# Date 2008-01-16 Time 06:53:34 PST -0800 (1200495214.67 s)
#phil __OFF__

Command line arguments: "../1323.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15493
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1323

-------------------------------------------------------------------------------
  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: (72.0062, 48.1033, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


================================== 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: (72.0062, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98146
Completeness in resolution range: 0.922443
Completeness with d_max=infinity: 0.919715

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9815

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: (72.0062, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.98146
Completeness in resolution range: 0.922443
Completeness with d_max=infinity: 0.919715

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2410 [2233/2262]  2011   222   9.9%
  bin  2:  4.2410 -  3.3783 [2131/2154]  1917   214  10.0%
  bin  3:  3.3783 -  2.9548 [2111/2136]  1896   215  10.2%
  bin  4:  2.9548 -  2.6863 [2094/2110]  1893   201   9.6%
  bin  5:  2.6863 -  2.4947 [2074/2118]  1864   210  10.1%
  bin  6:  2.4947 -  2.3481 [2077/2105]  1872   205   9.9%
  bin  7:  2.3481 -  2.2309 [2048/2084]  1837   211  10.3%
  bin  8:  2.2309 -  2.1341 [2047/2089]  1842   205  10.0%
  bin  9:  2.1341 -  2.0521 [2048/2093]  1847   201   9.8%
  bin 10:  2.0521 -  1.9815 [ 726/2085]   651    75  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/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:
        1.13 -     1.89: 6
        1.89 -     2.64: 71
        2.64 -     3.39: 4238
        3.39 -     4.15: 9247
        4.15 -     4.90: 14333
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.135 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.399 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.547 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.741 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.800 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27890 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_1323/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 72.00625 48.10325 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4784   r_free= 0.4597   ksol= 0.00   Bsol= 0.00   scale= 0.868    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.289108                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7308 0.99   1450  163 0.3817 0.4112      6.5761      6.5756|
|  2:  4.7308 -  3.7738 0.99   1386  150 0.4259 0.4267      6.8786      6.8673|
|  3:  3.7738 -  3.3023 0.99   1366  154 0.4626 0.4190       6.688      6.6287|
|  4:  3.3023 -  3.0029 0.99   1354  148 0.4773 0.4579       6.521      6.5231|
|  5:  3.0029 -  2.7891 0.98   1339  148 0.5000 0.5055      6.3637      6.3695|
|  6:  2.7891 -  2.6255 0.99   1344  156 0.5161 0.4775      6.2764      6.1946|
|  7:  2.6255 -  2.4947 0.98   1342  143 0.5182 0.4371      6.2418      6.1835|
|  8:  2.4947 -  2.3865 0.99   1324  147 0.5142 0.4889      6.1501      6.1781|
|  9:  2.3865 -  2.2949 0.99   1339  152 0.5364 0.5099      6.1429      6.0882|
| 10:  2.2949 -  2.2160 0.98   1323  149 0.5063 0.4804      6.0663      6.1108|
| 11:  2.2160 -  2.1469 0.97   1301  134 0.5311 0.5236      6.0331      5.9818|
| 12:  2.1469 -  2.0857 0.99   1332  154 0.5183 0.4941      5.9387      5.9814|
| 13:  2.0857 -  2.0309 0.84   1126  130 0.4940 0.4421      5.8546      5.8037|
| 14:  2.0309 -  1.9815 0.22    304   31 0.5419 0.4602      5.8034       5.759|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7308  1450   163  0.68  35.90   0.81     0.72      78285.05|
|  2:  4.7308 -  3.7738  1386   150  0.69  36.17   0.89     0.77     107642.74|
|  3:  3.7738 -  3.3023  1366   154  0.57  46.26   0.87     0.73     118163.80|
|  4:  3.3023 -  3.0029  1354   148  0.48  53.80   0.87     0.65     106889.27|
|  5:  3.0029 -  2.7891  1339   148  0.39  60.23   0.85     0.57      86799.91|
|  6:  2.7891 -  2.6255  1344   156  0.40  60.00   0.87     0.55      68732.51|
|  7:  2.6255 -  2.4947  1342   143  0.41  58.73   0.89     0.56      59418.60|
|  8:  2.4947 -  2.3865  1324   147  0.40  60.11   0.86     0.57      55213.69|
|  9:  2.3865 -  2.2949  1339   152  0.38  61.13   0.91     0.57      51850.60|
| 10:  2.2949 -  2.2160  1323   149  0.40  60.25   0.91     0.58      48148.63|
| 11:  2.2160 -  2.1469  1301   134  0.37  61.95   0.89     0.57      44230.58|
| 12:  2.1469 -  2.0857  1332   154  0.37  62.54   0.90     0.57      40482.46|
| 13:  2.0857 -  2.0309  1126   130  0.38  61.92   0.93     0.57      33529.77|
| 14:  2.0309 -  1.9815   304    31  0.39  60.53   0.90     0.59      26264.71|
|alpha:            min =        0.55 max =            0.77 mean =         0.61|
|beta:             min =    26264.71 max =       118163.80 mean =     69235.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.11|
|phase err.(test): min =        0.00 max =           89.99 mean =        54.91|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.473590             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.820   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.662997              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.433   (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 |  1.135 -  1.511:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.511 -  1.888:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.888 -  2.264:        8 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.264 -  2.641:       63 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.641 -  3.017:     1954 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.017 -  3.394:     2284 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.394 -  3.770:     3908 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.770 -  4.147:     5339 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.147 -  4.523:     6372 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.523 -  4.900:     7961 |
|-----------------------------------------------------------------------------|
|-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 |        0.183 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.135 |       0.443 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    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: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4784   r_free= 0.4597   ksol= 0.00   Bsol= 0.00   scale= 0.868    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.289108                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4712   r_free= 0.4505   ksol= 0.27   Bsol= 20.00   scale= 0.911   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,3.64,-1.59,0.00,-0.00,-0.00); trace/3= 0.95                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.285737                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.934631             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.604   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.331786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.246   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4712      final r-factor (work) = 0.3686          |
| start r-factor (free) = 0.4505      final r-factor (free) = 0.4126          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9487 = 13.93 * 0.50 * 6.2816 + 1.00 * 0.1826                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.1147 = 13.93 * 0.50 * 6.1639 + 1.00 * 0.1686                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3686      final r-factor (work) = 0.3375          |
| start r-factor (free) = 0.4126      final r-factor (free) = 0.4163          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2152 = 1.33 * 1.00 * 6.1639 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1270 = 1.33 * 1.00 * 6.0875 + 1.00 * 0.0197                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.66   18.42    None  None   None       |
|    all(noH): 2823   0      0.00    86.66   18.42    None  None   None       |
|    Sol.    : 438    0      0.00    86.66   36.27    None  None   None       |
|    Mac.    : 2385   0      0.00    76.68   15.14    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 -   8.666:  811   |   5:    43.331 -  51.998:  112        |
|      1:     8.666 -  17.333:  851   |   6:    51.998 -  60.664:   64        |
|      2:    17.333 -  25.999:  491   |   7:    60.664 -  69.330:   23        |
|      3:    25.999 -  34.665:  271   |   8:    69.330 -  77.996:   13        |
|      4:    34.665 -  43.331:  182   |   9:    77.996 -  86.663:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3375 r_free = 0.4163             target_work(ml) = 6.089         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3373 r_free = 0.4162             target_work(ml) = 6.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3373   r_free= 0.4162   ksol= 0.27   Bsol= 20.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,3.64,-1.59,0.00,-0.00,-0.00); trace/3= 0.95                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.088307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3359   r_free= 0.4142   ksol= 0.33   Bsol= 60.94   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.37,2.38,0.05,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.089029                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.571979             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.054  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.418088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3359      final r-factor (work) = 0.2730          |
| start r-factor (free) = 0.4142      final r-factor (free) = 0.3343          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.4920 = 13.57 * 0.50 * 6.0895 + 1.00 * 0.1688                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.9381 = 13.57 * 0.50 * 6.0156 + 1.00 * 0.1165                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2730      final r-factor (work) = 0.2484          |
| start r-factor (free) = 0.3343      final r-factor (free) = 0.3305          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 32.6127 = 5.42 * 1.00 * 6.0156 + 1.00 * 0.0197                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 31.8272 = 5.42 * 1.00 * 5.8688 + 1.00 * 0.0296                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.41  20.75    None  None   None       |
|    all(noH): 2823   0      0.00    112.41  20.75    None  None   None       |
|    Sol.    : 438    0      0.00    112.41  46.98    None  None   None       |
|    Mac.    : 2385   0      0.00    109.26  15.94    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 -  11.241: 1189   |   5:    56.204 -  67.445:   73        |
|      1:    11.241 -  22.482:  753   |   6:    67.445 -  78.686:   68        |
|      2:    22.482 -  33.723:  341   |   7:    78.686 -  89.927:   37        |
|      3:    33.723 -  44.963:  180   |   8:    89.927 - 101.167:   27        |
|      4:    44.963 -  56.204:  142   |   9:   101.167 - 112.408:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2484 r_free = 0.3305             target_work(ml) = 5.864         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2481 r_free = 0.3308             target_work(ml) = 5.863         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2481   r_free= 0.3308   ksol= 0.33   Bsol= 60.94   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.37,2.38,0.05,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.863440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2484   r_free= 0.3306   ksol= 0.33   Bsol= 77.68   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,1.69,0.34,0.00,0.00,0.00); trace/3= 0.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.862250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.805800              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.015  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.337425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.826  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2484      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.3306      final r-factor (free) = 0.2701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8914 = 9.81 * 0.50 * 5.8690 + 1.00 * 0.1165                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.4722 = 9.81 * 0.50 * 5.7879 + 1.00 * 0.0947                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2017      final r-factor (work) = 0.1807          |
| start r-factor (free) = 0.2701      final r-factor (free) = 0.2378          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7704 = 1.34 * 1.00 * 5.7879 + 1.00 * 0.0296                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5419 = 1.34 * 1.00 * 5.6247 + 1.00 * 0.0192                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.91  19.12    None  None   None       |
|    all(noH): 2823   0      0.00    115.91  19.12    None  None   None       |
|    Sol.    : 438    0      3.81    109.83  48.79    None  None   None       |
|    Mac.    : 2385   0      0.00    115.91  13.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.591: 1394   |   5:    57.955 -  69.546:   73        |
|      1:    11.591 -  23.182:  786   |   6:    69.546 -  81.137:   65        |
|      2:    23.182 -  34.773:  199   |   7:    81.137 -  92.728:   34        |
|      3:    34.773 -  46.364:  151   |   8:    92.728 - 104.319:   16        |
|      4:    46.364 -  57.955:   95   |   9:   104.319 - 115.910:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1807 r_free = 0.2378             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1806 r_free = 0.2378             target_work(ml) = 5.564         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1806   r_free= 0.2378   ksol= 0.33   Bsol= 77.68   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.50,1.69,0.34,0.00,0.00,0.00); trace/3= 0.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.563653                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1809   r_free= 0.2378   ksol= 0.34   Bsol= 84.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,0.61,-0.15,0.00,-0.00,-0.00); trace/3= 0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.564864                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.431898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.339898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.763  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1809      final r-factor (work) = 0.1532          |
| start r-factor (free) = 0.2378      final r-factor (free) = 0.2056          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5654 = 4.43 * 0.50 * 5.6277 + 1.00 * 0.0947                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2678 = 4.43 * 0.50 * 5.5007 + 1.00 * 0.0785                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1532      final r-factor (work) = 0.1443          |
| start r-factor (free) = 0.2056      final r-factor (free) = 0.1927          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8889 = 0.34 * 1.00 * 5.5007 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8510 = 0.34 * 1.00 * 5.4029 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.94  17.54    None  None   None       |
|    all(noH): 2823   0      0.00    115.94  17.54    None  None   None       |
|    Sol.    : 438    0      4.52    105.47  45.27    None  None   None       |
|    Mac.    : 2385   0      0.00    115.94  12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.594: 1518   |   5:    57.968 -  69.561:   88        |
|      1:    11.594 -  23.187:  753   |   6:    69.561 -  81.155:   34        |
|      2:    23.187 -  34.781:  176   |   7:    81.155 -  92.748:   23        |
|      3:    34.781 -  46.374:  121   |   8:    92.748 - 104.342:    7        |
|      4:    46.374 -  57.968:   98   |   9:   104.342 - 115.935:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1443 r_free = 0.1927             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1441 r_free = 0.1925             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1441   r_free= 0.1925   ksol= 0.34   Bsol= 84.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,0.61,-0.15,0.00,-0.00,-0.00); trace/3= 0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.365360                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1928   ksol= 0.33   Bsol= 77.95   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.06,-0.36,-0.00,-0.00,-0.00); trace/3= -0.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.367558                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.533645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.961  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.345212              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.098   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1444      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.1928      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6275 = 3.53 * 0.50 * 5.4046 + 1.00 * 0.0785                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4893 = 3.53 * 0.50 * 5.3249 + 1.00 * 0.0811                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8515 = 0.35 * 1.00 * 5.3249 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8309 = 0.35 * 1.00 * 5.2706 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    116.14  16.89    None  None   None       |
|    all(noH): 2823   0      0.52    116.14  16.89    None  None   None       |
|    Sol.    : 438    0      4.29    108.73  43.39    None  None   None       |
|    Mac.    : 2385   0      0.52    116.14  12.02    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:     0.516 -  12.078: 1642   |   5:    58.327 -  69.889:   72        |
|      1:    12.078 -  23.640:  669   |   6:    69.889 -  81.452:   33        |
|      2:    23.640 -  35.202:  162   |   7:    81.452 -  93.014:   15        |
|      3:    35.202 -  46.765:  114   |   8:    93.014 - 104.576:    3        |
|      4:    46.765 -  58.327:  108   |   9:   104.576 - 116.138:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1272 r_free = 0.1748             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1271 r_free = 0.1749             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1271   r_free= 0.1749   ksol= 0.33   Bsol= 77.95   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-0.06,-0.36,-0.00,-0.00,-0.00); trace/3= -0.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.261823                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7308 0.99   1450  163 0.1020 0.1313      5.4144      5.5784|
|  2:  4.7308 -  3.7738 0.99   1386  150 0.0872 0.1119      5.4532      5.6714|
|  3:  3.7738 -  3.3023 0.99   1366  154 0.1142 0.1719      5.5241       5.895|
|  4:  3.3023 -  3.0029 0.99   1354  148 0.1457 0.1759      5.5791      5.7187|
|  5:  3.0029 -  2.7891 0.98   1339  148 0.1597 0.2097      5.4808      5.6723|
|  6:  2.7891 -  2.6255 0.99   1344  156 0.1515 0.2098      5.3612      5.5586|
|  7:  2.6255 -  2.4947 0.98   1342  143 0.1439 0.2012      5.2878      5.5298|
|  8:  2.4947 -  2.3865 0.99   1324  147 0.1408 0.1866      5.1814      5.3758|
|  9:  2.3865 -  2.2949 0.99   1339  152 0.1382 0.2047       5.144      5.3833|
| 10:  2.2949 -  2.2160 0.98   1323  149 0.1282 0.1830      5.0798      5.3348|
| 11:  2.2160 -  2.1469 0.97   1301  134 0.1291 0.2124      5.0433       5.357|
| 12:  2.1469 -  2.0857 0.99   1332  154 0.1297 0.1869      4.9783      5.1943|
| 13:  2.0857 -  2.0309 0.84   1126  130 0.1322 0.1984      4.8918      5.1184|
| 14:  2.0309 -  1.9815 0.22    304   31 0.1251 0.1691      4.7606      4.9955|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7308  1450   163  0.93   9.74   0.96     0.94       7895.95|
|  2:  4.7308 -  3.7738  1386   150  0.95   8.42   1.00     0.98       9407.96|
|  3:  3.7738 -  3.3023  1366   154  0.92  12.70   1.02     1.01      11638.64|
|  4:  3.3023 -  3.0029  1354   148  0.90  16.64   1.01     0.98      13306.39|
|  5:  3.0029 -  2.7891  1339   148  0.86  19.99   1.00     0.97      11646.10|
|  6:  2.7891 -  2.6255  1344   156  0.88  18.83   0.99     0.96       9289.07|
|  7:  2.6255 -  2.4947  1342   143  0.88  18.01   0.98     0.94       7932.89|
|  8:  2.4947 -  2.3865  1324   147  0.88  18.29   1.00     0.96       6681.22|
|  9:  2.3865 -  2.2949  1339   152  0.88  18.41   1.00     0.94       6080.46|
| 10:  2.2949 -  2.2160  1323   149  0.89  17.44   0.99     0.95       5635.01|
| 11:  2.2160 -  2.1469  1301   134  0.88  19.02   0.99     0.94       5540.02|
| 12:  2.1469 -  2.0857  1332   154  0.88  18.73   0.99     0.97       5032.36|
| 13:  2.0857 -  2.0309  1126   130  0.88  18.53   0.98     0.97       4133.79|
| 14:  2.0309 -  1.9815   304    31  0.87  19.17   0.98     0.94       3271.99|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3271.99 max =        13306.39 mean =      8005.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.46|
|phase err.(test): min =        0.00 max =           89.61 mean =        15.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1748   ksol= 0.33   Bsol= 70.65   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,-0.26,-0.32,-0.00,-0.00,-0.00); trace/3= -0.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.261512                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1748   ksol= 0.33   Bsol= 70.65   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,-0.26,-0.32,-0.00,-0.00,-0.00); trace/3= -0.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.261512                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.7308 0.99   1450  163 0.1018 0.1306      5.4118      5.5742|
|  2:  4.7308 -  3.7738 0.99   1386  150 0.0869 0.1112      5.4499      5.6654|
|  3:  3.7738 -  3.3023 0.99   1366  154 0.1141 0.1718      5.5224      5.8961|
|  4:  3.3023 -  3.0029 0.99   1354  148 0.1457 0.1758      5.5796      5.7186|
|  5:  3.0029 -  2.7891 0.98   1339  148 0.1599 0.2100      5.4816      5.6732|
|  6:  2.7891 -  2.6255 0.99   1344  156 0.1516 0.2096      5.3619      5.5587|
|  7:  2.6255 -  2.4947 0.98   1342  143 0.1439 0.2013      5.2883      5.5297|
|  8:  2.4947 -  2.3865 0.99   1324  147 0.1407 0.1867       5.182      5.3763|
|  9:  2.3865 -  2.2949 0.99   1339  152 0.1381 0.2048      5.1439      5.3838|
| 10:  2.2949 -  2.2160 0.98   1323  149 0.1282 0.1833      5.0802      5.3358|
| 11:  2.2160 -  2.1469 0.97   1301  134 0.1291 0.2123      5.0432      5.3567|
| 12:  2.1469 -  2.0857 0.99   1332  154 0.1298 0.1874      4.9793      5.1961|
| 13:  2.0857 -  2.0309 0.84   1126  130 0.1322 0.1985      4.8918      5.1177|
| 14:  2.0309 -  1.9815 0.22    304   31 0.1252 0.1686      4.7602      4.9916|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2215 -  4.7308  1450   163  0.93   9.70   0.96     0.94       7847.74|
|  2:  4.7308 -  3.7738  1386   150  0.95   8.37   1.00     0.98       9329.28|
|  3:  3.7738 -  3.3023  1366   154  0.92  12.63   1.02     1.01      11554.78|
|  4:  3.3023 -  3.0029  1354   148  0.90  16.64   1.00     0.98      13305.44|
|  5:  3.0029 -  2.7891  1339   148  0.86  19.98   1.00     0.97      11646.69|
|  6:  2.7891 -  2.6255  1344   156  0.88  18.83   0.99     0.96       9298.31|
|  7:  2.6255 -  2.4947  1342   143  0.88  18.02   0.98     0.94       7938.92|
|  8:  2.4947 -  2.3865  1324   147  0.88  18.30   0.99     0.95       6693.12|
|  9:  2.3865 -  2.2949  1339   152  0.88  18.41   0.99     0.94       6088.67|
| 10:  2.2949 -  2.2160  1323   149  0.89  17.45   0.99     0.94       5643.45|
| 11:  2.2160 -  2.1469  1301   134  0.88  19.02   0.98     0.93       5541.30|
| 12:  2.1469 -  2.0857  1332   154  0.88  18.74   0.98     0.97       5042.10|
| 13:  2.0857 -  2.0309  1126   130  0.88  18.52   0.98     0.97       4131.62|
| 14:  2.0309 -  1.9815   304    31  0.87  19.15   0.97     0.94       3260.85|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3260.85 max =        13305.44 mean =      7992.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.45|
|phase err.(test): min =        0.00 max =           89.49 mean =        15.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.333)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    116.12  16.87    None  None   None       |
|    all(noH): 2823   0      0.50    116.12  16.87    None  None   None       |
|    Sol.    : 438    0      4.27    108.72  43.38    None  None   None       |
|    Mac.    : 2385   0      0.50    116.12  12.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.499 -  12.062: 1642   |   5:    58.311 -  69.873:   72        |
|      1:    12.062 -  23.624:  669   |   6:    69.873 -  81.435:   33        |
|      2:    23.624 -  35.186:  162   |   7:    81.435 -  92.998:   15        |
|      3:    35.186 -  46.748:  114   |   8:    92.998 - 104.560:    3        |
|      4:    46.748 -  58.311:  108   |   9:   104.560 - 116.122:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.391 - 5.877
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 343
   mapped sites are within: 0.740 - 5.877

peak=    8.852 closest distance to " O   HOH Z  41 " =    1.625
peak=    6.735 closest distance to " O   HOH Z 400 " =    1.165
peak=    5.669 closest distance to " CB  SER A  63 " =    1.354
peak=    5.504 closest distance to " CB  GLN A 223 " =    1.468
peak=    5.126 closest distance to " O   HOH Z 210 " =    1.379
peak=    5.097 closest distance to " O   HOH Z 126 " =    1.892
peak=    5.030 closest distance to " O   HOH Z 111 " =    1.798
peak=    4.994 closest distance to " CG  PRO A 213 " =    1.286
peak=    4.936 closest distance to " O   HOH Z  15 " =    2.219
peak=    4.936 closest distance to " O   HOH Z 433 " =    2.094
peak=    4.927 closest distance to " O   PRO A 198 " =    1.569
peak=    4.743 closest distance to " CA  TYR A  30 " =    1.029
peak=    4.701 closest distance to " CG  PRO A 280 " =    0.906
peak=    4.697 closest distance to " CG  PRO A  54 " =    1.203
peak=    4.687 closest distance to " CG  PRO A  90 " =    1.240
peak=    4.680 closest distance to " OE1 GLN A  88 " =    0.934
peak=    4.581 closest distance to " O  BHOH Z 338 " =    1.110
peak=    4.551 closest distance to " CG1 ILE A  33 " =    1.280
peak=    4.527 closest distance to " O   HOH Z 132 " =    2.030
peak=    4.478 closest distance to " CB  GLU A 152 " =    1.180
peak=    4.459 closest distance to " O   HOH Z 418 " =    1.906
peak=    4.438 closest distance to " O   HOH Z  68 " =    1.974
peak=    4.430 closest distance to " O   HOH Z 232 " =    2.188
peak=    4.392 closest distance to " CG  PRO A 198 " =    1.286
peak=    4.388 closest distance to " O   HOH Z 134 " =    1.936
peak=    4.372 closest distance to " CG2 THR A 221 " =    1.065
peak=    4.365 closest distance to " CB  VAL A 202 " =    1.504
peak=    4.357 closest distance to " CB  TRP A 179 " =    1.513
peak=    4.354 closest distance to " O   HOH Z 271 " =    2.512
peak=    4.335 closest distance to " O   HOH Z 404 " =    1.589
peak=    4.309 closest distance to " O   HOH Z 394 " =    1.723
peak=    4.294 closest distance to " O   HOH Z  47 " =    1.712
peak=    4.279 closest distance to " O   HOH Z  80 " =    2.218
peak=    4.264 closest distance to " O   HOH Z 132 " =    1.305
peak=    4.252 closest distance to " O   HOH Z   7 " =    1.273
peak=    4.215 closest distance to " O   HOH Z  97 " =    1.981
peak=    4.210 closest distance to " O   HOH Z  54 " =    1.288
peak=    4.178 closest distance to " CB  SER A 141 " =    0.985
peak=    4.177 closest distance to " O   HOH Z 406 " =    1.580
peak=    4.164 closest distance to " O   HOH Z 374 " =    2.704
peak=    4.139 closest distance to " O   HOH Z 411 " =    2.991
peak=    4.129 closest distance to " CB  PRO A  54 " =    0.751
peak=    4.119 closest distance to " CD2 LEU A 297 " =    1.063
peak=    4.106 closest distance to " O   HOH Z  20 " =    2.231
peak=    4.103 closest distance to " CB  ASN A 148 " =    1.279
peak=    4.082 closest distance to " O   HOH Z 425 " =    1.741
peak=    4.062 closest distance to " O   HOH Z 214 " =    1.492
peak=    4.061 closest distance to " O   HOH Z  40 " =    2.063
peak=    4.056 closest distance to " CB  GLU A 128 " =    1.161
peak=    4.055 closest distance to " O   HOH Z 234 " =    3.726
peak=    4.053 closest distance to " CB  LEU A 228 " =    1.124
peak=    4.048 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.044 closest distance to " NZ  LYS A 117 " =    3.211
peak=    4.040 closest distance to " O   HOH Z 196 " =    2.391
peak=    4.026 closest distance to " O   HOH Z  61 " =    1.672
peak=    4.018 closest distance to " O   HOH Z  78 " =    1.983
peak=    4.014 closest distance to " O   HOH Z  78 " =    1.285
peak=    4.012 closest distance to " CG2BVAL A  41 " =    0.995
peak=    4.007 closest distance to " CD1 LEU A 300 " =    1.285
peak=    4.005 closest distance to " CA  GLY A 196 " =    1.016
peak=    3.999 closest distance to " CE  LYS A 119 " =    1.100
peak=    3.987 closest distance to " O   HOH Z 174 " =    1.498
peak=    3.951 closest distance to " OE1 GLN A  11 " =    2.014
peak=    3.948 closest distance to " CA  ALA A 160 " =    1.011
peak=    3.944 closest distance to " O   HOH Z 209 " =    2.476
peak=    3.941 closest distance to " O   HOH Z 432 " =    2.131
peak=    3.932 closest distance to " CB  GLN A 183 " =    1.248
peak=    3.924 closest distance to " O   HOH Z 247 " =    1.446
peak=    3.917 closest distance to " CD  ARG A  66 " =    2.782
peak=    3.908 closest distance to " O   HOH Z 163 " =    1.900
peak=    3.899 closest distance to " CG2 VAL A 197 " =    1.315
peak=    3.879 closest distance to " O   HOH Z 301 " =    1.463
peak=    3.878 closest distance to " NH2AARG A 102 " =    1.059
peak=    3.875 closest distance to " CD  ARG A 269 " =    0.823
peak=    3.873 closest distance to " O   HOH Z 402 " =    1.697
peak=    3.861 closest distance to " CB  ARG A 190 " =    1.638
peak=    3.859 closest distance to " O   HOH Z 120 " =    1.074
peak=    3.853 closest distance to " ND1 HIS A  81 " =    1.418
peak=    3.845 closest distance to " O   HOH Z  57 " =    2.257
peak=    3.845 closest distance to " O   HOH Z 369 " =    2.101
peak=    3.843 closest distance to " O   HOH Z 118 " =    2.029
peak=    3.841 closest distance to " CG AARG A 275 " =    1.164
peak=    3.840 closest distance to " CB  ALA A 100 " =    1.585
peak=    3.824 closest distance to " CG2 VAL A  78 " =    1.003
peak=    3.818 closest distance to " O   HOH Z 112 " =    1.543
peak=    3.818 closest distance to " O   HOH Z  83 " =    1.234
peak=    3.808 closest distance to " CB  ASP A 140 " =    0.837
peak=    3.781 closest distance to " O   HOH Z 316 " =    3.158
peak=    3.779 closest distance to " CD  ARG A 159 " =    0.840
peak=    3.772 closest distance to " O   HOH Z 431 " =    1.284
peak=    3.767 closest distance to " O   HOH Z  43 " =    2.221
peak=    3.762 closest distance to " NE2 HIS A 115 " =    1.096
peak=    3.760 closest distance to " O   HOH Z   4 " =    1.135
peak=    3.759 closest distance to " CG  PRO A 243 " =    1.090
peak=    3.740 closest distance to " CA  ASP A 191 " =    0.853
peak=    3.733 closest distance to " CA  GLU A 152 " =    0.944
peak=    3.724 closest distance to " CA  ILE A 106 " =    0.804
peak=    3.723 closest distance to " NH2 ARG A 156 " =    1.210
peak=    3.716 closest distance to " O   GLY A  91 " =    1.163
peak=    3.711 closest distance to " CB  ASP A 124 " =    0.905
peak=    3.709 closest distance to " O   HOH Z 265 " =    1.874
peak=    3.709 closest distance to " N   ASN A  39 " =    1.240
peak=    3.706 closest distance to " O   HOH Z 102 " =    1.356
peak=    3.702 closest distance to " CB  ASN A 187 " =    1.142
peak=    3.700 closest distance to " O   HOH Z 119 " =    2.294
peak=    3.697 closest distance to " OG  SER A  97 " =    3.497
peak=    3.695 closest distance to " C   VAL A 265 " =    1.215
peak=    3.693 closest distance to " O   HOH Z  39 " =    1.396
peak=    3.692 closest distance to " CB  ARG A  79 " =    1.474
peak=    3.685 closest distance to " O   HOH Z 104 " =    2.914
peak=    3.680 closest distance to " O   HOH Z 192 " =    1.659
peak=    3.680 closest distance to " O   HOH Z 420 " =    2.085
peak=    3.675 closest distance to " O   HOH Z 389 " =    1.857
peak=    3.675 closest distance to " O   HOH Z 357 " =    2.107
peak=    3.675 closest distance to " CA  GLN A 223 " =    1.006
peak=    3.666 closest distance to " O   HOH Z 372 " =    1.167
peak=    3.663 closest distance to " O   HOH Z  35 " =    1.866
peak=    3.656 closest distance to " O   HOH Z 128 " =    2.250
peak=    3.655 closest distance to " CB  PRO A 198 " =    0.975
peak=    3.654 closest distance to " O   HOH Z 134 " =    2.323
peak=    3.649 closest distance to " CA  THR A 221 " =    1.519
peak=    3.643 closest distance to " OD1 ASN A 217 " =    1.771
peak=    3.641 closest distance to " O   HOH Z 172 " =    5.877
peak=    3.634 closest distance to " CZ  PHE A 218 " =    1.196
peak=    3.632 closest distance to " O   ALA A 165 " =    1.301
peak=    3.628 closest distance to " O   HOH Z 245 " =    1.360
peak=    3.627 closest distance to " CG1 VAL A 153 " =    1.080
peak=    3.627 closest distance to " CA  PRO A  54 " =    1.198
peak=    3.623 closest distance to " O   HOH Z 437 " =    1.895
peak=    3.612 closest distance to " CD BLYS A 290 " =    1.035
peak=    3.609 closest distance to " O   HOH Z 215 " =    1.573
peak=    3.608 closest distance to " O   HOH Z 207 " =    2.505
peak=    3.594 closest distance to " O   HOH Z  22 " =    2.416
peak=    3.593 closest distance to " CB  GLN A  88 " =    1.108
peak=    3.593 closest distance to " CD2 TRP A 179 " =    1.358
peak=    3.591 closest distance to " O   HOH Z  49 " =    0.807
peak=    3.586 closest distance to " O   HOH Z 298 " =    1.984
peak=    3.580 closest distance to " O   HOH Z 145 " =    2.041
peak=    3.579 closest distance to " CD2 LEU A 255 " =    1.423
peak=    3.578 closest distance to " CB  TYR A 116 " =    1.480
peak=    3.573 closest distance to " CB  SER A 216 " =    0.936
peak=    3.569 closest distance to " O   HOH Z 352 " =    1.909
peak=    3.568 closest distance to " O   HOH Z 292 " =    1.529
peak=    3.561 closest distance to " CD  ARG A 195 " =    1.044
peak=    3.556 closest distance to " O   HOH Z 214 " =    2.219
peak=    3.551 closest distance to " O   SER A 276 " =    1.215
peak=    3.549 closest distance to " CZ3 TRP A  85 " =    0.940
peak=    3.549 closest distance to " CA  ALA A  51 " =    1.047
peak=    3.545 closest distance to " CA  GLU A  46 " =    0.853
peak=    3.541 closest distance to " O   HOH Z  54 " =    1.569
peak=    3.541 closest distance to " O   THR A 251 " =    1.321
peak=    3.538 closest distance to " CB  TRP A 266 " =    1.018
peak=    3.537 closest distance to " O   HOH Z 377 " =    1.459
peak=    3.536 closest distance to " O   HOH Z 193 " =    2.357
peak=    3.536 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.532 closest distance to " O   HOH Z  91 " =    2.456
peak=    3.530 closest distance to " O   HOH Z  49 " =    2.203
peak=    3.528 closest distance to " O   HOH Z 182 " =    1.160
peak=    3.526 closest distance to " O   HOH Z 150 " =    1.817
peak=    3.524 closest distance to " CB  TRP A 150 " =    1.029
peak=    3.522 closest distance to " O   ARG A 275 " =    0.776
peak=    3.521 closest distance to " N   HIS A 108 " =    1.878
peak=    3.513 closest distance to " CD1 LEU A 222 " =    0.829
peak=    3.510 closest distance to " O   HOH Z 189 " =    2.468
peak=    3.510 closest distance to " ND2 ASN A 110 " =    1.567
peak=    3.506 closest distance to " O   HOH Z 130 " =    1.222
peak=    3.506 closest distance to " O   HOH Z 272 " =    1.930
peak=    3.489 closest distance to " CB  MET A 105 " =    1.174
peak=    3.486 closest distance to " O   HOH Z  24 " =    2.236
peak=    3.484 closest distance to " O   HOH Z   1 " =    3.084
peak=    3.479 closest distance to " CB  GLU A 277 " =    3.884
peak=    3.477 closest distance to " O   HOH Z 287 " =    2.074
peak=    3.475 closest distance to " O   HOH Z 155 " =    3.159
peak=    3.475 closest distance to " CA  LYS A  48 " =    1.390
peak=    3.473 closest distance to " O   HOH Z  20 " =    1.940
peak=    3.470 closest distance to " CA  ASP A 149 " =    1.436
peak=    3.470 closest distance to " CA  ARG A 156 " =    0.964
peak=    3.469 closest distance to " O   HOH Z 313 " =    2.114
peak=    3.463 closest distance to " CB  GLN A 194 " =    0.930
peak=    3.462 closest distance to " O   HOH Z 243 " =    1.077
peak=    3.462 closest distance to " CB  ILE A 120 " =    1.307
peak=    3.457 closest distance to " CA  TRP A 274 " =    0.986
peak=    3.452 closest distance to " CA  ASP A 124 " =    0.827
peak=    3.451 closest distance to " CD  LYS A 166 " =    1.418
peak=    3.450 closest distance to " O   HOH Z  88 " =    1.674
peak=    3.450 closest distance to " O   HOH Z 139 " =    3.236
peak=    3.450 closest distance to " O   HOH Z 344 " =    3.148
peak=    3.449 closest distance to " O   HOH Z 126 " =    1.838
peak=    3.448 closest distance to " CB  SER A 276 " =    1.318
peak=    3.447 closest distance to " O   HOH Z 132 " =    2.362
peak=    3.443 closest distance to " O   HOH Z 142 " =    1.533
peak=    3.440 closest distance to " CB  TYR A 169 " =    0.839
peak=    3.437 closest distance to " O   HOH Z  21 " =    1.787
peak=    3.435 closest distance to " O   HOH Z 184 " =    1.684
peak=    3.430 closest distance to " CG2 THR A  42 " =    0.946
peak=    3.415 closest distance to " O   HOH Z 260 " =    1.312
peak=    3.414 closest distance to " CD1 TRP A 266 " =    1.007
peak=    3.410 closest distance to " O   HOH Z 175 " =    3.853
peak=    3.408 closest distance to " O   HOH Z 327 " =    2.436
peak=    3.399 closest distance to " CA  ALA A 299 " =    1.086
peak=    3.398 closest distance to " O   HOH Z  19 " =    2.260
peak=    3.396 closest distance to " O   HOH Z 418 " =    5.737
peak=    3.395 closest distance to " O   HOH Z 255 " =    1.652
peak=    3.392 closest distance to " O   HOH Z 387 " =    2.518
peak=    3.391 closest distance to " CB  ARG A 259 " =    1.838
peak=    3.390 closest distance to " CB  ALA A 154 " =    1.150
peak=    3.387 closest distance to " CA  VAL A  41 " =    0.785
peak=    3.387 closest distance to " CB  LEU A  83 " =    0.836
peak=    3.387 closest distance to " O   HOH Z 423 " =    3.125
peak=    3.386 closest distance to " O   HOH Z 154 " =    1.313
peak=    3.382 closest distance to " CB  SER A   3 " =    1.534
peak=    3.377 closest distance to " CA  ASN A 127 " =    1.017
peak=    3.376 closest distance to " O   HOH Z 279 " =    2.431
peak=    3.374 closest distance to " CB  ASN A 148 " =    1.752
peak=    3.370 closest distance to " CB  SER A  62 " =    0.818
peak=    3.369 closest distance to " O   HOH Z 417 " =    3.207
peak=    3.368 closest distance to " O   HOH Z 174 " =    1.742
peak=    3.360 closest distance to " O   HOH Z  47 " =    1.855
peak=    3.359 closest distance to " O   HOH Z 180 " =    2.156
peak=    3.357 closest distance to " O   HOH Z 343 " =    2.260
peak=    3.357 closest distance to " O   HOH Z 131 " =    2.537
peak=    3.353 closest distance to " O   HOH Z 162 " =    1.969
peak=    3.353 closest distance to " CB  MET A  40 " =    0.822
peak=    3.352 closest distance to " CA  VAL A 125 " =    1.014
peak=    3.351 closest distance to " OG  SER A  62 " =    3.323
peak=    3.351 closest distance to " CA  LEU A  83 " =    1.533
peak=    3.345 closest distance to " CA  ARG A 195 " =    1.129
peak=    3.343 closest distance to " CG2 THR A 220 " =    0.740
peak=    3.342 closest distance to " O   HOH Z 303 " =    2.372
peak=    3.341 closest distance to " O   HOH Z 162 " =    2.308
peak=    3.336 closest distance to " CA  SER A  32 " =    1.646
peak=    3.336 closest distance to " CA  ILE A  33 " =    1.592
peak=    3.336 closest distance to " O   HOH Z  66 " =    2.181
peak=    3.329 closest distance to " O   HOH Z 298 " =    2.354
peak=    3.325 closest distance to " O   ASN A  74 " =    1.518
peak=    3.323 closest distance to " OD1 ASN A  69 " =    2.409
peak=    3.322 closest distance to " O   HOH Z 281 " =    4.055
peak=    3.322 closest distance to " CA  THR A 294 " =    1.733
peak=    3.318 closest distance to " CB  ALA A 256 " =    1.326
peak=    3.316 closest distance to " CB  GLU A 175 " =    1.441
peak=    3.308 closest distance to " CD2 PHE A  59 " =    1.840
peak=    3.303 closest distance to " CG  ARG A 219 " =    1.272
peak=    3.300 closest distance to " CD  LYS A 119 " =    1.366
peak=    3.298 closest distance to " O   HOH Z 413 " =    1.912
peak=    3.298 closest distance to " O   HOH Z 217 " =    2.363
peak=    3.296 closest distance to " O   HOH Z  95 " =    1.769
peak=    3.294 closest distance to " CG2 ILE A  20 " =    1.244
peak=    3.291 closest distance to " O   HOH Z 156 " =    2.667
peak=    3.289 closest distance to " O   HOH Z 298 " =    4.411
peak=    3.284 closest distance to " CG  GLN A  77 " =    0.761
peak=    3.283 closest distance to " O   HOH Z 426 " =    1.495
peak=    3.283 closest distance to " CG  LEU A 167 " =    1.082
peak=    3.283 closest distance to " O   HOH Z  42 " =    1.354
peak=    3.281 closest distance to " CZ  PHE A 192 " =    0.974
peak=    3.278 closest distance to " O   HOH Z 240 " =    2.050
peak=    3.276 closest distance to " O   HOH Z 108 " =    1.162
peak=    3.275 closest distance to " N   PHE A 130 " =    1.236
peak=    3.275 closest distance to " CD1 ILE A 106 " =    1.014
peak=    3.275 closest distance to " O   HOH Z 380 " =    1.828
peak=    3.272 closest distance to " CA  ALA A 100 " =    1.156
peak=    3.263 closest distance to " O   HOH Z 133 " =    1.447
peak=    3.262 closest distance to " N   TYR A  15 " =    0.848
peak=    3.261 closest distance to " CD  ARG A  56 " =    1.196
peak=    3.259 closest distance to " O   HOH Z 362 " =    3.221
peak=    3.259 closest distance to " CB  GLU A 277 " =    1.025
peak=    3.259 closest distance to " O   HOH Z 324 " =    1.465
peak=    3.258 closest distance to " CA  ARG A 139 " =    1.525
peak=    3.252 closest distance to " O   HOH Z 327 " =    1.688
peak=    3.247 closest distance to " OE1 GLN A  58 " =    0.984
peak=    3.245 closest distance to " O   HOH Z  63 " =    1.453
peak=    3.243 closest distance to " CG BARG A 275 " =    1.503
peak=    3.242 closest distance to " OD2 ASP A 286 " =    3.008
peak=    3.241 closest distance to " O   HOH Z 116 " =    1.762
peak=    3.239 closest distance to " O   HOH Z 234 " =    1.794
peak=    3.237 closest distance to " CA  MET A  40 " =    1.157
peak=    3.236 closest distance to " O   HOH Z  32 " =    1.924
peak=    3.236 closest distance to " CG2AVAL A 121 " =    2.123
peak=    3.235 closest distance to " OH  TYR A 169 " =    0.914
peak=    3.235 closest distance to " ND2 ASN A  69 " =    1.470
peak=    3.234 closest distance to " O   HOH Z 383 " =    1.968
peak=    3.234 closest distance to " CA  ALA A  21 " =    1.506
peak=    3.227 closest distance to " CG2 THR A  29 " =    1.458
peak=    3.224 closest distance to " CB  ALA A  51 " =    0.812
peak=    3.223 closest distance to " O   HOH Z 132 " =    2.636
peak=    3.222 closest distance to " CA  GLN A  88 " =    1.469
peak=    3.217 closest distance to " N   SER A 164 " =    1.086
peak=    3.216 closest distance to " CA  GLY A 267 " =    1.059
peak=    3.215 closest distance to " CB  ALA A 248 " =    1.095
peak=    3.211 closest distance to " CB  VAL A 265 " =    1.325
peak=    3.210 closest distance to " CA  ASP A 132 " =    1.234
peak=    3.210 closest distance to " CB  TYR A 247 " =    1.022
peak=    3.207 closest distance to " CE3 TRP A  85 " =    1.230
peak=    3.205 closest distance to " CA  ASP A 162 " =    1.205
peak=    3.205 closest distance to " NH2BARG A 145 " =    1.162
peak=    3.203 closest distance to " CB  VAL A 296 " =    1.454
peak=    3.202 closest distance to " NH1AARG A 145 " =    1.056
peak=    3.202 closest distance to " N   ILE A  33 " =    1.096
peak=    3.202 closest distance to " CB  SER A 212 " =    1.232
peak=    3.198 closest distance to " O   HOH Z 139 " =    4.805
peak=    3.197 closest distance to " CB  ALA A 242 " =    0.968
peak=    3.193 closest distance to " O   HOH Z 147 " =    1.665
peak=    3.193 closest distance to " CA  GLN A 103 " =    1.354
peak=    3.189 closest distance to " CD  PRO A  54 " =    1.013
peak=    3.187 closest distance to " CB  PHE A 283 " =    0.875
peak=    3.186 closest distance to " CB  ASN A  39 " =    0.831
peak=    3.186 closest distance to " O   HOH Z 217 " =    1.244
peak=    3.181 closest distance to " CB  ALA A  43 " =    0.886
peak=    3.180 closest distance to " O   HOH Z 415 " =    1.139
peak=    3.173 closest distance to " CB  GLN A 103 " =    0.954
peak=    3.169 closest distance to " CG  GLU A  37 " =    1.027
peak=    3.164 closest distance to " OE2 GLU A   2 " =    1.718
peak=    3.159 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.157 closest distance to " CB  PHE A  61 " =    0.776
peak=    3.157 closest distance to " CA  ALA A 295 " =    1.012
peak=    3.154 closest distance to " NH1BARG A 145 " =    1.231
peak=    3.141 closest distance to " CD  ARG A 195 " =    3.527
peak=    3.140 closest distance to " CB  PHE A  16 " =    1.359
peak=    3.135 closest distance to " O   HOH Z 275 " =    1.498
peak=    3.134 closest distance to " CZ3 TRP A 274 " =    4.656
peak=    3.130 closest distance to " O   HOH Z 435 " =    1.795
peak=    3.126 closest distance to " O   HOH Z 358 " =    1.442
peak=    3.114 closest distance to " CA  LYS A 117 " =    1.232
peak=    3.114 closest distance to " CG  GLN A  58 " =    2.400
peak=    3.112 closest distance to " O   HOH Z 185 " =    1.901
peak=    3.105 closest distance to " CB  PHE A 204 " =    1.184
peak=    3.100 closest distance to " O   HOH Z 411 " =    1.551
peak=    3.093 closest distance to " CG2 VAL A 265 " =    1.375
peak=    3.090 closest distance to " CE1 PHE A 225 " =    1.051
peak=    3.085 closest distance to " O   HOH Z 325 " =    3.884
peak=    3.081 closest distance to " O   HOH Z 215 " =    2.125
peak=    3.076 closest distance to " CB  MET A  47 " =    0.975
peak=    3.068 closest distance to " O   HOH Z 195 " =    1.294
peak=    3.066 closest distance to " O   HOH Z 109 " =    1.988
peak=    3.063 closest distance to " CA  SER A  87 " =    0.833
peak=    3.050 closest distance to " CD1 TRP A 274 " =    1.077
peak=    3.043 closest distance to " O   HOH Z 186 " =    3.040
peak=    3.012 closest distance to " CA  ALA A 154 " =    1.029

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 229         
Filter by distance & map next to the model:
   mapped sites are within: 0.564 - 5.851
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 228 from: 229
   mapped sites are within: 0.701 - 5.851

peak=   -4.403 closest distance to " O   HOH Z 166 " =    1.634
peak=   -4.362 closest distance to " OG  SER A  97 " =    2.232
peak=   -4.300 closest distance to " O   HOH Z 155 " =    1.660
peak=   -4.278 closest distance to " CD  GLN A  88 " =    0.811
peak=   -4.252 closest distance to " N   ARG A 275 " =    0.930
peak=   -4.126 closest distance to " O   HOH Z 411 " =    4.599
peak=   -4.121 closest distance to " O   HOH Z  19 " =    2.106
peak=   -4.111 closest distance to " CD1 LEU A 167 " =    2.182
peak=   -4.074 closest distance to " CD1 PHE A  59 " =    1.891
peak=   -4.044 closest distance to " CG1 VAL A  78 " =    2.822
peak=   -4.028 closest distance to " O   HOH Z 109 " =    3.496
peak=   -4.015 closest distance to " O   HOH Z 400 " =    0.847
peak=   -4.012 closest distance to " O   HOH Z 128 " =    4.294
peak=   -4.003 closest distance to " O   VAL A  67 " =    2.851
peak=   -4.001 closest distance to " O   HOH Z  38 " =    0.881
peak=   -3.987 closest distance to " CB  ASN A 285 " =    2.635
peak=   -3.956 closest distance to " O   HOH Z  10 " =    1.625
peak=   -3.956 closest distance to " O   HOH Z 103 " =    2.021
peak=   -3.920 closest distance to " OG1 THR A  82 " =    1.928
peak=   -3.907 closest distance to " O   HOH Z 400 " =    1.184
peak=   -3.906 closest distance to " OD2 ASP A 171 " =    2.255
peak=   -3.903 closest distance to " O   HOH Z 184 " =    1.281
peak=   -3.902 closest distance to " CA  GLY A 133 " =    2.406
peak=   -3.881 closest distance to " CD2 LEU A 237 " =    2.592
peak=   -3.875 closest distance to " O   PRO A 198 " =    1.377
peak=   -3.851 closest distance to " O   HOH Z 290 " =    1.086
peak=   -3.833 closest distance to " NH2 ARG A  66 " =    1.220
peak=   -3.821 closest distance to " OE1 GLN A  88 " =    1.022
peak=   -3.803 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.792 closest distance to " O   HOH Z  58 " =    0.974
peak=   -3.786 closest distance to " CA  VAL A  67 " =    2.963
peak=   -3.786 closest distance to " CD2 LEU A 255 " =    3.399
peak=   -3.781 closest distance to " C   SER A 206 " =    1.433
peak=   -3.780 closest distance to " O   HOH Z  52 " =    1.696
peak=   -3.767 closest distance to " O   HOH Z 231 " =    2.010
peak=   -3.764 closest distance to " O   ALA A   1 " =    2.053
peak=   -3.742 closest distance to " CE2 PHE A  38 " =    1.976
peak=   -3.741 closest distance to " O   SER A 276 " =    1.742
peak=   -3.738 closest distance to " CB  CYS A 254 " =    2.280
peak=   -3.735 closest distance to " CA  GLU A 277 " =    1.179
peak=   -3.724 closest distance to " CG  TRP A 266 " =    1.769
peak=   -3.724 closest distance to " OD1 ASN A 148 " =    1.702
peak=   -3.717 closest distance to " O   HOH Z 151 " =    1.603
peak=   -3.710 closest distance to " CG  MET A 105 " =    0.906
peak=   -3.698 closest distance to " OH  TYR A 169 " =    0.997
peak=   -3.691 closest distance to " CD  GLN A 223 " =    1.003
peak=   -3.679 closest distance to " O   HOH Z 377 " =    1.980
peak=   -3.658 closest distance to " O   HOH Z 377 " =    0.901
peak=   -3.654 closest distance to " O   HOH Z  43 " =    1.403
peak=   -3.651 closest distance to " O   HOH Z 231 " =    1.497
peak=   -3.627 closest distance to " CE  MET A  93 " =    1.338
peak=   -3.620 closest distance to " O   HOH Z  71 " =    1.502
peak=   -3.614 closest distance to " O   HOH Z  17 " =    1.334
peak=   -3.613 closest distance to " CA  GLY A 203 " =    2.329
peak=   -3.607 closest distance to " CG  LEU A 101 " =    2.543
peak=   -3.604 closest distance to " O   GLY A 196 " =    1.201
peak=   -3.597 closest distance to " O   HOH Z 308 " =    1.532
peak=   -3.595 closest distance to " O   HOH Z 185 " =    2.485
peak=   -3.591 closest distance to " CG  ARG A 269 " =    2.487
peak=   -3.588 closest distance to " O   HOH Z 348 " =    2.328
peak=   -3.587 closest distance to " O   HOH Z 426 " =    1.895
peak=   -3.587 closest distance to " O   HOH Z  83 " =    1.590
peak=   -3.585 closest distance to " CD2 PHE A  59 " =    2.213
peak=   -3.583 closest distance to " OG  SER A  62 " =    4.979
peak=   -3.572 closest distance to " O   HOH Z 275 " =    1.594
peak=   -3.563 closest distance to " O   HOH Z 150 " =    1.464
peak=   -3.559 closest distance to " O   HOH Z  41 " =    2.711
peak=   -3.558 closest distance to " CG  GLN A  58 " =    1.159
peak=   -3.549 closest distance to " O  BHOH Z 338 " =    1.049
peak=   -3.531 closest distance to " CG  ASP A 231 " =    0.804
peak=   -3.526 closest distance to " O   HOH Z 418 " =    1.530
peak=   -3.524 closest distance to " OG  SER A  26 " =    1.228
peak=   -3.521 closest distance to " O   PRO A 163 " =    2.231
peak=   -3.521 closest distance to " CH2 TRP A 179 " =    1.170
peak=   -3.516 closest distance to " CB  ASN A 170 " =    2.165
peak=   -3.515 closest distance to " CA  GLY A 241 " =    2.371
peak=   -3.508 closest distance to " O   HOH Z 350 " =    1.123
peak=   -3.507 closest distance to " CG  MET A  93 " =    2.446
peak=   -3.506 closest distance to " O   HOH Z   7 " =    0.849
peak=   -3.502 closest distance to " O   HOH Z  37 " =    1.461
peak=   -3.498 closest distance to " CG2 ILE A  49 " =    2.684
peak=   -3.497 closest distance to " CA  ASN A 127 " =    1.061
peak=   -3.493 closest distance to " N   ILE A 120 " =    1.120
peak=   -3.492 closest distance to " O   ILE A 109 " =    2.745
peak=   -3.489 closest distance to " O   HOH Z 281 " =    4.720
peak=   -3.485 closest distance to " O   GLY A 118 " =    2.367
peak=   -3.482 closest distance to " CB  SER A 146 " =    2.067
peak=   -3.480 closest distance to " C   THR A 279 " =    1.176
peak=   -3.479 closest distance to " CH2 TRP A 177 " =    1.910
peak=   -3.479 closest distance to " CG2BVAL A  41 " =    1.300
peak=   -3.478 closest distance to " O   HOH Z 234 " =    4.258
peak=   -3.472 closest distance to " CA  VAL A 232 " =    2.482
peak=   -3.462 closest distance to " O   HOH Z 221 " =    1.461
peak=   -3.461 closest distance to " ND2 ASN A  45 " =    1.710
peak=   -3.460 closest distance to " O   HOH Z 422 " =    1.178
peak=   -3.453 closest distance to " C   SER A 271 " =    1.222
peak=   -3.452 closest distance to " CD2 PHE A  61 " =    1.805
peak=   -3.449 closest distance to " O   HOH Z 399 " =    2.336
peak=   -3.447 closest distance to " O   HOH Z 414 " =    1.364
peak=   -3.442 closest distance to " OD2 ASP A 171 " =    1.974
peak=   -3.442 closest distance to " CD1 LEU A 228 " =    2.508
peak=   -3.440 closest distance to " O   HOH Z 213 " =    1.475
peak=   -3.433 closest distance to " CD  GLN A 223 " =    1.629
peak=   -3.427 closest distance to " CD1 LEU A  25 " =    2.434
peak=   -3.424 closest distance to " OXT GLY A 302 " =    3.016
peak=   -3.422 closest distance to " O   VAL A 174 " =    2.155
peak=   -3.417 closest distance to " CB  ALA A  43 " =    2.652
peak=   -3.411 closest distance to " CB  ALA A 227 " =    2.365
peak=   -3.410 closest distance to " CA  GLY A 241 " =    3.144
peak=   -3.409 closest distance to " CB  ALA A 291 " =    2.389
peak=   -3.409 closest distance to " C   LEU A 143 " =    1.774
peak=   -3.407 closest distance to " O   HOH Z 210 " =    1.069
peak=   -3.406 closest distance to " CG2 VAL A 189 " =    0.934
peak=   -3.402 closest distance to " O   HOH Z 111 " =    2.052
peak=   -3.391 closest distance to " OD1 ASP A 191 " =    1.746
peak=   -3.386 closest distance to " CG  ARG A 219 " =    2.447
peak=   -3.383 closest distance to " O   HOH Z 136 " =    1.901
peak=   -3.380 closest distance to " CB  PRO A 243 " =    2.736
peak=   -3.375 closest distance to " O   HOH Z  91 " =    2.130
peak=   -3.373 closest distance to " CD2 PHE A 225 " =    1.253
peak=   -3.368 closest distance to " O   PHE A 218 " =    1.436
peak=   -3.367 closest distance to " NH1 ARG A  36 " =    1.975
peak=   -3.366 closest distance to " O   HOH Z  11 " =    1.114
peak=   -3.356 closest distance to " CG2 THR A 221 " =    2.255
peak=   -3.355 closest distance to " C   ALA A 158 " =    1.221
peak=   -3.345 closest distance to " O   HOH Z 325 " =    1.673
peak=   -3.345 closest distance to " CB  ALA A 291 " =    2.257
peak=   -3.339 closest distance to " O   HOH Z 207 " =    1.351
peak=   -3.336 closest distance to " C   GLN A 240 " =    2.462
peak=   -3.336 closest distance to " O   HOH Z   7 " =    1.349
peak=   -3.335 closest distance to " CB  ALA A 248 " =    2.130
peak=   -3.334 closest distance to " CD2 LEU A 167 " =    1.802
peak=   -3.333 closest distance to " O   HOH Z 207 " =    2.132
peak=   -3.332 closest distance to " N   THR A 157 " =    1.713
peak=   -3.329 closest distance to " CD  ARG A 156 " =    2.070
peak=   -3.323 closest distance to " N   SER A 134 " =    1.211
peak=   -3.321 closest distance to " CA  HIS A  86 " =    2.279
peak=   -3.315 closest distance to " CB  ALA A  10 " =    1.974
peak=   -3.315 closest distance to " OD1 ASP A 171 " =    1.380
peak=   -3.309 closest distance to " CG  PRO A 243 " =    1.568
peak=   -3.308 closest distance to " CD  ARG A 195 " =    5.028
peak=   -3.304 closest distance to " O   HOH Z 198 " =    1.647
peak=   -3.296 closest distance to " O   HOH Z 417 " =    3.218
peak=   -3.295 closest distance to " O   HOH Z 137 " =    2.325
peak=   -3.294 closest distance to " C   GLY A  23 " =    2.248
peak=   -3.293 closest distance to " O   HOH Z 423 " =    1.780
peak=   -3.291 closest distance to " O   HOH Z 298 " =    3.014
peak=   -3.291 closest distance to " O   HOH Z 134 " =    2.318
peak=   -3.280 closest distance to " OD1 ASP A 298 " =    2.010
peak=   -3.276 closest distance to " O   HOH Z 118 " =    5.851
peak=   -3.276 closest distance to " OD1 ASN A  39 " =    2.286
peak=   -3.274 closest distance to " O   HOH Z 388 " =    1.977
peak=   -3.273 closest distance to " NZ  LYS A 119 " =    1.614
peak=   -3.271 closest distance to " O   HOH Z 118 " =    3.592
peak=   -3.271 closest distance to " OG ASER A 134 " =    1.264
peak=   -3.266 closest distance to " O   HOH Z 351 " =    1.573
peak=   -3.265 closest distance to " O   HOH Z 380 " =    4.270
peak=   -3.263 closest distance to " O   TYR A  15 " =    1.555
peak=   -3.261 closest distance to " O   HOH Z 389 " =    2.231
peak=   -3.256 closest distance to " CA  VAL A 197 " =    0.959
peak=   -3.252 closest distance to " O   HOH Z 283 " =    2.132
peak=   -3.251 closest distance to " O   HOH Z 165 " =    1.965
peak=   -3.251 closest distance to " NH1 ARG A 195 " =    0.957
peak=   -3.246 closest distance to " ND2 ASN A  45 " =    0.785
peak=   -3.245 closest distance to " CD  LYS A 289 " =    2.318
peak=   -3.239 closest distance to " CD  GLU A 236 " =    1.060
peak=   -3.239 closest distance to " CE2 TYR A  30 " =    2.612
peak=   -3.237 closest distance to " CB  ALA A   9 " =    2.726
peak=   -3.237 closest distance to " O   HOH Z 182 " =    0.909
peak=   -3.234 closest distance to " NH2 ARG A  66 " =    1.072
peak=   -3.232 closest distance to " O   HOH Z 252 " =    4.040
peak=   -3.224 closest distance to " O   HOH Z  94 " =    1.904
peak=   -3.222 closest distance to " N   GLN A  58 " =    1.676
peak=   -3.222 closest distance to " O   HOH Z 146 " =    1.110
peak=   -3.221 closest distance to " O   HOH Z 185 " =    1.866
peak=   -3.220 closest distance to " OE1 GLN A  58 " =    1.203
peak=   -3.219 closest distance to " O   GLY A  80 " =    2.396
peak=   -3.218 closest distance to " N   LEU A 261 " =    1.178
peak=   -3.218 closest distance to " O   HOH Z 436 " =    1.820
peak=   -3.216 closest distance to " O   HOH Z 322 " =    1.545
peak=   -3.206 closest distance to " O   HOH Z 259 " =    0.732
peak=   -3.205 closest distance to " O   LEU A 143 " =    1.357
peak=   -3.203 closest distance to " CD  ARG A 139 " =    1.607
peak=   -3.202 closest distance to " O   HOH Z  38 " =    1.364
peak=   -3.201 closest distance to " O   HOH Z  90 " =    3.218
peak=   -3.199 closest distance to " CG  LYS A 193 " =    2.741
peak=   -3.196 closest distance to " O   HOH Z 422 " =    1.785
peak=   -3.196 closest distance to " O   GLN A 194 " =    1.248
peak=   -3.195 closest distance to " CE  MET A 105 " =    2.065
peak=   -3.191 closest distance to " O   HOH Z 313 " =    1.278
peak=   -3.190 closest distance to " O   HOH Z 105 " =    1.939
peak=   -3.188 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.179 closest distance to " O   HOH Z  60 " =    2.454
peak=   -3.179 closest distance to " CG  GLU A  53 " =    1.431
peak=   -3.174 closest distance to " CD1 TYR A 247 " =    2.295
peak=   -3.170 closest distance to " O   HOH Z 124 " =    1.336
peak=   -3.168 closest distance to " O   ALA A  10 " =    1.881
peak=   -3.163 closest distance to " O   HOH Z 118 " =    0.799
peak=   -3.163 closest distance to " O   ALA A   1 " =    1.888
peak=   -3.162 closest distance to " O   THR A  18 " =    1.534
peak=   -3.160 closest distance to " OE1 GLN A  88 " =    1.178
peak=   -3.148 closest distance to " O   VAL A 125 " =    2.209
peak=   -3.143 closest distance to " C   ASN A 187 " =    1.904
peak=   -3.141 closest distance to " O   HOH Z 436 " =    1.321
peak=   -3.136 closest distance to " N   LEU A 281 " =    1.998
peak=   -3.131 closest distance to " SG  CYS A 260 " =    2.473
peak=   -3.128 closest distance to " CG  LYS A 166 " =    1.916
peak=   -3.125 closest distance to " ND2 ASN A 127 " =    1.593
peak=   -3.125 closest distance to " CG1 VAL A 125 " =    2.120
peak=   -3.121 closest distance to " O   THR A  31 " =    2.093
peak=   -3.112 closest distance to " CG2 ILE A 263 " =    2.239
peak=   -3.110 closest distance to " O   HOH Z  48 " =    0.701
peak=   -3.107 closest distance to " CD  GLN A  55 " =    0.883
peak=   -3.096 closest distance to " CA  ALA A 137 " =    2.533
peak=   -3.095 closest distance to " SG  CYS A 254 " =    3.278
peak=   -3.090 closest distance to " ND2 ASN A 252 " =    1.963
peak=   -3.089 closest distance to " O   HOH Z 366 " =    3.777
peak=   -3.088 closest distance to " CD  GLN A  11 " =    0.829
peak=   -3.081 closest distance to " SG  CYS A 168 " =    1.094
peak=   -3.080 closest distance to " O   GLN A 240 " =    2.738
peak=   -3.074 closest distance to " CD2 TRP A 274 " =    2.375
peak=   -3.048 closest distance to " CA  SER A 276 " =    1.503
peak=   -3.047 closest distance to " CG  ASP A 298 " =    0.807
peak=   -3.043 closest distance to " CE  LYS A 119 " =    0.955
peak=   -3.036 closest distance to " NE2 HIS A  86 " =    1.078
peak=   -3.036 closest distance to " CB  PHE A  16 " =    2.602
peak=   -3.022 closest distance to " O   HOH Z  24 " =    2.132
peak=   -3.016 closest distance to " O   LEU A 282 " =    1.787

================= 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    :  0.4784 0.4597   6.289108e+00   6.269139e+00
   1_bss:  0.4712 0.4505   6.285737e+00   6.260546e+00
   1_xyz:  0.3686 0.4126   6.131793e+00   6.195662e+00
   1_adp:  0.3375 0.4163   6.089185e+00   6.196872e+00
   1_occ:  0.3373 0.4162   6.088307e+00   6.196748e+00
   2_bss:  0.3359 0.4142   6.089029e+00   6.196203e+00
   2_xyz:  0.2730 0.3343   5.908322e+00   6.059858e+00
   2_adp:  0.2484 0.3305   5.863834e+00   6.049896e+00
   2_occ:  0.2481 0.3308   5.863440e+00   6.049917e+00
   3_bss:  0.2484 0.3306   5.862250e+00   6.049308e+00
   3_xyz:  0.2017 0.2701   5.668440e+00   5.877775e+00
   3_adp:  0.1807 0.2378   5.563997e+00   5.774294e+00
   3_occ:  0.1806 0.2378   5.563653e+00   5.773880e+00
   4_bss:  0.1809 0.2378   5.564864e+00   5.773792e+00
   4_xyz:  0.1532 0.2056   5.421617e+00   5.647420e+00
   4_adp:  0.1443 0.1927   5.365971e+00   5.581158e+00
   4_occ:  0.1441 0.1925   5.365360e+00   5.580611e+00
   5_bss:  0.1444 0.1928   5.367558e+00   5.581314e+00
   5_xyz:  0.1305 0.1783   5.279694e+00   5.504433e+00
   5_adp:  0.1272 0.1748   5.262144e+00   5.488997e+00
   5_occ:  0.1271 0.1749   5.261823e+00   5.489015e+00
   5_bss:  0.1270 0.1748   5.261512e+00   5.488523e+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:  0.274  20.001   0.789   3.640  -1.590   0.000  -0.000  -0.000
   1_xyz:  0.274  20.001   0.789   3.640  -1.590   0.000  -0.000  -0.000
   1_adp:  0.274  20.001   0.789   3.640  -1.590   0.000  -0.000  -0.000
   1_occ:  0.274  20.001   0.789   3.640  -1.590   0.000  -0.000  -0.000
   2_bss:  0.325  60.943   0.370   2.381   0.054   0.000   0.000   0.000
   2_xyz:  0.325  60.943   0.370   2.381   0.054   0.000   0.000   0.000
   2_adp:  0.325  60.943   0.370   2.381   0.054   0.000   0.000   0.000
   2_occ:  0.325  60.943   0.370   2.381   0.054   0.000   0.000   0.000
   3_bss:  0.331  77.684   0.501   1.688   0.340   0.000   0.000   0.000
   3_xyz:  0.331  77.684   0.501   1.688   0.340   0.000   0.000   0.000
   3_adp:  0.331  77.684   0.501   1.688   0.340   0.000   0.000   0.000
   3_occ:  0.331  77.684   0.501   1.688   0.340   0.000   0.000   0.000
   4_bss:  0.339  84.304  -0.279   0.610  -0.152   0.000  -0.000  -0.000
   4_xyz:  0.339  84.304  -0.279   0.610  -0.152   0.000  -0.000  -0.000
   4_adp:  0.339  84.304  -0.279   0.610  -0.152   0.000  -0.000  -0.000
   4_occ:  0.339  84.304  -0.279   0.610  -0.152   0.000  -0.000  -0.000
   5_bss:  0.334  77.954  -0.699  -0.058  -0.357  -0.000  -0.000  -0.000
   5_xyz:  0.334  77.954  -0.699  -0.058  -0.357  -0.000  -0.000  -0.000
   5_adp:  0.334  77.954  -0.699  -0.058  -0.357  -0.000  -0.000  -0.000
   5_occ:  0.334  77.954  -0.699  -0.058  -0.357  -0.000  -0.000  -0.000
   5_bss:  0.325  70.647  -0.719  -0.264  -0.325  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.086 0.4579  0.6147    69228.636
   1_bss:  54.318 0.4662  0.6465    66152.039
   1_xyz:  47.638 0.5489  0.7465    50628.618
   1_adp:  47.948 0.5446  0.7341    50736.333
   1_occ:  47.919 0.5448  0.7340    50621.790
   2_bss:  47.813 0.5461  0.7381    50381.109
   2_xyz:  36.723 0.6799  0.8910    31430.983
   2_adp:  35.788 0.6909  0.8815    30472.035
   2_occ:  35.781 0.6910  0.8811    30469.269
   3_bss:  35.687 0.6920  0.8797    30284.386
   3_xyz:  28.043 0.7772  0.9598    19140.618
   3_adp:  24.127 0.8195  0.9756    15007.852
   3_occ:  24.118 0.8196  0.9755    14997.609
   4_bss:  24.090 0.8199  0.9502    14996.828
   4_xyz:  20.416 0.8565  0.9704    11095.927
   4_adp:  18.541 0.8752  0.9723     9740.645
   4_occ:  18.529 0.8753  0.9723     9729.134
   5_bss:  18.544 0.8753  0.9580     9756.863
   5_xyz:  16.808 0.8908  0.9681     8223.439
   5_adp:  16.394 0.8948  0.9635     8004.553
   5_occ:  16.386 0.8949  0.9635     8004.510
   5_bss:  16.377 0.8949  0.9610     7991.657
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8259e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8259e-01
   1_xyz:   1.763  0.014  0.110 16.395  0.006  4.107   1.6864e-01
   1_adp:   1.763  0.014  0.110 16.395  0.006  4.107   1.6864e-01
   1_occ:   1.763  0.014  0.110 16.395  0.006  4.107   1.6864e-01
   2_bss:   1.763  0.014  0.110 16.395  0.006  4.107   1.6864e-01
   2_xyz:   1.490  0.011  0.094 15.373  0.007  4.117   1.1646e-01
   2_adp:   1.490  0.011  0.094 15.373  0.007  4.117   1.1646e-01
   2_occ:   1.490  0.011  0.094 15.373  0.007  4.117   1.1646e-01
   3_bss:   1.490  0.011  0.094 15.373  0.007  4.117   1.1646e-01
   3_xyz:   1.300  0.011  0.086 15.013  0.005  4.115   9.4740e-02
   3_adp:   1.300  0.011  0.086 15.013  0.005  4.115   9.4740e-02
   3_occ:   1.300  0.011  0.086 15.013  0.005  4.115   9.4740e-02
   4_bss:   1.300  0.011  0.086 15.013  0.005  4.115   9.4740e-02
   4_xyz:   1.157  0.010  0.082 14.822  0.004  4.129   7.8496e-02
   4_adp:   1.157  0.010  0.082 14.822  0.004  4.129   7.8496e-02
   4_occ:   1.157  0.010  0.082 14.822  0.004  4.129   7.8496e-02
   5_bss:   1.157  0.010  0.082 14.822  0.004  4.129   7.8496e-02
   5_xyz:   1.186  0.011  0.085 14.824  0.004  4.119   8.1138e-02
   5_adp:   1.186  0.011  0.085 14.824  0.004  4.119   8.1138e-02
   5_occ:   1.186  0.011  0.085 14.824  0.004  4.119   8.1138e-02
   5_bss:   1.186  0.011  0.085 14.824  0.004  4.119   8.1138e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.135   2.4513e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.135   2.4513e-01
   1_xyz:  11.418  0.086  0.459 89.330  0.022  1.893   1.1747e-01
   1_adp:  11.418  0.086  0.459 89.330  0.022  1.893   1.1747e-01
   1_occ:  11.418  0.086  0.459 89.330  0.022  1.893   1.1747e-01
   2_bss:  11.418  0.086  0.459 89.330  0.022  1.893   1.1747e-01
   2_xyz:   8.591  0.055  0.264 83.211  0.057  2.183   8.8683e-02
   2_adp:   8.591  0.055  0.264 83.211  0.057  2.183   8.8683e-02
   2_occ:   8.591  0.055  0.264 83.211  0.057  2.183   8.8683e-02
   3_bss:   8.591  0.055  0.264 83.211  0.057  2.183   8.8683e-02
   3_xyz:   8.038  0.059  0.273 86.091  0.045  2.153   9.3097e-02
   3_adp:   8.038  0.059  0.273 86.091  0.045  2.153   9.3097e-02
   3_occ:   8.038  0.059  0.273 86.091  0.045  2.153   9.3097e-02
   4_bss:   8.038  0.059  0.273 86.091  0.045  2.153   9.3097e-02
   4_xyz:   8.299  0.061  0.281 85.426  0.044  2.234   6.4183e-02
   4_adp:   8.299  0.061  0.281 85.426  0.044  2.234   6.4183e-02
   4_occ:   8.299  0.061  0.281 85.426  0.044  2.234   6.4183e-02
   5_bss:   8.299  0.061  0.281 85.426  0.044  2.234   6.4183e-02
   5_xyz:   8.626  0.053  0.255 85.099  0.036  2.106   6.8650e-02
   5_adp:   8.626  0.053  0.255 85.099  0.036  2.106   6.8650e-02
   5_occ:   8.626  0.053  0.255 85.099  0.036  2.106   6.8650e-02
   5_bss:   8.626  0.053  0.255 85.099  0.036  2.106   6.8650e-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:  86.66   0.00  18.42  76.68   0.00  15.14  86.66   0.00  36.27
   1_occ:  86.66   0.00  18.42  76.68   0.00  15.14  86.66   0.00  36.27
   2_bss:  86.66   0.00  18.42  76.68   0.00  15.14  86.66   0.00  36.27
   2_xyz:  86.66   0.00  18.42  76.68   0.00  15.14  86.66   0.00  36.27
   2_adp: 112.41   0.00  20.75 109.26   0.00  15.94 112.41   0.00  46.98
   2_occ: 112.41   0.00  20.75 109.26   0.00  15.94 112.41   0.00  46.98
   3_bss: 112.41   0.00  20.75 109.26   0.00  15.94 112.41   0.00  46.98
   3_xyz: 112.41   0.00  20.75 109.26   0.00  15.94 112.41   0.00  46.98
   3_adp: 115.91   0.00  19.12 115.91   0.00  13.67 109.83   3.81  48.79
   3_occ: 115.91   0.00  19.12 115.91   0.00  13.67 109.83   3.81  48.79
   4_bss: 115.91   0.00  19.12 115.91   0.00  13.67 109.83   3.81  48.79
   4_xyz: 115.91   0.00  19.12 115.91   0.00  13.67 109.83   3.81  48.79
   4_adp: 115.94   0.00  17.54 115.94   0.00  12.45 105.47   4.52  45.27
   4_occ: 115.94   0.00  17.54 115.94   0.00  12.45 105.47   4.52  45.27
   5_bss: 115.94   0.00  17.54 115.94   0.00  12.45 105.47   4.52  45.27
   5_xyz: 115.94   0.00  17.54 115.94   0.00  12.45 105.47   4.52  45.27
   5_adp: 116.14   0.52  16.89 116.14   0.52  12.02 108.73   4.29  43.39
   5_occ: 116.14   0.52  16.89 116.14   0.52  12.02 108.73   4.29  43.39
   5_bss: 116.12   0.50  16.87 116.12   0.50  12.00 108.72   4.27  43.38
------------------------------------------------------------------------
 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:    2.141    0.026    0.452
   1_adp:    2.141    0.026    0.452
   1_occ:    2.141    0.026    0.452
   2_bss:    2.141    0.026    0.452
   2_xyz:    1.792    0.034    0.647
   2_adp:    1.792    0.034    0.647
   2_occ:    1.792    0.034    0.647
   3_bss:    1.792    0.034    0.647
   3_xyz:    1.787    0.059    0.796
   3_adp:    1.787    0.059    0.796
   3_occ:    1.787    0.059    0.796
   4_bss:    1.787    0.059    0.796
   4_xyz:    1.809    0.082    0.866
   4_adp:    1.809    0.082    0.866
   4_occ:    1.809    0.082    0.866
   5_bss:    1.809    0.082    0.866
   5_xyz:    1.750    0.086    0.908
   5_adp:    1.750    0.086    0.908
   5_occ:    1.750    0.086    0.908
   5_bss:    1.750    0.086    0.908
------------------------------------------------------------------------

CPU time actual refinement: 365.04


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/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_1323/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1323/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.89 
  Macro-tasks:
    bulk solvent and scale       = 58.59  
    individual site refinement   = 142.25 
    weights calculation          = 29.66  
    collect and process          = 6.24   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 236.83 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 114.07 
    alpha_beta                      = 8.05   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 120.87 
    fmodel                         = 9.47   
    r_factors                      = 0.37   
    phase_errors                   = 10.26  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 266.87 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.192 micro seconds
Total CPU time: 6.31 minutes
from_scatterers_fft:    632 calls, 113.89 s
gradients_fft:          577 calls, 108.51 s

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

# Date 2008-01-16 Time 06:59:51 PST -0800 (1200495591.47 s)
Start R-work = 0.4784, R-free = 0.4597 (no bulk solvent and anisotropic scale)
Final R-work = 0.1431, R-free = 0.1908 (no bulk solvent and anisotropic scale)

Start R-work = 0.4712, R-free = 0.4505
Final R-work = 0.1270, R-free = 0.1748