# Date 2008-01-16 Time 04:26:13 PST -0800 (1200486373.36 s)
#phil __OFF__

Command line arguments: "../314.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1528
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 314

-------------------------------------------------------------------------------
  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: (69.1963, 47.1647, 86.822, 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: (69.1963, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97072
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.945963

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8486
                             d_min =   1.9707

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: (69.1963, 47.1647, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97072
Completeness in resolution range: 0.948896
Completeness with d_max=infinity: 0.945963

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8490 -  4.2164 [2174/2202]  1954   220  10.1%
  bin  2:  4.2164 -  3.3594 [2072/2091]  1867   205   9.9%
  bin  3:  3.3594 -  2.9385 [2065/2085]  1858   207  10.0%
  bin  4:  2.9385 -  2.6716 [2030/2055]  1828   202  10.0%
  bin  5:  2.6716 -  2.4810 [2019/2039]  1813   206  10.2%
  bin  6:  2.4810 -  2.3353 [2009/2056]  1812   197   9.8%
  bin  7:  2.3353 -  2.2188 [2003/2035]  1806   197   9.8%
  bin  8:  2.2188 -  2.1225 [1997/2032]  1791   206  10.3%
  bin  9:  2.1225 -  2.0410 [2001/2031]  1805   196   9.8%
  bin 10:  2.0410 -  1.9707 [1219/2018]  1096   123  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/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: 0.13 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:
        1.72 -     2.35: 18
        2.35 -     2.99: 1873
        2.99 -     3.63: 4609
        3.63 -     4.26: 9169
        4.26 -     4.90: 12720
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.719 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.745 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.881 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.980 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28384 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_314/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 69.19625 47.16465 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2937   r_free= 0.2877   ksol= 0.00   Bsol= 0.00   scale= 0.986    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.959313                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1407  157 0.2648 0.2716      6.3035      6.3312|
|  2:  4.7025 -  3.7524 0.99   1353  153 0.2237 0.1955       6.306      6.2481|
|  3:  3.7524 -  3.2839 0.99   1331  148 0.2504 0.2324      6.2261      6.2257|
|  4:  3.2839 -  2.9863 0.99   1322  138 0.2678 0.2973      6.1134      6.1599|
|  5:  2.9863 -  2.7738 0.99   1307  149 0.2993 0.2618      6.0075      5.9347|
|  6:  2.7738 -  2.6112 0.98   1306  145 0.3077 0.3523      5.9427      5.9199|
|  7:  2.6112 -  2.4810 0.99   1294  150 0.3041 0.2689      5.8962      5.7857|
|  8:  2.4810 -  2.3735 0.98   1302  140 0.3234 0.3035      5.8808      5.8547|
|  9:  2.3735 -  2.2824 0.98   1294  145 0.3281 0.3126       5.827      5.8247|
| 10:  2.2824 -  2.2039 0.98   1279  141 0.3271 0.3014      5.8256       5.694|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.3464 0.3406      5.7888      5.8338|
| 12:  2.1352 -  2.0744 0.98   1269  140 0.3382 0.3583      5.7245      5.8101|
| 13:  2.0744 -  2.0199 0.97   1266  136 0.3591 0.3454      5.6803       5.585|
| 14:  2.0199 -  1.9707 0.47    607   72 0.3710 0.3604      5.7031      5.5458|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1407   157  0.79  25.81   0.87     0.80      40574.72|
|  2:  4.7025 -  3.7524  1353   153  0.86  19.88   0.99     0.93      37370.81|
|  3:  3.7524 -  3.2839  1331   148  0.85  21.95   1.00     0.98      33449.97|
|  4:  3.2839 -  2.9863  1322   138  0.82  24.43   1.00     0.96      29602.35|
|  5:  2.9863 -  2.7738  1307   149  0.77  29.60   1.01     0.94      25672.55|
|  6:  2.7738 -  2.6112  1306   145  0.76  30.26   1.01     0.93      22370.65|
|  7:  2.6112 -  2.4810  1294   150  0.78  28.74   1.03     0.96      19148.01|
|  8:  2.4810 -  2.3735  1302   140  0.78  28.24   1.03     0.98      17068.43|
|  9:  2.3735 -  2.2824  1294   145  0.78  28.85   1.04     1.00      15799.65|
| 10:  2.2824 -  2.2039  1279   141  0.76  30.48   1.07     1.00      15683.34|
| 11:  2.2039 -  2.1352  1293   145  0.74  32.39   1.04     1.01      16503.82|
| 12:  2.1352 -  2.0744  1269   140  0.72  34.07   1.08     1.00      16430.48|
| 13:  2.0744 -  2.0199  1266   136  0.70  35.77   1.05     0.98      14694.49|
| 14:  2.0199 -  1.9707   607    72  0.74  32.77   1.04     0.93      11399.39|
|alpha:            min =        0.80 max =            1.01 mean =         0.96|
|beta:             min =    11399.39 max =        40574.72 mean =     23215.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.93 mean =        28.56|
|phase err.(test): min =        0.00 max =           89.99 mean =        28.63|
|-----------------------------------------------------------------------------|

============================== 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 = 3.005070              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.497   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472650              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.453   (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 |  1.719 -  2.037:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.037 -  2.355:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.355 -  2.673:       82 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.673 -  2.991:     1791 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.991 -  3.309:     1897 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.309 -  3.627:     2712 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.627 -  3.946:     4747 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.946 -  4.264:     4422 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.264 -  4.582:     5782 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.582 -  4.900:     6938 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.719 |       0.272 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2937   r_free= 0.2877   ksol= 0.00   Bsol= 0.00   scale= 0.986    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.959313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2806   r_free= 0.2745   ksol= 0.32   Bsol= 40.51   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-1.79,-0.91,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.932931                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.742040              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.280   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.262140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.209   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2806      final r-factor (work) = 0.1645          |
| start r-factor (free) = 0.2745      final r-factor (free) = 0.1839          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3353 = 2.74 * 0.50 * 5.9568 + 1.00 * 0.1684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7712 = 2.74 * 0.50 * 5.6249 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1645      final r-factor (work) = 0.1521          |
| start r-factor (free) = 0.1839      final r-factor (free) = 0.1879          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4810 = 0.26 * 1.00 * 5.6249 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4814 = 0.26 * 1.00 * 5.3703 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 5      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.39   16.57    None  None   None       |
|    all(noH): 2823   0      0.00    88.39   16.57    None  None   None       |
|    Sol.    : 438    0      7.21    62.90   37.30    None  None   None       |
|    Mac.    : 2385   0      0.00    88.39   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.839:  639   |   5:    44.193 -  53.032:  101        |
|      1:     8.839 -  17.677: 1419   |   6:    53.032 -  61.871:   44        |
|      2:    17.677 -  26.516:  320   |   7:    61.871 -  70.709:    2        |
|      3:    26.516 -  35.355:  146   |   8:    70.709 -  79.548:    0        |
|      4:    35.355 -  44.193:  151   |   9:    79.548 -  88.387:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1521 r_free = 0.1879             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1518 r_free = 0.1879             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1518   r_free= 0.1879   ksol= 0.32   Bsol= 40.51   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.89,-1.79,-0.91,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.383071                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1499   r_free= 0.1858   ksol= 0.32   Bsol= 47.76   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.43,-1.50,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.377647                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.141636              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.668   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.988   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1499      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1858      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8246 = 2.14 * 0.50 * 5.3839 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7126 = 2.14 * 0.50 * 5.2834 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1727 = 0.39 * 1.00 * 5.2834 + 1.00 * 0.1141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0205 = 0.39 * 1.00 * 5.1640 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    77.45   16.96    None  None   None       |
|    all(noH): 2823   0      0.83    77.45   16.96    None  None   None       |
|    Sol.    : 438    0      5.98    70.37   38.83    None  None   None       |
|    Mac.    : 2385   0      0.83    77.45   12.95    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:     0.830 -   8.491:  645   |   5:    39.138 -  46.799:  114        |
|      1:     8.491 -  16.153: 1300   |   6:    46.799 -  54.461:   92        |
|      2:    16.153 -  23.814:  353   |   7:    54.461 -  62.123:   53        |
|      3:    23.814 -  31.476:  122   |   8:    62.123 -  69.784:   21        |
|      4:    31.476 -  39.138:  119   |   9:    69.784 -  77.446:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1543             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1541             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1541   ksol= 0.32   Bsol= 47.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-2.43,-1.50,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1539   ksol= 0.32   Bsol= 48.60   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.17,-1.16,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.260451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.900  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.603208              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.364  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8922 = 2.26 * 0.50 * 5.1647 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8582 = 2.26 * 0.50 * 5.1291 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1022 = 0.60 * 1.00 * 5.1291 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0961 = 0.60 * 1.00 * 5.1181 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    81.94   16.88    None  None   None       |
|    all(noH): 2823   0      0.83    81.94   16.88    None  None   None       |
|    Sol.    : 438    0      2.74    74.73   39.01    None  None   None       |
|    Mac.    : 2385   0      0.83    81.94   12.82    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:     0.826 -   8.938:  789   |   5:    41.385 -  49.497:  100        |
|      1:     8.938 -  17.050: 1243   |   6:    49.497 -  57.609:   85        |
|      2:    17.050 -  25.162:  294   |   7:    57.609 -  65.721:   38        |
|      3:    25.162 -  33.274:  130   |   8:    65.721 -  73.833:   16        |
|      4:    33.274 -  41.385:  124   |   9:    73.833 -  81.944:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1525             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1525             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1525   ksol= 0.32   Bsol= 48.60   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.17,-1.16,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.118264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1525   ksol= 0.32   Bsol= 48.60   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.98,-0.95,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118324                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.382845              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.354  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.101515              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.555  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6003 = 1.38 * 0.50 * 5.1186 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5956 = 1.38 * 0.50 * 5.1280 + 1.00 * 0.0500                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1532          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5293 = 0.10 * 1.00 * 5.1280 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5287 = 0.10 * 1.00 * 5.1439 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    78.18   16.20    None  None   None       |
|    all(noH): 2823   0      1.79    78.18   16.20    None  None   None       |
|    Sol.    : 438    0      5.65    70.19   35.97    None  None   None       |
|    Mac.    : 2385   0      1.79    78.18   12.57    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:     1.792 -   9.430:  906   |   5:    39.985 -  47.624:   92        |
|      1:     9.430 -  17.069: 1157   |   6:    47.624 -  55.262:   75        |
|      2:    17.069 -  24.708:  280   |   7:    55.262 -  62.901:   27        |
|      3:    24.708 -  32.346:  134   |   8:    62.901 -  70.540:   11        |
|      4:    32.346 -  39.985:  139   |   9:    70.540 -  78.178:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1532             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1125 r_free = 0.1531             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1531   ksol= 0.32   Bsol= 48.60   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.98,-0.95,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1125   r_free= 0.1531   ksol= 0.32   Bsol= 48.60   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.97,-0.90,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140306                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.196351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.336  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.138760              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.778  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6986 = 2.20 * 0.50 * 5.1436 + 1.00 * 0.0500                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6892 = 2.20 * 0.50 * 5.1255 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9687 = 2.14 * 1.00 * 5.1255 + 1.00 * 0.0065                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9434 = 2.14 * 1.00 * 5.1124 + 1.00 * 0.0092                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    89.83   16.74    None  None   None       |
|    all(noH): 2823   0      0.52    89.83   16.74    None  None   None       |
|    Sol.    : 438    0      5.66    81.64   39.17    None  None   None       |
|    Mac.    : 2385   0      0.52    89.83   12.62    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:     0.521 -   9.452:  975   |   5:    45.176 -  54.106:  103        |
|      1:     9.452 -  18.383: 1160   |   6:    54.106 -  63.037:   63        |
|      2:    18.383 -  27.314:  236   |   7:    63.037 -  71.968:   26        |
|      3:    27.314 -  36.245:  130   |   8:    71.968 -  80.899:    8        |
|      4:    36.245 -  45.176:  117   |   9:    80.899 -  89.830:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1537             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1537             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1537   ksol= 0.32   Bsol= 48.60   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-1.97,-0.90,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117944                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1407  157 0.0982 0.1275      5.3775      5.5357|
|  2:  4.7025 -  3.7524 0.99   1353  153 0.0825 0.1080       5.407      5.5993|
|  3:  3.7524 -  3.2839 0.99   1331  148 0.1019 0.1502      5.4374      5.8302|
|  4:  3.2839 -  2.9863 0.99   1322  138 0.1162 0.1479       5.413      5.5668|
|  5:  2.9863 -  2.7738 0.99   1307  149 0.1253 0.1570      5.2833      5.4773|
|  6:  2.7738 -  2.6112 0.98   1306  145 0.1195 0.2030      5.1847      5.4788|
|  7:  2.6112 -  2.4810 0.99   1294  150 0.1179 0.1541      5.1254      5.2921|
|  8:  2.4810 -  2.3735 0.98   1302  140 0.1079 0.1582      5.0371      5.2815|
|  9:  2.3735 -  2.2824 0.98   1294  145 0.1147 0.1878      5.0019        5.35|
| 10:  2.2824 -  2.2039 0.98   1279  141 0.1073 0.1602      4.9312      5.1168|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.1066 0.1728      4.8911      5.2462|
| 12:  2.1352 -  2.0744 0.98   1269  140 0.1059 0.1698      4.8353      5.1666|
| 13:  2.0744 -  2.0199 0.97   1266  136 0.1057 0.1638      4.7522      4.9781|
| 14:  2.0199 -  1.9707 0.47    607   72 0.0970 0.1755      4.6647      4.9415|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1407   157  0.94   9.06   0.98     0.95       6982.59|
|  2:  4.7025 -  3.7524  1353   153  0.95   7.66   1.01     1.00       8544.42|
|  3:  3.7524 -  3.2839  1331   148  0.94  10.83   1.02     1.02       9660.10|
|  4:  3.2839 -  2.9863  1322   138  0.93  12.91   1.01     1.00       9657.98|
|  5:  2.9863 -  2.7738  1307   149  0.90  15.43   0.99     0.96       7779.58|
|  6:  2.7738 -  2.6112  1306   145  0.90  16.05   0.97     0.95       6712.42|
|  7:  2.6112 -  2.4810  1294   150  0.91  14.86   0.98     0.95       5734.36|
|  8:  2.4810 -  2.3735  1302   140  0.91  14.63   0.99     0.97       5203.55|
|  9:  2.3735 -  2.2824  1294   145  0.91  15.26   0.99     0.95       4659.87|
| 10:  2.2824 -  2.2039  1279   141  0.90  15.54   0.99     0.96       4331.62|
| 11:  2.2039 -  2.1352  1293   145  0.91  15.36   0.99     0.95       4062.13|
| 12:  2.1352 -  2.0744  1269   140  0.91  14.85   1.00     0.99       3709.13|
| 13:  2.0744 -  2.0199  1266   136  0.90  15.91   0.99     0.97       3212.90|
| 14:  2.0199 -  1.9707   607    72  0.91  14.45   0.96     0.92       2594.67|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2594.67 max =         9660.10 mean =      6086.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.68|
|phase err.(test): min =        0.00 max =           89.99 mean =        13.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1536   ksol= 0.32   Bsol= 49.11   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.72,-0.66,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117988                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1536   ksol= 0.32   Bsol= 49.11   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.72,-0.66,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.117988                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1407  157 0.0982 0.1278      5.3782      5.5373|
|  2:  4.7025 -  3.7524 0.99   1353  153 0.0826 0.1080      5.4079      5.5994|
|  3:  3.7524 -  3.2839 0.99   1331  148 0.1019 0.1502      5.4376      5.8303|
|  4:  3.2839 -  2.9863 0.99   1322  138 0.1162 0.1478      5.4127      5.5665|
|  5:  2.9863 -  2.7738 0.99   1307  149 0.1252 0.1569       5.283      5.4768|
|  6:  2.7738 -  2.6112 0.98   1306  145 0.1195 0.2029      5.1845      5.4786|
|  7:  2.6112 -  2.4810 0.99   1294  150 0.1179 0.1541      5.1253       5.292|
|  8:  2.4810 -  2.3735 0.98   1302  140 0.1079 0.1581       5.037      5.2812|
|  9:  2.3735 -  2.2824 0.98   1294  145 0.1146 0.1878       5.002      5.3504|
| 10:  2.2824 -  2.2039 0.98   1279  141 0.1073 0.1602      4.9311      5.1167|
| 11:  2.2039 -  2.1352 0.99   1293  145 0.1066 0.1728       4.891      5.2462|
| 12:  2.1352 -  2.0744 0.98   1269  140 0.1059 0.1698      4.8351      5.1663|
| 13:  2.0744 -  2.0199 0.97   1266  136 0.1057 0.1638      4.7521      4.9778|
| 14:  2.0199 -  1.9707 0.47    607   72 0.0970 0.1755      4.6649      4.9415|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1407   157  0.94   9.06   0.98     0.95       6988.98|
|  2:  4.7025 -  3.7524  1353   153  0.95   7.66   1.02     1.00       8554.34|
|  3:  3.7524 -  3.2839  1331   148  0.94  10.84   1.03     1.02       9665.89|
|  4:  3.2839 -  2.9863  1322   138  0.93  12.91   1.01     1.00       9653.35|
|  5:  2.9863 -  2.7738  1307   149  0.90  15.42   1.00     0.97       7774.56|
|  6:  2.7738 -  2.6112  1306   145  0.90  16.05   0.98     0.96       6707.52|
|  7:  2.6112 -  2.4810  1294   150  0.91  14.87   0.99     0.95       5730.89|
|  8:  2.4810 -  2.3735  1302   140  0.91  14.63   1.00     0.98       5200.88|
|  9:  2.3735 -  2.2824  1294   145  0.91  15.26   1.00     0.95       4658.33|
| 10:  2.2824 -  2.2039  1279   141  0.90  15.54   1.00     0.97       4329.27|
| 11:  2.2039 -  2.1352  1293   145  0.91  15.35   1.00     0.97       4060.10|
| 12:  2.1352 -  2.0744  1269   140  0.91  14.85   1.01     1.01       3707.70|
| 13:  2.0744 -  2.0199  1266   136  0.90  15.91   1.00     0.98       3212.61|
| 14:  2.0199 -  1.9707   607    72  0.91  14.46   0.98     0.93       2594.92|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2594.92 max =         9665.89 mean =      6086.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.68|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    89.81   16.72    None  None   None       |
|    all(noH): 2823   0      0.50    89.81   16.72    None  None   None       |
|    Sol.    : 438    0      5.64    81.63   39.15    None  None   None       |
|    Mac.    : 2385   0      0.50    89.81   12.61    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:     0.505 -   9.436:  975   |   5:    45.159 -  54.090:  103        |
|      1:     9.436 -  18.366: 1160   |   6:    54.090 -  63.021:   63        |
|      2:    18.366 -  27.297:  236   |   7:    63.021 -  71.951:   26        |
|      3:    27.297 -  36.228:  130   |   8:    71.951 -  80.882:    8        |
|      4:    36.228 -  45.159:  117   |   9:    80.882 -  89.813:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 272         
Filter by distance & map next to the model:
   mapped sites are within: 0.534 - 5.390
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 269 from: 272
   mapped sites are within: 0.721 - 5.390

peak=    5.721 closest distance to " CB  ARG A 275 " =    0.956
peak=    5.207 closest distance to " CG  PRO A  54 " =    1.245
peak=    5.180 closest distance to " O   HOH Z 232 " =    2.429
peak=    5.163 closest distance to " CB  GLN A 223 " =    1.436
peak=    5.049 closest distance to " NH2 ARG A  56 " =    2.211
peak=    4.989 closest distance to " O   HOH Z 142 " =    1.643
peak=    4.861 closest distance to " O   HOH Z 126 " =    1.903
peak=    4.723 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.719 closest distance to " CB  SER A  63 " =    1.166
peak=    4.669 closest distance to " CB  GLN A 183 " =    1.267
peak=    4.648 closest distance to " CB  GLU A 152 " =    1.185
peak=    4.637 closest distance to " NE2 GLN A  11 " =    1.010
peak=    4.538 closest distance to " C   PRO A 198 " =    1.493
peak=    4.525 closest distance to " CB  ARG A  79 " =    1.359
peak=    4.465 closest distance to " O   HOH Z 250 " =    1.485
peak=    4.450 closest distance to " O   HOH Z 209 " =    2.231
peak=    4.434 closest distance to " CB  PRO A  54 " =    0.930
peak=    4.430 closest distance to " CB  ASN A 148 " =    1.496
peak=    4.430 closest distance to " O   HOH Z 287 " =    2.109
peak=    4.387 closest distance to " CG  PRO A 213 " =    1.204
peak=    4.385 closest distance to " O   HOH Z 402 " =    1.460
peak=    4.383 closest distance to " O   HOH Z  15 " =    2.150
peak=    4.372 closest distance to " CB  ARG A 190 " =    1.700
peak=    4.371 closest distance to " O   HOH Z 427 " =    2.947
peak=    4.323 closest distance to " O   HOH Z 298 " =    1.834
peak=    4.319 closest distance to " CZ  PHE A 218 " =    1.080
peak=    4.313 closest distance to " O   HOH Z 369 " =    2.294
peak=    4.298 closest distance to " O   HOH Z 303 " =    2.075
peak=    4.252 closest distance to " O   HOH Z  78 " =    1.700
peak=    4.226 closest distance to " O   HOH Z 346 " =    1.694
peak=    4.221 closest distance to " O   HOH Z 403 " =    1.762
peak=    4.209 closest distance to " CD2 TRP A 179 " =    1.351
peak=    4.201 closest distance to " O   HOH Z 193 " =    1.770
peak=    4.194 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.177 closest distance to " O   HOH Z 392 " =    2.858
peak=    4.165 closest distance to " O   SER A  87 " =    2.157
peak=    4.143 closest distance to " O   HOH Z 234 " =    3.701
peak=    4.138 closest distance to " CG  PRO A  90 " =    1.174
peak=    4.120 closest distance to " O   HOH Z 128 " =    1.957
peak=    4.117 closest distance to " ND2 ASN A 187 " =    1.416
peak=    4.076 closest distance to " O   HOH Z 158 " =    3.043
peak=    4.072 closest distance to " CB  VAL A 265 " =    1.250
peak=    4.065 closest distance to " O   HOH Z  97 " =    2.419
peak=    4.053 closest distance to " CG  PRO A 243 " =    1.049
peak=    4.038 closest distance to " O   HOH Z 423 " =    2.003
peak=    4.028 closest distance to " O   HOH Z 203 " =    1.663
peak=    4.026 closest distance to " CB  TYR A 169 " =    0.721
peak=    4.020 closest distance to " CG  PRO A 198 " =    1.232
peak=    4.017 closest distance to " CA  ARG A  36 " =    1.033
peak=    4.014 closest distance to " OG ASER A 258 " =    3.053
peak=    4.004 closest distance to " O   HOH Z  61 " =    1.611
peak=    3.938 closest distance to " CA  ASN A 215 " =    1.067
peak=    3.931 closest distance to " O   HOH Z  40 " =    1.836
peak=    3.920 closest distance to " O   HOH Z  43 " =    1.954
peak=    3.907 closest distance to " O   HOH Z 389 " =    1.845
peak=    3.888 closest distance to " CB  GLU A 277 " =    3.579
peak=    3.888 closest distance to " CG1BVAL A  72 " =    1.681
peak=    3.887 closest distance to " O   HOH Z  97 " =    1.950
peak=    3.886 closest distance to " NZ  LYS A 117 " =    3.163
peak=    3.882 closest distance to " CB  TRP A 266 " =    0.972
peak=    3.864 closest distance to " CG1 ILE A  33 " =    1.204
peak=    3.857 closest distance to " O   HOH Z  54 " =    1.698
peak=    3.856 closest distance to " CG2 VAL A 257 " =    0.863
peak=    3.831 closest distance to " O   HOH Z  19 " =    2.127
peak=    3.821 closest distance to " O   HOH Z 189 " =    2.487
peak=    3.809 closest distance to " CB  VAL A 202 " =    1.499
peak=    3.784 closest distance to " O   HOH Z  44 " =    1.879
peak=    3.765 closest distance to " O   HOH Z 280 " =    2.947
peak=    3.764 closest distance to " CG  ARG A  66 " =    2.605
peak=    3.762 closest distance to " O   HOH Z 327 " =    1.580
peak=    3.761 closest distance to " CG2 ILE A 120 " =    1.052
peak=    3.750 closest distance to " NH2BARG A 145 " =    2.047
peak=    3.746 closest distance to " CD  ARG A 159 " =    0.727
peak=    3.743 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.738 closest distance to " O   HOH Z 180 " =    2.240
peak=    3.734 closest distance to " CB  GLU A 128 " =    1.060
peak=    3.729 closest distance to " CB  LEU A 228 " =    1.072
peak=    3.724 closest distance to " O   HOH Z 368 " =    2.143
peak=    3.716 closest distance to " O   HOH Z 291 " =    1.570
peak=    3.713 closest distance to " O   HOH Z 132 " =    2.830
peak=    3.710 closest distance to " N   TYR A 116 " =    1.557
peak=    3.706 closest distance to " O   HOH Z 421 " =    1.701
peak=    3.694 closest distance to " CB  ASN A  39 " =    0.852
peak=    3.692 closest distance to " CA  ARG A 195 " =    1.298
peak=    3.690 closest distance to " OD1 ASN A  69 " =    2.600
peak=    3.678 closest distance to " CB  THR A  31 " =    1.607
peak=    3.673 closest distance to " CB  SER A   3 " =    1.279
peak=    3.656 closest distance to " CB  GLU A  46 " =    1.028
peak=    3.654 closest distance to " O   HOH Z 407 " =    2.706
peak=    3.652 closest distance to " O   HOH Z 245 " =    1.320
peak=    3.647 closest distance to " O   HOH Z 227 " =    1.539
peak=    3.643 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.639 closest distance to " O   HOH Z 185 " =    1.752
peak=    3.632 closest distance to " CA  ALA A 291 " =    0.811
peak=    3.632 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.625 closest distance to " O   HOH Z 214 " =    2.111
peak=    3.619 closest distance to " CA  LYS A 117 " =    1.255
peak=    3.618 closest distance to " O   HOH Z 406 " =    1.535
peak=    3.617 closest distance to " O   HOH Z 265 " =    2.281
peak=    3.612 closest distance to " O   HOH Z 313 " =    1.945
peak=    3.612 closest distance to " O   HOH Z 371 " =    3.231
peak=    3.612 closest distance to " O   HOH Z  59 " =    2.063
peak=    3.612 closest distance to " CB  TYR A 169 " =    0.883
peak=    3.606 closest distance to " CB  ASN A 110 " =    1.147
peak=    3.601 closest distance to " O   HOH Z 147 " =    1.765
peak=    3.600 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.597 closest distance to " O   HOH Z 172 " =    3.828
peak=    3.594 closest distance to " O   HOH Z 261 " =    1.772
peak=    3.585 closest distance to " O   HOH Z 299 " =    4.425
peak=    3.585 closest distance to " CD  ARG A 269 " =    1.004
peak=    3.571 closest distance to " N   HIS A 108 " =    1.915
peak=    3.570 closest distance to " O   HOH Z 305 " =    3.545
peak=    3.568 closest distance to " O   HOH Z 128 " =    2.198
peak=    3.556 closest distance to " CD2 LEU A 297 " =    0.884
peak=    3.553 closest distance to " CB  SER A  26 " =    1.672
peak=    3.551 closest distance to " O   HOH Z 365 " =    2.825
peak=    3.546 closest distance to " CB  TRP A 179 " =    1.338
peak=    3.541 closest distance to " CG2 ILE A  20 " =    1.327
peak=    3.539 closest distance to " CA  ASN A 176 " =    1.199
peak=    3.539 closest distance to " O   HOH Z 403 " =    1.252
peak=    3.531 closest distance to " NE2 GLN A  77 " =    3.155
peak=    3.513 closest distance to " O  BHOH Z 338 " =    2.302
peak=    3.511 closest distance to " O   HOH Z 173 " =    1.978
peak=    3.507 closest distance to " O   HOH Z   1 " =    1.996
peak=    3.502 closest distance to " CB  ALA A 291 " =    1.257
peak=    3.497 closest distance to " O   HOH Z 411 " =    3.885
peak=    3.497 closest distance to " N   ARG A 156 " =    1.374
peak=    3.496 closest distance to " O   HOH Z 337 " =    3.621
peak=    3.485 closest distance to " O   HOH Z 368 " =    3.662
peak=    3.485 closest distance to " CB  GLN A  88 " =    1.151
peak=    3.485 closest distance to " O   HOH Z 357 " =    1.951
peak=    3.478 closest distance to " CB  ILE A 120 " =    1.289
peak=    3.478 closest distance to " OH  TYR A 116 " =    1.085
peak=    3.477 closest distance to " OG BSER A 164 " =    2.265
peak=    3.476 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.468 closest distance to " CB  SER A  62 " =    0.901
peak=    3.464 closest distance to " CA  ALA A  84 " =    1.252
peak=    3.462 closest distance to " O   HOH Z 425 " =    1.922
peak=    3.462 closest distance to " N   ASN A  39 " =    1.285
peak=    3.459 closest distance to " OD2 ASP A 286 " =    2.813
peak=    3.459 closest distance to " O   HOH Z 261 " =    2.022
peak=    3.451 closest distance to " CB  ARG A 139 " =    0.910
peak=    3.450 closest distance to " CZ2 TRP A 179 " =    1.698
peak=    3.449 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.445 closest distance to " O   ALA A 165 " =    1.482
peak=    3.442 closest distance to " O   HOH Z 344 " =    3.147
peak=    3.435 closest distance to " CA  THR A 221 " =    0.990
peak=    3.434 closest distance to " CA  MET A  40 " =    1.100
peak=    3.428 closest distance to " CA  ASN A 217 " =    1.210
peak=    3.426 closest distance to " CG  MET A 185 " =    1.075
peak=    3.426 closest distance to " O   HOH Z  66 " =    2.104
peak=    3.411 closest distance to " O   HOH Z 417 " =    3.163
peak=    3.411 closest distance to " CD1 ILE A 106 " =    0.852
peak=    3.408 closest distance to " CA  ALA A  51 " =    0.882
peak=    3.403 closest distance to " CB  ALA A 114 " =    1.133
peak=    3.401 closest distance to " CB  ALA A 248 " =    1.369
peak=    3.397 closest distance to " O   HOH Z 248 " =    1.557
peak=    3.395 closest distance to " CG  LEU A 167 " =    1.279
peak=    3.393 closest distance to " O   HOH Z 325 " =    2.484
peak=    3.391 closest distance to " O   HOH Z 156 " =    3.268
peak=    3.391 closest distance to " O   HOH Z  21 " =    1.809
peak=    3.387 closest distance to " O   HOH Z 148 " =    3.375
peak=    3.380 closest distance to " CG AARG A 275 " =    1.133
peak=    3.380 closest distance to " OE1 GLU A   2 " =    2.285
peak=    3.378 closest distance to " CA  MET A 105 " =    1.036
peak=    3.370 closest distance to " N   PHE A 130 " =    1.256
peak=    3.369 closest distance to " O   HOH Z  66 " =    2.147
peak=    3.367 closest distance to " O   HOH Z  35 " =    2.433
peak=    3.366 closest distance to " CA  ARG A 275 " =    1.906
peak=    3.366 closest distance to " O   HOH Z 426 " =    1.547
peak=    3.365 closest distance to " CG  GLN A  77 " =    2.095
peak=    3.365 closest distance to " O   HOH Z  10 " =    1.789
peak=    3.364 closest distance to " O   HOH Z 193 " =    2.040
peak=    3.360 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.358 closest distance to " O   HOH Z 108 " =    2.727
peak=    3.357 closest distance to " CB  SER A 141 " =    0.987
peak=    3.356 closest distance to " O   HOH Z 393 " =    3.202
peak=    3.354 closest distance to " CB  SER A 212 " =    1.037
peak=    3.351 closest distance to " O   ASN A  74 " =    1.962
peak=    3.346 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.329 closest distance to " CG  GLU A  37 " =    0.934
peak=    3.311 closest distance to " CA  ALA A 248 " =    1.193
peak=    3.310 closest distance to " NH1AARG A 145 " =    1.235
peak=    3.307 closest distance to " O   HOH Z 163 " =    1.927
peak=    3.296 closest distance to " C   TYR A 214 " =    1.432
peak=    3.290 closest distance to " CD1AILE A 234 " =    0.925
peak=    3.287 closest distance to " O   HOH Z 171 " =    1.847
peak=    3.284 closest distance to " O   THR A 220 " =    1.260
peak=    3.280 closest distance to " CG2 THR A 221 " =    1.196
peak=    3.280 closest distance to " CB  ALA A 242 " =    1.020
peak=    3.277 closest distance to " O   HOH Z  61 " =    1.460
peak=    3.261 closest distance to " O   HOH Z 286 " =    2.240
peak=    3.260 closest distance to " CB  TYR A 116 " =    0.721
peak=    3.260 closest distance to " O   HOH Z  88 " =    3.042
peak=    3.258 closest distance to " O   HOH Z  88 " =    2.531
peak=    3.256 closest distance to " O   HOH Z 258 " =    2.215
peak=    3.253 closest distance to " O   HOH Z 353 " =    2.660
peak=    3.253 closest distance to " CB  ARG A  79 " =    0.813
peak=    3.250 closest distance to " N   ASP A 162 " =    1.187
peak=    3.249 closest distance to " CB  ASN A 215 " =    1.181
peak=    3.243 closest distance to " O   HOH Z 336 " =    1.615
peak=    3.243 closest distance to " CA  VAL A 125 " =    1.031
peak=    3.241 closest distance to " CG1 ILE A  49 " =    1.480
peak=    3.241 closest distance to " CB  HIS A 108 " =    0.840
peak=    3.239 closest distance to " CD2 TYR A 186 " =    1.101
peak=    3.238 closest distance to " OG1 THR A 294 " =    2.419
peak=    3.237 closest distance to " CG2 VAL A 197 " =    1.118
peak=    3.237 closest distance to " NH2AARG A 190 " =    2.225
peak=    3.235 closest distance to " O   HOH Z 419 " =    1.988
peak=    3.231 closest distance to " O   HOH Z 411 " =    1.672
peak=    3.231 closest distance to " O   HOH Z 279 " =    2.187
peak=    3.229 closest distance to " CG  LYS A  76 " =    0.943
peak=    3.221 closest distance to " CG  GLN A  11 " =    1.529
peak=    3.221 closest distance to " CA  THR A 264 " =    0.931
peak=    3.218 closest distance to " OG  SER A  22 " =    2.612
peak=    3.218 closest distance to " O   HOH Z 345 " =    3.121
peak=    3.216 closest distance to " O   HOH Z 132 " =    2.535
peak=    3.211 closest distance to " CB  ALA A   9 " =    1.560
peak=    3.210 closest distance to " O   HOH Z 273 " =    2.868
peak=    3.207 closest distance to " O   HOH Z 391 " =    2.905
peak=    3.207 closest distance to " O   HOH Z  80 " =    1.645
peak=    3.203 closest distance to " CA  TYR A 116 " =    1.379
peak=    3.200 closest distance to " O   HOH Z 430 " =    5.390
peak=    3.199 closest distance to " O   HOH Z 422 " =    2.621
peak=    3.198 closest distance to " CB  THR A  52 " =    0.763
peak=    3.196 closest distance to " CB  ASP A 298 " =    1.137
peak=    3.195 closest distance to " O   HOH Z 126 " =    1.611
peak=    3.194 closest distance to " CA  ARG A 159 " =    1.302
peak=    3.191 closest distance to " O   HOH Z 380 " =    1.907
peak=    3.185 closest distance to " CB  ASN A 142 " =    1.109
peak=    3.182 closest distance to " O   HOH Z  44 " =    3.248
peak=    3.177 closest distance to " CB  THR A 279 " =    1.611
peak=    3.173 closest distance to " CD1 LEU A 300 " =    1.253
peak=    3.171 closest distance to " O   HOH Z 329 " =    3.974
peak=    3.169 closest distance to " CB  GLN A 103 " =    0.833
peak=    3.164 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.153 closest distance to " CE1 PHE A  38 " =    1.277
peak=    3.153 closest distance to " O   HOH Z 298 " =    2.380
peak=    3.152 closest distance to " CB  VAL A 126 " =    1.232
peak=    3.152 closest distance to " CB  PRO A  90 " =    1.104
peak=    3.151 closest distance to " CA  ASP A 140 " =    1.121
peak=    3.149 closest distance to " CB  SER A  62 " =    1.378
peak=    3.149 closest distance to " O   HOH Z 251 " =    1.589
peak=    3.148 closest distance to " CG  MET A 113 " =    1.102
peak=    3.143 closest distance to " CA  ASP A 191 " =    1.219
peak=    3.143 closest distance to " O   HOH Z  85 " =    1.299
peak=    3.140 closest distance to " CA  SER A 146 " =    1.732
peak=    3.137 closest distance to " CD  LYS A 119 " =    1.394
peak=    3.132 closest distance to " NE2 HIS A 207 " =    1.289
peak=    3.132 closest distance to " O   HOH Z 285 " =    2.817
peak=    3.131 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.129 closest distance to " O   HOH Z 267 " =    1.987
peak=    3.128 closest distance to " CB  ALA A  34 " =    1.128
peak=    3.125 closest distance to " CB  MET A  47 " =    1.062
peak=    3.124 closest distance to " O   HOH Z 425 " =    1.257
peak=    3.120 closest distance to " O   HOH Z 394 " =    3.853
peak=    3.117 closest distance to " O   HOH Z  49 " =    2.158
peak=    3.115 closest distance to " CB  GLN A 278 " =    0.887
peak=    3.114 closest distance to " O   HOH Z 213 " =    1.695
peak=    3.113 closest distance to " O   ALA A   1 " =    1.691
peak=    3.103 closest distance to " O   HOH Z 433 " =    1.732
peak=    3.099 closest distance to " ND1 HIS A  81 " =    1.618
peak=    3.098 closest distance to " CG  LYS A 119 " =    1.078
peak=    3.096 closest distance to " OG  SER A  62 " =    2.784
peak=    3.091 closest distance to " ND2 ASN A 110 " =    1.599
peak=    3.078 closest distance to " CA  ASN A 252 " =    1.689
peak=    3.061 closest distance to " CB  LEU A 300 " =    0.919
peak=    3.035 closest distance to " O   HOH Z  85 " =    1.800
peak=    3.018 closest distance to " O   HOH Z 281 " =    4.838

                           ----------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: 0.823 - 5.946
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 198
   mapped sites are within: 0.823 - 5.946

peak=   -4.746 closest distance to " O   HOH Z 266 " =    5.176
peak=   -4.670 closest distance to " CD  GLN A  58 " =    1.056
peak=   -4.644 closest distance to " C   HIS A 108 " =    1.094
peak=   -4.620 closest distance to " SG  CYS A 254 " =    3.418
peak=   -4.466 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.419 closest distance to " CG  GLN A 223 " =    2.010
peak=   -4.400 closest distance to " OG BSER A 134 " =    1.260
peak=   -4.359 closest distance to " CG1 VAL A 112 " =    2.788
peak=   -4.342 closest distance to " CB  PRO A 243 " =    2.612
peak=   -4.291 closest distance to " C   ILE A 239 " =    2.174
peak=   -4.272 closest distance to " O   VAL A  67 " =    2.676
peak=   -4.210 closest distance to " O   HOH Z 372 " =    2.281
peak=   -4.200 closest distance to " O   HOH Z 198 " =    1.766
peak=   -4.136 closest distance to " O   HOH Z 231 " =    2.266
peak=   -4.090 closest distance to " CA  VAL A  67 " =    2.972
peak=   -3.972 closest distance to " CB  PHE A 192 " =    1.976
peak=   -3.937 closest distance to " OG  SER A  97 " =    2.188
peak=   -3.930 closest distance to " OXT GLY A 302 " =    2.801
peak=   -3.900 closest distance to " CZ  TYR A 169 " =    1.777
peak=   -3.886 closest distance to " CB  ASP A 132 " =    2.284
peak=   -3.883 closest distance to " N   ALA A  43 " =    2.683
peak=   -3.882 closest distance to " CB  ALA A 161 " =    2.538
peak=   -3.874 closest distance to " OD2 ASP A 171 " =    2.392
peak=   -3.868 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.861 closest distance to " O   HOH Z 290 " =    1.254
peak=   -3.847 closest distance to " O   HOH Z  13 " =    1.671
peak=   -3.845 closest distance to " CZ3 TRP A 179 " =    1.225
peak=   -3.839 closest distance to " ND2 ASN A  45 " =    1.682
peak=   -3.819 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.814 closest distance to " CE2 TYR A  30 " =    2.761
peak=   -3.795 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.789 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.782 closest distance to " O   HOH Z 407 " =    2.817
peak=   -3.772 closest distance to " CB  ASN A  39 " =    2.357
peak=   -3.765 closest distance to " O   HOH Z 353 " =    2.170
peak=   -3.756 closest distance to " O   SER A 210 " =    1.948
peak=   -3.754 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.753 closest distance to " O   PHE A 218 " =    1.611
peak=   -3.730 closest distance to " O   HOH Z 114 " =    3.168
peak=   -3.710 closest distance to " OD2 ASP A 191 " =    1.416
peak=   -3.702 closest distance to " ND2 ASN A  45 " =    1.099
peak=   -3.695 closest distance to " O   HOH Z 211 " =    1.636
peak=   -3.687 closest distance to " O   HOH Z 126 " =    1.892
peak=   -3.673 closest distance to " O   HOH Z 351 " =    1.527
peak=   -3.652 closest distance to " N   ALA A 248 " =    1.649
peak=   -3.651 closest distance to " CB  ALA A 291 " =    2.313
peak=   -3.648 closest distance to " CD1 LEU A 255 " =    2.744
peak=   -3.643 closest distance to " O   HOH Z 196 " =    1.954
peak=   -3.637 closest distance to " CB  ALA A 248 " =    2.246
peak=   -3.628 closest distance to " CA  GLY A 203 " =    2.422
peak=   -3.614 closest distance to " O   HOH Z 389 " =    1.785
peak=   -3.614 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.610 closest distance to " CG1 VAL A 112 " =    2.773
peak=   -3.608 closest distance to " O   HOH Z 165 " =    1.983
peak=   -3.603 closest distance to " O   HOH Z  10 " =    1.517
peak=   -3.600 closest distance to " CB  ASP A 286 " =    1.826
peak=   -3.599 closest distance to " N   GLN A  58 " =    1.592
peak=   -3.596 closest distance to " N   THR A  52 " =    1.732
peak=   -3.582 closest distance to " CD1 LEU A  25 " =    2.513
peak=   -3.573 closest distance to " O   PRO A 163 " =    2.085
peak=   -3.570 closest distance to " O   HOH Z 348 " =    2.292
peak=   -3.559 closest distance to " CD1 ILE A 239 " =    2.395
peak=   -3.558 closest distance to " O   HOH Z 394 " =    1.466
peak=   -3.556 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.549 closest distance to " CG2 THR A 178 " =    2.242
peak=   -3.543 closest distance to " O   GLN A  89 " =    1.549
peak=   -3.535 closest distance to " OG  SER A   3 " =    1.753
peak=   -3.526 closest distance to " O   HOH Z  63 " =    1.553
peak=   -3.522 closest distance to " CB  ALA A  43 " =    2.462
peak=   -3.520 closest distance to " O   HOH Z 102 " =    1.580
peak=   -3.518 closest distance to " O   HOH Z 362 " =    5.946
peak=   -3.514 closest distance to " O   HOH Z 292 " =    4.491
peak=   -3.511 closest distance to " CD  ARG A 195 " =    5.216
peak=   -3.508 closest distance to " O   VAL A 174 " =    2.137
peak=   -3.499 closest distance to " CG  ARG A 269 " =    2.286
peak=   -3.497 closest distance to " NE2 GLN A  88 " =    1.799
peak=   -3.493 closest distance to " O   HOH Z 166 " =    1.889
peak=   -3.492 closest distance to " CZ  PHE A  59 " =    1.569
peak=   -3.492 closest distance to " O   MET A  40 " =    2.804
peak=   -3.487 closest distance to " N   TYR A  68 " =    3.198
peak=   -3.482 closest distance to " OD1 ASP A 171 " =    1.621
peak=   -3.466 closest distance to " CB  ALA A 291 " =    2.256
peak=   -3.465 closest distance to " CB  TYR A  15 " =    2.201
peak=   -3.463 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.463 closest distance to " ND2 ASN A 249 " =    2.324
peak=   -3.455 closest distance to " O   HOH Z 283 " =    2.434
peak=   -3.455 closest distance to " O   HOH Z 243 " =    2.008
peak=   -3.444 closest distance to " O   GLY A  75 " =    1.777
peak=   -3.444 closest distance to " NH2AARG A 275 " =    5.077
peak=   -3.441 closest distance to " CB  ALA A 248 " =    2.157
peak=   -3.439 closest distance to " O   HOH Z 123 " =    2.231
peak=   -3.438 closest distance to " CG  PHE A 283 " =    2.606
peak=   -3.436 closest distance to " O   VAL A 189 " =    1.689
peak=   -3.417 closest distance to " CG  GLU A  53 " =    1.505
peak=   -3.415 closest distance to " O   ALA A 161 " =    1.735
peak=   -3.409 closest distance to " O   HOH Z  11 " =    1.714
peak=   -3.408 closest distance to " CE  MET A 105 " =    2.296
peak=   -3.404 closest distance to " CG1 VAL A 230 " =    2.022
peak=   -3.399 closest distance to " OD1 ASN A 148 " =    1.494
peak=   -3.396 closest distance to " CG  GLU A 277 " =    1.238
peak=   -3.393 closest distance to " O   HOH Z 317 " =    1.523
peak=   -3.375 closest distance to " O   ALA A  10 " =    1.767
peak=   -3.374 closest distance to " N   ALA A 226 " =    1.960
peak=   -3.367 closest distance to " NE2 GLN A  11 " =    1.825
peak=   -3.367 closest distance to " CD2 TYR A 293 " =    2.009
peak=   -3.363 closest distance to " C   LEU A 143 " =    1.046
peak=   -3.361 closest distance to " O   LEU A 167 " =    1.515
peak=   -3.359 closest distance to " OG BSER A 134 " =    1.774
peak=   -3.356 closest distance to " O   HOH Z 421 " =    3.330
peak=   -3.353 closest distance to " CG  ASP A 231 " =    0.823
peak=   -3.346 closest distance to " CG1 VAL A 250 " =    2.631
peak=   -3.346 closest distance to " CZ  ARG A  66 " =    1.324
peak=   -3.343 closest distance to " CD2 PHE A 225 " =    1.219
peak=   -3.337 closest distance to " CD2 LEU A 237 " =    2.626
peak=   -3.332 closest distance to " O   HOH Z 313 " =    1.922
peak=   -3.318 closest distance to " O   HOH Z  71 " =    2.019
peak=   -3.317 closest distance to " O   HOH Z 252 " =    3.756
peak=   -3.312 closest distance to " O   ALA A 292 " =    2.038
peak=   -3.309 closest distance to " CB  PRO A 163 " =    2.423
peak=   -3.308 closest distance to " O   SER A 135 " =    1.516
peak=   -3.307 closest distance to " OD2 ASP A  50 " =    2.149
peak=   -3.307 closest distance to " O   HOH Z 166 " =    1.597
peak=   -3.304 closest distance to " CD  GLU A 236 " =    1.043
peak=   -3.300 closest distance to " OE2 GLU A 152 " =    1.266
peak=   -3.299 closest distance to " O   HOH Z 171 " =    2.028
peak=   -3.294 closest distance to " CD2 PHE A  61 " =    2.527
peak=   -3.291 closest distance to " CD2 LEU A 300 " =    2.830
peak=   -3.289 closest distance to " O   HOH Z 385 " =    2.110
peak=   -3.289 closest distance to " O   HOH Z  37 " =    1.768
peak=   -3.287 closest distance to " NE2 GLN A 194 " =    1.834
peak=   -3.284 closest distance to " O   HOH Z   6 " =    1.474
peak=   -3.273 closest distance to " CE3 TRP A 150 " =    2.184
peak=   -3.273 closest distance to " CG2 VAL A 189 " =    2.161
peak=   -3.272 closest distance to " SG ACYS A 201 " =    1.837
peak=   -3.271 closest distance to " O   PRO A 198 " =    1.611
peak=   -3.269 closest distance to " O   HOH Z 339 " =    1.744
peak=   -3.263 closest distance to " O   SER A  95 " =    1.569
peak=   -3.257 closest distance to " NE2 GLN A 278 " =    1.786
peak=   -3.251 closest distance to " O   ALA A  34 " =    2.276
peak=   -3.247 closest distance to " CA  GLY A 241 " =    3.254
peak=   -3.246 closest distance to " O   HOH Z 414 " =    1.489
peak=   -3.243 closest distance to " OE1 GLN A 183 " =    1.523
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.837
peak=   -3.235 closest distance to " CB  PHE A  16 " =    2.610
peak=   -3.232 closest distance to " O   HOH Z 177 " =    1.727
peak=   -3.227 closest distance to " O   PRO A 198 " =    1.277
peak=   -3.226 closest distance to " C   THR A 279 " =    1.188
peak=   -3.223 closest distance to " CA  ASN A 127 " =    1.316
peak=   -3.223 closest distance to " OE1 GLN A 194 " =    1.693
peak=   -3.222 closest distance to " CE1 TYR A 247 " =    2.786
peak=   -3.222 closest distance to " O   HOH Z 134 " =    2.999
peak=   -3.221 closest distance to " O   HOH Z  38 " =    1.722
peak=   -3.218 closest distance to " CG1 VAL A 125 " =    2.383
peak=   -3.216 closest distance to " CA  GLY A 241 " =    2.375
peak=   -3.215 closest distance to " ND2 ASN A  60 " =    1.372
peak=   -3.213 closest distance to " O   HOH Z  43 " =    1.681
peak=   -3.213 closest distance to " CB  TRP A  85 " =    2.579
peak=   -3.205 closest distance to " OG  SER A  62 " =    1.759
peak=   -3.204 closest distance to " OD2 ASP A  50 " =    1.487
peak=   -3.203 closest distance to " O   HOH Z 369 " =    2.147
peak=   -3.201 closest distance to " O   HOH Z 234 " =    4.071
peak=   -3.198 closest distance to " OE2 GLU A   2 " =    1.937
peak=   -3.196 closest distance to " C   GLY A 262 " =    1.925
peak=   -3.193 closest distance to " O   HOH Z 244 " =    1.990
peak=   -3.190 closest distance to " O   VAL A 189 " =    2.638
peak=   -3.189 closest distance to " O   HOH Z 309 " =    2.601
peak=   -3.187 closest distance to " O   HOH Z 357 " =    2.094
peak=   -3.182 closest distance to " CD1 LEU A 297 " =    2.347
peak=   -3.180 closest distance to " O   HOH Z 311 " =    3.596
peak=   -3.174 closest distance to " O   HOH Z 233 " =    2.386
peak=   -3.170 closest distance to " O   ILE A 106 " =    1.809
peak=   -3.159 closest distance to " O   SER A   3 " =    1.067
peak=   -3.158 closest distance to " CE2 PHE A 218 " =    2.433
peak=   -3.158 closest distance to " CE BMET A  47 " =    1.575
peak=   -3.157 closest distance to " CG1AVAL A  41 " =    2.881
peak=   -3.154 closest distance to " O   HOH Z 174 " =    4.157
peak=   -3.151 closest distance to " CA  GLY A  57 " =    2.204
peak=   -3.147 closest distance to " NE2 GLN A 223 " =    1.250
peak=   -3.146 closest distance to " CZ3 TRP A 274 " =    2.391
peak=   -3.139 closest distance to " CG  GLU A 152 " =    1.186
peak=   -3.135 closest distance to " OXT GLY A 302 " =    3.295
peak=   -3.128 closest distance to " NH2 ARG A  79 " =    2.007
peak=   -3.123 closest distance to " C   ALA A 158 " =    1.402
peak=   -3.110 closest distance to " CA  GLY A 133 " =    2.035
peak=   -3.104 closest distance to " NH2 ARG A  79 " =    1.606
peak=   -3.104 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.103 closest distance to " NH2BARG A 275 " =    2.215
peak=   -3.101 closest distance to " O   ALA A 227 " =    1.739
peak=   -3.098 closest distance to " CD1 ILE A 199 " =    2.417
peak=   -3.084 closest distance to " O   HOH Z 351 " =    1.358
peak=   -3.084 closest distance to " C   MET A 188 " =    1.427
peak=   -3.072 closest distance to " O   ASN A  45 " =    1.883
peak=   -3.056 closest distance to " O   HOH Z 377 " =    1.811
peak=   -3.042 closest distance to " O   ALA A  51 " =    1.291
peak=   -3.037 closest distance to " CG2 THR A 221 " =    2.293
peak=   -3.035 closest distance to " O   HOH Z 361 " =    3.423
peak=   -3.034 closest distance to " O   HOH Z  60 " =    2.093
peak=   -3.025 closest distance to " O   TRP A  70 " =    1.494

================= 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    :  0.2937 0.2877   5.959313e+00   5.930168e+00
   1_bss:  0.2806 0.2745   5.932931e+00   5.902084e+00
   1_xyz:  0.1645 0.1839   5.428237e+00   5.524772e+00
   1_adp:  0.1521 0.1879   5.384274e+00   5.557317e+00
   1_occ:  0.1518 0.1879   5.383071e+00   5.556447e+00
   2_bss:  0.1499 0.1858   5.377647e+00   5.548119e+00
   2_xyz:  0.1222 0.1563   5.193306e+00   5.387869e+00
   2_adp:  0.1158 0.1543   5.155239e+00   5.369773e+00
   2_occ:  0.1157 0.1541   5.154703e+00   5.369431e+00
   3_bss:  0.1156 0.1539   5.154442e+00   5.367342e+00
   3_xyz:  0.1094 0.1526   5.123071e+00   5.359986e+00
   3_adp:  0.1084 0.1525   5.118410e+00   5.359578e+00
   3_occ:  0.1083 0.1525   5.118264e+00   5.359601e+00
   4_bss:  0.1082 0.1525   5.118324e+00   5.359603e+00
   4_xyz:  0.1104 0.1537   5.133468e+00   5.369593e+00
   4_adp:  0.1126 0.1532   5.140360e+00   5.364691e+00
   4_occ:  0.1125 0.1531   5.140324e+00   5.364963e+00
   5_bss:  0.1125 0.1531   5.140306e+00   5.364894e+00
   5_xyz:  0.1091 0.1526   5.122231e+00   5.360294e+00
   5_adp:  0.1073 0.1537   5.118110e+00   5.367525e+00
   5_occ:  0.1073 0.1537   5.117944e+00   5.367395e+00
   5_bss:  0.1072 0.1536   5.117988e+00   5.367396e+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:  0.322  40.511  -0.887  -1.795  -0.910  -0.000  -0.000  -0.000
   1_xyz:  0.322  40.511  -0.887  -1.795  -0.910  -0.000  -0.000  -0.000
   1_adp:  0.322  40.511  -0.887  -1.795  -0.910  -0.000  -0.000  -0.000
   1_occ:  0.322  40.511  -0.887  -1.795  -0.910  -0.000  -0.000  -0.000
   2_bss:  0.323  47.761  -2.876  -2.434  -1.500  -0.000  -0.000  -0.000
   2_xyz:  0.323  47.761  -2.876  -2.434  -1.500  -0.000  -0.000  -0.000
   2_adp:  0.323  47.761  -2.876  -2.434  -1.500  -0.000  -0.000  -0.000
   2_occ:  0.323  47.761  -2.876  -2.434  -1.500  -0.000  -0.000  -0.000
   3_bss:  0.322  48.597  -2.869  -2.167  -1.162  -0.000  -0.000  -0.000
   3_xyz:  0.322  48.597  -2.869  -2.167  -1.162  -0.000  -0.000  -0.000
   3_adp:  0.322  48.597  -2.869  -2.167  -1.162  -0.000  -0.000  -0.000
   3_occ:  0.322  48.597  -2.869  -2.167  -1.162  -0.000  -0.000  -0.000
   4_bss:  0.322  48.597  -2.758  -1.981  -0.946  -0.000  -0.000  -0.000
   4_xyz:  0.322  48.597  -2.758  -1.981  -0.946  -0.000  -0.000  -0.000
   4_adp:  0.322  48.597  -2.758  -1.981  -0.946  -0.000  -0.000  -0.000
   4_occ:  0.322  48.597  -2.758  -1.981  -0.946  -0.000  -0.000  -0.000
   5_bss:  0.322  48.597  -2.808  -1.971  -0.900  -0.000  -0.000  -0.000
   5_xyz:  0.322  48.597  -2.808  -1.971  -0.900  -0.000  -0.000  -0.000
   5_adp:  0.322  48.597  -2.808  -1.971  -0.900  -0.000  -0.000  -0.000
   5_occ:  0.322  48.597  -2.808  -1.971  -0.900  -0.000  -0.000  -0.000
   5_bss:  0.321  49.106  -2.550  -1.723  -0.662  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.566 0.7774  0.9570    23215.253
   1_bss:  27.317 0.7890  0.9353    20282.809
   1_xyz:  16.952 0.8907  1.0063     8515.085
   1_adp:  17.780 0.8828  0.9993     9061.210
   1_occ:  17.769 0.8829  0.9991     9042.639
   2_bss:  17.565 0.8847  0.9614     8849.955
   2_xyz:  14.244 0.9128  0.9730     6342.821
   2_adp:  13.857 0.9159  0.9692     6120.301
   2_occ:  13.852 0.9160  0.9690     6111.500
   3_bss:  13.822 0.9162  0.9757     6072.244
   3_xyz:  13.564 0.9184  0.9776     6001.561
   3_adp:  13.533 0.9188  0.9719     5987.014
   3_occ:  13.532 0.9188  0.9719     5985.339
   4_bss:  13.534 0.9188  0.9777     5985.053
   4_xyz:  13.684 0.9178  0.9765     6105.844
   4_adp:  13.578 0.9186  0.9738     6098.900
   4_occ:  13.583 0.9185  0.9737     6100.047
   5_bss:  13.583 0.9185  0.9737     6098.915
   5_xyz:  13.495 0.9191  0.9746     6051.650
   5_adp:  13.644 0.9180  0.9682     6087.838
   5_occ:  13.639 0.9180  0.9682     6085.944
   5_bss:  13.640 0.9180  0.9762     6085.573
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6842e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6842e-01
   1_xyz:   1.001  0.007  0.070 14.988  0.004  4.109   5.9348e-02
   1_adp:   1.001  0.007  0.070 14.988  0.004  4.109   5.9348e-02
   1_occ:   1.001  0.007  0.070 14.988  0.004  4.109   5.9348e-02
   2_bss:   1.001  0.007  0.070 14.988  0.004  4.109   5.9348e-02
   2_xyz:   0.971  0.006  0.072 14.604  0.004  4.116   5.4965e-02
   2_adp:   0.971  0.006  0.072 14.604  0.004  4.116   5.4965e-02
   2_occ:   0.971  0.006  0.072 14.604  0.004  4.116   5.4965e-02
   3_bss:   0.971  0.006  0.072 14.604  0.004  4.116   5.4965e-02
   3_xyz:   1.013  0.008  0.077 14.754  0.004  4.111   6.1144e-02
   3_adp:   1.013  0.008  0.077 14.754  0.004  4.111   6.1144e-02
   3_occ:   1.013  0.008  0.077 14.754  0.004  4.111   6.1144e-02
   4_bss:   1.013  0.008  0.077 14.754  0.004  4.111   6.1144e-02
   4_xyz:   0.899  0.006  0.070 14.445  0.004  4.111   4.9995e-02
   4_adp:   0.899  0.006  0.070 14.445  0.004  4.111   4.9995e-02
   4_occ:   0.899  0.006  0.070 14.445  0.004  4.111   4.9995e-02
   5_bss:   0.899  0.006  0.070 14.445  0.004  4.111   4.9995e-02
   5_xyz:   1.009  0.007  0.078 14.660  0.004  4.111   6.0437e-02
   5_adp:   1.009  0.007  0.078 14.660  0.004  4.111   6.0437e-02
   5_occ:   1.009  0.007  0.078 14.660  0.004  4.111   6.0437e-02
   5_bss:   1.009  0.007  0.078 14.660  0.004  4.111   6.0437e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.719   2.4054e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.719   2.4054e-01
   1_xyz:   6.698  0.039  0.288 84.087  0.041  2.276   6.8023e-02
   1_adp:   6.698  0.039  0.288 84.087  0.041  2.276   6.8023e-02
   1_occ:   6.698  0.039  0.288 84.087  0.041  2.276   6.8023e-02
   2_bss:   6.698  0.039  0.288 84.087  0.041  2.276   6.8023e-02
   2_xyz:   6.650  0.040  0.230 81.832  0.036  2.333   3.8763e-02
   2_adp:   6.650  0.040  0.230 81.832  0.036  2.333   3.8763e-02
   2_occ:   6.650  0.040  0.230 81.832  0.036  2.333   3.8763e-02
   3_bss:   6.650  0.040  0.230 81.832  0.036  2.333   3.8763e-02
   3_xyz:   7.394  0.048  0.249 82.788  0.035  2.344   4.5856e-02
   3_adp:   7.394  0.048  0.249 82.788  0.035  2.344   4.5856e-02
   3_occ:   7.394  0.048  0.249 82.788  0.035  2.344   4.5856e-02
   4_bss:   7.394  0.048  0.249 82.788  0.035  2.344   4.5856e-02
   4_xyz:   6.396  0.044  0.224 82.395  0.035  2.407   2.9529e-02
   4_adp:   6.396  0.044  0.224 82.395  0.035  2.407   2.9529e-02
   4_occ:   6.396  0.044  0.224 82.395  0.035  2.407   2.9529e-02
   5_bss:   6.396  0.044  0.224 82.395  0.035  2.407   2.9529e-02
   5_xyz:   7.380  0.049  0.249 83.594  0.036  2.319   4.1386e-02
   5_adp:   7.380  0.049  0.249 83.594  0.036  2.319   4.1386e-02
   5_occ:   7.380  0.049  0.249 83.594  0.036  2.319   4.1386e-02
   5_bss:   7.380  0.049  0.249 83.594  0.036  2.319   4.1386e-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:  88.39   0.00  16.57  88.39   0.00  12.76  62.90   7.21  37.30
   1_occ:  88.39   0.00  16.57  88.39   0.00  12.76  62.90   7.21  37.30
   2_bss:  88.39   0.00  16.57  88.39   0.00  12.76  62.90   7.21  37.30
   2_xyz:  88.39   0.00  16.57  88.39   0.00  12.76  62.90   7.21  37.30
   2_adp:  77.45   0.83  16.96  77.45   0.83  12.95  70.37   5.98  38.83
   2_occ:  77.45   0.83  16.96  77.45   0.83  12.95  70.37   5.98  38.83
   3_bss:  77.45   0.83  16.96  77.45   0.83  12.95  70.37   5.98  38.83
   3_xyz:  77.45   0.83  16.96  77.45   0.83  12.95  70.37   5.98  38.83
   3_adp:  81.94   0.83  16.88  81.94   0.83  12.82  74.73   2.74  39.01
   3_occ:  81.94   0.83  16.88  81.94   0.83  12.82  74.73   2.74  39.01
   4_bss:  81.94   0.83  16.88  81.94   0.83  12.82  74.73   2.74  39.01
   4_xyz:  81.94   0.83  16.88  81.94   0.83  12.82  74.73   2.74  39.01
   4_adp:  78.18   1.79  16.20  78.18   1.79  12.57  70.19   5.65  35.97
   4_occ:  78.18   1.79  16.20  78.18   1.79  12.57  70.19   5.65  35.97
   5_bss:  78.18   1.79  16.20  78.18   1.79  12.57  70.19   5.65  35.97
   5_xyz:  78.18   1.79  16.20  78.18   1.79  12.57  70.19   5.65  35.97
   5_adp:  89.83   0.52  16.74  89.83   0.52  12.62  81.64   5.66  39.17
   5_occ:  89.83   0.52  16.74  89.83   0.52  12.62  81.64   5.66  39.17
   5_bss:  89.81   0.50  16.72  89.81   0.50  12.61  81.63   5.64  39.15
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.133    0.016    0.263
   1_adp:    1.133    0.016    0.263
   1_occ:    1.133    0.016    0.263
   2_bss:    1.133    0.016    0.263
   2_xyz:    0.820    0.031    0.313
   2_adp:    0.820    0.031    0.313
   2_occ:    0.820    0.031    0.313
   3_bss:    0.820    0.031    0.313
   3_xyz:    0.927    0.009    0.331
   3_adp:    0.927    0.009    0.331
   3_occ:    0.927    0.009    0.331
   4_bss:    0.927    0.009    0.331
   4_xyz:    1.046    0.011    0.336
   4_adp:    1.046    0.011    0.336
   4_occ:    1.046    0.011    0.336
   5_bss:    1.046    0.011    0.336
   5_xyz:    1.100    0.022    0.340
   5_adp:    1.100    0.022    0.340
   5_occ:    1.100    0.022    0.340
   5_bss:    1.100    0.022    0.340
------------------------------------------------------------------------

CPU time actual refinement: 320.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/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_314/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_314/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.95 
  Macro-tasks:
    bulk solvent and scale       = 38.53  
    individual site refinement   = 126.61 
    weights calculation          = 29.11  
    collect and process          = 6.65   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 201.01 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 100.99 
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.14 
    fmodel                         = 6.64   
    r_factors                      = 0.24   
    phase_errors                   = 11.29  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 239.13 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.595 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    641 calls, 100.65 s
gradients_fft:          586 calls,  96.40 s

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

# Date 2008-01-16 Time 04:31:47 PST -0800 (1200486707.31 s)
Start R-work = 0.2937, R-free = 0.2877 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1722 (no bulk solvent and anisotropic scale)

Start R-work = 0.2806, R-free = 0.2745
Final R-work = 0.1072, R-free = 0.1536