# Date 2008-01-16 Time 05:04:17 PST -0800 (1200488657.99 s)
#phil __OFF__

Command line arguments: "../580.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6483
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 580

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99072
Completeness in resolution range: 0.949678
Completeness with d_max=infinity: 0.94674

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9907

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99072
Completeness in resolution range: 0.949678
Completeness with d_max=infinity: 0.94674

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2592 [2174/2202]  1954   220  10.1%
  bin  2:  4.2592 -  3.3935 [2070/2089]  1865   205   9.9%
  bin  3:  3.3935 -  2.9684 [2065/2085]  1858   207  10.0%
  bin  4:  2.9684 -  2.6987 [2031/2056]  1829   202   9.9%
  bin  5:  2.6987 -  2.5062 [2015/2034]  1809   206  10.2%
  bin  6:  2.5062 -  2.3590 [2010/2056]  1813   197   9.8%
  bin  7:  2.3590 -  2.2413 [2000/2034]  1803   197   9.8%
  bin  8:  2.2413 -  2.1440 [1998/2033]  1792   206  10.3%
  bin  9:  2.1440 -  2.0617 [1994/2024]  1798   196   9.8%
  bin 10:  2.0617 -  1.9907 [1232/2014]  1109   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/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: 0.15 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:
        1.80 -     2.42: 19
        2.42 -     3.04: 2137
        3.04 -     3.66: 4604
        3.66 -     4.28: 8913
        4.28 -     4.90: 12289
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.800 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.971 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.092 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.125 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27957 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_580/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/model_refine_001.geo

CPU time processing inputs: 9.59


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.63395 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: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3962   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.187178                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1407  157 0.3098 0.3194      6.4165      6.3961|
|  2:  4.7503 -  3.7905 0.99   1352  152 0.3199 0.3288      6.6365      6.6711|
|  3:  3.7905 -  3.3172 0.99   1331  149 0.3604 0.3283      6.5449      6.4756|
|  4:  3.3172 -  3.0166 0.99   1320  137 0.3835 0.3954      6.3934      6.3642|
|  5:  3.0166 -  2.8019 0.99   1308  150 0.4135 0.3423      6.2637      6.2083|
|  6:  2.8019 -  2.6377 0.98   1304  145 0.4212 0.4529      6.1787      6.1243|
|  7:  2.6377 -  2.5062 0.99   1293  150 0.4117 0.4024      6.1364      6.0549|
|  8:  2.5062 -  2.3976 0.98   1305  139 0.4440 0.4372      6.1156       6.099|
|  9:  2.3976 -  2.3056 0.98   1293  146 0.4469 0.3883      6.0459      6.0385|
| 10:  2.3056 -  2.2263 0.98   1275  140 0.4640 0.4188      6.0649      5.9793|
| 11:  2.2263 -  2.1569 0.99   1292  145 0.4538 0.4344      5.9754        5.97|
| 12:  2.1569 -  2.0954 0.98   1277  139 0.4529 0.4859      5.9117      5.9962|
| 13:  2.0954 -  2.0404 0.97   1259  138 0.4889 0.4605      5.8606      5.7936|
| 14:  2.0404 -  1.9907 0.48    614   72 0.4362 0.5093      5.8078       5.788|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1407   157  0.76  28.65   0.85     0.78      51053.47|
|  2:  4.7503 -  3.7905  1352   152  0.79  27.06   0.94     0.86      67314.67|
|  3:  3.7905 -  3.3172  1331   149  0.73  32.48   0.93     0.87      67903.67|
|  4:  3.3172 -  3.0166  1320   137  0.68  36.85   0.94     0.83      59119.86|
|  5:  3.0166 -  2.8019  1308   150  0.63  41.77   0.94     0.78      47616.62|
|  6:  2.8019 -  2.6377  1304   145  0.59  44.87   0.94     0.75      43814.56|
|  7:  2.6377 -  2.5062  1293   150  0.59  44.92   0.97     0.75      40301.91|
|  8:  2.5062 -  2.3976  1305   139  0.59  45.08   0.94     0.77      37263.44|
|  9:  2.3976 -  2.3056  1293   146  0.59  45.29   0.96     0.80      33301.14|
| 10:  2.3056 -  2.2263  1275   140  0.58  45.44   0.96     0.80      30905.25|
| 11:  2.2263 -  2.1569  1292   145  0.55  48.29   0.95     0.78      31804.13|
| 12:  2.1569 -  2.0954  1277   139  0.48  53.58   0.97     0.70      33578.24|
| 13:  2.0954 -  2.0404  1259   138  0.41  59.56   0.93     0.60      32570.64|
| 14:  2.0404 -  1.9907   614    72  0.37  62.19   1.00     0.48      28194.05|
|alpha:            min =        0.48 max =            0.87 mean =         0.77|
|beta:             min =    28194.05 max =        67903.67 mean =     44025.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.97 mean =        43.07|
|phase err.(test): min =        0.00 max =           89.87 mean =        43.37|
|-----------------------------------------------------------------------------|

============================== 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 = 9.739359              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.725   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.018243              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.006   (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 |  1.800 -  2.110:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.110 -  2.420:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.420 -  2.730:      170 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.730 -  3.040:     1967 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.040 -  3.350:     1838 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.350 -  3.660:     2766 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.660 -  3.970:     4591 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.970 -  4.280:     4322 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.280 -  4.590:     5584 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.590 -  4.900:     6705 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.800 |       0.190 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3962   r_free= 0.3858   ksol= 0.00   Bsol= 0.00   scale= 0.926    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.187178                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3847   r_free= 0.3748   ksol= 0.30   Bsol= 50.00   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,2.67,1.89,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.171644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.664325              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.413   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.583324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3847      final r-factor (work) = 0.2145          |
| start r-factor (free) = 0.3748      final r-factor (free) = 0.2354          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.9055 = 8.66 * 0.50 * 6.1726 + 1.00 * 0.1648                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7226 = 8.66 * 0.50 * 5.9114 + 1.00 * 0.1134                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2145      final r-factor (work) = 0.1960          |
| start r-factor (free) = 0.2354      final r-factor (free) = 0.2419          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4546 = 0.58 * 1.00 * 5.9114 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2917 = 0.58 * 1.00 * 5.6119 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.32   16.89    None  None   None       |
|    all(noH): 2823   0      0.00    66.32   16.89    None  None   None       |
|    Sol.    : 438    0      6.83    66.32   38.69    None  None   None       |
|    Mac.    : 2385   0      0.00    65.58   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.632:  418   |   5:    33.161 -  39.793:  110        |
|      1:     6.632 -  13.264: 1109   |   6:    39.793 -  46.425:  113        |
|      2:    13.264 -  19.897:  579   |   7:    46.425 -  53.058:   81        |
|      3:    19.897 -  26.529:  232   |   8:    53.058 -  59.690:   57        |
|      4:    26.529 -  33.161:  110   |   9:    59.690 -  66.322:   14        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1960 r_free = 0.2419             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1958 r_free = 0.2425             target_work(ml) = 5.619         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.2425   ksol= 0.30   Bsol= 50.00   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,2.67,1.89,0.00,0.00,0.00); trace/3= 0.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.619455                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1922   r_free= 0.2384   ksol= 0.34   Bsol= 67.07   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-0.32,-0.09,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.610562                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.116934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.244   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.304031              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.923   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1922      final r-factor (work) = 0.1535          |
| start r-factor (free) = 0.2384      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0618 = 2.12 * 0.50 * 5.6198 + 1.00 * 0.1134                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8877 = 2.12 * 0.50 * 5.5130 + 1.00 * 0.0523                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1535      final r-factor (work) = 0.1446          |
| start r-factor (free) = 0.1878      final r-factor (free) = 0.1807          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6974 = 0.30 * 1.00 * 5.5130 + 1.00 * 0.0213                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6394 = 0.30 * 1.00 * 5.3615 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    72.54   16.97    None  None   None       |
|    all(noH): 2823   0      0.88    72.54   16.97    None  None   None       |
|    Sol.    : 438    0      5.89    71.16   39.67    None  None   None       |
|    Mac.    : 2385   0      0.88    72.54   12.80    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:     0.879 -   8.044:  632   |   5:    36.707 -  43.873:   86        |
|      1:     8.044 -  15.210: 1205   |   6:    43.873 -  51.038:  102        |
|      2:    15.210 -  22.376:  422   |   7:    51.038 -  58.204:   73        |
|      3:    22.376 -  29.541:  130   |   8:    58.204 -  65.370:   46        |
|      4:    29.541 -  36.707:  115   |   9:    65.370 -  72.535:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1446 r_free = 0.1807             target_work(ml) = 5.347         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1445 r_free = 0.1807             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1445   r_free= 0.1807   ksol= 0.34   Bsol= 67.07   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-0.32,-0.09,-0.00,-0.00,-0.00); trace/3= -1.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.346009                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1446   r_free= 0.1804   ksol= 0.34   Bsol= 67.07   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.14,-0.39,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.344432                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.274008              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.618  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1446      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8289 = 3.27 * 0.50 * 5.3614 + 1.00 * 0.0523                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6853 = 3.27 * 0.50 * 5.2618 + 1.00 * 0.0718                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1621          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7931 = 0.72 * 1.00 * 5.2618 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7432 = 0.72 * 1.00 * 5.1909 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    86.40   17.01    None  None   None       |
|    all(noH): 2823   0      0.43    86.40   17.01    None  None   None       |
|    Sol.    : 438    0      1.24    82.68   40.98    None  None   None       |
|    Mac.    : 2385   0      0.43    86.40   12.60    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:     0.426 -   9.023:  911   |   5:    43.412 -  52.010:  103        |
|      1:     9.023 -  17.621: 1165   |   6:    52.010 -  60.607:   78        |
|      2:    17.621 -  26.218:  266   |   7:    60.607 -  69.204:   47        |
|      3:    26.218 -  34.815:  127   |   8:    69.204 -  77.801:   17        |
|      4:    34.815 -  43.412:  104   |   9:    77.801 -  86.398:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1621             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1167 r_free = 0.1621             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1621   ksol= 0.34   Bsol= 67.07   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.14,-0.39,-0.00,-0.00,-0.00); trace/3= -1.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.183102                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1614   ksol= 0.34   Bsol= 67.07   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.28,-0.31,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.181902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.181855              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.358  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.261972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.957  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7351 = 2.18 * 0.50 * 5.1913 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7091 = 2.18 * 0.50 * 5.1772 + 1.00 * 0.0612                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1612      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5437 = 1.26 * 1.00 * 5.1772 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5374 = 1.26 * 1.00 * 5.1717 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.82   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    92.82   16.84    None  None   None       |
|    Sol.    : 438    0      1.17    90.11   40.92    None  None   None       |
|    Mac.    : 2385   0      0.00    92.82   12.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.282: 1016   |   5:    46.409 -  55.691:   92        |
|      1:     9.282 -  18.564: 1127   |   6:    55.691 -  64.973:   69        |
|      2:    18.564 -  27.846:  219   |   7:    64.973 -  74.255:   36        |
|      3:    27.846 -  37.127:  138   |   8:    74.255 -  83.537:    9        |
|      4:    37.127 -  46.409:  112   |   9:    83.537 -  92.818:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1616             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1145 r_free = 0.1616             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1145   r_free= 0.1616   ksol= 0.34   Bsol= 67.07   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.46,-1.28,-0.31,-0.00,-0.00,-0.00); trace/3= -1.35                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1614   ksol= 0.32   Bsol= 62.19   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.15,-0.12,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.173663                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.769441              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.778  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.943376              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.319  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6369 = 1.77 * 0.50 * 5.1719 + 1.00 * 0.0612                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6342 = 1.77 * 0.50 * 5.1734 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8914 = 0.94 * 1.00 * 5.1734 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8920 = 0.94 * 1.00 * 5.1740 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.22   16.61    None  None   None       |
|    all(noH): 2823   0      0.00    93.22   16.61    None  None   None       |
|    Sol.    : 438    0      3.84    90.60   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    93.22   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.322: 1079   |   5:    46.608 -  55.929:   93        |
|      1:     9.322 -  18.643: 1068   |   6:    55.929 -  65.251:   66        |
|      2:    18.643 -  27.965:  220   |   7:    65.251 -  74.572:   35        |
|      3:    27.965 -  37.286:  138   |   8:    74.572 -  83.894:    8        |
|      4:    37.286 -  46.608:  111   |   9:    83.894 -  93.215:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1622             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1622             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1622   ksol= 0.32   Bsol= 62.19   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-1.15,-0.12,-0.00,-0.00,-0.00); trace/3= -1.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174512                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1407  157 0.0977 0.1310      5.3832      5.5549|
|  2:  4.7503 -  3.7905 0.99   1352  152 0.0840 0.1067        5.42      5.6242|
|  3:  3.7905 -  3.3172 0.99   1331  149 0.1047 0.1487      5.4671      5.8304|
|  4:  3.3172 -  3.0166 0.99   1320  137 0.1232 0.1659      5.4653      5.6395|
|  5:  3.0166 -  2.8019 0.99   1308  150 0.1371 0.1694      5.3625      5.5343|
|  6:  2.8019 -  2.6377 0.98   1304  145 0.1302 0.2188      5.2566      5.5538|
|  7:  2.6377 -  2.5062 0.99   1293  150 0.1286 0.1658      5.1922      5.3378|
|  8:  2.5062 -  2.3976 0.98   1305  139 0.1158 0.1696      5.1041      5.3556|
|  9:  2.3976 -  2.3056 0.98   1293  146 0.1222 0.1971      5.0623      5.3917|
| 10:  2.3056 -  2.2263 0.98   1275  140 0.1191 0.1696      5.0125      5.1851|
| 11:  2.2263 -  2.1569 0.99   1292  145 0.1191 0.1864      4.9572      5.2934|
| 12:  2.1569 -  2.0954 0.98   1277  139 0.1158 0.1819      4.9052      5.2192|
| 13:  2.0954 -  2.0404 0.97   1259  138 0.1185 0.1763       4.825      5.0537|
| 14:  2.0404 -  1.9907 0.48    614   72 0.1072 0.1875      4.7411      5.0117|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1407   157  0.94   9.35   0.96     0.94       7400.46|
|  2:  4.7503 -  3.7905  1352   152  0.95   7.94   1.00     0.99       8845.53|
|  3:  3.7905 -  3.3172  1331   149  0.94  11.17   1.02     1.01      10331.68|
|  4:  3.3172 -  3.0166  1320   137  0.92  13.84   1.00     0.98      10610.95|
|  5:  3.0166 -  2.8019  1308   150  0.89  16.62   0.99     0.96       9000.11|
|  6:  2.8019 -  2.6377  1304   145  0.89  17.36   0.97     0.95       7754.60|
|  7:  2.6377 -  2.5062  1293   150  0.90  16.00   0.98     0.95       6520.64|
|  8:  2.5062 -  2.3976  1305   139  0.90  15.80   0.98     0.95       5937.90|
|  9:  2.3976 -  2.3056  1293   146  0.90  16.47   0.98     0.93       5283.15|
| 10:  2.3056 -  2.2263  1275   140  0.89  16.98   0.98     0.94       5014.93|
| 11:  2.2263 -  2.1569  1292   145  0.90  16.25   0.97     0.93       4472.38|
| 12:  2.1569 -  2.0954  1277   139  0.90  16.09   0.99     0.98       4204.31|
| 13:  2.0954 -  2.0404  1259   138  0.89  17.17   0.97     0.95       3631.90|
| 14:  2.0404 -  1.9907   614    72  0.91  15.71   0.94     0.89       2964.52|
|alpha:            min =        0.89 max =            1.01 mean =         0.96|
|beta:             min =     2964.52 max =        10610.95 mean =      6747.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.07 mean =        14.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1621   ksol= 0.32   Bsol= 62.19   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.97,0.10,-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: 5.174592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1621   ksol= 0.32   Bsol= 62.19   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-0.97,0.10,-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: 5.174592                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7503 0.99   1407  157 0.0977 0.1312      5.3835      5.5564|
|  2:  4.7503 -  3.7905 0.99   1352  152 0.0840 0.1067      5.4208      5.6243|
|  3:  3.7905 -  3.3172 0.99   1331  149 0.1048 0.1488      5.4674      5.8309|
|  4:  3.3172 -  3.0166 0.99   1320  137 0.1232 0.1659      5.4653      5.6394|
|  5:  3.0166 -  2.8019 0.99   1308  150 0.1371 0.1693      5.3622      5.5338|
|  6:  2.8019 -  2.6377 0.98   1304  145 0.1301 0.2187      5.2562      5.5534|
|  7:  2.6377 -  2.5062 0.99   1293  150 0.1286 0.1659      5.1922       5.338|
|  8:  2.5062 -  2.3976 0.98   1305  139 0.1158 0.1696      5.1043      5.3556|
|  9:  2.3976 -  2.3056 0.98   1293  146 0.1222 0.1971      5.0625      5.3919|
| 10:  2.3056 -  2.2263 0.98   1275  140 0.1192 0.1698      5.0126      5.1857|
| 11:  2.2263 -  2.1569 0.99   1292  145 0.1191 0.1862       4.957       5.293|
| 12:  2.1569 -  2.0954 0.98   1277  139 0.1158 0.1818      4.9049       5.219|
| 13:  2.0954 -  2.0404 0.97   1259  138 0.1185 0.1763       4.825      5.0534|
| 14:  2.0404 -  1.9907 0.48    614   72 0.1072 0.1872      4.7414      5.0112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7503  1407   157  0.94   9.36   0.96     0.94       7404.07|
|  2:  4.7503 -  3.7905  1352   152  0.95   7.94   1.00     0.99       8855.71|
|  3:  3.7905 -  3.3172  1331   149  0.94  11.18   1.02     1.02      10344.91|
|  4:  3.3172 -  3.0166  1320   137  0.92  13.85   1.01     0.99      10613.30|
|  5:  3.0166 -  2.8019  1308   150  0.89  16.62   1.00     0.97       8995.12|
|  6:  2.8019 -  2.6377  1304   145  0.89  17.36   0.98     0.95       7748.61|
|  7:  2.6377 -  2.5062  1293   150  0.90  16.00   0.99     0.96       6518.52|
|  8:  2.5062 -  2.3976  1305   139  0.90  15.81   0.99     0.96       5939.50|
|  9:  2.3976 -  2.3056  1293   146  0.90  16.47   0.99     0.94       5285.20|
| 10:  2.3056 -  2.2263  1275   140  0.89  16.98   0.99     0.95       5013.88|
| 11:  2.2263 -  2.1569  1292   145  0.90  16.25   0.98     0.94       4469.90|
| 12:  2.1569 -  2.0954  1277   139  0.90  16.09   1.00     0.99       4202.89|
| 13:  2.0954 -  2.0404  1259   138  0.89  17.17   0.98     0.96       3630.05|
| 14:  2.0404 -  1.9907   614    72  0.91  15.71   0.96     0.91       2962.09|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     2962.09 max =        10613.30 mean =      6748.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.66|
|phase err.(test): min =        0.00 max =           89.15 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.142)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.22   16.62    None  None   None       |
|    all(noH): 2823   0      0.00    93.22   16.62    None  None   None       |
|    Sol.    : 438    0      3.84    90.61   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    93.22   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.325: 1079   |   5:    46.611 -  55.932:   93        |
|      1:     9.325 -  18.646: 1068   |   6:    55.932 -  65.254:   66        |
|      2:    18.646 -  27.968:  220   |   7:    65.254 -  74.575:   35        |
|      3:    27.968 -  37.289:  138   |   8:    74.575 -  83.897:    8        |
|      4:    37.289 -  46.611:  111   |   9:    83.897 -  93.218:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.661 - 4.913
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 316
   mapped sites are within: 0.712 - 4.913

peak=    5.726 closest distance to " O   HOH Z 113 " =    2.198
peak=    5.168 closest distance to " CB  GLN A 223 " =    1.406
peak=    5.108 closest distance to " CG  PRO A  54 " =    1.372
peak=    4.905 closest distance to " CB  ARG A 190 " =    1.736
peak=    4.880 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.843 closest distance to " CG  PRO A  90 " =    1.210
peak=    4.818 closest distance to " CA  TYR A  30 " =    0.926
peak=    4.815 closest distance to " CB  ARG A 275 " =    0.966
peak=    4.787 closest distance to " CG  PRO A 280 " =    0.861
peak=    4.780 closest distance to " CB  SER A  63 " =    1.161
peak=    4.744 closest distance to " CG  PRO A 198 " =    1.236
peak=    4.743 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.567 closest distance to " C   PRO A 198 " =    1.532
peak=    4.561 closest distance to " CZ  PHE A 218 " =    1.086
peak=    4.466 closest distance to " CB  ARG A  79 " =    1.488
peak=    4.429 closest distance to " O   HOH Z 232 " =    2.331
peak=    4.389 closest distance to " O   HOH Z 234 " =    3.869
peak=    4.381 closest distance to " O   HOH Z 369 " =    2.204
peak=    4.326 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.281 closest distance to " CG  PRO A 243 " =    1.089
peak=    4.275 closest distance to " CB  PRO A  54 " =    0.937
peak=    4.250 closest distance to " O   HOH Z 298 " =    1.815
peak=    4.244 closest distance to " CA  ARG A  36 " =    1.103
peak=    4.216 closest distance to " CB  GLU A 128 " =    1.117
peak=    4.214 closest distance to " NE2 GLN A  11 " =    1.097
peak=    4.189 closest distance to " O   HOH Z 126 " =    1.889
peak=    4.176 closest distance to " O   HOH Z 142 " =    1.571
peak=    4.159 closest distance to " CD2 TRP A 179 " =    1.338
peak=    4.152 closest distance to " O   HOH Z 189 " =    2.772
peak=    4.138 closest distance to " O   HOH Z 403 " =    1.694
peak=    4.125 closest distance to " CD  ARG A 269 " =    1.004
peak=    4.098 closest distance to " CB  ASN A 148 " =    1.427
peak=    4.081 closest distance to " CE  LYS A  76 " =    0.853
peak=    4.078 closest distance to " CA  ARG A 195 " =    1.238
peak=    4.057 closest distance to " O   HOH Z  43 " =    1.963
peak=    4.022 closest distance to " CB  TRP A 266 " =    1.014
peak=    4.010 closest distance to " CA  ALA A  51 " =    0.945
peak=    4.002 closest distance to " O   HOH Z 303 " =    2.214
peak=    3.998 closest distance to " O   HOH Z 402 " =    1.447
peak=    3.988 closest distance to " O   HOH Z  40 " =    1.961
peak=    3.973 closest distance to " O   HOH Z  15 " =    2.184
peak=    3.970 closest distance to " O   HOH Z 265 " =    2.115
peak=    3.966 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.964 closest distance to " O   HOH Z 316 " =    3.105
peak=    3.950 closest distance to " O   HOH Z 362 " =    3.648
peak=    3.941 closest distance to " CB  ARG A  79 " =    1.010
peak=    3.934 closest distance to " O   HOH Z 214 " =    2.560
peak=    3.932 closest distance to " CB  TYR A 169 " =    0.739
peak=    3.926 closest distance to " CB  GLU A 277 " =    3.742
peak=    3.915 closest distance to " CD2 LEU A 297 " =    0.912
peak=    3.913 closest distance to " O   HOH Z 280 " =    2.938
peak=    3.911 closest distance to " CB  LEU A 228 " =    1.103
peak=    3.902 closest distance to " CG2 ILE A 120 " =    1.157
peak=    3.894 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.888 closest distance to " O   HOH Z 209 " =    2.280
peak=    3.886 closest distance to " NZ  LYS A 117 " =    3.167
peak=    3.880 closest distance to " O   HOH Z 158 " =    3.123
peak=    3.871 closest distance to " CZ3 TRP A 266 " =    1.121
peak=    3.860 closest distance to " O   HOH Z  21 " =    1.875
peak=    3.860 closest distance to " N   HIS A 108 " =    1.899
peak=    3.854 closest distance to " CD  LYS A 166 " =    1.297
peak=    3.853 closest distance to " CB  VAL A 202 " =    1.545
peak=    3.850 closest distance to " O   SER A  87 " =    2.227
peak=    3.835 closest distance to " CD  ARG A 159 " =    0.808
peak=    3.825 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.824 closest distance to " ND2 ASN A 249 " =    0.890
peak=    3.824 closest distance to " CG  MET A 185 " =    1.164
peak=    3.821 closest distance to " CG  ARG A  66 " =    2.496
peak=    3.820 closest distance to " O   HOH Z 412 " =    3.743
peak=    3.819 closest distance to " O   HOH Z 406 " =    1.630
peak=    3.809 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.809 closest distance to " O   HOH Z 368 " =    2.105
peak=    3.805 closest distance to " O   ASN A  74 " =    1.538
peak=    3.799 closest distance to " NH1AARG A 145 " =    1.326
peak=    3.783 closest distance to " ND2 ASN A 249 " =    1.949
peak=    3.778 closest distance to " O   THR A 251 " =    1.143
peak=    3.776 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.774 closest distance to " CA  ASN A 176 " =    1.402
peak=    3.772 closest distance to " O   HOH Z 128 " =    2.060
peak=    3.759 closest distance to " O   HOH Z 346 " =    1.661
peak=    3.755 closest distance to " O   HOH Z  59 " =    2.316
peak=    3.751 closest distance to " O   HOH Z 287 " =    1.882
peak=    3.743 closest distance to " O   HOH Z 203 " =    1.830
peak=    3.740 closest distance to " CZ  PHE A  38 " =    1.241
peak=    3.739 closest distance to " CB  ASN A  39 " =    0.858
peak=    3.739 closest distance to " O   HOH Z  19 " =    1.659
peak=    3.739 closest distance to " O   HOH Z  78 " =    1.647
peak=    3.732 closest distance to " CB  VAL A 265 " =    1.246
peak=    3.728 closest distance to " OG BSER A 134 " =    2.801
peak=    3.719 closest distance to " O   HOH Z 133 " =    2.745
peak=    3.717 closest distance to " N   ASN A  39 " =    1.284
peak=    3.710 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.706 closest distance to " O   HOH Z 258 " =    2.114
peak=    3.691 closest distance to " O   HOH Z 180 " =    2.179
peak=    3.685 closest distance to " CG1 ILE A  33 " =    1.216
peak=    3.679 closest distance to " NZ  LYS A  48 " =    1.221
peak=    3.676 closest distance to " O   HOH Z  44 " =    1.870
peak=    3.657 closest distance to " O   HOH Z 126 " =    1.904
peak=    3.647 closest distance to " CB  ASP A 124 " =    0.712
peak=    3.639 closest distance to " O   HOH Z  97 " =    1.997
peak=    3.637 closest distance to " O   ALA A 165 " =    1.442
peak=    3.635 closest distance to " CG2 VAL A 257 " =    0.833
peak=    3.633 closest distance to " NE2 GLN A  77 " =    3.363
peak=    3.630 closest distance to " O   HOH Z 371 " =    3.119
peak=    3.629 closest distance to " CB  ASN A 187 " =    1.486
peak=    3.627 closest distance to " O   HOH Z 291 " =    1.462
peak=    3.623 closest distance to " OD2 ASP A 298 " =    3.925
peak=    3.622 closest distance to " CG1BVAL A  72 " =    1.855
peak=    3.621 closest distance to " CB  GLU A  46 " =    0.964
peak=    3.616 closest distance to " O  BHOH Z 338 " =    2.244
peak=    3.615 closest distance to " O   HOH Z 359 " =    1.553
peak=    3.612 closest distance to " CB  TRP A 179 " =    1.433
peak=    3.612 closest distance to " CB  LEU A  83 " =    0.791
peak=    3.611 closest distance to " O   HOH Z 210 " =    0.804
peak=    3.606 closest distance to " O   HOH Z  80 " =    1.811
peak=    3.604 closest distance to " CA  ASN A 215 " =    1.042
peak=    3.603 closest distance to " O   HOH Z 426 " =    1.548
peak=    3.599 closest distance to " O   HOH Z 279 " =    2.185
peak=    3.597 closest distance to " O   HOH Z 365 " =    2.837
peak=    3.594 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.594 closest distance to " OG BSER A 164 " =    2.352
peak=    3.592 closest distance to " CB  ASP A 140 " =    1.042
peak=    3.590 closest distance to " O   HOH Z 383 " =    2.229
peak=    3.589 closest distance to " O   HOH Z 185 " =    1.772
peak=    3.588 closest distance to " O   HOH Z 271 " =    2.621
peak=    3.583 closest distance to " CB  PRO A  90 " =    1.035
peak=    3.579 closest distance to " NH2 ARG A 156 " =    1.185
peak=    3.574 closest distance to " O   HOH Z 421 " =    1.807
peak=    3.569 closest distance to " CA  ALA A  21 " =    1.224
peak=    3.567 closest distance to " O   THR A 220 " =    1.154
peak=    3.565 closest distance to " O   HOH Z 325 " =    2.264
peak=    3.548 closest distance to " O   HOH Z 353 " =    2.710
peak=    3.548 closest distance to " CB  ASN A 142 " =    1.109
peak=    3.545 closest distance to " CA  VAL A 125 " =    1.143
peak=    3.534 closest distance to " O   HOH Z 261 " =    1.896
peak=    3.527 closest distance to " O   HOH Z 148 " =    3.425
peak=    3.526 closest distance to " OD1 ASN A  69 " =    2.543
peak=    3.526 closest distance to " NH2BARG A 145 " =    2.141
peak=    3.526 closest distance to " O   HOH Z 285 " =    2.589
peak=    3.521 closest distance to " CG1 VAL A 153 " =    0.986
peak=    3.521 closest distance to " O   HOH Z 361 " =    2.692
peak=    3.518 closest distance to " O   HOH Z  48 " =    1.681
peak=    3.518 closest distance to " CB  THR A  31 " =    1.569
peak=    3.508 closest distance to " CG  GLU A  37 " =    0.893
peak=    3.505 closest distance to " O   HOH Z 392 " =    2.623
peak=    3.505 closest distance to " CB  ALA A 291 " =    1.200
peak=    3.499 closest distance to " CB  SER A  62 " =    0.827
peak=    3.496 closest distance to " CA  THR A 221 " =    1.027
peak=    3.494 closest distance to " CA  MET A 105 " =    1.069
peak=    3.489 closest distance to " O   HOH Z 134 " =    1.208
peak=    3.488 closest distance to " CA  SER A  87 " =    1.065
peak=    3.486 closest distance to " O   HOH Z 393 " =    3.186
peak=    3.484 closest distance to " O   HOH Z 299 " =    4.391
peak=    3.483 closest distance to " CD1 ILE A 199 " =    1.101
peak=    3.482 closest distance to " CB  ALA A 248 " =    1.330
peak=    3.476 closest distance to " O   HOH Z 345 " =    1.655
peak=    3.473 closest distance to " O   HOH Z 193 " =    1.772
peak=    3.470 closest distance to " O   HOH Z 403 " =    1.448
peak=    3.465 closest distance to " O   HOH Z 272 " =    1.864
peak=    3.465 closest distance to " O   THR A 182 " =    1.424
peak=    3.454 closest distance to " CG  GLN A  11 " =    1.462
peak=    3.453 closest distance to " O   HOH Z 227 " =    1.541
peak=    3.447 closest distance to " O   HOH Z  97 " =    2.255
peak=    3.445 closest distance to " O   HOH Z 173 " =    2.112
peak=    3.445 closest distance to " O   HOH Z 102 " =    1.235
peak=    3.440 closest distance to " NH2AARG A 275 " =    3.588
peak=    3.440 closest distance to " CG  LEU A 167 " =    1.160
peak=    3.428 closest distance to " O   HOH Z 327 " =    1.674
peak=    3.427 closest distance to " O   HOH Z 248 " =    1.628
peak=    3.425 closest distance to " CA  ALA A 295 " =    1.096
peak=    3.408 closest distance to " N   ARG A 156 " =    1.469
peak=    3.408 closest distance to " CB  GLN A  89 " =    1.314
peak=    3.407 closest distance to " CA  TYR A 116 " =    1.369
peak=    3.404 closest distance to " CG2 VAL A 197 " =    1.144
peak=    3.400 closest distance to " O   HOH Z  66 " =    2.155
peak=    3.400 closest distance to " CB  SER A   3 " =    1.303
peak=    3.400 closest distance to " O   HOH Z  61 " =    1.579
peak=    3.400 closest distance to " O   HOH Z 251 " =    1.585
peak=    3.399 closest distance to " CG AARG A 275 " =    1.180
peak=    3.395 closest distance to " O   HOH Z 357 " =    2.144
peak=    3.394 closest distance to " O   HOH Z 126 " =    1.507
peak=    3.388 closest distance to " CB  MET A  40 " =    0.883
peak=    3.369 closest distance to " O   HOH Z 128 " =    2.325
peak=    3.367 closest distance to " O   HOH Z 313 " =    1.920
peak=    3.363 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.363 closest distance to " O   HOH Z 285 " =    1.697
peak=    3.362 closest distance to " CB  SER A 141 " =    1.047
peak=    3.359 closest distance to " CB  GLN A  88 " =    1.174
peak=    3.358 closest distance to " CB  PRO A 198 " =    1.042
peak=    3.357 closest distance to " O   HOH Z 411 " =    1.699
peak=    3.357 closest distance to " CG2 ILE A  20 " =    1.323
peak=    3.355 closest distance to " CB  ASN A 215 " =    1.216
peak=    3.350 closest distance to " N   TYR A 116 " =    1.525
peak=    3.347 closest distance to " CB  TYR A 116 " =    0.776
peak=    3.346 closest distance to " CG2BVAL A  41 " =    0.870
peak=    3.343 closest distance to " CA  ALA A 154 " =    1.024
peak=    3.340 closest distance to " OG  SER A  22 " =    2.725
peak=    3.338 closest distance to " N   CYS A 260 " =    0.817
peak=    3.338 closest distance to " O   HOH Z  62 " =    2.237
peak=    3.336 closest distance to " CB  THR A  52 " =    0.740
peak=    3.332 closest distance to " O   ASP A 124 " =    1.306
peak=    3.332 closest distance to " O   HOH Z  63 " =    2.311
peak=    3.330 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.329 closest distance to " O   HOH Z 183 " =    1.502
peak=    3.328 closest distance to " O   HOH Z 298 " =    2.510
peak=    3.327 closest distance to " O   ASP A 191 " =    1.520
peak=    3.323 closest distance to " CB  TYR A 247 " =    0.955
peak=    3.323 closest distance to " O   HOH Z 247 " =    1.422
peak=    3.314 closest distance to " O   HOH Z 109 " =    2.625
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.536
peak=    3.312 closest distance to " CA  ILE A 106 " =    0.817
peak=    3.311 closest distance to " CB  ASP A 298 " =    1.180
peak=    3.307 closest distance to " N   GLY A  98 " =    1.212
peak=    3.307 closest distance to " O   HOH Z 391 " =    2.938
peak=    3.306 closest distance to " O   HOH Z 417 " =    3.020
peak=    3.304 closest distance to " O   HOH Z 171 " =    1.874
peak=    3.302 closest distance to " CA  ASP A 191 " =    1.215
peak=    3.298 closest distance to " CA  THR A 264 " =    0.922
peak=    3.289 closest distance to " CA  ASN A 217 " =    1.268
peak=    3.286 closest distance to " C   TYR A 214 " =    1.543
peak=    3.284 closest distance to " CB  GLN A 103 " =    0.858
peak=    3.282 closest distance to " CA  ALA A  84 " =    1.259
peak=    3.281 closest distance to " O   HOH Z 240 " =    2.602
peak=    3.277 closest distance to " O   HOH Z 227 " =    2.079
peak=    3.276 closest distance to " CB  PHE A 204 " =    0.723
peak=    3.275 closest distance to " OD1 ASN A 301 " =    1.550
peak=    3.269 closest distance to " CB  MET A  47 " =    0.934
peak=    3.265 closest distance to " O   HOH Z 294 " =    1.526
peak=    3.263 closest distance to " O   HOH Z 422 " =    2.670
peak=    3.263 closest distance to " CA  ALA A 248 " =    1.181
peak=    3.261 closest distance to " OG  SER A 245 " =    1.645
peak=    3.259 closest distance to " CG  PHE A 204 " =    0.804
peak=    3.258 closest distance to " N   ASN A 127 " =    1.266
peak=    3.257 closest distance to " CG2 THR A 221 " =    1.227
peak=    3.254 closest distance to " O   HOH Z  54 " =    1.663
peak=    3.251 closest distance to " CB  ARG A 138 " =    0.943
peak=    3.251 closest distance to " O   HOH Z 147 " =    1.848
peak=    3.250 closest distance to " CB  ALA A 114 " =    0.810
peak=    3.245 closest distance to " CB  SER A  26 " =    1.785
peak=    3.244 closest distance to " O   TRP A 274 " =    1.813
peak=    3.243 closest distance to " ND2 ASN A 110 " =    1.598
peak=    3.233 closest distance to " CB  MET A 105 " =    0.848
peak=    3.230 closest distance to " O   HOH Z 407 " =    2.987
peak=    3.225 closest distance to " CA  ASP A 124 " =    0.739
peak=    3.223 closest distance to " CB  TYR A 169 " =    0.799
peak=    3.223 closest distance to " O   HOH Z  68 " =    1.813
peak=    3.223 closest distance to " O   ALA A 158 " =    1.121
peak=    3.220 closest distance to " O   HOH Z 132 " =    2.732
peak=    3.219 closest distance to " CA  GLU A 152 " =    0.862
peak=    3.218 closest distance to " CB  ARG A 139 " =    1.054
peak=    3.216 closest distance to " NE2 HIS A 207 " =    1.128
peak=    3.214 closest distance to " O   HOH Z 332 " =    1.558
peak=    3.214 closest distance to " CA  ASN A 127 " =    1.233
peak=    3.209 closest distance to " OE1 GLU A 236 " =    1.067
peak=    3.209 closest distance to " CA  GLY A 241 " =    0.872
peak=    3.206 closest distance to " O   HOH Z 305 " =    3.742
peak=    3.205 closest distance to " O   TYR A 116 " =    1.423
peak=    3.201 closest distance to " OG  SER A  28 " =    1.487
peak=    3.200 closest distance to " O   HOH Z 345 " =    3.659
peak=    3.199 closest distance to " CD  ARG A  66 " =    2.429
peak=    3.197 closest distance to " N   VAL A 265 " =    1.228
peak=    3.197 closest distance to " CG1 ILE A 151 " =    1.029
peak=    3.197 closest distance to " CG1 ILE A  20 " =    1.273
peak=    3.192 closest distance to " CD1AILE A 234 " =    0.836
peak=    3.191 closest distance to " CG  ARG A 138 " =    1.193
peak=    3.187 closest distance to " O   HOH Z   1 " =    2.465
peak=    3.185 closest distance to " CA  ALA A 233 " =    1.604
peak=    3.185 closest distance to " OH  TYR A 169 " =    0.897
peak=    3.184 closest distance to " CG2 THR A 220 " =    0.758
peak=    3.182 closest distance to " CB  ALA A 227 " =    1.168
peak=    3.181 closest distance to " O   ALA A 242 " =    1.242
peak=    3.178 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.178 closest distance to " O   HOH Z 193 " =    2.115
peak=    3.177 closest distance to " N   PHE A 130 " =    1.277
peak=    3.175 closest distance to " O   HOH Z  20 " =    1.335
peak=    3.173 closest distance to " CB  PRO A 243 " =    1.435
peak=    3.173 closest distance to " O   HOH Z 380 " =    2.035
peak=    3.172 closest distance to " CA  LEU A  83 " =    1.284
peak=    3.169 closest distance to " CB  ALA A   1 " =    4.913
peak=    3.167 closest distance to " O   HOH Z 374 " =    2.692
peak=    3.167 closest distance to " O   HOH Z 199 " =    1.611
peak=    3.164 closest distance to " CA  LYS A 117 " =    1.199
peak=    3.163 closest distance to " CZ3 TRP A  85 " =    0.914
peak=    3.161 closest distance to " CG2 THR A  29 " =    1.295
peak=    3.159 closest distance to " CB  ALA A   9 " =    1.602
peak=    3.158 closest distance to " CG  ARG A 219 " =    1.118
peak=    3.155 closest distance to " CG2 VAL A 126 " =    0.755
peak=    3.153 closest distance to " NE  ARG A  79 " =    1.027
peak=    3.153 closest distance to " CB  ALA A 104 " =    0.732
peak=    3.145 closest distance to " CA  ASP A 191 " =    0.892
peak=    3.142 closest distance to " ND1 HIS A  81 " =    1.645
peak=    3.141 closest distance to " O   HOH Z 156 " =    2.622
peak=    3.140 closest distance to " CA  ALA A 100 " =    0.985
peak=    3.139 closest distance to " OG  SER A  62 " =    2.848
peak=    3.138 closest distance to " O   GLY A  91 " =    1.285
peak=    3.137 closest distance to " CB  SER A 212 " =    1.217
peak=    3.134 closest distance to " O   HOH Z 106 " =    4.004
peak=    3.127 closest distance to " CE3 TRP A 150 " =    1.092
peak=    3.121 closest distance to " CA  ALA A 158 " =    1.280
peak=    3.117 closest distance to " CD  PRO A  54 " =    1.050
peak=    3.112 closest distance to " NZ BLYS A 290 " =    0.998
peak=    3.099 closest distance to " CA  GLU A  46 " =    0.919
peak=    3.079 closest distance to " O   HOH Z 141 " =    1.661
peak=    3.070 closest distance to " CG1 ILE A 120 " =    1.018
peak=    3.068 closest distance to " O   HOH Z 392 " =    1.967
peak=    3.067 closest distance to " O  BHOH Z  74 " =    1.431
peak=    3.065 closest distance to " N   ASP A 162 " =    1.162
peak=    3.064 closest distance to " NH1AARG A 145 " =    0.987
peak=    3.062 closest distance to " CA  ARG A 156 " =    1.091
peak=    3.043 closest distance to " O   HOH Z 172 " =    3.575
peak=    3.038 closest distance to " O   HOH Z  88 " =    3.295
peak=    3.037 closest distance to " O   HOH Z 124 " =    2.279
peak=    3.030 closest distance to " O   HOH Z   9 " =    2.198
peak=    3.026 closest distance to " O   HOH Z 383 " =    1.670

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.983 - 5.996
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 204
   mapped sites are within: 0.983 - 5.996

peak=   -4.815 closest distance to " CD  GLN A  58 " =    0.985
peak=   -4.492 closest distance to " O   HOH Z 266 " =    5.254
peak=   -4.350 closest distance to " CD  ARG A  14 " =    3.400
peak=   -4.345 closest distance to " O   HOH Z 231 " =    2.359
peak=   -4.335 closest distance to " OXT GLY A 302 " =    2.921
peak=   -4.322 closest distance to " O   HOH Z  10 " =    1.573
peak=   -4.318 closest distance to " C   HIS A 108 " =    1.108
peak=   -4.315 closest distance to " CB  PRO A 243 " =    2.715
peak=   -4.175 closest distance to " O   PRO A 198 " =    1.292
peak=   -4.051 closest distance to " CD  ARG A 156 " =    2.124
peak=   -4.044 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -4.017 closest distance to " CE2 PHE A  61 " =    2.649
peak=   -4.017 closest distance to " CZ3 TRP A 179 " =    1.241
peak=   -4.016 closest distance to " CD1 LEU A 101 " =    2.445
peak=   -4.014 closest distance to " OG  SER A  97 " =    2.264
peak=   -3.989 closest distance to " O   VAL A  67 " =    2.726
peak=   -3.986 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.957 closest distance to " CG2 ILE A  49 " =    2.760
peak=   -3.936 closest distance to " CA  ASP A 298 " =    1.065
peak=   -3.934 closest distance to " CE2 TYR A  30 " =    2.700
peak=   -3.926 closest distance to " O   HOH Z 283 " =    2.348
peak=   -3.924 closest distance to " N   THR A  52 " =    1.686
peak=   -3.889 closest distance to " OD1 ASN A 148 " =    1.423
peak=   -3.887 closest distance to " O   HOH Z 377 " =    2.029
peak=   -3.882 closest distance to " O   HOH Z 196 " =    2.034
peak=   -3.880 closest distance to " OE1 GLN A 223 " =    1.926
peak=   -3.879 closest distance to " O   HOH Z 166 " =    1.758
peak=   -3.843 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.825 closest distance to " OG BSER A 134 " =    1.305
peak=   -3.817 closest distance to " CB  ALA A 161 " =    2.616
peak=   -3.817 closest distance to " CG  ASP A 132 " =    2.357
peak=   -3.812 closest distance to " CG  ARG A  66 " =    2.497
peak=   -3.800 closest distance to " CA  VAL A  67 " =    2.977
peak=   -3.796 closest distance to " CB  PHE A 192 " =    2.101
peak=   -3.776 closest distance to " O   HOH Z 290 " =    1.134
peak=   -3.766 closest distance to " CD1 PHE A  59 " =    1.995
peak=   -3.762 closest distance to " O   SER A 210 " =    1.958
peak=   -3.761 closest distance to " O   HOH Z  71 " =    2.040
peak=   -3.757 closest distance to " O   HOH Z 374 " =    1.937
peak=   -3.732 closest distance to " CG  PRO A 243 " =    1.699
peak=   -3.720 closest distance to " O   HOH Z 394 " =    1.544
peak=   -3.717 closest distance to " CE3 TRP A 150 " =    2.173
peak=   -3.705 closest distance to " O   HOH Z 348 " =    2.291
peak=   -3.694 closest distance to " O   HOH Z 198 " =    1.969
peak=   -3.693 closest distance to " CD1 ILE A 151 " =    2.400
peak=   -3.688 closest distance to " O   PRO A 163 " =    2.110
peak=   -3.680 closest distance to " O   ALA A  34 " =    2.316
peak=   -3.667 closest distance to " O   PHE A 218 " =    1.515
peak=   -3.667 closest distance to " O   HOH Z 372 " =    2.388
peak=   -3.661 closest distance to " CD  GLN A 223 " =    1.478
peak=   -3.658 closest distance to " O   HOH Z  13 " =    1.819
peak=   -3.645 closest distance to " O   HOH Z 292 " =    4.695
peak=   -3.638 closest distance to " ND2 ASN A 187 " =    1.599
peak=   -3.637 closest distance to " ND2 ASN A  45 " =    1.900
peak=   -3.631 closest distance to " CG  GLU A  53 " =    1.411
peak=   -3.618 closest distance to " N   ALA A  43 " =    2.618
peak=   -3.610 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.593 closest distance to " O   HOH Z 171 " =    2.254
peak=   -3.568 closest distance to " O   HOH Z 150 " =    2.363
peak=   -3.562 closest distance to " CG  GLN A  11 " =    1.725
peak=   -3.560 closest distance to " CD  ARG A 195 " =    5.088
peak=   -3.557 closest distance to " C   SER A 206 " =    1.509
peak=   -3.548 closest distance to " CB  ALA A 291 " =    2.449
peak=   -3.545 closest distance to " CG  ARG A 269 " =    2.374
peak=   -3.544 closest distance to " CA  GLY A 241 " =    2.367
peak=   -3.542 closest distance to " ND2 ASN A  45 " =    1.155
peak=   -3.528 closest distance to " CZ  PHE A 155 " =    1.206
peak=   -3.527 closest distance to " CG1 VAL A 265 " =    2.328
peak=   -3.521 closest distance to " OE1 GLN A 183 " =    1.603
peak=   -3.518 closest distance to " CD  ARG A  79 " =    1.163
peak=   -3.511 closest distance to " O   HOH Z 210 " =    1.125
peak=   -3.502 closest distance to " CG1 VAL A 112 " =    2.861
peak=   -3.500 closest distance to " CZ  TYR A 169 " =    1.820
peak=   -3.498 closest distance to " O   HOH Z 264 " =    1.754
peak=   -3.497 closest distance to " ND2BASN A 224 " =    1.789
peak=   -3.482 closest distance to " CG  GLU A 277 " =    1.173
peak=   -3.481 closest distance to " NH2 ARG A  79 " =    1.569
peak=   -3.481 closest distance to " CA  GLY A 241 " =    3.215
peak=   -3.470 closest distance to " NH2 ARG A  66 " =    2.185
peak=   -3.466 closest distance to " CE BMET A  47 " =    1.814
peak=   -3.451 closest distance to " O   HOH Z 421 " =    3.721
peak=   -3.444 closest distance to " O   HOH Z 102 " =    1.532
peak=   -3.441 closest distance to " O   HOH Z   6 " =    2.254
peak=   -3.426 closest distance to " ND2 ASN A 249 " =    2.426
peak=   -3.420 closest distance to " O   ALA A  10 " =    1.761
peak=   -3.415 closest distance to " O   HOH Z 111 " =    1.804
peak=   -3.410 closest distance to " NE2 GLN A  88 " =    0.996
peak=   -3.403 closest distance to " O   HOH Z 353 " =    2.310
peak=   -3.401 closest distance to " OG BSER A 210 " =    2.076
peak=   -3.400 closest distance to " CE  MET A 105 " =    2.460
peak=   -3.389 closest distance to " O   HOH Z 407 " =    3.051
peak=   -3.387 closest distance to " N   ALA A 226 " =    2.001
peak=   -3.386 closest distance to " O   HOH Z 185 " =    2.480
peak=   -3.386 closest distance to " O   HOH Z 426 " =    1.646
peak=   -3.385 closest distance to " CG  LEU A  83 " =    2.052
peak=   -3.380 closest distance to " O   HOH Z 128 " =    2.567
peak=   -3.379 closest distance to " CB  ALA A  43 " =    2.609
peak=   -3.378 closest distance to " CB  ALA A 248 " =    2.265
peak=   -3.376 closest distance to " O   VAL A 189 " =    2.670
peak=   -3.376 closest distance to " CG2 VAL A 189 " =    2.234
peak=   -3.365 closest distance to " O   HOH Z 211 " =    1.562
peak=   -3.353 closest distance to " O   HOH Z  37 " =    1.856
peak=   -3.350 closest distance to " CZ3 TRP A 274 " =    2.436
peak=   -3.350 closest distance to " CA  GLY A 203 " =    2.383
peak=   -3.349 closest distance to " O   HOH Z  52 " =    1.623
peak=   -3.348 closest distance to " NE2 GLN A  88 " =    1.842
peak=   -3.347 closest distance to " CB  ALA A  10 " =    2.263
peak=   -3.345 closest distance to " O   HOH Z 114 " =    3.211
peak=   -3.345 closest distance to " O   HOH Z 366 " =    1.753
peak=   -3.343 closest distance to " O   HOH Z 393 " =    1.357
peak=   -3.341 closest distance to " CG1AVAL A  41 " =    2.570
peak=   -3.332 closest distance to " O   GLY A 196 " =    1.138
peak=   -3.329 closest distance to " O   VAL A 174 " =    2.167
peak=   -3.329 closest distance to " OD1 ASP A 171 " =    1.554
peak=   -3.328 closest distance to " CD2 TYR A 247 " =    2.374
peak=   -3.327 closest distance to " O   HOH Z 106 " =    2.011
peak=   -3.326 closest distance to " N   ALA A 248 " =    1.717
peak=   -3.325 closest distance to " O   HOH Z   6 " =    1.579
peak=   -3.324 closest distance to " CB  TRP A  85 " =    2.433
peak=   -3.322 closest distance to " CG1 VAL A 125 " =    1.994
peak=   -3.322 closest distance to " N   TYR A  68 " =    3.009
peak=   -3.318 closest distance to " O   HOH Z 177 " =    1.771
peak=   -3.317 closest distance to " NH2AARG A 275 " =    5.298
peak=   -3.317 closest distance to " C   THR A 279 " =    1.162
peak=   -3.313 closest distance to " CB  ALA A 291 " =    2.156
peak=   -3.303 closest distance to " O   HOH Z 123 " =    2.466
peak=   -3.300 closest distance to " O   GLY A  17 " =    1.154
peak=   -3.297 closest distance to " OD1 ASP A 191 " =    1.547
peak=   -3.294 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.288 closest distance to " OD2 ASP A 191 " =    1.521
peak=   -3.288 closest distance to " CG  GLN A  58 " =    1.152
peak=   -3.284 closest distance to " CD  ARG A 139 " =    1.596
peak=   -3.281 closest distance to " N   SER A 276 " =    1.466
peak=   -3.281 closest distance to " O   HOH Z  78 " =    1.838
peak=   -3.280 closest distance to " ND2 ASN A  69 " =    1.806
peak=   -3.276 closest distance to " OG BSER A 134 " =    2.003
peak=   -3.275 closest distance to " O   SER A 271 " =    2.110
peak=   -3.272 closest distance to " N   MET A 188 " =    2.001
peak=   -3.269 closest distance to " NE  ARG A  66 " =    4.270
peak=   -3.260 closest distance to " CB  PHE A  16 " =    2.492
peak=   -3.255 closest distance to " O   HOH Z 166 " =    1.751
peak=   -3.254 closest distance to " O   HOH Z 145 " =    2.773
peak=   -3.247 closest distance to " NH2 ARG A  66 " =    3.708
peak=   -3.246 closest distance to " O   HOH Z 197 " =    2.184
peak=   -3.246 closest distance to " O   HOH Z 234 " =    4.325
peak=   -3.246 closest distance to " O   TYR A 186 " =    1.790
peak=   -3.243 closest distance to " CH2 TRP A 150 " =    1.117
peak=   -3.240 closest distance to " CD  GLU A 236 " =    1.108
peak=   -3.239 closest distance to " C   LEU A 143 " =    1.126
peak=   -3.229 closest distance to " O   HOH Z 165 " =    1.921
peak=   -3.228 closest distance to " O   HOH Z 396 " =    1.862
peak=   -3.224 closest distance to " CG  MET A 105 " =    0.983
peak=   -3.224 closest distance to " CG1 VAL A 265 " =    2.805
peak=   -3.223 closest distance to " CZ  PHE A  38 " =    1.992
peak=   -3.221 closest distance to " CG1BVAL A  41 " =    2.836
peak=   -3.221 closest distance to " NE2 GLN A 103 " =    1.828
peak=   -3.221 closest distance to " CB  ASP A 171 " =    2.482
peak=   -3.218 closest distance to " CG  TRP A 266 " =    1.934
peak=   -3.217 closest distance to " CE  MET A  93 " =    1.362
peak=   -3.214 closest distance to " CA  GLY A 133 " =    2.402
peak=   -3.212 closest distance to " CD2 LEU A 300 " =    2.900
peak=   -3.210 closest distance to " C   GLY A 262 " =    2.035
peak=   -3.205 closest distance to " O   SER A 276 " =    1.665
peak=   -3.204 closest distance to " O   HOH Z  38 " =    1.591
peak=   -3.199 closest distance to " C   THR A 264 " =    1.389
peak=   -3.195 closest distance to " CG  PHE A 283 " =    2.642
peak=   -3.194 closest distance to " CG  HIS A  86 " =    1.137
peak=   -3.189 closest distance to " O   HOH Z 156 " =    3.549
peak=   -3.186 closest distance to " O   HOH Z 191 " =    5.996
peak=   -3.183 closest distance to " O   HOH Z 150 " =    1.277
peak=   -3.178 closest distance to " ND2 ASN A  60 " =    4.083
peak=   -3.178 closest distance to " CD  LYS A 289 " =    2.409
peak=   -3.172 closest distance to " CZ  PHE A  59 " =    1.824
peak=   -3.168 closest distance to " CG2BVAL A  41 " =    1.850
peak=   -3.159 closest distance to " O   VAL A 189 " =    1.768
peak=   -3.158 closest distance to " CB  TYR A  15 " =    2.278
peak=   -3.157 closest distance to " O   HOH Z 252 " =    3.945
peak=   -3.155 closest distance to " O   HOH Z 174 " =    3.786
peak=   -3.149 closest distance to " CD  PRO A 213 " =    2.174
peak=   -3.144 closest distance to " O   ALA A 292 " =    2.157
peak=   -3.142 closest distance to " CD1 LEU A   5 " =    2.487
peak=   -3.142 closest distance to " O   GLU A 152 " =    1.373
peak=   -3.141 closest distance to " CB  ASP A 286 " =    1.876
peak=   -3.141 closest distance to " O   HOH Z 251 " =    1.686
peak=   -3.141 closest distance to " C   ALA A 158 " =    1.453
peak=   -3.140 closest distance to " CA  ILE A 263 " =    1.174
peak=   -3.137 closest distance to " O   TRP A  92 " =    1.926
peak=   -3.123 closest distance to " O   HOH Z  60 " =    1.796
peak=   -3.111 closest distance to " O   HOH Z 389 " =    1.904
peak=   -3.107 closest distance to " CD  PRO A 243 " =    2.071
peak=   -3.103 closest distance to " O   HOH Z 193 " =    1.648
peak=   -3.102 closest distance to " O   HOH Z 350 " =    2.037
peak=   -3.098 closest distance to " NE2 GLN A 223 " =    1.173
peak=   -3.093 closest distance to " O   TRP A  70 " =    1.609
peak=   -3.089 closest distance to " C   ARG A  79 " =    2.667
peak=   -3.087 closest distance to " OD1 ASN A 301 " =    2.011
peak=   -3.063 closest distance to " O   HOH Z 423 " =    2.373
peak=   -3.060 closest distance to " O   HOH Z 149 " =    2.151
peak=   -3.048 closest distance to " O   HOH Z 139 " =    4.918
peak=   -3.041 closest distance to " OE1 GLN A  88 " =    1.075
peak=   -3.027 closest distance to " O   HOH Z 287 " =    2.124
peak=   -3.017 closest distance to " O   PRO A 198 " =    1.378
peak=   -3.014 closest distance to " CA  GLY A 241 " =    2.872
peak=   -3.013 closest distance to " O   HOH Z 357 " =    2.069

================= 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    :  0.3962 0.3858   6.187178e+00   6.158409e+00
   1_bss:  0.3847 0.3748   6.171644e+00   6.139996e+00
   1_xyz:  0.2145 0.2354   5.669767e+00   5.764901e+00
   1_adp:  0.1960 0.2419   5.619660e+00   5.785955e+00
   1_occ:  0.1958 0.2425   5.619455e+00   5.786806e+00
   2_bss:  0.1922 0.2384   5.610562e+00   5.777521e+00
   2_xyz:  0.1535 0.1878   5.391623e+00   5.564151e+00
   2_adp:  0.1446 0.1807   5.346589e+00   5.530222e+00
   2_occ:  0.1445 0.1807   5.346009e+00   5.529862e+00
   3_bss:  0.1446 0.1804   5.344432e+00   5.527456e+00
   3_xyz:  0.1204 0.1644   5.206112e+00   5.429212e+00
   3_adp:  0.1168 0.1621   5.183296e+00   5.413737e+00
   3_occ:  0.1167 0.1621   5.183102e+00   5.413674e+00
   4_bss:  0.1167 0.1614   5.181902e+00   5.411091e+00
   4_xyz:  0.1152 0.1612   5.176031e+00   5.410848e+00
   4_adp:  0.1145 0.1616   5.174048e+00   5.413223e+00
   4_occ:  0.1145 0.1616   5.174043e+00   5.413459e+00
   5_bss:  0.1143 0.1614   5.173663e+00   5.413362e+00
   5_xyz:  0.1142 0.1624   5.175863e+00   5.418097e+00
   5_adp:  0.1143 0.1622   5.174559e+00   5.417596e+00
   5_occ:  0.1142 0.1622   5.174512e+00   5.417674e+00
   5_bss:  0.1141 0.1621   5.174592e+00   5.417773e+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:  0.300  50.000  -3.411   2.671   1.890   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -3.411   2.671   1.890   0.000   0.000   0.000
   1_adp:  0.300  50.000  -3.411   2.671   1.890   0.000   0.000   0.000
   1_occ:  0.300  50.000  -3.411   2.671   1.890   0.000   0.000   0.000
   2_bss:  0.336  67.065  -3.111  -0.318  -0.086  -0.000  -0.000  -0.000
   2_xyz:  0.336  67.065  -3.111  -0.318  -0.086  -0.000  -0.000  -0.000
   2_adp:  0.336  67.065  -3.111  -0.318  -0.086  -0.000  -0.000  -0.000
   2_occ:  0.336  67.065  -3.111  -0.318  -0.086  -0.000  -0.000  -0.000
   3_bss:  0.336  67.065  -2.854  -1.143  -0.385  -0.000  -0.000  -0.000
   3_xyz:  0.336  67.065  -2.854  -1.143  -0.385  -0.000  -0.000  -0.000
   3_adp:  0.336  67.065  -2.854  -1.143  -0.385  -0.000  -0.000  -0.000
   3_occ:  0.336  67.065  -2.854  -1.143  -0.385  -0.000  -0.000  -0.000
   4_bss:  0.336  67.065  -2.456  -1.278  -0.310  -0.000  -0.000  -0.000
   4_xyz:  0.336  67.065  -2.456  -1.278  -0.310  -0.000  -0.000  -0.000
   4_adp:  0.336  67.065  -2.456  -1.278  -0.310  -0.000  -0.000  -0.000
   4_occ:  0.336  67.065  -2.456  -1.278  -0.310  -0.000  -0.000  -0.000
   5_bss:  0.322  62.187  -2.165  -1.155  -0.122  -0.000  -0.000  -0.000
   5_xyz:  0.322  62.187  -2.165  -1.155  -0.122  -0.000  -0.000  -0.000
   5_adp:  0.322  62.187  -2.165  -1.155  -0.122  -0.000  -0.000  -0.000
   5_occ:  0.322  62.187  -2.165  -1.155  -0.122  -0.000  -0.000  -0.000
   5_bss:  0.320  62.190  -1.889  -0.974   0.097  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.100 0.6069  0.7667    44021.810
   1_bss:  42.039 0.6179  0.7930    40882.913
   1_xyz:  23.814 0.8242  0.9925    14750.480
   1_adp:  24.508 0.8164  0.9805    15400.071
   1_occ:  24.540 0.8160  0.9798    15429.784
   2_bss:  24.038 0.8214  0.9362    15045.744
   2_xyz:  18.132 0.8790  0.9713     9177.237
   2_adp:  17.166 0.8882  0.9669     8539.830
   2_occ:  17.153 0.8883  0.9669     8531.806
   3_bss:  17.080 0.8890  0.9584     8473.281
   3_xyz:  15.112 0.9056  0.9690     6944.444
   3_adp:  14.743 0.9089  0.9622     6774.355
   3_occ:  14.740 0.9090  0.9621     6773.104
   4_bss:  14.681 0.9094  0.9665     6721.012
   4_xyz:  14.537 0.9109  0.9664     6655.772
   4_adp:  14.549 0.9109  0.9574     6681.199
   4_occ:  14.552 0.9109  0.9573     6683.462
   5_bss:  14.548 0.9109  0.9641     6675.527
   5_xyz:  14.624 0.9103  0.9642     6756.078
   5_adp:  14.609 0.9104  0.9555     6745.744
   5_occ:  14.608 0.9104  0.9554     6746.508
   5_bss:  14.610 0.9104  0.9632     6747.473
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6480e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6480e-01
   1_xyz:   1.411  0.013  0.087 15.308  0.006  4.117   1.1340e-01
   1_adp:   1.411  0.013  0.087 15.308  0.006  4.117   1.1340e-01
   1_occ:   1.411  0.013  0.087 15.308  0.006  4.117   1.1340e-01
   2_bss:   1.411  0.013  0.087 15.308  0.006  4.117   1.1340e-01
   2_xyz:   0.940  0.006  0.067 14.344  0.004  4.130   5.2320e-02
   2_adp:   0.940  0.006  0.067 14.344  0.004  4.130   5.2320e-02
   2_occ:   0.940  0.006  0.067 14.344  0.004  4.130   5.2320e-02
   3_bss:   0.940  0.006  0.067 14.344  0.004  4.130   5.2320e-02
   3_xyz:   1.098  0.010  0.081 14.695  0.004  4.114   7.1756e-02
   3_adp:   1.098  0.010  0.081 14.695  0.004  4.114   7.1756e-02
   3_occ:   1.098  0.010  0.081 14.695  0.004  4.114   7.1756e-02
   4_bss:   1.098  0.010  0.081 14.695  0.004  4.114   7.1756e-02
   4_xyz:   1.011  0.008  0.077 14.336  0.004  4.117   6.1167e-02
   4_adp:   1.011  0.008  0.077 14.336  0.004  4.117   6.1167e-02
   4_occ:   1.011  0.008  0.077 14.336  0.004  4.117   6.1167e-02
   5_bss:   1.011  0.008  0.077 14.336  0.004  4.117   6.1167e-02
   5_xyz:   0.979  0.008  0.075 14.255  0.003  4.118   5.7177e-02
   5_adp:   0.979  0.008  0.075 14.255  0.003  4.118   5.7177e-02
   5_occ:   0.979  0.008  0.075 14.255  0.003  4.118   5.7177e-02
   5_bss:   0.979  0.008  0.075 14.255  0.003  4.118   5.7177e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.800   2.4322e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.800   2.4322e-01
   1_xyz:   8.527  0.070  0.292 86.851  0.030  2.125   2.0880e-01
   1_adp:   8.527  0.070  0.292 86.851  0.030  2.125   2.0880e-01
   1_occ:   8.527  0.070  0.292 86.851  0.030  2.125   2.0880e-01
   2_bss:   8.527  0.070  0.292 86.851  0.030  2.125   2.0880e-01
   2_xyz:   6.584  0.043  0.193 81.465  0.047  2.364   4.4556e-02
   2_adp:   6.584  0.043  0.193 81.465  0.047  2.364   4.4556e-02
   2_occ:   6.584  0.043  0.193 81.465  0.047  2.364   4.4556e-02
   3_bss:   6.584  0.043  0.193 81.465  0.047  2.364   4.4556e-02
   3_xyz:   8.453  0.046  0.277 83.936  0.035  2.333   5.2884e-02
   3_adp:   8.453  0.046  0.277 83.936  0.035  2.333   5.2884e-02
   3_occ:   8.453  0.046  0.277 83.936  0.035  2.333   5.2884e-02
   4_bss:   8.453  0.046  0.277 83.936  0.035  2.333   5.2884e-02
   4_xyz:   7.721  0.042  0.248 81.010  0.033  2.392   5.5316e-02
   4_adp:   7.721  0.042  0.248 81.010  0.033  2.392   5.5316e-02
   4_occ:   7.721  0.042  0.248 81.010  0.033  2.392   5.5316e-02
   5_bss:   7.721  0.042  0.248 81.010  0.033  2.392   5.5316e-02
   5_xyz:   7.372  0.041  0.244 82.172  0.029  2.380   3.5805e-02
   5_adp:   7.372  0.041  0.244 82.172  0.029  2.380   3.5805e-02
   5_occ:   7.372  0.041  0.244 82.172  0.029  2.380   3.5805e-02
   5_bss:   7.372  0.041  0.244 82.172  0.029  2.380   3.5805e-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:  66.32   0.00  16.89  65.58   0.00  12.89  66.32   6.83  38.69
   1_occ:  66.32   0.00  16.89  65.58   0.00  12.89  66.32   6.83  38.69
   2_bss:  66.32   0.00  16.89  65.58   0.00  12.89  66.32   6.83  38.69
   2_xyz:  66.32   0.00  16.89  65.58   0.00  12.89  66.32   6.83  38.69
   2_adp:  72.54   0.88  16.97  72.54   0.88  12.80  71.16   5.89  39.67
   2_occ:  72.54   0.88  16.97  72.54   0.88  12.80  71.16   5.89  39.67
   3_bss:  72.54   0.88  16.97  72.54   0.88  12.80  71.16   5.89  39.67
   3_xyz:  72.54   0.88  16.97  72.54   0.88  12.80  71.16   5.89  39.67
   3_adp:  86.40   0.43  17.01  86.40   0.43  12.60  82.68   1.24  40.98
   3_occ:  86.40   0.43  17.01  86.40   0.43  12.60  82.68   1.24  40.98
   4_bss:  86.40   0.43  17.01  86.40   0.43  12.60  82.68   1.24  40.98
   4_xyz:  86.40   0.43  17.01  86.40   0.43  12.60  82.68   1.24  40.98
   4_adp:  92.82   0.00  16.84  92.82   0.00  12.42  90.11   1.17  40.92
   4_occ:  92.82   0.00  16.84  92.82   0.00  12.42  90.11   1.17  40.92
   5_bss:  92.82   0.00  16.84  92.82   0.00  12.42  90.11   1.17  40.92
   5_xyz:  92.82   0.00  16.84  92.82   0.00  12.42  90.11   1.17  40.92
   5_adp:  93.22   0.00  16.61  93.22   0.00  12.19  90.60   3.84  40.72
   5_occ:  93.22   0.00  16.61  93.22   0.00  12.19  90.60   3.84  40.72
   5_bss:  93.22   0.00  16.62  93.22   0.00  12.19  90.61   3.84  40.72
------------------------------------------------------------------------
 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:    1.193    0.041    0.463
   1_adp:    1.193    0.041    0.463
   1_occ:    1.193    0.041    0.463
   2_bss:    1.193    0.041    0.463
   2_xyz:    1.032    0.053    0.486
   2_adp:    1.032    0.053    0.486
   2_occ:    1.032    0.053    0.486
   3_bss:    1.032    0.053    0.486
   3_xyz:    1.083    0.037    0.552
   3_adp:    1.083    0.037    0.552
   3_occ:    1.083    0.037    0.552
   4_bss:    1.083    0.037    0.552
   4_xyz:    1.162    0.062    0.567
   4_adp:    1.162    0.062    0.567
   4_occ:    1.162    0.062    0.567
   5_bss:    1.162    0.062    0.567
   5_xyz:    1.222    0.081    0.578
   5_adp:    1.222    0.081    0.578
   5_occ:    1.222    0.081    0.578
   5_bss:    1.222    0.081    0.578
------------------------------------------------------------------------

CPU time actual refinement: 334.34


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/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_580/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_580/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.20 
  Macro-tasks:
    bulk solvent and scale       = 38.50  
    individual site refinement   = 138.13 
    weights calculation          = 28.93  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.15 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 107.16 
    alpha_beta                      = 8.26   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.28 
    fmodel                         = 6.61   
    r_factors                      = 0.21   
    phase_errors                   = 10.65  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 252.48 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.694 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    667 calls, 106.86 s
gradients_fft:          612 calls, 102.55 s

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

# Date 2008-01-16 Time 05:10:04 PST -0800 (1200489004.77 s)
Start R-work = 0.3962, R-free = 0.3858 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1772 (no bulk solvent and anisotropic scale)

Start R-work = 0.3847, R-free = 0.3748
Final R-work = 0.1141, R-free = 0.1621