# Date 2008-01-16 Time 05:18:41 PST -0800 (1200489521.29 s)
#phil __OFF__

Command line arguments: "../679.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31259
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 679

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.1647, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00062
Completeness in resolution range: 0.968123
Completeness with d_max=infinity: 0.96507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00062
Completeness in resolution range: 0.968123
Completeness with d_max=infinity: 0.96507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2803 [2136/2160]  1920   216  10.1%
  bin  2:  4.2803 -  3.4104 [2035/2054]  1836   199   9.8%
  bin  3:  3.4104 -  2.9831 [2017/2036]  1815   202  10.0%
  bin  4:  2.9831 -  2.7121 [1989/2019]  1783   206  10.4%
  bin  5:  2.7121 -  2.5187 [1996/2015]  1801   195   9.8%
  bin  6:  2.5187 -  2.3708 [1970/1995]  1774   196   9.9%
  bin  7:  2.3708 -  2.2524 [1959/1987]  1763   196  10.0%
  bin  8:  2.2524 -  2.1547 [1975/2011]  1776   199  10.1%
  bin  9:  2.1547 -  2.0720 [1922/1964]  1728   194  10.1%
  bin 10:  2.0720 -  2.0006 [1590/1993]  1434   156   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2179
        3.04 -     3.66: 4588
        3.66 -     4.28: 8945
        4.28 -     4.90: 12282
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.834 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.013 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.063 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.097 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28002 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_679/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3008   r_free= 0.2891   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.985339                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7737 0.99   1385  153 0.2678 0.2659      6.3055      6.2308|
|  2:  4.7737 -  3.8093 0.99   1319  150 0.2254 0.2217       6.341      6.3613|
|  3:  3.8093 -  3.3337 0.99   1312  144 0.2660 0.2398      6.3121       6.274|
|  4:  3.3337 -  3.0316 0.99   1296  138 0.2773 0.2967      6.1814      6.2081|
|  5:  3.0316 -  2.8158 0.99   1274  144 0.3069 0.2439      6.0499      5.9144|
|  6:  2.8158 -  2.6508 0.99   1293  149 0.3084 0.3297      5.9638       5.958|
|  7:  2.6508 -  2.5187 0.99   1276  140 0.3141 0.2937      5.9251      5.9221|
|  8:  2.5187 -  2.4095 0.98   1273  137 0.3373 0.2934      5.9449      5.8714|
|  9:  2.4095 -  2.3171 0.98   1251  143 0.3254 0.3013      5.8559      5.8048|
| 10:  2.3171 -  2.2374 0.99   1278  139 0.3520 0.2988      5.9061      5.7458|
| 11:  2.2374 -  2.1676 0.98   1255  140 0.3516 0.3554       5.817       5.833|
| 12:  2.1676 -  2.1058 0.97   1251  140 0.3410 0.3391      5.7489      5.8747|
| 13:  2.1058 -  2.0505 1.00   1255  139 0.3528 0.3327       5.685      5.6286|
| 14:  2.0505 -  2.0006 0.72    912  103 0.3302 0.3532      5.5746      5.5983|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7737  1385   153  0.81  24.28   0.86     0.82      37535.48|
|  2:  4.7737 -  3.8093  1319   150  0.86  20.25   0.98     0.92      39191.70|
|  3:  3.8093 -  3.3337  1312   144  0.84  22.89   0.98     0.95      35721.92|
|  4:  3.3337 -  3.0316  1296   138  0.82  24.73   0.98     0.92      30422.73|
|  5:  3.0316 -  2.8158  1274   144  0.77  29.00   1.01     0.91      23984.40|
|  6:  2.8158 -  2.6508  1293   149  0.76  30.16   0.99     0.90      22342.41|
|  7:  2.6508 -  2.5187  1276   140  0.75  31.50   1.02     0.91      21078.22|
|  8:  2.5187 -  2.4095  1273   137  0.75  30.95   0.99     0.93      19856.52|
|  9:  2.4095 -  2.3171  1251   143  0.76  30.76   1.03     0.95      17680.70|
| 10:  2.3171 -  2.2374  1278   139  0.75  31.50   1.06     0.95      16372.51|
| 11:  2.2374 -  2.1676  1255   140  0.74  32.64   1.02     0.96      16881.59|
| 12:  2.1676 -  2.1058  1251   140  0.72  33.90   1.05     0.96      16750.66|
| 13:  2.1058 -  2.0505  1255   139  0.71  35.42   1.03     0.95      15380.47|
| 14:  2.0505 -  2.0006   912   103  0.71  35.30   1.06     0.92      12641.92|
|alpha:            min =        0.82 max =            0.96 mean =         0.92|
|beta:             min =    12641.92 max =        39191.70 mean =     23687.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           89.93 mean =        29.31|
|phase err.(test): min =        0.00 max =           89.17 mean =        28.78|
|-----------------------------------------------------------------------------|

============================== 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 = 4.948951              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.554   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521071              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.486   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      178 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2001 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1818 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2770 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4622 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4323 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5597 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6685 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.167 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3008   r_free= 0.2891   ksol= 0.00   Bsol= 0.00   scale= 0.971    |
|                                                                             |
| 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:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.985339                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2844   r_free= 0.2727   ksol= 0.32   Bsol= 59.35   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,-2.00,2.50,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.953875                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.468167              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.351   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303947              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.336   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2844      final r-factor (work) = 0.1568          |
| start r-factor (free) = 0.2727      final r-factor (free) = 0.1787          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4871 = 4.47 * 0.50 * 5.9640 + 1.00 * 0.1630                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6332 = 4.47 * 0.50 * 5.6229 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1568      final r-factor (work) = 0.1462          |
| start r-factor (free) = 0.1787      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7161 = 0.30 * 1.00 * 5.6229 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7447 = 0.30 * 1.00 * 5.3336 + 1.00 * 0.1235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.35   16.28    None  None   None       |
|    all(noH): 2823   0      0.00    86.35   16.28    None  None   None       |
|    Sol.    : 438    0      6.75    63.19   37.25    None  None   None       |
|    Mac.    : 2385   0      0.00    86.35   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.635:  604   |   5:    43.176 -  51.811:  101        |
|      1:     8.635 -  17.271: 1492   |   6:    51.811 -  60.447:   54        |
|      2:    17.271 -  25.906:  280   |   7:    60.447 -  69.082:    5        |
|      3:    25.906 -  34.541:  147   |   8:    69.082 -  77.717:    0        |
|      4:    34.541 -  43.176:  139   |   9:    77.717 -  86.352:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1462 r_free = 0.1783             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1457 r_free = 0.1782             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1457   r_free= 0.1782   ksol= 0.32   Bsol= 59.35   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.46,-2.00,2.50,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.333863                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1435   r_free= 0.1751   ksol= 0.33   Bsol= 65.86   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.25,-2.37,-0.19,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.320153                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.411224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.262  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659334              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.233   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1435      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8383 = 1.41 * 0.50 * 5.3389 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7650 = 1.41 * 0.50 * 5.2607 + 1.00 * 0.0530                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4927 = 0.66 * 1.00 * 5.2607 + 1.00 * 0.0241                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4268 = 0.66 * 1.00 * 5.1828 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    84.03   17.14    None  None   None       |
|    all(noH): 2823   0      0.50    84.03   17.14    None  None   None       |
|    Sol.    : 438    0      4.23    79.39   40.44    None  None   None       |
|    Mac.    : 2385   0      0.50    84.03   12.86    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:     0.499 -   8.852:  766   |   5:    42.265 -  50.618:   97        |
|      1:     8.852 -  17.205: 1279   |   6:    50.618 -  58.971:   83        |
|      2:    17.205 -  25.558:  285   |   7:    58.971 -  67.324:   52        |
|      3:    25.558 -  33.911:  127   |   8:    67.324 -  75.677:   19        |
|      4:    33.911 -  42.265:  110   |   9:    75.677 -  84.031:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1597             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1596             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1596   ksol= 0.33   Bsol= 65.86   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.25,-2.37,-0.19,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188138                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1593   ksol= 0.33   Bsol= 65.86   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.07,-0.43,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186837                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.537531              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.064  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.166607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.017  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2202 = 3.54 * 0.50 * 5.1828 + 1.00 * 0.0530                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1746 = 3.54 * 0.50 * 5.1421 + 1.00 * 0.0795                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8662 = 0.17 * 1.00 * 5.1421 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8629 = 0.17 * 1.00 * 5.1326 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    82.08   16.52    None  None   None       |
|    all(noH): 2823   0      1.71    82.08   16.52    None  None   None       |
|    Sol.    : 438    0      3.89    76.94   37.98    None  None   None       |
|    Mac.    : 2385   0      1.71    82.08   12.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.710 -   9.747: 1005   |   5:    41.894 -  49.931:   83        |
|      1:     9.747 -  17.783: 1108   |   6:    49.931 -  57.967:   77        |
|      2:    17.783 -  25.820:  243   |   7:    57.967 -  66.004:   34        |
|      3:    25.820 -  33.857:  123   |   8:    66.004 -  74.041:   13        |
|      4:    33.857 -  41.894:  134   |   9:    74.041 -  82.078:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1547             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1094 r_free = 0.1547             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1547   ksol= 0.33   Bsol= 65.86   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.73,-2.07,-0.43,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1537   ksol= 0.32   Bsol= 56.51   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.90,-0.43,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.121934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.015432              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.451  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.389  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8181 = 3.02 * 0.50 * 5.1327 + 1.00 * 0.0795                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7919 = 3.02 * 0.50 * 5.1189 + 1.00 * 0.0740                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6795 = 0.33 * 1.00 * 5.1189 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6807 = 0.33 * 1.00 * 5.1211 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    82.03   16.37    None  None   None       |
|    all(noH): 2823   0      0.84    82.03   16.37    None  None   None       |
|    Sol.    : 438    0      4.53    76.46   38.02    None  None   None       |
|    Mac.    : 2385   0      0.84    82.03   12.39    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:     0.844 -   8.963:  871   |   5:    41.439 -  49.557:   89        |
|      1:     8.963 -  17.082: 1194   |   6:    49.557 -  57.676:   77        |
|      2:    17.082 -  25.201:  279   |   7:    57.676 -  65.795:   36        |
|      3:    25.201 -  33.320:  124   |   8:    65.795 -  73.914:   14        |
|      4:    33.320 -  41.439:  136   |   9:    73.914 -  82.033:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1551             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1551             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1551   ksol= 0.32   Bsol= 56.51   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.45,-1.90,-0.43,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.123400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1551   ksol= 0.32   Bsol= 56.51   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.78,-0.35,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.123354                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.486660              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.969  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.649951              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8809 = 1.49 * 0.50 * 5.1214 + 1.00 * 0.0740                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8762 = 1.49 * 0.50 * 5.1396 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3486 = 0.65 * 1.00 * 5.1396 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3522 = 0.65 * 1.00 * 5.1435 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.98   16.33    None  None   None       |
|    all(noH): 2823   0      0.00    82.98   16.33    None  None   None       |
|    Sol.    : 438    0      5.26    76.14   38.48    None  None   None       |
|    Mac.    : 2385   0      0.00    82.98   12.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.298:  769   |   5:    41.490 -  49.788:   99        |
|      1:     8.298 -  16.596: 1252   |   6:    49.788 -  58.086:   84        |
|      2:    16.596 -  24.894:  312   |   7:    58.086 -  66.384:   34        |
|      3:    24.894 -  33.192:  129   |   8:    66.384 -  74.682:   15        |
|      4:    33.192 -  41.490:  125   |   9:    74.682 -  82.980:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1580             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1580             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1580   ksol= 0.32   Bsol= 56.51   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-1.78,-0.35,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.148976                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7737 0.99   1385  153 0.1002 0.1246      5.3897      5.4967|
|  2:  4.7737 -  3.8093 0.99   1319  150 0.0861 0.1093      5.4358      5.6307|
|  3:  3.8093 -  3.3337 0.99   1312  144 0.1041 0.1506      5.4668      5.8593|
|  4:  3.3337 -  3.0316 0.99   1296  138 0.1199 0.1495      5.4447      5.5622|
|  5:  3.0316 -  2.8158 0.99   1274  144 0.1325 0.1701      5.3311      5.5431|
|  6:  2.8158 -  2.6508 0.99   1293  149 0.1213 0.2026      5.2211      5.5269|
|  7:  2.6508 -  2.5187 0.99   1276  140 0.1271 0.1609       5.172      5.3257|
|  8:  2.5187 -  2.4095 0.98   1273  137 0.1157 0.1707      5.0786      5.3522|
|  9:  2.4095 -  2.3171 0.98   1251  143 0.1160 0.1850      5.0355       5.317|
| 10:  2.3171 -  2.2374 0.99   1278  139 0.1129 0.1707      4.9769      5.2383|
| 11:  2.2374 -  2.1676 0.98   1255  140 0.1172 0.1816      4.9655       5.231|
| 12:  2.1676 -  2.1058 0.97   1251  140 0.1152 0.1710      4.8988      5.2696|
| 13:  2.1058 -  2.0505 1.00   1255  139 0.1085 0.1781      4.8026      5.0544|
| 14:  2.0505 -  2.0006 0.72    912  103 0.1013 0.1735      4.6695      4.9501|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7737  1385   153  0.94   9.07   0.97     0.94       7101.04|
|  2:  4.7737 -  3.8093  1319   150  0.95   7.80   1.00     0.99       8788.70|
|  3:  3.8093 -  3.3337  1312   144  0.94  10.92   1.01     1.01      10051.08|
|  4:  3.3337 -  3.0316  1296   138  0.92  13.23   1.00     0.98       9991.34|
|  5:  3.0316 -  2.8158  1274   144  0.90  15.65   0.99     0.96       8281.76|
|  6:  2.8158 -  2.6508  1293   149  0.90  16.12   0.98     0.95       7218.42|
|  7:  2.6508 -  2.5187  1276   140  0.90  15.71   0.98     0.95       6272.40|
|  8:  2.5187 -  2.4095  1273   137  0.91  14.82   0.98     0.96       5353.11|
|  9:  2.4095 -  2.3171  1251   143  0.91  15.42   0.99     0.95       5118.22|
| 10:  2.3171 -  2.2374  1278   139  0.90  15.94   0.98     0.93       4469.79|
| 11:  2.2374 -  2.1676  1255   140  0.90  16.45   0.98     0.94       4630.82|
| 12:  2.1676 -  2.1058  1251   140  0.90  15.90   0.99     0.98       4123.82|
| 13:  2.1058 -  2.0505  1255   139  0.90  15.89   0.97     0.95       3506.80|
| 14:  2.0505 -  2.0006   912   103  0.92  14.59   0.95     0.91       2598.01|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2598.01 max =        10051.08 mean =      6359.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.04|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1580   ksol= 0.32   Bsol= 56.51   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.59,-0.19,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149067                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1580   ksol= 0.32   Bsol= 56.51   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.59,-0.19,-0.00,-0.00,-0.00); trace/3= -1.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149067                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7737 0.99   1385  153 0.1002 0.1247      5.3902      5.4977|
|  2:  4.7737 -  3.8093 0.99   1319  150 0.0861 0.1093      5.4362      5.6307|
|  3:  3.8093 -  3.3337 0.99   1312  144 0.1041 0.1507      5.4669      5.8597|
|  4:  3.3337 -  3.0316 0.99   1296  138 0.1199 0.1495      5.4447      5.5623|
|  5:  3.0316 -  2.8158 0.99   1274  144 0.1325 0.1701       5.331      5.5429|
|  6:  2.8158 -  2.6508 0.99   1293  149 0.1212 0.2028      5.2211       5.527|
|  7:  2.6508 -  2.5187 0.99   1276  140 0.1271 0.1609      5.1721      5.3257|
|  8:  2.5187 -  2.4095 0.98   1273  137 0.1157 0.1706      5.0787      5.3521|
|  9:  2.4095 -  2.3171 0.98   1251  143 0.1160 0.1851      5.0355       5.317|
| 10:  2.3171 -  2.2374 0.99   1278  139 0.1130 0.1706      4.9769       5.238|
| 11:  2.2374 -  2.1676 0.98   1255  140 0.1172 0.1815      4.9654      5.2306|
| 12:  2.1676 -  2.1058 0.97   1251  140 0.1152 0.1709      4.8987      5.2691|
| 13:  2.1058 -  2.0505 1.00   1255  139 0.1084 0.1782      4.8027      5.0548|
| 14:  2.0505 -  2.0006 0.72    912  103 0.1014 0.1735      4.6698        4.95|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7737  1385   153  0.94   9.08   0.97     0.94       7113.02|
|  2:  4.7737 -  3.8093  1319   150  0.95   7.81   1.00     0.99       8797.49|
|  3:  3.8093 -  3.3337  1312   144  0.94  10.92   1.02     1.01      10053.17|
|  4:  3.3337 -  3.0316  1296   138  0.92  13.23   1.00     0.99       9990.66|
|  5:  3.0316 -  2.8158  1274   144  0.90  15.65   1.00     0.96       8281.01|
|  6:  2.8158 -  2.6508  1293   149  0.90  16.11   0.98     0.96       7216.83|
|  7:  2.6508 -  2.5187  1276   140  0.90  15.71   0.98     0.96       6273.01|
|  8:  2.5187 -  2.4095  1273   137  0.91  14.83   0.99     0.97       5354.09|
|  9:  2.4095 -  2.3171  1251   143  0.91  15.42   1.00     0.96       5119.52|
| 10:  2.3171 -  2.2374  1278   139  0.90  15.94   0.99     0.94       4468.34|
| 11:  2.2374 -  2.1676  1255   140  0.90  16.45   0.99     0.95       4628.12|
| 12:  2.1676 -  2.1058  1251   140  0.90  15.90   1.00     0.99       4122.67|
| 13:  2.1058 -  2.0505  1255   139  0.90  15.89   0.98     0.96       3507.13|
| 14:  2.0505 -  2.0006   912   103  0.92  14.60   0.96     0.92       2599.50|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2599.50 max =        10053.17 mean =      6361.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.04|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.116)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.98   16.33    None  None   None       |
|    all(noH): 2823   0      0.00    82.98   16.33    None  None   None       |
|    Sol.    : 438    0      5.26    76.15   38.48    None  None   None       |
|    Mac.    : 2385   0      0.00    82.98   12.27    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 -   8.301:  769   |   5:    41.493 -  49.791:   99        |
|      1:     8.301 -  16.599: 1252   |   6:    49.791 -  58.089:   84        |
|      2:    16.599 -  24.897:  312   |   7:    58.089 -  66.387:   34        |
|      3:    24.897 -  33.195:  129   |   8:    66.387 -  74.685:   15        |
|      4:    33.195 -  41.493:  125   |   9:    74.685 -  82.983:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 290         
Filter by distance & map next to the model:
   mapped sites are within: 0.489 - 4.848
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 290
   mapped sites are within: 0.704 - 4.848

peak=    5.581 closest distance to " CB  GLN A 223 " =    1.423
peak=    5.524 closest distance to " NH2 ARG A  56 " =    2.293
peak=    5.326 closest distance to " CG  PRO A  54 " =    1.365
peak=    5.086 closest distance to " CB  ARG A 275 " =    0.940
peak=    4.883 closest distance to " O   HOH Z 126 " =    1.873
peak=    4.685 closest distance to " CB  ARG A  79 " =    1.313
peak=    4.670 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.644 closest distance to " CB  ARG A 190 " =    1.664
peak=    4.639 closest distance to " CZ  PHE A 218 " =    1.086
peak=    4.632 closest distance to " CB  SER A  63 " =    1.177
peak=    4.611 closest distance to " CB  PRO A  54 " =    0.959
peak=    4.605 closest distance to " O   HOH Z 232 " =    2.355
peak=    4.564 closest distance to " CG  PRO A 213 " =    1.198
peak=    4.556 closest distance to " CA  TYR A  30 " =    0.933
peak=    4.523 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.464 closest distance to " O   HOH Z 298 " =    1.881
peak=    4.441 closest distance to " CG  PRO A  90 " =    1.220
peak=    4.429 closest distance to " CB  LEU A 228 " =    1.103
peak=    4.381 closest distance to " NE2 GLN A  11 " =    1.073
peak=    4.368 closest distance to " O   HOH Z  15 " =    2.181
peak=    4.364 closest distance to " C   PRO A 198 " =    1.525
peak=    4.328 closest distance to " O   HOH Z 142 " =    1.643
peak=    4.320 closest distance to " CB  GLU A 152 " =    1.170
peak=    4.292 closest distance to " CB  TYR A 169 " =    0.764
peak=    4.250 closest distance to " O   HOH Z 287 " =    2.192
peak=    4.226 closest distance to " O   HOH Z  78 " =    1.660
peak=    4.224 closest distance to " O   HOH Z 369 " =    2.275
peak=    4.213 closest distance to " O   HOH Z 303 " =    2.155
peak=    4.209 closest distance to " CE  LYS A  76 " =    0.851
peak=    4.197 closest distance to " CB  ASN A 148 " =    1.414
peak=    4.164 closest distance to " CG  PRO A 243 " =    1.024
peak=    4.160 closest distance to " CG2 VAL A 257 " =    0.886
peak=    4.148 closest distance to " CA  ARG A  36 " =    1.077
peak=    4.135 closest distance to " CA  ASN A 215 " =    1.094
peak=    4.099 closest distance to " O   HOH Z 189 " =    2.704
peak=    4.098 closest distance to " OD1 ASN A  69 " =    2.571
peak=    4.097 closest distance to " CB  TRP A 266 " =    1.013
peak=    4.072 closest distance to " ND2 ASN A 187 " =    1.493
peak=    4.065 closest distance to " O   HOH Z 265 " =    2.275
peak=    4.036 closest distance to " O   HOH Z  61 " =    1.641
peak=    4.025 closest distance to " O   HOH Z  19 " =    2.426
peak=    4.015 closest distance to " O   HOH Z 158 " =    3.142
peak=    4.004 closest distance to " CB  GLU A 128 " =    1.004
peak=    4.002 closest distance to " O   HOH Z 427 " =    3.006
peak=    3.994 closest distance to " O   HOH Z  63 " =    2.085
peak=    3.987 closest distance to " CB  VAL A 265 " =    1.227
peak=    3.971 closest distance to " O   HOH Z 272 " =    1.894
peak=    3.967 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.966 closest distance to " O   HOH Z 346 " =    1.685
peak=    3.951 closest distance to " CD2 TRP A 179 " =    1.327
peak=    3.946 closest distance to " CB  GLU A 277 " =    3.677
peak=    3.941 closest distance to " O   HOH Z 250 " =    1.449
peak=    3.941 closest distance to " O   HOH Z 234 " =    3.794
peak=    3.924 closest distance to " ND2 ASN A 249 " =    0.874
peak=    3.924 closest distance to " CD1 LEU A 300 " =    1.191
peak=    3.919 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.919 closest distance to " O   HOH Z  40 " =    1.771
peak=    3.915 closest distance to " O   SER A  87 " =    2.283
peak=    3.909 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.899 closest distance to " CZ  PHE A  38 " =    1.265
peak=    3.888 closest distance to " CA  TYR A  30 " =    1.058
peak=    3.887 closest distance to " CB  ASP A 140 " =    1.028
peak=    3.884 closest distance to " CB  GLU A  46 " =    0.976
peak=    3.845 closest distance to " O   HOH Z  21 " =    1.889
peak=    3.844 closest distance to " CB  VAL A 202 " =    1.547
peak=    3.843 closest distance to " CB  ASP A 124 " =    0.704
peak=    3.843 closest distance to " O   HOH Z 147 " =    1.816
peak=    3.827 closest distance to " O   HOH Z 389 " =    1.881
peak=    3.814 closest distance to " O   HOH Z 368 " =    2.077
peak=    3.810 closest distance to " O   HOH Z 423 " =    1.955
peak=    3.798 closest distance to " NH1AARG A 145 " =    1.288
peak=    3.794 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.794 closest distance to " O   HOH Z  43 " =    1.938
peak=    3.790 closest distance to " CG2 ILE A 120 " =    1.063
peak=    3.789 closest distance to " CA  SER A  87 " =    1.049
peak=    3.784 closest distance to " O   HOH Z 214 " =    2.063
peak=    3.783 closest distance to " O   HOH Z  44 " =    2.289
peak=    3.781 closest distance to " O   HOH Z 406 " =    1.595
peak=    3.777 closest distance to " O   HOH Z 402 " =    1.399
peak=    3.750 closest distance to " CG  ARG A  66 " =    2.475
peak=    3.742 closest distance to " CD  ARG A 159 " =    0.742
peak=    3.725 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.720 closest distance to " O   HOH Z 316 " =    3.178
peak=    3.711 closest distance to " O   HOH Z 203 " =    1.701
peak=    3.707 closest distance to " O   HOH Z 392 " =    3.021
peak=    3.705 closest distance to " O   HOH Z 128 " =    2.093
peak=    3.704 closest distance to " CA  ALA A  51 " =    0.912
peak=    3.701 closest distance to " O   HOH Z 313 " =    1.981
peak=    3.696 closest distance to " CB  ASN A 142 " =    1.092
peak=    3.671 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.659 closest distance to " O   HOH Z 261 " =    1.914
peak=    3.655 closest distance to " CZ3 TRP A 266 " =    1.136
peak=    3.652 closest distance to " O   MET A 105 " =    1.924
peak=    3.652 closest distance to " CB  TRP A 179 " =    1.468
peak=    3.645 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.642 closest distance to " CG  MET A 185 " =    1.127
peak=    3.640 closest distance to " O  BHOH Z 338 " =    2.305
peak=    3.628 closest distance to " O   HOH Z 291 " =    1.553
peak=    3.622 closest distance to " NH2 ARG A 156 " =    1.176
peak=    3.615 closest distance to " CB  ALA A 291 " =    1.120
peak=    3.612 closest distance to " CG1 VAL A 153 " =    0.995
peak=    3.599 closest distance to " O   HOH Z 368 " =    3.654
peak=    3.598 closest distance to " O   HOH Z 359 " =    1.551
peak=    3.591 closest distance to " O   HOH Z 180 " =    2.169
peak=    3.589 closest distance to " O   ASN A  74 " =    1.480
peak=    3.584 closest distance to " CA  THR A 264 " =    0.896
peak=    3.583 closest distance to " O   HOH Z 403 " =    1.447
peak=    3.580 closest distance to " O   HOH Z 403 " =    1.612
peak=    3.578 closest distance to " CB  ALA A 104 " =    0.714
peak=    3.577 closest distance to " CG  GLN A  11 " =    1.565
peak=    3.577 closest distance to " CB  SER A   3 " =    1.288
peak=    3.576 closest distance to " CG1BVAL A  72 " =    1.780
peak=    3.573 closest distance to " CB  ASN A 187 " =    1.081
peak=    3.572 closest distance to " O   HOH Z 353 " =    2.643
peak=    3.565 closest distance to " CB  THR A  31 " =    1.595
peak=    3.552 closest distance to " CA  ASP A 124 " =    0.710
peak=    3.551 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.540 closest distance to " O   HOH Z 305 " =    3.667
peak=    3.538 closest distance to " CA  MET A 105 " =    1.012
peak=    3.534 closest distance to " NE2 HIS A 207 " =    1.226
peak=    3.533 closest distance to " O   HOH Z   1 " =    2.003
peak=    3.533 closest distance to " N   GLY A  98 " =    1.092
peak=    3.526 closest distance to " CD2 LEU A 297 " =    0.846
peak=    3.521 closest distance to " O   HOH Z 411 " =    3.855
peak=    3.521 closest distance to " O   HOH Z 261 " =    1.722
peak=    3.513 closest distance to " CD1 ILE A 106 " =    0.840
peak=    3.511 closest distance to " O   THR A 220 " =    1.220
peak=    3.506 closest distance to " CG1 ILE A  33 " =    1.270
peak=    3.502 closest distance to " N   ASN A  39 " =    1.292
peak=    3.499 closest distance to " CB  ILE A 120 " =    1.277
peak=    3.495 closest distance to " OG BSER A 164 " =    2.340
peak=    3.493 closest distance to " O   HOH Z 172 " =    3.569
peak=    3.489 closest distance to " N   ARG A 156 " =    1.432
peak=    3.487 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.487 closest distance to " O   HOH Z 248 " =    1.668
peak=    3.486 closest distance to " O   HOH Z 371 " =    3.005
peak=    3.485 closest distance to " CE1 TYR A 186 " =    1.357
peak=    3.484 closest distance to " O   HOH Z 185 " =    1.839
peak=    3.476 closest distance to " O   HOH Z 148 " =    3.396
peak=    3.474 closest distance to " O   THR A 251 " =    1.150
peak=    3.473 closest distance to " O   HOH Z 419 " =    2.001
peak=    3.467 closest distance to " CB  TYR A 116 " =    0.766
peak=    3.458 closest distance to " CA  ASN A 217 " =    1.222
peak=    3.457 closest distance to " CG2 ILE A  20 " =    1.413
peak=    3.455 closest distance to " CG  GLU A  37 " =    0.853
peak=    3.450 closest distance to " NE2 GLN A  77 " =    3.281
peak=    3.439 closest distance to " O   HOH Z  59 " =    2.077
peak=    3.438 closest distance to " O   HOH Z   9 " =    2.128
peak=    3.435 closest distance to " O   ALA A 165 " =    1.545
peak=    3.433 closest distance to " O   HOH Z 294 " =    1.527
peak=    3.432 closest distance to " CB  MET A  47 " =    0.995
peak=    3.431 closest distance to " O   HOH Z 213 " =    1.935
peak=    3.431 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.429 closest distance to " CZ2 TRP A 179 " =    1.752
peak=    3.419 closest distance to " CB  TYR A 169 " =    0.712
peak=    3.419 closest distance to " CA  VAL A 125 " =    1.127
peak=    3.409 closest distance to " CD BLYS A 290 " =    0.950
peak=    3.409 closest distance to " CA  ALA A 291 " =    0.807
peak=    3.408 closest distance to " CB  SER A 212 " =    1.168
peak=    3.400 closest distance to " O   HOH Z 126 " =    1.614
peak=    3.399 closest distance to " CA  TYR A 116 " =    1.427
peak=    3.398 closest distance to " CA  ALA A 160 " =    0.925
peak=    3.390 closest distance to " O   HOH Z  68 " =    2.147
peak=    3.387 closest distance to " O   HOH Z  40 " =    1.431
peak=    3.383 closest distance to " CB  LEU A  83 " =    0.740
peak=    3.381 closest distance to " O   HOH Z 325 " =    2.425
peak=    3.381 closest distance to " OG  SER A  22 " =    2.699
peak=    3.378 closest distance to " O   HOH Z  10 " =    1.787
peak=    3.377 closest distance to " O   HOH Z 128 " =    2.235
peak=    3.374 closest distance to " CB  ALA A 114 " =    0.843
peak=    3.374 closest distance to " CA  THR A 221 " =    0.999
peak=    3.371 closest distance to " O   HOH Z  97 " =    1.977
peak=    3.369 closest distance to " CG  LEU A 167 " =    1.231
peak=    3.359 closest distance to " O   HOH Z 329 " =    4.015
peak=    3.358 closest distance to " CB  SER A 141 " =    1.017
peak=    3.357 closest distance to " CB  ALA A 242 " =    0.934
peak=    3.349 closest distance to " O   HOH Z 421 " =    1.879
peak=    3.346 closest distance to " O   HOH Z 426 " =    1.654
peak=    3.340 closest distance to " O   HOH Z 273 " =    2.886
peak=    3.337 closest distance to " O   HOH Z 337 " =    3.562
peak=    3.337 closest distance to " CB  GLN A  89 " =    1.295
peak=    3.334 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.334 closest distance to " NZ  LYS A  48 " =    1.238
peak=    3.332 closest distance to " CA  ASN A 127 " =    1.166
peak=    3.332 closest distance to " O   ASP A 124 " =    1.066
peak=    3.329 closest distance to " O   HOH Z  14 " =    2.251
peak=    3.329 closest distance to " O   HOH Z 234 " =    1.901
peak=    3.325 closest distance to " CB  GLN A  88 " =    1.173
peak=    3.325 closest distance to " CB  PRO A  90 " =    1.115
peak=    3.322 closest distance to " CA  ALA A  21 " =    1.163
peak=    3.318 closest distance to " O   HOH Z 425 " =    1.953
peak=    3.315 closest distance to " CA  ALA A  84 " =    1.224
peak=    3.310 closest distance to " O   TRP A 274 " =    1.836
peak=    3.309 closest distance to " CB  ARG A 139 " =    0.939
peak=    3.305 closest distance to " CA  ALA A 233 " =    1.491
peak=    3.304 closest distance to " OG1 THR A 294 " =    2.486
peak=    3.303 closest distance to " CA  ALA A 158 " =    1.308
peak=    3.291 closest distance to " O   HOH Z  62 " =    2.147
peak=    3.291 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.290 closest distance to " CB  SER A 210 " =    0.834
peak=    3.279 closest distance to " CG2 ILE A 234 " =    0.766
peak=    3.277 closest distance to " CB  SER A 273 " =    0.908
peak=    3.277 closest distance to " O   HOH Z 383 " =    1.906
peak=    3.272 closest distance to " CD1 ILE A 199 " =    0.886
peak=    3.270 closest distance to " O   HOH Z 133 " =    2.617
peak=    3.269 closest distance to " O   HOH Z  88 " =    1.896
peak=    3.266 closest distance to " O   THR A 182 " =    1.320
peak=    3.263 closest distance to " CB  SER A  62 " =    0.825
peak=    3.263 closest distance to " O   HOH Z  88 " =    3.252
peak=    3.256 closest distance to " O   HOH Z 193 " =    1.694
peak=    3.252 closest distance to " CA  ILE A 234 " =    0.936
peak=    3.252 closest distance to " O   HOH Z 285 " =    2.555
peak=    3.251 closest distance to " O   HOH Z 344 " =    3.206
peak=    3.248 closest distance to " N   TYR A 116 " =    1.545
peak=    3.246 closest distance to " CA  ASP A 162 " =    1.018
peak=    3.245 closest distance to " OG BSER A 134 " =    2.885
peak=    3.245 closest distance to " N   CYS A 260 " =    0.811
peak=    3.244 closest distance to " CG  PHE A 204 " =    0.928
peak=    3.238 closest distance to " N   ASN A 127 " =    1.255
peak=    3.238 closest distance to " CA  ASN A 176 " =    1.266
peak=    3.233 closest distance to " C   TYR A 214 " =    1.502
peak=    3.230 closest distance to " O   HOH Z  97 " =    2.478
peak=    3.226 closest distance to " CB  ALA A  34 " =    1.050
peak=    3.225 closest distance to " O   HOH Z 193 " =    2.119
peak=    3.224 closest distance to " NH2BARG A 145 " =    2.209
peak=    3.224 closest distance to " CG2 THR A 220 " =    0.868
peak=    3.223 closest distance to " CB  GLN A 103 " =    0.834
peak=    3.220 closest distance to " O   HOH Z  88 " =    2.504
peak=    3.219 closest distance to " CA  ARG A 159 " =    1.286
peak=    3.215 closest distance to " CB  LYS A 117 " =    1.227
peak=    3.214 closest distance to " CD  ARG A  66 " =    2.349
peak=    3.212 closest distance to " CA  ALA A 154 " =    0.979
peak=    3.210 closest distance to " CD1AILE A 234 " =    0.901
peak=    3.208 closest distance to " N   PHE A 130 " =    1.243
peak=    3.207 closest distance to " CG  LYS A  76 " =    0.978
peak=    3.205 closest distance to " O   HOH Z  80 " =    1.599
peak=    3.204 closest distance to " CG2 VAL A 197 " =    1.121
peak=    3.202 closest distance to " O   HOH Z 299 " =    4.405
peak=    3.201 closest distance to " CB  ALA A 248 " =    1.351
peak=    3.201 closest distance to " CG1 ILE A  49 " =    1.519
peak=    3.200 closest distance to " O   HOH Z 175 " =    2.127
peak=    3.198 closest distance to " CB  GLN A 205 " =    1.043
peak=    3.197 closest distance to " O   HOH Z 417 " =    2.032
peak=    3.185 closest distance to " CA  ALA A 248 " =    1.125
peak=    3.182 closest distance to " CB  SER A  26 " =    1.740
peak=    3.174 closest distance to " O   HOH Z 171 " =    3.990
peak=    3.172 closest distance to " CB  PRO A 198 " =    1.123
peak=    3.171 closest distance to " CB  MET A  40 " =    0.815
peak=    3.169 closest distance to " O   SER A 164 " =    1.339
peak=    3.156 closest distance to " O   HOH Z 116 " =    1.805
peak=    3.156 closest distance to " OE1 GLU A   2 " =    2.100
peak=    3.155 closest distance to " O   ALA A   1 " =    1.683
peak=    3.154 closest distance to " CG1 ILE A 151 " =    1.014
peak=    3.148 closest distance to " OG BSER A  99 " =    2.341
peak=    3.148 closest distance to " O   HOH Z 365 " =    2.858
peak=    3.146 closest distance to " CB  THR A  52 " =    0.760
peak=    3.143 closest distance to " ND1 HIS A  81 " =    1.688
peak=    3.138 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.136 closest distance to " CB  ALA A  43 " =    0.790
peak=    3.132 closest distance to " O   HOH Z 407 " =    2.527
peak=    3.129 closest distance to " O   HOH Z  44 " =    1.598
peak=    3.128 closest distance to " O   TYR A 116 " =    1.452
peak=    3.127 closest distance to " N   SER A 135 " =    1.356
peak=    3.126 closest distance to " CG2 THR A 221 " =    1.115
peak=    3.126 closest distance to " NE  ARG A  79 " =    0.963
peak=    3.122 closest distance to " CB  ALA A 227 " =    1.109
peak=    3.113 closest distance to " O   HOH Z 336 " =    1.651
peak=    3.113 closest distance to " CA  ASP A 140 " =    1.228
peak=    3.109 closest distance to " O   HOH Z 285 " =    1.764
peak=    3.105 closest distance to " O   HOH Z 271 " =    2.010
peak=    3.104 closest distance to " CE  MET A 113 " =    1.688
peak=    3.104 closest distance to " CB  ALA A   1 " =    4.848
peak=    3.103 closest distance to " CA  ARG A 139 " =    0.961
peak=    3.100 closest distance to " CB  ASN A 224 " =    1.019
peak=    3.098 closest distance to " OH  TYR A  30 " =    1.077
peak=    3.093 closest distance to " O   HOH Z 371 " =    3.370
peak=    3.076 closest distance to " ND2 ASN A 110 " =    1.622
peak=    3.073 closest distance to " OE2 GLU A  53 " =    1.965
peak=    3.071 closest distance to " O   HOH Z 327 " =    1.616
peak=    3.067 closest distance to " CD1 ILE A 263 " =    1.272
peak=    3.067 closest distance to " CB  SER A 216 " =    0.846
peak=    3.063 closest distance to " N   ASP A 162 " =    1.147
peak=    3.040 closest distance to " CA  ILE A 106 " =    0.787
peak=    3.036 closest distance to " O   HOH Z 345 " =    3.261
peak=    3.022 closest distance to " CZ3 TRP A  85 " =    0.961

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.770 - 5.701
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 193
   mapped sites are within: 0.770 - 5.701

peak=   -4.831 closest distance to " CD  GLN A  58 " =    0.955
peak=   -4.602 closest distance to " O   HOH Z 266 " =    5.359
peak=   -4.512 closest distance to " CD  ARG A  14 " =    3.444
peak=   -4.482 closest distance to " CB  PRO A 243 " =    2.697
peak=   -4.444 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.325 closest distance to " C   HIS A 108 " =    1.080
peak=   -4.317 closest distance to " O   HOH Z 231 " =    2.329
peak=   -4.313 closest distance to " O   VAL A  67 " =    2.649
peak=   -4.240 closest distance to " CZ3 TRP A 179 " =    1.174
peak=   -4.103 closest distance to " O   HOH Z 198 " =    2.029
peak=   -4.060 closest distance to " OG BSER A 134 " =    1.314
peak=   -4.032 closest distance to " O   HOH Z 377 " =    2.146
peak=   -4.000 closest distance to " CB  ALA A 161 " =    2.567
peak=   -3.999 closest distance to " O   HOH Z  73 " =    2.292
peak=   -3.994 closest distance to " CG1 VAL A 112 " =    2.835
peak=   -3.990 closest distance to " O   PRO A 198 " =    1.293
peak=   -3.980 closest distance to " CA  VAL A  67 " =    2.951
peak=   -3.963 closest distance to " O   HOH Z 196 " =    2.017
peak=   -3.951 closest distance to " CD2 PHE A 192 " =    2.045
peak=   -3.938 closest distance to " OG  SER A  97 " =    2.280
peak=   -3.918 closest distance to " O   HOH Z 372 " =    2.334
peak=   -3.907 closest distance to " CG1 VAL A 112 " =    2.643
peak=   -3.892 closest distance to " CG  GLN A 223 " =    1.966
peak=   -3.864 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.864 closest distance to " CE2 TYR A  30 " =    2.702
peak=   -3.857 closest distance to " OD1 ASN A 148 " =    1.445
peak=   -3.857 closest distance to " OXT GLY A 302 " =    2.869
peak=   -3.855 closest distance to " CE2 PHE A  61 " =    2.635
peak=   -3.838 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.838 closest distance to " O   HOH Z 114 " =    3.110
peak=   -3.809 closest distance to " CG1 VAL A 265 " =    2.358
peak=   -3.795 closest distance to " O   HOH Z  10 " =    1.528
peak=   -3.777 closest distance to " N   SER A 212 " =    2.016
peak=   -3.771 closest distance to " CE  MET A 105 " =    2.463
peak=   -3.770 closest distance to " O   HOH Z 290 " =    1.187
peak=   -3.758 closest distance to " ND2 ASN A  45 " =    1.770
peak=   -3.745 closest distance to " N   ALA A  43 " =    2.603
peak=   -3.733 closest distance to " CG1 VAL A 250 " =    2.662
peak=   -3.714 closest distance to " CG  ARG A 269 " =    2.526
peak=   -3.671 closest distance to " CB  ASN A  39 " =    2.350
peak=   -3.644 closest distance to " O   HOH Z 389 " =    1.898
peak=   -3.628 closest distance to " CZ  PHE A 155 " =    1.178
peak=   -3.623 closest distance to " CB  ALA A 291 " =    2.382
peak=   -3.618 closest distance to " ND2 ASN A  45 " =    1.133
peak=   -3.618 closest distance to " CB  ALA A 248 " =    2.346
peak=   -3.609 closest distance to " CD1 PHE A  59 " =    2.047
peak=   -3.599 closest distance to " CB  ALA A  43 " =    2.643
peak=   -3.597 closest distance to " O   HOH Z 185 " =    2.363
peak=   -3.593 closest distance to " CD1 LEU A 101 " =    2.404
peak=   -3.591 closest distance to " CD  GLN A 223 " =    1.253
peak=   -3.585 closest distance to " O   HOH Z 394 " =    1.518
peak=   -3.582 closest distance to " O   HOH Z 407 " =    3.140
peak=   -3.579 closest distance to " CB  ASP A 132 " =    2.349
peak=   -3.574 closest distance to " NH2AARG A 275 " =    5.329
peak=   -3.565 closest distance to " O   ALA A  10 " =    1.701
peak=   -3.564 closest distance to " O   HOH Z  60 " =    2.337
peak=   -3.556 closest distance to " O   HOH Z 211 " =    1.621
peak=   -3.554 closest distance to " CD  ARG A 139 " =    1.609
peak=   -3.553 closest distance to " CG  ARG A  66 " =    2.407
peak=   -3.552 closest distance to " ND2 ASN A 249 " =    2.422
peak=   -3.541 closest distance to " CA  GLY A 241 " =    3.270
peak=   -3.540 closest distance to " O   HOH Z 435 " =    2.829
peak=   -3.539 closest distance to " CA  GLY A 203 " =    2.441
peak=   -3.537 closest distance to " NE2 GLN A  88 " =    1.884
peak=   -3.535 closest distance to " CD  ARG A 195 " =    5.131
peak=   -3.530 closest distance to " O   HOH Z 166 " =    1.992
peak=   -3.527 closest distance to " NE2 GLN A 194 " =    1.898
peak=   -3.525 closest distance to " CG  GLU A 277 " =    1.189
peak=   -3.521 closest distance to " N   THR A  52 " =    1.688
peak=   -3.521 closest distance to " CD  GLU A 236 " =    1.104
peak=   -3.517 closest distance to " OD1 ASP A 171 " =    1.559
peak=   -3.506 closest distance to " NH2 ARG A  79 " =    1.509
peak=   -3.504 closest distance to " CZ  TYR A 169 " =    1.780
peak=   -3.504 closest distance to " O   HOH Z 351 " =    1.491
peak=   -3.503 closest distance to " O   HOH Z 348 " =    2.241
peak=   -3.491 closest distance to " O   HOH Z 353 " =    2.197
peak=   -3.486 closest distance to " N   ALA A 248 " =    1.672
peak=   -3.481 closest distance to " CG2 ILE A  49 " =    2.728
peak=   -3.479 closest distance to " CG  GLN A  11 " =    1.686
peak=   -3.476 closest distance to " O   PHE A 218 " =    1.549
peak=   -3.472 closest distance to " CG  HIS A  86 " =    1.131
peak=   -3.470 closest distance to " OD2 ASP A 191 " =    1.497
peak=   -3.457 closest distance to " CA  GLY A 241 " =    2.350
peak=   -3.454 closest distance to " CB  ALA A 248 " =    2.218
peak=   -3.451 closest distance to " CB  ALA A   7 " =    2.393
peak=   -3.436 closest distance to " O   HOH Z 292 " =    4.694
peak=   -3.435 closest distance to " CD1 ILE A 151 " =    2.452
peak=   -3.433 closest distance to " NH2 ARG A 159 " =    2.392
peak=   -3.427 closest distance to " O   PRO A 163 " =    2.112
peak=   -3.415 closest distance to " O   HOH Z 313 " =    1.981
peak=   -3.413 closest distance to " CG  ASP A 231 " =    0.770
peak=   -3.412 closest distance to " CB  ALA A 291 " =    2.286
peak=   -3.405 closest distance to " O   VAL A 189 " =    2.645
peak=   -3.404 closest distance to " O   HOH Z 243 " =    2.015
peak=   -3.392 closest distance to " CE BMET A  47 " =    1.635
peak=   -3.392 closest distance to " C   SER A 206 " =    1.571
peak=   -3.390 closest distance to " O   HOH Z 357 " =    2.083
peak=   -3.377 closest distance to " CG  PHE A 283 " =    2.725
peak=   -3.373 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.369 closest distance to " CA  ILE A 263 " =    1.120
peak=   -3.368 closest distance to " O   ALA A  34 " =    2.440
peak=   -3.364 closest distance to " CG1 VAL A  67 " =    3.072
peak=   -3.361 closest distance to " C   LEU A 143 " =    1.051
peak=   -3.360 closest distance to " O   HOH Z  37 " =    1.814
peak=   -3.360 closest distance to " C   MET A 188 " =    1.392
peak=   -3.353 closest distance to " O   SER A 135 " =    1.437
peak=   -3.351 closest distance to " O   HOH Z   6 " =    1.417
peak=   -3.344 closest distance to " C   GLY A 262 " =    1.911
peak=   -3.342 closest distance to " CD1 ILE A 239 " =    2.243
peak=   -3.341 closest distance to " O   HOH Z  71 " =    2.085
peak=   -3.341 closest distance to " O   HOH Z 253 " =    4.021
peak=   -3.335 closest distance to " O   SER A  95 " =    1.687
peak=   -3.330 closest distance to " CB  ASP A 286 " =    1.828
peak=   -3.327 closest distance to " O   GLY A  17 " =    1.153
peak=   -3.317 closest distance to " O   HOH Z  13 " =    1.629
peak=   -3.309 closest distance to " O   VAL A 174 " =    2.135
peak=   -3.308 closest distance to " O   VAL A 189 " =    1.630
peak=   -3.306 closest distance to " CG1 VAL A 125 " =    1.951
peak=   -3.296 closest distance to " O   HOH Z  38 " =    1.479
peak=   -3.295 closest distance to " CD2 LEU A 237 " =    2.790
peak=   -3.290 closest distance to " CE3 TRP A 150 " =    2.228
peak=   -3.289 closest distance to " OE1 GLN A  88 " =    1.119
peak=   -3.288 closest distance to " O   HOH Z  11 " =    1.650
peak=   -3.288 closest distance to " CD  ARG A  79 " =    1.154
peak=   -3.285 closest distance to " CG  LEU A  83 " =    1.980
peak=   -3.283 closest distance to " O   HOH Z 265 " =    2.355
peak=   -3.283 closest distance to " NE2 GLN A 278 " =    1.734
peak=   -3.279 closest distance to " O   HOH Z 191 " =    5.701
peak=   -3.278 closest distance to " CD2 HIS A 207 " =    2.400
peak=   -3.276 closest distance to " O   HOH Z 311 " =    3.739
peak=   -3.276 closest distance to " O   HOH Z 177 " =    1.766
peak=   -3.267 closest distance to " O   HOH Z  52 " =    1.416
peak=   -3.264 closest distance to " CZ  PHE A  59 " =    1.634
peak=   -3.264 closest distance to " O   HOH Z 298 " =    2.602
peak=   -3.264 closest distance to " CD  GLN A 223 " =    0.796
peak=   -3.258 closest distance to " O   HOH Z 134 " =    3.019
peak=   -3.255 closest distance to " CD1 LEU A   5 " =    2.540
peak=   -3.254 closest distance to " CG2 THR A 178 " =    2.357
peak=   -3.253 closest distance to " OD2 ASP A 171 " =    1.856
peak=   -3.252 closest distance to " CE3 TRP A 274 " =    2.519
peak=   -3.247 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.247 closest distance to " N   MET A 188 " =    1.903
peak=   -3.246 closest distance to " O   HOH Z 322 " =    1.648
peak=   -3.244 closest distance to " O   HOH Z 421 " =    3.236
peak=   -3.240 closest distance to " CG  PRO A 243 " =    1.769
peak=   -3.239 closest distance to " O   HOH Z  51 " =    1.786
peak=   -3.238 closest distance to " O   ALA A  34 " =    2.109
peak=   -3.230 closest distance to " CG2 VAL A 189 " =    2.190
peak=   -3.229 closest distance to " O   HOH Z  43 " =    1.633
peak=   -3.227 closest distance to " CB  PRO A 163 " =    2.478
peak=   -3.224 closest distance to " O   HOH Z 368 " =    1.710
peak=   -3.218 closest distance to " N   ALA A 226 " =    2.112
peak=   -3.216 closest distance to " O   HOH Z 298 " =    1.271
peak=   -3.215 closest distance to " OD2 ASP A 171 " =    2.471
peak=   -3.211 closest distance to " N   MET A 105 " =    2.646
peak=   -3.199 closest distance to " O   HOH Z 171 " =    1.971
peak=   -3.196 closest distance to " O   GLN A 240 " =    2.165
peak=   -3.193 closest distance to " O   HOH Z 322 " =    1.285
peak=   -3.188 closest distance to " O   LEU A 101 " =    2.167
peak=   -3.185 closest distance to " O   HOH Z 426 " =    1.589
peak=   -3.176 closest distance to " OG  SER A  62 " =    1.750
peak=   -3.170 closest distance to " OD1 ASP A 191 " =    1.622
peak=   -3.168 closest distance to " CB  TRP A  85 " =    2.566
peak=   -3.167 closest distance to " O   HOH Z 165 " =    1.956
peak=   -3.165 closest distance to " CB  PHE A  16 " =    2.562
peak=   -3.165 closest distance to " O   GLY A 211 " =    1.346
peak=   -3.165 closest distance to " C   ALA A 158 " =    1.358
peak=   -3.159 closest distance to " CD1 TRP A  70 " =    1.067
peak=   -3.150 closest distance to " O   TRP A  70 " =    1.445
peak=   -3.148 closest distance to " CB  TYR A  15 " =    2.257
peak=   -3.147 closest distance to " CA  GLY A 241 " =    2.859
peak=   -3.143 closest distance to " O   HOH Z 123 " =    2.453
peak=   -3.143 closest distance to " OG BSER A 134 " =    1.873
peak=   -3.136 closest distance to " O   HOH Z 393 " =    1.381
peak=   -3.134 closest distance to " OH  TYR A 247 " =    1.907
peak=   -3.133 closest distance to " CA  GLY A 133 " =    2.325
peak=   -3.122 closest distance to " O   HOH Z 264 " =    1.816
peak=   -3.121 closest distance to " CE2 PHE A 218 " =    2.455
peak=   -3.121 closest distance to " O   HOH Z 262 " =    2.865
peak=   -3.111 closest distance to " O   HOH Z  47 " =    1.664
peak=   -3.104 closest distance to " O   HOH Z 128 " =    2.599
peak=   -3.101 closest distance to " CG1AVAL A  41 " =    2.812
peak=   -3.096 closest distance to " O   HOH Z 377 " =    1.668
peak=   -3.090 closest distance to " CA  SER A 135 " =    1.288
peak=   -3.086 closest distance to " O   GLU A 152 " =    1.379
peak=   -3.075 closest distance to " O   HOH Z 210 " =    1.202
peak=   -3.073 closest distance to " CD1 LEU A 255 " =    2.687
peak=   -3.070 closest distance to " SG ACYS A 201 " =    1.999
peak=   -3.068 closest distance to " O   HOH Z 166 " =    1.599
peak=   -3.060 closest distance to " O   HOH Z 106 " =    1.923
peak=   -3.050 closest distance to " CB  ALA A  10 " =    2.257
peak=   -3.024 closest distance to " O   HOH Z 236 " =    1.576
peak=   -3.010 closest distance to " CG2 VAL A 189 " =    2.214

================= 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    :  0.3008 0.2891   5.985339e+00   5.955783e+00
   1_bss:  0.2844 0.2727   5.953875e+00   5.920329e+00
   1_xyz:  0.1568 0.1787   5.384889e+00   5.493738e+00
   1_adp:  0.1462 0.1783   5.335494e+00   5.502531e+00
   1_occ:  0.1457 0.1782   5.333863e+00   5.502101e+00
   2_bss:  0.1435 0.1751   5.320153e+00   5.486363e+00
   2_xyz:  0.1274 0.1577   5.214491e+00   5.390150e+00
   2_adp:  0.1209 0.1597   5.188381e+00   5.395681e+00
   2_occ:  0.1209 0.1596   5.188138e+00   5.395634e+00
   3_bss:  0.1206 0.1593   5.186837e+00   5.394557e+00
   3_xyz:  0.1095 0.1573   5.131572e+00   5.378679e+00
   3_adp:  0.1095 0.1547   5.125288e+00   5.367470e+00
   3_occ:  0.1094 0.1547   5.125180e+00   5.367713e+00
   4_bss:  0.1094 0.1537   5.121934e+00   5.361715e+00
   4_xyz:  0.1088 0.1551   5.124637e+00   5.372995e+00
   4_adp:  0.1084 0.1551   5.123246e+00   5.374709e+00
   4_occ:  0.1083 0.1551   5.123400e+00   5.375073e+00
   5_bss:  0.1083 0.1551   5.123354e+00   5.375036e+00
   5_xyz:  0.1121 0.1567   5.147409e+00   5.388082e+00
   5_adp:  0.1118 0.1580   5.148910e+00   5.394637e+00
   5_occ:  0.1117 0.1580   5.148976e+00   5.394818e+00
   5_bss:  0.1117 0.1580   5.149067e+00   5.394862e+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:  0.318  59.347  -3.458  -1.996   2.497  -0.000   0.000   0.000
   1_xyz:  0.318  59.347  -3.458  -1.996   2.497  -0.000   0.000   0.000
   1_adp:  0.318  59.347  -3.458  -1.996   2.497  -0.000   0.000   0.000
   1_occ:  0.318  59.347  -3.458  -1.996   2.497  -0.000   0.000   0.000
   2_bss:  0.335  65.857  -3.255  -2.374  -0.191  -0.000  -0.000  -0.000
   2_xyz:  0.335  65.857  -3.255  -2.374  -0.191  -0.000  -0.000  -0.000
   2_adp:  0.335  65.857  -3.255  -2.374  -0.191  -0.000  -0.000  -0.000
   2_occ:  0.335  65.857  -3.255  -2.374  -0.191  -0.000  -0.000  -0.000
   3_bss:  0.335  65.857  -2.732  -2.074  -0.429  -0.000  -0.000  -0.000
   3_xyz:  0.335  65.857  -2.732  -2.074  -0.429  -0.000  -0.000  -0.000
   3_adp:  0.335  65.857  -2.732  -2.074  -0.429  -0.000  -0.000  -0.000
   3_occ:  0.335  65.857  -2.732  -2.074  -0.429  -0.000  -0.000  -0.000
   4_bss:  0.322  56.507  -2.452  -1.904  -0.428  -0.000  -0.000  -0.000
   4_xyz:  0.322  56.507  -2.452  -1.904  -0.428  -0.000  -0.000  -0.000
   4_adp:  0.322  56.507  -2.452  -1.904  -0.428  -0.000  -0.000  -0.000
   4_occ:  0.322  56.507  -2.452  -1.904  -0.428  -0.000  -0.000  -0.000
   5_bss:  0.320  56.507  -2.286  -1.776  -0.346  -0.000  -0.000  -0.000
   5_xyz:  0.320  56.507  -2.286  -1.776  -0.346  -0.000  -0.000  -0.000
   5_adp:  0.320  56.507  -2.286  -1.776  -0.346  -0.000  -0.000  -0.000
   5_occ:  0.320  56.507  -2.286  -1.776  -0.346  -0.000  -0.000  -0.000
   5_bss:  0.319  56.510  -2.083  -1.587  -0.193  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.257 0.7699  0.9234    23685.753
   1_bss:  27.974 0.7821  0.9069    20751.187
   1_xyz:  16.306 0.8963  0.9971     8015.357
   1_adp:  16.507 0.8942  0.9915     8105.758
   1_occ:  16.501 0.8942  0.9912     8092.365
   2_bss:  16.077 0.8981  0.9628     7892.962
   2_xyz:  14.013 0.9152  0.9674     6368.680
   2_adp:  14.134 0.9142  0.9598     6372.367
   2_occ:  14.134 0.9142  0.9597     6371.288
   3_bss:  14.106 0.9144  0.9670     6364.456
   3_xyz:  13.792 0.9168  0.9704     6239.111
   3_adp:  13.531 0.9189  0.9659     6116.258
   3_occ:  13.540 0.9188  0.9658     6117.401
   4_bss:  13.430 0.9196  0.9709     5973.826
   4_xyz:  13.593 0.9185  0.9703     6126.437
   4_adp:  13.621 0.9183  0.9634     6135.792
   4_occ:  13.626 0.9183  0.9633     6139.685
   5_bss:  13.625 0.9183  0.9676     6139.349
   5_xyz:  13.846 0.9167  0.9664     6290.065
   5_adp:  13.986 0.9156  0.9587     6357.134
   5_occ:  13.989 0.9155  0.9586     6358.988
   5_bss:  13.991 0.9155  0.9649     6360.452
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6299e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6299e-01
   1_xyz:   1.119  0.010  0.073 15.189  0.004  4.123   7.1195e-02
   1_adp:   1.119  0.010  0.073 15.189  0.004  4.123   7.1195e-02
   1_occ:   1.119  0.010  0.073 15.189  0.004  4.123   7.1195e-02
   2_bss:   1.119  0.010  0.073 15.189  0.004  4.123   7.1195e-02
   2_xyz:   0.936  0.007  0.072 14.589  0.004  4.125   5.2967e-02
   2_adp:   0.936  0.007  0.072 14.589  0.004  4.125   5.2967e-02
   2_occ:   0.936  0.007  0.072 14.589  0.004  4.125   5.2967e-02
   3_bss:   0.936  0.007  0.072 14.589  0.004  4.125   5.2967e-02
   3_xyz:   1.136  0.011  0.088 14.981  0.005  4.133   7.9472e-02
   3_adp:   1.136  0.011  0.088 14.981  0.005  4.133   7.9472e-02
   3_occ:   1.136  0.011  0.088 14.981  0.005  4.133   7.9472e-02
   4_bss:   1.136  0.011  0.088 14.981  0.005  4.133   7.9472e-02
   4_xyz:   1.100  0.011  0.085 14.810  0.004  4.136   7.4032e-02
   4_adp:   1.100  0.011  0.085 14.810  0.004  4.136   7.4032e-02
   4_occ:   1.100  0.011  0.085 14.810  0.004  4.136   7.4032e-02
   5_bss:   1.100  0.011  0.085 14.810  0.004  4.136   7.4032e-02
   5_xyz:   0.960  0.007  0.076 14.523  0.004  4.134   5.5791e-02
   5_adp:   0.960  0.007  0.076 14.523  0.004  4.134   5.5791e-02
   5_occ:   0.960  0.007  0.076 14.523  0.004  4.134   5.5791e-02
   5_bss:   0.960  0.007  0.076 14.523  0.004  4.134   5.5791e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4288e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4288e-01
   1_xyz:   7.706  0.055  0.261 81.920  0.034  2.296   6.8976e-02
   1_adp:   7.706  0.055  0.261 81.920  0.034  2.296   6.8976e-02
   1_occ:   7.706  0.055  0.261 81.920  0.034  2.296   6.8976e-02
   2_bss:   7.706  0.055  0.261 81.920  0.034  2.296   6.8976e-02
   2_xyz:   6.555  0.035  0.211 82.024  0.040  2.417   3.1321e-02
   2_adp:   6.555  0.035  0.211 82.024  0.040  2.417   3.1321e-02
   2_occ:   6.555  0.035  0.211 82.024  0.040  2.417   3.1321e-02
   3_bss:   6.555  0.035  0.211 82.024  0.040  2.417   3.1321e-02
   3_xyz:   7.742  0.056  0.315 83.383  0.041  2.319   6.4250e-02
   3_adp:   7.742  0.056  0.315 83.383  0.041  2.319   6.4250e-02
   3_occ:   7.742  0.056  0.315 83.383  0.041  2.319   6.4250e-02
   4_bss:   7.742  0.056  0.315 83.383  0.041  2.319   6.4250e-02
   4_xyz:   7.683  0.057  0.279 83.160  0.038  2.276   5.6815e-02
   4_adp:   7.683  0.057  0.279 83.160  0.038  2.276   5.6815e-02
   4_occ:   7.683  0.057  0.279 83.160  0.038  2.276   5.6815e-02
   5_bss:   7.683  0.057  0.279 83.160  0.038  2.276   5.6815e-02
   5_xyz:   6.718  0.045  0.230 82.662  0.035  2.368   3.3144e-02
   5_adp:   6.718  0.045  0.230 82.662  0.035  2.368   3.3144e-02
   5_occ:   6.718  0.045  0.230 82.662  0.035  2.368   3.3144e-02
   5_bss:   6.718  0.045  0.230 82.662  0.035  2.368   3.3144e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  86.35   0.00  16.28  86.35   0.00  12.43  63.19   6.75  37.25
   1_occ:  86.35   0.00  16.28  86.35   0.00  12.43  63.19   6.75  37.25
   2_bss:  86.35   0.00  16.28  86.35   0.00  12.43  63.19   6.75  37.25
   2_xyz:  86.35   0.00  16.28  86.35   0.00  12.43  63.19   6.75  37.25
   2_adp:  84.03   0.50  17.14  84.03   0.50  12.86  79.39   4.23  40.44
   2_occ:  84.03   0.50  17.14  84.03   0.50  12.86  79.39   4.23  40.44
   3_bss:  84.03   0.50  17.14  84.03   0.50  12.86  79.39   4.23  40.44
   3_xyz:  84.03   0.50  17.14  84.03   0.50  12.86  79.39   4.23  40.44
   3_adp:  82.08   1.71  16.52  82.08   1.71  12.57  76.94   3.89  37.98
   3_occ:  82.08   1.71  16.52  82.08   1.71  12.57  76.94   3.89  37.98
   4_bss:  82.08   1.71  16.52  82.08   1.71  12.57  76.94   3.89  37.98
   4_xyz:  82.08   1.71  16.52  82.08   1.71  12.57  76.94   3.89  37.98
   4_adp:  82.03   0.84  16.37  82.03   0.84  12.39  76.46   4.53  38.02
   4_occ:  82.03   0.84  16.37  82.03   0.84  12.39  76.46   4.53  38.02
   5_bss:  82.03   0.84  16.37  82.03   0.84  12.39  76.46   4.53  38.02
   5_xyz:  82.03   0.84  16.37  82.03   0.84  12.39  76.46   4.53  38.02
   5_adp:  82.98   0.00  16.33  82.98   0.00  12.26  76.14   5.26  38.48
   5_occ:  82.98   0.00  16.33  82.98   0.00  12.26  76.14   5.26  38.48
   5_bss:  82.98   0.00  16.33  82.98   0.00  12.27  76.15   5.26  38.48
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.820    0.013    0.295
   1_adp:    0.820    0.013    0.295
   1_occ:    0.820    0.013    0.295
   2_bss:    0.820    0.013    0.295
   2_xyz:    0.770    0.020    0.312
   2_adp:    0.770    0.020    0.312
   2_occ:    0.770    0.020    0.312
   3_bss:    0.770    0.020    0.312
   3_xyz:    1.096    0.013    0.344
   3_adp:    1.096    0.013    0.344
   3_occ:    1.096    0.013    0.344
   4_bss:    1.096    0.013    0.344
   4_xyz:    1.264    0.046    0.355
   4_adp:    1.264    0.046    0.355
   4_occ:    1.264    0.046    0.355
   5_bss:    1.264    0.046    0.355
   5_xyz:    1.315    0.035    0.358
   5_adp:    1.315    0.035    0.358
   5_occ:    1.315    0.035    0.358
   5_bss:    1.315    0.035    0.358
------------------------------------------------------------------------

CPU time actual refinement: 325.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/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_679/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_679/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.92 
  Macro-tasks:
    bulk solvent and scale       = 38.09  
    individual site refinement   = 132.84 
    weights calculation          = 29.51  
    collect and process          = 6.59   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 207.13 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 103.07 
    alpha_beta                      = 7.99   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 112.27 
    fmodel                         = 6.75   
    r_factors                      = 0.16   
    phase_errors                   = 11.34  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 244.19 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.599 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    650 calls, 102.70 s
gradients_fft:          595 calls,  98.59 s

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

# Date 2008-01-16 Time 05:24:19 PST -0800 (1200489859.85 s)
Start R-work = 0.3008, R-free = 0.2891 (no bulk solvent and anisotropic scale)
Final R-work = 0.1328, R-free = 0.1758 (no bulk solvent and anisotropic scale)

Start R-work = 0.2844, R-free = 0.2727
Final R-work = 0.1117, R-free = 0.1580