# Date 2008-01-16 Time 05:54:52 PST -0800 (1200491692.22 s)
#phil __OFF__

Command line arguments: "../932.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19260
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 932

-------------------------------------------------------------------------------
  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: (70.9525, 47.3993, 87.6859, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0201

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: (70.9525, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02009
Completeness in resolution range: 0.981364
Completeness with d_max=infinity: 0.978227

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1645 -  4.3217 [2096/2119]  1886   210  10.0%
  bin  2:  4.3217 -  3.4435 [2023/2043]  1821   202  10.0%
  bin  3:  3.4435 -  3.0121 [1990/2009]  1792   198   9.9%
  bin  4:  3.0121 -  2.7384 [1953/1983]  1757   196  10.0%
  bin  5:  2.7384 -  2.5431 [1970/1989]  1773   197  10.0%
  bin  6:  2.5431 -  2.3938 [1951/1976]  1754   197  10.1%
  bin  7:  2.3938 -  2.2743 [1925/1953]  1733   192  10.0%
  bin  8:  2.2743 -  2.1756 [1933/1969]  1739   194  10.0%
  bin  9:  2.1756 -  2.0921 [1922/1964]  1732   190   9.9%
  bin 10:  2.0921 -  2.0201 [1826/1956]  1643   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2150
        3.04 -     3.66: 4585
        3.66 -     4.28: 8845
        4.28 -     4.90: 12230
  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
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.879 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.084 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.228 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27816 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_932/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 70.9525 47.3993 87.68585 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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3692   r_free= 0.3594   ksol= 0.00   Bsol= 0.00   scale= 0.937    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.131534                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.2962 0.2924      6.3708      6.2966|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.2860 0.2824      6.5386      6.5467|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.3240 0.2965      6.4682      6.4379|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.3463 0.3678      6.3545      6.3371|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.3790 0.3286      6.2046      6.1215|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.3915 0.3959      6.1388      6.1158|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.3936 0.3889       6.088      6.0829|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.4138 0.3988      6.0897      6.0731|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.4158 0.3822      6.0084      5.9942|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.4304 0.3828      6.0272      5.9519|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.4375 0.4247        5.96      5.9804|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.4360 0.4589       5.908      6.0055|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.4339 0.4060      5.8252      5.7834|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.4381 0.4576      5.7666      5.7233|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8198  1371   152  0.79  26.43   0.85     0.81      43820.60|
|  2:  4.8198 -  3.8462  1299   146  0.82  24.09   0.95     0.88      54207.48|
|  3:  3.8462 -  3.3661  1286   141  0.77  28.81   0.95     0.89      54576.33|
|  4:  3.3661 -  3.0611  1280   142  0.73  32.60   0.95     0.85      49354.97|
|  5:  3.0611 -  2.8432  1261   141  0.67  38.29   0.95     0.81      41039.78|
|  6:  2.8432 -  2.6765  1268   141  0.64  40.31   0.95     0.80      38479.93|
|  7:  2.6765 -  2.5431  1264   140  0.63  41.84   0.96     0.79      35680.75|
|  8:  2.5431 -  2.4329  1247   137  0.63  41.44   0.96     0.81      33331.33|
|  9:  2.4329 -  2.3396  1243   141  0.64  41.19   0.97     0.83      29395.52|
| 10:  2.3396 -  2.2591  1243   138  0.62  42.23   1.00     0.82      27821.19|
| 11:  2.2591 -  2.1887  1249   138  0.60  44.23   0.96     0.80      27938.47|
| 12:  2.1887 -  2.1263  1239   139  0.57  46.90   0.98     0.79      28153.81|
| 13:  2.1263 -  2.0705  1247   137  0.55  48.01   0.97     0.76      25333.22|
| 14:  2.0705 -  2.0201  1133   126  0.55  48.05   0.97     0.72      20748.01|
|alpha:            min =        0.72 max =            0.89 mean =         0.81|
|beta:             min =    20748.01 max =        54576.33 mean =     36702.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.66|
|phase err.(work): min =        0.00 max =           89.97 mean =        38.66|
|phase err.(test): min =        0.00 max =           89.93 mean =        38.41|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.519969              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.191   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.915333              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.227   (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:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      172 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1978 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1823 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2762 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4552 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4293 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5565 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6665 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.116    4.900  1.806 |       0.148 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3692   r_free= 0.3594   ksol= 0.00   Bsol= 0.00   scale= 0.937    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.131534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3591   r_free= 0.3510   ksol= 0.31   Bsol= 62.27   scale= 0.961   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.02,2.02,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.114889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.212325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.049   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.534782              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.110   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3591      final r-factor (work) = 0.2324          |
| start r-factor (free) = 0.3510      final r-factor (free) = 0.2520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9894 = 3.21 * 0.50 * 6.1182 + 1.00 * 0.1626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5250 = 3.21 * 0.50 * 5.8836 + 1.00 * 0.0749                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2324      final r-factor (work) = 0.2113          |
| start r-factor (free) = 0.2520      final r-factor (free) = 0.2596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1525 = 0.53 * 1.00 * 5.8836 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0460 = 0.53 * 1.00 * 5.6739 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.36   17.46    None  None   None       |
|    all(noH): 2823   0      0.00    86.36   17.46    None  None   None       |
|    Sol.    : 438    0      3.75    86.36   40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    75.55   13.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.636:  737   |   5:    43.178 -  51.814:  100        |
|      1:     8.636 -  17.271: 1197   |   6:    51.814 -  60.450:   72        |
|      2:    17.271 -  25.907:  363   |   7:    60.450 -  69.085:   43        |
|      3:    25.907 -  34.543:  169   |   8:    69.085 -  77.721:   13        |
|      4:    34.543 -  43.178:  124   |   9:    77.721 -  86.357:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2113 r_free = 0.2596             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2108 r_free = 0.2594             target_work(ml) = 5.684         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2108   r_free= 0.2594   ksol= 0.31   Bsol= 62.27   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.02,2.02,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.683779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2099   r_free= 0.2580   ksol= 0.33   Bsol= 79.61   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.13,-0.09,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.682897                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.407367              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.608   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.252042              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2099      final r-factor (work) = 0.1481          |
| start r-factor (free) = 0.2580      final r-factor (free) = 0.1906          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7507 = 3.41 * 0.50 * 5.6793 + 1.00 * 0.0749                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5090 = 3.41 * 0.50 * 5.5425 + 1.00 * 0.0663                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1481      final r-factor (work) = 0.1371          |
| start r-factor (free) = 0.1906      final r-factor (free) = 0.1765          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4086 = 0.25 * 1.00 * 5.5425 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3540 = 0.25 * 1.00 * 5.3354 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    85.81   17.00    None  None   None       |
|    all(noH): 2823   0      1.60    85.81   17.00    None  None   None       |
|    Sol.    : 438    0      5.28    85.81   40.13    None  None   None       |
|    Mac.    : 2385   0      1.60    76.17   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.599 -  10.020: 1066   |   5:    43.706 -  52.127:  118        |
|      1:    10.020 -  18.442: 1031   |   6:    52.127 -  60.549:   64        |
|      2:    18.442 -  26.863:  253   |   7:    60.549 -  68.970:   35        |
|      3:    26.863 -  35.284:  133   |   8:    68.970 -  77.392:   14        |
|      4:    35.284 -  43.706:  105   |   9:    77.392 -  85.813:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1371 r_free = 0.1765             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1369 r_free = 0.1765             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1765   ksol= 0.33   Bsol= 79.61   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.13,-0.09,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.296633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1763   ksol= 0.33   Bsol= 72.09   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.50,-0.27,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.296770                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.920180              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.657  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.056568              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.356  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1371      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1887 = 1.92 * 0.50 * 5.3354 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0995 = 1.92 * 0.50 * 5.2501 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1238      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8064 = 2.06 * 1.00 * 5.2501 + 1.00 * 0.0091                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6991 = 2.06 * 1.00 * 5.1968 + 1.00 * 0.0115                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.65   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    90.65   17.21    None  None   None       |
|    Sol.    : 438    0      5.36    88.23   42.12    None  None   None       |
|    Mac.    : 2385   0      0.00    90.65   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.065:  942   |   5:    45.327 -  54.392:   85        |
|      1:     9.065 -  18.131: 1158   |   6:    54.392 -  63.458:   85        |
|      2:    18.131 -  27.196:  248   |   7:    63.458 -  72.523:   41        |
|      3:    27.196 -  36.262:  129   |   8:    72.523 -  81.588:   16        |
|      4:    36.262 -  45.327:  109   |   9:    81.588 -  90.654:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1650             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1203 r_free = 0.1649             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1649   ksol= 0.33   Bsol= 72.09   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.14,-1.50,-0.27,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.198600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1649   ksol= 0.33   Bsol= 68.93   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.45,-0.26,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.198584                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.471519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.265  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.767488              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8825 = 1.47 * 0.50 * 5.1968 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8809 = 1.47 * 0.50 * 5.1961 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9995 = 0.77 * 1.00 * 5.1961 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9973 = 0.77 * 1.00 * 5.1931 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.08   16.94    None  None   None       |
|    all(noH): 2823   0      0.00    91.08   16.94    None  None   None       |
|    Sol.    : 438    0      5.29    88.55   41.92    None  None   None       |
|    Mac.    : 2385   0      0.00    91.08   12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.108: 1019   |   5:    45.538 -  54.646:   81        |
|      1:     9.108 -  18.215: 1101   |   6:    54.646 -  63.754:   84        |
|      2:    18.215 -  27.323:  232   |   7:    63.754 -  72.861:   39        |
|      3:    27.323 -  36.431:  131   |   8:    72.861 -  81.969:   16        |
|      4:    36.431 -  45.538:  111   |   9:    81.969 -  91.077:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1646             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1646             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1646   ksol= 0.33   Bsol= 68.93   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.45,-0.26,-0.00,-0.00,-0.00); trace/3= -1.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.192877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1644   ksol= 0.33   Bsol= 69.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-1.18,0.01,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.192984                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.109377              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.039  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.806233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5365 = 2.11 * 0.50 * 5.1946 + 1.00 * 0.0578                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5229 = 2.11 * 0.50 * 5.1752 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5342 = 2.81 * 1.00 * 5.1752 + 1.00 * 0.0115                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5126 = 2.81 * 1.00 * 5.1672 + 1.00 * 0.0123                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.04   16.72    None  None   None       |
|    all(noH): 2823   0      0.00    99.04   16.72    None  None   None       |
|    Sol.    : 438    0      5.01    92.66   41.58    None  None   None       |
|    Mac.    : 2385   0      0.00    99.04   12.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.904: 1234   |   5:    49.522 -  59.426:   87        |
|      1:     9.904 -  19.809:  955   |   6:    59.426 -  69.331:   60        |
|      2:    19.809 -  29.713:  206   |   7:    69.331 -  79.235:   28        |
|      3:    29.713 -  39.618:  141   |   8:    79.235 -  89.140:    9        |
|      4:    39.618 -  49.522:   97   |   9:    89.140 -  99.044:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1632             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1633             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1633   ksol= 0.33   Bsol= 69.56   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,-1.18,0.01,-0.00,0.00,0.00); trace/3= -0.92                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.169408                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.0999 0.1307      5.4014      5.5304|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.0829 0.1095      5.4207      5.6208|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.1062 0.1445      5.4869      5.8197|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.1216 0.1676       5.468      5.6652|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.1382 0.1872      5.3765      5.5856|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.1278 0.1938      5.2681      5.5374|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.1322 0.1704      5.2078      5.3755|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.1198 0.1822      5.1164      5.4075|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.1197 0.1784      5.0606      5.2951|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.1170 0.1882      5.0148      5.3023|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.1197 0.1753      4.9847      5.2423|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.1205 0.1860      4.9431      5.3068|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.1158 0.1810      4.8415      5.1118|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.1045 0.1805      4.6783      4.9816|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8198  1371   152  0.94   9.63   0.96     0.93       7622.70|
|  2:  4.8198 -  3.8462  1299   146  0.95   7.94   1.00     0.98       8976.90|
|  3:  3.8462 -  3.3661  1286   141  0.94  11.05   1.02     1.01      10411.62|
|  4:  3.3661 -  3.0611  1280   142  0.92  13.53   1.00     0.98      10460.21|
|  5:  3.0611 -  2.8432  1261   141  0.90  16.42   0.99     0.97       9241.07|
|  6:  2.8432 -  2.6765  1268   141  0.89  16.76   0.98     0.95       7833.66|
|  7:  2.6765 -  2.5431  1264   140  0.90  16.29   0.98     0.96       6706.27|
|  8:  2.5431 -  2.4329  1247   137  0.91  15.42   0.98     0.96       5782.63|
|  9:  2.4329 -  2.3396  1243   141  0.90  15.90   0.98     0.94       5317.50|
| 10:  2.3396 -  2.2591  1243   138  0.90  16.15   0.98     0.93       4810.90|
| 11:  2.2591 -  2.1887  1249   138  0.90  16.66   0.97     0.93       4756.17|
| 12:  2.1887 -  2.1263  1239   139  0.90  16.60   0.98     0.97       4480.55|
| 13:  2.1263 -  2.0705  1247   137  0.90  16.07   0.97     0.95       3683.04|
| 14:  2.0705 -  2.0201  1133   126  0.92  14.56   0.94     0.90       2599.81|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2599.81 max =        10460.21 mean =      6680.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.44|
|phase err.(test): min =        0.00 max =           88.05 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1626   ksol= 0.33   Bsol= 69.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.98,0.20,-0.00,0.00,0.00); trace/3= -0.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1626   ksol= 0.33   Bsol= 69.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.98,0.20,-0.00,0.00,0.00); trace/3= -0.70                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168136                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8198 0.99   1371  152 0.1001 0.1264      5.3913      5.5017|
|  2:  4.8198 -  3.8462 0.99   1299  146 0.0835 0.1076      5.4182      5.6109|
|  3:  3.8462 -  3.3661 0.99   1286  141 0.1063 0.1433      5.4846       5.814|
|  4:  3.3661 -  3.0611 0.99   1280  142 0.1212 0.1680      5.4666      5.6695|
|  5:  3.0611 -  2.8432 0.99   1261  141 0.1379 0.1872      5.3764      5.5853|
|  6:  2.8432 -  2.6765 0.99   1268  141 0.1275 0.1936      5.2677      5.5381|
|  7:  2.6765 -  2.5431 0.99   1264  140 0.1323 0.1708       5.208       5.377|
|  8:  2.5431 -  2.4329 0.98   1247  137 0.1196 0.1821      5.1163      5.4074|
|  9:  2.4329 -  2.3396 0.98   1243  141 0.1198 0.1785      5.0606      5.2949|
| 10:  2.3396 -  2.2591 1.00   1243  138 0.1169 0.1882      5.0148      5.3031|
| 11:  2.2591 -  2.1887 0.97   1249  138 0.1196 0.1753      4.9845      5.2427|
| 12:  2.1887 -  2.1263 0.98   1239  139 0.1205 0.1859      4.9431      5.3064|
| 13:  2.1263 -  2.0705 0.99   1247  137 0.1157 0.1810      4.8415      5.1123|
| 14:  2.0705 -  2.0201 0.91   1133  126 0.1045 0.1806      4.6785      4.9819|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1645 -  4.8198  1371   152  0.94   9.25   0.96     0.93       7228.36|
|  2:  4.8198 -  3.8462  1299   146  0.95   7.79   1.00     0.99       8693.78|
|  3:  3.8462 -  3.3661  1286   141  0.94  10.95   1.02     1.02      10287.74|
|  4:  3.3661 -  3.0611  1280   142  0.92  13.54   1.00     0.98      10447.96|
|  5:  3.0611 -  2.8432  1261   141  0.90  16.44   1.00     0.98       9254.47|
|  6:  2.8432 -  2.6765  1268   141  0.89  16.76   0.99     0.96       7837.64|
|  7:  2.6765 -  2.5431  1264   140  0.90  16.30   0.99     0.96       6712.48|
|  8:  2.5431 -  2.4329  1247   137  0.91  15.42   0.99     0.97       5785.16|
|  9:  2.4329 -  2.3396  1243   141  0.90  15.92   0.99     0.95       5324.56|
| 10:  2.3396 -  2.2591  1243   138  0.90  16.15   0.99     0.94       4812.46|
| 11:  2.2591 -  2.1887  1249   138  0.90  16.66   0.98     0.94       4757.04|
| 12:  2.1887 -  2.1263  1239   139  0.90  16.60   1.00     0.98       4482.27|
| 13:  2.1263 -  2.0705  1247   137  0.90  16.07   0.98     0.96       3683.99|
| 14:  2.0705 -  2.0201  1133   126  0.92  14.57   0.95     0.92       2601.81|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2601.81 max =        10447.96 mean =      6622.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.40|
|phase err.(test): min =        0.00 max =           88.18 mean =        13.90|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.313)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.05   16.72    None  None   None       |
|    all(noH): 2823   0      0.00    99.05   16.72    None  None   None       |
|    Sol.    : 438    0      5.01    92.66   41.59    None  None   None       |
|    Mac.    : 2385   0      0.00    99.05   12.16    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:     0.003 -   9.907: 1234   |   5:    49.525 -  59.429:   87        |
|      1:     9.907 -  19.812:  955   |   6:    59.429 -  69.334:   60        |
|      2:    19.812 -  29.716:  206   |   7:    69.334 -  79.238:   28        |
|      3:    29.716 -  39.621:  141   |   8:    79.238 -  89.143:    9        |
|      4:    39.621 -  49.525:   97   |   9:    89.143 -  99.047:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.482 - 4.860
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 308
   mapped sites are within: 0.710 - 4.860

peak=    5.624 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.474 closest distance to " NH2 ARG A  56 " =    2.274
peak=    5.027 closest distance to " CB  ARG A 190 " =    1.611
peak=    5.022 closest distance to " CG  PRO A  54 " =    1.346
peak=    4.908 closest distance to " CB  SER A  63 " =    1.225
peak=    4.848 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.834 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.742 closest distance to " CZ  PHE A 218 " =    1.097
peak=    4.598 closest distance to " O   HOH Z 232 " =    2.292
peak=    4.590 closest distance to " O   HOH Z 369 " =    2.233
peak=    4.585 closest distance to " CG  PRO A 213 " =    1.186
peak=    4.584 closest distance to " CB  PRO A  54 " =    0.927
peak=    4.470 closest distance to " CB  ARG A 275 " =    0.944
peak=    4.444 closest distance to " O   HOH Z 298 " =    2.016
peak=    4.402 closest distance to " CD  ARG A 269 " =    0.896
peak=    4.352 closest distance to " O   HOH Z 189 " =    2.836
peak=    4.317 closest distance to " O   HOH Z 368 " =    2.157
peak=    4.305 closest distance to " CB  ARG A  79 " =    1.436
peak=    4.269 closest distance to " CA  TYR A  30 " =    0.973
peak=    4.260 closest distance to " O   HOH Z  15 " =    2.154
peak=    4.254 closest distance to " CB  TYR A 169 " =    0.793
peak=    4.204 closest distance to " O   HOH Z 265 " =    2.290
peak=    4.196 closest distance to " CB  GLU A 277 " =    3.772
peak=    4.165 closest distance to " C   PRO A 198 " =    1.505
peak=    4.156 closest distance to " NH1AARG A 145 " =    1.335
peak=    4.124 closest distance to " NE2 GLN A  11 " =    1.007
peak=    4.116 closest distance to " CD1 LEU A 300 " =    1.211
peak=    4.112 closest distance to " O   HOH Z  19 " =    2.295
peak=    4.103 closest distance to " O   HOH Z  40 " =    1.912
peak=    4.085 closest distance to " CB  VAL A 202 " =    1.608
peak=    4.080 closest distance to " CA  ALA A  51 " =    0.915
peak=    4.078 closest distance to " CA  ARG A 195 " =    1.213
peak=    4.072 closest distance to " O   HOH Z 126 " =    1.983
peak=    4.069 closest distance to " O   HOH Z 234 " =    3.857
peak=    4.061 closest distance to " CD  LYS A 166 " =    1.317
peak=    4.043 closest distance to " O   HOH Z  78 " =    1.602
peak=    4.025 closest distance to " ND2 ASN A 187 " =    1.446
peak=    4.022 closest distance to " O   HOH Z 427 " =    3.164
peak=    4.020 closest distance to " CB  TRP A 266 " =    1.027
peak=    4.018 closest distance to " CB  LEU A 228 " =    1.119
peak=    4.008 closest distance to " O   HOH Z 133 " =    2.626
peak=    3.997 closest distance to " O   HOH Z  63 " =    1.955
peak=    3.976 closest distance to " CB  ASN A 148 " =    1.502
peak=    3.970 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.944 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.936 closest distance to " CD2 LEU A 297 " =    0.955
peak=    3.928 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.911 closest distance to " CB  ASN A  39 " =    0.906
peak=    3.910 closest distance to " O   HOH Z 287 " =    2.000
peak=    3.904 closest distance to " O   HOH Z 214 " =    2.186
peak=    3.902 closest distance to " O   SER A  87 " =    2.258
peak=    3.885 closest distance to " CZ3 TRP A 266 " =    1.154
peak=    3.885 closest distance to " CB  GLU A 128 " =    1.014
peak=    3.874 closest distance to " CA  ARG A  36 " =    1.131
peak=    3.870 closest distance to " CB  ASP A 124 " =    0.718
peak=    3.858 closest distance to " CD1 LEU A  96 " =    0.710
peak=    3.856 closest distance to " O   HOH Z 361 " =    3.606
peak=    3.855 closest distance to " O   HOH Z 203 " =    1.756
peak=    3.855 closest distance to " CA  PRO A  54 " =    1.389
peak=    3.852 closest distance to " O   HOH Z 346 " =    1.629
peak=    3.851 closest distance to " CD  ARG A 159 " =    0.788
peak=    3.841 closest distance to " O   HOH Z 180 " =    2.141
peak=    3.838 closest distance to " CB  GLU A 152 " =    1.180
peak=    3.838 closest distance to " CB  VAL A 265 " =    1.294
peak=    3.832 closest distance to " CB  ASP A 140 " =    1.012
peak=    3.812 closest distance to " O   HOH Z 412 " =    3.872
peak=    3.807 closest distance to " O   HOH Z 261 " =    1.691
peak=    3.802 closest distance to " O   HOH Z 402 " =    1.425
peak=    3.798 closest distance to " CA  ALA A 160 " =    0.930
peak=    3.789 closest distance to " OD1 ASN A  69 " =    2.533
peak=    3.788 closest distance to " O   HOH Z 303 " =    2.141
peak=    3.780 closest distance to " O   HOH Z  21 " =    1.856
peak=    3.778 closest distance to " NZ  LYS A 117 " =    3.221
peak=    3.777 closest distance to " CG  PRO A 243 " =    1.068
peak=    3.771 closest distance to " O   HOH Z 193 " =    1.767
peak=    3.763 closest distance to " O   HOH Z  43 " =    1.946
peak=    3.759 closest distance to " O   HOH Z 316 " =    3.161
peak=    3.749 closest distance to " C   ILE A 106 " =    1.918
peak=    3.740 closest distance to " NH2 ARG A 156 " =    1.179
peak=    3.735 closest distance to " CB  GLU A  46 " =    0.974
peak=    3.735 closest distance to " CA  VAL A 125 " =    1.282
peak=    3.732 closest distance to " CA  MET A 105 " =    1.069
peak=    3.727 closest distance to " CD  ARG A  66 " =    2.507
peak=    3.727 closest distance to " O   HOH Z 406 " =    1.596
peak=    3.713 closest distance to " O   HOH Z 158 " =    3.056
peak=    3.713 closest distance to " O   HOH Z  80 " =    1.691
peak=    3.697 closest distance to " O   HOH Z 142 " =    1.556
peak=    3.687 closest distance to " O   HOH Z  59 " =    2.305
peak=    3.682 closest distance to " O  BHOH Z 338 " =    2.323
peak=    3.676 closest distance to " O   HOH Z 193 " =    1.962
peak=    3.658 closest distance to " O   HOH Z 271 " =    2.719
peak=    3.655 closest distance to " CD ALYS A 290 " =    0.959
peak=    3.629 closest distance to " CZ  PHE A  38 " =    1.264
peak=    3.628 closest distance to " CA  ALA A 154 " =    1.018
peak=    3.627 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.627 closest distance to " CG1 ILE A  33 " =    1.202
peak=    3.621 closest distance to " O   HOH Z 280 " =    2.981
peak=    3.616 closest distance to " ND2 ASN A 249 " =    0.816
peak=    3.616 closest distance to " O   HOH Z 285 " =    2.541
peak=    3.613 closest distance to " O   HOH Z 403 " =    1.479
peak=    3.612 closest distance to " CA  THR A 221 " =    0.944
peak=    3.609 closest distance to " O   THR A 251 " =    1.152
peak=    3.603 closest distance to " O   HOH Z 353 " =    2.673
peak=    3.602 closest distance to " O   ALA A 165 " =    1.472
peak=    3.594 closest distance to " N   ASN A  39 " =    1.364
peak=    3.590 closest distance to " O   ASN A  74 " =    1.594
peak=    3.579 closest distance to " OG BSER A 164 " =    2.403
peak=    3.577 closest distance to " O   HOH Z 294 " =    1.544
peak=    3.573 closest distance to " O   HOH Z   1 " =    2.357
peak=    3.567 closest distance to " O   THR A 220 " =    1.161
peak=    3.563 closest distance to " O   HOH Z 172 " =    3.890
peak=    3.558 closest distance to " CG1 VAL A 153 " =    1.021
peak=    3.557 closest distance to " O   HOH Z  44 " =    2.151
peak=    3.556 closest distance to " CB  ASN A 142 " =    1.077
peak=    3.555 closest distance to " CG2 THR A 221 " =    1.152
peak=    3.554 closest distance to " O   HOH Z 365 " =    2.865
peak=    3.544 closest distance to " O   HOH Z 126 " =    1.812
peak=    3.540 closest distance to " CB  GLN A  89 " =    1.229
peak=    3.533 closest distance to " CB  SER A  62 " =    0.794
peak=    3.532 closest distance to " O   HOH Z 325 " =    2.317
peak=    3.528 closest distance to " OE1 GLN A  11 " =    2.019
peak=    3.523 closest distance to " CB  SER A 212 " =    1.089
peak=    3.522 closest distance to " O   HOH Z 422 " =    2.713
peak=    3.519 closest distance to " CA  SER A  87 " =    1.123
peak=    3.514 closest distance to " O   HOH Z 106 " =    4.123
peak=    3.507 closest distance to " CB  LEU A  83 " =    0.819
peak=    3.504 closest distance to " O   HOH Z 392 " =    2.813
peak=    3.502 closest distance to " O   HOH Z  66 " =    2.270
peak=    3.497 closest distance to " O   HOH Z 128 " =    2.236
peak=    3.495 closest distance to " O   HOH Z 213 " =    1.950
peak=    3.495 closest distance to " O   ASN A  74 " =    2.065
peak=    3.484 closest distance to " O   TYR A 116 " =    1.318
peak=    3.480 closest distance to " CB  SER A 141 " =    1.058
peak=    3.479 closest distance to " O   HOH Z  97 " =    2.019
peak=    3.473 closest distance to " CG  GLU A  37 " =    0.878
peak=    3.468 closest distance to " CB  LYS A 117 " =    1.163
peak=    3.467 closest distance to " O   HOH Z 261 " =    1.737
peak=    3.464 closest distance to " O   HOH Z 134 " =    1.199
peak=    3.463 closest distance to " CG2 ILE A 234 " =    0.874
peak=    3.462 closest distance to " O   ALA A 158 " =    1.216
peak=    3.457 closest distance to " CB  TYR A 116 " =    0.789
peak=    3.456 closest distance to " CB  MET A  47 " =    0.965
peak=    3.452 closest distance to " CA  ALA A 295 " =    1.103
peak=    3.451 closest distance to " CG2AVAL A  72 " =    1.914
peak=    3.450 closest distance to " O   HOH Z 313 " =    1.834
peak=    3.450 closest distance to " CB  ALA A 291 " =    1.247
peak=    3.449 closest distance to " ND2 ASN A 249 " =    1.931
peak=    3.449 closest distance to " N   ARG A 156 " =    1.430
peak=    3.448 closest distance to " CD  ARG A  66 " =    2.468
peak=    3.447 closest distance to " O   HOH Z 391 " =    2.975
peak=    3.447 closest distance to " O   HOH Z 425 " =    1.339
peak=    3.445 closest distance to " CA  MET A  40 " =    1.193
peak=    3.444 closest distance to " CB  MET A  40 " =    0.793
peak=    3.442 closest distance to " O   HOH Z 126 " =    1.682
peak=    3.440 closest distance to " O   HOH Z 147 " =    1.819
peak=    3.438 closest distance to " CA  GLU A  46 " =    0.851
peak=    3.436 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.435 closest distance to " CA  ASP A 124 " =    0.783
peak=    3.433 closest distance to " O   HOH Z 128 " =    2.208
peak=    3.431 closest distance to " CA  ASN A 215 " =    1.165
peak=    3.425 closest distance to " O   HOH Z 423 " =    1.852
peak=    3.425 closest distance to " O   HOH Z 290 " =    1.006
peak=    3.424 closest distance to " O   HOH Z 272 " =    1.882
peak=    3.423 closest distance to " O   HOH Z 250 " =    1.442
peak=    3.415 closest distance to " CB  TRP A 179 " =    1.456
peak=    3.412 closest distance to " O   HOH Z 102 " =    1.301
peak=    3.411 closest distance to " CA  ALA A 100 " =    1.067
peak=    3.406 closest distance to " O   HOH Z 403 " =    1.540
peak=    3.403 closest distance to " N   ASN A 127 " =    1.293
peak=    3.402 closest distance to " O   ASP A 124 " =    1.173
peak=    3.402 closest distance to " CG2 ILE A 120 " =    1.062
peak=    3.394 closest distance to " O   HOH Z 371 " =    3.222
peak=    3.393 closest distance to " O   THR A 182 " =    1.426
peak=    3.392 closest distance to " CB  SER A   3 " =    1.383
peak=    3.392 closest distance to " CG  GLN A  11 " =    1.567
peak=    3.391 closest distance to " O   HOH Z  66 " =    2.125
peak=    3.389 closest distance to " CB  PRO A 243 " =    1.482
peak=    3.388 closest distance to " O   HOH Z  62 " =    2.240
peak=    3.386 closest distance to " CB  ALA A  43 " =    0.873
peak=    3.385 closest distance to " CA  GLU A 152 " =    0.901
peak=    3.384 closest distance to " O   HOH Z 340 " =    2.222
peak=    3.382 closest distance to " O   HOH Z 305 " =    3.665
peak=    3.381 closest distance to " CB  ASN A 187 " =    1.286
peak=    3.380 closest distance to " CA  GLY A 241 " =    0.811
peak=    3.371 closest distance to " CA  ASN A 217 " =    1.259
peak=    3.368 closest distance to " CB  ALA A 248 " =    1.243
peak=    3.365 closest distance to " N   GLY A  98 " =    1.143
peak=    3.365 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.360 closest distance to " O   HOH Z  88 " =    1.782
peak=    3.359 closest distance to " CA  ASP A 191 " =    0.865
peak=    3.358 closest distance to " CA  ALA A 291 " =    0.773
peak=    3.356 closest distance to " O   HOH Z 248 " =    1.609
peak=    3.356 closest distance to " O   HOH Z 199 " =    1.648
peak=    3.354 closest distance to " CB  THR A  82 " =    1.424
peak=    3.353 closest distance to " CG  ARG A 138 " =    1.170
peak=    3.351 closest distance to " CB  PRO A  90 " =    1.175
peak=    3.347 closest distance to " N   CYS A 260 " =    0.829
peak=    3.334 closest distance to " CA  ASP A 162 " =    1.080
peak=    3.331 closest distance to " O   HOH Z 285 " =    1.790
peak=    3.330 closest distance to " CG  MET A 185 " =    1.232
peak=    3.329 closest distance to " CD1 LEU A 255 " =    1.730
peak=    3.328 closest distance to " NE2 GLN A  77 " =    3.441
peak=    3.322 closest distance to " NH2AARG A 275 " =    3.528
peak=    3.318 closest distance to " O   HOH Z 417 " =    3.151
peak=    3.314 closest distance to " O   HOH Z  44 " =    2.598
peak=    3.313 closest distance to " O   HOH Z 166 " =    3.848
peak=    3.313 closest distance to " O   HOH Z 163 " =    1.913
peak=    3.311 closest distance to " O   HOH Z 193 " =    2.174
peak=    3.310 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.310 closest distance to " CB  ALA A  34 " =    0.891
peak=    3.309 closest distance to " CA  THR A 264 " =    0.913
peak=    3.305 closest distance to " C   TYR A 214 " =    1.589
peak=    3.305 closest distance to " O   HOH Z  20 " =    1.626
peak=    3.301 closest distance to " CG1 ILE A 120 " =    0.986
peak=    3.291 closest distance to " CE1 TYR A 186 " =    1.313
peak=    3.289 closest distance to " O   HOH Z 247 " =    1.430
peak=    3.287 closest distance to " OG  SER A 245 " =    1.752
peak=    3.282 closest distance to " O   HOH Z 383 " =    2.224
peak=    3.282 closest distance to " NE  ARG A  79 " =    1.055
peak=    3.281 closest distance to " OG BSER A 134 " =    2.813
peak=    3.276 closest distance to " CB  GLN A  88 " =    1.207
peak=    3.274 closest distance to " O   HOH Z 299 " =    4.560
peak=    3.273 closest distance to " O   HOH Z 359 " =    1.520
peak=    3.273 closest distance to " O   HOH Z 132 " =    2.709
peak=    3.270 closest distance to " CA  THR A 221 " =    1.320
peak=    3.269 closest distance to " CA  TYR A 116 " =    1.408
peak=    3.269 closest distance to " CA  ALA A 158 " =    1.204
peak=    3.265 closest distance to " OG  SER A  22 " =    2.804
peak=    3.263 closest distance to " O   HOH Z 248 " =    1.675
peak=    3.259 closest distance to " CE1 HIS A 115 " =    1.021
peak=    3.255 closest distance to " CG2 THR A 220 " =    0.960
peak=    3.252 closest distance to " CA  ALA A 233 " =    1.526
peak=    3.252 closest distance to " CA  ASN A 176 " =    1.784
peak=    3.251 closest distance to " CB  ALA A   1 " =    4.860
peak=    3.249 closest distance to " O   HOH Z 234 " =    1.859
peak=    3.247 closest distance to " CB  GLN A 103 " =    0.829
peak=    3.243 closest distance to " NH2BARG A 145 " =    2.212
peak=    3.243 closest distance to " CA  ARG A 139 " =    1.135
peak=    3.242 closest distance to " CB  GLN A 205 " =    1.034
peak=    3.241 closest distance to " CD  GLU A 152 " =    0.829
peak=    3.241 closest distance to " CB  ALA A 104 " =    0.757
peak=    3.239 closest distance to " O   HOH Z 258 " =    1.990
peak=    3.232 closest distance to " O   HOH Z 185 " =    1.890
peak=    3.227 closest distance to " O   HOH Z  90 " =    2.341
peak=    3.224 closest distance to " O   HOH Z 148 " =    3.356
peak=    3.219 closest distance to " CB  ASN A 285 " =    0.913
peak=    3.219 closest distance to " O   HOH Z 135 " =    1.736
peak=    3.212 closest distance to " CB  ASP A 298 " =    1.210
peak=    3.212 closest distance to " O   HOH Z 291 " =    1.545
peak=    3.211 closest distance to " CB  LEU A  96 " =    1.293
peak=    3.210 closest distance to " CA  ASN A 127 " =    1.142
peak=    3.206 closest distance to " O   HOH Z 124 " =    1.808
peak=    3.205 closest distance to " O   HOH Z 258 " =    1.633
peak=    3.205 closest distance to " CB  ASN A 215 " =    1.168
peak=    3.204 closest distance to " NE2 HIS A 207 " =    1.169
peak=    3.201 closest distance to " NZ  LYS A  48 " =    1.306
peak=    3.194 closest distance to " CG2BVAL A  41 " =    0.853
peak=    3.193 closest distance to " CA  GLY A 211 " =    1.302
peak=    3.193 closest distance to " CB  THR A  31 " =    1.659
peak=    3.193 closest distance to " CB  THR A  52 " =    0.755
peak=    3.192 closest distance to " CB  ILE A 120 " =    1.217
peak=    3.185 closest distance to " CB  ARG A 139 " =    0.898
peak=    3.185 closest distance to " CA  LEU A  83 " =    1.408
peak=    3.184 closest distance to " CB  ALA A 242 " =    0.846
peak=    3.183 closest distance to " O   HOH Z 273 " =    2.861
peak=    3.180 closest distance to " O   HOH Z  44 " =    1.581
peak=    3.177 closest distance to " OE2 GLU A  53 " =    2.029
peak=    3.172 closest distance to " CA  ALA A  21 " =    1.230
peak=    3.169 closest distance to " CD2 TYR A 186 " =    1.026
peak=    3.169 closest distance to " CA  ASP A 191 " =    1.124
peak=    3.159 closest distance to " CB  ASN A 110 " =    1.190
peak=    3.159 closest distance to " O   THR A 251 " =    1.695
peak=    3.155 closest distance to " CB  SER A 210 " =    0.882
peak=    3.151 closest distance to " CB  SER A 216 " =    0.892
peak=    3.150 closest distance to " O   ASP A 191 " =    1.511
peak=    3.148 closest distance to " CG  ARG A 159 " =    0.907
peak=    3.148 closest distance to " O   HOH Z 116 " =    1.802
peak=    3.143 closest distance to " O   HOH Z 171 " =    3.941
peak=    3.140 closest distance to " CB  ARG A 138 " =    0.998
peak=    3.134 closest distance to " OH  TYR A 116 " =    1.130
peak=    3.118 closest distance to " O   GLU A   2 " =    1.617
peak=    3.113 closest distance to " CA  ARG A 102 " =    1.160
peak=    3.112 closest distance to " N   ALA A 256 " =    1.143
peak=    3.105 closest distance to " CD1 ILE A 199 " =    0.852
peak=    3.102 closest distance to " CB  ALA A 248 " =    0.992
peak=    3.100 closest distance to " CG  MET A 185 " =    1.006
peak=    3.100 closest distance to " CB  SER A  26 " =    1.858
peak=    3.099 closest distance to " CA  ILE A 106 " =    0.846
peak=    3.094 closest distance to " O   HOH Z 419 " =    1.916
peak=    3.091 closest distance to " O   HOH Z 167 " =    1.711
peak=    3.087 closest distance to " ND1 HIS A  81 " =    1.562
peak=    3.086 closest distance to " CZ2 TRP A 179 " =    1.737
peak=    3.075 closest distance to " O   HOH Z  46 " =    1.556
peak=    3.065 closest distance to " N   TYR A 247 " =    1.116
peak=    3.063 closest distance to " N   PHE A 130 " =    1.237
peak=    3.052 closest distance to " CZ  PHE A 192 " =    0.995
peak=    3.050 closest distance to " NH1BARG A 145 " =    0.954
peak=    3.048 closest distance to " CB  PHE A 204 " =    0.876
peak=    3.045 closest distance to " CG2 ILE A  20 " =    1.275
peak=    3.033 closest distance to " CA  ARG A 156 " =    1.055
peak=    3.015 closest distance to " CE  MET A 113 " =    1.741
peak=    3.008 closest distance to " OD2 ASP A 200 " =    1.242
peak=    3.001 closest distance to " O   HOH Z 203 " =    1.231

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.944 - 5.764
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 208
   mapped sites are within: 0.944 - 5.764

peak=   -4.820 closest distance to " CD  GLN A  58 " =    0.944
peak=   -4.537 closest distance to " CD  ARG A 156 " =    2.089
peak=   -4.399 closest distance to " CD  ARG A  14 " =    3.542
peak=   -4.348 closest distance to " O   HOH Z 266 " =    5.567
peak=   -4.342 closest distance to " O   HOH Z 231 " =    2.334
peak=   -4.326 closest distance to " CG1 VAL A 112 " =    2.613
peak=   -4.267 closest distance to " C   HIS A 108 " =    1.030
peak=   -4.254 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.173 closest distance to " O   HOH Z  10 " =    1.604
peak=   -4.130 closest distance to " CG1 VAL A 250 " =    2.733
peak=   -4.128 closest distance to " CD2 TYR A 293 " =    1.984
peak=   -4.123 closest distance to " O   VAL A  67 " =    2.694
peak=   -4.107 closest distance to " O   HOH Z 196 " =    2.158
peak=   -4.069 closest distance to " O   HOH Z  73 " =    2.354
peak=   -4.053 closest distance to " OE1 GLN A 223 " =    2.010
peak=   -4.045 closest distance to " O   HOH Z 377 " =    1.974
peak=   -4.044 closest distance to " OG  SER A  97 " =    2.245
peak=   -4.024 closest distance to " CB  ALA A 161 " =    2.708
peak=   -4.014 closest distance to " CG2 ILE A  49 " =    2.795
peak=   -3.969 closest distance to " CE2 TYR A  30 " =    2.748
peak=   -3.961 closest distance to " O   PRO A 198 " =    1.354
peak=   -3.918 closest distance to " O   HOH Z 198 " =    2.166
peak=   -3.915 closest distance to " N   ALA A  43 " =    2.731
peak=   -3.913 closest distance to " CE2 PHE A  61 " =    2.617
peak=   -3.908 closest distance to " O   HOH Z 211 " =    1.393
peak=   -3.892 closest distance to " OD1 ASN A 148 " =    1.479
peak=   -3.889 closest distance to " OG BSER A 134 " =    1.328
peak=   -3.876 closest distance to " CG  ARG A 269 " =    2.449
peak=   -3.831 closest distance to " CZ3 TRP A 179 " =    1.175
peak=   -3.829 closest distance to " CA  GLY A 241 " =    3.280
peak=   -3.820 closest distance to " O   HOH Z   6 " =    2.267
peak=   -3.764 closest distance to " CD1 LEU A 101 " =    2.452
peak=   -3.759 closest distance to " CA  ASP A 298 " =    1.056
peak=   -3.756 closest distance to " O   HOH Z 185 " =    2.250
peak=   -3.748 closest distance to " OXT GLY A 302 " =    3.120
peak=   -3.729 closest distance to " CD1 PHE A  59 " =    2.002
peak=   -3.728 closest distance to " O   HOH Z  38 " =    1.314
peak=   -3.723 closest distance to " CB  ALA A 129 " =    2.438
peak=   -3.720 closest distance to " CG  GLU A 277 " =    1.251
peak=   -3.693 closest distance to " CG  GLN A  11 " =    1.716
peak=   -3.693 closest distance to " CA  GLY A 241 " =    2.341
peak=   -3.689 closest distance to " ND2 ASN A  45 " =    1.935
peak=   -3.687 closest distance to " O   HOH Z 166 " =    1.817
peak=   -3.687 closest distance to " O   HOH Z 128 " =    2.688
peak=   -3.686 closest distance to " CE3 TRP A 150 " =    2.189
peak=   -3.668 closest distance to " O   HOH Z 394 " =    1.570
peak=   -3.658 closest distance to " CA  VAL A  67 " =    2.937
peak=   -3.640 closest distance to " NE2 GLN A  88 " =    1.994
peak=   -3.620 closest distance to " CG1 VAL A 125 " =    1.921
peak=   -3.616 closest distance to " O   HOH Z 393 " =    1.325
peak=   -3.609 closest distance to " CG2 ILE A 263 " =    2.351
peak=   -3.607 closest distance to " NE2 GLN A 194 " =    1.875
peak=   -3.597 closest distance to " O   HOH Z  51 " =    1.714
peak=   -3.595 closest distance to " CG1 VAL A 112 " =    2.888
peak=   -3.588 closest distance to " CG  HIS A  86 " =    1.081
peak=   -3.581 closest distance to " O   HOH Z   6 " =    1.422
peak=   -3.577 closest distance to " CE  MET A 105 " =    2.522
peak=   -3.564 closest distance to " CG2 VAL A 189 " =    2.196
peak=   -3.561 closest distance to " CB  ASN A  39 " =    2.376
peak=   -3.559 closest distance to " O   HOH Z 348 " =    2.271
peak=   -3.553 closest distance to " CB  ALA A 291 " =    2.368
peak=   -3.549 closest distance to " NH2 ARG A  79 " =    1.516
peak=   -3.546 closest distance to " O   HOH Z  37 " =    1.864
peak=   -3.544 closest distance to " C   GLY A  17 " =    1.215
peak=   -3.534 closest distance to " ND2 ASN A  45 " =    1.184
peak=   -3.532 closest distance to " ND2BASN A 224 " =    1.801
peak=   -3.528 closest distance to " O   PRO A 163 " =    2.164
peak=   -3.509 closest distance to " O   HOH Z 102 " =    1.594
peak=   -3.508 closest distance to " O   HOH Z 114 " =    3.440
peak=   -3.506 closest distance to " NE2 GLN A 103 " =    1.879
peak=   -3.499 closest distance to " O   HOH Z 292 " =    4.676
peak=   -3.496 closest distance to " O   HOH Z 216 " =    1.413
peak=   -3.495 closest distance to " ND2 ASN A  69 " =    1.762
peak=   -3.494 closest distance to " CA  GLY A 203 " =    2.432
peak=   -3.488 closest distance to " CG  ARG A  66 " =    2.361
peak=   -3.476 closest distance to " O   HOH Z 290 " =    1.223
peak=   -3.475 closest distance to " OD2 ASP A 171 " =    1.887
peak=   -3.474 closest distance to " O   HOH Z 264 " =    1.786
peak=   -3.474 closest distance to " C   ASN A 285 " =    2.510
peak=   -3.446 closest distance to " O   HOH Z 106 " =    1.957
peak=   -3.439 closest distance to " C   LEU A 143 " =    1.121
peak=   -3.437 closest distance to " O   HOH Z 174 " =    3.859
peak=   -3.427 closest distance to " CE3 TRP A  70 " =    1.873
peak=   -3.427 closest distance to " CA  GLY A 133 " =    2.303
peak=   -3.426 closest distance to " N   ALA A 226 " =    2.119
peak=   -3.426 closest distance to " CB  ASP A 132 " =    2.367
peak=   -3.422 closest distance to " O   HOH Z 114 " =    1.298
peak=   -3.417 closest distance to " O   HOH Z  52 " =    1.421
peak=   -3.408 closest distance to " O   HOH Z 421 " =    3.446
peak=   -3.407 closest distance to " CB  ALA A  43 " =    2.708
peak=   -3.406 closest distance to " NH2AARG A 275 " =    5.445
peak=   -3.405 closest distance to " O   PHE A 218 " =    1.472
peak=   -3.404 closest distance to " O   ALA A  34 " =    2.499
peak=   -3.403 closest distance to " O   ALA A  10 " =    1.678
peak=   -3.403 closest distance to " O   SER A 210 " =    1.850
peak=   -3.402 closest distance to " ND2 ASN A 249 " =    2.465
peak=   -3.394 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.379 closest distance to " CG  PRO A 243 " =    1.782
peak=   -3.376 closest distance to " O   GLY A 211 " =    1.376
peak=   -3.375 closest distance to " N   THR A 264 " =    1.376
peak=   -3.374 closest distance to " OD2 ASP A 191 " =    1.538
peak=   -3.365 closest distance to " O   SER A 276 " =    1.753
peak=   -3.361 closest distance to " CG  GLU A  53 " =    1.483
peak=   -3.361 closest distance to " NH2 ARG A 159 " =    2.388
peak=   -3.358 closest distance to " O   HOH Z  19 " =    2.210
peak=   -3.358 closest distance to " O   HOH Z 111 " =    1.922
peak=   -3.357 closest distance to " O   HOH Z 275 " =    1.595
peak=   -3.354 closest distance to " C   SER A 206 " =    1.432
peak=   -3.351 closest distance to " O   HOH Z 407 " =    3.443
peak=   -3.348 closest distance to " OG BSER A 134 " =    1.960
peak=   -3.343 closest distance to " OD1 ASP A 171 " =    1.514
peak=   -3.340 closest distance to " CB  PHE A 192 " =    2.023
peak=   -3.339 closest distance to " CG  MET A 105 " =    0.969
peak=   -3.329 closest distance to " CA  GLY A 241 " =    2.897
peak=   -3.328 closest distance to " OH  TYR A 247 " =    1.792
peak=   -3.323 closest distance to " O   HOH Z 372 " =    2.362
peak=   -3.321 closest distance to " O   TYR A 186 " =    1.809
peak=   -3.316 closest distance to " O   HOH Z 265 " =    2.309
peak=   -3.315 closest distance to " O   SER A 135 " =    1.404
peak=   -3.306 closest distance to " OD1 ASP A 191 " =    1.579
peak=   -3.299 closest distance to " C   ARG A  79 " =    2.666
peak=   -3.296 closest distance to " O   HOH Z 426 " =    1.678
peak=   -3.295 closest distance to " CD2 LEU A 167 " =    1.881
peak=   -3.295 closest distance to " N   THR A  52 " =    1.620
peak=   -3.286 closest distance to " O   HOH Z 357 " =    2.160
peak=   -3.281 closest distance to " O   HOH Z 234 " =    4.487
peak=   -3.278 closest distance to " O   HOH Z  60 " =    2.372
peak=   -3.266 closest distance to " O   HOH Z 351 " =    1.596
peak=   -3.265 closest distance to " O   HOH Z 177 " =    1.756
peak=   -3.260 closest distance to " O   HOH Z 299 " =    2.707
peak=   -3.257 closest distance to " CG  TRP A 266 " =    1.840
peak=   -3.256 closest distance to " OE1 GLN A  88 " =    1.098
peak=   -3.247 closest distance to " O   HOH Z  43 " =    1.559
peak=   -3.245 closest distance to " NH2 ARG A  66 " =    2.094
peak=   -3.241 closest distance to " CB  PHE A  16 " =    2.532
peak=   -3.238 closest distance to " SG  CYS A 168 " =    1.219
peak=   -3.231 closest distance to " ND2 ASN A  60 " =    1.375
peak=   -3.228 closest distance to " O   HOH Z 193 " =    1.631
peak=   -3.224 closest distance to " C   ASN A 187 " =    1.920
peak=   -3.224 closest distance to " CD1 LEU A 228 " =    2.363
peak=   -3.223 closest distance to " O   HOH Z 396 " =    1.855
peak=   -3.222 closest distance to " O   HOH Z 409 " =    4.623
peak=   -3.218 closest distance to " O   HOH Z 236 " =    1.405
peak=   -3.213 closest distance to " O   VAL A 189 " =    2.581
peak=   -3.212 closest distance to " NE1 TRP A 266 " =    2.217
peak=   -3.210 closest distance to " CB  PRO A  54 " =    2.577
peak=   -3.209 closest distance to " O   GLN A 240 " =    2.593
peak=   -3.209 closest distance to " O   HOH Z 389 " =    1.964
peak=   -3.209 closest distance to " CG  LEU A  83 " =    2.066
peak=   -3.208 closest distance to " OD1 ASN A 187 " =    1.508
peak=   -3.207 closest distance to " O   HOH Z 357 " =    2.101
peak=   -3.204 closest distance to " O   HOH Z 191 " =    5.764
peak=   -3.201 closest distance to " O   HOH Z 298 " =    2.519
peak=   -3.197 closest distance to " CD1 LEU A   5 " =    2.541
peak=   -3.196 closest distance to " O   HOH Z 353 " =    2.175
peak=   -3.195 closest distance to " CZ  PHE A 155 " =    1.302
peak=   -3.192 closest distance to " CD2 PHE A 225 " =    1.175
peak=   -3.192 closest distance to " O   HOH Z 139 " =    3.052
peak=   -3.191 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.183 closest distance to " CG  PRO A 163 " =    2.208
peak=   -3.181 closest distance to " O   HOH Z 326 " =    5.002
peak=   -3.179 closest distance to " CG1AVAL A  41 " =    2.756
peak=   -3.173 closest distance to " O   HOH Z  70 " =    2.159
peak=   -3.171 closest distance to " O   HOH Z 183 " =    1.727
peak=   -3.166 closest distance to " O   VAL A 189 " =    1.681
peak=   -3.161 closest distance to " O   HOH Z 285 " =    1.515
peak=   -3.161 closest distance to " O   HOH Z 323 " =    1.463
peak=   -3.160 closest distance to " O   HOH Z 156 " =    3.579
peak=   -3.156 closest distance to " CD  ARG A  79 " =    1.178
peak=   -3.153 closest distance to " O   GLY A  98 " =    2.172
peak=   -3.148 closest distance to " O   HOH Z 350 " =    2.022
peak=   -3.147 closest distance to " O   HOH Z 189 " =    2.130
peak=   -3.147 closest distance to " CD  GLU A 236 " =    1.134
peak=   -3.146 closest distance to " O   HOH Z 418 " =    1.466
peak=   -3.145 closest distance to " CD  GLN A  88 " =    1.153
peak=   -3.144 closest distance to " CB  ALA A  10 " =    2.181
peak=   -3.143 closest distance to " O   HOH Z 251 " =    5.126
peak=   -3.143 closest distance to " O   HOH Z  71 " =    2.325
peak=   -3.143 closest distance to " CB  ALA A 100 " =    2.045
peak=   -3.143 closest distance to " O   HOH Z 197 " =    2.117
peak=   -3.142 closest distance to " O   HOH Z 322 " =    1.692
peak=   -3.142 closest distance to " O   HOH Z 150 " =    1.531
peak=   -3.131 closest distance to " CG2 VAL A 189 " =    1.936
peak=   -3.130 closest distance to " CE3 TRP A 274 " =    2.439
peak=   -3.127 closest distance to " O   HOH Z 252 " =    4.140
peak=   -3.127 closest distance to " O   HOH Z 311 " =    3.832
peak=   -3.125 closest distance to " C   GLY A 262 " =    2.113
peak=   -3.124 closest distance to " O   HOH Z  44 " =    2.325
peak=   -3.123 closest distance to " CB  TRP A  85 " =    2.454
peak=   -3.123 closest distance to " CB  ALA A 248 " =    2.365
peak=   -3.120 closest distance to " CB  ASP A 286 " =    2.186
peak=   -3.105 closest distance to " O   SER A  95 " =    1.857
peak=   -3.102 closest distance to " CE  MET A  93 " =    1.993
peak=   -3.100 closest distance to " O   HOH Z  64 " =    1.626
peak=   -3.089 closest distance to " CD2 PHE A  59 " =    2.500
peak=   -3.088 closest distance to " OE1 GLN A 183 " =    1.647
peak=   -3.083 closest distance to " OD1 ASN A 301 " =    1.970
peak=   -3.081 closest distance to " CG1 VAL A 197 " =    2.289
peak=   -3.079 closest distance to " N   SER A 276 " =    1.411
peak=   -3.078 closest distance to " CB  TYR A  15 " =    2.223
peak=   -3.067 closest distance to " O   HOH Z 435 " =    2.697
peak=   -3.058 closest distance to " O   HOH Z 166 " =    1.730
peak=   -3.057 closest distance to " NE2 GLN A 223 " =    1.565
peak=   -3.055 closest distance to " O   HOH Z 137 " =    2.434
peak=   -3.054 closest distance to " OD1 ASN A 173 " =    1.342
peak=   -3.051 closest distance to " O   HOH Z  89 " =    3.016
peak=   -3.045 closest distance to " O   HOH Z 414 " =    1.650
peak=   -3.042 closest distance to " O   HOH Z 227 " =    1.360

================= 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    :  0.3692 0.3594   6.131534e+00   6.110081e+00
   1_bss:  0.3591 0.3510   6.114889e+00   6.091865e+00
   1_xyz:  0.2324 0.2520   5.740575e+00   5.809801e+00
   1_adp:  0.2113 0.2596   5.684480e+00   5.838814e+00
   1_occ:  0.2108 0.2594   5.683779e+00   5.839327e+00
   2_bss:  0.2099 0.2580   5.682897e+00   5.836901e+00
   2_xyz:  0.1481 0.1906   5.369751e+00   5.570955e+00
   2_adp:  0.1371 0.1765   5.297472e+00   5.499670e+00
   2_occ:  0.1369 0.1765   5.296633e+00   5.499496e+00
   3_bss:  0.1371 0.1763   5.296770e+00   5.497828e+00
   3_xyz:  0.1238 0.1647   5.212962e+00   5.430415e+00
   3_adp:  0.1204 0.1650   5.198676e+00   5.428324e+00
   3_occ:  0.1203 0.1649   5.198600e+00   5.428440e+00
   4_bss:  0.1202 0.1649   5.198584e+00   5.428677e+00
   4_xyz:  0.1196 0.1648   5.195173e+00   5.426732e+00
   4_adp:  0.1198 0.1646   5.192891e+00   5.423830e+00
   4_occ:  0.1197 0.1646   5.192877e+00   5.423913e+00
   5_bss:  0.1196 0.1644   5.192984e+00   5.424025e+00
   5_xyz:  0.1151 0.1631   5.170912e+00   5.416244e+00
   5_adp:  0.1147 0.1632   5.169324e+00   5.418443e+00
   5_occ:  0.1147 0.1633   5.169408e+00   5.418805e+00
   5_bss:  0.1146 0.1626   5.168136e+00   5.415961e+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:  0.310  62.273  -2.182  -0.024   2.017  -0.000   0.000   0.000
   1_xyz:  0.310  62.273  -2.182  -0.024   2.017  -0.000   0.000   0.000
   1_adp:  0.310  62.273  -2.182  -0.024   2.017  -0.000   0.000   0.000
   1_occ:  0.310  62.273  -2.182  -0.024   2.017  -0.000   0.000   0.000
   2_bss:  0.332  79.611  -2.325  -1.128  -0.093  -0.000  -0.000  -0.000
   2_xyz:  0.332  79.611  -2.325  -1.128  -0.093  -0.000  -0.000  -0.000
   2_adp:  0.332  79.611  -2.325  -1.128  -0.093  -0.000  -0.000  -0.000
   2_occ:  0.332  79.611  -2.325  -1.128  -0.093  -0.000  -0.000  -0.000
   3_bss:  0.332  72.090  -2.138  -1.502  -0.267  -0.000  -0.000  -0.000
   3_xyz:  0.332  72.090  -2.138  -1.502  -0.267  -0.000  -0.000  -0.000
   3_adp:  0.332  72.090  -2.138  -1.502  -0.267  -0.000  -0.000  -0.000
   3_occ:  0.332  72.090  -2.138  -1.502  -0.267  -0.000  -0.000  -0.000
   4_bss:  0.327  68.927  -1.894  -1.448  -0.259  -0.000  -0.000  -0.000
   4_xyz:  0.327  68.927  -1.894  -1.448  -0.259  -0.000  -0.000  -0.000
   4_adp:  0.327  68.927  -1.894  -1.448  -0.259  -0.000  -0.000  -0.000
   4_occ:  0.327  68.927  -1.894  -1.448  -0.259  -0.000  -0.000  -0.000
   5_bss:  0.327  69.561  -1.575  -1.183   0.008  -0.000   0.000   0.000
   5_xyz:  0.327  69.561  -1.575  -1.183   0.008  -0.000   0.000   0.000
   5_adp:  0.327  69.561  -1.575  -1.183   0.008  -0.000   0.000   0.000
   5_occ:  0.327  69.561  -1.575  -1.183   0.008  -0.000   0.000   0.000
   5_bss:  0.327  69.564  -1.320  -0.982   0.203  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  38.638 0.6612  0.8127    36701.625
   1_bss:  37.837 0.6692  0.8261    34522.220
   1_xyz:  24.697 0.8161  0.9662    16200.663
   1_adp:  25.908 0.8025  0.9478    17447.967
   1_occ:  25.925 0.8023  0.9473    17460.228
   2_bss:  25.744 0.8043  0.9135    17325.964
   2_xyz:  18.252 0.8775  0.9669     9219.787
   2_adp:  16.307 0.8957  0.9663     7927.048
   2_occ:  16.296 0.8958  0.9663     7919.570
   3_bss:  16.265 0.8960  0.9622     7880.223
   3_xyz:  14.697 0.9094  0.9685     6827.101
   3_adp:  14.625 0.9104  0.9579     6815.763
   3_occ:  14.624 0.9104  0.9578     6814.863
   4_bss:  14.625 0.9104  0.9613     6819.510
   4_xyz:  14.582 0.9107  0.9616     6792.656
   4_adp:  14.506 0.9114  0.9518     6753.666
   4_occ:  14.505 0.9114  0.9517     6754.961
   5_bss:  14.507 0.9114  0.9614     6757.373
   5_xyz:  14.370 0.9124  0.9643     6659.020
   5_adp:  14.383 0.9124  0.9553     6677.963
   5_occ:  14.388 0.9124  0.9552     6680.787
   5_bss:  14.347 0.9126  0.9626     6622.186
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.116   1.6257e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.116   1.6257e-01
   1_xyz:   1.189  0.009  0.073 15.077  0.005  4.115   7.4941e-02
   1_adp:   1.189  0.009  0.073 15.077  0.005  4.115   7.4941e-02
   1_occ:   1.189  0.009  0.073 15.077  0.005  4.115   7.4941e-02
   2_bss:   1.189  0.009  0.073 15.077  0.005  4.115   7.4941e-02
   2_xyz:   1.094  0.008  0.079 14.773  0.004  4.134   6.6295e-02
   2_adp:   1.094  0.008  0.079 14.773  0.004  4.134   6.6295e-02
   2_occ:   1.094  0.008  0.079 14.773  0.004  4.134   6.6295e-02
   3_bss:   1.094  0.008  0.079 14.773  0.004  4.134   6.6295e-02
   3_xyz:   0.990  0.008  0.074 14.767  0.003  4.142   5.8924e-02
   3_adp:   0.990  0.008  0.074 14.767  0.003  4.142   5.8924e-02
   3_occ:   0.990  0.008  0.074 14.767  0.003  4.142   5.8924e-02
   4_bss:   0.990  0.008  0.074 14.767  0.003  4.142   5.8924e-02
   4_xyz:   0.973  0.008  0.074 14.708  0.003  4.115   5.7814e-02
   4_adp:   0.973  0.008  0.074 14.708  0.003  4.115   5.7814e-02
   4_occ:   0.973  0.008  0.074 14.708  0.003  4.115   5.7814e-02
   5_bss:   0.973  0.008  0.074 14.708  0.003  4.115   5.7814e-02
   5_xyz:   1.028  0.009  0.079 14.734  0.004  4.119   6.4695e-02
   5_adp:   1.028  0.009  0.079 14.734  0.004  4.119   6.4695e-02
   5_occ:   1.028  0.009  0.079 14.734  0.004  4.119   6.4695e-02
   5_bss:   1.028  0.009  0.079 14.734  0.004  4.119   6.4695e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4416e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4416e-01
   1_xyz:   7.408  0.045  0.328 84.169  0.042  2.163   7.3265e-02
   1_adp:   7.408  0.045  0.328 84.169  0.042  2.163   7.3265e-02
   1_occ:   7.408  0.045  0.328 84.169  0.042  2.163   7.3265e-02
   2_bss:   7.408  0.045  0.328 84.169  0.042  2.163   7.3265e-02
   2_xyz:   7.645  0.045  0.256 83.187  0.043  2.314   7.4863e-02
   2_adp:   7.645  0.045  0.256 83.187  0.043  2.314   7.4863e-02
   2_occ:   7.645  0.045  0.256 83.187  0.043  2.314   7.4863e-02
   3_bss:   7.645  0.045  0.256 83.187  0.043  2.314   7.4863e-02
   3_xyz:   7.133  0.038  0.227 84.514  0.037  2.371   3.5714e-02
   3_adp:   7.133  0.038  0.227 84.514  0.037  2.371   3.5714e-02
   3_occ:   7.133  0.038  0.227 84.514  0.037  2.371   3.5714e-02
   4_bss:   7.133  0.038  0.227 84.514  0.037  2.371   3.5714e-02
   4_xyz:   7.301  0.042  0.222 83.454  0.038  2.384   3.6059e-02
   4_adp:   7.301  0.042  0.222 83.454  0.038  2.384   3.6059e-02
   4_occ:   7.301  0.042  0.222 83.454  0.038  2.384   3.6059e-02
   5_bss:   7.301  0.042  0.222 83.454  0.038  2.384   3.6059e-02
   5_xyz:   7.340  0.047  0.262 82.549  0.037  2.365   4.2755e-02
   5_adp:   7.340  0.047  0.262 82.549  0.037  2.365   4.2755e-02
   5_occ:   7.340  0.047  0.262 82.549  0.037  2.365   4.2755e-02
   5_bss:   7.340  0.047  0.262 82.549  0.037  2.365   4.2755e-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:  86.36   0.00  17.46  75.55   0.00  13.28  86.36   3.75  40.21
   1_occ:  86.36   0.00  17.46  75.55   0.00  13.28  86.36   3.75  40.21
   2_bss:  86.36   0.00  17.46  75.55   0.00  13.28  86.36   3.75  40.21
   2_xyz:  86.36   0.00  17.46  75.55   0.00  13.28  86.36   3.75  40.21
   2_adp:  85.81   1.60  17.00  76.17   1.60  12.75  85.81   5.28  40.13
   2_occ:  85.81   1.60  17.00  76.17   1.60  12.75  85.81   5.28  40.13
   3_bss:  85.81   1.60  17.00  76.17   1.60  12.75  85.81   5.28  40.13
   3_xyz:  85.81   1.60  17.00  76.17   1.60  12.75  85.81   5.28  40.13
   3_adp:  90.65   0.00  17.21  90.65   0.00  12.63  88.23   5.36  42.12
   3_occ:  90.65   0.00  17.21  90.65   0.00  12.63  88.23   5.36  42.12
   4_bss:  90.65   0.00  17.21  90.65   0.00  12.63  88.23   5.36  42.12
   4_xyz:  90.65   0.00  17.21  90.65   0.00  12.63  88.23   5.36  42.12
   4_adp:  91.08   0.00  16.94  91.08   0.00  12.36  88.55   5.29  41.92
   4_occ:  91.08   0.00  16.94  91.08   0.00  12.36  88.55   5.29  41.92
   5_bss:  91.08   0.00  16.94  91.08   0.00  12.36  88.55   5.29  41.92
   5_xyz:  91.08   0.00  16.94  91.08   0.00  12.36  88.55   5.29  41.92
   5_adp:  99.04   0.00  16.72  99.04   0.00  12.15  92.66   5.01  41.58
   5_occ:  99.04   0.00  16.72  99.04   0.00  12.15  92.66   5.01  41.58
   5_bss:  99.05   0.00  16.72  99.05   0.00  12.16  92.66   5.01  41.59
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.532    0.009    0.293
   1_adp:    1.532    0.009    0.293
   1_occ:    1.532    0.009    0.293
   2_bss:    1.532    0.009    0.293
   2_xyz:    1.132    0.022    0.416
   2_adp:    1.132    0.022    0.416
   2_occ:    1.132    0.022    0.416
   3_bss:    1.132    0.022    0.416
   3_xyz:    1.061    0.041    0.459
   3_adp:    1.061    0.041    0.459
   3_occ:    1.061    0.041    0.459
   4_bss:    1.061    0.041    0.459
   4_xyz:    1.053    0.044    0.461
   4_adp:    1.053    0.044    0.461
   4_occ:    1.053    0.044    0.461
   5_bss:    1.053    0.044    0.461
   5_xyz:    1.130    0.051    0.481
   5_adp:    1.130    0.051    0.481
   5_occ:    1.130    0.051    0.481
   5_bss:    1.130    0.051    0.481
------------------------------------------------------------------------

CPU time actual refinement: 325.77


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/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_932/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_932/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.62 
  Macro-tasks:
    bulk solvent and scale       = 42.98  
    individual site refinement   = 136.68 
    weights calculation          = 28.25  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.53 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 100.84 
    alpha_beta                      = 8.01   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.16 
    fmodel                         = 7.18   
    r_factors                      = 0.15   
    phase_errors                   = 11.12  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 241.57 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.554 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    644 calls, 100.56 s
gradients_fft:          589 calls,  97.23 s

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

# Date 2008-01-16 Time 06:00:30 PST -0800 (1200492030.02 s)
Start R-work = 0.3692, R-free = 0.3594 (no bulk solvent and anisotropic scale)
Final R-work = 0.1322, R-free = 0.1777 (no bulk solvent and anisotropic scale)

Start R-work = 0.3591, R-free = 0.3510
Final R-work = 0.1146, R-free = 0.1626