# Date 2008-01-16 Time 04:59:31 PST -0800 (1200488371.49 s)
#phil __OFF__

Command line arguments: "../544.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15410
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 544

-------------------------------------------------------------------------------
  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: (69.8988, 46.93, 86.39, 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: 3.34, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99053
Completeness in resolution range: 0.977007
Completeness with d_max=infinity: 0.973899

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9905

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: (69.8988, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99053
Completeness in resolution range: 0.977007
Completeness with d_max=infinity: 0.973899

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2585 [2105/2129]  1894   211  10.0%
  bin  2:  4.2585 -  3.3931 [2028/2047]  1826   202  10.0%
  bin  3:  3.3931 -  2.9680 [1994/2013]  1795   199  10.0%
  bin  4:  2.9680 -  2.6984 [1972/2002]  1774   198  10.0%
  bin  5:  2.6984 -  2.5059 [1977/1996]  1781   196   9.9%
  bin  6:  2.5059 -  2.3588 [1946/1971]  1747   199  10.2%
  bin  7:  2.3588 -  2.2411 [1948/1976]  1756   192   9.9%
  bin  8:  2.2411 -  2.1438 [1953/1989]  1758   195  10.0%
  bin  9:  2.1438 -  2.0615 [1906/1948]  1713   193  10.1%
  bin 10:  2.0615 -  1.9905 [1760/1979]  1586   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/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:
        1.81 -     2.42: 10
        2.42 -     3.04: 2214
        3.04 -     3.66: 4643
        3.66 -     4.28: 9094
        4.28 -     4.90: 12363
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.274 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.298 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28319 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_544/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 69.89875 46.93 86.39 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: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1741   r_free= 0.1743   ksol= 0.00   Bsol= 0.00   scale= 1.021    |
|                                                                             |
| 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:   0.10 A                  |
| x-ray target function (ml) for work reflections: 5.409358                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.2363 0.2330      6.2103      6.1771|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.1376 0.1338      5.8774       5.848|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.1404 0.1350      5.6996      5.7482|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.1442 0.1525      5.5498      5.5617|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.1611 0.1456       5.451      5.3984|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.1581 0.1731      5.3584      5.3537|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.1683 0.1558      5.3414      5.2756|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.1657 0.1582      5.2987      5.2911|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.1635 0.1688      5.2286      5.2276|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.1619 0.1807       5.187      5.2024|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.1644 0.1567        5.14       5.152|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.1669 0.1528      5.1202      5.1582|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.1756 0.1648      5.0902      4.9865|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.1713 0.1631      5.0039      4.9035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7493  1375   153  0.82  22.91   0.88     0.83      33141.77|
|  2:  4.7493 -  3.7899  1306   146  0.91  13.71   1.01     0.96      19371.56|
|  3:  3.7899 -  3.3168  1294   143  0.93  11.57   1.03     1.03      11156.04|
|  4:  3.3168 -  3.0163  1285   139  0.93  11.72   1.04     1.03       8540.44|
|  5:  3.0163 -  2.8016  1266   144  0.92  13.74   1.05     1.03       6975.00|
|  6:  2.8016 -  2.6374  1277   141  0.92  13.52   1.06     1.04       5748.91|
|  7:  2.6374 -  2.5059  1267   140  0.92  13.53   1.07     1.06       5014.17|
|  8:  2.5059 -  2.3973  1248   140  0.92  13.57   1.08     1.08       4596.85|
|  9:  2.3973 -  2.3054  1253   142  0.92  13.92   1.11     1.09       4379.39|
| 10:  2.3054 -  2.2261  1247   136  0.91  14.52   1.13     1.10       4156.27|
| 11:  2.2261 -  2.1567  1254   137  0.92  14.42   1.12     1.12       3850.85|
| 12:  2.1567 -  2.0952  1241   142  0.92  13.66   1.14     1.14       3420.62|
| 13:  2.0952 -  2.0402  1248   136  0.92  13.57   1.13     1.14       2887.74|
| 14:  2.0402 -  1.9905  1069   120  0.92  13.58   1.14     1.11       2304.06|
|alpha:            min =        0.83 max =            1.14 mean =         1.05|
|beta:             min =     2304.06 max =        33141.77 mean =      8528.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.19|
|phase err.(test): min =        0.00 max =           88.92 mean =        14.21|
|-----------------------------------------------------------------------------|

============================== 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 = 1.998771              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.660   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.246158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.932   (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 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2020 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1829 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2814 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4695 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4399 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5629 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6734 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.139 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    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: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1741   r_free= 0.1743   ksol= 0.00   Bsol= 0.00   scale= 1.021    |
|                                                                             |
| 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:   0.10 A                  |
| x-ray target function (ml) for work reflections: 5.409358                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1513   r_free= 0.1496   ksol= 0.33   Bsol= 50.00   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.73,-1.63,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.12 A                  |
| x-ray target function (ml) for work reflections: 5.350100                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.853593              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.784   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.133481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.835   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1513      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1496      final r-factor (free) = 0.1436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2969 = 1.85 * 0.50 * 5.5430 + 1.00 * 0.1596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8597 = 1.85 * 0.50 * 5.1715 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1436      final r-factor (free) = 0.1444          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6963 = 0.13 * 1.00 * 5.1715 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6987 = 0.13 * 1.00 * 5.0996 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    62.67   16.35    None  None   None       |
|    all(noH): 2823   0      0.00    62.67   16.35    None  None   None       |
|    Sol.    : 438    0      4.41    62.67   36.66    None  None   None       |
|    Mac.    : 2385   0      0.00    53.40   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:     0.000 -   6.268:  129   |   5:    31.337 -  37.605:   93        |
|      1:     6.268 -  12.535: 1382   |   6:    37.605 -  43.872:  108        |
|      2:    12.535 -  18.802:  652   |   7:    43.872 -  50.140:   73        |
|      3:    18.802 -  25.070:  200   |   8:    50.140 -  56.407:   54        |
|      4:    25.070 -  31.337:  113   |   9:    56.407 -  62.675:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1444             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1442             target_work(ml) = 5.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1442   ksol= 0.33   Bsol= 50.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.89,-2.73,-1.63,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.103684                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1440   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.64,-1.55,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.105767                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.215341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.092  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.124818              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.404   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1440      final r-factor (free) = 0.1462          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1658 = 1.22 * 0.50 * 5.0998 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.1565 = 1.22 * 0.50 * 5.1054 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1462      final r-factor (free) = 0.1464          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7363 = 0.12 * 1.00 * 5.1054 + 1.00 * 1.0991                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6437 = 0.12 * 1.00 * 5.1069 + 1.00 * 0.0062                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    63.25   16.36    None  None   None       |
|    all(noH): 2823   0      2.03    63.25   16.36    None  None   None       |
|    Sol.    : 438    0      5.69    63.25   36.34    None  None   None       |
|    Mac.    : 2385   0      2.03    55.74   12.69    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:     2.035 -   8.157:  485   |   5:    32.644 -  38.766:  109        |
|      1:     8.157 -  14.278: 1293   |   6:    38.766 -  44.887:   90        |
|      2:    14.278 -  20.400:  451   |   7:    44.887 -  51.009:   80        |
|      3:    20.400 -  26.522:  148   |   8:    51.009 -  57.131:   53        |
|      4:    26.522 -  32.644:  107   |   9:    57.131 -  63.253:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1464             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1465             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1465   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.02,-2.64,-1.55,-0.00,-0.00,-0.00); trace/3= -2.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1465   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.47,-1.38,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.109009                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.827916              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.106  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 9.995842              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.581  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1465      final r-factor (free) = 0.1489          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7220 = 1.83 * 0.50 * 5.1073 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7178 = 1.83 * 0.50 * 5.0950 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1489      final r-factor (free) = 0.1510          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.9349 = 10.00 * 1.00 * 5.0950 + 1.00 * 0.0062                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.8732 = 10.00 * 1.00 * 5.0885 + 1.00 * 0.0091                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    79.13   16.98    None  None   None       |
|    all(noH): 2823   0      0.55    79.13   16.98    None  None   None       |
|    Sol.    : 438    0      6.38    72.48   39.23    None  None   None       |
|    Mac.    : 2385   0      0.55    79.13   12.89    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:     0.550 -   8.409:  635   |   5:    39.842 -  47.700:  108        |
|      1:     8.409 -  16.267: 1331   |   6:    47.700 -  55.559:   81        |
|      2:    16.267 -  24.125:  343   |   7:    55.559 -  63.417:   56        |
|      3:    24.125 -  31.984:  131   |   8:    63.417 -  71.275:   26        |
|      4:    31.984 -  39.842:  105   |   9:    71.275 -  79.134:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1510             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1510             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1510   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.47,-1.38,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.098449                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1510   ksol= 0.32   Bsol= 47.36   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.18,-1.12,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.098282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.926681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.177  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.098256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.904  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1510      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9642 = 1.93 * 0.50 * 5.0900 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9686 = 1.93 * 0.50 * 5.0974 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1512          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5104 = 0.10 * 1.00 * 5.0974 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5088 = 0.10 * 1.00 * 5.1155 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.03    73.96   16.02    None  None   None       |
|    all(noH): 2823   0      2.03    73.96   16.02    None  None   None       |
|    Sol.    : 438    0      6.11    67.00   35.13    None  None   None       |
|    Mac.    : 2385   0      2.03    73.96   12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.033 -   9.225:  822   |   5:    37.997 -  45.190:  107        |
|      1:     9.225 -  16.418: 1195   |   6:    45.190 -  52.383:   73        |
|      2:    16.418 -  23.611:  314   |   7:    52.383 -  59.576:   32        |
|      3:    23.611 -  30.804:  126   |   8:    59.576 -  66.769:    8        |
|      4:    30.804 -  37.997:  142   |   9:    66.769 -  73.962:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1090 r_free = 0.1512             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1089 r_free = 0.1514             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1514   ksol= 0.32   Bsol= 47.36   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.18,-1.12,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1089   r_free= 0.1514   ksol= 0.33   Bsol= 47.36   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.11,-1.03,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.419612              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.852  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.988  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1514      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6893 = 1.42 * 0.50 * 5.1159 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6845 = 1.42 * 0.50 * 5.1154 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9764 = 0.39 * 1.00 * 5.1154 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9756 = 0.39 * 1.00 * 5.1093 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    76.22   16.26    None  None   None       |
|    all(noH): 2823   0      0.96    76.22   16.26    None  None   None       |
|    Sol.    : 438    0      6.15    66.67   37.02    None  None   None       |
|    Mac.    : 2385   0      0.96    76.22   12.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.965 -   8.490:  687   |   5:    38.591 -  46.116:  112        |
|      1:     8.490 -  16.015: 1289   |   6:    46.116 -  53.641:   94        |
|      2:    16.015 -  23.541:  336   |   7:    53.641 -  61.166:   42        |
|      3:    23.541 -  31.066:  132   |   8:    61.166 -  68.692:   10        |
|      4:    31.066 -  38.591:  117   |   9:    68.692 -  76.217:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1082 r_free = 0.1524             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1081 r_free = 0.1523             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1523   ksol= 0.33   Bsol= 47.36   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.11,-1.03,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112215                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.1014 0.1265      5.3964      5.5155|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.0863 0.1133      5.4459      5.6332|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.1042 0.1454      5.4646      5.8449|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.1165 0.1466      5.4214       5.556|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.1259 0.1660      5.2964      5.5212|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.1166 0.1778      5.1803      5.4242|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.1188 0.1579      5.1193        5.33|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.1123 0.1674      5.0456      5.3229|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.1104 0.1676      4.9887      5.2273|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.1074 0.1663      4.9352      5.1951|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.1087 0.1636      4.8965      5.1877|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.1068 0.1596      4.8425      5.1889|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.1045 0.1689      4.7597      5.0469|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.0992 0.1756        4.64      4.9396|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7493  1375   153  0.94   9.27   0.98     0.95       7202.94|
|  2:  4.7493 -  3.7899  1306   146  0.95   7.81   1.01     1.00       8999.84|
|  3:  3.7899 -  3.3168  1294   143  0.94  10.90   1.02     1.01      10051.01|
|  4:  3.3168 -  3.0163  1285   139  0.93  12.75   1.00     0.99       9579.21|
|  5:  3.0163 -  2.8016  1266   144  0.91  14.98   0.99     0.96       7746.59|
|  6:  2.8016 -  2.6374  1277   141  0.91  15.19   0.98     0.95       6571.29|
|  7:  2.6374 -  2.5059  1267   140  0.91  14.72   0.98     0.96       5663.54|
|  8:  2.5059 -  2.3973  1248   140  0.92  13.89   0.99     0.96       4930.40|
|  9:  2.3973 -  2.3054  1253   142  0.91  14.64   1.00     0.97       4615.74|
| 10:  2.3054 -  2.2261  1247   136  0.91  15.05   0.99     0.95       4132.71|
| 11:  2.2261 -  2.1567  1254   137  0.91  14.97   0.99     0.96       3981.01|
| 12:  2.1567 -  2.0952  1241   142  0.92  14.38   1.00     0.99       3636.82|
| 13:  2.0952 -  2.0402  1248   136  0.92  14.49   0.99     0.98       3139.62|
| 14:  2.0402 -  1.9905  1069   120  0.92  14.30   0.97     0.93       2450.06|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2450.06 max =        10051.01 mean =      5983.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.32|
|phase err.(test): min =        0.00 max =           89.34 mean =        12.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1523   ksol= 0.32   Bsol= 47.33   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.92,-0.85,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112079                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1523   ksol= 0.32   Bsol= 47.33   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-1.92,-0.85,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.112079                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.1012 0.1265      5.3947      5.5134|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.0865 0.1134      5.4463      5.6336|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.1043 0.1454      5.4648      5.8449|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.1165 0.1466      5.4213      5.5559|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.1259 0.1660      5.2962      5.5208|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.1166 0.1778      5.1801      5.4241|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.1188 0.1578      5.1192      5.3298|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.1123 0.1674      5.0455      5.3227|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.1104 0.1676      4.9887      5.2273|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.1074 0.1663      4.9352       5.195|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.1087 0.1636      4.8964      5.1875|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.1068 0.1596      4.8424      5.1888|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.1045 0.1689      4.7596      5.0468|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.0992 0.1756        4.64      4.9397|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9396 -  4.7493  1375   153  0.94   9.25   0.98     0.95       7163.92|
|  2:  4.7493 -  3.7899  1306   146  0.95   7.81   1.01     1.00       8986.52|
|  3:  3.7899 -  3.3168  1294   143  0.94  10.90   1.02     1.01      10054.99|
|  4:  3.3168 -  3.0163  1285   139  0.93  12.75   1.01     0.99       9574.95|
|  5:  3.0163 -  2.8016  1266   144  0.91  14.98   1.00     0.97       7743.21|
|  6:  2.8016 -  2.6374  1277   141  0.91  15.19   0.99     0.96       6568.28|
|  7:  2.6374 -  2.5059  1267   140  0.91  14.72   0.99     0.96       5661.96|
|  8:  2.5059 -  2.3973  1248   140  0.92  13.89   0.99     0.97       4929.45|
|  9:  2.3973 -  2.3054  1253   142  0.91  14.64   1.01     0.98       4615.41|
| 10:  2.3054 -  2.2261  1247   136  0.91  15.05   1.00     0.96       4131.97|
| 11:  2.2261 -  2.1567  1254   137  0.91  14.96   1.00     0.97       3979.90|
| 12:  2.1567 -  2.0952  1241   142  0.92  14.38   1.01     1.00       3635.93|
| 13:  2.0952 -  2.0402  1248   136  0.92  14.49   1.00     0.99       3139.22|
| 14:  2.0402 -  1.9905  1069   120  0.92  14.30   0.98     0.94       2450.31|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2450.31 max =        10054.99 mean =      5978.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.32|
|phase err.(test): min =        0.00 max =           89.32 mean =        12.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.93    76.18   16.23    None  None   None       |
|    all(noH): 2823   0      0.93    76.18   16.23    None  None   None       |
|    Sol.    : 438    0      6.12    66.64   36.98    None  None   None       |
|    Mac.    : 2385   0      0.93    76.18   12.42    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:     0.932 -   8.457:  687   |   5:    38.558 -  46.083:  112        |
|      1:     8.457 -  15.982: 1289   |   6:    46.083 -  53.608:   94        |
|      2:    15.982 -  23.507:  336   |   7:    53.608 -  61.133:   42        |
|      3:    23.507 -  31.032:  132   |   8:    61.133 -  68.658:   10        |
|      4:    31.032 -  38.558:  117   |   9:    68.658 -  76.184:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.571 - 4.723
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 287
   mapped sites are within: 0.707 - 4.723

peak=    5.635 closest distance to " CB  ARG A 275 " =    0.943
peak=    5.314 closest distance to " NH2 ARG A  56 " =    2.230
peak=    5.309 closest distance to " CB  GLN A 223 " =    1.391
peak=    5.183 closest distance to " O   HOH Z 126 " =    1.851
peak=    5.163 closest distance to " O   HOH Z 232 " =    2.366
peak=    4.923 closest distance to " CB  SER A  63 " =    1.167
peak=    4.905 closest distance to " O   HOH Z 142 " =    1.688
peak=    4.771 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.578 closest distance to " CB  GLU A 152 " =    1.189
peak=    4.568 closest distance to " NE2 GLN A  11 " =    1.051
peak=    4.555 closest distance to " C   PRO A 198 " =    1.449
peak=    4.515 closest distance to " O   HOH Z  78 " =    1.691
peak=    4.495 closest distance to " CG  PRO A 198 " =    1.294
peak=    4.464 closest distance to " O   HOH Z 236 " =    1.948
peak=    4.449 closest distance to " O   HOH Z 298 " =    1.880
peak=    4.441 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.414 closest distance to " O   HOH Z  15 " =    2.260
peak=    4.367 closest distance to " O   HOH Z 209 " =    2.301
peak=    4.349 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.344 closest distance to " O   HOH Z 250 " =    1.492
peak=    4.338 closest distance to " ND2 ASN A 187 " =    1.475
peak=    4.316 closest distance to " CG2 VAL A 257 " =    0.924
peak=    4.307 closest distance to " CB  ARG A  79 " =    1.297
peak=    4.288 closest distance to " O   HOH Z 234 " =    3.693
peak=    4.287 closest distance to " O   HOH Z  40 " =    1.716
peak=    4.282 closest distance to " CG  PRO A 243 " =    1.033
peak=    4.281 closest distance to " O   HOH Z 427 " =    2.910
peak=    4.274 closest distance to " O   HOH Z 303 " =    2.053
peak=    4.274 closest distance to " CB  ARG A 190 " =    1.687
peak=    4.272 closest distance to " CB  TYR A 169 " =    0.707
peak=    4.253 closest distance to " O   HOH Z  61 " =    1.636
peak=    4.206 closest distance to " CZ  PHE A 218 " =    1.074
peak=    4.198 closest distance to " O   HOH Z 189 " =    2.291
peak=    4.172 closest distance to " CB  LEU A 228 " =    1.068
peak=    4.152 closest distance to " O   HOH Z 158 " =    3.056
peak=    4.120 closest distance to " O   HOH Z 402 " =    1.409
peak=    4.113 closest distance to " CB  VAL A 265 " =    1.255
peak=    4.112 closest distance to " O   HOH Z  43 " =    1.923
peak=    4.099 closest distance to " O   HOH Z 369 " =    2.193
peak=    4.087 closest distance to " OD1 ASN A  69 " =    2.558
peak=    4.066 closest distance to " CB  GLU A 128 " =    1.011
peak=    4.044 closest distance to " O   HOH Z 193 " =    1.844
peak=    4.044 closest distance to " CA  ASN A 215 " =    1.104
peak=    4.034 closest distance to " O   HOH Z  66 " =    2.125
peak=    4.027 closest distance to " CB  TRP A 266 " =    0.983
peak=    4.017 closest distance to " O   HOH Z 203 " =    1.707
peak=    4.007 closest distance to " O   HOH Z 346 " =    1.694
peak=    4.001 closest distance to " O   HOH Z 389 " =    1.858
peak=    3.993 closest distance to " O   HOH Z 392 " =    3.159
peak=    3.948 closest distance to " O   SER A  87 " =    2.211
peak=    3.945 closest distance to " CA  ARG A  36 " =    1.015
peak=    3.935 closest distance to " OG ASER A 258 " =    3.116
peak=    3.925 closest distance to " O   HOH Z 368 " =    2.015
peak=    3.893 closest distance to " CB  SER A   3 " =    1.292
peak=    3.879 closest distance to " O   HOH Z 261 " =    2.193
peak=    3.875 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.872 closest distance to " O   HOH Z 403 " =    1.639
peak=    3.862 closest distance to " CD2 TRP A 179 " =    1.378
peak=    3.842 closest distance to " O   HOH Z  10 " =    1.776
peak=    3.834 closest distance to " CB  ASP A 140 " =    0.899
peak=    3.822 closest distance to " CB  ASN A  39 " =    0.877
peak=    3.822 closest distance to " CD  ARG A 159 " =    0.717
peak=    3.802 closest distance to " CB  ALA A 291 " =    1.293
peak=    3.801 closest distance to " O   HOH Z 423 " =    1.883
peak=    3.801 closest distance to " O   HOH Z  19 " =    2.414
peak=    3.790 closest distance to " O   HOH Z  44 " =    1.813
peak=    3.772 closest distance to " O   HOH Z   9 " =    2.138
peak=    3.752 closest distance to " NZ  LYS A 117 " =    3.249
peak=    3.751 closest distance to " NH1AARG A 145 " =    1.208
peak=    3.749 closest distance to " O   HOH Z 126 " =    2.075
peak=    3.739 closest distance to " O   HOH Z  97 " =    2.542
peak=    3.731 closest distance to " CB  GLU A 277 " =    3.543
peak=    3.721 closest distance to " O   HOH Z 344 " =    3.138
peak=    3.718 closest distance to " O   HOH Z 245 " =    1.303
peak=    3.714 closest distance to " O   HOH Z  97 " =    1.951
peak=    3.707 closest distance to " CB  VAL A 202 " =    1.517
peak=    3.700 closest distance to " CG2 ILE A 120 " =    1.183
peak=    3.690 closest distance to " CB  TRP A 179 " =    1.297
peak=    3.689 closest distance to " CB  ILE A 120 " =    1.242
peak=    3.668 closest distance to " O   HOH Z 248 " =    1.604
peak=    3.668 closest distance to " CG1BVAL A  72 " =    1.614
peak=    3.665 closest distance to " O   HOH Z 148 " =    3.342
peak=    3.660 closest distance to " O   HOH Z 147 " =    1.774
peak=    3.660 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.660 closest distance to " O   HOH Z 172 " =    3.433
peak=    3.659 closest distance to " N   ARG A 156 " =    1.341
peak=    3.656 closest distance to " O   HOH Z  54 " =    1.696
peak=    3.653 closest distance to " O   HOH Z 291 " =    1.522
peak=    3.649 closest distance to " CG  ARG A  66 " =    2.665
peak=    3.641 closest distance to " O   HOH Z   1 " =    2.060
peak=    3.634 closest distance to " O   HOH Z 305 " =    3.656
peak=    3.619 closest distance to " O   HOH Z 371 " =    3.163
peak=    3.616 closest distance to " OE1 GLU A   2 " =    2.203
peak=    3.594 closest distance to " CA  ARG A 195 " =    1.153
peak=    3.588 closest distance to " OD2 ASP A 286 " =    2.824
peak=    3.584 closest distance to " N   ASN A  39 " =    1.208
peak=    3.581 closest distance to " O   HOH Z 280 " =    2.951
peak=    3.580 closest distance to " O   HOH Z 173 " =    1.911
peak=    3.573 closest distance to " CG1 VAL A 153 " =    0.986
peak=    3.570 closest distance to " CB  ASN A 110 " =    1.072
peak=    3.567 closest distance to " O   HOH Z 407 " =    2.436
peak=    3.565 closest distance to " CA  ALA A  51 " =    0.877
peak=    3.563 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.561 closest distance to " CA  ALA A  21 " =    1.152
peak=    3.554 closest distance to " CB  PRO A  54 " =    0.751
peak=    3.553 closest distance to " CA  SER A  87 " =    1.034
peak=    3.549 closest distance to " CD BLYS A 290 " =    1.031
peak=    3.546 closest distance to " O   HOH Z 128 " =    2.059
peak=    3.537 closest distance to " O   HOH Z 419 " =    1.974
peak=    3.536 closest distance to " CG  GLN A  77 " =    2.049
peak=    3.526 closest distance to " CB  SER A  26 " =    1.642
peak=    3.521 closest distance to " O   HOH Z 433 " =    1.828
peak=    3.518 closest distance to " NH2BARG A 145 " =    2.030
peak=    3.510 closest distance to " NE2 GLN A  77 " =    3.168
peak=    3.502 closest distance to " O   TRP A 274 " =    1.853
peak=    3.497 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.495 closest distance to " CD1 ILE A 106 " =    0.818
peak=    3.494 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.491 closest distance to " O   HOH Z 265 " =    2.459
peak=    3.489 closest distance to " O   HOH Z 214 " =    2.083
peak=    3.485 closest distance to " CB  ALA A 248 " =    1.371
peak=    3.485 closest distance to " O   HOH Z 313 " =    1.994
peak=    3.482 closest distance to " CD1 LEU A 300 " =    1.275
peak=    3.473 closest distance to " O   HOH Z 421 " =    1.746
peak=    3.471 closest distance to " O   HOH Z 132 " =    2.557
peak=    3.470 closest distance to " O   HOH Z 185 " =    1.760
peak=    3.459 closest distance to " O   HOH Z  21 " =    1.794
peak=    3.459 closest distance to " CB  ARG A 139 " =    0.944
peak=    3.456 closest distance to " O   MET A 105 " =    1.868
peak=    3.455 closest distance to " O   HOH Z 187 " =    2.241
peak=    3.449 closest distance to " CA  THR A 221 " =    0.993
peak=    3.445 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.444 closest distance to " CB  THR A  31 " =    1.630
peak=    3.444 closest distance to " CA  THR A 264 " =    0.895
peak=    3.443 closest distance to " O   HOH Z 417 " =    3.115
peak=    3.434 closest distance to " CB  MET A  47 " =    0.978
peak=    3.431 closest distance to " O   HOH Z  59 " =    1.930
peak=    3.430 closest distance to " O   HOH Z 403 " =    1.327
peak=    3.428 closest distance to " O   HOH Z 272 " =    1.794
peak=    3.426 closest distance to " CA  ASP A 162 " =    1.085
peak=    3.426 closest distance to " CZ2 TRP A 179 " =    1.788
peak=    3.425 closest distance to " CD  LYS A 166 " =    1.192
peak=    3.423 closest distance to " CD  ARG A 269 " =    0.955
peak=    3.423 closest distance to " O   HOH Z 368 " =    3.552
peak=    3.419 closest distance to " CA  ALA A  84 " =    1.187
peak=    3.419 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.409 closest distance to " CB  ASN A 142 " =    1.062
peak=    3.409 closest distance to " NE2 GLN A  73 " =    3.837
peak=    3.402 closest distance to " CD2 LEU A 297 " =    0.861
peak=    3.394 closest distance to " O   HOH Z 234 " =    1.910
peak=    3.390 closest distance to " O   HOH Z  88 " =    2.672
peak=    3.387 closest distance to " O   HOH Z 383 " =    1.771
peak=    3.386 closest distance to " CB  SER A 212 " =    1.147
peak=    3.384 closest distance to " CA  GLY A  80 " =    0.819
peak=    3.382 closest distance to " O   THR A 220 " =    1.265
peak=    3.379 closest distance to " O   HOH Z 261 " =    1.603
peak=    3.378 closest distance to " O   HOH Z 329 " =    3.841
peak=    3.375 closest distance to " O   HOH Z 213 " =    1.728
peak=    3.375 closest distance to " OG1 THR A 294 " =    2.407
peak=    3.374 closest distance to " CB  TYR A 116 " =    0.759
peak=    3.372 closest distance to " O   HOH Z 193 " =    2.040
peak=    3.371 closest distance to " O   HOH Z 175 " =    2.178
peak=    3.366 closest distance to " O   HOH Z 426 " =    1.599
peak=    3.362 closest distance to " CB  ALA A 242 " =    0.892
peak=    3.353 closest distance to " OG BSER A 164 " =    2.281
peak=    3.351 closest distance to " NH2 ARG A 156 " =    1.110
peak=    3.351 closest distance to " CG  LEU A 167 " =    1.242
peak=    3.350 closest distance to " CG2 ILE A  20 " =    1.412
peak=    3.345 closest distance to " NH1BARG A 145 " =    1.204
peak=    3.343 closest distance to " CD  LYS A 119 " =    1.383
peak=    3.342 closest distance to " O   HOH Z 133 " =    2.653
peak=    3.342 closest distance to " CB  ALA A  34 " =    0.962
peak=    3.341 closest distance to " O   HOH Z 337 " =    3.632
peak=    3.337 closest distance to " O   HOH Z 193 " =    1.619
peak=    3.333 closest distance to " CA  ALA A  43 " =    1.227
peak=    3.330 closest distance to " ND2 ASN A 110 " =    1.677
peak=    3.329 closest distance to " O   HOH Z 273 " =    2.746
peak=    3.328 closest distance to " CA  MET A  40 " =    1.091
peak=    3.328 closest distance to " CB  MET A  40 " =    0.812
peak=    3.323 closest distance to " O   ALA A   1 " =    1.675
peak=    3.319 closest distance to " O   THR A 251 " =    1.165
peak=    3.318 closest distance to " CB  LYS A 290 " =    0.981
peak=    3.317 closest distance to " CB  SER A 216 " =    0.787
peak=    3.316 closest distance to " CB  ALA A 114 " =    1.086
peak=    3.313 closest distance to " CA  ILE A 234 " =    0.909
peak=    3.313 closest distance to " O   HOH Z 411 " =    3.895
peak=    3.310 closest distance to " O   HOH Z 435 " =    1.944
peak=    3.306 closest distance to " CB  SER A  62 " =    1.283
peak=    3.302 closest distance to " O   HOH Z 219 " =    2.011
peak=    3.294 closest distance to " N   TYR A 116 " =    1.517
peak=    3.292 closest distance to " O   HOH Z 258 " =    1.667
peak=    3.291 closest distance to " CA  ALA A 291 " =    0.811
peak=    3.290 closest distance to " CG1 ILE A 120 " =    1.056
peak=    3.290 closest distance to " O   HOH Z 128 " =    2.198
peak=    3.288 closest distance to " CB  ASN A 224 " =    1.060
peak=    3.287 closest distance to " O   ALA A 165 " =    1.517
peak=    3.285 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.283 closest distance to " CB  PRO A 198 " =    1.081
peak=    3.282 closest distance to " CG2 THR A 221 " =    1.149
peak=    3.281 closest distance to " O   HOH Z  44 " =    3.190
peak=    3.280 closest distance to " O   HOH Z  88 " =    1.928
peak=    3.279 closest distance to " CB  THR A 157 " =    1.082
peak=    3.278 closest distance to " O  BHOH Z 338 " =    2.321
peak=    3.273 closest distance to " O   HOH Z 180 " =    2.194
peak=    3.271 closest distance to " O   HOH Z 285 " =    2.836
peak=    3.266 closest distance to " CD1AILE A 234 " =    0.945
peak=    3.266 closest distance to " CG  LYS A  76 " =    0.964
peak=    3.264 closest distance to " O   HOH Z  61 " =    1.441
peak=    3.261 closest distance to " CA  ILE A  33 " =    1.420
peak=    3.259 closest distance to " CB  GLN A  89 " =    1.308
peak=    3.253 closest distance to " CD  ARG A  36 " =    0.977
peak=    3.253 closest distance to " CA  ASP A 140 " =    1.135
peak=    3.253 closest distance to " O   HOH Z  66 " =    2.078
peak=    3.251 closest distance to " CA  ALA A 248 " =    1.251
peak=    3.248 closest distance to " CA  ALA A 233 " =    1.312
peak=    3.246 closest distance to " O   HOH Z 298 " =    2.513
peak=    3.245 closest distance to " CB  SER A 141 " =    1.020
peak=    3.241 closest distance to " CD2 LEU A 255 " =    1.417
peak=    3.240 closest distance to " CA  ALA A 158 " =    1.301
peak=    3.240 closest distance to " N   SER A 135 " =    1.231
peak=    3.239 closest distance to " O   HOH Z 327 " =    1.624
peak=    3.236 closest distance to " O   HOH Z 359 " =    1.464
peak=    3.236 closest distance to " CG  GLN A  11 " =    1.579
peak=    3.219 closest distance to " O   HOH Z 261 " =    2.247
peak=    3.211 closest distance to " CA  ASN A 217 " =    1.233
peak=    3.210 closest distance to " CB  SER A  62 " =    0.928
peak=    3.210 closest distance to " CB  ASN A 215 " =    1.131
peak=    3.207 closest distance to " O   HOH Z 406 " =    1.523
peak=    3.206 closest distance to " NZ  LYS A  76 " =    1.543
peak=    3.204 closest distance to " CD2 HIS A  81 " =    1.137
peak=    3.203 closest distance to " CB  GLN A  88 " =    1.137
peak=    3.201 closest distance to " C   TYR A 214 " =    1.432
peak=    3.201 closest distance to " CA  TYR A 116 " =    1.343
peak=    3.200 closest distance to " CB  ALA A   9 " =    1.497
peak=    3.200 closest distance to " N   PHE A 130 " =    1.276
peak=    3.198 closest distance to " CB  GLN A 278 " =    0.819
peak=    3.198 closest distance to " N   ASN A 127 " =    1.218
peak=    3.194 closest distance to " O   HOH Z 126 " =    1.692
peak=    3.192 closest distance to " O   HOH Z 365 " =    2.989
peak=    3.182 closest distance to " O   HOH Z 163 " =    1.806
peak=    3.181 closest distance to " O   HOH Z 357 " =    1.850
peak=    3.175 closest distance to " O   HOH Z  62 " =    2.104
peak=    3.175 closest distance to " CA  MET A 105 " =    0.995
peak=    3.169 closest distance to " O   HOH Z 345 " =    3.332
peak=    3.169 closest distance to " O   HOH Z 371 " =    1.731
peak=    3.167 closest distance to " O   HOH Z 257 " =    2.195
peak=    3.164 closest distance to " CB  VAL A 126 " =    1.011
peak=    3.158 closest distance to " O   HOH Z 286 " =    2.292
peak=    3.151 closest distance to " O   HOH Z 380 " =    1.802
peak=    3.150 closest distance to " CG  MET A 185 " =    1.082
peak=    3.143 closest distance to " CB  LEU A 300 " =    0.918
peak=    3.136 closest distance to " OG1 THR A 294 " =    1.662
peak=    3.132 closest distance to " O   HOH Z 353 " =    2.596
peak=    3.130 closest distance to " OG  SER A 206 " =    1.299
peak=    3.130 closest distance to " O   HOH Z 271 " =    2.345
peak=    3.116 closest distance to " O   HOH Z  85 " =    2.305
peak=    3.116 closest distance to " CA  ASN A 176 " =    1.123
peak=    3.113 closest distance to " NH1 ARG A 138 " =    1.145
peak=    3.110 closest distance to " CG  MET A 113 " =    1.089
peak=    3.107 closest distance to " O   HOH Z 336 " =    1.749
peak=    3.105 closest distance to " O   HOH Z 171 " =    2.229
peak=    3.103 closest distance to " O   HOH Z 391 " =    2.930
peak=    3.102 closest distance to " CB  PRO A 243 " =    1.785
peak=    3.100 closest distance to " O   HOH Z 423 " =    3.016
peak=    3.095 closest distance to " ND1 HIS A  86 " =    1.772
peak=    3.094 closest distance to " O   HOH Z 417 " =    2.463
peak=    3.089 closest distance to " O   HOH Z 201 " =    3.221
peak=    3.087 closest distance to " CG2 VAL A 197 " =    1.058
peak=    3.085 closest distance to " CD  ARG A 156 " =    1.534
peak=    3.083 closest distance to " CB  ALA A   1 " =    4.723
peak=    3.083 closest distance to " CB  LEU A 255 " =    0.789
peak=    3.083 closest distance to " O   HOH Z 263 " =    1.691
peak=    3.071 closest distance to " CE AMET A  47 " =    1.347
peak=    3.044 closest distance to " CB  ALA A 291 " =    0.802
peak=    3.041 closest distance to " N   GLY A  98 " =    1.029
peak=    3.031 closest distance to " O   HOH Z 302 " =    1.936
peak=    3.030 closest distance to " ND1 HIS A  81 " =    1.664
peak=    3.015 closest distance to " CA  LYS A 290 " =    1.426
peak=    3.010 closest distance to " O   SER A 164 " =    1.241
peak=    3.003 closest distance to " NH1AARG A 145 " =    0.872

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 186         
Filter by distance & map next to the model:
   mapped sites are within: 0.578 - 5.970
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 186
   mapped sites are within: 0.804 - 5.970

peak=   -4.697 closest distance to " O   HOH Z 266 " =    5.018
peak=   -4.580 closest distance to " CD  GLN A  58 " =    0.995
peak=   -4.465 closest distance to " CD  ARG A 156 " =    2.013
peak=   -4.459 closest distance to " O   VAL A  67 " =    2.677
peak=   -4.386 closest distance to " C   HIS A 108 " =    1.090
peak=   -4.372 closest distance to " SG  CYS A 254 " =    3.509
peak=   -4.290 closest distance to " CG  GLN A 223 " =    1.822
peak=   -4.289 closest distance to " O   HOH Z 290 " =    1.063
peak=   -4.243 closest distance to " CB  PRO A 243 " =    2.666
peak=   -4.132 closest distance to " CZ3 TRP A 179 " =    1.178
peak=   -4.128 closest distance to " OG BSER A 134 " =    1.188
peak=   -4.121 closest distance to " CA  VAL A  67 " =    2.871
peak=   -4.095 closest distance to " CG1 VAL A 112 " =    2.811
peak=   -4.088 closest distance to " ND2 ASN A  45 " =    1.641
peak=   -4.056 closest distance to " CD2 PHE A 192 " =    2.037
peak=   -4.042 closest distance to " O   HOH Z 372 " =    2.254
peak=   -4.033 closest distance to " CA  ASN A 110 " =    2.595
peak=   -3.985 closest distance to " CB  ASN A  39 " =    2.306
peak=   -3.984 closest distance to " O   HOH Z 231 " =    2.266
peak=   -3.962 closest distance to " O   HOH Z 198 " =    1.970
peak=   -3.933 closest distance to " OG  SER A  97 " =    2.191
peak=   -3.912 closest distance to " N   ALA A  43 " =    2.523
peak=   -3.905 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -3.903 closest distance to " O   HOH Z 377 " =    2.061
peak=   -3.896 closest distance to " CG2 ILE A 263 " =    2.296
peak=   -3.888 closest distance to " CE  MET A 105 " =    2.351
peak=   -3.872 closest distance to " O   PRO A 198 " =    1.233
peak=   -3.868 closest distance to " CD  ARG A 139 " =    1.495
peak=   -3.865 closest distance to " O   HOH Z 389 " =    1.901
peak=   -3.830 closest distance to " CG  ASP A 231 " =    0.804
peak=   -3.826 closest distance to " O   HOH Z 114 " =    3.060
peak=   -3.752 closest distance to " O   HOH Z 351 " =    1.473
peak=   -3.751 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.735 closest distance to " O   HOH Z 435 " =    2.844
peak=   -3.721 closest distance to " O   HOH Z 211 " =    1.716
peak=   -3.717 closest distance to " O   HOH Z 407 " =    2.997
peak=   -3.712 closest distance to " ND2 ASN A  45 " =    1.090
peak=   -3.708 closest distance to " O   HOH Z 185 " =    2.347
peak=   -3.687 closest distance to " OXT GLY A 302 " =    2.794
peak=   -3.685 closest distance to " O   HOH Z 126 " =    1.926
peak=   -3.668 closest distance to " O   HOH Z 196 " =    1.990
peak=   -3.654 closest distance to " O   HOH Z  10 " =    1.491
peak=   -3.644 closest distance to " CA  GLY A 203 " =    2.341
peak=   -3.631 closest distance to " OD1 ASP A 171 " =    1.596
peak=   -3.631 closest distance to " CG  PHE A 283 " =    2.607
peak=   -3.626 closest distance to " CD1 LEU A 101 " =    2.323
peak=   -3.625 closest distance to " CG  ASP A 132 " =    2.295
peak=   -3.607 closest distance to " O   HOH Z 353 " =    2.110
peak=   -3.600 closest distance to " O   HOH Z 313 " =    1.853
peak=   -3.598 closest distance to " O   PRO A 163 " =    2.034
peak=   -3.590 closest distance to " OD1 ASN A 187 " =    1.636
peak=   -3.559 closest distance to " CZ  TYR A 169 " =    1.745
peak=   -3.558 closest distance to " CB  ALA A 248 " =    2.178
peak=   -3.545 closest distance to " CB  ALA A 248 " =    2.343
peak=   -3.533 closest distance to " CD1 LEU A 228 " =    2.176
peak=   -3.530 closest distance to " O   HOH Z 311 " =    3.630
peak=   -3.522 closest distance to " CD1 PHE A  59 " =    1.877
peak=   -3.517 closest distance to " CB  ALA A 291 " =    2.371
peak=   -3.515 closest distance to " O   ALA A 161 " =    1.652
peak=   -3.506 closest distance to " N   SER A 212 " =    1.937
peak=   -3.503 closest distance to " CA  GLY A 241 " =    3.034
peak=   -3.501 closest distance to " CG  GLU A 277 " =    1.164
peak=   -3.494 closest distance to " O   HOH Z  43 " =    1.605
peak=   -3.488 closest distance to " OD1 ASN A 148 " =    1.515
peak=   -3.486 closest distance to " NH2 ARG A  79 " =    1.571
peak=   -3.481 closest distance to " CA  GLY A 133 " =    1.987
peak=   -3.474 closest distance to " NE2 GLN A 278 " =    1.806
peak=   -3.471 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.469 closest distance to " OD2 ASP A 191 " =    1.419
peak=   -3.456 closest distance to " N   ALA A 248 " =    1.711
peak=   -3.448 closest distance to " N   ASP A 286 " =    2.378
peak=   -3.444 closest distance to " NH2AARG A 275 " =    5.200
peak=   -3.442 closest distance to " O   HOH Z 394 " =    1.471
peak=   -3.439 closest distance to " CZ  PHE A  59 " =    1.509
peak=   -3.434 closest distance to " N   THR A 157 " =    1.555
peak=   -3.432 closest distance to " CG  ARG A  66 " =    2.478
peak=   -3.432 closest distance to " CD2 PHE A  61 " =    2.487
peak=   -3.431 closest distance to " NH1 ARG A 195 " =    2.543
peak=   -3.412 closest distance to " CD1 ILE A 239 " =    2.181
peak=   -3.402 closest distance to " OD2 ASP A 171 " =    2.372
peak=   -3.398 closest distance to " O   HOH Z  44 " =    2.256
peak=   -3.390 closest distance to " O   HOH Z  60 " =    2.273
peak=   -3.386 closest distance to " CZ  PHE A 155 " =    1.195
peak=   -3.385 closest distance to " O   HOH Z 166 " =    2.023
peak=   -3.385 closest distance to " C   MET A 188 " =    1.339
peak=   -3.378 closest distance to " O   ARG A 145 " =    1.565
peak=   -3.373 closest distance to " CG  GLN A  11 " =    1.749
peak=   -3.372 closest distance to " C   ALA A 158 " =    1.296
peak=   -3.372 closest distance to " NH1 ARG A  36 " =    2.090
peak=   -3.368 closest distance to " N   GLN A  58 " =    1.648
peak=   -3.368 closest distance to " CG1 VAL A 230 " =    2.134
peak=   -3.357 closest distance to " CB  PRO A 163 " =    2.492
peak=   -3.355 closest distance to " CG  ARG A 269 " =    2.339
peak=   -3.353 closest distance to " ND2 ASN A 187 " =    1.496
peak=   -3.353 closest distance to " CD  ARG A 195 " =    5.171
peak=   -3.352 closest distance to " O   HOH Z 198 " =    1.330
peak=   -3.343 closest distance to " C   LEU A 143 " =    1.014
peak=   -3.341 closest distance to " O   HOH Z  13 " =    1.462
peak=   -3.340 closest distance to " O   HOH Z 385 " =    2.072
peak=   -3.334 closest distance to " O   HOH Z 298 " =    1.264
peak=   -3.331 closest distance to " O   HOH Z  73 " =    2.291
peak=   -3.331 closest distance to " O   HOH Z 362 " =    5.970
peak=   -3.328 closest distance to " O   HOH Z 134 " =    2.952
peak=   -3.318 closest distance to " O   HOH Z 102 " =    1.570
peak=   -3.315 closest distance to " CB  ASP A 286 " =    1.825
peak=   -3.313 closest distance to " CD1 LEU A 297 " =    2.370
peak=   -3.312 closest distance to " O   HOH Z 322 " =    1.647
peak=   -3.307 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.303 closest distance to " N   ALA A 226 " =    1.997
peak=   -3.302 closest distance to " O   ALA A  10 " =    1.662
peak=   -3.300 closest distance to " O   HOH Z  11 " =    1.719
peak=   -3.297 closest distance to " O   PHE A 218 " =    1.593
peak=   -3.293 closest distance to " OG  SER A  62 " =    1.665
peak=   -3.290 closest distance to " CB  TYR A  15 " =    2.173
peak=   -3.285 closest distance to " CG1 VAL A  78 " =    3.182
peak=   -3.279 closest distance to " O   HOH Z 174 " =    4.306
peak=   -3.278 closest distance to " O   ALA A  51 " =    1.411
peak=   -3.278 closest distance to " O   HOH Z  52 " =    1.304
peak=   -3.273 closest distance to " ND2 ASN A 249 " =    2.329
peak=   -3.270 closest distance to " CB  ALA A  43 " =    2.419
peak=   -3.269 closest distance to " CB  PHE A 208 " =    2.228
peak=   -3.268 closest distance to " OE1 GLN A  88 " =    1.146
peak=   -3.268 closest distance to " N   MET A 105 " =    2.687
peak=   -3.267 closest distance to " O   HOH Z 193 " =    2.000
peak=   -3.265 closest distance to " NE2 GLN A 194 " =    1.726
peak=   -3.265 closest distance to " O   HOH Z 317 " =    1.576
peak=   -3.256 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.252 closest distance to " CG1 VAL A 250 " =    2.665
peak=   -3.251 closest distance to " O   ALA A  34 " =    2.510
peak=   -3.244 closest distance to " CD2 TYR A 293 " =    2.036
peak=   -3.242 closest distance to " O   SER A  95 " =    1.573
peak=   -3.242 closest distance to " O   HOH Z 165 " =    1.981
peak=   -3.241 closest distance to " CA  PRO A 243 " =    2.339
peak=   -3.239 closest distance to " CE2 PHE A 218 " =    2.449
peak=   -3.229 closest distance to " O   HOH Z 377 " =    1.718
peak=   -3.228 closest distance to " O   GLY A 211 " =    1.297
peak=   -3.224 closest distance to " OG  SER A 206 " =    1.732
peak=   -3.224 closest distance to " CA  GLY A 241 " =    2.788
peak=   -3.219 closest distance to " CA  GLY A  98 " =    1.935
peak=   -3.219 closest distance to " O   SER A 135 " =    1.461
peak=   -3.218 closest distance to " O   GLN A 240 " =    2.098
peak=   -3.217 closest distance to " NE2 GLN A  88 " =    1.808
peak=   -3.202 closest distance to " O   HOH Z 253 " =    3.882
peak=   -3.200 closest distance to " CD1 LEU A   5 " =    2.488
peak=   -3.195 closest distance to " CE3 TRP A 150 " =    2.158
peak=   -3.190 closest distance to " N   PHE A  59 " =    2.116
peak=   -3.187 closest distance to " O   HOH Z  93 " =    2.262
peak=   -3.185 closest distance to " O   HOH Z 166 " =    1.627
peak=   -3.183 closest distance to " OG BSER A 134 " =    1.810
peak=   -3.181 closest distance to " NH2 ARG A  79 " =    2.050
peak=   -3.179 closest distance to " O   HOH Z  51 " =    1.615
peak=   -3.175 closest distance to " CG1 VAL A 125 " =    1.964
peak=   -3.173 closest distance to " O   HOH Z 421 " =    3.056
peak=   -3.170 closest distance to " OD2 ASP A  50 " =    2.243
peak=   -3.169 closest distance to " OG BSER A 210 " =    2.408
peak=   -3.169 closest distance to " SG ACYS A 201 " =    1.988
peak=   -3.164 closest distance to " C   PRO A  90 " =    1.513
peak=   -3.164 closest distance to " O   HOH Z  38 " =    1.602
peak=   -3.164 closest distance to " O   LEU A 167 " =    1.430
peak=   -3.164 closest distance to " O   HOH Z  91 " =    1.606
peak=   -3.160 closest distance to " O   HOH Z  63 " =    1.648
peak=   -3.153 closest distance to " CD2 LEU A 300 " =    2.904
peak=   -3.150 closest distance to " O   TRP A  70 " =    1.472
peak=   -3.148 closest distance to " CD2 PHE A 192 " =    2.328
peak=   -3.136 closest distance to " O   HOH Z 123 " =    2.297
peak=   -3.129 closest distance to " OD1AASN A 224 " =    1.781
peak=   -3.126 closest distance to " CE1 TYR A 247 " =    2.775
peak=   -3.124 closest distance to " O   HOH Z 250 " =    1.394
peak=   -3.121 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.120 closest distance to " CG2 THR A 221 " =    2.220
peak=   -3.118 closest distance to " CB  LEU A  83 " =    2.381
peak=   -3.113 closest distance to " OXT GLY A 302 " =    3.339
peak=   -3.107 closest distance to " CD2 LEU A 237 " =    2.733
peak=   -3.107 closest distance to " O   HOH Z   6 " =    1.404
peak=   -3.104 closest distance to " O   HOH Z  37 " =    1.768
peak=   -3.101 closest distance to " O   HOH Z 351 " =    1.402
peak=   -3.101 closest distance to " CZ  PHE A 130 " =    1.002
peak=   -3.096 closest distance to " O   HOH Z 210 " =    1.097
peak=   -3.094 closest distance to " NH2BARG A 275 " =    2.033
peak=   -3.071 closest distance to " O   ALA A 292 " =    2.000
peak=   -3.066 closest distance to " CG1AVAL A  41 " =    2.917
peak=   -3.063 closest distance to " O   HOH Z  41 " =    2.438
peak=   -3.055 closest distance to " CG  GLU A   2 " =    1.864
peak=   -3.037 closest distance to " O   HOH Z 111 " =    2.276

================= 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    :  0.1741 0.1743   5.409358e+00   5.390653e+00
   1_bss:  0.1513 0.1496   5.350100e+00   5.324533e+00
   1_xyz:  0.1228 0.1436   5.158194e+00   5.288648e+00
   1_adp:  0.1132 0.1444   5.105826e+00   5.301434e+00
   1_occ:  0.1128 0.1442   5.103684e+00   5.300159e+00
   2_bss:  0.1132 0.1440   5.105767e+00   5.299547e+00
   2_xyz:  0.1131 0.1462   5.112973e+00   5.316968e+00
   2_adp:  0.1119 0.1464   5.108992e+00   5.320646e+00
   2_occ:  0.1118 0.1465   5.108940e+00   5.321134e+00
   3_bss:  0.1118 0.1465   5.109009e+00   5.321082e+00
   3_xyz:  0.1088 0.1489   5.100416e+00   5.333788e+00
   3_adp:  0.1065 0.1510   5.098344e+00   5.346651e+00
   3_occ:  0.1065 0.1510   5.098449e+00   5.346968e+00
   4_bss:  0.1063 0.1510   5.098282e+00   5.346784e+00
   4_xyz:  0.1062 0.1524   5.103197e+00   5.357085e+00
   4_adp:  0.1090 0.1512   5.111477e+00   5.352676e+00
   4_occ:  0.1089 0.1514   5.111858e+00   5.353561e+00
   5_bss:  0.1089 0.1514   5.112123e+00   5.353893e+00
   5_xyz:  0.1097 0.1520   5.117993e+00   5.358408e+00
   5_adp:  0.1082 0.1524   5.112198e+00   5.360399e+00
   5_occ:  0.1081 0.1523   5.112215e+00   5.360464e+00
   5_bss:  0.1081 0.1523   5.112079e+00   5.360243e+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:  0.333  50.000  -2.886  -2.734  -1.629  -0.000  -0.000  -0.000
   1_xyz:  0.333  50.000  -2.886  -2.734  -1.629  -0.000  -0.000  -0.000
   1_adp:  0.333  50.000  -2.886  -2.734  -1.629  -0.000  -0.000  -0.000
   1_occ:  0.333  50.000  -2.886  -2.734  -1.629  -0.000  -0.000  -0.000
   2_bss:  0.333  50.000  -3.016  -2.645  -1.550  -0.000  -0.000  -0.000
   2_xyz:  0.333  50.000  -3.016  -2.645  -1.550  -0.000  -0.000  -0.000
   2_adp:  0.333  50.000  -3.016  -2.645  -1.550  -0.000  -0.000  -0.000
   2_occ:  0.333  50.000  -3.016  -2.645  -1.550  -0.000  -0.000  -0.000
   3_bss:  0.333  50.000  -2.923  -2.468  -1.377  -0.000  -0.000  -0.000
   3_xyz:  0.333  50.000  -2.923  -2.468  -1.377  -0.000  -0.000  -0.000
   3_adp:  0.333  50.000  -2.923  -2.468  -1.377  -0.000  -0.000  -0.000
   3_occ:  0.333  50.000  -2.923  -2.468  -1.377  -0.000  -0.000  -0.000
   4_bss:  0.323  47.361  -2.626  -2.182  -1.124  -0.000  -0.000  -0.000
   4_xyz:  0.323  47.361  -2.626  -2.182  -1.124  -0.000  -0.000  -0.000
   4_adp:  0.323  47.361  -2.626  -2.182  -1.124  -0.000  -0.000  -0.000
   4_occ:  0.323  47.361  -2.626  -2.182  -1.124  -0.000  -0.000  -0.000
   5_bss:  0.329  47.361  -2.563  -2.106  -1.028  -0.000  -0.000  -0.000
   5_xyz:  0.329  47.361  -2.563  -2.106  -1.028  -0.000  -0.000  -0.000
   5_adp:  0.329  47.361  -2.563  -2.106  -1.028  -0.000  -0.000  -0.000
   5_occ:  0.329  47.361  -2.563  -2.106  -1.028  -0.000  -0.000  -0.000
   5_bss:  0.325  47.328  -2.370  -1.919  -0.851  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  14.195 0.9146  1.0508     8528.448
   1_bss:  12.541 0.9276  0.9768     5586.152
   1_xyz:  11.907 0.9318  0.9774     5281.029
   1_adp:  12.225 0.9290  0.9755     5358.249
   1_occ:  12.196 0.9292  0.9753     5325.592
   2_bss:  12.185 0.9293  0.9757     5308.463
   2_xyz:  12.473 0.9273  0.9742     5527.797
   2_adp:  12.530 0.9269  0.9706     5539.106
   2_occ:  12.541 0.9268  0.9704     5541.829
   3_bss:  12.543 0.9268  0.9755     5541.756
   3_xyz:  12.753 0.9252  0.9754     5712.000
   3_adp:  13.052 0.9228  0.9684     5803.656
   3_occ:  13.059 0.9227  0.9683     5807.730
   4_bss:  13.058 0.9227  0.9781     5799.960
   4_xyz:  13.246 0.9213  0.9771     5939.677
   4_adp:  13.109 0.9224  0.9732     5918.144
   4_occ:  13.124 0.9223  0.9731     5927.668
   5_bss:  13.131 0.9222  0.9759     5935.732
   5_xyz:  13.202 0.9217  0.9757     5982.542
   5_adp:  13.278 0.9211  0.9700     5981.310
   5_occ:  13.281 0.9211  0.9699     5982.485
   5_bss:  13.277 0.9211  0.9753     5977.563
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5964e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5964e-01
   1_xyz:   1.029  0.008  0.077 15.655  0.004  4.109   6.6732e-02
   1_adp:   1.029  0.008  0.077 15.655  0.004  4.109   6.6732e-02
   1_occ:   1.029  0.008  0.077 15.655  0.004  4.109   6.6732e-02
   2_bss:   1.029  0.008  0.077 15.655  0.004  4.109   6.6732e-02
   2_xyz:   0.910  0.006  0.072 15.375  0.004  4.110   5.4127e-02
   2_adp:   0.910  0.006  0.072 15.375  0.004  4.110   5.4127e-02
   2_occ:   0.910  0.006  0.072 15.375  0.004  4.110   5.4127e-02
   3_bss:   0.910  0.006  0.072 15.375  0.004  4.110   5.4127e-02
   3_xyz:   0.978  0.007  0.077 15.494  0.004  4.111   6.1169e-02
   3_adp:   0.978  0.007  0.077 15.494  0.004  4.111   6.1169e-02
   3_occ:   0.978  0.007  0.077 15.494  0.004  4.111   6.1169e-02
   4_bss:   0.978  0.007  0.077 15.494  0.004  4.111   6.1169e-02
   4_xyz:   0.949  0.007  0.074 15.411  0.004  4.117   5.8014e-02
   4_adp:   0.949  0.007  0.074 15.411  0.004  4.117   5.8014e-02
   4_occ:   0.949  0.007  0.074 15.411  0.004  4.117   5.8014e-02
   5_bss:   0.949  0.007  0.074 15.411  0.004  4.117   5.8014e-02
   5_xyz:   0.904  0.006  0.071 15.290  0.003  4.117   5.3593e-02
   5_adp:   0.904  0.006  0.071 15.290  0.003  4.117   5.3593e-02
   5_occ:   0.904  0.006  0.071 15.290  0.003  4.117   5.3593e-02
   5_bss:   0.904  0.006  0.071 15.290  0.003  4.117   5.3593e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4067e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4067e-01
   1_xyz:   7.247  0.044  0.239 84.722  0.039  2.285   5.8138e-02
   1_adp:   7.247  0.044  0.239 84.722  0.039  2.285   5.8138e-02
   1_occ:   7.247  0.044  0.239 84.722  0.039  2.285   5.8138e-02
   2_bss:   7.247  0.044  0.239 84.722  0.039  2.285   5.8138e-02
   2_xyz:   6.322  0.038  0.220 84.050  0.033  2.379   3.1426e-02
   2_adp:   6.322  0.038  0.220 84.050  0.033  2.379   3.1426e-02
   2_occ:   6.322  0.038  0.220 84.050  0.033  2.379   3.1426e-02
   3_bss:   6.322  0.038  0.220 84.050  0.033  2.379   3.1426e-02
   3_xyz:   6.810  0.043  0.249 84.242  0.032  2.307   3.9729e-02
   3_adp:   6.810  0.043  0.249 84.242  0.032  2.307   3.9729e-02
   3_occ:   6.810  0.043  0.249 84.242  0.032  2.307   3.9729e-02
   4_bss:   6.810  0.043  0.249 84.242  0.032  2.307   3.9729e-02
   4_xyz:   6.387  0.043  0.240 83.097  0.034  2.360   3.9320e-02
   4_adp:   6.387  0.043  0.240 83.097  0.034  2.360   3.9320e-02
   4_occ:   6.387  0.043  0.240 83.097  0.034  2.360   3.9320e-02
   5_bss:   6.387  0.043  0.240 83.097  0.034  2.360   3.9320e-02
   5_xyz:   6.308  0.040  0.224 83.730  0.031  2.349   3.0861e-02
   5_adp:   6.308  0.040  0.224 83.730  0.031  2.349   3.0861e-02
   5_occ:   6.308  0.040  0.224 83.730  0.031  2.349   3.0861e-02
   5_bss:   6.308  0.040  0.224 83.730  0.031  2.349   3.0861e-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:  62.67   0.00  16.35  53.40   0.00  12.62  62.67   4.41  36.66
   1_occ:  62.67   0.00  16.35  53.40   0.00  12.62  62.67   4.41  36.66
   2_bss:  62.67   0.00  16.35  53.40   0.00  12.62  62.67   4.41  36.66
   2_xyz:  62.67   0.00  16.35  53.40   0.00  12.62  62.67   4.41  36.66
   2_adp:  63.25   2.03  16.36  55.74   2.03  12.69  63.25   5.69  36.34
   2_occ:  63.25   2.03  16.36  55.74   2.03  12.69  63.25   5.69  36.34
   3_bss:  63.25   2.03  16.36  55.74   2.03  12.69  63.25   5.69  36.34
   3_xyz:  63.25   2.03  16.36  55.74   2.03  12.69  63.25   5.69  36.34
   3_adp:  79.13   0.55  16.98  79.13   0.55  12.89  72.48   6.38  39.23
   3_occ:  79.13   0.55  16.98  79.13   0.55  12.89  72.48   6.38  39.23
   4_bss:  79.13   0.55  16.98  79.13   0.55  12.89  72.48   6.38  39.23
   4_xyz:  79.13   0.55  16.98  79.13   0.55  12.89  72.48   6.38  39.23
   4_adp:  73.96   2.03  16.02  73.96   2.03  12.51  67.00   6.11  35.13
   4_occ:  73.96   2.03  16.02  73.96   2.03  12.51  67.00   6.11  35.13
   5_bss:  73.96   2.03  16.02  73.96   2.03  12.51  67.00   6.11  35.13
   5_xyz:  73.96   2.03  16.02  73.96   2.03  12.51  67.00   6.11  35.13
   5_adp:  76.22   0.96  16.26  76.22   0.96  12.45  66.67   6.15  37.02
   5_occ:  76.22   0.96  16.26  76.22   0.96  12.45  66.67   6.15  37.02
   5_bss:  76.18   0.93  16.23  76.18   0.93  12.42  66.64   6.12  36.98
------------------------------------------------------------------------
 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:    0.439    0.004    0.102
   1_adp:    0.439    0.004    0.102
   1_occ:    0.439    0.004    0.102
   2_bss:    0.439    0.004    0.102
   2_xyz:    0.684    0.004    0.109
   2_adp:    0.684    0.004    0.109
   2_occ:    0.684    0.004    0.109
   3_bss:    0.684    0.004    0.109
   3_xyz:    0.864    0.008    0.120
   3_adp:    0.864    0.008    0.120
   3_occ:    0.864    0.008    0.120
   4_bss:    0.864    0.008    0.120
   4_xyz:    0.948    0.009    0.125
   4_adp:    0.948    0.009    0.125
   4_occ:    0.948    0.009    0.125
   5_bss:    0.948    0.009    0.125
   5_xyz:    0.994    0.006    0.126
   5_adp:    0.994    0.006    0.126
   5_occ:    0.994    0.006    0.126
   5_bss:    0.994    0.006    0.126
------------------------------------------------------------------------

CPU time actual refinement: 328.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/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_544/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_544/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.59 
  Macro-tasks:
    bulk solvent and scale       = 39.07  
    individual site refinement   = 131.84 
    weights calculation          = 29.75  
    collect and process          = 6.72   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.48 
  Micro-tasks:
    mask                            = 0.55   
    f_calc                          = 106.36 
    alpha_beta                      = 7.97   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 110.25 
    fmodel                         = 6.92   
    r_factors                      = 0.26   
    phase_errors                   = 12.24  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 246.05 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.650 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    663 calls, 105.90 s
gradients_fft:          608 calls,  98.41 s

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

# Date 2008-01-16 Time 05:05:14 PST -0800 (1200488714.35 s)
Start R-work = 0.1741, R-free = 0.1743 (no bulk solvent and anisotropic scale)
Final R-work = 0.1325, R-free = 0.1720 (no bulk solvent and anisotropic scale)

Start R-work = 0.1513, R-free = 0.1496
Final R-work = 0.1081, R-free = 0.1523