# Date 2008-01-16 Time 05:33:14 PST -0800 (1200490394.18 s)
#phil __OFF__

Command line arguments: "../783.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23684
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 783

-------------------------------------------------------------------------------
  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: (70.6012, 46.93, 85.0941, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (70.6012, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97116
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9712

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: (70.6012, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97116
Completeness in resolution range: 0.95449
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2181 [2153/2181]  1941   212   9.8%
  bin  2:  4.2181 -  3.3605 [2061/2077]  1852   209  10.1%
  bin  3:  3.3605 -  2.9393 [2048/2067]  1843   205  10.0%
  bin  4:  2.9393 -  2.6722 [2035/2065]  1835   200   9.8%
  bin  5:  2.6722 -  2.4816 [2018/2037]  1818   200   9.9%
  bin  6:  2.4816 -  2.3359 [2007/2043]  1799   208  10.4%
  bin  7:  2.3359 -  2.2193 [1971/2004]  1773   198  10.0%
  bin  8:  2.2193 -  2.1230 [1997/2031]  1800   197   9.9%
  bin  9:  2.1230 -  2.0414 [1974/2002]  1777   197  10.0%
  bin 10:  2.0414 -  1.9712 [1325/2016]  1192   133  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/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: 0.11 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: 22
        2.42 -     3.04: 2202
        3.04 -     3.66: 4723
        3.66 -     4.28: 9051
        4.28 -     4.90: 12426
  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 100 " - " O   HOH Z 352 "  1.962 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.969 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.149 3.120 -x,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28419 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_783/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/model_refine_001.geo

CPU time processing inputs: 8.01


============================ 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 = 70.60125 46.93 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2862   r_free= 0.2902   ksol= 0.00   Bsol= 0.00   scale= 0.989    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.949475                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7048 0.99   1390  155 0.2701 0.2683       6.316      6.2846|
|  2:  4.7048 -  3.7537 0.99   1361  147 0.2214 0.2112      6.3127      6.2914|
|  3:  3.7537 -  3.2849 0.99   1317  151 0.2458 0.2427      6.2134      6.3356|
|  4:  3.2849 -  2.9872 0.99   1315  148 0.2475 0.2694       6.091      6.0977|
|  5:  2.9872 -  2.7745 0.99   1311  143 0.2795 0.2630      5.9838      5.9723|
|  6:  2.7745 -  2.6118 0.99   1286  145 0.3036 0.3101      5.9446      5.9548|
|  7:  2.6118 -  2.4816 0.99   1309  137 0.2938 0.2717      5.9205       5.859|
|  8:  2.4816 -  2.3740 0.98   1275  151 0.3140 0.3061      5.8777      5.8809|
|  9:  2.3740 -  2.2830 0.98   1277  144 0.3130 0.3217      5.8368      5.8109|
| 10:  2.2830 -  2.2045 0.98   1288  132 0.3159 0.3934       5.807      5.9805|
| 11:  2.2045 -  2.1357 1.00   1274  146 0.3266 0.3417      5.7763      5.8577|
| 12:  2.1357 -  2.0748 0.97   1269  140 0.3234 0.3503      5.7213      5.7806|
| 13:  2.0748 -  2.0203 0.98   1270  140 0.3301 0.3251      5.6245      5.5811|
| 14:  2.0203 -  1.9712 0.54    688   80 0.3713 0.3931      5.6638      5.6105|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7048  1390   155  0.81  24.59   0.87     0.81      38392.55|
|  2:  4.7048 -  3.7537  1361   147  0.86  20.32   0.99     0.93      38621.23|
|  3:  3.7537 -  3.2849  1317   151  0.83  23.47   1.01     0.98      36158.83|
|  4:  3.2849 -  2.9872  1315   148  0.82  25.10   1.02     0.98      31158.70|
|  5:  2.9872 -  2.7745  1311   143  0.77  29.23   1.00     0.95      26246.38|
|  6:  2.7745 -  2.6118  1286   145  0.76  30.32   1.02     0.95      22971.32|
|  7:  2.6118 -  2.4816  1309   137  0.77  29.38   1.02     0.97      20880.81|
|  8:  2.4816 -  2.3740  1275   151  0.75  31.41   1.02     0.97      20097.28|
|  9:  2.3740 -  2.2830  1277   144  0.74  32.35   1.06     0.95      19278.62|
| 10:  2.2830 -  2.2045  1288   132  0.71  35.06   1.07     0.95      20160.59|
| 11:  2.2045 -  2.1357  1274   146  0.70  35.46   1.08     0.95      18972.28|
| 12:  2.1357 -  2.0748  1269   140  0.71  35.39   1.08     0.99      18103.35|
| 13:  2.0748 -  2.0203  1270   140  0.68  37.18   1.06     0.95      15569.79|
| 14:  2.0203 -  1.9712   688    80  0.67  38.87   1.05     0.85      14187.12|
|alpha:            min =        0.81 max =            0.99 mean =         0.94|
|beta:             min =    14187.12 max =        38621.23 mean =     24883.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.97 mean =        30.18|
|phase err.(test): min =        0.00 max =           89.56 mean =        30.16|
|-----------------------------------------------------------------------------|

============================== 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 = 4.844814              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.224   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.567838              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.822   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      196 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2006 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2850 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4646 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4405 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5657 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6769 |
|-----------------------------------------------------------------------------|
|-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 |   4.112    4.900  1.806 |       0.187 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2862   r_free= 0.2902   ksol= 0.00   Bsol= 0.00   scale= 0.989    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.949475                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2684   r_free= 0.2724   ksol= 0.32   Bsol= 38.57   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.87,1.26,-0.00,0.00,0.00); trace/3= -1.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.923544                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.161392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.289   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.278135              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.715   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2684      final r-factor (work) = 0.1536          |
| start r-factor (free) = 0.2724      final r-factor (free) = 0.1777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5150 = 4.16 * 0.50 * 5.9367 + 1.00 * 0.1625                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7689 = 4.16 * 0.50 * 5.6266 + 1.00 * 0.0616                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1536      final r-factor (work) = 0.1404          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5711 = 0.28 * 1.00 * 5.6266 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4856 = 0.28 * 1.00 * 5.3139 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.16    72.03   16.92    None  None   None       |
|    all(noH): 2823   0      1.16    72.03   16.92    None  None   None       |
|    Sol.    : 438    0      7.36    66.58   38.10    None  None   None       |
|    Mac.    : 2385   0      1.16    72.03   13.03    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:     1.158 -   8.245:  547   |   5:    36.594 -  43.681:  108        |
|      1:     8.245 -  15.333: 1315   |   6:    43.681 -  50.768:  108        |
|      2:    15.333 -  22.420:  398   |   7:    50.768 -  57.856:   61        |
|      3:    22.420 -  29.507:  149   |   8:    57.856 -  64.943:   28        |
|      4:    29.507 -  36.594:  104   |   9:    64.943 -  72.030:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1404 r_free = 0.1804             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1400 r_free = 0.1804             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1400   r_free= 0.1804   ksol= 0.32   Bsol= 38.57   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.87,1.26,-0.00,0.00,0.00); trace/3= -1.40                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.321131                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1384   r_free= 0.1769   ksol= 0.33   Bsol= 45.10   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.84,-1.17,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.306129                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.125476              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.284  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.179067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.600  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1384      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1769      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7130 = 2.13 * 0.50 * 5.3178 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6147 = 2.13 * 0.50 * 5.2311 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9444 = 0.18 * 1.00 * 5.2311 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9294 = 0.18 * 1.00 * 5.1514 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.16    72.91   16.74    None  None   None       |
|    all(noH): 2823   0      2.16    72.91   16.74    None  None   None       |
|    Sol.    : 438    0      5.33    67.86   37.44    None  None   None       |
|    Mac.    : 2385   0      2.16    72.91   12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.156 -   9.231:  747   |   5:    37.531 -  44.606:  110        |
|      1:     9.231 -  16.306: 1215   |   6:    44.606 -  51.681:   95        |
|      2:    16.306 -  23.381:  339   |   7:    51.681 -  58.756:   49        |
|      3:    23.381 -  30.456:  125   |   8:    58.756 -  65.831:   19        |
|      4:    30.456 -  37.531:  117   |   9:    65.831 -  72.906:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1530             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1529             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1529   ksol= 0.33   Bsol= 45.10   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.84,-1.17,-0.00,-0.00,-0.00); trace/3= -2.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141296                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1526   ksol= 0.33   Bsol= 45.10   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.57,-1.60,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139614                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.738579              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.138  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.465655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5323 = 1.74 * 0.50 * 5.1501 + 1.00 * 0.0554                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5100 = 1.74 * 0.50 * 5.1242 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3931 = 0.47 * 1.00 * 5.1242 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3898 = 0.47 * 1.00 * 5.1148 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    77.02   16.87    None  None   None       |
|    all(noH): 2823   0      1.39    77.02   16.87    None  None   None       |
|    Sol.    : 438    0      4.98    69.87   38.41    None  None   None       |
|    Mac.    : 2385   0      1.39    77.02   12.91    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:     1.391 -   8.954:  728   |   5:    39.206 -  46.769:  114        |
|      1:     8.954 -  16.517: 1258   |   6:    46.769 -  54.332:   92        |
|      2:    16.517 -  24.080:  332   |   7:    54.332 -  61.895:   48        |
|      3:    24.080 -  31.643:  119   |   8:    61.895 -  69.458:   19        |
|      4:    31.643 -  39.206:  107   |   9:    69.458 -  77.021:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1528             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1529             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1529   ksol= 0.33   Bsol= 45.10   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.57,-1.60,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1530   ksol= 0.32   Bsol= 45.10   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.37,-1.64,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.196436              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.555  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.114482              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.299  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6724 = 2.20 * 0.50 * 5.1146 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6733 = 2.20 * 0.50 * 5.1107 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1063      final r-factor (work) = 0.1057          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7038 = 1.11 * 1.00 * 5.1107 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7029 = 1.11 * 1.00 * 5.1089 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.66    88.93   16.99    None  None   None       |
|    all(noH): 2823   0      0.66    88.93   16.99    None  None   None       |
|    Sol.    : 438    0      6.47    76.10   39.32    None  None   None       |
|    Mac.    : 2385   0      0.66    88.93   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.662 -   9.489:  917   |   5:    44.796 -  53.623:  106        |
|      1:     9.489 -  18.315: 1192   |   6:    53.623 -  62.450:   68        |
|      2:    18.315 -  27.142:  248   |   7:    62.450 -  71.277:   23        |
|      3:    27.142 -  35.969:  140   |   8:    71.277 -  80.104:    8        |
|      4:    35.969 -  44.796:  115   |   9:    80.104 -  88.931:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1057 r_free = 0.1553             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1057 r_free = 0.1553             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1553   ksol= 0.32   Bsol= 45.10   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.37,-1.64,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.114808                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1553   ksol= 0.32   Bsol= 45.10   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.12,-1.46,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.114922                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.012097              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.927  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.541023              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.661  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1056      final r-factor (work) = 0.1062          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2014 = 2.01 * 0.50 * 5.1099 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2045 = 2.01 * 0.50 * 5.1173 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1062      final r-factor (work) = 0.1063          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7777 = 0.54 * 1.00 * 5.1173 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7797 = 0.54 * 1.00 * 5.1212 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    89.33   16.82    None  None   None       |
|    all(noH): 2823   0      0.68    89.33   16.82    None  None   None       |
|    Sol.    : 438    0      6.31    76.16   39.12    None  None   None       |
|    Mac.    : 2385   0      0.68    89.33   12.73    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:     0.677 -   9.542:  977   |   5:    45.002 -  53.867:  105        |
|      1:     9.542 -  18.407: 1144   |   6:    53.867 -  62.732:   65        |
|      2:    18.407 -  27.272:  240   |   7:    62.732 -  71.597:   23        |
|      3:    27.272 -  36.137:  141   |   8:    71.597 -  80.462:    7        |
|      4:    36.137 -  45.002:  115   |   9:    80.462 -  89.327:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1063 r_free = 0.1561             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1561             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1561   ksol= 0.32   Bsol= 45.10   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.12,-1.46,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120284                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7048 0.99   1390  155 0.0963 0.1268       5.364      5.5218|
|  2:  4.7048 -  3.7537 0.99   1361  147 0.0818 0.1074      5.4097      5.5984|
|  3:  3.7537 -  3.2849 0.99   1317  151 0.1015 0.1505      5.4405      5.8503|
|  4:  3.2849 -  2.9872 0.99   1315  148 0.1144 0.1503      5.4289      5.5657|
|  5:  2.9872 -  2.7745 0.99   1311  143 0.1242 0.1820      5.2939      5.5525|
|  6:  2.7745 -  2.6118 0.99   1286  145 0.1164 0.1762      5.1839      5.4247|
|  7:  2.6118 -  2.4816 0.99   1309  137 0.1185 0.1616      5.1332      5.3594|
|  8:  2.4816 -  2.3740 0.98   1275  151 0.1079 0.1698      5.0209      5.2873|
|  9:  2.3740 -  2.2830 0.98   1277  144 0.1115 0.1836      5.0042      5.3317|
| 10:  2.2830 -  2.2045 0.98   1288  132 0.1051 0.1696       4.929      5.1988|
| 11:  2.2045 -  2.1357 1.00   1274  146 0.1102 0.1749      4.9271      5.2784|
| 12:  2.1357 -  2.0748 0.97   1269  140 0.1040 0.1612       4.849      5.0862|
| 13:  2.0748 -  2.0203 0.98   1270  140 0.1096 0.1763        4.77      5.0682|
| 14:  2.0203 -  1.9712 0.54    688   80 0.1005 0.1621      4.6406      4.8973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7048  1390   155  0.94   9.08   0.98     0.95       6945.21|
|  2:  4.7048 -  3.7537  1361   147  0.95   7.68   1.02     1.00       8693.53|
|  3:  3.7537 -  3.2849  1317   151  0.93  11.18   1.03     1.02       9983.48|
|  4:  3.2849 -  2.9872  1315   148  0.92  13.58   1.01     0.99      10278.49|
|  5:  2.9872 -  2.7745  1311   143  0.90  15.82   0.99     0.97       8102.60|
|  6:  2.7745 -  2.6118  1286   145  0.90  15.76   0.98     0.96       6944.15|
|  7:  2.6118 -  2.4816  1309   137  0.91  15.04   0.99     0.95       5927.51|
|  8:  2.4816 -  2.3740  1275   151  0.91  14.77   0.99     0.97       5054.96|
|  9:  2.3740 -  2.2830  1277   144  0.91  14.80   1.00     0.97       4794.65|
| 10:  2.2830 -  2.2045  1288   132  0.90  15.33   0.99     0.95       4233.01|
| 11:  2.2045 -  2.1357  1274   146  0.90  16.30   1.00     0.96       4367.04|
| 12:  2.1357 -  2.0748  1269   140  0.92  14.70   1.00     0.98       3872.41|
| 13:  2.0748 -  2.0203  1270   140  0.90  16.33   1.00     0.99       3314.86|
| 14:  2.0203 -  1.9712   688    80  0.91  14.57   0.98     0.95       2499.93|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2499.93 max =        10278.49 mean =      6233.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.84|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1561   ksol= 0.32   Bsol= 45.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.93,-1.28,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1062   r_free= 0.1561   ksol= 0.32   Bsol= 45.08   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.93,-1.28,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.120378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7048 0.99   1390  155 0.0963 0.1269      5.3648      5.5229|
|  2:  4.7048 -  3.7537 0.99   1361  147 0.0818 0.1073        5.41      5.5981|
|  3:  3.7537 -  3.2849 0.99   1317  151 0.1015 0.1505      5.4403      5.8503|
|  4:  3.2849 -  2.9872 0.99   1315  148 0.1144 0.1503      5.4288      5.5658|
|  5:  2.9872 -  2.7745 0.99   1311  143 0.1242 0.1820      5.2939      5.5523|
|  6:  2.7745 -  2.6118 0.99   1286  145 0.1164 0.1762       5.184      5.4249|
|  7:  2.6118 -  2.4816 0.99   1309  137 0.1185 0.1616      5.1334      5.3595|
|  8:  2.4816 -  2.3740 0.98   1275  151 0.1079 0.1698       5.021      5.2873|
|  9:  2.3740 -  2.2830 0.98   1277  144 0.1115 0.1836      5.0043      5.3317|
| 10:  2.2830 -  2.2045 0.98   1288  132 0.1051 0.1696      4.9291      5.1985|
| 11:  2.2045 -  2.1357 1.00   1274  146 0.1101 0.1749      4.9271      5.2785|
| 12:  2.1357 -  2.0748 0.97   1269  140 0.1040 0.1613      4.8489      5.0863|
| 13:  2.0748 -  2.0203 0.98   1270  140 0.1097 0.1763      4.7699      5.0678|
| 14:  2.0203 -  1.9712 0.54    688   80 0.1005 0.1621      4.6407      4.8976|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7048  1390   155  0.94   9.09   0.98     0.95       6958.36|
|  2:  4.7048 -  3.7537  1361   147  0.95   7.68   1.02     1.01       8700.49|
|  3:  3.7537 -  3.2849  1317   151  0.93  11.18   1.03     1.03       9981.62|
|  4:  3.2849 -  2.9872  1315   148  0.92  13.58   1.01     1.00      10277.20|
|  5:  2.9872 -  2.7745  1311   143  0.90  15.82   1.00     0.97       8103.17|
|  6:  2.7745 -  2.6118  1286   145  0.90  15.76   0.99     0.97       6944.99|
|  7:  2.6118 -  2.4816  1309   137  0.91  15.04   0.99     0.96       5928.54|
|  8:  2.4816 -  2.3740  1275   151  0.91  14.77   1.00     0.98       5055.36|
|  9:  2.3740 -  2.2830  1277   144  0.91  14.80   1.01     0.98       4794.66|
| 10:  2.2830 -  2.2045  1288   132  0.90  15.33   1.00     0.96       4233.22|
| 11:  2.2045 -  2.1357  1274   146  0.90  16.30   1.01     0.97       4366.35|
| 12:  2.1357 -  2.0748  1269   140  0.92  14.70   1.01     0.99       3870.99|
| 13:  2.0748 -  2.0203  1270   140  0.90  16.33   1.01     1.00       3314.20|
| 14:  2.0203 -  1.9712   688    80  0.91  14.58   0.99     0.96       2500.62|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2500.62 max =        10277.20 mean =      6234.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.84|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.817)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    89.30   16.80    None  None   None       |
|    all(noH): 2823   0      0.65    89.30   16.80    None  None   None       |
|    Sol.    : 438    0      6.28    76.14   39.09    None  None   None       |
|    Mac.    : 2385   0      0.65    89.30   12.71    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:     0.654 -   9.519:  977   |   5:    44.979 -  53.844:  105        |
|      1:     9.519 -  18.384: 1144   |   6:    53.844 -  62.710:   65        |
|      2:    18.384 -  27.249:  240   |   7:    62.710 -  71.575:   23        |
|      3:    27.249 -  36.114:  141   |   8:    71.575 -  80.440:    7        |
|      4:    36.114 -  44.979:  115   |   9:    80.440 -  89.305:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.552 - 4.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 293
   mapped sites are within: 0.753 - 4.606

peak=    5.907 closest distance to " NH2 ARG A  56 " =    2.205
peak=    5.534 closest distance to " CG  PRO A  54 " =    1.238
peak=    5.349 closest distance to " CB  SER A  63 " =    1.184
peak=    5.303 closest distance to " CB  GLN A 223 " =    1.467
peak=    5.197 closest distance to " O   HOH Z 126 " =    1.859
peak=    5.092 closest distance to " NE2 GLN A  11 " =    1.092
peak=    4.996 closest distance to " CB  ARG A 275 " =    0.899
peak=    4.881 closest distance to " O   HOH Z 142 " =    1.713
peak=    4.869 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.817 closest distance to " CB  PRO A  54 " =    0.932
peak=    4.731 closest distance to " C   PRO A 198 " =    1.508
peak=    4.700 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.682 closest distance to " CG  PRO A  90 " =    1.114
peak=    4.574 closest distance to " O   HOH Z 236 " =    2.007
peak=    4.572 closest distance to " OD1 ASN A  69 " =    2.503
peak=    4.570 closest distance to " O   HOH Z  78 " =    1.658
peak=    4.543 closest distance to " O   HOH Z  15 " =    2.203
peak=    4.525 closest distance to " O   HOH Z 232 " =    2.311
peak=    4.463 closest distance to " O   HOH Z 193 " =    1.883
peak=    4.462 closest distance to " CB  LEU A 228 " =    1.090
peak=    4.451 closest distance to " O   HOH Z 298 " =    1.840
peak=    4.433 closest distance to " O   HOH Z 427 " =    2.913
peak=    4.359 closest distance to " ND2 ASN A 187 " =    1.463
peak=    4.343 closest distance to " CB  ASN A 148 " =    1.404
peak=    4.334 closest distance to " O   HOH Z 234 " =    3.719
peak=    4.313 closest distance to " O   HOH Z 203 " =    1.878
peak=    4.302 closest distance to " CB  GLU A 128 " =    1.071
peak=    4.301 closest distance to " CG  PRO A 198 " =    1.271
peak=    4.285 closest distance to " O   HOH Z 272 " =    1.829
peak=    4.285 closest distance to " O   HOH Z 369 " =    2.061
peak=    4.273 closest distance to " CB  TYR A 169 " =    0.756
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.182
peak=    4.248 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.199 closest distance to " O   HOH Z 316 " =    3.057
peak=    4.164 closest distance to " O   HOH Z 144 " =    2.248
peak=    4.153 closest distance to " O   HOH Z 303 " =    2.019
peak=    4.150 closest distance to " OD2 ASP A 286 " =    2.852
peak=    4.127 closest distance to " CA  ALA A  21 " =    1.176
peak=    4.108 closest distance to " CB  TRP A 179 " =    1.309
peak=    4.082 closest distance to " CB  SER A   3 " =    1.338
peak=    4.037 closest distance to " CB  ARG A  79 " =    1.410
peak=    4.022 closest distance to " CB  VAL A 265 " =    1.244
peak=    4.013 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.994 closest distance to " O   HOH Z  61 " =    1.609
peak=    3.975 closest distance to " CB  ARG A 190 " =    1.701
peak=    3.975 closest distance to " CA  ASN A 215 " =    1.202
peak=    3.973 closest distance to " O   HOH Z 368 " =    1.966
peak=    3.972 closest distance to " NZ  LYS A 117 " =    3.302
peak=    3.930 closest distance to " O   HOH Z  44 " =    1.755
peak=    3.920 closest distance to " CG  ARG A  66 " =    2.423
peak=    3.916 closest distance to " CG2 VAL A 257 " =    0.928
peak=    3.901 closest distance to " O   HOH Z 344 " =    3.078
peak=    3.891 closest distance to " O   HOH Z 346 " =    1.648
peak=    3.866 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.860 closest distance to " O   HOH Z  40 " =    1.670
peak=    3.847 closest distance to " O   HOH Z 132 " =    2.486
peak=    3.835 closest distance to " CB  TRP A 266 " =    0.969
peak=    3.835 closest distance to " O   MET A 105 " =    1.793
peak=    3.833 closest distance to " O   HOH Z  54 " =    1.702
peak=    3.824 closest distance to " CZ  PHE A 218 " =    1.050
peak=    3.814 closest distance to " CA  THR A 264 " =    0.854
peak=    3.805 closest distance to " O   HOH Z 158 " =    3.053
peak=    3.802 closest distance to " O   HOH Z 403 " =    1.682
peak=    3.785 closest distance to " O   HOH Z  43 " =    1.857
peak=    3.762 closest distance to " O   HOH Z  97 " =    1.948
peak=    3.758 closest distance to " O   SER A  87 " =    2.338
peak=    3.757 closest distance to " ND2 ASN A 249 " =    1.937
peak=    3.755 closest distance to " O   HOH Z 189 " =    2.021
peak=    3.749 closest distance to " CD2 LEU A 297 " =    0.886
peak=    3.749 closest distance to " O   HOH Z 214 " =    2.024
peak=    3.736 closest distance to " CB  SER A 216 " =    0.801
peak=    3.724 closest distance to " CA  THR A 221 " =    0.990
peak=    3.724 closest distance to " CD1 LEU A 300 " =    1.210
peak=    3.723 closest distance to " O   HOH Z 128 " =    2.084
peak=    3.712 closest distance to " O   HOH Z 133 " =    1.584
peak=    3.708 closest distance to " NH1AARG A 145 " =    1.132
peak=    3.704 closest distance to " CB  GLU A 277 " =    3.568
peak=    3.698 closest distance to " OE1 GLU A   2 " =    2.208
peak=    3.698 closest distance to " O   HOH Z 197 " =    3.063
peak=    3.690 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.685 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.683 closest distance to " O   HOH Z  21 " =    1.685
peak=    3.682 closest distance to " CA  MET A  40 " =    1.120
peak=    3.670 closest distance to " N   ARG A 156 " =    1.317
peak=    3.669 closest distance to " O   HOH Z  88 " =    3.316
peak=    3.662 closest distance to " O   HOH Z 426 " =    1.565
peak=    3.653 closest distance to " CB  TYR A 169 " =    0.774
peak=    3.651 closest distance to " O   HOH Z  61 " =    1.562
peak=    3.647 closest distance to " O   HOH Z 207 " =    1.817
peak=    3.640 closest distance to " CB  VAL A 202 " =    1.601
peak=    3.639 closest distance to " O   HOH Z  93 " =    2.573
peak=    3.638 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.637 closest distance to " CD BLYS A 290 " =    1.180
peak=    3.635 closest distance to " O   HOH Z  66 " =    1.998
peak=    3.628 closest distance to " O   HOH Z  10 " =    1.869
peak=    3.625 closest distance to " O   HOH Z 425 " =    1.942
peak=    3.624 closest distance to " O   HOH Z 345 " =    3.377
peak=    3.622 closest distance to " NH2 ARG A 156 " =    1.154
peak=    3.620 closest distance to " CA  ASP A 140 " =    1.144
peak=    3.618 closest distance to " O   HOH Z 368 " =    3.605
peak=    3.618 closest distance to " CA  ALA A 291 " =    0.922
peak=    3.614 closest distance to " O   HOH Z 402 " =    1.417
peak=    3.604 closest distance to " O   HOH Z 273 " =    2.685
peak=    3.604 closest distance to " O   HOH Z   9 " =    2.090
peak=    3.599 closest distance to " O   HOH Z 371 " =    3.226
peak=    3.596 closest distance to " ND1 HIS A  86 " =    1.866
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.246
peak=    3.593 closest distance to " NH2BARG A 145 " =    2.058
peak=    3.585 closest distance to " CB  ASP A 140 " =    0.904
peak=    3.582 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.581 closest distance to " CD  LYS A 119 " =    1.230
peak=    3.575 closest distance to " O   HOH Z 108 " =    2.263
peak=    3.574 closest distance to " O   HOH Z  59 " =    1.942
peak=    3.563 closest distance to " CB  SER A 212 " =    1.085
peak=    3.562 closest distance to " CG2 ILE A 120 " =    1.220
peak=    3.556 closest distance to " O   HOH Z 423 " =    1.876
peak=    3.553 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.553 closest distance to " O   HOH Z 193 " =    2.083
peak=    3.552 closest distance to " O   HOH Z 407 " =    2.588
peak=    3.549 closest distance to " CD  ARG A 269 " =    0.942
peak=    3.545 closest distance to " O   HOH Z 411 " =    3.877
peak=    3.543 closest distance to " CB  GLN A  88 " =    1.230
peak=    3.542 closest distance to " OG BSER A 164 " =    2.334
peak=    3.540 closest distance to " O   HOH Z 327 " =    1.617
peak=    3.539 closest distance to " O   HOH Z 135 " =    1.602
peak=    3.532 closest distance to " CD2 TRP A 179 " =    1.375
peak=    3.530 closest distance to " CB  LEU A 255 " =    0.763
peak=    3.527 closest distance to " O   HOH Z 406 " =    1.625
peak=    3.527 closest distance to " CG1BVAL A  72 " =    1.528
peak=    3.526 closest distance to " O   HOH Z 280 " =    3.025
peak=    3.520 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.510 closest distance to " O   HOH Z   1 " =    1.878
peak=    3.503 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.486 closest distance to " O   HOH Z 337 " =    3.734
peak=    3.485 closest distance to " CD1 ILE A 106 " =    0.854
peak=    3.484 closest distance to " CG2BVAL A  41 " =    0.824
peak=    3.483 closest distance to " O   HOH Z 291 " =    1.495
peak=    3.478 closest distance to " CA  ARG A 195 " =    1.249
peak=    3.478 closest distance to " O   HOH Z 295 " =    1.480
peak=    3.475 closest distance to " CA  ALA A  51 " =    0.944
peak=    3.474 closest distance to " CB  LEU A 143 " =    1.087
peak=    3.461 closest distance to " CG  LEU A 167 " =    1.214
peak=    3.459 closest distance to " CB  ARG A 139 " =    0.925
peak=    3.431 closest distance to " CB  SER A  62 " =    1.240
peak=    3.429 closest distance to " CA  ALA A 158 " =    1.162
peak=    3.426 closest distance to " CD  LYS A 166 " =    1.241
peak=    3.424 closest distance to " O   HOH Z 172 " =    3.544
peak=    3.424 closest distance to " O   HOH Z 209 " =    2.282
peak=    3.423 closest distance to " CG  LYS A  76 " =    1.024
peak=    3.421 closest distance to " CD  ARG A  66 " =    2.442
peak=    3.419 closest distance to " ND1 HIS A  81 " =    1.599
peak=    3.412 closest distance to " CB  SER A 141 " =    1.030
peak=    3.410 closest distance to " CB  ALA A 291 " =    1.373
peak=    3.406 closest distance to " CA  ARG A  36 " =    1.065
peak=    3.403 closest distance to " CB  ASN A  39 " =    0.901
peak=    3.398 closest distance to " O   HOH Z   3 " =    1.736
peak=    3.395 closest distance to " O   HOH Z  64 " =    2.265
peak=    3.394 closest distance to " NH1BARG A 145 " =    1.212
peak=    3.391 closest distance to " O   TRP A 274 " =    1.874
peak=    3.391 closest distance to " O   HOH Z 175 " =    2.103
peak=    3.388 closest distance to " O   HOH Z 353 " =    2.778
peak=    3.385 closest distance to " O   HOH Z 305 " =    3.643
peak=    3.384 closest distance to " CA  ASN A 176 " =    1.245
peak=    3.383 closest distance to " O   HOH Z 329 " =    3.706
peak=    3.379 closest distance to " CA  ALA A  43 " =    1.246
peak=    3.378 closest distance to " CE1 TYR A 186 " =    1.296
peak=    3.376 closest distance to " CZ2 TRP A 179 " =    1.649
peak=    3.374 closest distance to " CB  MET A  47 " =    1.033
peak=    3.358 closest distance to " O   HOH Z  63 " =    2.088
peak=    3.355 closest distance to " CD2 LEU A 255 " =    1.370
peak=    3.348 closest distance to " OD1BASN A 224 " =    2.333
peak=    3.348 closest distance to " O   HOH Z 133 " =    2.421
peak=    3.347 closest distance to " O   HOH Z 213 " =    1.619
peak=    3.346 closest distance to " O   HOH Z 173 " =    1.826
peak=    3.341 closest distance to " CA  ALA A 248 " =    1.232
peak=    3.328 closest distance to " O   HOH Z 163 " =    1.667
peak=    3.326 closest distance to " O   HOH Z 299 " =    4.410
peak=    3.321 closest distance to " CB  THR A 157 " =    1.101
peak=    3.315 closest distance to " CG  MET A 113 " =    1.262
peak=    3.313 closest distance to " CB  ILE A 120 " =    1.261
peak=    3.312 closest distance to " O   HOH Z  49 " =    2.132
peak=    3.310 closest distance to " CA  ALA A  84 " =    1.372
peak=    3.307 closest distance to " O   HOH Z  19 " =    2.498
peak=    3.300 closest distance to " CA  ILE A 234 " =    0.931
peak=    3.297 closest distance to " O   HOH Z 409 " =    2.975
peak=    3.295 closest distance to " CB  GLN A  89 " =    1.293
peak=    3.292 closest distance to " O   HOH Z  66 " =    2.034
peak=    3.292 closest distance to " CG  GLU A 277 " =    2.118
peak=    3.285 closest distance to " O   HOH Z 183 " =    1.366
peak=    3.283 closest distance to " O   HOH Z 227 " =    1.620
peak=    3.283 closest distance to " CB  TYR A 116 " =    0.813
peak=    3.280 closest distance to " O   HOH Z 437 " =    1.489
peak=    3.279 closest distance to " CD2 HIS A  81 " =    1.181
peak=    3.279 closest distance to " O   HOH Z 134 " =    1.275
peak=    3.276 closest distance to " OG1 THR A 294 " =    2.456
peak=    3.276 closest distance to " NH2 ARG A 219 " =    1.838
peak=    3.271 closest distance to " O   HOH Z 219 " =    1.916
peak=    3.270 closest distance to " CG  MET A 185 " =    1.113
peak=    3.267 closest distance to " CA  SER A  87 " =    1.017
peak=    3.266 closest distance to " N   ASN A 127 " =    1.245
peak=    3.261 closest distance to " CG1 ILE A 151 " =    0.959
peak=    3.258 closest distance to " O   HOH Z 366 " =    3.129
peak=    3.258 closest distance to " O   HOH Z 234 " =    1.733
peak=    3.255 closest distance to " O   ALA A 165 " =    1.402
peak=    3.252 closest distance to " CA  ASP A 162 " =    1.114
peak=    3.251 closest distance to " O   HOH Z 359 " =    1.375
peak=    3.247 closest distance to " CA  ALA A 233 " =    1.353
peak=    3.246 closest distance to " OG BSER A 134 " =    2.790
peak=    3.241 closest distance to " CB  ALA A  34 " =    1.092
peak=    3.238 closest distance to " CB  SER A  26 " =    1.586
peak=    3.237 closest distance to " O   HOH Z 125 " =    2.349
peak=    3.237 closest distance to " O   HOH Z 421 " =    1.725
peak=    3.236 closest distance to " O   HOH Z 267 " =    2.088
peak=    3.235 closest distance to " O   HOH Z 166 " =    3.790
peak=    3.231 closest distance to " O   HOH Z 411 " =    1.750
peak=    3.229 closest distance to " O   HOH Z 327 " =    2.277
peak=    3.229 closest distance to " CG  MET A 185 " =    1.083
peak=    3.229 closest distance to " O   HOH Z  85 " =    2.159
peak=    3.228 closest distance to " OG  SER A  22 " =    2.698
peak=    3.228 closest distance to " N   VAL A 126 " =    1.279
peak=    3.224 closest distance to " O   THR A 220 " =    1.350
peak=    3.222 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.220 closest distance to " O   HOH Z 410 " =    1.956
peak=    3.215 closest distance to " O   HOH Z  44 " =    3.314
peak=    3.213 closest distance to " O   HOH Z 419 " =    1.878
peak=    3.212 closest distance to " CB  PHE A  16 " =    0.997
peak=    3.211 closest distance to " CB  ASN A 215 " =    1.105
peak=    3.210 closest distance to " O   HOH Z 279 " =    2.180
peak=    3.209 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.207 closest distance to " CB  ALA A   1 " =    4.606
peak=    3.205 closest distance to " O   HOH Z 374 " =    2.593
peak=    3.205 closest distance to " CB  VAL A 126 " =    1.153
peak=    3.204 closest distance to " CA  ALA A 154 " =    0.944
peak=    3.204 closest distance to " O   HOH Z 391 " =    2.938
peak=    3.198 closest distance to " O   HOH Z 403 " =    1.330
peak=    3.193 closest distance to " O   HOH Z 334 " =    1.479
peak=    3.184 closest distance to " O   HOH Z 422 " =    2.683
peak=    3.182 closest distance to " O   HOH Z 261 " =    2.124
peak=    3.175 closest distance to " CB  GLU A  46 " =    1.055
peak=    3.175 closest distance to " O   HOH Z 417 " =    1.937
peak=    3.172 closest distance to " O   HOH Z 423 " =    3.041
peak=    3.172 closest distance to " O   ALA A 158 " =    1.283
peak=    3.171 closest distance to " CB  ASN A 142 " =    0.986
peak=    3.171 closest distance to " CA  GLY A 267 " =    1.165
peak=    3.168 closest distance to " O   HOH Z  96 " =    2.029
peak=    3.165 closest distance to " NZ  LYS A  76 " =    1.223
peak=    3.161 closest distance to " CD1 LEU A  96 " =    0.753
peak=    3.161 closest distance to " N   SER A 135 " =    1.325
peak=    3.154 closest distance to " O   HOH Z 148 " =    3.225
peak=    3.153 closest distance to " CB  ASN A 224 " =    1.058
peak=    3.150 closest distance to " CG  GLN A  89 " =    1.487
peak=    3.150 closest distance to " O   HOH Z 433 " =    1.812
peak=    3.149 closest distance to " O  BHOH Z 338 " =    2.335
peak=    3.148 closest distance to " O   HOH Z 425 " =    1.220
peak=    3.145 closest distance to " O   GLY A  57 " =    2.562
peak=    3.144 closest distance to " OD1 ASP A 231 " =    1.876
peak=    3.141 closest distance to " O   ALA A   1 " =    1.493
peak=    3.137 closest distance to " O   HOH Z  30 " =    2.160
peak=    3.135 closest distance to " CB  ALA A   9 " =    1.552
peak=    3.132 closest distance to " CB  THR A  31 " =    1.768
peak=    3.127 closest distance to " N   TYR A 116 " =    1.730
peak=    3.126 closest distance to " O   HOH Z 286 " =    2.226
peak=    3.126 closest distance to " CA  ARG A 102 " =    1.113
peak=    3.118 closest distance to " C   TYR A 214 " =    1.449
peak=    3.117 closest distance to " O   HOH Z 435 " =    1.913
peak=    3.109 closest distance to " CB  GLN A 278 " =    0.862
peak=    3.106 closest distance to " O   HOH Z 336 " =    1.786
peak=    3.105 closest distance to " CB  LYS A 117 " =    1.137
peak=    3.104 closest distance to " CG2 VAL A 202 " =    1.213
peak=    3.103 closest distance to " OG  SER A 206 " =    1.295
peak=    3.099 closest distance to " O   HOH Z 383 " =    1.727
peak=    3.099 closest distance to " OG1 THR A 246 " =    3.215
peak=    3.094 closest distance to " N   GLN A 278 " =    1.063
peak=    3.094 closest distance to " CB  GLU A 152 " =    1.444
peak=    3.088 closest distance to " N   ASN A 252 " =    1.388
peak=    3.083 closest distance to " O   HOH Z 227 " =    1.920
peak=    3.081 closest distance to " CA  GLY A  80 " =    1.028
peak=    3.081 closest distance to " CG BARG A 102 " =    1.853
peak=    3.078 closest distance to " CA  ASP A 191 " =    0.861
peak=    3.078 closest distance to " CA  MET A 105 " =    1.015
peak=    3.077 closest distance to " O   HOH Z 357 " =    1.875
peak=    3.069 closest distance to " N   ALA A 154 " =    0.998
peak=    3.067 closest distance to " O   HOH Z 393 " =    3.323
peak=    3.067 closest distance to " O   HOH Z   3 " =    1.515
peak=    3.050 closest distance to " O   HOH Z 380 " =    1.815
peak=    3.043 closest distance to " CB  ARG A 138 " =    0.941
peak=    3.034 closest distance to " O   HOH Z 371 " =    1.621
peak=    3.021 closest distance to " O   HOH Z 261 " =    1.533
peak=    3.008 closest distance to " CB  ALA A 114 " =    1.157

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.801 - 5.335
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.801 - 5.335

peak=   -4.794 closest distance to " O   HOH Z 266 " =    4.527
peak=   -4.561 closest distance to " CB  PRO A 243 " =    2.618
peak=   -4.388 closest distance to " CB  PRO A 280 " =    2.085
peak=   -4.358 closest distance to " CD  ARG A 156 " =    2.007
peak=   -4.331 closest distance to " O   ILE A 109 " =    2.580
peak=   -4.331 closest distance to " CG  GLN A 223 " =    1.922
peak=   -4.312 closest distance to " O   HOH Z 198 " =    2.116
peak=   -4.290 closest distance to " O   VAL A  67 " =    2.749
peak=   -4.233 closest distance to " SG  CYS A 254 " =    3.296
peak=   -4.200 closest distance to " O   HOH Z 372 " =    2.390
peak=   -4.125 closest distance to " C   HIS A 108 " =    1.083
peak=   -4.107 closest distance to " O   HOH Z 290 " =    1.107
peak=   -4.089 closest distance to " N   ALA A  43 " =    2.542
peak=   -4.054 closest distance to " ND2 ASN A  45 " =    1.300
peak=   -4.034 closest distance to " CG1 VAL A 112 " =    2.800
peak=   -4.031 closest distance to " ND2 ASN A  45 " =    0.978
peak=   -4.004 closest distance to " OG BSER A 134 " =    1.196
peak=   -3.984 closest distance to " O   HOH Z 126 " =    1.888
peak=   -3.977 closest distance to " O   HOH Z 118 " =    3.160
peak=   -3.972 closest distance to " O   HOH Z 231 " =    2.213
peak=   -3.967 closest distance to " CE2 TYR A  30 " =    2.777
peak=   -3.892 closest distance to " O   HOH Z 353 " =    2.203
peak=   -3.889 closest distance to " CD1 LEU A 228 " =    2.259
peak=   -3.888 closest distance to " CG  PHE A 283 " =    2.782
peak=   -3.879 closest distance to " CA  VAL A  67 " =    2.701
peak=   -3.863 closest distance to " O   HOH Z 185 " =    2.255
peak=   -3.838 closest distance to " O   HOH Z  43 " =    1.616
peak=   -3.834 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.820 closest distance to " O   PRO A 163 " =    2.062
peak=   -3.800 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.788 closest distance to " CD  ARG A 139 " =    1.520
peak=   -3.786 closest distance to " CD2 LEU A 300 " =    2.876
peak=   -3.772 closest distance to " CB  ALA A 291 " =    2.225
peak=   -3.770 closest distance to " OXT GLY A 302 " =    2.807
peak=   -3.760 closest distance to " CD1 PHE A  59 " =    1.810
peak=   -3.752 closest distance to " C   ALA A 158 " =    1.260
peak=   -3.744 closest distance to " OG  SER A  97 " =    2.170
peak=   -3.731 closest distance to " O   HOH Z 389 " =    1.811
peak=   -3.725 closest distance to " CZ  PHE A  59 " =    1.606
peak=   -3.720 closest distance to " CZ3 TRP A 179 " =    1.148
peak=   -3.716 closest distance to " O   HOH Z  10 " =    1.498
peak=   -3.704 closest distance to " O   HOH Z 435 " =    2.758
peak=   -3.703 closest distance to " CG2 ILE A 263 " =    2.268
peak=   -3.685 closest distance to " NH2AARG A 275 " =    5.335
peak=   -3.683 closest distance to " O   HOH Z  52 " =    1.358
peak=   -3.680 closest distance to " CE  MET A 105 " =    2.195
peak=   -3.676 closest distance to " N   SER A 212 " =    2.032
peak=   -3.640 closest distance to " O   HOH Z  13 " =    1.561
peak=   -3.639 closest distance to " CZ  TYR A 169 " =    1.716
peak=   -3.633 closest distance to " O   HOH Z 196 " =    2.113
peak=   -3.632 closest distance to " CE2 PHE A 218 " =    2.482
peak=   -3.612 closest distance to " O   HOH Z 313 " =    2.021
peak=   -3.606 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.590 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.586 closest distance to " O   HOH Z 407 " =    3.033
peak=   -3.580 closest distance to " CD1 LEU A 101 " =    2.429
peak=   -3.579 closest distance to " CG  ARG A 269 " =    2.716
peak=   -3.570 closest distance to " OD1 ASN A 187 " =    1.540
peak=   -3.564 closest distance to " SG ACYS A 201 " =    1.914
peak=   -3.556 closest distance to " CB  ALA A 291 " =    2.415
peak=   -3.543 closest distance to " CD  GLN A  58 " =    1.125
peak=   -3.539 closest distance to " CD2 PHE A 192 " =    2.084
peak=   -3.537 closest distance to " O   SER A 135 " =    1.508
peak=   -3.535 closest distance to " CB  ASN A  39 " =    2.228
peak=   -3.533 closest distance to " O   HOH Z 102 " =    1.594
peak=   -3.525 closest distance to " OG BSER A 134 " =    1.728
peak=   -3.524 closest distance to " O   HOH Z 351 " =    1.512
peak=   -3.522 closest distance to " O   HOH Z 198 " =    1.447
peak=   -3.512 closest distance to " O   HOH Z 292 " =    4.499
peak=   -3.498 closest distance to " N   ALA A 248 " =    1.574
peak=   -3.495 closest distance to " O   HOH Z  47 " =    1.572
peak=   -3.493 closest distance to " O   HOH Z 311 " =    3.537
peak=   -3.487 closest distance to " C   LEU A 143 " =    1.129
peak=   -3.482 closest distance to " N   GLN A  58 " =    1.705
peak=   -3.480 closest distance to " CG1 VAL A 250 " =    2.616
peak=   -3.474 closest distance to " C   ASN A 285 " =    2.526
peak=   -3.471 closest distance to " O   HOH Z 211 " =    1.682
peak=   -3.470 closest distance to " CB  CYS A 201 " =    2.633
peak=   -3.466 closest distance to " O   HOH Z  11 " =    1.758
peak=   -3.459 closest distance to " OD1 ASP A 191 " =    1.716
peak=   -3.455 closest distance to " CA  GLY A 203 " =    2.223
peak=   -3.450 closest distance to " O   GLY A 196 " =    1.050
peak=   -3.441 closest distance to " CA  ASP A 298 " =    1.040
peak=   -3.438 closest distance to " OD1 ASP A 171 " =    1.581
peak=   -3.425 closest distance to " OG  SER A  62 " =    1.621
peak=   -3.418 closest distance to " CA  GLY A  98 " =    1.973
peak=   -3.411 closest distance to " ND2 ASN A 249 " =    2.093
peak=   -3.405 closest distance to " N   ALA A 226 " =    2.077
peak=   -3.401 closest distance to " O   MET A  40 " =    2.721
peak=   -3.400 closest distance to " NH2 ARG A  79 " =    1.916
peak=   -3.400 closest distance to " O   HOH Z  11 " =    2.079
peak=   -3.399 closest distance to " CD  GLU A 236 " =    1.043
peak=   -3.394 closest distance to " O   HOH Z 417 " =    2.451
peak=   -3.389 closest distance to " CD2 TYR A 247 " =    2.494
peak=   -3.382 closest distance to " CB  ALA A 248 " =    1.984
peak=   -3.375 closest distance to " O   HOH Z 388 " =    1.989
peak=   -3.373 closest distance to " NH1 ARG A  36 " =    2.069
peak=   -3.370 closest distance to " C   ILE A 234 " =    1.352
peak=   -3.366 closest distance to " CB  PRO A 163 " =    2.536
peak=   -3.351 closest distance to " O   HOH Z 395 " =    5.179
peak=   -3.350 closest distance to " C   MET A 188 " =    1.463
peak=   -3.350 closest distance to " O   VAL A 189 " =    2.522
peak=   -3.350 closest distance to " NE2 GLN A  88 " =    1.870
peak=   -3.347 closest distance to " CB  ALA A 131 " =    2.089
peak=   -3.340 closest distance to " O   HOH Z 385 " =    1.961
peak=   -3.338 closest distance to " O   HOH Z  63 " =    1.436
peak=   -3.338 closest distance to " CG  ARG A  66 " =    2.398
peak=   -3.336 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.336 closest distance to " O   HOH Z 111 " =    2.242
peak=   -3.336 closest distance to " CE3 TRP A 150 " =    2.052
peak=   -3.335 closest distance to " OD2 ASP A 171 " =    2.364
peak=   -3.334 closest distance to " CB  PHE A 208 " =    2.243
peak=   -3.329 closest distance to " O   PHE A 218 " =    1.545
peak=   -3.328 closest distance to " CD2 PHE A  61 " =    2.489
peak=   -3.326 closest distance to " O   LYS A 117 " =    1.693
peak=   -3.323 closest distance to " O   HOH Z 166 " =    1.884
peak=   -3.319 closest distance to " CD  LYS A 289 " =    2.440
peak=   -3.315 closest distance to " O   HOH Z  60 " =    2.558
peak=   -3.311 closest distance to " CG  MET A 105 " =    0.954
peak=   -3.309 closest distance to " OE1 GLN A  88 " =    1.161
peak=   -3.308 closest distance to " OD1 ASP A 191 " =    1.506
peak=   -3.306 closest distance to " O   GLY A 211 " =    1.501
peak=   -3.304 closest distance to " CG  GLU A   2 " =    1.920
peak=   -3.301 closest distance to " O   HOH Z 385 " =    2.048
peak=   -3.286 closest distance to " CD1 ILE A 239 " =    2.091
peak=   -3.285 closest distance to " O   HOH Z  93 " =    1.942
peak=   -3.282 closest distance to " O   HOH Z  73 " =    2.355
peak=   -3.281 closest distance to " CD2 LEU A 237 " =    2.673
peak=   -3.276 closest distance to " O   TRP A  70 " =    1.509
peak=   -3.275 closest distance to " O   HOH Z  98 " =    2.305
peak=   -3.272 closest distance to " O   GLY A  80 " =    2.447
peak=   -3.272 closest distance to " O   HOH Z 394 " =    1.508
peak=   -3.271 closest distance to " CB  ASP A 132 " =    2.307
peak=   -3.265 closest distance to " O   HOH Z 317 " =    2.422
peak=   -3.265 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.262 closest distance to " OD2 ASP A 171 " =    1.743
peak=   -3.259 closest distance to " CB  ASP A 286 " =    2.239
peak=   -3.257 closest distance to " O   VAL A 174 " =    2.026
peak=   -3.248 closest distance to " CB  TRP A  85 " =    2.493
peak=   -3.248 closest distance to " O   HOH Z 281 " =    2.729
peak=   -3.248 closest distance to " O   HOH Z 166 " =    1.469
peak=   -3.246 closest distance to " NE  ARG A  36 " =    1.929
peak=   -3.237 closest distance to " OH  TYR A 214 " =    1.229
peak=   -3.234 closest distance to " CG  TRP A 266 " =    1.805
peak=   -3.232 closest distance to " OD2 ASP A  50 " =    1.540
peak=   -3.227 closest distance to " OD2 ASP A 191 " =    1.505
peak=   -3.223 closest distance to " CE3 TRP A 274 " =    2.407
peak=   -3.222 closest distance to " OD2 ASP A 270 " =    1.493
peak=   -3.222 closest distance to " O   SER A  95 " =    1.525
peak=   -3.220 closest distance to " O   ALA A 161 " =    1.607
peak=   -3.218 closest distance to " CA  GLY A 241 " =    3.074
peak=   -3.217 closest distance to " CG  GLU A 277 " =    1.168
peak=   -3.217 closest distance to " OG BSER A 210 " =    2.183
peak=   -3.215 closest distance to " CB  ALA A  43 " =    2.423
peak=   -3.214 closest distance to " O   HOH Z  90 " =    2.746
peak=   -3.214 closest distance to " CE  MET A  93 " =    1.230
peak=   -3.210 closest distance to " CA  GLY A 133 " =    1.987
peak=   -3.210 closest distance to " CG2 VAL A 189 " =    2.006
peak=   -3.209 closest distance to " O   HOH Z 148 " =    3.367
peak=   -3.205 closest distance to " N   MET A 105 " =    2.788
peak=   -3.203 closest distance to " O   HOH Z 322 " =    1.581
peak=   -3.195 closest distance to " O   HOH Z   6 " =    1.519
peak=   -3.194 closest distance to " O   HOH Z 298 " =    1.273
peak=   -3.190 closest distance to " O   ALA A  51 " =    1.355
peak=   -3.187 closest distance to " O   HOH Z  44 " =    2.158
peak=   -3.187 closest distance to " CG1 VAL A 197 " =    2.195
peak=   -3.185 closest distance to " O   HOH Z 252 " =    3.759
peak=   -3.184 closest distance to " NH2BARG A 275 " =    2.028
peak=   -3.183 closest distance to " OG1 THR A 178 " =    1.284
peak=   -3.181 closest distance to " ND2 ASN A  60 " =    1.493
peak=   -3.179 closest distance to " O   HOH Z 222 " =    1.175
peak=   -3.176 closest distance to " ND2 ASN A 187 " =    1.506
peak=   -3.176 closest distance to " OG  SER A  87 " =    1.381
peak=   -3.172 closest distance to " CD2 PHE A 225 " =    1.198
peak=   -3.170 closest distance to " O   ALA A  34 " =    2.529
peak=   -3.167 closest distance to " OG ASER A 134 " =    1.133
peak=   -3.164 closest distance to " O   HOH Z 357 " =    2.019
peak=   -3.162 closest distance to " NZ  LYS A 119 " =    3.491
peak=   -3.160 closest distance to " CD2 TYR A 293 " =    1.990
peak=   -3.158 closest distance to " O   HOH Z 324 " =    2.170
peak=   -3.152 closest distance to " O   ASN A 249 " =    1.519
peak=   -3.151 closest distance to " O   HOH Z  76 " =    1.914
peak=   -3.147 closest distance to " CB  ALA A 248 " =    2.392
peak=   -3.146 closest distance to " O   GLY A  80 " =    2.450
peak=   -3.146 closest distance to " CG  ASN A 301 " =    1.937
peak=   -3.144 closest distance to " CB  ASP A 132 " =    2.341
peak=   -3.137 closest distance to " CG  PRO A 163 " =    2.511
peak=   -3.135 closest distance to " O   HOH Z 323 " =    1.337
peak=   -3.135 closest distance to " O   HOH Z 350 " =    1.944
peak=   -3.133 closest distance to " O   HOH Z  71 " =    2.291
peak=   -3.132 closest distance to " O   HOH Z  51 " =    1.608
peak=   -3.131 closest distance to " O   HOH Z 252 " =    4.251
peak=   -3.130 closest distance to " O   HOH Z 414 " =    1.669
peak=   -3.125 closest distance to " NH2 ARG A  66 " =    2.122
peak=   -3.123 closest distance to " O   HOH Z 174 " =    2.990
peak=   -3.120 closest distance to " O   ALA A 292 " =    1.941
peak=   -3.118 closest distance to " O   ALA A   1 " =    1.859
peak=   -3.112 closest distance to " O   HOH Z 168 " =    1.837
peak=   -3.109 closest distance to " OG  SER A  26 " =    1.277
peak=   -3.101 closest distance to " O   HOH Z  51 " =    1.369
peak=   -3.100 closest distance to " O   HOH Z 298 " =    2.604
peak=   -3.097 closest distance to " O   HOH Z 234 " =    4.123
peak=   -3.088 closest distance to " O   HOH Z 263 " =    2.997
peak=   -3.071 closest distance to " NH2 ARG A  79 " =    1.594
peak=   -3.058 closest distance to " CD1 ILE A 199 " =    2.499
peak=   -3.044 closest distance to " CD1 TYR A 247 " =    2.599
peak=   -3.039 closest distance to " N   TYR A  68 " =    3.091
peak=   -3.006 closest distance to " OD2 ASP A  50 " =    2.324

================= 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    :  0.2862 0.2902   5.949475e+00   5.965866e+00
   1_bss:  0.2684 0.2724   5.923544e+00   5.925519e+00
   1_xyz:  0.1536 0.1777   5.378238e+00   5.500422e+00
   1_adp:  0.1404 0.1804   5.322792e+00   5.524250e+00
   1_occ:  0.1400 0.1804   5.321131e+00   5.523172e+00
   2_bss:  0.1384 0.1769   5.306129e+00   5.504460e+00
   2_xyz:  0.1171 0.1551   5.162047e+00   5.380558e+00
   2_adp:  0.1144 0.1530   5.141961e+00   5.360322e+00
   2_occ:  0.1143 0.1529   5.141296e+00   5.359745e+00
   3_bss:  0.1141 0.1526   5.139614e+00   5.358280e+00
   3_xyz:  0.1103 0.1516   5.121842e+00   5.353527e+00
   3_adp:  0.1087 0.1528   5.120006e+00   5.360183e+00
   3_occ:  0.1087 0.1529   5.120003e+00   5.360363e+00
   4_bss:  0.1086 0.1530   5.121041e+00   5.361704e+00
   4_xyz:  0.1063 0.1540   5.112468e+00   5.364791e+00
   4_adp:  0.1057 0.1553   5.114710e+00   5.371872e+00
   4_occ:  0.1057 0.1553   5.114808e+00   5.372144e+00
   5_bss:  0.1056 0.1553   5.114922e+00   5.372217e+00
   5_xyz:  0.1062 0.1564   5.121898e+00   5.380900e+00
   5_adp:  0.1063 0.1561   5.120219e+00   5.378703e+00
   5_occ:  0.1063 0.1561   5.120284e+00   5.378872e+00
   5_bss:  0.1062 0.1561   5.120378e+00   5.378931e+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:  0.323  38.567  -2.593  -2.872   1.262  -0.000   0.000   0.000
   1_xyz:  0.323  38.567  -2.593  -2.872   1.262  -0.000   0.000   0.000
   1_adp:  0.323  38.567  -2.593  -2.872   1.262  -0.000   0.000   0.000
   1_occ:  0.323  38.567  -2.593  -2.872   1.262  -0.000   0.000   0.000
   2_bss:  0.326  45.099  -2.763  -2.843  -1.169  -0.000  -0.000  -0.000
   2_xyz:  0.326  45.099  -2.763  -2.843  -1.169  -0.000  -0.000  -0.000
   2_adp:  0.326  45.099  -2.763  -2.843  -1.169  -0.000  -0.000  -0.000
   2_occ:  0.326  45.099  -2.763  -2.843  -1.169  -0.000  -0.000  -0.000
   3_bss:  0.326  45.099  -2.650  -2.569  -1.599  -0.000  -0.000  -0.000
   3_xyz:  0.326  45.099  -2.650  -2.569  -1.599  -0.000  -0.000  -0.000
   3_adp:  0.326  45.099  -2.650  -2.569  -1.599  -0.000  -0.000  -0.000
   3_occ:  0.326  45.099  -2.650  -2.569  -1.599  -0.000  -0.000  -0.000
   4_bss:  0.322  45.099  -2.485  -2.373  -1.638  -0.000  -0.000  -0.000
   4_xyz:  0.322  45.099  -2.485  -2.373  -1.638  -0.000  -0.000  -0.000
   4_adp:  0.322  45.099  -2.485  -2.373  -1.638  -0.000  -0.000  -0.000
   4_occ:  0.322  45.099  -2.485  -2.373  -1.638  -0.000  -0.000  -0.000
   5_bss:  0.322  45.099  -2.250  -2.123  -1.455  -0.000  -0.000  -0.000
   5_xyz:  0.322  45.099  -2.250  -2.123  -1.455  -0.000  -0.000  -0.000
   5_adp:  0.322  45.099  -2.250  -2.123  -1.455  -0.000  -0.000  -0.000
   5_occ:  0.322  45.099  -2.250  -2.123  -1.455  -0.000  -0.000  -0.000
   5_bss:  0.322  45.076  -2.064  -1.931  -1.284  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.179 0.7591  0.9430    24882.871
   1_bss:  28.496 0.7751  0.9180    21178.784
   1_xyz:  16.157 0.8981  1.0035     8128.486
   1_adp:  16.782 0.8921  1.0017     8399.256
   1_occ:  16.762 0.8922  1.0015     8367.338
   2_bss:  16.285 0.8963  0.9741     8022.838
   2_xyz:  13.883 0.9157  0.9830     6219.207
   2_adp:  13.476 0.9192  0.9817     6014.891
   2_occ:  13.460 0.9193  0.9817     6002.621
   3_bss:  13.433 0.9195  0.9811     5990.570
   3_xyz:  13.300 0.9207  0.9809     5923.059
   3_adp:  13.418 0.9198  0.9757     5979.608
   3_occ:  13.422 0.9198  0.9756     5982.543
   4_bss:  13.462 0.9195  0.9791     6016.642
   4_xyz:  13.550 0.9187  0.9787     6072.008
   4_adp:  13.706 0.9175  0.9727     6148.517
   4_occ:  13.710 0.9175  0.9726     6152.787
   5_bss:  13.716 0.9174  0.9804     6154.850
   5_xyz:  13.841 0.9165  0.9800     6262.296
   5_adp:  13.797 0.9168  0.9746     6230.819
   5_occ:  13.800 0.9168  0.9745     6233.427
   5_bss:  13.803 0.9168  0.9801     6234.817
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6250e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6250e-01
   1_xyz:   1.024  0.007  0.071 15.071  0.004  4.112   6.1592e-02
   1_adp:   1.024  0.007  0.071 15.071  0.004  4.112   6.1592e-02
   1_occ:   1.024  0.007  0.071 15.071  0.004  4.112   6.1592e-02
   2_bss:   1.024  0.007  0.071 15.071  0.004  4.112   6.1592e-02
   2_xyz:   0.959  0.006  0.071 14.846  0.004  4.116   5.5396e-02
   2_adp:   0.959  0.006  0.071 14.846  0.004  4.116   5.5396e-02
   2_occ:   0.959  0.006  0.071 14.846  0.004  4.116   5.5396e-02
   3_bss:   0.959  0.006  0.071 14.846  0.004  4.116   5.5396e-02
   3_xyz:   0.946  0.006  0.073 14.874  0.004  4.117   5.5539e-02
   3_adp:   0.946  0.006  0.073 14.874  0.004  4.117   5.5539e-02
   3_occ:   0.946  0.006  0.073 14.874  0.004  4.117   5.5539e-02
   4_bss:   0.946  0.006  0.073 14.874  0.004  4.117   5.5539e-02
   4_xyz:   0.999  0.007  0.075 14.959  0.004  4.118   6.0571e-02
   4_adp:   0.999  0.007  0.075 14.959  0.004  4.118   6.0571e-02
   4_occ:   0.999  0.007  0.075 14.959  0.004  4.118   6.0571e-02
   5_bss:   0.999  0.007  0.075 14.959  0.004  4.118   6.0571e-02
   5_xyz:   0.956  0.006  0.073 14.818  0.004  4.118   5.6223e-02
   5_adp:   0.956  0.006  0.073 14.818  0.004  4.118   5.6223e-02
   5_occ:   0.956  0.006  0.073 14.818  0.004  4.118   5.6223e-02
   5_bss:   0.956  0.006  0.073 14.818  0.004  4.118   5.6223e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4011e-01
   1_xyz:   7.314  0.048  0.320 83.240  0.038  2.353   6.0688e-02
   1_adp:   7.314  0.048  0.320 83.240  0.038  2.353   6.0688e-02
   1_occ:   7.314  0.048  0.320 83.240  0.038  2.353   6.0688e-02
   2_bss:   7.314  0.048  0.320 83.240  0.038  2.353   6.0688e-02
   2_xyz:   6.913  0.034  0.223 84.886  0.037  2.359   3.8042e-02
   2_adp:   6.913  0.034  0.223 84.886  0.037  2.359   3.8042e-02
   2_occ:   6.913  0.034  0.223 84.886  0.037  2.359   3.8042e-02
   3_bss:   6.913  0.034  0.223 84.886  0.037  2.359   3.8042e-02
   3_xyz:   6.737  0.037  0.232 82.995  0.036  2.328   3.6918e-02
   3_adp:   6.737  0.037  0.232 82.995  0.036  2.328   3.6918e-02
   3_occ:   6.737  0.037  0.232 82.995  0.036  2.328   3.6918e-02
   4_bss:   6.737  0.037  0.232 82.995  0.036  2.328   3.6918e-02
   4_xyz:   6.692  0.041  0.237 83.606  0.037  2.322   4.3282e-02
   4_adp:   6.692  0.041  0.237 83.606  0.037  2.322   4.3282e-02
   4_occ:   6.692  0.041  0.237 83.606  0.037  2.322   4.3282e-02
   5_bss:   6.692  0.041  0.237 83.606  0.037  2.322   4.3282e-02
   5_xyz:   6.555  0.041  0.229 83.085  0.035  2.344   3.7863e-02
   5_adp:   6.555  0.041  0.229 83.085  0.035  2.344   3.7863e-02
   5_occ:   6.555  0.041  0.229 83.085  0.035  2.344   3.7863e-02
   5_bss:   6.555  0.041  0.229 83.085  0.035  2.344   3.7863e-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:  72.03   1.16  16.92  72.03   1.16  13.03  66.58   7.36  38.10
   1_occ:  72.03   1.16  16.92  72.03   1.16  13.03  66.58   7.36  38.10
   2_bss:  72.03   1.16  16.92  72.03   1.16  13.03  66.58   7.36  38.10
   2_xyz:  72.03   1.16  16.92  72.03   1.16  13.03  66.58   7.36  38.10
   2_adp:  72.91   2.16  16.74  72.91   2.16  12.94  67.86   5.33  37.44
   2_occ:  72.91   2.16  16.74  72.91   2.16  12.94  67.86   5.33  37.44
   3_bss:  72.91   2.16  16.74  72.91   2.16  12.94  67.86   5.33  37.44
   3_xyz:  72.91   2.16  16.74  72.91   2.16  12.94  67.86   5.33  37.44
   3_adp:  77.02   1.39  16.87  77.02   1.39  12.91  69.87   4.98  38.41
   3_occ:  77.02   1.39  16.87  77.02   1.39  12.91  69.87   4.98  38.41
   4_bss:  77.02   1.39  16.87  77.02   1.39  12.91  69.87   4.98  38.41
   4_xyz:  77.02   1.39  16.87  77.02   1.39  12.91  69.87   4.98  38.41
   4_adp:  88.93   0.66  16.99  88.93   0.66  12.89  76.10   6.47  39.32
   4_occ:  88.93   0.66  16.99  88.93   0.66  12.89  76.10   6.47  39.32
   5_bss:  88.93   0.66  16.99  88.93   0.66  12.89  76.10   6.47  39.32
   5_xyz:  88.93   0.66  16.99  88.93   0.66  12.89  76.10   6.47  39.32
   5_adp:  89.33   0.68  16.82  89.33   0.68  12.73  76.16   6.31  39.12
   5_occ:  89.33   0.68  16.82  89.33   0.68  12.73  76.16   6.31  39.12
   5_bss:  89.30   0.65  16.80  89.30   0.65  12.71  76.14   6.28  39.09
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.025    0.014    0.265
   1_adp:    1.025    0.014    0.265
   1_occ:    1.025    0.014    0.265
   2_bss:    1.025    0.014    0.265
   2_xyz:    0.772    0.021    0.296
   2_adp:    0.772    0.021    0.296
   2_occ:    0.772    0.021    0.296
   3_bss:    0.772    0.021    0.296
   3_xyz:    0.990    0.023    0.314
   3_adp:    0.990    0.023    0.314
   3_occ:    0.990    0.023    0.314
   4_bss:    0.990    0.023    0.314
   4_xyz:    0.970    0.025    0.325
   4_adp:    0.970    0.025    0.325
   4_occ:    0.970    0.025    0.325
   5_bss:    0.970    0.025    0.325
   5_xyz:    1.075    0.025    0.328
   5_adp:    1.075    0.025    0.328
   5_occ:    1.075    0.025    0.328
   5_bss:    1.075    0.025    0.328
------------------------------------------------------------------------

CPU time actual refinement: 263.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/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_783/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_783/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 262.97 
  Macro-tasks:
    bulk solvent and scale       = 30.67  
    individual site refinement   = 103.91 
    weights calculation          = 24.46  
    collect and process          = 5.54   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 164.66 
  Micro-tasks:
    mask                            = 1.01   
    f_calc                          = 83.22  
    alpha_beta                      = 7.11   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 89.74  
    fmodel                         = 5.48   
    r_factors                      = 0.10   
    phase_errors                   = 9.17   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 197.08 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.801 micro seconds
Total CPU time: 4.58 minutes
from_scatterers_fft:    631 calls, 82.87 s
gradients_fft:          576 calls, 78.74 s

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

# Date 2008-01-16 Time 05:37:47 PST -0800 (1200490667.87 s)
Start R-work = 0.2862, R-free = 0.2902 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.2684, R-free = 0.2724
Final R-work = 0.1062, R-free = 0.1561