# Date 2008-01-16 Time 04:04:08 PST -0800 (1200485048.52 s)
#phil __OFF__

Command line arguments: "../166.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22817
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 166

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.6953, 84.6622, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96047
Completeness in resolution range: 0.97158
Completeness with d_max=infinity: 0.968506

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6941
                             d_min =   1.9605

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96047
Completeness in resolution range: 0.97158
Completeness with d_max=infinity: 0.968506

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6945 -  4.1940 [2114/2141]  1903   211  10.0%
  bin  2:  4.1940 -  3.3418 [2031/2047]  1827   204  10.0%
  bin  3:  3.3418 -  2.9232 [2016/2035]  1813   203  10.1%
  bin  4:  2.9232 -  2.6576 [1981/2011]  1789   192   9.7%
  bin  5:  2.6576 -  2.4681 [1970/1989]  1769   201  10.2%
  bin  6:  2.4681 -  2.3232 [1963/1999]  1768   195   9.9%
  bin  7:  2.3232 -  2.2072 [1958/1991]  1764   194   9.9%
  bin  8:  2.2072 -  2.1114 [1944/1979]  1746   198  10.2%
  bin  9:  2.1114 -  2.0304 [1939/1966]  1745   194  10.0%
  bin 10:  2.0304 -  1.9605 [1673/2004]  1506   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.06 -     1.83: 11
        1.83 -     2.60: 98
        2.60 -     3.36: 4230
        3.36 -     4.13: 9627
        4.13 -     4.90: 15041
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.059 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.330 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.503 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.581 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.655 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29002 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_166/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4160   r_free= 0.4185   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.209134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.3362 0.3334      6.4718      6.4693|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.3444 0.3347      6.6624      6.6702|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.3697 0.3948       6.561       6.693|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.3877 0.4102      6.4215      6.4576|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.4273 0.4297      6.2966      6.2745|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.4459 0.4489      6.2236      6.1862|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.4460 0.4123       6.181      6.1201|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.4594 0.4426      6.1485      6.1574|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.4880 0.4845      6.0863      6.0839|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.4681 0.5179      6.0688      6.0887|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.4732 0.4738       6.005      6.0524|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.4806 0.4330      5.9548      5.9538|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.4701 0.5137      5.8659      5.8798|
| 14:  2.0094 -  1.9605 0.79    993  118 0.4826 0.4334      5.8315      5.7024|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6774  1374   153  0.72  32.13   0.85     0.74      60502.41|
|  2:  4.6774 -  3.7326  1322   146  0.75  30.86   0.95     0.85      84741.95|
|  3:  3.7326 -  3.2667  1299   146  0.67  37.81   0.98     0.87      90196.40|
|  4:  3.2667 -  2.9707  1285   139  0.60  43.62   0.99     0.82      80548.46|
|  5:  2.9707 -  2.7593  1275   142  0.55  48.02   0.94     0.77      64030.93|
|  6:  2.7593 -  2.5975  1279   146  0.54  48.86   0.94     0.75      54715.41|
|  7:  2.5975 -  2.4681  1267   139  0.54  48.72   0.95     0.76      49843.68|
|  8:  2.4681 -  2.3611  1269   142  0.52  50.77   0.97     0.73      45843.33|
|  9:  2.3611 -  2.2705  1264   139  0.49  53.27   0.96     0.71      42535.01|
| 10:  2.2705 -  2.1925  1243   136  0.50  52.49   1.01     0.70      38895.49|
| 11:  2.1925 -  2.1241  1267   147  0.48  53.95   0.99     0.70      36784.34|
| 12:  2.1241 -  2.0636  1252   128  0.48  53.52   1.01     0.74      33994.55|
| 13:  2.0636 -  2.0094  1241   138  0.49  53.36   1.00     0.73      29370.64|
| 14:  2.0094 -  1.9605   993   118  0.53  50.04   0.98     0.71      21477.97|
|alpha:            min =        0.70 max =            0.87 mean =         0.76|
|beta:             min =    21477.97 max =        90196.40 mean =     53195.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.98 mean =        46.73|
|phase err.(test): min =        0.00 max =           89.96 mean =        46.81|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.319810             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.475558              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.807   (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 |  1.059 -  1.443:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.443 -  1.827:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.827 -  2.211:       23 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.211 -  2.595:       75 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.595 -  2.979:     1822 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.979 -  3.364:     2408 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.364 -  3.748:     3969 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.748 -  4.132:     5658 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.132 -  4.516:     6678 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.516 -  4.900:     8363 |
|-----------------------------------------------------------------------------|
|-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 |        0.210 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.059 |       0.937 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4160   r_free= 0.4185   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.209134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4056   r_free= 0.4053   ksol= 0.33   Bsol= 20.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,-2.29,2.15,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.196129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.482672              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.227   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.744206              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.686   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4056      final r-factor (work) = 0.2291          |
| start r-factor (free) = 0.4053      final r-factor (free) = 0.2498          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.6025 = 9.48 * 0.50 * 6.1992 + 1.00 * 0.2101                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.4143 = 9.48 * 0.50 * 5.9716 + 1.00 * 0.1009                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2291      final r-factor (work) = 0.2090          |
| start r-factor (free) = 0.2498      final r-factor (free) = 0.2591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4503 = 0.74 * 1.00 * 5.9716 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2190 = 0.74 * 1.00 * 5.6470 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.77   18.40    None  None   None       |
|    all(noH): 2823   0      0.00    90.77   18.40    None  None   None       |
|    Sol.    : 438    0      7.42    84.58   42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    90.77   14.03    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 -   9.077:  783   |   5:    45.385 -  54.462:  117        |
|      1:     9.077 -  18.154: 1145   |   6:    54.462 -  63.539:   68        |
|      2:    18.154 -  27.231:  357   |   7:    63.539 -  72.616:   27        |
|      3:    27.231 -  36.308:  160   |   8:    72.616 -  81.693:   22        |
|      4:    36.308 -  45.385:  140   |   9:    81.693 -  90.770:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2090 r_free = 0.2591             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2088 r_free = 0.2589             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2088   r_free= 0.2589   ksol= 0.33   Bsol= 20.00   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.22,-2.29,2.15,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.663040                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2023   r_free= 0.2543   ksol= 0.32   Bsol= 29.76   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.58,-0.95,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.648657                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.822319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.489   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.979   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2023      final r-factor (work) = 0.1478          |
| start r-factor (free) = 0.2543      final r-factor (free) = 0.1951          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0916 = 2.82 * 0.50 * 5.6626 + 1.00 * 0.1009                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8522 = 2.82 * 0.50 * 5.5241 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1478      final r-factor (work) = 0.1380          |
| start r-factor (free) = 0.1951      final r-factor (free) = 0.1820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0629 = 0.19 * 1.00 * 5.5241 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0233 = 0.19 * 1.00 * 5.3422 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.43    92.02   17.56    None  None   None       |
|    all(noH): 2823   0      1.43    92.02   17.56    None  None   None       |
|    Sol.    : 438    0      7.03    80.50   40.02    None  None   None       |
|    Mac.    : 2385   0      1.43    92.02   13.44    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:     1.428 -  10.487: 1056   |   5:    46.726 -  55.786:  110        |
|      1:    10.487 -  19.547: 1083   |   6:    55.786 -  64.846:   47        |
|      2:    19.547 -  28.607:  227   |   7:    64.846 -  73.905:   23        |
|      3:    28.607 -  37.666:  138   |   8:    73.905 -  82.965:    9        |
|      4:    37.666 -  46.726:  129   |   9:    82.965 -  92.025:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1380 r_free = 0.1820             target_work(ml) = 5.299         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1822             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1822   ksol= 0.32   Bsol= 29.76   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-2.58,-0.95,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.298030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1807   ksol= 0.32   Bsol= 30.16   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.55,-1.72,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.294512                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.156605              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.390  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348522              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1376      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1807      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8171 = 2.16 * 0.50 * 5.3420 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6938 = 2.16 * 0.50 * 5.2275 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8296 = 0.35 * 1.00 * 5.2275 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8059 = 0.35 * 1.00 * 5.1583 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    95.12   17.51    None  None   None       |
|    all(noH): 2823   0      1.65    95.12   17.51    None  None   None       |
|    Sol.    : 438    0      6.26    81.11   40.54    None  None   None       |
|    Mac.    : 2385   0      1.65    95.12   13.28    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:     1.648 -  10.995: 1170   |   5:    48.383 -  57.730:  106        |
|      1:    10.995 -  20.342: 1024   |   6:    57.730 -  67.077:   42        |
|      2:    20.342 -  29.689:  195   |   7:    67.077 -  76.425:   19        |
|      3:    29.689 -  39.036:  129   |   8:    76.425 -  85.772:    8        |
|      4:    39.036 -  48.383:  129   |   9:    85.772 -  95.119:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1584             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1583             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1583   ksol= 0.32   Bsol= 30.16   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.55,-1.72,-0.00,-0.00,-0.00); trace/3= -2.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150233                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1582   ksol= 0.31   Bsol= 32.37   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.54,-1.92,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149219                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.249479              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.704  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362555              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.527  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2788 = 1.25 * 0.50 * 5.1578 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2627 = 1.25 * 0.50 * 5.1474 + 1.00 * 0.0469                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8743 = 0.36 * 1.00 * 5.1474 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8711 = 0.36 * 1.00 * 5.1383 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.58    97.49   17.40    None  None   None       |
|    all(noH): 2823   0      1.58    97.49   17.40    None  None   None       |
|    Sol.    : 438    0      6.17    81.72   40.29    None  None   None       |
|    Mac.    : 2385   0      1.58    97.49   13.20    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:     1.577 -  11.168: 1244   |   5:    49.534 -  59.125:   88        |
|      1:    11.168 -  20.759:  977   |   6:    59.125 -  68.717:   41        |
|      2:    20.759 -  30.351:  182   |   7:    68.717 -  78.308:   11        |
|      3:    30.351 -  39.942:  133   |   8:    78.308 -  87.900:    7        |
|      4:    39.942 -  49.534:  138   |   9:    87.900 -  97.491:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1572             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1572             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1572   ksol= 0.31   Bsol= 32.37   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.54,-1.92,-0.00,-0.00,-0.00); trace/3= -2.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.138391                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1570   ksol= 0.31   Bsol= 32.37   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.40,-1.84,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139355                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.294673              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.913  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.412614              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.747  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3736 = 1.29 * 0.50 * 5.1391 + 1.00 * 0.0469                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3682 = 1.29 * 0.50 * 5.1271 + 1.00 * 0.0492                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1237 = 0.41 * 1.00 * 5.1271 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1219 = 0.41 * 1.00 * 5.1225 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.44    97.79   17.29    None  None   None       |
|    all(noH): 2823   0      1.44    97.79   17.29    None  None   None       |
|    Sol.    : 438    0      6.01    81.62   40.13    None  None   None       |
|    Mac.    : 2385   0      1.44    97.79   13.10    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:     1.441 -  11.077: 1230   |   5:    49.617 -  59.252:   83        |
|      1:    11.077 -  20.712:  990   |   6:    59.252 -  68.887:   41        |
|      2:    20.712 -  30.347:  186   |   7:    68.887 -  78.523:   11        |
|      3:    30.347 -  39.982:  129   |   8:    78.523 -  88.158:    7        |
|      4:    39.982 -  49.617:  144   |   9:    88.158 -  97.793:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1559             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1559             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1559   ksol= 0.31   Bsol= 32.37   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.40,-1.84,-0.00,-0.00,-0.00); trace/3= -2.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122232                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.0995 0.1230      5.3719      5.5014|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.0846 0.1157      5.4304      5.6284|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.1042 0.1510       5.463      5.8409|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.1180 0.1559      5.4302      5.5876|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.1216 0.1601      5.2731      5.4574|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.1189 0.1721      5.1828      5.4015|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.1180 0.1602      5.1133      5.3341|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.1154 0.1691      5.0685      5.3203|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.1158 0.1880      5.0061      5.2827|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.1113 0.1759      4.9634      5.2011|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.1107 0.1706      4.9094      5.2686|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.1088 0.1614      4.8509       5.129|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.1113 0.1652      4.7871      5.0292|
| 14:  2.0094 -  1.9605 0.79    993  118 0.1096 0.1871      4.7096      4.9777|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6774  1374   153  0.94   8.72   0.99     0.97       6672.56|
|  2:  4.6774 -  3.7326  1322   146  0.95   7.69   1.03     1.02       8720.97|
|  3:  3.7326 -  3.2667  1299   146  0.94  11.02   1.04     1.03      10104.28|
|  4:  3.2667 -  2.9707  1285   139  0.93  12.57   1.02     1.02       9524.30|
|  5:  2.9707 -  2.7593  1275   142  0.91  14.49   1.00     0.98       7397.88|
|  6:  2.7593 -  2.5975  1279   146  0.91  15.11   0.99     0.96       6495.28|
|  7:  2.5975 -  2.4681  1267   139  0.91  14.83   0.99     0.97       5641.85|
|  8:  2.4681 -  2.3611  1269   142  0.91  14.60   1.00     0.99       5204.66|
|  9:  2.3611 -  2.2705  1264   139  0.91  14.99   1.01     0.99       4729.17|
| 10:  2.2705 -  2.1925  1243   136  0.91  15.14   1.01     0.98       4379.47|
| 11:  2.1925 -  2.1241  1267   147  0.91  15.55   1.01     0.98       4108.63|
| 12:  2.1241 -  2.0636  1252   128  0.92  14.60   1.02     1.00       3714.10|
| 13:  2.0636 -  2.0094  1241   138  0.91  15.34   1.01     1.00       3273.78|
| 14:  2.0094 -  1.9605   993   118  0.91  15.32   1.00     0.97       2759.64|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2759.64 max =        10104.28 mean =      5991.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.49|
|phase err.(test): min =        0.00 max =           89.60 mean =        13.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1559   ksol= 0.32   Bsol= 33.34   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.23,-1.69,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122297                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1559   ksol= 0.32   Bsol= 33.34   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.93,-2.23,-1.69,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122297                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.0996 0.1233      5.3743      5.5046|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.0847 0.1157      5.4312      5.6282|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.1042 0.1510      5.4631      5.8412|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.1180 0.1559      5.4302      5.5874|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.1216 0.1601      5.2729      5.4572|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.1189 0.1720      5.1826       5.401|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.1180 0.1601      5.1129      5.3335|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.1154 0.1690       5.068      5.3198|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.1158 0.1881      5.0059      5.2827|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.1112 0.1758      4.9632      5.2008|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.1107 0.1706      4.9092      5.2685|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.1087 0.1614      4.8507      5.1288|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.1113 0.1652      4.7869      5.0292|
| 14:  2.0094 -  1.9605 0.79    993  118 0.1096 0.1870      4.7092      4.9775|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6945 -  4.6774  1374   153  0.94   8.75   0.99     0.97       6724.48|
|  2:  4.6774 -  3.7326  1322   146  0.95   7.70   1.03     1.03       8748.81|
|  3:  3.7326 -  3.2667  1299   146  0.94  11.02   1.04     1.04      10103.04|
|  4:  3.2667 -  2.9707  1285   139  0.93  12.57   1.03     1.02       9524.39|
|  5:  2.9707 -  2.7593  1275   142  0.91  14.49   1.01     0.98       7395.58|
|  6:  2.7593 -  2.5975  1279   146  0.91  15.11   0.99     0.96       6491.74|
|  7:  2.5975 -  2.4681  1267   139  0.91  14.82   1.00     0.97       5635.18|
|  8:  2.4681 -  2.3611  1269   142  0.91  14.59   1.01     0.99       5198.26|
|  9:  2.3611 -  2.2705  1264   139  0.91  14.99   1.02     1.00       4725.60|
| 10:  2.2705 -  2.1925  1243   136  0.91  15.14   1.02     0.98       4377.96|
| 11:  2.1925 -  2.1241  1267   147  0.91  15.54   1.01     0.98       4106.44|
| 12:  2.1241 -  2.0636  1252   128  0.92  14.59   1.02     1.01       3712.34|
| 13:  2.0636 -  2.0094  1241   138  0.91  15.34   1.02     1.01       3272.13|
| 14:  2.0094 -  1.9605   993   118  0.91  15.32   1.01     0.97       2758.03|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2758.03 max =        10103.04 mean =      5995.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.49|
|phase err.(test): min =        0.00 max =           89.63 mean =        13.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    97.74   17.24    None  None   None       |
|    all(noH): 2823   0      1.39    97.74   17.24    None  None   None       |
|    Sol.    : 438    0      5.96    81.57   40.08    None  None   None       |
|    Mac.    : 2385   0      1.39    97.74   13.05    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:     1.390 -  11.025: 1230   |   5:    49.566 -  59.201:   83        |
|      1:    11.025 -  20.661:  990   |   6:    59.201 -  68.836:   41        |
|      2:    20.661 -  30.296:  186   |   7:    68.836 -  78.472:   11        |
|      3:    30.296 -  39.931:  129   |   8:    78.472 -  88.107:    7        |
|      4:    39.931 -  49.566:  144   |   9:    88.107 -  97.742:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.407 - 5.816
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 296
   mapped sites are within: 0.715 - 5.816

peak=    6.208 closest distance to " O   HOH Z 142 " =    1.892
peak=    5.964 closest distance to " O   HOH Z 126 " =    1.933
peak=    5.726 closest distance to " NE2 GLN A  11 " =    1.123
peak=    5.641 closest distance to " O   HOH Z  52 " =    1.527
peak=    5.633 closest distance to " CB  ARG A 275 " =    0.969
peak=    5.586 closest distance to " NH2 ARG A  56 " =    2.078
peak=    5.550 closest distance to " CG  PRO A  54 " =    1.240
peak=    5.514 closest distance to " O   HOH Z 236 " =    1.452
peak=    5.379 closest distance to " O   HOH Z 193 " =    1.671
peak=    5.277 closest distance to " CG  PRO A 213 " =    1.314
peak=    5.182 closest distance to " O   HOH Z 124 " =    1.487
peak=    4.962 closest distance to " O   HOH Z 272 " =    1.902
peak=    4.931 closest distance to " CG  PRO A  90 " =    1.172
peak=    4.868 closest distance to " CB  GLN A 223 " =    1.526
peak=    4.847 closest distance to " O   HOH Z 427 " =    2.714
peak=    4.793 closest distance to " O   HOH Z  78 " =    1.745
peak=    4.765 closest distance to " O   HOH Z 402 " =    1.449
peak=    4.763 closest distance to " O   HOH Z 209 " =    2.234
peak=    4.713 closest distance to " CB  SER A  63 " =    1.147
peak=    4.654 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.643 closest distance to " O   HOH Z 232 " =    2.331
peak=    4.589 closest distance to " C   PRO A 198 " =    1.548
peak=    4.543 closest distance to " CB  GLN A 183 " =    1.205
peak=    4.534 closest distance to " O   HOH Z  59 " =    1.872
peak=    4.524 closest distance to " CB  SER A   3 " =    1.278
peak=    4.444 closest distance to " CB  GLU A 152 " =    1.223
peak=    4.435 closest distance to " NZ  LYS A 117 " =    3.131
peak=    4.422 closest distance to " O   HOH Z 234 " =    3.556
peak=    4.378 closest distance to " ND2 ASN A 187 " =    1.436
peak=    4.361 closest distance to " O   HOH Z 213 " =    1.733
peak=    4.331 closest distance to " CB  ASN A 148 " =    1.446
peak=    4.290 closest distance to " O   HOH Z 250 " =    1.394
peak=    4.261 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.244 closest distance to " O   HOH Z  97 " =    1.982
peak=    4.240 closest distance to " O   HOH Z 316 " =    2.926
peak=    4.235 closest distance to " O   HOH Z 346 " =    1.653
peak=    4.232 closest distance to " O   HOH Z 368 " =    2.024
peak=    4.216 closest distance to " O   HOH Z 298 " =    1.762
peak=    4.211 closest distance to " O   HOH Z  93 " =    2.222
peak=    4.210 closest distance to " O   HOH Z 203 " =    1.700
peak=    4.193 closest distance to " O   SER A  87 " =    2.383
peak=    4.192 closest distance to " CG  PRO A 243 " =    1.159
peak=    4.187 closest distance to " O   HOH Z 132 " =    1.020
peak=    4.179 closest distance to " O   HOH Z  54 " =    1.682
peak=    4.178 closest distance to " O   HOH Z 278 " =    1.073
peak=    4.173 closest distance to " CB  VAL A 265 " =    1.283
peak=    4.165 closest distance to " OE1 GLU A   2 " =    2.294
peak=    4.162 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.147 closest distance to " O   HOH Z 369 " =    2.100
peak=    4.144 closest distance to " CB  TYR A 169 " =    0.809
peak=    4.084 closest distance to " CB  GLU A 128 " =    1.062
peak=    4.059 closest distance to " O   HOH Z 287 " =    1.782
peak=    4.030 closest distance to " CA  ALA A  21 " =    1.088
peak=    4.010 closest distance to " O   HOH Z   9 " =    2.332
peak=    4.008 closest distance to " O   HOH Z 134 " =    1.297
peak=    3.995 closest distance to " CG AARG A 275 " =    1.013
peak=    3.980 closest distance to " O   HOH Z 303 " =    2.061
peak=    3.971 closest distance to " O   HOH Z 403 " =    1.857
peak=    3.964 closest distance to " NH2BARG A 145 " =    2.127
peak=    3.952 closest distance to " O   HOH Z 130 " =    2.867
peak=    3.952 closest distance to " O   HOH Z 207 " =    1.737
peak=    3.950 closest distance to " O   HOH Z 183 " =    1.842
peak=    3.945 closest distance to " CG2 VAL A 257 " =    0.885
peak=    3.944 closest distance to " CG1 ILE A  33 " =    1.241
peak=    3.933 closest distance to " N   ASN A  39 " =    1.190
peak=    3.925 closest distance to " O   HOH Z 173 " =    2.016
peak=    3.917 closest distance to " O   HOH Z  43 " =    1.965
peak=    3.903 closest distance to " O   HOH Z  61 " =    1.531
peak=    3.902 closest distance to " O   HOH Z 344 " =    2.955
peak=    3.895 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.886 closest distance to " NH1BARG A 145 " =    1.336
peak=    3.878 closest distance to " CD BLYS A 290 " =    1.195
peak=    3.874 closest distance to " O   HOH Z 407 " =    2.417
peak=    3.873 closest distance to " O   HOH Z  66 " =    2.063
peak=    3.869 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.869 closest distance to " O   HOH Z 260 " =    1.065
peak=    3.867 closest distance to " OD2 ASP A 286 " =    2.623
peak=    3.854 closest distance to " OD1 ASN A  69 " =    2.584
peak=    3.854 closest distance to " O   HOH Z  10 " =    1.794
peak=    3.846 closest distance to " O   HOH Z 108 " =    1.053
peak=    3.833 closest distance to " O   HOH Z  40 " =    1.446
peak=    3.823 closest distance to " O   HOH Z 365 " =    2.800
peak=    3.822 closest distance to " C   ALA A   1 " =    1.673
peak=    3.815 closest distance to " OG BSER A 164 " =    2.263
peak=    3.807 closest distance to " O   HOH Z  44 " =    1.897
peak=    3.795 closest distance to " CB  LEU A 228 " =    1.113
peak=    3.794 closest distance to " CB  ARG A  79 " =    1.372
peak=    3.785 closest distance to " CB  SER A  26 " =    1.611
peak=    3.764 closest distance to " O   HOH Z   3 " =    1.808
peak=    3.753 closest distance to " O   HOH Z 425 " =    1.271
peak=    3.742 closest distance to " O   HOH Z 389 " =    1.717
peak=    3.741 closest distance to " CA  GLY A  80 " =    0.715
peak=    3.740 closest distance to " O   HOH Z 327 " =    1.655
peak=    3.732 closest distance to " N   ARG A 156 " =    1.296
peak=    3.728 closest distance to " O   HOH Z 156 " =    3.180
peak=    3.726 closest distance to " O   HOH Z 128 " =    2.024
peak=    3.723 closest distance to " CB  TRP A 179 " =    1.171
peak=    3.698 closest distance to " O   HOH Z 345 " =    3.094
peak=    3.682 closest distance to " O   HOH Z  88 " =    2.636
peak=    3.682 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.664 closest distance to " O   HOH Z 411 " =    3.685
peak=    3.649 closest distance to " O   HOH Z 108 " =    2.084
peak=    3.643 closest distance to " O   HOH Z 423 " =    1.973
peak=    3.641 closest distance to " O   HOH Z 261 " =    1.651
peak=    3.630 closest distance to " CB  TRP A 266 " =    1.086
peak=    3.626 closest distance to " O   HOH Z 361 " =    3.667
peak=    3.621 closest distance to " O   HOH Z 286 " =    2.174
peak=    3.616 closest distance to " O   HOH Z  89 " =    2.199
peak=    3.615 closest distance to " OE2 GLU A  53 " =    2.031
peak=    3.613 closest distance to " O   HOH Z 357 " =    1.791
peak=    3.609 closest distance to " O   HOH Z 144 " =    2.053
peak=    3.607 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.597 closest distance to " CD2 TRP A 179 " =    1.369
peak=    3.595 closest distance to " CA  ASN A 176 " =    1.104
peak=    3.589 closest distance to " CG  MET A 185 " =    1.241
peak=    3.577 closest distance to " O   HOH Z 425 " =    1.968
peak=    3.570 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.565 closest distance to " CG  GLU A 277 " =    2.069
peak=    3.564 closest distance to " O   HOH Z 112 " =    1.041
peak=    3.562 closest distance to " O   HOH Z 247 " =    1.307
peak=    3.557 closest distance to " CB  THR A  31 " =    1.693
peak=    3.556 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.548 closest distance to " O   HOH Z 222 " =    2.382
peak=    3.547 closest distance to " O   HOH Z 371 " =    1.573
peak=    3.547 closest distance to " O   HOH Z 227 " =    1.522
peak=    3.541 closest distance to " O   HOH Z  85 " =    1.520
peak=    3.537 closest distance to " O   HOH Z  71 " =    1.346
peak=    3.536 closest distance to " O   HOH Z  21 " =    1.777
peak=    3.528 closest distance to " O   HOH Z 132 " =    2.101
peak=    3.524 closest distance to " O  BHOH Z  74 " =    1.391
peak=    3.520 closest distance to " O   HOH Z 291 " =    1.760
peak=    3.516 closest distance to " O   HOH Z 106 " =    2.282
peak=    3.512 closest distance to " CB  SER A  62 " =    1.322
peak=    3.512 closest distance to " O   HOH Z   1 " =    1.696
peak=    3.511 closest distance to " O   HOH Z 172 " =    3.565
peak=    3.505 closest distance to " O   HOH Z  48 " =    1.554
peak=    3.480 closest distance to " CG1BVAL A  72 " =    1.422
peak=    3.478 closest distance to " O   HOH Z  50 " =    1.547
peak=    3.473 closest distance to " CG  LEU A 167 " =    1.145
peak=    3.467 closest distance to " CB  SER A  62 " =    1.032
peak=    3.465 closest distance to " CG  MET A 113 " =    0.972
peak=    3.458 closest distance to " O   HOH Z  49 " =    2.103
peak=    3.457 closest distance to " O   HOH Z 189 " =    1.540
peak=    3.455 closest distance to " O   HOH Z 433 " =    1.819
peak=    3.455 closest distance to " O   HOH Z 273 " =    2.744
peak=    3.448 closest distance to " CE  LYS A 119 " =    1.151
peak=    3.446 closest distance to " O   HOH Z  19 " =    2.153
peak=    3.442 closest distance to " O   HOH Z 426 " =    1.497
peak=    3.427 closest distance to " OG  SER A  62 " =    2.819
peak=    3.426 closest distance to " CG  GLN A  77 " =    2.095
peak=    3.426 closest distance to " CA  THR A 264 " =    0.797
peak=    3.424 closest distance to " CD2 LEU A 297 " =    0.992
peak=    3.420 closest distance to " CA  ALA A 233 " =    1.110
peak=    3.418 closest distance to " CA  THR A 221 " =    0.927
peak=    3.415 closest distance to " CB  ARG A 190 " =    1.775
peak=    3.410 closest distance to " O   HOH Z 392 " =    2.725
peak=    3.409 closest distance to " CB  HIS A 108 " =    0.894
peak=    3.407 closest distance to " O   MET A 105 " =    1.820
peak=    3.403 closest distance to " CG  ARG A  66 " =    0.928
peak=    3.402 closest distance to " CB  GLU A 277 " =    3.483
peak=    3.401 closest distance to " CG AARG A 275 " =    1.125
peak=    3.399 closest distance to " O   HOH Z 263 " =    2.332
peak=    3.389 closest distance to " CB  GLN A 278 " =    0.826
peak=    3.386 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.383 closest distance to " CD  ARG A 269 " =    1.036
peak=    3.377 closest distance to " NH1 ARG A  14 " =    1.099
peak=    3.375 closest distance to " O   SER A  26 " =    1.583
peak=    3.370 closest distance to " O   HOH Z 214 " =    2.264
peak=    3.365 closest distance to " NE2 GLN A  73 " =    3.561
peak=    3.359 closest distance to " CB  ALA A 291 " =    1.301
peak=    3.355 closest distance to " O   HOH Z 219 " =    2.159
peak=    3.352 closest distance to " O   HOH Z 421 " =    1.538
peak=    3.350 closest distance to " O   HOH Z 163 " =    1.735
peak=    3.346 closest distance to " CB  SER A 141 " =    1.133
peak=    3.343 closest distance to " O   HOH Z 261 " =    2.076
peak=    3.341 closest distance to " OG BSER A 258 " =    2.963
peak=    3.338 closest distance to " CG2BVAL A  41 " =    0.775
peak=    3.330 closest distance to " O   HOH Z 163 " =    1.892
peak=    3.327 closest distance to " O   HOH Z 334 " =    1.522
peak=    3.322 closest distance to " O   HOH Z 192 " =    1.577
peak=    3.322 closest distance to " CE BLYS A 290 " =    0.997
peak=    3.320 closest distance to " O   HOH Z 299 " =    4.305
peak=    3.318 closest distance to " CB  ILE A 120 " =    1.267
peak=    3.316 closest distance to " O   HOH Z 245 " =    1.283
peak=    3.308 closest distance to " O   HOH Z 132 " =    2.214
peak=    3.307 closest distance to " O   HOH Z  63 " =    2.292
peak=    3.304 closest distance to " O   HOH Z 251 " =    1.667
peak=    3.302 closest distance to " O   HOH Z 234 " =    1.836
peak=    3.302 closest distance to " CB  ARG A 102 " =    0.786
peak=    3.300 closest distance to " O   HOH Z  73 " =    1.681
peak=    3.296 closest distance to " O   HOH Z 279 " =    2.160
peak=    3.295 closest distance to " O   HOH Z 353 " =    2.534
peak=    3.292 closest distance to " O   HOH Z 194 " =    1.806
peak=    3.291 closest distance to " O   HOH Z 326 " =    1.392
peak=    3.289 closest distance to " O   HOH Z 135 " =    1.676
peak=    3.288 closest distance to " CA  PHE A 283 " =    1.277
peak=    3.286 closest distance to " CB  ALA A 248 " =    1.367
peak=    3.285 closest distance to " CD2 HIS A  81 " =    1.132
peak=    3.283 closest distance to " O   HOH Z 180 " =    2.246
peak=    3.283 closest distance to " O   HOH Z 337 " =    3.467
peak=    3.282 closest distance to " O   HOH Z 112 " =    2.343
peak=    3.276 closest distance to " CZ2 TRP A 179 " =    1.718
peak=    3.276 closest distance to " C   ALA A 299 " =    0.990
peak=    3.275 closest distance to " O   HOH Z 214 " =    2.416
peak=    3.269 closest distance to " CE AMET A  47 " =    1.326
peak=    3.267 closest distance to " O   HOH Z 257 " =    2.143
peak=    3.261 closest distance to " O   TRP A 274 " =    1.886
peak=    3.259 closest distance to " O   HOH Z  30 " =    2.258
peak=    3.259 closest distance to " CA  MET A  40 " =    1.077
peak=    3.253 closest distance to " CE  LYS A  48 " =    1.535
peak=    3.253 closest distance to " CD  GLN A  58 " =    5.816
peak=    3.252 closest distance to " CE1 TYR A 186 " =    1.294
peak=    3.245 closest distance to " O   HOH Z 185 " =    1.513
peak=    3.239 closest distance to " O   HOH Z  44 " =    3.365
peak=    3.239 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.237 closest distance to " N   ASN A 127 " =    1.186
peak=    3.235 closest distance to " O   HOH Z  43 " =    2.714
peak=    3.235 closest distance to " NE  ARG A  14 " =    1.270
peak=    3.235 closest distance to " O   HOH Z 148 " =    3.179
peak=    3.233 closest distance to " O   HOH Z 281 " =    4.471
peak=    3.233 closest distance to " OD1BASN A 224 " =    2.141
peak=    3.233 closest distance to " CB  ASN A  39 " =    0.831
peak=    3.233 closest distance to " O   HOH Z 336 " =    1.662
peak=    3.232 closest distance to " O   HOH Z 284 " =    2.803
peak=    3.231 closest distance to " O   HOH Z 272 " =    2.313
peak=    3.226 closest distance to " CB  SER A 216 " =    0.744
peak=    3.221 closest distance to " O   HOH Z  19 " =    2.391
peak=    3.220 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.220 closest distance to " CA  ILE A  33 " =    1.299
peak=    3.216 closest distance to " O   HOH Z 163 " =    1.643
peak=    3.214 closest distance to " CB  ALA A  34 " =    1.042
peak=    3.213 closest distance to " O   HOH Z 417 " =    3.112
peak=    3.213 closest distance to " O   HOH Z 276 " =    1.159
peak=    3.212 closest distance to " O   HOH Z 234 " =    2.197
peak=    3.212 closest distance to " O   HOH Z 189 " =    1.514
peak=    3.206 closest distance to " O  BHOH Z 338 " =    2.293
peak=    3.206 closest distance to " CD2 LEU A 255 " =    1.031
peak=    3.206 closest distance to " CA  ALA A 291 " =    0.888
peak=    3.204 closest distance to " O   HOH Z 383 " =    1.818
peak=    3.204 closest distance to " O   HOH Z 419 " =    1.838
peak=    3.204 closest distance to " O   HOH Z  59 " =    2.183
peak=    3.203 closest distance to " NZ  LYS A  76 " =    1.309
peak=    3.198 closest distance to " CA  LEU A 282 " =    1.256
peak=    3.197 closest distance to " CG  ARG A 269 " =    1.270
peak=    3.196 closest distance to " NE AARG A 275 " =    1.835
peak=    3.194 closest distance to " O   HOH Z 291 " =    1.533
peak=    3.193 closest distance to " O   HOH Z 435 " =    1.811
peak=    3.188 closest distance to " CA  ARG A  36 " =    0.994
peak=    3.187 closest distance to " O   HOH Z 183 " =    1.573
peak=    3.184 closest distance to " CG2 THR A 294 " =    1.562
peak=    3.183 closest distance to " CH2 TRP A 150 " =    1.158
peak=    3.181 closest distance to " CB  THR A 279 " =    1.592
peak=    3.177 closest distance to " O   HOH Z 343 " =    1.328
peak=    3.175 closest distance to " O   HOH Z 248 " =    1.826
peak=    3.171 closest distance to " CA  ALA A  51 " =    0.880
peak=    3.171 closest distance to " CG2 ILE A  20 " =    1.501
peak=    3.170 closest distance to " OG1 THR A 294 " =    2.332
peak=    3.167 closest distance to " CA  LEU A 300 " =    1.035
peak=    3.163 closest distance to " O   HOH Z 374 " =    2.434
peak=    3.162 closest distance to " O   HOH Z 365 " =    1.823
peak=    3.155 closest distance to " O   HOH Z  47 " =    1.503
peak=    3.153 closest distance to " O   HOH Z 313 " =    1.636
peak=    3.152 closest distance to " CA  ASP A 140 " =    1.082
peak=    3.152 closest distance to " N   CYS A 260 " =    0.797
peak=    3.148 closest distance to " O   HOH Z 299 " =    2.261
peak=    3.144 closest distance to " O   HOH Z 417 " =    1.934
peak=    3.142 closest distance to " N   ASP A 162 " =    1.235
peak=    3.141 closest distance to " CB  ALA A  21 " =    1.839
peak=    3.141 closest distance to " CB  GLN A  88 " =    1.182
peak=    3.138 closest distance to " NH1AARG A 145 " =    1.086
peak=    3.136 closest distance to " CB  ASN A 215 " =    1.039
peak=    3.136 closest distance to " O   HOH Z 211 " =    2.565
peak=    3.134 closest distance to " NH2 ARG A 219 " =    1.936
peak=    3.133 closest distance to " CB  TRP A 179 " =    1.377
peak=    3.131 closest distance to " O   GLY A  91 " =    1.575
peak=    3.129 closest distance to " CB  VAL A 126 " =    1.152
peak=    3.125 closest distance to " CG  MET A  93 " =    0.924
peak=    3.123 closest distance to " O   HOH Z 114 " =    3.829
peak=    3.122 closest distance to " CG  LYS A  76 " =    0.960
peak=    3.119 closest distance to " CA  ALA A  84 " =    1.272
peak=    3.116 closest distance to " CG1 ILE A 120 " =    1.251
peak=    3.106 closest distance to " N   SER A 135 " =    1.228
peak=    3.101 closest distance to " O   HOH Z 287 " =    2.116
peak=    3.095 closest distance to " O   HOH Z  88 " =    1.965
peak=    3.090 closest distance to " NH2AARG A 190 " =    1.764
peak=    3.086 closest distance to " O   HOH Z 329 " =    3.460
peak=    3.075 closest distance to " O   HOH Z 325 " =    3.485
peak=    3.074 closest distance to " O   HOH Z 261 " =    1.658
peak=    3.060 closest distance to " O   HOH Z 269 " =    3.630
peak=    3.057 closest distance to " O   HOH Z 303 " =    1.623
peak=    3.043 closest distance to " O   HOH Z  80 " =    1.875
peak=    3.041 closest distance to " NH1 ARG A 138 " =    1.315
peak=    3.031 closest distance to " O   HOH Z  98 " =    1.550

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.631 - 5.711
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.743 - 5.711

peak=   -4.474 closest distance to " C   HIS A 108 " =    1.090
peak=   -4.445 closest distance to " O   VAL A  67 " =    2.688
peak=   -4.437 closest distance to " O   HOH Z 266 " =    4.495
peak=   -4.388 closest distance to " OXT GLY A 302 " =    2.700
peak=   -4.358 closest distance to " O   HOH Z 290 " =    1.015
peak=   -4.198 closest distance to " O   HOH Z  13 " =    1.435
peak=   -4.173 closest distance to " O   PRO A 198 " =    1.244
peak=   -4.162 closest distance to " O   ALA A 161 " =    1.582
peak=   -4.141 closest distance to " SG  CYS A 254 " =    3.304
peak=   -4.138 closest distance to " N   GLN A  58 " =    1.773
peak=   -4.133 closest distance to " CD  ARG A 156 " =    1.983
peak=   -4.116 closest distance to " CA  VAL A  67 " =    2.778
peak=   -4.095 closest distance to " ND2 ASN A  45 " =    1.039
peak=   -4.057 closest distance to " CB  PRO A 243 " =    2.580
peak=   -4.002 closest distance to " OG BSER A 134 " =    1.254
peak=   -3.984 closest distance to " CG  LYS A 193 " =    2.233
peak=   -3.952 closest distance to " N   ALA A 248 " =    1.662
peak=   -3.947 closest distance to " O   HOH Z 377 " =    1.992
peak=   -3.931 closest distance to " CB  ASN A  39 " =    2.241
peak=   -3.930 closest distance to " O   HOH Z 102 " =    1.782
peak=   -3.921 closest distance to " O   HOH Z 126 " =    1.842
peak=   -3.920 closest distance to " O   HOH Z 198 " =    1.776
peak=   -3.920 closest distance to " OG  SER A   3 " =    1.627
peak=   -3.908 closest distance to " OD2 ASP A 191 " =    1.431
peak=   -3.898 closest distance to " O   HOH Z   6 " =    1.987
peak=   -3.874 closest distance to " O   HOH Z   3 " =    1.774
peak=   -3.858 closest distance to " O   HOH Z 407 " =    2.732
peak=   -3.833 closest distance to " CE2 TYR A  30 " =    2.897
peak=   -3.829 closest distance to " C   ALA A 158 " =    1.184
peak=   -3.826 closest distance to " O   SER A 146 " =    0.913
peak=   -3.825 closest distance to " O   HOH Z 362 " =    5.711
peak=   -3.815 closest distance to " O   HOH Z 351 " =    1.508
peak=   -3.794 closest distance to " CZ  TYR A 169 " =    1.731
peak=   -3.787 closest distance to " CG  PHE A 283 " =    2.659
peak=   -3.773 closest distance to " CG  GLN A 223 " =    1.846
peak=   -3.771 closest distance to " O   HOH Z  52 " =    2.030
peak=   -3.766 closest distance to " CB  ALA A 161 " =    2.480
peak=   -3.734 closest distance to " O   HOH Z  43 " =    1.797
peak=   -3.729 closest distance to " O   HOH Z  47 " =    1.626
peak=   -3.729 closest distance to " O   SER A 135 " =    1.483
peak=   -3.702 closest distance to " CD1 LEU A 255 " =    2.778
peak=   -3.700 closest distance to " O   HOH Z  24 " =    1.389
peak=   -3.685 closest distance to " CB  TYR A  15 " =    2.148
peak=   -3.680 closest distance to " N   HIS A 115 " =    1.965
peak=   -3.679 closest distance to " CA  GLY A  98 " =    1.927
peak=   -3.667 closest distance to " CG1 VAL A  78 " =    3.018
peak=   -3.667 closest distance to " OD2 ASP A  50 " =    1.435
peak=   -3.665 closest distance to " O   HOH Z 114 " =    2.827
peak=   -3.664 closest distance to " O   HOH Z 385 " =    1.879
peak=   -3.663 closest distance to " N   ASP A 286 " =    2.234
peak=   -3.659 closest distance to " O   HOH Z 388 " =    1.938
peak=   -3.656 closest distance to " CD1 LEU A 101 " =    2.302
peak=   -3.655 closest distance to " O   HOH Z 166 " =    1.534
peak=   -3.645 closest distance to " CZ  PHE A  59 " =    1.401
peak=   -3.643 closest distance to " OXT GLY A 302 " =    3.490
peak=   -3.633 closest distance to " N   GLN A 122 " =    1.442
peak=   -3.630 closest distance to " CB  ALA A 291 " =    2.354
peak=   -3.630 closest distance to " O   HOH Z  11 " =    1.737
peak=   -3.628 closest distance to " CD2 LEU A 237 " =    2.385
peak=   -3.614 closest distance to " O   HOH Z 250 " =    1.434
peak=   -3.599 closest distance to " O   PRO A 163 " =    1.797
peak=   -3.588 closest distance to " O   HOH Z 263 " =    2.927
peak=   -3.585 closest distance to " CA  GLY A 133 " =    1.804
peak=   -3.576 closest distance to " OG  SER A  97 " =    1.962
peak=   -3.572 closest distance to " CD1 LEU A 228 " =    2.035
peak=   -3.570 closest distance to " O   TRP A  92 " =    1.700
peak=   -3.564 closest distance to " O   ALA A  51 " =    1.246
peak=   -3.556 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.556 closest distance to " O   HOH Z 429 " =    1.814
peak=   -3.549 closest distance to " O   MET A  40 " =    2.608
peak=   -3.542 closest distance to " O   HOH Z 197 " =    4.911
peak=   -3.541 closest distance to " O   HOH Z 185 " =    2.135
peak=   -3.536 closest distance to " O   HOH Z 353 " =    2.243
peak=   -3.534 closest distance to " CD2 LEU A 300 " =    2.887
peak=   -3.533 closest distance to " O   HOH Z 313 " =    1.965
peak=   -3.531 closest distance to " OD1 ASP A 191 " =    1.619
peak=   -3.521 closest distance to " CB  PHE A 192 " =    1.858
peak=   -3.520 closest distance to " CG1 VAL A 112 " =    2.819
peak=   -3.520 closest distance to " CB  ALA A 291 " =    2.177
peak=   -3.519 closest distance to " OE1 GLN A  88 " =    1.095
peak=   -3.501 closest distance to " O   HOH Z 395 " =    5.080
peak=   -3.493 closest distance to " O   HOH Z 427 " =    1.432
peak=   -3.490 closest distance to " OD1 ASP A 191 " =    1.419
peak=   -3.488 closest distance to " O   VAL A 174 " =    1.967
peak=   -3.487 closest distance to " O   SER A  95 " =    1.429
peak=   -3.484 closest distance to " CD1 PHE A  59 " =    1.962
peak=   -3.480 closest distance to " NH2 ARG A  66 " =    4.484
peak=   -3.476 closest distance to " O   HOH Z 231 " =    2.231
peak=   -3.474 closest distance to " ND2 ASN A 187 " =    1.577
peak=   -3.472 closest distance to " O   HOH Z  52 " =    1.474
peak=   -3.467 closest distance to " N   SER A 276 " =    1.185
peak=   -3.464 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.460 closest distance to " O   HOH Z 385 " =    1.938
peak=   -3.452 closest distance to " N   SER A 206 " =    1.868
peak=   -3.445 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.444 closest distance to " CE  MET A 105 " =    2.205
peak=   -3.432 closest distance to " O   HOH Z 423 " =    2.153
peak=   -3.431 closest distance to " O   TRP A  70 " =    1.471
peak=   -3.427 closest distance to " OH  TYR A 172 " =    1.649
peak=   -3.426 closest distance to " ND2 ASN A  39 " =    1.246
peak=   -3.425 closest distance to " CG  GLN A  58 " =    1.334
peak=   -3.397 closest distance to " O   HOH Z 165 " =    2.144
peak=   -3.397 closest distance to " CG  ASP A 231 " =    0.743
peak=   -3.391 closest distance to " CD  ARG A 139 " =    1.446
peak=   -3.388 closest distance to " C   LEU A 143 " =    1.019
peak=   -3.381 closest distance to " O   HOH Z  63 " =    1.441
peak=   -3.379 closest distance to " CD1 LEU A  25 " =    2.456
peak=   -3.378 closest distance to " CG2 ILE A 263 " =    2.164
peak=   -3.376 closest distance to " CA  ASP A 298 " =    1.085
peak=   -3.373 closest distance to " CZ3 TRP A 274 " =    2.238
peak=   -3.366 closest distance to " O   THR A 182 " =    1.200
peak=   -3.365 closest distance to " CZ3 TRP A 274 " =    1.161
peak=   -3.364 closest distance to " O   ALA A  34 " =    2.601
peak=   -3.361 closest distance to " O   HOH Z 421 " =    3.208
peak=   -3.350 closest distance to " CG2 THR A 178 " =    2.148
peak=   -3.347 closest distance to " O   ILE A  49 " =    1.723
peak=   -3.346 closest distance to " CB  SER A 210 " =    1.338
peak=   -3.345 closest distance to " OG ASER A 134 " =    1.141
peak=   -3.344 closest distance to " O   ASP A 162 " =    2.130
peak=   -3.331 closest distance to " O   HOH Z 191 " =    5.354
peak=   -3.330 closest distance to " ND2 ASN A 142 " =    1.903
peak=   -3.329 closest distance to " O   SER A 146 " =    0.925
peak=   -3.323 closest distance to " O   ASN A  45 " =    1.881
peak=   -3.321 closest distance to " OG  SER A 206 " =    1.474
peak=   -3.314 closest distance to " CB  PRO A 163 " =    2.643
peak=   -3.306 closest distance to " O   HOH Z 326 " =    1.622
peak=   -3.305 closest distance to " C   ASP A 231 " =    2.414
peak=   -3.295 closest distance to " CD2 LEU A 300 " =    2.812
peak=   -3.286 closest distance to " CZ  PHE A 130 " =    0.861
peak=   -3.284 closest distance to " CD  GLN A  88 " =    0.994
peak=   -3.274 closest distance to " CG  GLU A 152 " =    0.961
peak=   -3.270 closest distance to " CA  TRP A  70 " =    2.381
peak=   -3.267 closest distance to " O   VAL A 125 " =    1.967
peak=   -3.262 closest distance to " OG1 THR A 178 " =    1.179
peak=   -3.262 closest distance to " O   SER A 210 " =    1.889
peak=   -3.261 closest distance to " O   HOH Z 417 " =    2.388
peak=   -3.238 closest distance to " O   GLN A 205 " =    1.593
peak=   -3.238 closest distance to " CA  GLY A  57 " =    2.161
peak=   -3.237 closest distance to " O   HOH Z  93 " =    1.464
peak=   -3.234 closest distance to " CG1 VAL A 230 " =    1.895
peak=   -3.230 closest distance to " O   HOH Z 286 " =    1.812
peak=   -3.227 closest distance to " CG  ASN A 110 " =    1.092
peak=   -3.220 closest distance to " CG  PRO A 243 " =    1.475
peak=   -3.217 closest distance to " CZ3 TRP A 179 " =    1.377
peak=   -3.216 closest distance to " OD1 ASN A 301 " =    2.009
peak=   -3.214 closest distance to " ND2 ASN A 209 " =    1.779
peak=   -3.213 closest distance to " O   HOH Z  71 " =    1.248
peak=   -3.210 closest distance to " O   HOH Z 134 " =    2.699
peak=   -3.210 closest distance to " CA  GLY A 203 " =    2.240
peak=   -3.199 closest distance to " O   SER A 273 " =    1.361
peak=   -3.195 closest distance to " OD1 ASP A 200 " =    1.256
peak=   -3.193 closest distance to " SG ACYS A 201 " =    1.783
peak=   -3.192 closest distance to " CB  ALA A 244 " =    1.989
peak=   -3.190 closest distance to " CG  MET A 105 " =    0.875
peak=   -3.188 closest distance to " O   HOH Z 122 " =    2.024
peak=   -3.185 closest distance to " O   HOH Z  60 " =    1.800
peak=   -3.184 closest distance to " O   HOH Z 389 " =    1.784
peak=   -3.183 closest distance to " O   HOH Z 113 " =    1.884
peak=   -3.182 closest distance to " CB  ASP A 132 " =    2.158
peak=   -3.180 closest distance to " CA  TYR A  30 " =    2.912
peak=   -3.178 closest distance to " CG2BVAL A  72 " =    1.966
peak=   -3.173 closest distance to " O   PHE A 218 " =    1.536
peak=   -3.173 closest distance to " O   HOH Z 198 " =    1.463
peak=   -3.170 closest distance to " O   HOH Z 211 " =    1.648
peak=   -3.166 closest distance to " O   HOH Z 251 " =    1.366
peak=   -3.165 closest distance to " O   HOH Z 193 " =    1.633
peak=   -3.162 closest distance to " CD1 ILE A 239 " =    2.268
peak=   -3.149 closest distance to " O   HOH Z 139 " =    2.987
peak=   -3.147 closest distance to " CA  TRP A 274 " =    1.470
peak=   -3.147 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.145 closest distance to " C   MET A 188 " =    1.558
peak=   -3.130 closest distance to " O   HOH Z 424 " =    2.880
peak=   -3.128 closest distance to " O   HOH Z 210 " =    1.160
peak=   -3.127 closest distance to " CE  LYS A  76 " =    2.884
peak=   -3.125 closest distance to " O   HOH Z 137 " =    1.374
peak=   -3.124 closest distance to " O   HOH Z 166 " =    2.071
peak=   -3.121 closest distance to " O   HOH Z 150 " =    1.659
peak=   -3.121 closest distance to " O   HOH Z  56 " =    0.982
peak=   -3.115 closest distance to " CD1 TYR A 247 " =    2.284
peak=   -3.109 closest distance to " O   HOH Z 234 " =    3.834
peak=   -3.105 closest distance to " O   HOH Z 298 " =    2.431
peak=   -3.104 closest distance to " O   HOH Z 174 " =    4.254
peak=   -3.103 closest distance to " O   SER A  22 " =    2.308
peak=   -3.095 closest distance to " OE2 GLU A 152 " =    1.285
peak=   -3.091 closest distance to " O   HOH Z  97 " =    1.437
peak=   -3.087 closest distance to " O   HOH Z 346 " =    1.795
peak=   -3.078 closest distance to " OD1 ASP A 171 " =    1.613
peak=   -3.077 closest distance to " O   HOH Z 281 " =    2.792
peak=   -3.075 closest distance to " O   HOH Z 345 " =    1.476
peak=   -3.070 closest distance to " NE2 GLN A  58 " =    1.123
peak=   -3.066 closest distance to " O   HOH Z 396 " =    1.651
peak=   -3.061 closest distance to " O   HOH Z 389 " =    4.685
peak=   -3.059 closest distance to " O   HOH Z 210 " =    2.004
peak=   -3.056 closest distance to " O   ASP A 191 " =    1.530
peak=   -3.008 closest distance to " O   LYS A 117 " =    1.512
peak=   -3.007 closest distance to " O   ASN A 249 " =    1.509

================= 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    :  0.4160 0.4185   6.209134e+00   6.211048e+00
   1_bss:  0.4056 0.4053   6.196129e+00   6.186854e+00
   1_xyz:  0.2291 0.2498   5.718515e+00   5.804170e+00
   1_adp:  0.2090 0.2591   5.663602e+00   5.838416e+00
   1_occ:  0.2088 0.2589   5.663040e+00   5.838290e+00
   2_bss:  0.2023 0.2543   5.648657e+00   5.826888e+00
   2_xyz:  0.1478 0.1951   5.373271e+00   5.579796e+00
   2_adp:  0.1380 0.1820   5.299427e+00   5.502450e+00
   2_occ:  0.1376 0.1822   5.298030e+00   5.501641e+00
   3_bss:  0.1376 0.1807   5.294512e+00   5.495813e+00
   3_xyz:  0.1184 0.1607   5.173717e+00   5.396931e+00
   3_adp:  0.1147 0.1584   5.150672e+00   5.381352e+00
   3_occ:  0.1146 0.1583   5.150233e+00   5.380997e+00
   4_bss:  0.1145 0.1582   5.149219e+00   5.379863e+00
   4_xyz:  0.1134 0.1572   5.141346e+00   5.368650e+00
   4_adp:  0.1127 0.1572   5.138585e+00   5.368897e+00
   4_occ:  0.1126 0.1572   5.138391e+00   5.368851e+00
   5_bss:  0.1127 0.1570   5.139355e+00   5.368272e+00
   5_xyz:  0.1098 0.1560   5.123829e+00   5.363727e+00
   5_adp:  0.1096 0.1559   5.122307e+00   5.363633e+00
   5_occ:  0.1096 0.1559   5.122232e+00   5.363680e+00
   5_bss:  0.1095 0.1559   5.122297e+00   5.363728e+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:  0.326  20.000  -0.224  -2.292   2.150  -0.000   0.000   0.000
   1_xyz:  0.326  20.000  -0.224  -2.292   2.150  -0.000   0.000   0.000
   1_adp:  0.326  20.000  -0.224  -2.292   2.150  -0.000   0.000   0.000
   1_occ:  0.326  20.000  -0.224  -2.292   2.150  -0.000   0.000   0.000
   2_bss:  0.316  29.758  -2.674  -2.584  -0.951  -0.000  -0.000  -0.000
   2_xyz:  0.316  29.758  -2.674  -2.584  -0.951  -0.000  -0.000  -0.000
   2_adp:  0.316  29.758  -2.674  -2.584  -0.951  -0.000  -0.000  -0.000
   2_occ:  0.316  29.758  -2.674  -2.584  -0.951  -0.000  -0.000  -0.000
   3_bss:  0.315  30.164  -3.136  -2.551  -1.722  -0.000  -0.000  -0.000
   3_xyz:  0.315  30.164  -3.136  -2.551  -1.722  -0.000  -0.000  -0.000
   3_adp:  0.315  30.164  -3.136  -2.551  -1.722  -0.000  -0.000  -0.000
   3_occ:  0.315  30.164  -3.136  -2.551  -1.722  -0.000  -0.000  -0.000
   4_bss:  0.309  32.372  -3.176  -2.540  -1.915  -0.000  -0.000  -0.000
   4_xyz:  0.309  32.372  -3.176  -2.540  -1.915  -0.000  -0.000  -0.000
   4_adp:  0.309  32.372  -3.176  -2.540  -1.915  -0.000  -0.000  -0.000
   4_occ:  0.309  32.372  -3.176  -2.540  -1.915  -0.000  -0.000  -0.000
   5_bss:  0.313  32.372  -3.082  -2.405  -1.843  -0.000  -0.000  -0.000
   5_xyz:  0.313  32.372  -3.082  -2.405  -1.843  -0.000  -0.000  -0.000
   5_adp:  0.313  32.372  -3.082  -2.405  -1.843  -0.000  -0.000  -0.000
   5_occ:  0.313  32.372  -3.082  -2.405  -1.843  -0.000  -0.000  -0.000
   5_bss:  0.317  33.337  -2.927  -2.235  -1.688  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.737 0.5633  0.7572    53187.646
   1_bss:  45.346 0.5787  0.7777    48965.702
   1_xyz:  23.901 0.8246  1.0285    15754.356
   1_adp:  25.392 0.8081  1.0231    17071.873
   1_occ:  25.390 0.8081  1.0231    17069.761
   2_bss:  24.939 0.8123  0.9561    16461.211
   2_xyz:  18.365 0.8768  0.9967     9423.622
   2_adp:  16.351 0.8955  1.0039     8070.568
   2_occ:  16.333 0.8957  1.0036     8039.669
   3_bss:  16.196 0.8968  0.9888     7897.706
   3_xyz:  14.243 0.9127  0.9965     6390.502
   3_adp:  13.898 0.9158  0.9942     6246.177
   3_occ:  13.888 0.9159  0.9942     6236.653
   4_bss:  13.865 0.9161  0.9916     6218.858
   4_xyz:  13.608 0.9182  0.9920     6050.070
   4_adp:  13.592 0.9184  0.9889     6054.451
   4_occ:  13.590 0.9184  0.9888     6051.984
   5_bss:  13.588 0.9184  0.9926     6059.875
   5_xyz:  13.484 0.9193  0.9929     5995.493
   5_adp:  13.454 0.9196  0.9894     5990.806
   5_occ:  13.455 0.9196  0.9894     5991.083
   5_bss:  13.454 0.9196  0.9935     5994.918
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.1013e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.1013e-01
   1_xyz:   1.330  0.011  0.085 15.573  0.007  4.103   1.0086e-01
   1_adp:   1.330  0.011  0.085 15.573  0.007  4.103   1.0086e-01
   1_occ:   1.330  0.011  0.085 15.573  0.007  4.103   1.0086e-01
   2_bss:   1.330  0.011  0.085 15.573  0.007  4.103   1.0086e-01
   2_xyz:   0.972  0.006  0.068 14.492  0.004  4.112   5.6862e-02
   2_adp:   0.972  0.006  0.068 14.492  0.004  4.112   5.6862e-02
   2_occ:   0.972  0.006  0.068 14.492  0.004  4.112   5.6862e-02
   3_bss:   0.972  0.006  0.068 14.492  0.004  4.112   5.6862e-02
   3_xyz:   0.988  0.006  0.068 14.728  0.004  4.111   5.6968e-02
   3_adp:   0.988  0.006  0.068 14.728  0.004  4.111   5.6968e-02
   3_occ:   0.988  0.006  0.068 14.728  0.004  4.111   5.6968e-02
   4_bss:   0.988  0.006  0.068 14.728  0.004  4.111   5.6968e-02
   4_xyz:   0.868  0.004  0.062 14.373  0.004  4.107   4.6872e-02
   4_adp:   0.868  0.004  0.062 14.373  0.004  4.107   4.6872e-02
   4_occ:   0.868  0.004  0.062 14.373  0.004  4.107   4.6872e-02
   5_bss:   0.868  0.004  0.062 14.373  0.004  4.107   4.6872e-02
   5_xyz:   0.900  0.005  0.065 14.419  0.004  4.106   4.9216e-02
   5_adp:   0.900  0.005  0.065 14.419  0.004  4.106   4.9216e-02
   5_occ:   0.900  0.005  0.065 14.419  0.004  4.106   4.9216e-02
   5_bss:   0.900  0.005  0.065 14.419  0.004  4.106   4.9216e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.059   2.3962e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.059   2.3962e-01
   1_xyz:   9.264  0.063  0.336 86.863  0.057  2.030   1.0897e-01
   1_adp:   9.264  0.063  0.336 86.863  0.057  2.030   1.0897e-01
   1_occ:   9.264  0.063  0.336 86.863  0.057  2.030   1.0897e-01
   2_bss:   9.264  0.063  0.336 86.863  0.057  2.030   1.0897e-01
   2_xyz:   6.621  0.040  0.208 81.069  0.044  2.381   8.9861e-02
   2_adp:   6.621  0.040  0.208 81.069  0.044  2.381   8.9861e-02
   2_occ:   6.621  0.040  0.208 81.069  0.044  2.381   8.9861e-02
   3_bss:   6.621  0.040  0.208 81.069  0.044  2.381   8.9861e-02
   3_xyz:   6.319  0.042  0.220 84.092  0.042  2.325   4.1431e-02
   3_adp:   6.319  0.042  0.220 84.092  0.042  2.325   4.1431e-02
   3_occ:   6.319  0.042  0.220 84.092  0.042  2.325   4.1431e-02
   4_bss:   6.319  0.042  0.220 84.092  0.042  2.325   4.1431e-02
   4_xyz:   6.032  0.038  0.193 82.262  0.038  2.387   2.6115e-02
   4_adp:   6.032  0.038  0.193 82.262  0.038  2.387   2.6115e-02
   4_occ:   6.032  0.038  0.193 82.262  0.038  2.387   2.6115e-02
   5_bss:   6.032  0.038  0.193 82.262  0.038  2.387   2.6115e-02
   5_xyz:   6.254  0.040  0.222 83.415  0.037  2.342   3.2284e-02
   5_adp:   6.254  0.040  0.222 83.415  0.037  2.342   3.2284e-02
   5_occ:   6.254  0.040  0.222 83.415  0.037  2.342   3.2284e-02
   5_bss:   6.254  0.040  0.222 83.415  0.037  2.342   3.2284e-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:  90.77   0.00  18.40  90.77   0.00  14.03  84.58   7.42  42.20
   1_occ:  90.77   0.00  18.40  90.77   0.00  14.03  84.58   7.42  42.20
   2_bss:  90.77   0.00  18.40  90.77   0.00  14.03  84.58   7.42  42.20
   2_xyz:  90.77   0.00  18.40  90.77   0.00  14.03  84.58   7.42  42.20
   2_adp:  92.02   1.43  17.56  92.02   1.43  13.44  80.50   7.03  40.02
   2_occ:  92.02   1.43  17.56  92.02   1.43  13.44  80.50   7.03  40.02
   3_bss:  92.02   1.43  17.56  92.02   1.43  13.44  80.50   7.03  40.02
   3_xyz:  92.02   1.43  17.56  92.02   1.43  13.44  80.50   7.03  40.02
   3_adp:  95.12   1.65  17.51  95.12   1.65  13.28  81.11   6.26  40.54
   3_occ:  95.12   1.65  17.51  95.12   1.65  13.28  81.11   6.26  40.54
   4_bss:  95.12   1.65  17.51  95.12   1.65  13.28  81.11   6.26  40.54
   4_xyz:  95.12   1.65  17.51  95.12   1.65  13.28  81.11   6.26  40.54
   4_adp:  97.49   1.58  17.40  97.49   1.58  13.20  81.72   6.17  40.29
   4_occ:  97.49   1.58  17.40  97.49   1.58  13.20  81.72   6.17  40.29
   5_bss:  97.49   1.58  17.40  97.49   1.58  13.20  81.72   6.17  40.29
   5_xyz:  97.49   1.58  17.40  97.49   1.58  13.20  81.72   6.17  40.29
   5_adp:  97.79   1.44  17.29  97.79   1.44  13.10  81.62   6.01  40.13
   5_occ:  97.79   1.44  17.29  97.79   1.44  13.10  81.62   6.01  40.13
   5_bss:  97.74   1.39  17.24  97.74   1.39  13.05  81.57   5.96  40.08
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.471    0.035    0.432
   1_adp:    2.471    0.035    0.432
   1_occ:    2.471    0.035    0.432
   2_bss:    2.471    0.035    0.432
   2_xyz:    2.346    0.015    0.496
   2_adp:    2.346    0.015    0.496
   2_occ:    2.346    0.015    0.496
   3_bss:    2.346    0.015    0.496
   3_xyz:    2.158    0.033    0.547
   3_adp:    2.158    0.033    0.547
   3_occ:    2.158    0.033    0.547
   4_bss:    2.158    0.033    0.547
   4_xyz:    2.026    0.049    0.555
   4_adp:    2.026    0.049    0.555
   4_occ:    2.026    0.049    0.555
   5_bss:    2.026    0.049    0.555
   5_xyz:    1.877    0.024    0.565
   5_adp:    1.877    0.024    0.565
   5_occ:    1.877    0.024    0.565
   5_bss:    1.877    0.024    0.565
------------------------------------------------------------------------

CPU time actual refinement: 331.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/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_166/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_166/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.59 
  Macro-tasks:
    bulk solvent and scale       = 42.74  
    individual site refinement   = 135.88 
    weights calculation          = 29.16  
    collect and process          = 6.49   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 214.36 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 103.75 
    alpha_beta                      = 7.96   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 113.60 
    fmodel                         = 7.37   
    r_factors                      = 0.22   
    phase_errors                   = 10.89  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 246.97 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.645 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    659 calls, 103.49 s
gradients_fft:          604 calls,  99.67 s

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

# Date 2008-01-16 Time 04:09:52 PST -0800 (1200485392.64 s)
Start R-work = 0.4160, R-free = 0.4185 (no bulk solvent and anisotropic scale)
Final R-work = 0.1368, R-free = 0.1778 (no bulk solvent and anisotropic scale)

Start R-work = 0.4056, R-free = 0.4053
Final R-work = 0.1095, R-free = 0.1559