# Date 2008-01-16 Time 06:51:41 PST -0800 (1200495101.89 s)
#phil __OFF__

Command line arguments: "../1311.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29077
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1311

-------------------------------------------------------------------------------
  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, 47.8686, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


================================== 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, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97146
Completeness in resolution range: 0.917732
Completeness with d_max=infinity: 0.915032

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9715

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, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97146
Completeness in resolution range: 0.917732
Completeness with d_max=infinity: 0.915032

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2199 [2242/2271]  2020   222   9.9%
  bin  2:  4.2199 -  3.3614 [2146/2169]  1930   216  10.1%
  bin  3:  3.3614 -  2.9400 [2121/2146]  1905   216  10.2%
  bin  4:  2.9400 -  2.6728 [2100/2116]  1895   205   9.8%
  bin  5:  2.6728 -  2.4821 [2081/2125]  1877   204   9.8%
  bin  6:  2.4821 -  2.3363 [2084/2112]  1871   213  10.2%
  bin  7:  2.3363 -  2.2197 [2071/2107]  1861   210  10.1%
  bin  8:  2.2197 -  2.1233 [2052/2094]  1849   203   9.9%
  bin  9:  2.1233 -  2.0418 [2036/2105]  1832   204  10.0%
  bin 10:  2.0418 -  1.9715 [ 656/2100]   590    66  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/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:
        1.31 -     2.03: 8
        2.03 -     2.75: 289
        2.75 -     3.46: 4545
        3.46 -     4.18: 9304
        4.18 -     4.90: 13899
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.309 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.561 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.654 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.676 3.120 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28040 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_1311/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/model_refine_001.geo

CPU time processing inputs: 9.73


============================ 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 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4739   r_free= 0.4601   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282013                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7074 0.99   1455  165 0.3685 0.3873      6.5497      6.5519|
|  2:  4.7074 -  3.7550 0.99   1394  151 0.4087 0.3988      6.8386      6.8293|
|  3:  3.7550 -  3.2858 0.99   1372  152 0.4507 0.4071      6.6662      6.6194|
|  4:  3.2858 -  2.9878 0.99   1365  149 0.4726 0.4557       6.504      6.5018|
|  5:  2.9878 -  2.7751 0.98   1352  151 0.4892 0.4964       6.352      6.3599|
|  6:  2.7751 -  2.6123 0.99   1352  156 0.5188 0.4945      6.2743      6.1997|
|  7:  2.6123 -  2.4821 0.98   1337  139 0.5135 0.4406      6.2349      6.1994|
|  8:  2.4821 -  2.3745 0.99   1329  155 0.5205 0.5036       6.153      6.1813|
|  9:  2.3745 -  2.2834 0.99   1350  152 0.5422 0.5086      6.1475      6.1009|
| 10:  2.2834 -  2.2048 0.98   1321  149 0.5170 0.5393      6.0616      6.1366|
| 11:  2.2048 -  2.1361 0.97   1327  134 0.5386 0.5462      6.0397      5.9819|
| 12:  2.1361 -  2.0752 0.99   1322  158 0.5169 0.5187      5.9275      5.9656|
| 13:  2.0752 -  2.0207 0.80   1070  123 0.5068 0.4504      5.8625       5.822|
| 14:  2.0207 -  1.9715 0.21    284   25 0.5690 0.4639      5.8118      5.7875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7074  1455   165  0.71  33.71   0.82     0.74      69664.85|
|  2:  4.7074 -  3.7550  1394   151  0.71  34.36   0.90     0.79      98723.72|
|  3:  3.7550 -  3.2858  1372   152  0.59  44.50   0.88     0.75     109863.56|
|  4:  3.2858 -  2.9878  1365   149  0.49  52.85   0.88     0.67     102702.64|
|  5:  2.9878 -  2.7751  1352   151  0.39  60.17   0.86     0.56      86104.67|
|  6:  2.7751 -  2.6123  1352   156  0.38  61.72   0.88     0.54      72355.36|
|  7:  2.6123 -  2.4821  1337   139  0.38  61.07   0.90     0.52      61468.93|
|  8:  2.4821 -  2.3745  1329   155  0.37  62.47   0.86     0.54      57859.56|
|  9:  2.3745 -  2.2834  1350   152  0.33  64.93   0.91     0.49      54328.94|
| 10:  2.2834 -  2.2048  1321   149  0.30  67.78   0.90     0.44      54176.42|
| 11:  2.2048 -  2.1361  1327   134  0.25  71.15   0.90     0.39      50898.23|
| 12:  2.1361 -  2.0752  1322   158  0.25  71.30   0.90     0.41      46808.30|
| 13:  2.0752 -  2.0207  1070   123  0.30  67.43   0.92     0.48      37450.58|
| 14:  2.0207 -  1.9715   284    25  0.38  61.74   0.88     0.58      26526.57|
|alpha:            min =        0.39 max =            0.79 mean =         0.57|
|beta:             min =    26526.57 max =       109863.56 mean =     69493.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.58|
|phase err.(test): min =        0.00 max =           89.78 mean =        57.55|
|-----------------------------------------------------------------------------|

============================== 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 = 13.324945             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.442   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.255672              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.720   (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 |  1.309 -  1.668:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.668 -  2.027:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.027 -  2.387:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.387 -  2.746:      268 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.746 -  3.105:     2279 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.105 -  3.464:     2266 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.464 -  3.823:     4262 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.823 -  4.182:     5042 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.182 -  4.541:     6252 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.541 -  4.900:     7647 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| 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  1.309 |       0.422 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4739   r_free= 0.4601   ksol= 0.00   Bsol= 0.00   scale= 0.877    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4671   r_free= 0.4518   ksol= 0.28   Bsol= 27.83   scale= 0.925   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,2.84,-0.52,0.00,-0.00,-0.00); trace/3= 1.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.278511                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.649178             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.532   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.466257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.377   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4671      final r-factor (work) = 0.3589          |
| start r-factor (free) = 0.4518      final r-factor (free) = 0.4013          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5926 = 10.65 * 0.50 * 6.2751 + 1.00 * 0.1804                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.9162 = 10.65 * 0.50 * 6.1555 + 1.00 * 0.1407                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3589      final r-factor (work) = 0.3244          |
| start r-factor (free) = 0.4013      final r-factor (free) = 0.4048          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0318 = 1.47 * 1.00 * 6.1555 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8996 = 1.47 * 1.00 * 6.0554 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.92  18.93    None  None   None       |
|    all(noH): 2823   0      0.00    111.92  18.93    None  None   None       |
|    Sol.    : 438    0      0.00    111.92  39.08    None  None   None       |
|    Mac.    : 2385   0      0.00    90.08   15.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.192: 1096   |   5:    55.959 -  67.151:   58        |
|      1:    11.192 -  22.384:  883   |   6:    67.151 -  78.342:   28        |
|      2:    22.384 -  33.575:  405   |   7:    78.342 -  89.534:   14        |
|      3:    33.575 -  44.767:  208   |   8:    89.534 - 100.726:    3        |
|      4:    44.767 -  55.959:  127   |   9:   100.726 - 111.918:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3244 r_free = 0.4048             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3240 r_free = 0.4051             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3240   r_free= 0.4051   ksol= 0.28   Bsol= 27.83   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,2.84,-0.52,0.00,-0.00,-0.00); trace/3= 1.11                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.059258                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3234   r_free= 0.4031   ksol= 0.33   Bsol= 69.51   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,1.62,-0.17,0.00,-0.00,-0.00); trace/3= 0.62                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.060113                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.756871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.867   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.885111              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.434  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3234      final r-factor (work) = 0.2712          |
| start r-factor (free) = 0.4031      final r-factor (free) = 0.3438          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.6015 = 6.76 * 0.50 * 6.0560 + 1.00 * 0.1416                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3411 = 6.76 * 0.50 * 5.9989 + 1.00 * 0.0741                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2712      final r-factor (work) = 0.2586          |
| start r-factor (free) = 0.3438      final r-factor (free) = 0.3329          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3304 = 0.89 * 1.00 * 5.9989 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2413 = 0.89 * 1.00 * 5.9036 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.83  18.88    None  None   None       |
|    all(noH): 2823   0      0.00    126.83  18.88    None  None   None       |
|    Sol.    : 438    0      0.00    126.83  41.03    None  None   None       |
|    Mac.    : 2385   0      0.00    94.95   14.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.683: 1311   |   5:    63.414 -  76.097:   52        |
|      1:    12.683 -  25.366:  850   |   6:    76.097 -  88.779:   22        |
|      2:    25.366 -  38.048:  325   |   7:    88.779 - 101.462:    7        |
|      3:    38.048 -  50.731:  157   |   8:   101.462 - 114.145:    2        |
|      4:    50.731 -  63.414:   96   |   9:   114.145 - 126.828:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2586 r_free = 0.3329             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2585 r_free = 0.3329             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2585   r_free= 0.3329   ksol= 0.33   Bsol= 69.51   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,1.62,-0.17,0.00,-0.00,-0.00); trace/3= 0.62                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.890044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2588   r_free= 0.3323   ksol= 0.33   Bsol= 71.47   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,1.04,-0.43,0.00,-0.00,-0.00); trace/3= 0.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.889368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.045126              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.686  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.377117              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.408  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2588      final r-factor (work) = 0.1934          |
| start r-factor (free) = 0.3323      final r-factor (free) = 0.2496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.7744 = 9.05 * 0.50 * 5.9038 + 1.00 * 0.0741                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2626 = 9.05 * 0.50 * 5.7875 + 1.00 * 0.0882                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1934      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.2496      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1987 = 0.38 * 1.00 * 5.7875 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1082 = 0.38 * 1.00 * 5.5615 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.93  17.81    None  None   None       |
|    all(noH): 2823   0      0.00    116.93  17.81    None  None   None       |
|    Sol.    : 438    0      4.67    116.93  42.94    None  None   None       |
|    Mac.    : 2385   0      0.00    97.91   13.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.694: 1381   |   5:    58.467 -  70.161:   67        |
|      1:    11.694 -  23.387:  860   |   6:    70.161 -  81.854:   23        |
|      2:    23.387 -  35.080:  193   |   7:    81.854 -  93.548:    9        |
|      3:    35.080 -  46.774:  162   |   8:    93.548 - 105.241:    4        |
|      4:    46.774 -  58.467:  123   |   9:   105.241 - 116.934:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1708 r_free = 0.2197             target_work(ml) = 5.501         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1707 r_free = 0.2196             target_work(ml) = 5.500         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1707   r_free= 0.2196   ksol= 0.33   Bsol= 71.47   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.01,1.04,-0.43,0.00,-0.00,-0.00); trace/3= 0.20                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.500386                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1701   r_free= 0.2192   ksol= 0.33   Bsol= 66.85   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.59,-1.23,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.502079                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.949644              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.649640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.700  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1701      final r-factor (work) = 0.1441          |
| start r-factor (free) = 0.2192      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3013 = 2.95 * 0.50 * 5.5689 + 1.00 * 0.0882                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0769 = 2.95 * 0.50 * 5.4324 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1441      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5399 = 0.65 * 1.00 * 5.4324 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4751 = 0.65 * 1.00 * 5.3307 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    106.68  17.83    None  None   None       |
|    all(noH): 2823   0      0.63    106.68  17.83    None  None   None       |
|    Sol.    : 438    0      4.75    106.20  44.68    None  None   None       |
|    Mac.    : 2385   0      0.63    106.68  12.90    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:     0.629 -  11.234: 1352   |   5:    53.652 -  64.257:   87        |
|      1:    11.234 -  21.838:  878   |   6:    64.257 -  74.862:   57        |
|      2:    21.838 -  32.443:  190   |   7:    74.862 -  85.466:   20        |
|      3:    32.443 -  43.048:  118   |   8:    85.466 -  96.071:    8        |
|      4:    43.048 -  53.652:  106   |   9:    96.071 - 106.676:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1362 r_free = 0.1850             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1361 r_free = 0.1848             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1848   ksol= 0.33   Bsol= 66.85   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.59,-1.23,-0.00,-0.00,-0.00); trace/3= -1.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319420                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1854   ksol= 0.33   Bsol= 70.11   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-1.06,-1.35,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.750268              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.028  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180513              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1367      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.1854      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7317 = 1.75 * 0.50 * 5.3325 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6953 = 1.75 * 0.50 * 5.3020 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1296      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9690 = 0.18 * 1.00 * 5.3020 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9630 = 0.18 * 1.00 * 5.2851 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    102.84  16.92    None  None   None       |
|    all(noH): 2823   0      1.67    102.84  16.92    None  None   None       |
|    Sol.    : 438    0      4.39    95.87   40.94    None  None   None       |
|    Mac.    : 2385   0      1.67    102.84  12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.666 -  11.783: 1493   |   5:    52.253 -  62.371:   74        |
|      1:    11.783 -  21.901:  775   |   6:    62.371 -  72.488:   40        |
|      2:    21.901 -  32.018:  178   |   7:    72.488 -  82.606:   15        |
|      3:    32.018 -  42.136:  135   |   8:    82.606 -  92.723:    5        |
|      4:    42.136 -  52.253:  102   |   9:    92.723 - 102.841:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1749             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1748             target_work(ml) = 5.277         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1748   ksol= 0.33   Bsol= 70.11   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.52,-1.06,-1.35,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7074 0.99   1455  165 0.1045 0.1341      5.4269      5.6021|
|  2:  4.7074 -  3.7550 0.99   1394  151 0.0927 0.1141      5.4957      5.6983|
|  3:  3.7550 -  3.2858 0.99   1372  152 0.1193 0.1765      5.5589      5.9332|
|  4:  3.2858 -  2.9878 0.99   1365  149 0.1495 0.1721      5.5937      5.7205|
|  5:  2.9878 -  2.7751 0.98   1352  151 0.1617 0.2106      5.4919      5.6752|
|  6:  2.7751 -  2.6123 0.99   1352  156 0.1500 0.2164        5.35      5.5488|
|  7:  2.6123 -  2.4821 0.98   1337  139 0.1434 0.1792      5.2788      5.4672|
|  8:  2.4821 -  2.3745 0.99   1329  155 0.1420 0.1901      5.1923      5.3828|
|  9:  2.3745 -  2.2834 0.99   1350  152 0.1417 0.2142      5.1686       5.415|
| 10:  2.2834 -  2.2048 0.98   1321  149 0.1334 0.1828      5.0971       5.347|
| 11:  2.2048 -  2.1361 0.97   1327  134 0.1315 0.1919      5.0407       5.284|
| 12:  2.1361 -  2.0752 0.99   1322  158 0.1369 0.2053      4.9874      5.2397|
| 13:  2.0752 -  2.0207 0.80   1070  123 0.1404 0.1778      4.9021      5.0594|
| 14:  2.0207 -  1.9715 0.21    284   25 0.1295 0.1844      4.7571      5.0126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7074  1455   165  0.94   9.69   0.96     0.94       7811.56|
|  2:  4.7074 -  3.7550  1394   151  0.95   8.74   1.00     0.98       9990.60|
|  3:  3.7550 -  3.2858  1372   152  0.92  13.20   1.01     1.01      12374.15|
|  4:  3.2858 -  2.9878  1365   149  0.89  17.21   1.00     0.96      13573.59|
|  5:  2.9878 -  2.7751  1352   151  0.87  19.37   0.99     0.97      11564.22|
|  6:  2.7751 -  2.6123  1352   156  0.88  18.61   0.99     0.96       9041.84|
|  7:  2.6123 -  2.4821  1337   139  0.89  17.75   0.99     0.96       7692.44|
|  8:  2.4821 -  2.3745  1329   155  0.89  18.03   0.99     0.95       6696.44|
|  9:  2.3745 -  2.2834  1350   152  0.88  18.88   1.00     0.94       6337.67|
| 10:  2.2834 -  2.2048  1321   149  0.89  17.68   0.98     0.94       5743.94|
| 11:  2.2048 -  2.1361  1327   134  0.88  18.50   0.98     0.93       5230.11|
| 12:  2.1361 -  2.0752  1322   158  0.88  18.47   0.98     0.97       4952.38|
| 13:  2.0752 -  2.0207  1070   123  0.88  18.56   0.98     0.97       4039.37|
| 14:  2.0207 -  1.9715   284    25  0.89  17.52   0.96     0.94       3010.17|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3010.17 max =        13573.59 mean =      8091.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.43|
|phase err.(test): min =        0.00 max =           89.12 mean =        15.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1747   ksol= 0.32   Bsol= 61.90   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,-1.22,-1.32,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276235                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1747   ksol= 0.32   Bsol= 61.90   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,-1.22,-1.32,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.276235                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7074 0.99   1455  165 0.1040 0.1334      5.4241      5.5964|
|  2:  4.7074 -  3.7550 0.99   1394  151 0.0922 0.1132       5.491      5.6912|
|  3:  3.7550 -  3.2858 0.99   1372  152 0.1192 0.1760      5.5564      5.9328|
|  4:  3.2858 -  2.9878 0.99   1365  149 0.1496 0.1719       5.594      5.7196|
|  5:  2.9878 -  2.7751 0.98   1352  151 0.1619 0.2109      5.4928      5.6763|
|  6:  2.7751 -  2.6123 0.99   1352  156 0.1502 0.2163      5.3509      5.5493|
|  7:  2.6123 -  2.4821 0.98   1337  139 0.1434 0.1792      5.2797      5.4678|
|  8:  2.4821 -  2.3745 0.99   1329  155 0.1421 0.1904      5.1932      5.3843|
|  9:  2.3745 -  2.2834 0.99   1350  152 0.1418 0.2142       5.169      5.4158|
| 10:  2.2834 -  2.2048 0.98   1321  149 0.1334 0.1830      5.0979      5.3484|
| 11:  2.2048 -  2.1361 0.97   1327  134 0.1315 0.1918      5.0409      5.2835|
| 12:  2.1361 -  2.0752 0.99   1322  158 0.1370 0.2058      4.9884      5.2413|
| 13:  2.0752 -  2.0207 0.80   1070  123 0.1405 0.1778      4.9025      5.0593|
| 14:  2.0207 -  1.9715 0.21    284   25 0.1296 0.1840      4.7568      5.0099|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7074  1455   165  0.94   9.65   0.96     0.94       7759.70|
|  2:  4.7074 -  3.7550  1394   151  0.95   8.68   1.00     0.98       9878.79|
|  3:  3.7550 -  3.2858  1372   152  0.92  13.09   1.01     1.01      12246.44|
|  4:  3.2858 -  2.9878  1365   149  0.89  17.17   0.99     0.96      13549.75|
|  5:  2.9878 -  2.7751  1352   151  0.87  19.35   0.98     0.97      11560.85|
|  6:  2.7751 -  2.6123  1352   156  0.88  18.62   0.98     0.95       9055.11|
|  7:  2.6123 -  2.4821  1337   139  0.89  17.76   0.98     0.96       7705.98|
|  8:  2.4821 -  2.3745  1329   155  0.88  18.06   0.98     0.94       6715.71|
|  9:  2.3745 -  2.2834  1350   152  0.88  18.89   0.99     0.94       6351.50|
| 10:  2.2834 -  2.2048  1321   149  0.89  17.70   0.98     0.94       5758.17|
| 11:  2.2048 -  2.1361  1327   134  0.88  18.51   0.97     0.92       5237.17|
| 12:  2.1361 -  2.0752  1322   158  0.88  18.49   0.98     0.96       4963.32|
| 13:  2.0752 -  2.0207  1070   123  0.88  18.55   0.98     0.96       4039.59|
| 14:  2.0207 -  1.9715   284    25  0.89  17.52   0.96     0.94       3004.05|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3004.05 max =        13549.75 mean =      8073.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        16.41|
|phase err.(test): min =        0.00 max =           88.67 mean =        15.69|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.213)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    102.78  16.86    None  None   None       |
|    all(noH): 2823   0      1.61    102.78  16.86    None  None   None       |
|    Sol.    : 438    0      4.33    95.81   40.88    None  None   None       |
|    Mac.    : 2385   0      1.61    102.78  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:     1.606 -  11.724: 1493   |   5:    52.194 -  62.311:   74        |
|      1:    11.724 -  21.841:  775   |   6:    62.311 -  72.429:   40        |
|      2:    21.841 -  31.959:  178   |   7:    72.429 -  82.546:   15        |
|      3:    31.959 -  42.076:  135   |   8:    82.546 -  92.664:    5        |
|      4:    42.076 -  52.194:  102   |   9:    92.664 - 102.781:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 354         
Filter by distance & map next to the model:
   mapped sites are within: 0.666 - 5.921
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 348 from: 354
   mapped sites are within: 0.724 - 5.921

peak=    5.817 closest distance to " CB  SER A  63 " =    1.439
peak=    5.509 closest distance to " CB  GLN A 223 " =    1.550
peak=    5.293 closest distance to " CG  PRO A  54 " =    1.317
peak=    5.089 closest distance to " CG  PRO A  90 " =    1.227
peak=    5.027 closest distance to " CG  PRO A 280 " =    0.917
peak=    4.955 closest distance to " CG  PRO A 213 " =    1.339
peak=    4.806 closest distance to " NH2AARG A 102 " =    1.074
peak=    4.707 closest distance to " O   HOH Z 111 " =    1.938
peak=    4.697 closest distance to " O   HOH Z  15 " =    2.058
peak=    4.668 closest distance to " CB  PRO A  54 " =    0.861
peak=    4.627 closest distance to " O   PRO A 198 " =    1.542
peak=    4.607 closest distance to " CB  LEU A 228 " =    1.110
peak=    4.599 closest distance to " O   HOH Z 126 " =    1.784
peak=    4.590 closest distance to " O   HOH Z 207 " =    1.923
peak=    4.570 closest distance to " O   HOH Z 232 " =    2.202
peak=    4.529 closest distance to " CG  PRO A 198 " =    1.288
peak=    4.497 closest distance to " O   HOH Z 112 " =    1.546
peak=    4.489 closest distance to " O   HOH Z 134 " =    1.787
peak=    4.473 closest distance to " O   HOH Z  68 " =    2.036
peak=    4.462 closest distance to " CB  ARG A 275 " =    0.842
peak=    4.451 closest distance to " O   ASP A 132 " =    3.929
peak=    4.425 closest distance to " O   HOH Z 132 " =    1.223
peak=    4.424 closest distance to " CA  TYR A  30 " =    1.090
peak=    4.402 closest distance to " O   HOH Z 425 " =    1.715
peak=    4.399 closest distance to " CA  GLU A 152 " =    0.905
peak=    4.327 closest distance to " O   HOH Z  47 " =    1.675
peak=    4.269 closest distance to " O   HOH Z 411 " =    2.956
peak=    4.260 closest distance to " CG1 ILE A  33 " =    1.333
peak=    4.253 closest distance to " O   HOH Z 132 " =    2.058
peak=    4.246 closest distance to " CB  PRO A 198 " =    1.016
peak=    4.243 closest distance to " O   HOH Z  61 " =    1.821
peak=    4.220 closest distance to " O   HOH Z  78 " =    2.179
peak=    4.218 closest distance to " CG  PRO A 243 " =    1.128
peak=    4.216 closest distance to " O   HOH Z  40 " =    2.051
peak=    4.209 closest distance to " CG2 THR A 221 " =    0.968
peak=    4.208 closest distance to " OE1 GLN A  11 " =    1.998
peak=    4.185 closest distance to " CB  TRP A 179 " =    1.559
peak=    4.168 closest distance to " O   HOH Z 287 " =    2.113
peak=    4.164 closest distance to " OD1 ASN A 217 " =    1.654
peak=    4.163 closest distance to " CD  ARG A 269 " =    0.933
peak=    4.142 closest distance to " O   HOH Z 118 " =    1.983
peak=    4.130 closest distance to " CA  GLN A 223 " =    0.932
peak=    4.129 closest distance to " CA  ASP A 124 " =    0.833
peak=    4.128 closest distance to " O   HOH Z  47 " =    1.631
peak=    4.128 closest distance to " O   HOH Z 196 " =    1.555
peak=    4.127 closest distance to " O   HOH Z 163 " =    1.898
peak=    4.115 closest distance to " CB  GLU A 128 " =    1.142
peak=    4.109 closest distance to " O   HOH Z 404 " =    1.513
peak=    4.103 closest distance to " CZ  PHE A 218 " =    1.098
peak=    4.095 closest distance to " CB  ASN A 148 " =    1.194
peak=    4.088 closest distance to " O   HOH Z 374 " =    2.733
peak=    4.078 closest distance to " CB  GLN A 183 " =    1.209
peak=    4.067 closest distance to " CA  ASP A 191 " =    0.830
peak=    4.064 closest distance to " O   HOH Z 154 " =    2.443
peak=    4.058 closest distance to " CB  GLU A 152 " =    1.217
peak=    4.048 closest distance to " NE2 HIS A 115 " =    0.999
peak=    4.045 closest distance to " O   HOH Z 433 " =    1.676
peak=    4.040 closest distance to " CD  ARG A  66 " =    2.637
peak=    4.017 closest distance to " CB  PRO A  54 " =    1.344
peak=    4.001 closest distance to " CG1 VAL A 153 " =    1.028
peak=    3.995 closest distance to " CG2BVAL A  41 " =    1.088
peak=    3.995 closest distance to " CB  VAL A 202 " =    1.491
peak=    3.989 closest distance to " O   HOH Z  80 " =    2.130
peak=    3.981 closest distance to " O   HOH Z 389 " =    1.916
peak=    3.964 closest distance to " O   HOH Z 247 " =    1.524
peak=    3.959 closest distance to " O   HOH Z 214 " =    1.157
peak=    3.939 closest distance to " NH2 ARG A 156 " =    1.302
peak=    3.935 closest distance to " CD2 LEU A 297 " =    0.966
peak=    3.934 closest distance to " CD1 TRP A 266 " =    1.080
peak=    3.929 closest distance to " CB  ASN A 187 " =    1.086
peak=    3.917 closest distance to " O   HOH Z 298 " =    1.858
peak=    3.910 closest distance to " O   HOH Z  49 " =    1.085
peak=    3.909 closest distance to " O   HOH Z 243 " =    1.247
peak=    3.906 closest distance to " O   HOH Z  22 " =    2.543
peak=    3.905 closest distance to " N   ASN A  39 " =    1.269
peak=    3.890 closest distance to " O   HOH Z 102 " =    1.385
peak=    3.889 closest distance to " CG2 VAL A  78 " =    1.043
peak=    3.885 closest distance to " O   HOH Z 104 " =    3.059
peak=    3.879 closest distance to " O   HOH Z 227 " =    1.823
peak=    3.876 closest distance to " CD BLYS A 290 " =    1.035
peak=    3.871 closest distance to " CZ  PHE A 192 " =    0.941
peak=    3.869 closest distance to " O   HOH Z 189 " =    2.385
peak=    3.865 closest distance to " O   HOH Z 128 " =    2.305
peak=    3.864 closest distance to " O   HOH Z 395 " =    1.409
peak=    3.849 closest distance to " CB  SER A   3 " =    1.494
peak=    3.837 closest distance to " O   HOH Z 387 " =    2.542
peak=    3.833 closest distance to " OE1 GLN A  58 " =    1.294
peak=    3.831 closest distance to " O   HOH Z 108 " =    1.384
peak=    3.831 closest distance to " O   HOH Z 200 " =    1.452
peak=    3.829 closest distance to " O   HOH Z 210 " =    1.319
peak=    3.826 closest distance to " CB  TRP A 266 " =    0.968
peak=    3.825 closest distance to " CB  ILE A 199 " =    1.023
peak=    3.822 closest distance to " CD1 LEU A 300 " =    1.288
peak=    3.812 closest distance to " O   HOH Z 394 " =    1.657
peak=    3.810 closest distance to " CD  ARG A 159 " =    0.831
peak=    3.810 closest distance to " C   SER A  32 " =    1.107
peak=    3.770 closest distance to " CB  ARG A 190 " =    1.806
peak=    3.768 closest distance to " O   HOH Z  97 " =    1.907
peak=    3.744 closest distance to " O   HOH Z 369 " =    2.166
peak=    3.741 closest distance to " O   HOH Z 437 " =    1.782
peak=    3.741 closest distance to " O   HOH Z 193 " =    2.002
peak=    3.739 closest distance to " CA  ALA A  21 " =    1.401
peak=    3.736 closest distance to " CB  ARG A  79 " =    1.352
peak=    3.736 closest distance to " CB  MET A  47 " =    0.989
peak=    3.718 closest distance to " O   HOH Z 108 " =    2.393
peak=    3.715 closest distance to " CB  ASP A 124 " =    0.872
peak=    3.708 closest distance to " O   HOH Z 368 " =    2.007
peak=    3.708 closest distance to " CA  GLY A 196 " =    0.902
peak=    3.699 closest distance to " CB  TYR A 169 " =    0.904
peak=    3.694 closest distance to " CA  SER A  87 " =    0.829
peak=    3.693 closest distance to " O   HOH Z 316 " =    3.083
peak=    3.690 closest distance to " CG2 ILE A 151 " =    0.825
peak=    3.688 closest distance to " CG  LEU A 167 " =    1.069
peak=    3.685 closest distance to " O   HOH Z 432 " =    1.807
peak=    3.678 closest distance to " O   HOH Z 132 " =    2.466
peak=    3.677 closest distance to " CD2 LEU A 255 " =    1.503
peak=    3.670 closest distance to " O   HOH Z 272 " =    1.997
peak=    3.668 closest distance to " O   HOH Z  88 " =    1.545
peak=    3.666 closest distance to " CG AARG A 275 " =    1.160
peak=    3.665 closest distance to " CB  GLN A  58 " =    0.893
peak=    3.654 closest distance to " O   HOH Z 357 " =    2.122
peak=    3.652 closest distance to " O   HOH Z  44 " =    2.437
peak=    3.646 closest distance to " CA  GLU A 152 " =    1.580
peak=    3.643 closest distance to " O   THR A 251 " =    1.332
peak=    3.643 closest distance to " O   HOH Z 344 " =    3.224
peak=    3.640 closest distance to " O   HOH Z 154 " =    1.395
peak=    3.634 closest distance to " OD2 ASP A 286 " =    3.092
peak=    3.634 closest distance to " O   HOH Z  30 " =    1.772
peak=    3.634 closest distance to " O   HOH Z 182 " =    1.240
peak=    3.626 closest distance to " CB  VAL A 265 " =    1.338
peak=    3.625 closest distance to " NH1 ARG A  56 " =    1.271
peak=    3.624 closest distance to " O   HOH Z 406 " =    1.568
peak=    3.618 closest distance to " CB  SER A 141 " =    1.006
peak=    3.617 closest distance to " O   HOH Z 265 " =    2.009
peak=    3.615 closest distance to " CA  GLY A 241 " =    0.748
peak=    3.614 closest distance to " CB  GLU A 277 " =    1.052
peak=    3.607 closest distance to " CA  ARG A 195 " =    1.173
peak=    3.606 closest distance to " O   HOH Z  41 " =    1.037
peak=    3.604 closest distance to " O   GLY A  91 " =    1.115
peak=    3.603 closest distance to " O   HOH Z  43 " =    2.302
peak=    3.599 closest distance to " O   HOH Z 411 " =    1.435
peak=    3.595 closest distance to " O   HOH Z 418 " =    1.565
peak=    3.586 closest distance to " O   HOH Z 261 " =    1.880
peak=    3.583 closest distance to " CB  ALA A 256 " =    1.380
peak=    3.579 closest distance to " O   HOH Z 124 " =    1.259
peak=    3.575 closest distance to " O   HOH Z 172 " =    5.921
peak=    3.574 closest distance to " O   HOH Z 139 " =    3.423
peak=    3.574 closest distance to " CB  SER A 216 " =    0.807
peak=    3.570 closest distance to " NZ  LYS A 117 " =    3.256
peak=    3.565 closest distance to " CG2 VAL A 197 " =    1.252
peak=    3.562 closest distance to " O   HOH Z  20 " =    2.284
peak=    3.558 closest distance to " CB  GLN A 194 " =    0.893
peak=    3.554 closest distance to " CD  LYS A 166 " =    1.408
peak=    3.545 closest distance to " O   HOH Z 403 " =    1.817
peak=    3.542 closest distance to " O   HOH Z 426 " =    1.403
peak=    3.541 closest distance to " O   HOH Z   4 " =    1.118
peak=    3.535 closest distance to " CA  ARG A  36 " =    1.113
peak=    3.533 closest distance to " O   HOH Z  66 " =    2.237
peak=    3.533 closest distance to " O   HOH Z  54 " =    1.306
peak=    3.533 closest distance to " O   HOH Z 174 " =    1.362
peak=    3.530 closest distance to " CB  PHE A  16 " =    1.065
peak=    3.528 closest distance to " CG1 ILE A 120 " =    1.117
peak=    3.527 closest distance to " O   HOH Z 128 " =    2.271
peak=    3.523 closest distance to " CD  PRO A 280 " =    1.079
peak=    3.523 closest distance to " O   HOH Z 197 " =    2.113
peak=    3.516 closest distance to " O   HOH Z 313 " =    2.171
peak=    3.501 closest distance to " CG  ASP A 231 " =    1.201
peak=    3.501 closest distance to " O   HOH Z  19 " =    2.375
peak=    3.500 closest distance to " OG  SER A  97 " =    3.523
peak=    3.492 closest distance to " CA  ALA A 160 " =    0.958
peak=    3.492 closest distance to " O   HOH Z 135 " =    1.981
peak=    3.490 closest distance to " CA  LYS A  48 " =    1.352
peak=    3.488 closest distance to " NH1 ARG A 269 " =    0.815
peak=    3.487 closest distance to " CB  ASP A 132 " =    3.836
peak=    3.473 closest distance to " O   HOH Z 145 " =    2.077
peak=    3.470 closest distance to " O   HOH Z 345 " =    3.652
peak=    3.469 closest distance to " O   HOH Z 183 " =    1.624
peak=    3.467 closest distance to " O   HOH Z 174 " =    1.981
peak=    3.462 closest distance to " O   HOH Z  21 " =    1.822
peak=    3.459 closest distance to " CB  ALA A 248 " =    1.110
peak=    3.458 closest distance to " CD  ARG A 219 " =    1.034
peak=    3.457 closest distance to " CD  LYS A 119 " =    1.298
peak=    3.451 closest distance to " CD  ARG A 195 " =    1.023
peak=    3.447 closest distance to " O   HOH Z 281 " =    4.009
peak=    3.446 closest distance to " CA  ILE A 106 " =    0.860
peak=    3.441 closest distance to " CA  THR A  42 " =    0.978
peak=    3.437 closest distance to " CB  ILE A 120 " =    1.221
peak=    3.436 closest distance to " N   PHE A 130 " =    1.345
peak=    3.435 closest distance to " N   TYR A  15 " =    0.804
peak=    3.435 closest distance to " O   HOH Z 184 " =    1.240
peak=    3.433 closest distance to " C   GLY A  80 " =    1.219
peak=    3.430 closest distance to " O   HOH Z 126 " =    1.836
peak=    3.424 closest distance to " CB  TYR A 247 " =    1.023
peak=    3.424 closest distance to " CB  ASP A 140 " =    0.724
peak=    3.417 closest distance to " O   HOH Z  32 " =    1.791
peak=    3.415 closest distance to " O   HOH Z 362 " =    3.138
peak=    3.414 closest distance to " ND1 HIS A  81 " =    1.457
peak=    3.411 closest distance to " CA  ILE A  33 " =    1.632
peak=    3.411 closest distance to " O   HOH Z 410 " =    1.426
peak=    3.410 closest distance to " CD  ARG A  56 " =    1.253
peak=    3.410 closest distance to " N   SER A 164 " =    1.068
peak=    3.410 closest distance to " CB  GLN A  73 " =    0.960
peak=    3.407 closest distance to " O   SER A  87 " =    2.302
peak=    3.406 closest distance to " O   HOH Z 245 " =    1.363
peak=    3.405 closest distance to " O   HOH Z 363 " =    1.192
peak=    3.405 closest distance to " O   HOH Z 116 " =    1.830
peak=    3.402 closest distance to " NH2AARG A 190 " =    1.513
peak=    3.400 closest distance to " CB  ARG A 259 " =    1.857
peak=    3.397 closest distance to " CD2 TRP A 179 " =    1.316
peak=    3.396 closest distance to " CB  MET A  40 " =    0.739
peak=    3.392 closest distance to " O   HOH Z 279 " =    2.373
peak=    3.390 closest distance to " CB  LEU A 143 " =    1.016
peak=    3.388 closest distance to " OD1 ASP A 238 " =    0.956
peak=    3.385 closest distance to " O   HOH Z 180 " =    2.159
peak=    3.385 closest distance to " CB  ALA A 154 " =    1.262
peak=    3.384 closest distance to " O   HOH Z  50 " =    3.499
peak=    3.383 closest distance to " O   HOH Z 127 " =    1.119
peak=    3.381 closest distance to " OD1 ASN A  69 " =    2.486
peak=    3.378 closest distance to " CA  GLY A  75 " =    1.097
peak=    3.378 closest distance to " O   HOH Z 352 " =    1.864
peak=    3.377 closest distance to " O   HOH Z  11 " =    1.251
peak=    3.377 closest distance to " CA  GLY A 267 " =    1.128
peak=    3.372 closest distance to " NZ  LYS A  76 " =    1.560
peak=    3.368 closest distance to " NH1 ARG A 138 " =    1.067
peak=    3.368 closest distance to " CG  GLN A  77 " =    0.776
peak=    3.365 closest distance to " CA  VAL A  41 " =    0.851
peak=    3.364 closest distance to " O   HOH Z 383 " =    1.975
peak=    3.363 closest distance to " O   HOH Z  87 " =    1.950
peak=    3.359 closest distance to " O   HOH Z 373 " =    1.677
peak=    3.358 closest distance to " CG  GLN A  58 " =    2.286
peak=    3.351 closest distance to " O   HOH Z 207 " =    1.906
peak=    3.351 closest distance to " O   HOH Z 336 " =    1.632
peak=    3.349 closest distance to " CB  SER A  62 " =    0.880
peak=    3.349 closest distance to " CD  ARG A  14 " =    1.361
peak=    3.343 closest distance to " CE  LYS A 119 " =    1.115
peak=    3.343 closest distance to " CA  GLU A  46 " =    0.778
peak=    3.337 closest distance to " OE1 GLU A   2 " =    2.338
peak=    3.337 closest distance to " C   VAL A 265 " =    1.162
peak=    3.336 closest distance to " O   HOH Z 192 " =    2.069
peak=    3.334 closest distance to " CB  ALA A 100 " =    1.577
peak=    3.333 closest distance to " CB  ARG A 139 " =    0.930
peak=    3.330 closest distance to " O   HOH Z 214 " =    1.842
peak=    3.322 closest distance to " O   HOH Z 377 " =    1.538
peak=    3.322 closest distance to " CB  ALA A 137 " =    1.154
peak=    3.314 closest distance to " CB  ARG A 269 " =    0.937
peak=    3.312 closest distance to " CA  THR A 221 " =    0.927
peak=    3.312 closest distance to " NZ  LYS A 193 " =    1.413
peak=    3.309 closest distance to " CB  MET A 105 " =    1.164
peak=    3.306 closest distance to " CE3 TRP A 274 " =    3.658
peak=    3.305 closest distance to " O   HOH Z 400 " =    0.826
peak=    3.304 closest distance to " CG  GLN A  89 " =    1.323
peak=    3.303 closest distance to " CA  ALA A  51 " =    0.921
peak=    3.303 closest distance to " CA  MET A  40 " =    1.134
peak=    3.303 closest distance to " O   HOH Z 260 " =    1.363
peak=    3.299 closest distance to " O   HOH Z 294 " =    1.648
peak=    3.297 closest distance to " CZ  PHE A 208 " =    1.124
peak=    3.296 closest distance to " NH2BARG A 145 " =    1.979
peak=    3.295 closest distance to " CA  GLN A  88 " =    1.408
peak=    3.290 closest distance to " CB  PHE A 204 " =    1.118
peak=    3.285 closest distance to " CG2 THR A  42 " =    0.924
peak=    3.281 closest distance to " CB  GLU A 277 " =    3.803
peak=    3.279 closest distance to " CG1 ILE A  49 " =    1.675
peak=    3.277 closest distance to " CB  TRP A 123 " =    1.135
peak=    3.274 closest distance to " O   HOH Z 139 " =    4.712
peak=    3.273 closest distance to " O   HOH Z 301 " =    1.515
peak=    3.272 closest distance to " O   HOH Z 185 " =    1.908
peak=    3.269 closest distance to " O   HOH Z 263 " =    2.170
peak=    3.263 closest distance to " O   HOH Z 371 " =    3.233
peak=    3.260 closest distance to " O   HOH Z 186 " =    1.226
peak=    3.259 closest distance to " O   HOH Z 147 " =    1.729
peak=    3.256 closest distance to " O   HOH Z   1 " =    2.613
peak=    3.254 closest distance to " O   HOH Z 134 " =    2.289
peak=    3.250 closest distance to " N   HIS A 108 " =    1.901
peak=    3.249 closest distance to " O   ARG A 275 " =    0.781
peak=    3.245 closest distance to " NZ ALYS A 290 " =    1.064
peak=    3.245 closest distance to " CB  TYR A 116 " =    1.427
peak=    3.244 closest distance to " O   HOH Z 368 " =    2.674
peak=    3.240 closest distance to " CA  LEU A 282 " =    1.039
peak=    3.233 closest distance to " CB  TRP A 150 " =    1.059
peak=    3.232 closest distance to " CA  ASP A 162 " =    1.167
peak=    3.232 closest distance to " CB  GLU A 236 " =    1.190
peak=    3.231 closest distance to " O   TRP A 274 " =    1.643
peak=    3.230 closest distance to " O   HOH Z 215 " =    1.436
peak=    3.230 closest distance to " O   HOH Z 420 " =    2.051
peak=    3.223 closest distance to " O   HOH Z 409 " =    3.200
peak=    3.222 closest distance to " NE AARG A 275 " =    1.513
peak=    3.220 closest distance to " N   LYS A 166 " =    0.804
peak=    3.219 closest distance to " O   HOH Z 343 " =    2.350
peak=    3.213 closest distance to " CG  GLU A  37 " =    1.080
peak=    3.211 closest distance to " CG  GLU A 277 " =    2.721
peak=    3.210 closest distance to " NZ  LYS A 166 " =    3.177
peak=    3.206 closest distance to " CB  LEU A  83 " =    0.818
peak=    3.202 closest distance to " NH1 ARG A  14 " =    1.234
peak=    3.201 closest distance to " NH1AARG A 145 " =    1.056
peak=    3.200 closest distance to " CB  TYR A  30 " =    1.099
peak=    3.197 closest distance to " CB  ALA A  34 " =    0.868
peak=    3.192 closest distance to " O   HOH Z 248 " =    1.728
peak=    3.192 closest distance to " CE  LYS A  76 " =    0.940
peak=    3.184 closest distance to " O   HOH Z 109 " =    2.490
peak=    3.184 closest distance to " O   HOH Z 402 " =    1.582
peak=    3.183 closest distance to " CZ3 TRP A  85 " =    0.991
peak=    3.182 closest distance to " CD1 ILE A 106 " =    0.922
peak=    3.181 closest distance to " O   HOH Z 178 " =    1.128
peak=    3.180 closest distance to " CZ  PHE A  38 " =    1.381
peak=    3.175 closest distance to " CB  ALA A 291 " =    1.251
peak=    3.174 closest distance to " N   THR A  52 " =    1.093
peak=    3.174 closest distance to " O   HOH Z 172 " =    2.031
peak=    3.168 closest distance to " CA  THR A 294 " =    1.754
peak=    3.167 closest distance to " CG2 VAL A 296 " =    0.922
peak=    3.167 closest distance to " O   HOH Z  78 " =    1.225
peak=    3.166 closest distance to " O   HOH Z  87 " =    2.594
peak=    3.166 closest distance to " CZ3 TRP A 274 " =    4.705
peak=    3.163 closest distance to " O   HOH Z  39 " =    1.487
peak=    3.162 closest distance to " CB  GLU A 175 " =    1.357
peak=    3.162 closest distance to " O   HOH Z  54 " =    1.561
peak=    3.161 closest distance to " CB  ALA A  71 " =    1.293
peak=    3.157 closest distance to " CA  ALA A 299 " =    1.384
peak=    3.153 closest distance to " CA  ILE A 263 " =    0.955
peak=    3.152 closest distance to " CD  GLU A 236 " =    1.141
peak=    3.151 closest distance to " CB  GLN A  89 " =    1.165
peak=    3.146 closest distance to " O   HOH Z 142 " =    1.576
peak=    3.138 closest distance to " CD1 PHE A  59 " =    1.799
peak=    3.136 closest distance to " CA  TRP A 274 " =    1.022
peak=    3.135 closest distance to " O   HOH Z 193 " =    2.445
peak=    3.135 closest distance to " O   HOH Z   2 " =    1.796
peak=    3.130 closest distance to " O   HOH Z 155 " =    3.079
peak=    3.128 closest distance to " O   ALA A 180 " =    1.483
peak=    3.127 closest distance to " CB  ASN A 148 " =    1.690
peak=    3.126 closest distance to " CA  TYR A 116 " =    1.450
peak=    3.121 closest distance to " O   HOH Z 424 " =    2.897
peak=    3.120 closest distance to " O   HOH Z 305 " =    3.637
peak=    3.117 closest distance to " OE1 GLN A  58 " =    5.858
peak=    3.117 closest distance to " CD1 TYR A 169 " =    1.387
peak=    3.115 closest distance to " O   ASN A 209 " =    1.216
peak=    3.104 closest distance to " CA  ARG A 156 " =    0.966
peak=    3.101 closest distance to " O   HOH Z 303 " =    2.239
peak=    3.093 closest distance to " O   ALA A 165 " =    1.357
peak=    3.087 closest distance to " CA  ALA A 100 " =    1.165
peak=    3.081 closest distance to " CD1 TRP A 274 " =    1.043
peak=    3.081 closest distance to " CB  ASP A 253 " =    1.053
peak=    3.081 closest distance to " O   HOH Z 186 " =    3.000
peak=    3.072 closest distance to " CB  ALA A  51 " =    0.800
peak=    3.070 closest distance to " O   HOH Z 293 " =    1.868
peak=    3.069 closest distance to " O   HOH Z 188 " =    1.928
peak=    3.059 closest distance to " O   HOH Z 126 " =    1.976
peak=    3.044 closest distance to " CA  ALA A 158 " =    1.081
peak=    3.037 closest distance to " O   HOH Z 327 " =    1.730
peak=    3.007 closest distance to " O   HOH Z 409 " =    2.901

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.569 - 5.614
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 216
   mapped sites are within: 0.729 - 5.614

peak=   -4.705 closest distance to " O   HOH Z 290 " =    0.886
peak=   -4.442 closest distance to " O   HOH Z 411 " =    4.609
peak=   -4.400 closest distance to " C   ASN A 285 " =    2.627
peak=   -4.392 closest distance to " NH2 ARG A  66 " =    1.227
peak=   -4.388 closest distance to " O   HOH Z 166 " =    1.685
peak=   -4.369 closest distance to " CD  GLN A  88 " =    0.799
peak=   -4.152 closest distance to " N   ALA A  43 " =    2.619
peak=   -4.096 closest distance to " OD2 ASP A 171 " =    2.282
peak=   -4.061 closest distance to " O   HOH Z  19 " =    1.806
peak=   -4.000 closest distance to " O   HOH Z 184 " =    1.094
peak=   -3.993 closest distance to " CD  GLN A 223 " =    0.802
peak=   -3.967 closest distance to " CE  MET A  93 " =    1.153
peak=   -3.966 closest distance to " O   HOH Z  13 " =    1.536
peak=   -3.965 closest distance to " OG  SER A  97 " =    2.256
peak=   -3.960 closest distance to " CD2 LEU A 300 " =    3.374
peak=   -3.957 closest distance to " N   GLN A  58 " =    1.527
peak=   -3.952 closest distance to " O   HOH Z  43 " =    1.315
peak=   -3.951 closest distance to " O   HOH Z 231 " =    1.276
peak=   -3.922 closest distance to " N   ARG A 275 " =    0.973
peak=   -3.906 closest distance to " O   HOH Z 222 " =    1.172
peak=   -3.905 closest distance to " O   HOH Z  71 " =    1.254
peak=   -3.897 closest distance to " NH2 ARG A  66 " =    1.033
peak=   -3.892 closest distance to " O   HOH Z 109 " =    3.883
peak=   -3.891 closest distance to " CG  ARG A 269 " =    2.356
peak=   -3.865 closest distance to " O   HOH Z 377 " =    0.879
peak=   -3.859 closest distance to " O   VAL A  67 " =    2.694
peak=   -3.856 closest distance to " CG1 VAL A 112 " =    2.646
peak=   -3.848 closest distance to " CG  GLU A  53 " =    1.269
peak=   -3.845 closest distance to " CD2 PHE A  59 " =    2.382
peak=   -3.833 closest distance to " CG  GLN A  58 " =    1.075
peak=   -3.831 closest distance to " O   PRO A 198 " =    1.308
peak=   -3.829 closest distance to " O   HOH Z  52 " =    1.817
peak=   -3.828 closest distance to " O   HOH Z 308 " =    1.317
peak=   -3.826 closest distance to " CA  GLU A 277 " =    1.204
peak=   -3.816 closest distance to " OH  TYR A 169 " =    1.010
peak=   -3.804 closest distance to " CG  ASP A 231 " =    0.729
peak=   -3.787 closest distance to " O   HOH Z  10 " =    1.627
peak=   -3.777 closest distance to " O   HOH Z 351 " =    1.571
peak=   -3.769 closest distance to " CD1 PHE A  59 " =    1.926
peak=   -3.768 closest distance to " O   HOH Z 231 " =    1.902
peak=   -3.764 closest distance to " CG  ARG A  66 " =    2.457
peak=   -3.763 closest distance to " O   HOH Z 418 " =    1.307
peak=   -3.762 closest distance to " O   HOH Z  38 " =    0.891
peak=   -3.759 closest distance to " CG  MET A 105 " =    0.948
peak=   -3.736 closest distance to " CB  LEU A 167 " =    2.199
peak=   -3.732 closest distance to " O   HOH Z 185 " =    2.509
peak=   -3.724 closest distance to " OE2 GLU A   2 " =    1.353
peak=   -3.709 closest distance to " CH2 TRP A 179 " =    1.124
peak=   -3.704 closest distance to " O   HOH Z  17 " =    1.242
peak=   -3.699 closest distance to " O   HOH Z 377 " =    1.730
peak=   -3.688 closest distance to " OG1 THR A  82 " =    1.917
peak=   -3.684 closest distance to " CA  VAL A  67 " =    2.834
peak=   -3.683 closest distance to " O   HOH Z  91 " =    2.231
peak=   -3.666 closest distance to " CA  GLY A  23 " =    2.352
peak=   -3.658 closest distance to " O   GLY A 196 " =    1.171
peak=   -3.656 closest distance to " O   HOH Z 213 " =    1.403
peak=   -3.654 closest distance to " CD2 LEU A 237 " =    2.506
peak=   -3.641 closest distance to " O   HOH Z  94 " =    1.734
peak=   -3.637 closest distance to " OE1 GLN A  88 " =    0.964
peak=   -3.620 closest distance to " OD1 ASN A 148 " =    1.733
peak=   -3.607 closest distance to " CB  CYS A 254 " =    2.292
peak=   -3.606 closest distance to " CD1 LEU A 228 " =    2.583
peak=   -3.598 closest distance to " OG ASER A 134 " =    1.217
peak=   -3.597 closest distance to " O   HOH Z 407 " =    0.754
peak=   -3.590 closest distance to " O   HOH Z  37 " =    1.536
peak=   -3.586 closest distance to " O   HOH Z 221 " =    1.179
peak=   -3.585 closest distance to " N   ALA A 226 " =    2.115
peak=   -3.583 closest distance to " O   HOH Z  58 " =    0.757
peak=   -3.573 closest distance to " CH2 TRP A 177 " =    2.062
peak=   -3.561 closest distance to " CG  LEU A 101 " =    2.524
peak=   -3.553 closest distance to " CD2 LEU A 300 " =    2.836
peak=   -3.552 closest distance to " C   SER A 271 " =    1.237
peak=   -3.550 closest distance to " O   GLY A 118 " =    2.319
peak=   -3.548 closest distance to " OXT GLY A 302 " =    2.856
peak=   -3.540 closest distance to " ND2 ASN A  45 " =    0.945
peak=   -3.518 closest distance to " C   ALA A 158 " =    1.203
peak=   -3.517 closest distance to " CA  ASN A 127 " =    1.135
peak=   -3.502 closest distance to " O   HOH Z 426 " =    2.003
peak=   -3.502 closest distance to " CA  VAL A 197 " =    1.067
peak=   -3.502 closest distance to " O   HOH Z  98 " =    1.995
peak=   -3.494 closest distance to " O   HOH Z 283 " =    2.002
peak=   -3.493 closest distance to " CD  ARG A 156 " =    2.084
peak=   -3.493 closest distance to " CB  ALA A 161 " =    2.717
peak=   -3.492 closest distance to " C   THR A 279 " =    1.229
peak=   -3.488 closest distance to " OD2 ASP A 171 " =    1.837
peak=   -3.473 closest distance to " CD2 LEU A 167 " =    1.872
peak=   -3.471 closest distance to " CG  ASP A 298 " =    0.852
peak=   -3.470 closest distance to " CA  GLY A 241 " =    2.289
peak=   -3.461 closest distance to " CG  ARG A 219 " =    2.401
peak=   -3.453 closest distance to " O   HOH Z 351 " =    1.335
peak=   -3.449 closest distance to " CD1 LEU A 101 " =    2.915
peak=   -3.444 closest distance to " SG  CYS A 168 " =    0.975
peak=   -3.442 closest distance to " O   HOH Z 275 " =    1.614
peak=   -3.430 closest distance to " N   SER A 134 " =    1.214
peak=   -3.426 closest distance to " CE2 TYR A  30 " =    2.689
peak=   -3.418 closest distance to " O   HOH Z 251 " =    1.818
peak=   -3.412 closest distance to " CG  ASP A  50 " =    2.280
peak=   -3.410 closest distance to " O   HOH Z 234 " =    4.446
peak=   -3.410 closest distance to " CB  PRO A 243 " =    2.687
peak=   -3.407 closest distance to " CD  GLU A 236 " =    1.075
peak=   -3.398 closest distance to " C   SER A 206 " =    1.462
peak=   -3.392 closest distance to " O   HOH Z 389 " =    2.139
peak=   -3.392 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.384 closest distance to " O   HOH Z 103 " =    1.911
peak=   -3.384 closest distance to " C   GLN A 240 " =    2.238
peak=   -3.380 closest distance to " CB  ALA A 227 " =    2.353
peak=   -3.378 closest distance to " CA  PRO A 198 " =    1.103
peak=   -3.352 closest distance to " O   HOH Z 423 " =    1.129
peak=   -3.350 closest distance to " NH2AARG A 275 " =    5.405
peak=   -3.347 closest distance to " O   HOH Z 325 " =    1.565
peak=   -3.347 closest distance to " O   HOH Z 177 " =    1.424
peak=   -3.346 closest distance to " O   ALA A  10 " =    1.825
peak=   -3.341 closest distance to " OD1 ASP A 191 " =    1.603
peak=   -3.340 closest distance to " CG2 THR A 221 " =    2.225
peak=   -3.338 closest distance to " CB  ALA A 291 " =    2.310
peak=   -3.337 closest distance to " O   HOH Z 298 " =    2.943
peak=   -3.334 closest distance to " CD1 TRP A 179 " =    0.910
peak=   -3.333 closest distance to " CB  ARG A 219 " =    2.347
peak=   -3.333 closest distance to " OG  SER A  32 " =    0.990
peak=   -3.331 closest distance to " O   HOH Z 414 " =    1.401
peak=   -3.330 closest distance to " O   PHE A 218 " =    1.435
peak=   -3.328 closest distance to " O  BHOH Z 338 " =    1.312
peak=   -3.327 closest distance to " O   HOH Z 380 " =    4.650
peak=   -3.326 closest distance to " O   ALA A   7 " =    1.642
peak=   -3.324 closest distance to " O   HOH Z 128 " =    4.331
peak=   -3.324 closest distance to " O   HOH Z 124 " =    1.293
peak=   -3.321 closest distance to " CD  LYS A 289 " =    2.387
peak=   -3.318 closest distance to " CA  GLY A 203 " =    2.185
peak=   -3.314 closest distance to " O   HOH Z 111 " =    1.141
peak=   -3.311 closest distance to " CD2 TRP A 274 " =    2.379
peak=   -3.311 closest distance to " N   LEU A 281 " =    1.920
peak=   -3.302 closest distance to " CG  LEU A  83 " =    2.070
peak=   -3.302 closest distance to " O   HOH Z 259 " =    0.843
peak=   -3.297 closest distance to " CZ  ARG A 259 " =    0.776
peak=   -3.296 closest distance to " O   VAL A 125 " =    2.179
peak=   -3.296 closest distance to " OG  SER A  63 " =    0.943
peak=   -3.295 closest distance to " O   HOH Z 243 " =    2.006
peak=   -3.292 closest distance to " SG ACYS A 201 " =    2.195
peak=   -3.278 closest distance to " OG  SER A  63 " =    1.468
peak=   -3.271 closest distance to " ND2 ASN A  45 " =    1.857
peak=   -3.263 closest distance to " CB  GLN A  55 " =    1.404
peak=   -3.263 closest distance to " C   ASN A 187 " =    1.844
peak=   -3.262 closest distance to " O   HOH Z 385 " =    4.106
peak=   -3.260 closest distance to " O   ALA A 256 " =    1.592
peak=   -3.259 closest distance to " O   HOH Z 368 " =    2.069
peak=   -3.256 closest distance to " O   HOH Z 313 " =    1.137
peak=   -3.255 closest distance to " CB  ALA A  10 " =    1.969
peak=   -3.253 closest distance to " CG2 VAL A 189 " =    0.936
peak=   -3.250 closest distance to " CD2 PHE A  61 " =    1.828
peak=   -3.244 closest distance to " CG1 VAL A 125 " =    2.042
peak=   -3.242 closest distance to " O   HOH Z 312 " =    1.531
peak=   -3.242 closest distance to " O   HOH Z 348 " =    2.248
peak=   -3.236 closest distance to " N   LEU A 261 " =    1.301
peak=   -3.235 closest distance to " O   HOH Z 252 " =    4.191
peak=   -3.233 closest distance to " O   HOH Z 118 " =    0.867
peak=   -3.232 closest distance to " CA  GLY A 133 " =    2.415
peak=   -3.229 closest distance to " O   HOH Z 151 " =    1.505
peak=   -3.223 closest distance to " O   HOH Z 100 " =    0.822
peak=   -3.222 closest distance to " O   HOH Z 198 " =    1.624
peak=   -3.218 closest distance to " CD  ARG A 195 " =    5.109
peak=   -3.217 closest distance to " CE2 TRP A  85 " =    1.113
peak=   -3.215 closest distance to " O   HOH Z 423 " =    1.922
peak=   -3.215 closest distance to " O   HOH Z 396 " =    1.564
peak=   -3.213 closest distance to " O   HOH Z  11 " =    1.395
peak=   -3.200 closest distance to " CD2 LEU A 237 " =    2.620
peak=   -3.199 closest distance to " O   VAL A 121 " =    0.930
peak=   -3.199 closest distance to " CA  GLY A 241 " =    3.123
peak=   -3.199 closest distance to " NE2 GLN A  58 " =    0.828
peak=   -3.198 closest distance to " O   TRP A  92 " =    1.827
peak=   -3.190 closest distance to " O   HOH Z 388 " =    1.958
peak=   -3.188 closest distance to " O   PRO A 163 " =    2.229
peak=   -3.188 closest distance to " O   SER A 276 " =    1.848
peak=   -3.186 closest distance to " NH1 ARG A 195 " =    2.287
peak=   -3.184 closest distance to " O   HOH Z 221 " =    1.526
peak=   -3.183 closest distance to " OD2 ASP A  65 " =    1.988
peak=   -3.172 closest distance to " O   VAL A 174 " =    2.052
peak=   -3.169 closest distance to " OG  SER A  62 " =    4.858
peak=   -3.166 closest distance to " O   HOH Z 136 " =    1.541
peak=   -3.165 closest distance to " O   HOH Z 111 " =    2.219
peak=   -3.165 closest distance to " O   GLY A 211 " =    1.546
peak=   -3.163 closest distance to " CE  LYS A 119 " =    0.957
peak=   -3.161 closest distance to " O   HOH Z  95 " =    0.845
peak=   -3.149 closest distance to " O   HOH Z 118 " =    5.614
peak=   -3.147 closest distance to " ND2 ASN A  60 " =    1.374
peak=   -3.146 closest distance to " O   HOH Z 417 " =    3.047
peak=   -3.146 closest distance to " N   THR A 157 " =    1.767
peak=   -3.145 closest distance to " CD  GLN A 223 " =    1.094
peak=   -3.136 closest distance to " CG  LYS A 166 " =    1.933
peak=   -3.133 closest distance to " O   HOH Z  93 " =    1.933
peak=   -3.130 closest distance to " CD  PRO A 198 " =    1.092
peak=   -3.121 closest distance to " CA  ASP A 107 " =    2.433
peak=   -3.116 closest distance to " O   HOH Z  30 " =    0.975
peak=   -3.110 closest distance to " CG  GLU A   2 " =    1.623
peak=   -3.110 closest distance to " CD2 TYR A 293 " =    1.901
peak=   -3.108 closest distance to " O   ARG A 275 " =    1.884
peak=   -3.105 closest distance to " O   HOH Z 186 " =    1.168
peak=   -3.104 closest distance to " O   SER A 135 " =    1.860
peak=   -3.103 closest distance to " CG2BVAL A  41 " =    1.128
peak=   -3.102 closest distance to " O   GLN A 194 " =    1.273
peak=   -3.087 closest distance to " CE  MET A 105 " =    2.016
peak=   -3.087 closest distance to " CG2 THR A   4 " =    1.955
peak=   -3.083 closest distance to " CG  LYS A 193 " =    2.665
peak=   -3.079 closest distance to " OG  SER A  87 " =    1.792
peak=   -3.075 closest distance to " O   HOH Z 141 " =    0.874
peak=   -3.073 closest distance to " O   ALA A  34 " =    2.037
peak=   -3.066 closest distance to " CD1 LEU A   5 " =    2.508
peak=   -3.063 closest distance to " O   HOH Z 132 " =    1.468
peak=   -3.060 closest distance to " O   HOH Z 399 " =    2.314
peak=   -3.060 closest distance to " O   HOH Z 231 " =    0.868
peak=   -3.053 closest distance to " OG1 THR A  82 " =    1.459
peak=   -3.052 closest distance to " O   HOH Z 326 " =    4.597
peak=   -3.044 closest distance to " O   ALA A 160 " =    1.540
peak=   -3.008 closest distance to " O   HOH Z  86 " =    2.404

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4739 0.4601   6.282013e+00   6.269089e+00
   1_bss:  0.4671 0.4518   6.278511e+00   6.259945e+00
   1_xyz:  0.3589 0.4013   6.103924e+00   6.175791e+00
   1_adp:  0.3244 0.4048   6.060138e+00   6.182853e+00
   1_occ:  0.3240 0.4051   6.059258e+00   6.182833e+00
   2_bss:  0.3234 0.4031   6.060113e+00   6.181816e+00
   2_xyz:  0.2712 0.3438   5.918003e+00   6.084375e+00
   2_adp:  0.2586 0.3329   5.890388e+00   6.062899e+00
   2_occ:  0.2585 0.3329   5.890044e+00   6.062614e+00
   3_bss:  0.2588 0.3323   5.889368e+00   6.061866e+00
   3_xyz:  0.1934 0.2496   5.614054e+00   5.816405e+00
   3_adp:  0.1708 0.2197   5.500777e+00   5.704658e+00
   3_occ:  0.1707 0.2196   5.500386e+00   5.704291e+00
   4_bss:  0.1701 0.2192   5.502079e+00   5.704290e+00
   4_xyz:  0.1441 0.1888   5.352776e+00   5.565374e+00
   4_adp:  0.1362 0.1850   5.319718e+00   5.544623e+00
   4_occ:  0.1361 0.1848   5.319420e+00   5.544250e+00
   5_bss:  0.1367 0.1854   5.322102e+00   5.546145e+00
   5_xyz:  0.1296 0.1783   5.280751e+00   5.506580e+00
   5_adp:  0.1303 0.1749   5.276715e+00   5.492147e+00
   5_occ:  0.1302 0.1748   5.276538e+00   5.492182e+00
   5_bss:  0.1301 0.1747   5.276235e+00   5.491551e+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:  0.280  27.827   1.024   2.836  -0.524   0.000  -0.000  -0.000
   1_xyz:  0.280  27.827   1.024   2.836  -0.524   0.000  -0.000  -0.000
   1_adp:  0.280  27.827   1.024   2.836  -0.524   0.000  -0.000  -0.000
   1_occ:  0.280  27.827   1.024   2.836  -0.524   0.000  -0.000  -0.000
   2_bss:  0.330  69.515   0.401   1.625  -0.166   0.000  -0.000  -0.000
   2_xyz:  0.330  69.515   0.401   1.625  -0.166   0.000  -0.000  -0.000
   2_adp:  0.330  69.515   0.401   1.625  -0.166   0.000  -0.000  -0.000
   2_occ:  0.330  69.515   0.401   1.625  -0.166   0.000  -0.000  -0.000
   3_bss:  0.329  71.473  -0.007   1.042  -0.432   0.000  -0.000  -0.000
   3_xyz:  0.329  71.473  -0.007   1.042  -0.432   0.000  -0.000  -0.000
   3_adp:  0.329  71.473  -0.007   1.042  -0.432   0.000  -0.000  -0.000
   3_occ:  0.329  71.473  -0.007   1.042  -0.432   0.000  -0.000  -0.000
   4_bss:  0.331  66.853  -1.242  -0.595  -1.231  -0.000  -0.000  -0.000
   4_xyz:  0.331  66.853  -1.242  -0.595  -1.231  -0.000  -0.000  -0.000
   4_adp:  0.331  66.853  -1.242  -0.595  -1.231  -0.000  -0.000  -0.000
   4_occ:  0.331  66.853  -1.242  -0.595  -1.231  -0.000  -0.000  -0.000
   5_bss:  0.327  70.108  -1.521  -1.062  -1.348  -0.000  -0.000  -0.000
   5_xyz:  0.327  70.108  -1.521  -1.062  -1.348  -0.000  -0.000  -0.000
   5_adp:  0.327  70.108  -1.521  -1.062  -1.348  -0.000  -0.000  -0.000
   5_occ:  0.327  70.108  -1.521  -1.062  -1.348  -0.000  -0.000  -0.000
   5_bss:  0.318  61.897  -1.528  -1.220  -1.320  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.580 0.4244  0.5676    69487.123
   1_bss:  56.773 0.4330  0.6031    66486.628
   1_xyz:  45.407 0.5760  0.7893    46507.522
   1_adp:  46.581 0.5606  0.7665    47872.863
   1_occ:  46.564 0.5608  0.7662    47833.527
   2_bss:  46.437 0.5624  0.7583    47684.040
   2_xyz:  38.204 0.6620  0.8775    33806.001
   2_adp:  36.282 0.6854  0.8895    31662.180
   2_occ:  36.261 0.6857  0.8895    31629.106
   3_bss:  36.163 0.6867  0.8771    31439.130
   3_xyz:  25.569 0.8038  0.9789    16309.579
   3_adp:  21.787 0.8435  0.9908    12693.813
   3_occ:  21.782 0.8435  0.9907    12686.913
   4_bss:  21.758 0.8438  0.9505    12690.459
   4_xyz:  18.175 0.8783  0.9721     9272.387
   4_adp:  17.512 0.8849  0.9709     8885.385
   4_occ:  17.502 0.8849  0.9708     8878.433
   5_bss:  17.543 0.8847  0.9614     8945.195
   5_xyz:  16.692 0.8923  0.9626     8242.047
   5_adp:  16.354 0.8955  0.9594     8085.958
   5_occ:  16.353 0.8956  0.9595     8090.719
   5_bss:  16.339 0.8957  0.9561     8072.475
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.8037e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.8037e-01
   1_xyz:   1.613  0.012  0.100 15.764  0.006  4.118   1.4074e-01
   1_adp:   1.613  0.012  0.100 15.764  0.006  4.118   1.4074e-01
   1_occ:   1.613  0.012  0.100 15.764  0.006  4.118   1.4074e-01
   2_bss:   1.613  0.012  0.100 15.764  0.006  4.118   1.4074e-01
   2_xyz:   1.199  0.008  0.077 14.418  0.005  4.123   7.4050e-02
   2_adp:   1.199  0.008  0.077 14.418  0.005  4.123   7.4050e-02
   2_occ:   1.199  0.008  0.077 14.418  0.005  4.123   7.4050e-02
   3_bss:   1.199  0.008  0.077 14.418  0.005  4.123   7.4050e-02
   3_xyz:   1.257  0.010  0.085 14.786  0.005  4.121   8.8157e-02
   3_adp:   1.257  0.010  0.085 14.786  0.005  4.121   8.8157e-02
   3_occ:   1.257  0.010  0.085 14.786  0.005  4.121   8.8157e-02
   4_bss:   1.257  0.010  0.085 14.786  0.005  4.121   8.8157e-02
   4_xyz:   1.061  0.008  0.076 14.467  0.004  4.133   6.5039e-02
   4_adp:   1.061  0.008  0.076 14.467  0.004  4.133   6.5039e-02
   4_occ:   1.061  0.008  0.076 14.467  0.004  4.133   6.5039e-02
   5_bss:   1.061  0.008  0.076 14.467  0.004  4.133   6.5039e-02
   5_xyz:   0.975  0.007  0.070 14.240  0.003  4.117   5.5307e-02
   5_adp:   0.975  0.007  0.070 14.240  0.003  4.117   5.5307e-02
   5_occ:   0.975  0.007  0.070 14.240  0.003  4.117   5.5307e-02
   5_bss:   0.975  0.007  0.070 14.240  0.003  4.117   5.5307e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.309   2.4373e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.309   2.4373e-01
   1_xyz:  10.207  0.067  0.380 86.574  0.029  2.040   1.0527e-01
   1_adp:  10.207  0.067  0.380 86.574  0.029  2.040   1.0527e-01
   1_occ:  10.207  0.067  0.380 86.574  0.029  2.040   1.0527e-01
   2_bss:  10.207  0.067  0.380 86.574  0.029  2.040   1.0527e-01
   2_xyz:   7.815  0.043  0.202 80.431  0.049  2.277   6.1501e-02
   2_adp:   7.815  0.043  0.202 80.431  0.049  2.277   6.1501e-02
   2_occ:   7.815  0.043  0.202 80.431  0.049  2.277   6.1501e-02
   3_bss:   7.815  0.043  0.202 80.431  0.049  2.277   6.1501e-02
   3_xyz:   8.903  0.063  0.283 77.008  0.033  2.205   8.8183e-02
   3_adp:   8.903  0.063  0.283 77.008  0.033  2.205   8.8183e-02
   3_occ:   8.903  0.063  0.283 77.008  0.033  2.205   8.8183e-02
   4_bss:   8.903  0.063  0.283 77.008  0.033  2.205   8.8183e-02
   4_xyz:   8.713  0.051  0.264 88.836  0.037  2.299   5.1791e-02
   4_adp:   8.713  0.051  0.264 88.836  0.037  2.299   5.1791e-02
   4_occ:   8.713  0.051  0.264 88.836  0.037  2.299   5.1791e-02
   5_bss:   8.713  0.051  0.264 88.836  0.037  2.299   5.1791e-02
   5_xyz:   8.186  0.045  0.236 80.802  0.032  2.399   3.4128e-02
   5_adp:   8.186  0.045  0.236 80.802  0.032  2.399   3.4128e-02
   5_occ:   8.186  0.045  0.236 80.802  0.032  2.399   3.4128e-02
   5_bss:   8.186  0.045  0.236 80.802  0.032  2.399   3.4128e-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: 111.92   0.00  18.93  90.08   0.00  15.23 111.92   0.00  39.08
   1_occ: 111.92   0.00  18.93  90.08   0.00  15.23 111.92   0.00  39.08
   2_bss: 111.92   0.00  18.93  90.08   0.00  15.23 111.92   0.00  39.08
   2_xyz: 111.92   0.00  18.93  90.08   0.00  15.23 111.92   0.00  39.08
   2_adp: 126.83   0.00  18.88  94.95   0.00  14.81 126.83   0.00  41.03
   2_occ: 126.83   0.00  18.88  94.95   0.00  14.81 126.83   0.00  41.03
   3_bss: 126.83   0.00  18.88  94.95   0.00  14.81 126.83   0.00  41.03
   3_xyz: 126.83   0.00  18.88  94.95   0.00  14.81 126.83   0.00  41.03
   3_adp: 116.93   0.00  17.81  97.91   0.00  13.19 116.93   4.67  42.94
   3_occ: 116.93   0.00  17.81  97.91   0.00  13.19 116.93   4.67  42.94
   4_bss: 116.93   0.00  17.81  97.91   0.00  13.19 116.93   4.67  42.94
   4_xyz: 116.93   0.00  17.81  97.91   0.00  13.19 116.93   4.67  42.94
   4_adp: 106.68   0.63  17.83 106.68   0.63  12.90 106.20   4.75  44.68
   4_occ: 106.68   0.63  17.83 106.68   0.63  12.90 106.20   4.75  44.68
   5_bss: 106.68   0.63  17.83 106.68   0.63  12.90 106.20   4.75  44.68
   5_xyz: 106.68   0.63  17.83 106.68   0.63  12.90 106.20   4.75  44.68
   5_adp: 102.84   1.67  16.92 102.84   1.67  12.51  95.87   4.39  40.94
   5_occ: 102.84   1.67  16.92 102.84   1.67  12.51  95.87   4.39  40.94
   5_bss: 102.78   1.61  16.86 102.78   1.61  12.45  95.81   4.33  40.88
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.932    0.027    0.396
   1_adp:    1.932    0.027    0.396
   1_occ:    1.932    0.027    0.396
   2_bss:    1.932    0.027    0.396
   2_xyz:    1.831    0.024    0.513
   2_adp:    1.831    0.024    0.513
   2_occ:    1.831    0.024    0.513
   3_bss:    1.831    0.024    0.513
   3_xyz:    1.636    0.062    0.739
   3_adp:    1.636    0.062    0.739
   3_occ:    1.636    0.062    0.739
   4_bss:    1.636    0.062    0.739
   4_xyz:    1.545    0.067    0.784
   4_adp:    1.545    0.067    0.784
   4_occ:    1.545    0.067    0.784
   5_bss:    1.545    0.067    0.784
   5_xyz:    1.489    0.052    0.814
   5_adp:    1.489    0.052    0.814
   5_occ:    1.489    0.052    0.814
   5_bss:    1.489    0.052    0.814
------------------------------------------------------------------------

CPU time actual refinement: 345.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/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_1311/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1311/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.38 
  Macro-tasks:
    bulk solvent and scale       = 37.03  
    individual site refinement   = 142.41 
    weights calculation          = 30.97  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 217.01 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 114.43 
    alpha_beta                      = 8.43   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 121.07 
    fmodel                         = 6.69   
    r_factors                      = 0.11   
    phase_errors                   = 10.21  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 264.96 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.987 micro seconds
Total CPU time: 5.99 minutes
from_scatterers_fft:    624 calls, 114.12 s
gradients_fft:          569 calls, 108.62 s

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

# Date 2008-01-16 Time 06:57:39 PST -0800 (1200495459.76 s)
Start R-work = 0.4739, R-free = 0.4601 (no bulk solvent and anisotropic scale)
Final R-work = 0.1490, R-free = 0.1930 (no bulk solvent and anisotropic scale)

Start R-work = 0.4671, R-free = 0.4518
Final R-work = 0.1301, R-free = 0.1747