# Date 2008-01-16 Time 06:15:42 PST -0800 (1200492942.50 s)
#phil __OFF__

Command line arguments: "../1070.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3233
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1070

-------------------------------------------------------------------------------
  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: (71.3037, 47.8686, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, 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: (71.3037, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98138
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933521

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9814

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: (71.3037, 47.8686, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98138
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933521

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2403 [2203/2232]  1984   219   9.9%
  bin  2:  4.2403 -  3.3780 [2100/2123]  1891   209  10.0%
  bin  3:  3.3780 -  2.9546 [2073/2098]  1860   213  10.3%
  bin  4:  2.9546 -  2.6861 [2074/2090]  1874   200   9.6%
  bin  5:  2.6861 -  2.4945 [2046/2084]  1837   209  10.2%
  bin  6:  2.4945 -  2.3480 [2055/2088]  1854   201   9.8%
  bin  7:  2.3480 -  2.2308 [2013/2050]  1810   203  10.1%
  bin  8:  2.2308 -  2.1340 [2011/2053]  1810   201  10.0%
  bin  9:  2.1340 -  2.0520 [2016/2052]  1812   204  10.1%
  bin 10:  2.0520 -  1.9814 [ 998/2051]   898   100  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/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: 0.12 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:
        1.51 -     2.19: 9
        2.19 -     2.86: 1159
        2.86 -     3.54: 4392
        3.54 -     4.22: 9105
        4.22 -     4.90: 13363
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.508 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.630 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.717 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.918 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28023 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_1070/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/model_refine_001.geo

CPU time processing inputs: 9.01


============================ 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 = 71.30375 47.8686 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4292   r_free= 0.4141   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.236023                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7297 0.99   1425  161 0.3382 0.3616      6.4841      6.4808|
|  2:  4.7297 -  3.7733 0.99   1370  145 0.3574 0.3670      6.7511      6.7224|
|  3:  3.7733 -  3.3020 0.99   1344  157 0.3939 0.3481      6.5969      6.5388|
|  4:  3.3020 -  3.0027 0.99   1343  146 0.4158 0.4110      6.4548      6.4466|
|  5:  3.0027 -  2.7889 0.98   1321  148 0.4365 0.4324      6.3074      6.3127|
|  6:  2.7889 -  2.6254 0.99   1330  143 0.4733 0.4233      6.2438      6.1199|
|  7:  2.6254 -  2.4945 0.99   1313  150 0.4695 0.4083      6.2121      6.1177|
|  8:  2.4945 -  2.3864 0.99   1302  143 0.4818 0.4615      6.1192      6.1775|
|  9:  2.3864 -  2.2948 0.99   1319  151 0.5000 0.4513      6.1019      6.0938|
| 10:  2.2948 -  2.2159 0.98   1301  144 0.4674 0.5047      6.0625      6.0681|
| 11:  2.2159 -  2.1468 0.98   1296  136 0.4946 0.4731      6.0165       6.007|
| 12:  2.1468 -  2.0856 1.00   1286  151 0.4864 0.4910       5.927      5.9594|
| 13:  2.0856 -  2.0308 0.95   1274  143 0.4710 0.4102      5.8449      5.7913|
| 14:  2.0308 -  1.9814 0.31    406   41 0.4846 0.4886      5.8012      5.7628|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7297  1425   161  0.73  31.43   0.84     0.76      61673.45|
|  2:  4.7297 -  3.7733  1370   145  0.76  30.01   0.93     0.83      78340.94|
|  3:  3.7733 -  3.3020  1344   157  0.68  37.25   0.92     0.83      83993.53|
|  4:  3.3020 -  3.0027  1343   146  0.61  42.85   0.92     0.78      76165.80|
|  5:  3.0027 -  2.7889  1321   148  0.54  48.56   0.90     0.73      63916.31|
|  6:  2.7889 -  2.6254  1330   143  0.53  49.49   0.92     0.71      52329.92|
|  7:  2.6254 -  2.4945  1313   150  0.54  48.85   0.93     0.71      46466.78|
|  8:  2.4945 -  2.3864  1302   143  0.49  53.05   0.89     0.69      45808.83|
|  9:  2.3864 -  2.2948  1319   151  0.46  55.37   0.92     0.66      45028.28|
| 10:  2.2948 -  2.2159  1301   144  0.46  55.64   0.97     0.65      43787.03|
| 11:  2.2159 -  2.1468  1296   136  0.45  56.17   0.92     0.66      39683.83|
| 12:  2.1468 -  2.0856  1286   151  0.45  56.28   0.95     0.68      35702.40|
| 13:  2.0856 -  2.0308  1274   143  0.47  54.90   0.93     0.68      28948.17|
| 14:  2.0308 -  1.9814   406    41  0.50  52.03   0.96     0.70      22487.68|
|alpha:            min =        0.65 max =            0.83 mean =         0.72|
|beta:             min =    22487.68 max =        83993.53 mean =     53589.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.98 mean =        47.55|
|phase err.(test): min =        0.00 max =           90.00 mean =        47.54|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.774422              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.550   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.711394              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.520   (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 |  1.508 -  1.847:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.847 -  2.186:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.186 -  2.526:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.526 -  2.865:     1128 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.865 -  3.204:     1914 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.204 -  3.543:     2478 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.543 -  3.882:     4597 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.882 -  4.222:     4508 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.222 -  4.561:     6069 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.561 -  4.900:     7294 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.508 |       0.282 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4292   r_free= 0.4141   ksol= 0.00   Bsol= 0.00   scale= 0.907    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.236023                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4195   r_free= 0.4052   ksol= 0.28   Bsol= 20.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,4.38,-0.96,0.00,-0.00,-0.00); trace/3= 0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.226523                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.718902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.471   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.846965              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.318   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4195      final r-factor (work) = 0.3097          |
| start r-factor (free) = 0.4052      final r-factor (free) = 0.3417          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0828 = 6.72 * 0.50 * 6.2248 + 1.00 * 0.1709                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4770 = 6.72 * 0.50 * 6.0620 + 1.00 * 0.1119                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3097      final r-factor (work) = 0.2831          |
| start r-factor (free) = 0.3417      final r-factor (free) = 0.3488          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1404 = 0.85 * 1.00 * 6.0620 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0556 = 0.85 * 1.00 * 5.9514 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.88   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    94.88   17.74    None  None   None       |
|    Sol.    : 438    0      1.71    94.88   37.38    None  None   None       |
|    Mac.    : 2385   0      0.00    84.50   14.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.488:  908   |   5:    47.442 -  56.930:   89        |
|      1:     9.488 -  18.977:  993   |   6:    56.930 -  66.418:   50        |
|      2:    18.977 -  28.465:  424   |   7:    66.418 -  75.907:   19        |
|      3:    28.465 -  37.953:  201   |   8:    75.907 -  85.395:    5        |
|      4:    37.953 -  47.442:  133   |   9:    85.395 -  94.883:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2831 r_free = 0.3488             target_work(ml) = 5.956         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2828 r_free = 0.3485             target_work(ml) = 5.954         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2828   r_free= 0.3485   ksol= 0.28   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,4.38,-0.96,0.00,-0.00,-0.00); trace/3= 0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.954454                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2813   r_free= 0.3464   ksol= 0.32   Bsol= 60.18   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,1.89,-0.92,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.953643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.824866              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.697   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.543333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.767  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2813      final r-factor (work) = 0.2025          |
| start r-factor (free) = 0.3464      final r-factor (free) = 0.2496          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3711 = 8.82 * 0.50 * 5.9512 + 1.00 * 0.1119                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8388 = 8.82 * 0.50 * 5.8323 + 1.00 * 0.1044                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2025      final r-factor (work) = 0.1758          |
| start r-factor (free) = 0.2496      final r-factor (free) = 0.2235          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1837 = 0.54 * 1.00 * 5.8323 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0407 = 0.54 * 1.00 * 5.5752 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.52   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    89.52   17.44    None  None   None       |
|    Sol.    : 438    0      3.15    89.52   41.30    None  None   None       |
|    Mac.    : 2385   0      0.00    88.07   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.952:  930   |   5:    44.758 -  53.710:  110        |
|      1:     8.952 -  17.903: 1091   |   6:    53.710 -  62.662:   80        |
|      2:    17.903 -  26.855:  303   |   7:    62.662 -  71.613:   34        |
|      3:    26.855 -  35.807:  140   |   8:    71.613 -  80.565:   17        |
|      4:    35.807 -  44.758:  109   |   9:    80.565 -  89.517:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1758 r_free = 0.2235             target_work(ml) = 5.527         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1757 r_free = 0.2234             target_work(ml) = 5.526         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1757   r_free= 0.2234   ksol= 0.32   Bsol= 60.18   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,1.89,-0.92,0.00,-0.00,-0.00); trace/3= -0.09                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.526217                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1751   r_free= 0.2227   ksol= 0.32   Bsol= 60.18   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.05,-0.97,0.00,-0.00,-0.00); trace/3= -0.79                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.522846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.804125              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.870   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303019              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.749  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1751      final r-factor (work) = 0.1365          |
| start r-factor (free) = 0.2227      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4991 = 4.80 * 0.50 * 5.5763 + 1.00 * 0.1044                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0931 = 4.80 * 0.50 * 5.4188 + 1.00 * 0.0768                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1365      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6534 = 0.30 * 1.00 * 5.4188 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6097 = 0.30 * 1.00 * 5.2802 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.34    91.36   16.91    None  None   None       |
|    all(noH): 2823   0      1.34    91.36   16.91    None  None   None       |
|    Sol.    : 438    0      2.88    90.07   40.79    None  None   None       |
|    Mac.    : 2385   0      1.34    91.36   12.53    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:     1.341 -  10.343: 1223   |   5:    46.351 -  55.354:   99        |
|      1:    10.343 -  19.345:  943   |   6:    55.354 -  64.356:   60        |
|      2:    19.345 -  28.347:  208   |   7:    64.356 -  73.358:   30        |
|      3:    28.347 -  37.349:  138   |   8:    73.358 -  82.360:    9        |
|      4:    37.349 -  46.351:  105   |   9:    82.360 -  91.362:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1279 r_free = 0.1727             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1278 r_free = 0.1725             target_work(ml) = 5.254         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1725   ksol= 0.32   Bsol= 60.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.44,0.05,-0.97,0.00,-0.00,-0.00); trace/3= -0.79                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.253873                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1280   r_free= 0.1729   ksol= 0.33   Bsol= 64.16   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,-0.80,-1.12,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.254773                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.615487              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.087  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.450  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3434 = 1.62 * 0.50 * 5.2821 + 1.00 * 0.0768                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2923 = 1.62 * 0.50 * 5.2451 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0767 = 0.20 * 1.00 * 5.2451 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0730 = 0.20 * 1.00 * 5.2318 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    90.03   16.48    None  None   None       |
|    all(noH): 2823   0      1.28    90.03   16.48    None  None   None       |
|    Sol.    : 438    0      3.82    87.16   39.28    None  None   None       |
|    Mac.    : 2385   0      1.28    90.03   12.29    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:     1.283 -  10.157: 1201   |   5:    45.656 -  54.531:   98        |
|      1:    10.157 -  19.032:  973   |   6:    54.531 -  63.405:   53        |
|      2:    19.032 -  27.907:  215   |   7:    63.405 -  72.280:   22        |
|      3:    27.907 -  36.781:  128   |   8:    72.280 -  81.155:    7        |
|      4:    36.781 -  45.656:  118   |   9:    81.155 -  90.029:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1241 r_free = 0.1680             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1240 r_free = 0.1680             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1680   ksol= 0.33   Bsol= 64.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.70,-0.80,-1.12,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.229028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1680   ksol= 0.32   Bsol= 61.45   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-1.05,-1.09,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.228959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.281168              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.011  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.522428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.270  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1240      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0224 = 2.28 * 0.50 * 5.2314 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0019 = 2.28 * 0.50 * 5.2017 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7260 = 0.52 * 1.00 * 5.2017 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7142 = 0.52 * 1.00 * 5.1768 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    95.30   16.49    None  None   None       |
|    all(noH): 2823   0      0.54    95.30   16.49    None  None   None       |
|    Sol.    : 438    0      4.69    88.82   39.92    None  None   None       |
|    Mac.    : 2385   0      0.54    95.30   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:     0.544 -  10.019: 1213   |   5:    47.921 -  57.397:  101        |
|      1:    10.019 -  19.495:  982   |   6:    57.397 -  66.872:   44        |
|      2:    19.495 -  28.970:  211   |   7:    66.872 -  76.348:   21        |
|      3:    28.970 -  38.446:  126   |   8:    76.348 -  85.823:    5        |
|      4:    38.446 -  47.921:  114   |   9:    85.823 -  95.299:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1151 r_free = 0.1633             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1633             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1633   ksol= 0.32   Bsol= 61.45   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.74,-1.05,-1.09,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.179251                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7297 0.99   1425  161 0.0976 0.1269      5.3635      5.5256|
|  2:  4.7297 -  3.7733 0.99   1370  145 0.0847 0.1088      5.4187      5.6245|
|  3:  3.7733 -  3.3020 0.99   1344  157 0.1072 0.1621      5.4793      5.8982|
|  4:  3.3020 -  3.0027 0.99   1343  146 0.1290 0.1562      5.4961      5.6249|
|  5:  3.0027 -  2.7889 0.98   1321  148 0.1416 0.1915      5.3894      5.5648|
|  6:  2.7889 -  2.6254 0.99   1330  143 0.1328 0.1981      5.2717      5.4944|
|  7:  2.6254 -  2.4945 0.99   1313  150 0.1268 0.1859      5.1927       5.456|
|  8:  2.4945 -  2.3864 0.99   1302  143 0.1240 0.1717      5.0981      5.3086|
|  9:  2.3864 -  2.2948 0.99   1319  151 0.1210 0.1827      5.0563      5.3273|
| 10:  2.2948 -  2.2159 0.98   1301  144 0.1164 0.1765      5.0003      5.2433|
| 11:  2.2159 -  2.1468 0.98   1296  136 0.1146 0.1899       4.948      5.3111|
| 12:  2.1468 -  2.0856 1.00   1286  151 0.1142 0.1741      4.8962      5.1264|
| 13:  2.0856 -  2.0308 0.95   1274  143 0.1177 0.1741        4.81      5.0403|
| 14:  2.0308 -  1.9814 0.31    406   41 0.1114 0.1745      4.6799      4.9811|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7297  1425   161  0.94   8.72   0.97     0.95       6883.73|
|  2:  4.7297 -  3.7733  1370   145  0.95   8.02   1.00     0.99       8632.46|
|  3:  3.7733 -  3.3020  1344   157  0.93  11.56   1.01     1.01      10563.93|
|  4:  3.3020 -  3.0027  1343   146  0.91  14.97   0.99     0.97      11472.18|
|  5:  3.0027 -  2.7889  1321   148  0.88  17.76   0.98     0.96       9613.57|
|  6:  2.7889 -  2.6254  1330   143  0.89  17.23   0.98     0.96       7982.79|
|  7:  2.6254 -  2.4945  1313   150  0.90  16.13   0.98     0.95       6639.14|
|  8:  2.4945 -  2.3864  1302   143  0.90  16.40   0.98     0.95       5748.58|
|  9:  2.3864 -  2.2948  1319   151  0.90  16.58   0.98     0.94       5279.47|
| 10:  2.2948 -  2.2159  1301   144  0.90  16.05   0.98     0.94       4823.96|
| 11:  2.2159 -  2.1468  1296   136  0.89  16.86   0.97     0.93       4561.84|
| 12:  2.1468 -  2.0856  1286   151  0.91  15.99   0.98     0.96       4169.41|
| 13:  2.0856 -  2.0308  1274   143  0.89  17.30   0.97     0.96       3576.43|
| 14:  2.0308 -  1.9814   406    41  0.90  16.24   0.96     0.92       2712.71|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2712.71 max =        11472.18 mean =      6859.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.85|
|phase err.(test): min =        0.00 max =           87.39 mean =        14.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1632   ksol= 0.32   Bsol= 61.43   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.93,-0.84,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.179358                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1632   ksol= 0.32   Bsol= 61.43   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,-0.93,-0.84,-0.00,-0.00,-0.00); trace/3= -1.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.179358                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7297 0.99   1425  161 0.0976 0.1270      5.3644      5.5272|
|  2:  4.7297 -  3.7733 0.99   1370  145 0.0847 0.1089      5.4195      5.6247|
|  3:  3.7733 -  3.3020 0.99   1344  157 0.1072 0.1621      5.4797      5.8985|
|  4:  3.3020 -  3.0027 0.99   1343  146 0.1290 0.1563      5.4962      5.6251|
|  5:  3.0027 -  2.7889 0.98   1321  148 0.1416 0.1914      5.3891      5.5644|
|  6:  2.7889 -  2.6254 0.99   1330  143 0.1328 0.1978      5.2712      5.4937|
|  7:  2.6254 -  2.4945 0.99   1313  150 0.1269 0.1860      5.1927      5.4561|
|  8:  2.4945 -  2.3864 0.99   1302  143 0.1240 0.1716      5.0981      5.3082|
|  9:  2.3864 -  2.2948 0.99   1319  151 0.1209 0.1828      5.0564      5.3281|
| 10:  2.2948 -  2.2159 0.98   1301  144 0.1164 0.1766      5.0005      5.2431|
| 11:  2.2159 -  2.1468 0.98   1296  136 0.1147 0.1897       4.948      5.3111|
| 12:  2.1468 -  2.0856 1.00   1286  151 0.1142 0.1742      4.8962      5.1269|
| 13:  2.0856 -  2.0308 0.95   1274  143 0.1178 0.1743      4.8098      5.0397|
| 14:  2.0308 -  1.9814 0.31    406   41 0.1114 0.1741      4.6796      4.9799|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7297  1425   161  0.94   8.74   0.97     0.95       6897.42|
|  2:  4.7297 -  3.7733  1370   145  0.95   8.03   1.00     0.99       8644.36|
|  3:  3.7733 -  3.3020  1344   157  0.93  11.57   1.02     1.01      10575.38|
|  4:  3.3020 -  3.0027  1343   146  0.91  14.98   1.00     0.97      11474.94|
|  5:  3.0027 -  2.7889  1321   148  0.88  17.75   0.99     0.96       9604.13|
|  6:  2.7889 -  2.6254  1330   143  0.89  17.22   0.99     0.96       7972.40|
|  7:  2.6254 -  2.4945  1313   150  0.90  16.13   0.98     0.95       6635.34|
|  8:  2.4945 -  2.3864  1302   143  0.90  16.40   0.99     0.96       5749.91|
|  9:  2.3864 -  2.2948  1319   151  0.90  16.59   0.99     0.94       5283.46|
| 10:  2.2948 -  2.2159  1301   144  0.90  16.06   0.99     0.95       4825.80|
| 11:  2.2159 -  2.1468  1296   136  0.89  16.86   0.98     0.94       4560.85|
| 12:  2.1468 -  2.0856  1286   151  0.91  16.00   0.99     0.97       4170.73|
| 13:  2.0856 -  2.0308  1274   143  0.89  17.30   0.98     0.97       3573.05|
| 14:  2.0308 -  1.9814   406    41  0.90  16.23   0.97     0.93       2707.24|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2707.24 max =        11474.94 mean =      6860.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.85|
|phase err.(test): min =        0.00 max =           87.39 mean =        14.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.186)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    95.28   16.48    None  None   None       |
|    all(noH): 2823   0      0.53    95.28   16.48    None  None   None       |
|    Sol.    : 438    0      4.68    88.80   39.90    None  None   None       |
|    Mac.    : 2385   0      0.53    95.28   12.17    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:     0.526 -  10.002: 1213   |   5:    47.904 -  57.379:  101        |
|      1:    10.002 -  19.477:  982   |   6:    57.379 -  66.855:   44        |
|      2:    19.477 -  28.953:  211   |   7:    66.855 -  76.330:   21        |
|      3:    28.953 -  38.428:  126   |   8:    76.330 -  85.806:    5        |
|      4:    38.428 -  47.904:  114   |   9:    85.806 -  95.281:    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)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.705 - 4.547
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 309
   mapped sites are within: 0.705 - 4.547

peak=    5.920 closest distance to " O   HOH Z 111 " =    2.128
peak=    5.595 closest distance to " CB  GLN A 223 " =    1.414
peak=    5.504 closest distance to " CB  SER A  63 " =    1.244
peak=    5.320 closest distance to " CG  PRO A  54 " =    1.224
peak=    4.892 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.872 closest distance to " CG  PRO A 213 " =    1.232
peak=    4.770 closest distance to " O   HOH Z  15 " =    2.070
peak=    4.657 closest distance to " CB  GLN A 183 " =    1.299
peak=    4.633 closest distance to " O   HOH Z 134 " =    1.772
peak=    4.587 closest distance to " CA  TYR A  30 " =    0.965
peak=    4.568 closest distance to " O   HOH Z 108 " =    2.614
peak=    4.514 closest distance to " C   PRO A 198 " =    1.530
peak=    4.492 closest distance to " CB  PRO A  54 " =    0.791
peak=    4.484 closest distance to " CB  GLU A 152 " =    1.150
peak=    4.477 closest distance to " O   HOH Z  47 " =    1.445
peak=    4.416 closest distance to " CB  ARG A 190 " =    1.659
peak=    4.408 closest distance to " CB  GLU A 128 " =    1.169
peak=    4.367 closest distance to " O   HOH Z  67 " =    2.022
peak=    4.353 closest distance to " CG1 ILE A  33 " =    1.208
peak=    4.344 closest distance to " CB  ARG A 275 " =    0.857
peak=    4.343 closest distance to " O   HOH Z 298 " =    1.972
peak=    4.309 closest distance to " O   HOH Z  20 " =    1.831
peak=    4.290 closest distance to " O   HOH Z 369 " =    2.300
peak=    4.257 closest distance to " NH2 ARG A 156 " =    1.248
peak=    4.255 closest distance to " O   HOH Z 132 " =    2.302
peak=    4.252 closest distance to " CG  PRO A 198 " =    1.302
peak=    4.246 closest distance to " CB  LEU A 228 " =    1.140
peak=    4.240 closest distance to " CB  TYR A 169 " =    0.852
peak=    4.236 closest distance to " O   HOH Z  97 " =    1.983
peak=    4.235 closest distance to " O   HOH Z 234 " =    3.842
peak=    4.193 closest distance to " O   HOH Z 193 " =    1.983
peak=    4.179 closest distance to " CB  ARG A  79 " =    1.379
peak=    4.172 closest distance to " CG2 THR A 221 " =    1.070
peak=    4.159 closest distance to " O   HOH Z  80 " =    1.800
peak=    4.132 closest distance to " O   HOH Z 403 " =    1.794
peak=    4.127 closest distance to " CA  ASP A 191 " =    0.794
peak=    4.125 closest distance to " O   HOH Z 265 " =    2.171
peak=    4.123 closest distance to " CB  ASN A 148 " =    1.351
peak=    4.122 closest distance to " O   HOH Z 412 " =    3.599
peak=    4.119 closest distance to " O   HOH Z  40 " =    1.865
peak=    4.116 closest distance to " O   HOH Z 163 " =    1.665
peak=    4.114 closest distance to " CG  PRO A  90 " =    1.099
peak=    4.103 closest distance to " CG  PRO A 243 " =    1.183
peak=    4.096 closest distance to " OD1 ASN A  69 " =    2.662
peak=    4.088 closest distance to " CA  ALA A  21 " =    1.375
peak=    4.086 closest distance to " O   HOH Z  78 " =    2.030
peak=    4.081 closest distance to " CB  SER A   3 " =    1.374
peak=    4.070 closest distance to " CB  GLU A 277 " =    3.732
peak=    4.061 closest distance to " O   HOH Z 402 " =    1.540
peak=    4.058 closest distance to " O   HOH Z 247 " =    1.445
peak=    4.042 closest distance to " O   HOH Z 126 " =    1.601
peak=    4.031 closest distance to " CG  PRO A 280 " =    0.705
peak=    4.020 closest distance to " O   HOH Z 209 " =    2.284
peak=    4.008 closest distance to " O   HOH Z 131 " =    2.612
peak=    3.990 closest distance to " CG  ARG A  66 " =    2.606
peak=    3.988 closest distance to " O   HOH Z 189 " =    2.394
peak=    3.981 closest distance to " CA  ALA A  51 " =    1.001
peak=    3.974 closest distance to " CD  LYS A 166 " =    1.364
peak=    3.972 closest distance to " CD1 LEU A 300 " =    1.213
peak=    3.967 closest distance to " O   SER A  87 " =    2.298
peak=    3.948 closest distance to " O   HOH Z 423 " =    1.906
peak=    3.935 closest distance to " CB  SER A 141 " =    1.035
peak=    3.934 closest distance to " O   HOH Z 425 " =    1.373
peak=    3.933 closest distance to " O   HOH Z 418 " =    1.537
peak=    3.922 closest distance to " O   HOH Z  21 " =    1.751
peak=    3.919 closest distance to " CB  TRP A 266 " =    0.937
peak=    3.899 closest distance to " CB  TRP A 179 " =    1.392
peak=    3.886 closest distance to " O   HOH Z  61 " =    1.560
peak=    3.886 closest distance to " O   HOH Z 433 " =    1.506
peak=    3.884 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.882 closest distance to " NH2BARG A 145 " =    2.059
peak=    3.882 closest distance to " C   ILE A 106 " =    1.889
peak=    3.870 closest distance to " O   HOH Z 132 " =    2.620
peak=    3.860 closest distance to " O   HOH Z 214 " =    2.249
peak=    3.835 closest distance to " O   HOH Z  43 " =    2.160
peak=    3.833 closest distance to " CB  PRO A  54 " =    1.290
peak=    3.815 closest distance to " CA  ARG A 195 " =    1.215
peak=    3.813 closest distance to " O   HOH Z 352 " =    1.858
peak=    3.812 closest distance to " O   HOH Z 368 " =    2.096
peak=    3.802 closest distance to " OD2 ASP A 286 " =    2.956
peak=    3.799 closest distance to " O   HOH Z 383 " =    2.117
peak=    3.798 closest distance to " NE2 GLN A  11 " =    1.040
peak=    3.790 closest distance to " CA  THR A 221 " =    0.928
peak=    3.787 closest distance to " O   HOH Z 284 " =    2.903
peak=    3.781 closest distance to " O   HOH Z 374 " =    2.807
peak=    3.772 closest distance to " CG2BVAL A  41 " =    0.909
peak=    3.757 closest distance to " O   HOH Z 174 " =    2.385
peak=    3.755 closest distance to " O   HOH Z  48 " =    1.619
peak=    3.732 closest distance to " CD2 LEU A 297 " =    0.947
peak=    3.725 closest distance to " O   HOH Z 126 " =    2.012
peak=    3.723 closest distance to " O   HOH Z 426 " =    1.495
peak=    3.715 closest distance to " O   HOH Z 236 " =    2.010
peak=    3.713 closest distance to " CG2 VAL A  78 " =    0.986
peak=    3.702 closest distance to " O   HOH Z 196 " =    1.165
peak=    3.697 closest distance to " O   HOH Z 180 " =    2.284
peak=    3.693 closest distance to " O   HOH Z 279 " =    2.213
peak=    3.692 closest distance to " CD  ARG A 269 " =    0.908
peak=    3.688 closest distance to " O   HOH Z 357 " =    2.046
peak=    3.684 closest distance to " CZ  PHE A 218 " =    1.122
peak=    3.674 closest distance to " O   HOH Z 245 " =    1.368
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.845
peak=    3.657 closest distance to " O   THR A 251 " =    1.197
peak=    3.654 closest distance to " CB  ALA A 100 " =    1.400
peak=    3.650 closest distance to " O   HOH Z 118 " =    1.486
peak=    3.637 closest distance to " O   HOH Z 128 " =    2.209
peak=    3.636 closest distance to " N   ASN A  39 " =    1.303
peak=    3.630 closest distance to " CB  ASP A 140 " =    0.795
peak=    3.629 closest distance to " NZ  LYS A 117 " =    3.206
peak=    3.626 closest distance to " O   HOH Z 250 " =    1.480
peak=    3.619 closest distance to " ND1 HIS A  81 " =    1.644
peak=    3.618 closest distance to " O   HOH Z  49 " =    1.905
peak=    3.614 closest distance to " NE2 HIS A 115 " =    1.030
peak=    3.612 closest distance to " O   HOH Z 197 " =    2.179
peak=    3.610 closest distance to " NZ  LYS A  76 " =    1.487
peak=    3.609 closest distance to " CA  ARG A  36 " =    1.197
peak=    3.609 closest distance to " O   HOH Z  88 " =    3.557
peak=    3.602 closest distance to " O   HOH Z 316 " =    3.025
peak=    3.602 closest distance to " O   ALA A 165 " =    1.355
peak=    3.600 closest distance to " O   HOH Z 272 " =    1.932
peak=    3.593 closest distance to " O   HOH Z  63 " =    1.794
peak=    3.592 closest distance to " CB  ASN A 187 " =    1.087
peak=    3.591 closest distance to " O   HOH Z 386 " =    2.311
peak=    3.591 closest distance to " OE1 GLN A  11 " =    2.014
peak=    3.587 closest distance to " O   HOH Z 344 " =    3.129
peak=    3.584 closest distance to " O   HOH Z  44 " =    1.806
peak=    3.584 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.579 closest distance to " CB  ALA A 291 " =    1.300
peak=    3.578 closest distance to " O   HOH Z  19 " =    1.859
peak=    3.576 closest distance to " O   HOH Z 303 " =    2.177
peak=    3.572 closest distance to " NZ  LYS A 117 " =    1.779
peak=    3.571 closest distance to " CB  ARG A 139 " =    0.796
peak=    3.565 closest distance to " OG1 THR A 294 " =    2.469
peak=    3.564 closest distance to " CG  GLN A  58 " =    2.599
peak=    3.562 closest distance to " CD2 LEU A 255 " =    1.295
peak=    3.560 closest distance to " CA  GLU A 152 " =    0.910
peak=    3.559 closest distance to " CA  ASP A 162 " =    1.219
peak=    3.556 closest distance to " CD BLYS A 290 " =    1.013
peak=    3.552 closest distance to " CB  ARG A 190 " =    1.075
peak=    3.550 closest distance to " O   HOH Z  30 " =    1.561
peak=    3.550 closest distance to " C   SER A  32 " =    1.044
peak=    3.549 closest distance to " O   HOH Z 389 " =    1.934
peak=    3.543 closest distance to " O   HOH Z 142 " =    1.487
peak=    3.540 closest distance to " O   HOH Z 362 " =    3.552
peak=    3.538 closest distance to " CG2 VAL A 197 " =    1.145
peak=    3.537 closest distance to " CE  LYS A  76 " =    0.825
peak=    3.532 closest distance to " O   HOH Z 102 " =    1.288
peak=    3.530 closest distance to " O   HOH Z 391 " =    2.973
peak=    3.528 closest distance to " O   HOH Z  54 " =    1.621
peak=    3.526 closest distance to " OG BSER A 164 " =    2.352
peak=    3.519 closest distance to " CB  MET A  40 " =    0.816
peak=    3.515 closest distance to " CG AARG A 275 " =    1.161
peak=    3.513 closest distance to " CB  TYR A 116 " =    1.111
peak=    3.513 closest distance to " OD1 ASN A 217 " =    1.679
peak=    3.508 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.506 closest distance to " O   HOH Z 192 " =    1.786
peak=    3.502 closest distance to " O   HOH Z 419 " =    2.948
peak=    3.498 closest distance to " O   HOH Z 227 " =    1.679
peak=    3.494 closest distance to " O   HOH Z   6 " =    2.157
peak=    3.494 closest distance to " CA  ALA A 160 " =    0.894
peak=    3.489 closest distance to " CD2 TRP A 179 " =    1.341
peak=    3.485 closest distance to " CZ  PHE A 192 " =    0.920
peak=    3.481 closest distance to " O   HOH Z 158 " =    2.879
peak=    3.480 closest distance to " O   HOH Z 336 " =    1.700
peak=    3.480 closest distance to " CG1 VAL A 153 " =    1.025
peak=    3.479 closest distance to " CB  ILE A 120 " =    1.284
peak=    3.479 closest distance to " O   HOH Z 327 " =    2.272
peak=    3.477 closest distance to " CA  MET A  40 " =    1.097
peak=    3.472 closest distance to " O   HOH Z 281 " =    4.338
peak=    3.470 closest distance to " O   HOH Z 255 " =    1.682
peak=    3.468 closest distance to " CD1 LEU A  96 " =    0.766
peak=    3.466 closest distance to " O   HOH Z 394 " =    1.721
peak=    3.466 closest distance to " ND2 ASN A 187 " =    1.507
peak=    3.461 closest distance to " CA  ALA A 295 " =    1.089
peak=    3.460 closest distance to " CD1 ILE A 106 " =    0.886
peak=    3.458 closest distance to " CB  ALA A  71 " =    1.282
peak=    3.457 closest distance to " O   HOH Z 419 " =    1.788
peak=    3.455 closest distance to " O   HOH Z 147 " =    1.809
peak=    3.445 closest distance to " O   HOH Z 128 " =    2.163
peak=    3.443 closest distance to " O   HOH Z 124 " =    1.366
peak=    3.443 closest distance to " CA  ASP A 124 " =    0.741
peak=    3.433 closest distance to " OD2 ASP A 298 " =    4.016
peak=    3.432 closest distance to " CB  THR A 157 " =    1.153
peak=    3.423 closest distance to " O   HOH Z 250 " =    1.662
peak=    3.420 closest distance to " O   HOH Z 313 " =    1.957
peak=    3.419 closest distance to " O   HOH Z  64 " =    2.152
peak=    3.417 closest distance to " CB  MET A  47 " =    1.053
peak=    3.409 closest distance to " CA  ALA A  84 " =    1.320
peak=    3.407 closest distance to " O   HOH Z 345 " =    3.260
peak=    3.402 closest distance to " CD  ARG A  66 " =    2.532
peak=    3.399 closest distance to " O   HOH Z 371 " =    3.458
peak=    3.398 closest distance to " O   HOH Z 417 " =    3.286
peak=    3.396 closest distance to " NZ  LYS A 166 " =    3.069
peak=    3.396 closest distance to " CZ  PHE A  38 " =    1.359
peak=    3.395 closest distance to " CA  GLU A  46 " =    0.752
peak=    3.395 closest distance to " O   HOH Z 133 " =    1.674
peak=    3.393 closest distance to " O   ALA A 158 " =    1.257
peak=    3.391 closest distance to " OG  SER A  62 " =    3.005
peak=    3.390 closest distance to " CB  PRO A 198 " =    1.077
peak=    3.388 closest distance to " O   HOH Z 345 " =    1.718
peak=    3.386 closest distance to " O   HOH Z 409 " =    2.903
peak=    3.385 closest distance to " O   HOH Z 358 " =    2.093
peak=    3.382 closest distance to " CG  MET A 185 " =    1.202
peak=    3.382 closest distance to " O   HOH Z 185 " =    1.756
peak=    3.381 closest distance to " O   HOH Z 109 " =    2.370
peak=    3.378 closest distance to " CA  GLY A 241 " =    0.774
peak=    3.374 closest distance to " CA  GLN A 223 " =    0.917
peak=    3.365 closest distance to " O   HOH Z 432 " =    1.772
peak=    3.363 closest distance to " CG2 VAL A 257 " =    0.902
peak=    3.361 closest distance to " O   GLN A 278 " =    1.268
peak=    3.361 closest distance to " CG  ARG A 219 " =    1.302
peak=    3.360 closest distance to " O   HOH Z 406 " =    1.565
peak=    3.356 closest distance to " CA  GLU A 152 " =    1.304
peak=    3.348 closest distance to " CD1 TRP A 266 " =    1.160
peak=    3.347 closest distance to " O   HOH Z   1 " =    2.709
peak=    3.344 closest distance to " CA  TYR A 116 " =    1.354
peak=    3.344 closest distance to " O   HOH Z 437 " =    1.433
peak=    3.341 closest distance to " O   HOH Z 387 " =    2.516
peak=    3.339 closest distance to " O   HOH Z 261 " =    1.850
peak=    3.330 closest distance to " CE1 TYR A 186 " =    1.228
peak=    3.329 closest distance to " NH2AARG A 190 " =    1.366
peak=    3.324 closest distance to " OG  SER A  97 " =    3.541
peak=    3.321 closest distance to " O   HOH Z 145 " =    2.439
peak=    3.317 closest distance to " CB  ALA A 242 " =    0.955
peak=    3.314 closest distance to " CA  GLY A 196 " =    0.966
peak=    3.301 closest distance to " O   HOH Z 173 " =    2.137
peak=    3.299 closest distance to " CA  VAL A 125 " =    1.228
peak=    3.299 closest distance to " CD  ARG A 195 " =    0.920
peak=    3.299 closest distance to " O   HOH Z 346 " =    1.539
peak=    3.297 closest distance to " CA  LEU A  83 " =    1.461
peak=    3.290 closest distance to " O   ASP A 124 " =    1.290
peak=    3.290 closest distance to " CA  ILE A  33 " =    1.481
peak=    3.289 closest distance to " CB  SER A  62 " =    0.774
peak=    3.285 closest distance to " ND2 ASN A 301 " =    1.318
peak=    3.285 closest distance to " CB  ASP A 124 " =    0.705
peak=    3.285 closest distance to " O   HOH Z 197 " =    2.163
peak=    3.275 closest distance to " O   HOH Z 132 " =    0.922
peak=    3.275 closest distance to " O   HOH Z 286 " =    2.196
peak=    3.273 closest distance to " CB  LEU A  83 " =    0.841
peak=    3.272 closest distance to " O   HOH Z 427 " =    2.948
peak=    3.270 closest distance to " O   HOH Z 295 " =    1.455
peak=    3.266 closest distance to " O   HOH Z 423 " =    3.357
peak=    3.265 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.262 closest distance to " O   HOH Z 299 " =    2.336
peak=    3.257 closest distance to " OG  SER A 245 " =    1.625
peak=    3.251 closest distance to " CG  GLU A  37 " =    0.975
peak=    3.246 closest distance to " CG BARG A 275 " =    1.449
peak=    3.242 closest distance to " CB  VAL A 265 " =    1.190
peak=    3.242 closest distance to " CB  TYR A  30 " =    1.404
peak=    3.241 closest distance to " O   TRP A 274 " =    1.861
peak=    3.241 closest distance to " CB  SER A 216 " =    0.828
peak=    3.240 closest distance to " CB  ASN A 127 " =    1.034
peak=    3.238 closest distance to " O   VAL A  72 " =    3.278
peak=    3.238 closest distance to " O   HOH Z 305 " =    3.754
peak=    3.235 closest distance to " NH1AARG A 145 " =    1.049
peak=    3.235 closest distance to " CB  ARG A 259 " =    1.888
peak=    3.226 closest distance to " CG2 THR A 220 " =    0.806
peak=    3.224 closest distance to " CG1 VAL A 174 " =    1.227
peak=    3.223 closest distance to " O   HOH Z  66 " =    2.199
peak=    3.219 closest distance to " O   HOH Z 104 " =    2.642
peak=    3.217 closest distance to " O   HOH Z 416 " =    2.933
peak=    3.215 closest distance to " O   GLY A  57 " =    2.613
peak=    3.213 closest distance to " O   HOH Z 162 " =    1.603
peak=    3.212 closest distance to " O   HOH Z  20 " =    1.906
peak=    3.211 closest distance to " CG1BVAL A  72 " =    1.793
peak=    3.206 closest distance to " O   HOH Z 411 " =    1.755
peak=    3.203 closest distance to " CG2 ILE A  20 " =    1.287
peak=    3.195 closest distance to " CA  ASP A 140 " =    1.156
peak=    3.193 closest distance to " ND2 ASN A 110 " =    1.611
peak=    3.192 closest distance to " CB  ASN A 142 " =    1.184
peak=    3.176 closest distance to " O   HOH Z  97 " =    2.687
peak=    3.173 closest distance to " O   HOH Z 301 " =    1.433
peak=    3.164 closest distance to " O   HOH Z 130 " =    2.158
peak=    3.161 closest distance to " CA  ALA A 100 " =    1.239
peak=    3.160 closest distance to " CB  PHE A  16 " =    1.040
peak=    3.159 closest distance to " CZ3 TRP A  85 " =    0.959
peak=    3.158 closest distance to " CB  PRO A 243 " =    1.120
peak=    3.157 closest distance to " O   HOH Z 134 " =    2.377
peak=    3.155 closest distance to " O   HOH Z 368 " =    4.547
peak=    3.152 closest distance to " O   HOH Z 258 " =    2.221
peak=    3.151 closest distance to " O   HOH Z 126 " =    1.651
peak=    3.148 closest distance to " O   HOH Z 353 " =    2.837
peak=    3.146 closest distance to " CA  SER A  87 " =    0.980
peak=    3.139 closest distance to " CB  ALA A   9 " =    1.538
peak=    3.137 closest distance to " CB  ALA A 256 " =    1.236
peak=    3.135 closest distance to " CA  SER A  32 " =    1.648
peak=    3.135 closest distance to " O   HOH Z 359 " =    3.947
peak=    3.134 closest distance to " C   GLY A  80 " =    1.097
peak=    3.131 closest distance to " N   ASN A 127 " =    1.234
peak=    3.129 closest distance to " OG  SER A  22 " =    2.878
peak=    3.123 closest distance to " O   HOH Z 420 " =    1.947
peak=    3.122 closest distance to " CD1AILE A 234 " =    0.860
peak=    3.111 closest distance to " O   HOH Z 368 " =    2.604
peak=    3.110 closest distance to " O   HOH Z 112 " =    1.583
peak=    3.110 closest distance to " CG2 ILE A 120 " =    0.993
peak=    3.110 closest distance to " O   HOH Z 214 " =    2.355
peak=    3.103 closest distance to " O   HOH Z 365 " =    2.945
peak=    3.094 closest distance to " CB  PRO A 163 " =    4.059
peak=    3.092 closest distance to " CA  VAL A  41 " =    0.891
peak=    3.092 closest distance to " CG2 THR A  42 " =    0.921
peak=    3.089 closest distance to " CA  ALA A 158 " =    1.122
peak=    3.088 closest distance to " CB  GLU A  46 " =    1.114
peak=    3.083 closest distance to " O   HOH Z  99 " =    2.283
peak=    3.083 closest distance to " OH  TYR A 116 " =    1.127
peak=    3.078 closest distance to " O   HOH Z  29 " =    2.771
peak=    3.067 closest distance to " O  BHOH Z 338 " =    2.222
peak=    3.027 closest distance to " O   HOH Z 137 " =    1.714
peak=    3.013 closest distance to " O   PHE A 155 " =    1.444
peak=    3.004 closest distance to " O   HOH Z 421 " =    2.116

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 224         
Filter by distance & map next to the model:
   mapped sites are within: 0.785 - 5.835
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 224
   mapped sites are within: 0.785 - 5.835

peak=   -4.666 closest distance to " O   HOH Z 266 " =    4.686
peak=   -4.351 closest distance to " CD  ARG A 156 " =    2.085
peak=   -4.222 closest distance to " O   HOH Z 155 " =    1.675
peak=   -4.145 closest distance to " CH2 TRP A 179 " =    1.177
peak=   -4.118 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -4.088 closest distance to " CD2 LEU A 237 " =    2.627
peak=   -4.088 closest distance to " N   ALA A  43 " =    2.637
peak=   -4.030 closest distance to " O   HOH Z  52 " =    1.688
peak=   -4.029 closest distance to " O   HOH Z   5 " =    1.586
peak=   -4.015 closest distance to " OXT GLY A 302 " =    2.868
peak=   -3.971 closest distance to " O   HOH Z 210 " =    0.785
peak=   -3.968 closest distance to " O   HOH Z 166 " =    1.720
peak=   -3.965 closest distance to " O   HOH Z 377 " =    1.071
peak=   -3.958 closest distance to " NH2 ARG A  66 " =    1.578
peak=   -3.954 closest distance to " CG  ARG A  66 " =    2.456
peak=   -3.951 closest distance to " O   PRO A 163 " =    2.163
peak=   -3.947 closest distance to " O   HOH Z 407 " =    3.744
peak=   -3.945 closest distance to " CD1 LEU A 101 " =    2.580
peak=   -3.908 closest distance to " O   PRO A 198 " =    1.331
peak=   -3.892 closest distance to " O   HOH Z 292 " =    4.515
peak=   -3.853 closest distance to " O   HOH Z 290 " =    1.123
peak=   -3.846 closest distance to " O   HOH Z 283 " =    2.071
peak=   -3.845 closest distance to " C   HIS A 108 " =    1.114
peak=   -3.832 closest distance to " OG  SER A  97 " =    2.230
peak=   -3.827 closest distance to " CD1 PHE A  59 " =    1.921
peak=   -3.802 closest distance to " CG  ASP A 231 " =    0.862
peak=   -3.787 closest distance to " CD  GLN A 223 " =    1.234
peak=   -3.786 closest distance to " CB  PRO A 243 " =    2.658
peak=   -3.778 closest distance to " O   VAL A  67 " =    2.717
peak=   -3.770 closest distance to " C   SER A 206 " =    1.459
peak=   -3.765 closest distance to " CB  ALA A 291 " =    2.475
peak=   -3.765 closest distance to " CD2 LEU A 300 " =    2.863
peak=   -3.765 closest distance to " C   ASN A 285 " =    2.481
peak=   -3.763 closest distance to " ND2 ASN A  45 " =    1.824
peak=   -3.762 closest distance to " O   HOH Z 394 " =    1.540
peak=   -3.759 closest distance to " OD1 ASN A 148 " =    1.573
peak=   -3.757 closest distance to " O   HOH Z 377 " =    2.142
peak=   -3.749 closest distance to " O   HOH Z 165 " =    1.941
peak=   -3.736 closest distance to " O   HOH Z  43 " =    1.456
peak=   -3.715 closest distance to " O   HOH Z  17 " =    1.367
peak=   -3.715 closest distance to " OH  TYR A 169 " =    1.036
peak=   -3.714 closest distance to " O   HOH Z  19 " =    2.171
peak=   -3.713 closest distance to " CA  ASP A 298 " =    1.062
peak=   -3.674 closest distance to " CD1 LEU A 228 " =    2.415
peak=   -3.673 closest distance to " O   HOH Z 234 " =    4.388
peak=   -3.667 closest distance to " OD1 ASP A 191 " =    1.798
peak=   -3.655 closest distance to " CG1 VAL A 112 " =    2.566
peak=   -3.648 closest distance to " CA  VAL A  67 " =    2.794
peak=   -3.635 closest distance to " ND2 ASN A 187 " =    1.626
peak=   -3.617 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.612 closest distance to " CD  ARG A 139 " =    1.558
peak=   -3.605 closest distance to " CD  ARG A  14 " =    3.524
peak=   -3.604 closest distance to " O   HOH Z 196 " =    2.497
peak=   -3.601 closest distance to " OG  SER A  26 " =    1.402
peak=   -3.600 closest distance to " CD2 LEU A 167 " =    1.788
peak=   -3.596 closest distance to " O   HOH Z 353 " =    2.258
peak=   -3.595 closest distance to " O   ALA A   1 " =    2.006
peak=   -3.590 closest distance to " N   THR A 235 " =    1.316
peak=   -3.590 closest distance to " O   HOH Z  58 " =    1.055
peak=   -3.581 closest distance to " CG  GLU A  53 " =    1.450
peak=   -3.581 closest distance to " CD2 TYR A 293 " =    2.051
peak=   -3.580 closest distance to " O   ILE A 109 " =    2.647
peak=   -3.580 closest distance to " O   HOH Z 426 " =    1.761
peak=   -3.550 closest distance to " ND2 ASN A  45 " =    1.065
peak=   -3.550 closest distance to " O   HOH Z  71 " =    1.630
peak=   -3.549 closest distance to " O   HOH Z 252 " =    3.948
peak=   -3.547 closest distance to " O   HOH Z  15 " =    1.529
peak=   -3.547 closest distance to " O   HOH Z  37 " =    1.871
peak=   -3.539 closest distance to " O   HOH Z 150 " =    1.240
peak=   -3.539 closest distance to " CB  ALA A 291 " =    2.391
peak=   -3.538 closest distance to " O   HOH Z 372 " =    2.580
peak=   -3.537 closest distance to " OG ASER A 134 " =    1.218
peak=   -3.524 closest distance to " OG  SER A  62 " =    1.486
peak=   -3.517 closest distance to " CB  CYS A 254 " =    2.522
peak=   -3.516 closest distance to " C   ALA A 158 " =    1.184
peak=   -3.509 closest distance to " O   SER A 210 " =    1.924
peak=   -3.509 closest distance to " CD  GLN A  58 " =    1.200
peak=   -3.494 closest distance to " N   MET A 188 " =    1.896
peak=   -3.494 closest distance to " O   HOH Z 118 " =    3.384
peak=   -3.487 closest distance to " CA  GLY A  98 " =    2.196
peak=   -3.484 closest distance to " OD2 ASP A 171 " =    1.916
peak=   -3.483 closest distance to " O   VAL A 189 " =    2.661
peak=   -3.467 closest distance to " O   HOH Z 313 " =    1.255
peak=   -3.459 closest distance to " CB  ASP A 132 " =    2.374
peak=   -3.459 closest distance to " CA  GLY A 203 " =    2.241
peak=   -3.455 closest distance to " O   HOH Z 185 " =    2.471
peak=   -3.452 closest distance to " ND2 ASN A  60 " =    1.700
peak=   -3.451 closest distance to " OE2 GLU A   2 " =    1.440
peak=   -3.450 closest distance to " N   GLN A  58 " =    1.592
peak=   -3.447 closest distance to " O   HOH Z 417 " =    2.765
peak=   -3.447 closest distance to " O   HOH Z 111 " =    1.327
peak=   -3.442 closest distance to " CA  GLY A 133 " =    2.353
peak=   -3.439 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -3.427 closest distance to " CZ  PHE A  38 " =    1.946
peak=   -3.424 closest distance to " CB  ALA A  10 " =    2.119
peak=   -3.423 closest distance to " O   HOH Z  38 " =    1.281
peak=   -3.420 closest distance to " NE2 GLN A 103 " =    1.709
peak=   -3.420 closest distance to " O   VAL A 125 " =    2.211
peak=   -3.419 closest distance to " O   HOH Z 231 " =    2.307
peak=   -3.416 closest distance to " N   ALA A 226 " =    2.134
peak=   -3.410 closest distance to " O   ALA A  10 " =    1.844
peak=   -3.408 closest distance to " O   HOH Z 298 " =    2.841
peak=   -3.405 closest distance to " CA  TYR A  68 " =    2.743
peak=   -3.399 closest distance to " CG2 ILE A 263 " =    2.334
peak=   -3.379 closest distance to " CD2 PHE A  59 " =    2.443
peak=   -3.376 closest distance to " O   HOH Z 117 " =    4.494
peak=   -3.375 closest distance to " O   HOH Z 241 " =    1.100
peak=   -3.369 closest distance to " CG  MET A 105 " =    0.872
peak=   -3.366 closest distance to " O   HOH Z 351 " =    1.579
peak=   -3.366 closest distance to " CE2 PHE A  61 " =    2.541
peak=   -3.365 closest distance to " O   HOH Z 414 " =    1.581
peak=   -3.358 closest distance to " CB  PRO A 163 " =    2.704
peak=   -3.358 closest distance to " CZ  ARG A  66 " =    1.201
peak=   -3.358 closest distance to " CB  ALA A 248 " =    2.049
peak=   -3.355 closest distance to " CD1 LEU A 167 " =    2.137
peak=   -3.353 closest distance to " O   HOH Z   6 " =    1.631
peak=   -3.348 closest distance to " O   HOH Z 128 " =    2.476
peak=   -3.342 closest distance to " O   HOH Z 311 " =    3.762
peak=   -3.341 closest distance to " O   GLY A 196 " =    1.129
peak=   -3.336 closest distance to " CD  GLN A  88 " =    0.871
peak=   -3.336 closest distance to " CG  ARG A 269 " =    2.339
peak=   -3.335 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.332 closest distance to " CD  GLN A 223 " =    0.906
peak=   -3.327 closest distance to " O   HOH Z  30 " =    0.845
peak=   -3.324 closest distance to " CA  GLY A 241 " =    2.260
peak=   -3.324 closest distance to " OD1 ASN A 187 " =    1.761
peak=   -3.323 closest distance to " CD2 PHE A 225 " =    1.264
peak=   -3.319 closest distance to " O   HOH Z 399 " =    2.208
peak=   -3.319 closest distance to " N   SER A 276 " =    1.485
peak=   -3.319 closest distance to " O   HOH Z 166 " =    1.795
peak=   -3.317 closest distance to " CB  ASN A  39 " =    2.229
peak=   -3.317 closest distance to " OD2 ASP A 171 " =    2.433
peak=   -3.316 closest distance to " O   HOH Z 393 " =    1.622
peak=   -3.315 closest distance to " CG  PRO A 243 " =    1.778
peak=   -3.314 closest distance to " O   HOH Z 350 " =    1.767
peak=   -3.305 closest distance to " CG  PRO A 163 " =    2.480
peak=   -3.303 closest distance to " OE1 GLN A 223 " =    2.142
peak=   -3.301 closest distance to " O   ALA A  34 " =    2.529
peak=   -3.297 closest distance to " O   HOH Z 150 " =    1.617
peak=   -3.296 closest distance to " CD  LYS A 289 " =    2.443
peak=   -3.293 closest distance to " O   HOH Z 236 " =    1.437
peak=   -3.293 closest distance to " OG BSER A 210 " =    1.294
peak=   -3.292 closest distance to " OE2 GLU A 152 " =    2.309
peak=   -3.292 closest distance to " ND2 ASN A 249 " =    2.235
peak=   -3.292 closest distance to " NH1 ARG A 195 " =    2.656
peak=   -3.290 closest distance to " CB  ASP A 286 " =    2.281
peak=   -3.286 closest distance to " O   HOH Z  90 " =    1.866
peak=   -3.286 closest distance to " CA  VAL A 197 " =    1.006
peak=   -3.286 closest distance to " O   HOH Z 177 " =    1.691
peak=   -3.281 closest distance to " O   HOH Z 322 " =    1.427
peak=   -3.280 closest distance to " CE3 TRP A 274 " =    2.464
peak=   -3.277 closest distance to " O   HOH Z 198 " =    2.391
peak=   -3.277 closest distance to " C   THR A 279 " =    1.096
peak=   -3.272 closest distance to " O   HOH Z 407 " =    0.969
peak=   -3.268 closest distance to " OG BSER A 134 " =    1.233
peak=   -3.267 closest distance to " CB  PHE A  16 " =    2.673
peak=   -3.257 closest distance to " OG BSER A 134 " =    1.885
peak=   -3.252 closest distance to " OD2 ASP A  50 " =    2.313
peak=   -3.243 closest distance to " O   HOH Z 111 " =    2.033
peak=   -3.243 closest distance to " O   HOH Z 396 " =    1.739
peak=   -3.239 closest distance to " O   GLY A 211 " =    1.486
peak=   -3.239 closest distance to " O   GLY A 118 " =    2.244
peak=   -3.236 closest distance to " O   HOH Z 252 " =    3.894
peak=   -3.230 closest distance to " C   LEU A 143 " =    1.197
peak=   -3.224 closest distance to " CG2 THR A   4 " =    1.964
peak=   -3.223 closest distance to " O   HOH Z 275 " =    1.515
peak=   -3.208 closest distance to " O   HOH Z  91 " =    2.119
peak=   -3.206 closest distance to " OG BSER A 210 " =    2.186
peak=   -3.205 closest distance to " CD  ARG A 195 " =    5.080
peak=   -3.200 closest distance to " CA  GLY A 241 " =    3.064
peak=   -3.195 closest distance to " CE  MET A  93 " =    1.308
peak=   -3.193 closest distance to " O   HOH Z  97 " =    1.663
peak=   -3.189 closest distance to " CB  PHE A 192 " =    1.933
peak=   -3.188 closest distance to " CD1 LEU A 222 " =    2.516
peak=   -3.187 closest distance to " CB  TRP A  85 " =    2.390
peak=   -3.182 closest distance to " NE2 GLN A  58 " =    1.018
peak=   -3.182 closest distance to " CD1 LEU A 101 " =    2.922
peak=   -3.181 closest distance to " OD1 ASN A  39 " =    2.304
peak=   -3.180 closest distance to " O   PHE A 218 " =    1.548
peak=   -3.171 closest distance to " O   HOH Z 385 " =    3.945
peak=   -3.170 closest distance to " O   LEU A 167 " =    1.641
peak=   -3.169 closest distance to " O   HOH Z 156 " =    3.479
peak=   -3.167 closest distance to " OD1 ASP A 171 " =    1.450
peak=   -3.162 closest distance to " N   LEU A 281 " =    1.742
peak=   -3.161 closest distance to " O   HOH Z 423 " =    2.344
peak=   -3.161 closest distance to " CE  MET A 105 " =    2.087
peak=   -3.159 closest distance to " O   HOH Z 191 " =    5.835
peak=   -3.158 closest distance to " O   HOH Z  11 " =    1.787
peak=   -3.156 closest distance to " CG  LYS A 119 " =    2.927
peak=   -3.154 closest distance to " O   ASN A 301 " =    1.351
peak=   -3.154 closest distance to " NE1 TRP A 266 " =    2.251
peak=   -3.152 closest distance to " CE BMET A  47 " =    2.322
peak=   -3.148 closest distance to " NH2 ARG A 159 " =    2.421
peak=   -3.145 closest distance to " O   HOH Z 380 " =    4.592
peak=   -3.145 closest distance to " NE  ARG A 259 " =    1.119
peak=   -3.142 closest distance to " O   HOH Z 231 " =    1.525
peak=   -3.141 closest distance to " O   HOH Z 200 " =    1.352
peak=   -3.139 closest distance to " ND2 ASN A  60 " =    1.695
peak=   -3.128 closest distance to " O   HOH Z 134 " =    2.098
peak=   -3.113 closest distance to " O   GLN A 240 " =    2.371
peak=   -3.111 closest distance to " O   HOH Z 389 " =    1.789
peak=   -3.110 closest distance to " CG  GLN A  58 " =    1.182
peak=   -3.109 closest distance to " O   PRO A 198 " =    1.366
peak=   -3.105 closest distance to " O   HOH Z 246 " =    1.501
peak=   -3.103 closest distance to " NE2 GLN A  88 " =    1.924
peak=   -3.101 closest distance to " O   HOH Z 418 " =    1.437
peak=   -3.091 closest distance to " O   HOH Z 151 " =    1.560
peak=   -3.088 closest distance to " O   HOH Z 422 " =    1.122
peak=   -3.085 closest distance to " O   HOH Z 171 " =    2.305
peak=   -3.083 closest distance to " CG1 VAL A 197 " =    2.326
peak=   -3.079 closest distance to " O   HOH Z 176 " =    1.067
peak=   -3.077 closest distance to " CG2 VAL A 189 " =    2.204
peak=   -3.072 closest distance to " OG1 THR A 178 " =    1.414
peak=   -3.068 closest distance to " O   HOH Z 149 " =    1.955
peak=   -3.052 closest distance to " O   ASP A  27 " =    2.171
peak=   -3.050 closest distance to " O   HOH Z 430 " =    5.685
peak=   -3.042 closest distance to " O   HOH Z 264 " =    1.840
peak=   -3.038 closest distance to " O   HOH Z  61 " =    1.536
peak=   -3.032 closest distance to " CD  GLN A  88 " =    0.923
peak=   -3.030 closest distance to " CD1 TYR A 247 " =    2.121
peak=   -3.026 closest distance to " SD  MET A 188 " =    2.362
peak=   -3.020 closest distance to " OD2 ASP A  65 " =    1.894
peak=   -3.016 closest distance to " O   PRO A 198 " =    1.727

================= 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    :  0.4292 0.4141   6.236023e+00   6.213192e+00
   1_bss:  0.4195 0.4052   6.226523e+00   6.197655e+00
   1_xyz:  0.3097 0.3417   6.005310e+00   6.077803e+00
   1_adp:  0.2831 0.3488   5.955761e+00   6.089615e+00
   1_occ:  0.2828 0.3485   5.954454e+00   6.089236e+00
   2_bss:  0.2813 0.3464   5.953643e+00   6.087191e+00
   2_xyz:  0.2025 0.2496   5.641822e+00   5.811008e+00
   2_adp:  0.1758 0.2235   5.526843e+00   5.717100e+00
   2_occ:  0.1757 0.2234   5.526217e+00   5.716501e+00
   3_bss:  0.1751 0.2227   5.522846e+00   5.711688e+00
   3_xyz:  0.1365 0.1813   5.306766e+00   5.526647e+00
   3_adp:  0.1279 0.1727   5.254324e+00   5.479681e+00
   3_occ:  0.1278 0.1725   5.253873e+00   5.479504e+00
   4_bss:  0.1280 0.1729   5.254773e+00   5.479870e+00
   4_xyz:  0.1244 0.1683   5.232698e+00   5.455341e+00
   4_adp:  0.1241 0.1680   5.229147e+00   5.450313e+00
   4_occ:  0.1240 0.1680   5.229028e+00   5.450491e+00
   5_bss:  0.1240 0.1680   5.228959e+00   5.450369e+00
   5_xyz:  0.1164 0.1632   5.183066e+00   5.418912e+00
   5_adp:  0.1151 0.1633   5.178978e+00   5.420628e+00
   5_occ:  0.1151 0.1633   5.179251e+00   5.421181e+00
   5_bss:  0.1150 0.1632   5.179358e+00   5.421273e+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:  0.278  20.000  -0.857   4.375  -0.963   0.000  -0.000  -0.000
   1_xyz:  0.278  20.000  -0.857   4.375  -0.963   0.000  -0.000  -0.000
   1_adp:  0.278  20.000  -0.857   4.375  -0.963   0.000  -0.000  -0.000
   1_occ:  0.278  20.000  -0.857   4.375  -0.963   0.000  -0.000  -0.000
   2_bss:  0.319  60.177  -1.245   1.891  -0.917   0.000  -0.000  -0.000
   2_xyz:  0.319  60.177  -1.245   1.891  -0.917   0.000  -0.000  -0.000
   2_adp:  0.319  60.177  -1.245   1.891  -0.917   0.000  -0.000  -0.000
   2_occ:  0.319  60.177  -1.245   1.891  -0.917   0.000  -0.000  -0.000
   3_bss:  0.315  60.177  -1.440   0.048  -0.975   0.000  -0.000  -0.000
   3_xyz:  0.315  60.177  -1.440   0.048  -0.975   0.000  -0.000  -0.000
   3_adp:  0.315  60.177  -1.440   0.048  -0.975   0.000  -0.000  -0.000
   3_occ:  0.315  60.177  -1.440   0.048  -0.975   0.000  -0.000  -0.000
   4_bss:  0.325  64.163  -1.695  -0.804  -1.119  -0.000  -0.000  -0.000
   4_xyz:  0.325  64.163  -1.695  -0.804  -1.119  -0.000  -0.000  -0.000
   4_adp:  0.325  64.163  -1.695  -0.804  -1.119  -0.000  -0.000  -0.000
   4_occ:  0.325  64.163  -1.695  -0.804  -1.119  -0.000  -0.000  -0.000
   5_bss:  0.323  61.450  -1.742  -1.046  -1.087  -0.000  -0.000  -0.000
   5_xyz:  0.323  61.450  -1.742  -1.046  -1.087  -0.000  -0.000  -0.000
   5_adp:  0.323  61.450  -1.742  -1.046  -1.087  -0.000  -0.000  -0.000
   5_occ:  0.323  61.450  -1.742  -1.046  -1.087  -0.000  -0.000  -0.000
   5_bss:  0.323  61.433  -1.481  -0.927  -0.843  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.551 0.5527  0.7218    53591.426
   1_bss:  46.702 0.5613  0.7532    50461.371
   1_xyz:  37.471 0.6728  0.8768    33717.152
   1_adp:  38.220 0.6633  0.8561    34697.842
   1_occ:  38.173 0.6638  0.8562    34596.108
   2_bss:  37.921 0.6669  0.8371    34319.351
   2_xyz:  25.565 0.8041  0.9625    16173.798
   2_adp:  22.228 0.8392  0.9738    13047.951
   2_occ:  22.210 0.8394  0.9739    13022.762
   3_bss:  22.023 0.8412  0.9524    12803.152
   3_xyz:  17.325 0.8858  0.9802     8468.132
   3_adp:  16.107 0.8972  0.9797     7775.827
   3_occ:  16.097 0.8973  0.9796     7771.100
   4_bss:  16.109 0.8972  0.9660     7789.820
   4_xyz:  15.526 0.9024  0.9674     7329.295
   4_adp:  15.379 0.9038  0.9630     7301.185
   4_occ:  15.382 0.9038  0.9629     7305.281
   5_bss:  15.379 0.9038  0.9602     7300.757
   5_xyz:  14.760 0.9088  0.9635     6841.171
   5_adp:  14.772 0.9087  0.9577     6852.289
   5_occ:  14.783 0.9087  0.9575     6859.507
   5_bss:  14.786 0.9086  0.9640     6861.038
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.7086e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.7086e-01
   1_xyz:   1.470  0.011  0.091 15.779  0.006  4.116   1.1193e-01
   1_adp:   1.470  0.011  0.091 15.779  0.006  4.116   1.1193e-01
   1_occ:   1.470  0.011  0.091 15.779  0.006  4.116   1.1193e-01
   2_bss:   1.470  0.011  0.091 15.779  0.006  4.116   1.1193e-01
   2_xyz:   1.377  0.011  0.091 14.829  0.005  4.116   1.0436e-01
   2_adp:   1.377  0.011  0.091 14.829  0.005  4.116   1.0436e-01
   2_occ:   1.377  0.011  0.091 14.829  0.005  4.116   1.0436e-01
   3_bss:   1.377  0.011  0.091 14.829  0.005  4.116   1.0436e-01
   3_xyz:   1.149  0.010  0.079 14.750  0.004  4.129   7.6816e-02
   3_adp:   1.149  0.010  0.079 14.750  0.004  4.129   7.6816e-02
   3_occ:   1.149  0.010  0.079 14.750  0.004  4.129   7.6816e-02
   4_bss:   1.149  0.010  0.079 14.750  0.004  4.129   7.6816e-02
   4_xyz:   0.976  0.007  0.071 14.279  0.004  4.133   5.5563e-02
   4_adp:   0.976  0.007  0.071 14.279  0.004  4.133   5.5563e-02
   4_occ:   0.976  0.007  0.071 14.279  0.004  4.133   5.5563e-02
   5_bss:   0.976  0.007  0.071 14.279  0.004  4.133   5.5563e-02
   5_xyz:   1.101  0.009  0.080 14.594  0.004  4.116   6.8985e-02
   5_adp:   1.101  0.009  0.080 14.594  0.004  4.116   6.8985e-02
   5_occ:   1.101  0.009  0.080 14.594  0.004  4.116   6.8985e-02
   5_bss:   1.101  0.009  0.080 14.594  0.004  4.116   6.8985e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.508   2.4324e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.508   2.4324e-01
   1_xyz:  11.443  0.067  0.364 85.109  0.030  2.125   1.0628e-01
   1_adp:  11.443  0.067  0.364 85.109  0.030  2.125   1.0628e-01
   1_occ:  11.443  0.067  0.364 85.109  0.030  2.125   1.0628e-01
   2_bss:  11.443  0.067  0.364 85.109  0.030  2.125   1.0628e-01
   2_xyz:   8.359  0.082  0.280 82.305  0.050  2.153   1.9917e-01
   2_adp:   8.359  0.082  0.280 82.305  0.050  2.153   1.9917e-01
   2_occ:   8.359  0.082  0.280 82.305  0.050  2.153   1.9917e-01
   3_bss:   8.359  0.082  0.280 82.305  0.050  2.153   1.9917e-01
   3_xyz:   7.714  0.071  0.249 83.270  0.034  2.214   6.2528e-02
   3_adp:   7.714  0.071  0.249 83.270  0.034  2.214   6.2528e-02
   3_occ:   7.714  0.071  0.249 83.270  0.034  2.214   6.2528e-02
   4_bss:   7.714  0.071  0.249 83.270  0.034  2.214   6.2528e-02
   4_xyz:   7.212  0.037  0.241 82.763  0.036  2.384   4.8419e-02
   4_adp:   7.212  0.037  0.241 82.763  0.036  2.384   4.8419e-02
   4_occ:   7.212  0.037  0.241 82.763  0.036  2.384   4.8419e-02
   5_bss:   7.212  0.037  0.241 82.763  0.036  2.384   4.8419e-02
   5_xyz:   8.138  0.046  0.263 82.687  0.031  2.297   4.3051e-02
   5_adp:   8.138  0.046  0.263 82.687  0.031  2.297   4.3051e-02
   5_occ:   8.138  0.046  0.263 82.687  0.031  2.297   4.3051e-02
   5_bss:   8.138  0.046  0.263 82.687  0.031  2.297   4.3051e-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:  94.88   0.00  17.74  84.50   0.00  14.13  94.88   1.71  37.38
   1_occ:  94.88   0.00  17.74  84.50   0.00  14.13  94.88   1.71  37.38
   2_bss:  94.88   0.00  17.74  84.50   0.00  14.13  94.88   1.71  37.38
   2_xyz:  94.88   0.00  17.74  84.50   0.00  14.13  94.88   1.71  37.38
   2_adp:  89.52   0.00  17.44  88.07   0.00  13.06  89.52   3.15  41.30
   2_occ:  89.52   0.00  17.44  88.07   0.00  13.06  89.52   3.15  41.30
   3_bss:  89.52   0.00  17.44  88.07   0.00  13.06  89.52   3.15  41.30
   3_xyz:  89.52   0.00  17.44  88.07   0.00  13.06  89.52   3.15  41.30
   3_adp:  91.36   1.34  16.91  91.36   1.34  12.53  90.07   2.88  40.79
   3_occ:  91.36   1.34  16.91  91.36   1.34  12.53  90.07   2.88  40.79
   4_bss:  91.36   1.34  16.91  91.36   1.34  12.53  90.07   2.88  40.79
   4_xyz:  91.36   1.34  16.91  91.36   1.34  12.53  90.07   2.88  40.79
   4_adp:  90.03   1.28  16.48  90.03   1.28  12.29  87.16   3.82  39.28
   4_occ:  90.03   1.28  16.48  90.03   1.28  12.29  87.16   3.82  39.28
   5_bss:  90.03   1.28  16.48  90.03   1.28  12.29  87.16   3.82  39.28
   5_xyz:  90.03   1.28  16.48  90.03   1.28  12.29  87.16   3.82  39.28
   5_adp:  95.30   0.54  16.49  95.30   0.54  12.19  88.82   4.69  39.92
   5_occ:  95.30   0.54  16.49  95.30   0.54  12.19  88.82   4.69  39.92
   5_bss:  95.28   0.53  16.48  95.28   0.53  12.17  88.80   4.68  39.90
------------------------------------------------------------------------
 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:    1.796    0.025    0.350
   1_adp:    1.796    0.025    0.350
   1_occ:    1.796    0.025    0.350
   2_bss:    1.796    0.025    0.350
   2_xyz:    1.304    0.045    0.601
   2_adp:    1.304    0.045    0.601
   2_occ:    1.304    0.045    0.601
   3_bss:    1.304    0.045    0.601
   3_xyz:    1.414    0.032    0.669
   3_adp:    1.414    0.032    0.669
   3_occ:    1.414    0.032    0.669
   4_bss:    1.414    0.032    0.669
   4_xyz:    1.373    0.033    0.689
   4_adp:    1.373    0.033    0.689
   4_occ:    1.373    0.033    0.689
   5_bss:    1.373    0.033    0.689
   5_xyz:    1.370    0.048    0.709
   5_adp:    1.370    0.048    0.709
   5_occ:    1.370    0.048    0.709
   5_bss:    1.370    0.048    0.709
------------------------------------------------------------------------

CPU time actual refinement: 328.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/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_1070/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1070/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.06 
  Macro-tasks:
    bulk solvent and scale       = 47.25  
    individual site refinement   = 129.60 
    weights calculation          = 28.20  
    collect and process          = 6.54   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 211.67 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 102.91 
    alpha_beta                      = 8.20   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 106.48 
    fmodel                         = 7.51   
    r_factors                      = 0.23   
    phase_errors                   = 11.46  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 239.90 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.702 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    624 calls, 102.36 s
gradients_fft:          569 calls,  95.60 s

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

# Date 2008-01-16 Time 06:21:24 PST -0800 (1200493284.08 s)
Start R-work = 0.4292, R-free = 0.4141 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4195, R-free = 0.4052
Final R-work = 0.1150, R-free = 0.1632