  0.320  50.446  -2.704  -2.064  -0.104  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.724 0.5378  0.7178    55242.144
   1_bss:  47.225 0.5550  0.7645    51782.551
   1_xyz:  29.043 0.7690  0.9916    21958.911
   1_adp:  30.436 0.7529  0.9759    23713.508
   1_occ:  30.494 0.7522  0.9749    23783.370
   2_bss:  30.161 0.7556  0.9133    23319.651
   2_xyz:  22.215 0.8394  0.9788    13265.075
   2_adp:  20.217 0.8600  0.9873    11656.610
   2_occ:  20.204 0.8601  0.9872    11630.385
   3_bss:  20.145 0.8606  0.9736    11563.678
   3_xyz:  16.454 0.8940  0.9893     8077.649
   3_adp:  15.888 0.8991  0.9823     7656.630
   3_occ:  15.892 0.8991  0.9822     7659.450
   4_bss:  15.862 0.8993  0.9820     7645.294
   4_xyz:  14.941 0.9072  0.9864     6996.792
   4_adp:  14.566 0.9105  0.9838     6809.594
   4_occ:  14.574 0.9104  0.9836     6806.364
   5_bss:  14.580 0.9104  0.9786     6814.149
   5_xyz:  14.341 0.9123  0.9796     6637.522
   5_adp:  14.401 0.9119  0.9732     6665.279
   5_occ:  14.401 0.9119  0.9731     6666.054
   5_bss:  14.396 0.9120  0.9773     6662.151
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9540e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9540e-01
   1_xyz:   1.475  0.011  0.095 15.870  0.007  4.104   1.1586e-01
   1_adp:   1.475  0.011  0.095 15.870  0.007  4.104   1.1586e-01
   1_occ:   1.475  0.011  0.095 15.870  0.007  4.104   1.1586e-01
   2_bss:   1.475  0.011  0.095 15.870  0.007  4.104   1.1586e-01
   2_xyz:   0.986  0.006  0.072 14.705  0.004  4.119   5.5618e-02
   2_adp:   0.986  0.006  0.072 14.705  0.004  4.119   5.5618e-02
   2_occ:   0.986  0.006  0.072 14.705  0.004  4.119   5.5618e-02
   3_bss:   0.986  0.006  0.072 14.705  0.004  4.119   5.5618e-02
   3_xyz:   0.974  0.006  0.070 14.596  0.004  4.126   5.5647e-02
   3_adp:   0.974  0.006  0.070 14.596  0.004  4.126   5.5647e-02
   3_occ:   0.974  0.006  0.070 14.596  0.004  4.126   5.5647e-02
   4_bss:   0.974  0.006  0.070 14.596  0.004  4.126   5.5647e-02
   4_xyz:   0.941  0.006  0.071 14.436  0.004  4.118   5.2679e-02
   4_adp:   0.941  0.006  0.071 14.436  0.004  4.118   5.2679e-02
   4_occ:   0.941  0.006  0.071 14.436  0.004  4.118   5.2679e-02
   5_bss:   0.941  0.006  0.071 14.436  0.004  4.118   5.2679e-02
   5_xyz:   0.944  0.006  0.072 14.335  0.004  4.119   5.2727e-02
   5_adp:   0.944  0.006  0.072 14.335  0.004  4.119   5.2727e-02
   5_occ:   0.944  0.006  0.072 14.335  0.004  4.119   5.2727e-02
   5_bss:   0.944  0.006  0.072 14.335  0.004  4.119   5.2727e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.266   2.4126e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.266   2.4126e-01
   1_xyz:  11.141  0.065  0.354 88.446  0.055  1.991   8.0919e-02
   1_adp:  11.141  0.065  0.354 88.446  0.055  1.991   8.0919e-02
   1_occ:  11.141  0.065  0.354 88.446  0.055  1.991   8.0919e-02
   2_bss:  11.141  0.065  0.354 88.446  0.055  1.991   8.0919e-02
   2_xyz:   5.950  0.053  0.251 82.296  0.041  2.362   4.7856e-02
   2_adp:   5.950  0.053  0.251 82.296  0.041  2.362   4.7856e-02
   2_occ:   5.950  0.053  0.251 82.296  0.041  2.362   4.7856e-02
   3_bss:   5.950  0.053  0.251 82.296  0.041  2.362   4.7856e-02
   3_xyz:   6.554  0.039  0.231 82.611  0.035  2.258   3.7788e-02
   3_adp:   6.554  0.039  0.231 82.611  0.035  2.258   3.7788e-02
   3_occ:   6.554  0.039  0.231 82.611  0.035  2.258   3.7788e-02
   4_bss:   6.554  0.039  0.231 82.611  0.035  2.258   3.7788e-02
   4_xyz:   6.330  0.044  0.228 81.399  0.031  2.320   3.4873e-02
   4_adp:   6.330  0.044  0.228 81.399  0.031  2.320   3.4873e-02
   4_occ:   6.330  0.044  0.228 81.399  0.031  2.320   3.4873e-02
   5_bss:   6.330  0.044  0.228 81.399  0.031  2.320   3.4873e-02
   5_xyz:   6.241  0.037  0.237 83.769  0.035  2.235   3.2889e-02
   5_adp:   6.241  0.037  0.237 83.769  0.035  2.235   3.2889e-02
   5_occ:   6.241  0.037  0.237 83.769  0.035  2.235   3.2889e-02
   5_bss:   6.241  0.037  0.237 83.769  0.035  2.235   3.2889e-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:  89.71   0.00  18.04  78.61   0.00  13.71  89.71   3.90  41.58
   1_occ:  89.71   0.00  18.04  78.61   0.00  13.71  89.71   3.90  41.58
   2_bss:  89.71   0.00  18.04  78.61   0.00  13.71  89.71   3.90  41.58
   2_xyz:  89.71   0.00  18.04  78.61   0.00  13.71  89.71   3.90  41.58
   2_adp:  86.24   0.00  17.49  79.09   0.00  13.19  86.24   5.72  40.92
   2_occ:  86.24   0.00  17.49  79.09   0.00  13.19  86.24   5.72  40.92
   3_bss:  86.24   0.00  17.49  79.09   0.00  13.19  86.24   5.72  40.92
   3_xyz:  86.24   0.00  17.49  79.09   0.00  13.19  86.24   5.72  40.92
   3_adp:  92.94   0.54  17.99  92.94   0.54  13.15  92.80   6.06  44.38
   3_occ:  92.94   0.54  17.99  92.94   0.54  13.15  92.80   6.06  44.38
   4_bss:  92.94   0.54  17.99  92.94   0.54  13.15  92.80   6.06  44.38
   4_xyz:  92.94   0.54  17.99  92.94   0.54  13.15  92.80   6.06  44.38
   4_adp:  90.77   1.78  16.92  90.77   1.78  12.74  83.88   5.97  39.69
   4_occ:  90.77   1.78  16.92  90.77   1.78  12.74  83.88   5.97  39.69
   5_bss:  90.77   1.78  16.92  90.77   1.78  12.74  83.88   5.97  39.69
   5_xyz:  90.77   1.78  16.92  90.77   1.78  12.74  83.88   5.97  39.69
   5_adp:  95.98   1.08  17.04  95.98   1.08  12.67  87.29   5.75  40.83
   5_occ:  95.98   1.08  17.04  95.98   1.08  12.67  87.29   5.75  40.83
   5_bss:  95.94   1.04  17.00  95.94   1.04  12.63  87.25   5.71  40.79
------------------------------------------------------------------------
 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:    2.333    0.016    0.457
   1_adp:    2.333    0.016    0.457
   1_occ:    2.333    0.016    0.457
   2_bss:    2.333    0.016    0.457
   2_xyz:    1.925    0.033    0.521
   2_adp:    1.925    0.033    0.521
   2_occ:    1.925    0.033    0.521
   3_bss:    1.925    0.033    0.521
   3_xyz:    1.783    0.070    0.602
   3_adp:    1.783    0.070    0.602
   3_occ:    1.783    0.070    0.602
   4_bss:    1.783    0.070    0.602
   4_xyz:    1.858    0.080    0.617
   4_adp:    1.858    0.080    0.617
   4_occ:    1.858    0.080    0.617
   5_bss:    1.858    0.080    0.617
   5_xyz:    2.016    0.074    0.633
   5_adp:    2.016    0.074    0.633
   5_occ:    2.016    0.074    0.633
   5_bss:    2.016    0.074    0.633
------------------------------------------------------------------------

CPU time actual refinement: 315.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/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_163/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_163/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.22 
  Macro-tasks:
    bulk solvent and scale       = 42.25  
    individual site refinement   = 122.56 
    weights calculation          = 29.23  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 200.66 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 97.75  
    alpha_beta                      = 8.20   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 105.01 
    fmodel                         = 6.90   
    r_factors                      = 0.26   
    phase_errors                   = 10.95  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 232.14 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.550 micro seconds
Total CPU time: 5.48 minutes
from_scatterers_fft:    622 calls, 97.47 s
gradients_fft:          567 calls, 92.57 s

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

# Date 2008-01-16 Time 04:09:17 PST -0800 (1200485357.39 s)
Start R-work = 0.4383, R-free = 0.4330 (no bulk solvent and anisotropic scale)
Final R-work = 0.1382, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.4293, R-free = 0.4229
Final R-work = 0.1142, R-free = 0.1595