# Date 2008-01-16 Time 06:07:39 PST -0800 (1200492459.37 s)
#phil __OFF__

Command line arguments: "../1019.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28129
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1019

-------------------------------------------------------------------------------
  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: (71.3037, 46.6953, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.99287
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953468

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9929

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: (71.3037, 46.6953, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.99287
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953468

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2649 [2153/2178]  1938   215  10.0%
  bin  2:  4.2649 -  3.3976 [2053/2073]  1848   205  10.0%
  bin  3:  3.3976 -  2.9717 [2057/2076]  1848   209  10.2%
  bin  4:  2.9717 -  2.7017 [2007/2037]  1810   197   9.8%
  bin  5:  2.7017 -  2.5090 [2023/2042]  1824   199   9.8%
  bin  6:  2.5090 -  2.3616 [1997/2022]  1790   207  10.4%
  bin  7:  2.3616 -  2.2437 [1981/2009]  1785   196   9.9%
  bin  8:  2.2437 -  2.1463 [1988/2024]  1792   196   9.9%
  bin  9:  2.1463 -  2.0639 [1963/2005]  1763   200  10.2%
  bin 10:  2.0639 -  1.9929 [1367/2017]  1232   135   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2172
        3.04 -     3.66: 4634
        3.66 -     4.28: 8944
        4.28 -     4.90: 12274
  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 341 " - " O   HOH Z 207 "  2.154 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.154 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28029 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_1019/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 = 71.30375 46.69535 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3262   r_free= 0.3194   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.036562                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.2837 0.2603      6.3439      6.2508|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.2597 0.2476      6.4334      6.3783|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.2733 0.2653      6.3003      6.3463|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.2946 0.3134      6.2055      6.2033|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.3448 0.3166      6.1118      6.1129|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.3268 0.3204      5.9916       5.942|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.3555 0.3741      6.0169      6.0911|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.3648 0.3301      5.9803      5.9232|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.3659 0.3394      5.9211      5.8721|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.3736 0.3769      5.9079      5.8851|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.3904 0.4032      5.8797      5.9432|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.3751 0.3847      5.8071      5.8672|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.3952 0.3879      5.7139      5.6513|
| 14:  2.0426 -  1.9929 0.55    720   81 0.3731 0.3922      5.6724      5.6788|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7571  1397   155  0.81  24.06   0.86     0.83      36737.26|
|  2:  4.7571 -  3.7952  1345   152  0.86  20.50   0.97     0.92      40773.10|
|  3:  3.7952 -  3.3212  1318   141  0.81  25.13   0.99     0.94      42050.62|
|  4:  3.3212 -  3.0201  1314   152  0.79  27.88   0.99     0.92      37863.81|
|  5:  3.0201 -  2.8051  1305   147  0.72  33.84   0.98     0.89      33193.19|
|  6:  2.8051 -  2.6406  1301   136  0.72  34.09   0.99     0.87      27990.69|
|  7:  2.6406 -  2.5090  1288   142  0.71  34.50   0.99     0.87      26175.02|
|  8:  2.5090 -  2.4002  1274   145  0.71  34.67   0.99     0.89      23750.41|
|  9:  2.4002 -  2.3081  1260   147  0.71  34.86   1.01     0.91      22702.62|
| 10:  2.3081 -  2.2287  1300   142  0.68  37.23   1.04     0.90      22171.72|
| 11:  2.2287 -  2.1592  1276   138  0.66  39.02   1.02     0.88      22578.90|
| 12:  2.1592 -  2.0977  1250   139  0.66  39.56   1.03     0.87      21181.10|
| 13:  2.0977 -  2.0426  1282   142  0.64  41.16   1.01     0.88      18169.30|
| 14:  2.0426 -  1.9929   720    81  0.68  37.34   1.04     0.89      14310.86|
|alpha:            min =        0.83 max =            0.94 mean =         0.89|
|beta:             min =    14310.86 max =        42050.62 mean =     28437.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.73|
|phase err.(work): min =        0.00 max =           89.93 mean =        32.86|
|phase err.(test): min =        0.00 max =           89.87 mean =        32.42|
|-----------------------------------------------------------------------------|

============================== 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 = 5.051230              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.719   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658506              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.756   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      194 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1978 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1828 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2806 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4598 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4346 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5606 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6668 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.138 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3262   r_free= 0.3194   ksol= 0.00   Bsol= 0.00   scale= 0.963    |
|                                                                             |
| 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:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.036562                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3139   r_free= 0.3099   ksol= 0.33   Bsol= 63.80   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-2.59,0.27,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 6.015778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.502136              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.853   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362729              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.505   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3139      final r-factor (work) = 0.1693          |
| start r-factor (free) = 0.3099      final r-factor (free) = 0.1915          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7141 = 4.50 * 0.50 * 6.0208 + 1.00 * 0.1609                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9331 = 4.50 * 0.50 * 5.7159 + 1.00 * 0.0662                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1693      final r-factor (work) = 0.1533          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0795 = 0.36 * 1.00 * 5.7159 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9632 = 0.36 * 1.00 * 5.3876 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    74.20   17.30    None  None   None       |
|    all(noH): 2823   0      0.87    74.20   17.30    None  None   None       |
|    Sol.    : 438    0      4.15    74.20   39.99    None  None   None       |
|    Mac.    : 2385   0      0.87    67.72   13.13    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:     0.872 -   8.205:  541   |   5:    37.537 -  44.871:   97        |
|      1:     8.205 -  15.538: 1320   |   6:    44.871 -  52.204:   87        |
|      2:    15.538 -  22.871:  401   |   7:    52.204 -  59.537:   77        |
|      3:    22.871 -  30.204:  157   |   8:    59.537 -  66.870:   34        |
|      4:    30.204 -  37.537:   96   |   9:    66.870 -  74.203:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1533 r_free = 0.1982             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1529 r_free = 0.1978             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1529   r_free= 0.1978   ksol= 0.33   Bsol= 63.80   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,-2.59,0.27,-0.00,0.00,0.00); trace/3= -0.83                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.399069                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.1956   ksol= 0.33   Bsol= 63.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-3.08,-1.09,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.398579                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.205562              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.713  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.168172              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.782  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1517      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0265 = 2.21 * 0.50 * 5.4047 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9186 = 2.21 * 0.50 * 5.3138 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1675      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9026 = 0.17 * 1.00 * 5.3138 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8853 = 0.17 * 1.00 * 5.2201 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    75.39   17.00    None  None   None       |
|    all(noH): 2823   0      1.61    75.39   17.00    None  None   None       |
|    Sol.    : 438    0      6.50    75.39   38.46    None  None   None       |
|    Mac.    : 2385   0      1.61    70.34   13.05    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:     1.609 -   8.987:  685   |   5:    38.500 -  45.878:  100        |
|      1:     8.987 -  16.365: 1271   |   6:    45.878 -  53.256:   87        |
|      2:    16.365 -  23.743:  349   |   7:    53.256 -  60.634:   57        |
|      3:    23.743 -  31.122:  135   |   8:    60.634 -  68.012:   20        |
|      4:    31.122 -  38.500:  110   |   9:    68.012 -  75.391:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1623             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1622             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1622   ksol= 0.33   Bsol= 63.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-3.08,-1.09,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.201849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1619   ksol= 0.33   Bsol= 63.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.94,-1.23,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200307                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.216345              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.231  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198342              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.115  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8423 = 2.22 * 0.50 * 5.2191 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7952 = 2.22 * 0.50 * 5.1718 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0331 = 0.20 * 1.00 * 5.1718 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0297 = 0.20 * 1.00 * 5.1540 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.46    75.95   16.91    None  None   None       |
|    all(noH): 2823   0      1.46    75.95   16.91    None  None   None       |
|    Sol.    : 438    0      6.51    75.95   38.30    None  None   None       |
|    Mac.    : 2385   0      1.46    71.35   12.99    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:     1.458 -   8.907:  682   |   5:    38.704 -  46.153:   99        |
|      1:     8.907 -  16.356: 1283   |   6:    46.153 -  53.602:   88        |
|      2:    16.356 -  23.805:  342   |   7:    53.602 -  61.051:   53        |
|      3:    23.805 -  31.254:  132   |   8:    61.051 -  68.500:   19        |
|      4:    31.254 -  38.704:  118   |   9:    68.500 -  75.949:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1131 r_free = 0.1565             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1565             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1565   ksol= 0.33   Bsol= 63.80   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.94,-1.23,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1566   ksol= 0.32   Bsol= 57.15   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.78,-1.18,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150326                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.402425              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.264  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619454              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.771  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6780 = 1.40 * 0.50 * 5.1539 + 1.00 * 0.0640                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6705 = 1.40 * 0.50 * 5.1594 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2034 = 0.62 * 1.00 * 5.1594 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2058 = 0.62 * 1.00 * 5.1607 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    78.32   17.10    None  None   None       |
|    all(noH): 2823   0      0.50    78.32   17.10    None  None   None       |
|    Sol.    : 438    0      6.11    78.32   39.49    None  None   None       |
|    Mac.    : 2385   0      0.50    77.46   12.98    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:     0.501 -   8.283:  598   |   5:    39.413 -  47.195:  101        |
|      1:     8.283 -  16.066: 1336   |   6:    47.195 -  54.977:   92        |
|      2:    16.066 -  23.848:  362   |   7:    54.977 -  62.760:   57        |
|      3:    23.848 -  31.630:  137   |   8:    62.760 -  70.542:   24        |
|      4:    31.630 -  39.413:  108   |   9:    70.542 -  78.324:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1595             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1142 r_free = 0.1594             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1594   ksol= 0.32   Bsol= 57.15   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.78,-1.18,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165171                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1593   ksol= 0.32   Bsol= 57.15   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.60,-1.03,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.457541              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 163.363  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.257982              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.571  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9749 = 3.46 * 0.50 * 5.1611 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9657 = 3.46 * 0.50 * 5.1419 + 1.00 * 0.0766                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1079          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 42.4703 = 8.26 * 1.00 * 5.1419 + 1.00 * 0.0089                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 42.3984 = 8.26 * 1.00 * 5.1330 + 1.00 * 0.0105                              |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.41   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    87.41   17.24    None  None   None       |
|    Sol.    : 438    0      5.85    85.99   40.79    None  None   None       |
|    Mac.    : 2385   0      0.00    87.41   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.741:  776   |   5:    43.704 -  52.445:   95        |
|      1:     8.741 -  17.482: 1271   |   6:    52.445 -  61.186:   84        |
|      2:    17.482 -  26.223:  298   |   7:    61.186 -  69.927:   42        |
|      3:    26.223 -  34.963:  133   |   8:    69.927 -  78.668:   16        |
|      4:    34.963 -  43.704:  101   |   9:    78.668 -  87.409:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1079 r_free = 0.1596             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1596             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1596   ksol= 0.32   Bsol= 57.15   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-2.60,-1.03,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.134775                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.0959 0.1311      5.3751      5.5413|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.0815 0.1108      5.4147      5.6134|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.1023 0.1508      5.4532      5.8627|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.1163 0.1671      5.4446      5.5989|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.1312 0.1795      5.3216      5.5945|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.1180 0.1840       5.202      5.4471|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.1235 0.1620      5.1583      5.3616|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.1093 0.1689      5.0382      5.3063|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.1117 0.1762      5.0127      5.2984|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.1060 0.1797      4.9329      5.2484|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.1098 0.1749      4.9365      5.2542|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.1076 0.1737        4.88      5.1764|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.1099 0.1797      4.7837      5.0651|
| 14:  2.0426 -  1.9929 0.55    720   81 0.0989 0.1655       4.663       4.922|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7571  1397   155  0.94   9.39   0.97     0.94       7481.63|
|  2:  4.7571 -  3.7952  1345   152  0.95   7.94   1.00     0.99       9098.57|
|  3:  3.7952 -  3.3212  1318   141  0.93  11.13   1.02     1.01      10089.36|
|  4:  3.3212 -  3.0201  1314   152  0.92  13.85   1.00     0.98      10518.10|
|  5:  3.0201 -  2.8051  1305   147  0.90  16.12   0.99     0.97       8562.05|
|  6:  2.8051 -  2.6406  1301   136  0.90  16.51   0.98     0.95       7270.74|
|  7:  2.6406 -  2.5090  1288   142  0.91  15.56   0.98     0.95       6262.86|
|  8:  2.5090 -  2.4002  1274   145  0.91  15.04   0.98     0.96       5151.32|
|  9:  2.4002 -  2.3081  1260   147  0.91  15.10   0.99     0.95       4885.39|
| 10:  2.3081 -  2.2287  1300   142  0.90  15.70   0.98     0.95       4369.08|
| 11:  2.2287 -  2.1592  1276   138  0.90  16.31   0.97     0.93       4387.44|
| 12:  2.1592 -  2.0977  1250   139  0.91  15.34   0.99     0.98       4105.77|
| 13:  2.0977 -  2.0426  1282   142  0.90  16.72   0.97     0.95       3440.56|
| 14:  2.0426 -  1.9929   720    81  0.92  14.52   0.95     0.92       2675.11|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2675.11 max =        10518.10 mean =      6464.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.16|
|phase err.(test): min =        0.00 max =           89.61 mean =        13.65|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1595   ksol= 0.32   Bsol= 57.76   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.27,-0.74,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.134872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1595   ksol= 0.32   Bsol= 57.76   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,-2.27,-0.74,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.134872                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7571 0.99   1397  155 0.0960 0.1314      5.3758       5.543|
|  2:  4.7571 -  3.7952 0.99   1345  152 0.0816 0.1108      5.4156      5.6135|
|  3:  3.7952 -  3.3212 0.99   1318  141 0.1024 0.1507      5.4532      5.8628|
|  4:  3.3212 -  3.0201 0.99   1314  152 0.1163 0.1671      5.4444      5.5988|
|  5:  3.0201 -  2.8051 0.99   1305  147 0.1311 0.1793      5.3213      5.5936|
|  6:  2.8051 -  2.6406 0.99   1301  136 0.1180 0.1840      5.2019      5.4472|
|  7:  2.6406 -  2.5090 0.99   1288  142 0.1235 0.1620      5.1584      5.3617|
|  8:  2.5090 -  2.4002 0.98   1274  145 0.1093 0.1689      5.0382      5.3059|
|  9:  2.4002 -  2.3081 0.98   1260  147 0.1116 0.1763      5.0129      5.2987|
| 10:  2.3081 -  2.2287 1.00   1300  142 0.1060 0.1796       4.933      5.2474|
| 11:  2.2287 -  2.1592 0.98   1276  138 0.1097 0.1749      4.9366      5.2542|
| 12:  2.1592 -  2.0977 0.98   1250  139 0.1076 0.1737      4.8796      5.1761|
| 13:  2.0977 -  2.0426 0.99   1282  142 0.1099 0.1797      4.7837      5.0647|
| 14:  2.0426 -  1.9929 0.55    720   81 0.0989 0.1656      4.6635      4.9227|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7571  1397   155  0.94   9.41   0.97     0.94       7498.58|
|  2:  4.7571 -  3.7952  1345   152  0.95   7.95   1.01     1.00       9112.22|
|  3:  3.7952 -  3.3212  1318   141  0.93  11.14   1.02     1.02      10091.43|
|  4:  3.3212 -  3.0201  1314   152  0.92  13.85   1.01     0.99      10515.05|
|  5:  3.0201 -  2.8051  1305   147  0.90  16.13   1.00     0.98       8559.55|
|  6:  2.8051 -  2.6406  1301   136  0.90  16.51   0.99     0.96       7267.25|
|  7:  2.6406 -  2.5090  1288   142  0.91  15.56   0.99     0.96       6262.06|
|  8:  2.5090 -  2.4002  1274   145  0.91  15.04   0.99     0.97       5150.92|
|  9:  2.4002 -  2.3081  1260   147  0.91  15.11   1.00     0.96       4886.22|
| 10:  2.3081 -  2.2287  1300   142  0.90  15.70   1.00     0.97       4368.20|
| 11:  2.2287 -  2.1592  1276   138  0.90  16.31   0.99     0.94       4384.41|
| 12:  2.1592 -  2.0977  1250   139  0.91  15.33   1.01     1.00       4102.42|
| 13:  2.0977 -  2.0426  1282   142  0.90  16.72   0.99     0.96       3439.92|
| 14:  2.0426 -  1.9929   720    81  0.92  14.53   0.97     0.94       2677.64|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2677.64 max =        10515.05 mean =      6466.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.17|
|phase err.(test): min =        0.00 max =           89.64 mean =        13.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.141)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.41   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    87.41   17.25    None  None   None       |
|    Sol.    : 438    0      5.85    85.99   40.79    None  None   None       |
|    Mac.    : 2385   0      0.00    87.41   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.744:  776   |   5:    43.707 -  52.448:   95        |
|      1:     8.744 -  17.485: 1271   |   6:    52.448 -  61.189:   84        |
|      2:    17.485 -  26.226:  298   |   7:    61.189 -  69.930:   42        |
|      3:    26.226 -  34.966:  133   |   8:    69.930 -  78.671:   16        |
|      4:    34.966 -  43.707:  101   |   9:    78.671 -  87.411:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 4.737
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 291
   mapped sites are within: 0.704 - 4.737

peak=    5.672 closest distance to " NH2 ARG A  56 " =    2.196
peak=    5.364 closest distance to " NE2 GLN A  11 " =    1.118
peak=    5.171 closest distance to " CB  GLN A 223 " =    1.438
peak=    5.160 closest distance to " O   HOH Z 232 " =    2.292
peak=    5.123 closest distance to " CG  PRO A  54 " =    1.241
peak=    5.032 closest distance to " O   HOH Z 144 " =    1.783
peak=    4.930 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.802 closest distance to " O   HOH Z 298 " =    2.004
peak=    4.733 closest distance to " CB  SER A  63 " =    1.196
peak=    4.730 closest distance to " O   HOH Z  78 " =    1.725
peak=    4.684 closest distance to " CB  ARG A  79 " =    1.440
peak=    4.657 closest distance to " O   HOH Z 126 " =    1.891
peak=    4.563 closest distance to " CB  ARG A 275 " =    0.941
peak=    4.554 closest distance to " CB  LEU A 228 " =    1.117
peak=    4.519 closest distance to " O   HOH Z  15 " =    2.180
peak=    4.455 closest distance to " CB  ARG A 190 " =    1.618
peak=    4.378 closest distance to " CA  TYR A  30 " =    0.982
peak=    4.336 closest distance to " CG  PRO A 213 " =    1.157
peak=    4.279 closest distance to " O   HOH Z 427 " =    2.984
peak=    4.268 closest distance to " C   PRO A 198 " =    1.505
peak=    4.268 closest distance to " CB  PRO A  54 " =    0.922
peak=    4.256 closest distance to " CD  ARG A 159 " =    0.776
peak=    4.249 closest distance to " O   HOH Z 369 " =    2.178
peak=    4.201 closest distance to " O   HOH Z 287 " =    2.224
peak=    4.180 closest distance to " O   HOH Z  78 " =    2.145
peak=    4.179 closest distance to " O   HOH Z 250 " =    1.509
peak=    4.178 closest distance to " CB  ASN A 148 " =    1.440
peak=    4.114 closest distance to " CZ  PHE A 218 " =    1.055
peak=    4.108 closest distance to " CB  TRP A 266 " =    1.028
peak=    4.087 closest distance to " O   HOH Z 158 " =    3.013
peak=    4.068 closest distance to " CE  LYS A  76 " =    0.842
peak=    4.064 closest distance to " CB  SER A 212 " =    1.094
peak=    4.055 closest distance to " NZ  LYS A 117 " =    3.202
peak=    4.043 closest distance to " O   HOH Z 272 " =    1.823
peak=    4.035 closest distance to " O   HOH Z 303 " =    2.188
peak=    4.033 closest distance to " NH1AARG A 145 " =    1.244
peak=    4.029 closest distance to " O   HOH Z 193 " =    1.850
peak=    4.024 closest distance to " O   HOH Z 234 " =    3.822
peak=    4.023 closest distance to " CB  VAL A 265 " =    1.257
peak=    4.006 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.003 closest distance to " CD  ARG A  66 " =    2.246
peak=    4.003 closest distance to " O   HOH Z 180 " =    2.111
peak=    3.999 closest distance to " ND2 ASN A 187 " =    1.382
peak=    3.989 closest distance to " OD1 ASN A  69 " =    2.628
peak=    3.969 closest distance to " CG  LEU A 167 " =    1.263
peak=    3.969 closest distance to " CB  ASP A 140 " =    1.053
peak=    3.968 closest distance to " CB  GLU A 152 " =    1.254
peak=    3.961 closest distance to " O   HOH Z 316 " =    3.099
peak=    3.957 closest distance to " O   HOH Z 133 " =    2.444
peak=    3.942 closest distance to " O   HOH Z  61 " =    1.591
peak=    3.934 closest distance to " O   HOH Z  53 " =    2.539
peak=    3.916 closest distance to " O   HOH Z 368 " =    2.174
peak=    3.908 closest distance to " CG2 VAL A 257 " =    0.899
peak=    3.906 closest distance to " O   HOH Z 189 " =    2.753
peak=    3.886 closest distance to " CB  GLU A 277 " =    3.686
peak=    3.884 closest distance to " CD  ARG A  66 " =    2.281
peak=    3.874 closest distance to " O   HOH Z 214 " =    2.138
peak=    3.856 closest distance to " O   HOH Z 346 " =    1.619
peak=    3.843 closest distance to " O   HOH Z  54 " =    2.371
peak=    3.837 closest distance to " O   HOH Z   1 " =    2.027
peak=    3.825 closest distance to " O   HOH Z 261 " =    1.957
peak=    3.822 closest distance to " CB  GLU A 128 " =    1.010
peak=    3.816 closest distance to " CA  ASN A 215 " =    1.214
peak=    3.815 closest distance to " CD1 LEU A 300 " =    1.185
peak=    3.812 closest distance to " CB  TYR A 169 " =    0.808
peak=    3.806 closest distance to " CD2 TRP A 179 " =    1.356
peak=    3.805 closest distance to " O   HOH Z  63 " =    2.010
peak=    3.805 closest distance to " O   HOH Z 392 " =    3.097
peak=    3.801 closest distance to " ND1 HIS A  86 " =    1.797
peak=    3.751 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.741 closest distance to " CD BLYS A 290 " =    0.951
peak=    3.732 closest distance to " CG2 THR A 221 " =    1.081
peak=    3.722 closest distance to " O   HOH Z 371 " =    3.038
peak=    3.713 closest distance to " CA  ARG A 195 " =    1.252
peak=    3.702 closest distance to " C   ILE A 106 " =    1.922
peak=    3.700 closest distance to " CB  GLN A  88 " =    1.261
peak=    3.689 closest distance to " O   HOH Z 285 " =    2.545
peak=    3.686 closest distance to " O   HOH Z 313 " =    1.932
peak=    3.676 closest distance to " O   HOH Z 391 " =    2.886
peak=    3.676 closest distance to " O   HOH Z  88 " =    3.910
peak=    3.674 closest distance to " CB  ASN A 187 " =    1.292
peak=    3.663 closest distance to " NH2 ARG A 156 " =    1.248
peak=    3.663 closest distance to " CA  ALA A 158 " =    1.197
peak=    3.663 closest distance to " CB  SER A   3 " =    1.361
peak=    3.660 closest distance to " N   ASN A 127 " =    1.298
peak=    3.657 closest distance to " CA  ALA A  51 " =    0.936
peak=    3.649 closest distance to " O   HOH Z 172 " =    3.284
peak=    3.648 closest distance to " O   HOH Z 426 " =    1.846
peak=    3.644 closest distance to " O   HOH Z 132 " =    2.582
peak=    3.633 closest distance to " CD  LYS A 166 " =    1.229
peak=    3.629 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.622 closest distance to " O   HOH Z 193 " =    1.711
peak=    3.621 closest distance to " O  BHOH Z 338 " =    2.368
peak=    3.614 closest distance to " O   HOH Z 213 " =    2.121
peak=    3.613 closest distance to " O   HOH Z  10 " =    1.838
peak=    3.597 closest distance to " CA  THR A 221 " =    0.992
peak=    3.586 closest distance to " CB  ALA A  34 " =    0.923
peak=    3.581 closest distance to " O   HOH Z 185 " =    1.881
peak=    3.578 closest distance to " CA  MET A  40 " =    1.221
peak=    3.576 closest distance to " O   HOH Z 203 " =    1.785
peak=    3.574 closest distance to " O   HOH Z 368 " =    3.630
peak=    3.569 closest distance to " O   HOH Z  21 " =    1.737
peak=    3.562 closest distance to " CB  THR A  82 " =    1.360
peak=    3.548 closest distance to " O   SER A  87 " =    2.300
peak=    3.546 closest distance to " CB  ASN A 142 " =    1.016
peak=    3.545 closest distance to " CD  ARG A 269 " =    0.904
peak=    3.545 closest distance to " O   HOH Z 280 " =    3.035
peak=    3.543 closest distance to " CA  PRO A  54 " =    1.360
peak=    3.542 closest distance to " CB  GLU A  46 " =    0.998
peak=    3.541 closest distance to " O   HOH Z 389 " =    1.944
peak=    3.532 closest distance to " O   HOH Z 406 " =    1.553
peak=    3.532 closest distance to " CA  THR A 264 " =    0.896
peak=    3.529 closest distance to " O   HOH Z 411 " =    3.770
peak=    3.527 closest distance to " CB  MET A  40 " =    0.805
peak=    3.522 closest distance to " CB  ASN A  39 " =    0.907
peak=    3.522 closest distance to " O   TYR A 116 " =    1.273
peak=    3.522 closest distance to " CG  PRO A 243 " =    1.099
peak=    3.515 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.515 closest distance to " CD2 LEU A 297 " =    0.876
peak=    3.514 closest distance to " OD2 ASP A 286 " =    2.866
peak=    3.510 closest distance to " CA  MET A 105 " =    1.024
peak=    3.509 closest distance to " O   HOH Z 166 " =    3.829
peak=    3.506 closest distance to " CG1 ILE A  33 " =    1.193
peak=    3.503 closest distance to " O   HOH Z 329 " =    3.984
peak=    3.502 closest distance to " CD2 LEU A 255 " =    1.495
peak=    3.496 closest distance to " O   HOH Z 148 " =    3.377
peak=    3.495 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.486 closest distance to " NH2BARG A 145 " =    2.120
peak=    3.479 closest distance to " CB  ASN A 110 " =    1.129
peak=    3.474 closest distance to " O   HOH Z 213 " =    2.684
peak=    3.468 closest distance to " O   HOH Z 344 " =    3.151
peak=    3.464 closest distance to " OD1BASN A 224 " =    2.389
peak=    3.461 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.461 closest distance to " O   HOH Z  61 " =    1.465
peak=    3.459 closest distance to " O   HOH Z 218 " =    4.599
peak=    3.451 closest distance to " O   HOH Z  66 " =    2.235
peak=    3.451 closest distance to " CB  ALA A   1 " =    4.737
peak=    3.449 closest distance to " CB  ALA A 104 " =    0.717
peak=    3.447 closest distance to " O   HOH Z 403 " =    1.671
peak=    3.443 closest distance to " O   HOH Z 345 " =    1.728
peak=    3.440 closest distance to " CB  MET A  47 " =    1.039
peak=    3.438 closest distance to " O   HOH Z 108 " =    2.743
peak=    3.433 closest distance to " O   HOH Z 305 " =    3.533
peak=    3.432 closest distance to " CG2AVAL A  72 " =    1.628
peak=    3.431 closest distance to " O   HOH Z 409 " =    2.678
peak=    3.428 closest distance to " O   HOH Z 147 " =    1.822
peak=    3.425 closest distance to " O   HOH Z 425 " =    2.058
peak=    3.415 closest distance to " O   HOH Z 116 " =    3.088
peak=    3.415 closest distance to " O   HOH Z   1 " =    1.662
peak=    3.412 closest distance to " O   THR A 220 " =    1.283
peak=    3.412 closest distance to " CB  TRP A 179 " =    1.522
peak=    3.411 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.411 closest distance to " O   ALA A 158 " =    1.312
peak=    3.410 closest distance to " OG BSER A 164 " =    2.309
peak=    3.404 closest distance to " CG BARG A 275 " =    1.475
peak=    3.404 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.399 closest distance to " CA  TYR A 116 " =    1.302
peak=    3.397 closest distance to " CG1 VAL A 189 " =    2.056
peak=    3.395 closest distance to " N   ARG A 156 " =    1.343
peak=    3.388 closest distance to " O   HOH Z 384 " =    3.030
peak=    3.387 closest distance to " O   HOH Z 227 " =    1.735
peak=    3.382 closest distance to " CB  SER A 216 " =    0.903
peak=    3.374 closest distance to " O   HOH Z 128 " =    2.365
peak=    3.374 closest distance to " CB  PRO A  90 " =    1.210
peak=    3.374 closest distance to " O   HOH Z 282 " =    1.874
peak=    3.373 closest distance to " O   HOH Z 353 " =    2.703
peak=    3.369 closest distance to " O   HOH Z 419 " =    1.986
peak=    3.368 closest distance to " CA  ALA A 291 " =    0.820
peak=    3.368 closest distance to " O   THR A 251 " =    1.179
peak=    3.366 closest distance to " O   HOH Z 325 " =    4.019
peak=    3.358 closest distance to " O   HOH Z 425 " =    1.232
peak=    3.358 closest distance to " O   HOH Z 193 " =    2.113
peak=    3.351 closest distance to " CG1 VAL A 153 " =    0.975
peak=    3.347 closest distance to " ND2 ASN A 249 " =    0.848
peak=    3.346 closest distance to " O   HOH Z 245 " =    1.233
peak=    3.343 closest distance to " OG  SER A  22 " =    2.854
peak=    3.342 closest distance to " CA  ALA A 160 " =    0.954
peak=    3.341 closest distance to " O   HOH Z 291 " =    1.643
peak=    3.337 closest distance to " O   HOH Z 135 " =    1.728
peak=    3.337 closest distance to " CA  ALA A 233 " =    1.225
peak=    3.327 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.322 closest distance to " CA  ALA A  21 " =    1.197
peak=    3.318 closest distance to " CB  VAL A 265 " =    1.969
peak=    3.317 closest distance to " CD  ARG A 219 " =    1.167
peak=    3.315 closest distance to " O   HOH Z  59 " =    1.946
peak=    3.311 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.311 closest distance to " CG2 ILE A 120 " =    1.041
peak=    3.309 closest distance to " CG2 ILE A  20 " =    1.414
peak=    3.304 closest distance to " CA  SER A 146 " =    1.740
peak=    3.304 closest distance to " O   HOH Z 365 " =    2.989
peak=    3.304 closest distance to " O   HOH Z 299 " =    4.407
peak=    3.303 closest distance to " O   HOH Z 133 " =    1.653
peak=    3.301 closest distance to " CA  GLU A  46 " =    0.816
peak=    3.300 closest distance to " O   HOH Z 327 " =    1.829
peak=    3.298 closest distance to " O   HOH Z 273 " =    2.824
peak=    3.298 closest distance to " O   HOH Z 109 " =    2.637
peak=    3.298 closest distance to " CZ3 TRP A 266 " =    1.127
peak=    3.296 closest distance to " CZ  ARG A  14 " =    2.116
peak=    3.296 closest distance to " CA  ALA A 295 " =    1.012
peak=    3.295 closest distance to " CB  ARG A 138 " =    0.994
peak=    3.295 closest distance to " CE  LYS A  48 " =    1.085
peak=    3.294 closest distance to " O   HOH Z 238 " =    3.753
peak=    3.289 closest distance to " NE2 HIS A 207 " =    1.348
peak=    3.285 closest distance to " CB  ASP A 298 " =    1.174
peak=    3.262 closest distance to " CB  THR A 235 " =    1.212
peak=    3.258 closest distance to " N   PHE A 130 " =    1.221
peak=    3.250 closest distance to " NE  ARG A  79 " =    1.154
peak=    3.245 closest distance to " O   HOH Z 371 " =    1.830
peak=    3.244 closest distance to " O   HOH Z 422 " =    2.701
peak=    3.239 closest distance to " CG1 ILE A 151 " =    1.047
peak=    3.233 closest distance to " O   HOH Z 188 " =    2.021
peak=    3.231 closest distance to " CB  ALA A 248 " =    0.916
peak=    3.230 closest distance to " O   HOH Z  44 " =    2.958
peak=    3.230 closest distance to " ND1 HIS A  81 " =    1.619
peak=    3.226 closest distance to " CB  SER A  26 " =    1.727
peak=    3.224 closest distance to " O   HOH Z 437 " =    1.196
peak=    3.220 closest distance to " ND2 ASN A 110 " =    1.607
peak=    3.217 closest distance to " CA  VAL A 125 " =    1.149
peak=    3.217 closest distance to " O   HOH Z 423 " =    1.717
peak=    3.215 closest distance to " O   HOH Z 359 " =    1.396
peak=    3.208 closest distance to " O   HOH Z  40 " =    2.009
peak=    3.203 closest distance to " O   HOH Z 421 " =    2.029
peak=    3.202 closest distance to " OE1 GLN A  55 " =    1.418
peak=    3.201 closest distance to " O   HOH Z  20 " =    1.674
peak=    3.201 closest distance to " CD  GLU A 152 " =    0.808
peak=    3.201 closest distance to " CA  GLY A 267 " =    1.165
peak=    3.201 closest distance to " CD1 ILE A 106 " =    0.714
peak=    3.199 closest distance to " CB  LEU A 237 " =    0.720
peak=    3.196 closest distance to " CB  HIS A 108 " =    0.792
peak=    3.190 closest distance to " CB  ILE A 120 " =    1.363
peak=    3.189 closest distance to " O   HOH Z 407 " =    2.427
peak=    3.189 closest distance to " CB  ASP A 200 " =    1.101
peak=    3.188 closest distance to " CA  SER A  87 " =    1.008
peak=    3.188 closest distance to " CA  ASN A 217 " =    1.208
peak=    3.187 closest distance to " CG  GLN A  89 " =    1.489
peak=    3.186 closest distance to " O   HOH Z 163 " =    1.774
peak=    3.185 closest distance to " CG2 ILE A 234 " =    0.806
peak=    3.181 closest distance to " CB  ALA A 291 " =    1.369
peak=    3.179 closest distance to " CA  LYS A 117 " =    1.226
peak=    3.173 closest distance to " O   HOH Z 383 " =    2.162
peak=    3.170 closest distance to " O   HOH Z 248 " =    1.592
peak=    3.168 closest distance to " CG  ARG A 159 " =    0.882
peak=    3.167 closest distance to " NZ  LYS A  48 " =    1.363
peak=    3.166 closest distance to " CB  PRO A 163 " =    4.178
peak=    3.164 closest distance to " O   HOH Z 126 " =    1.601
peak=    3.161 closest distance to " NH2AARG A 275 " =    3.649
peak=    3.159 closest distance to " OG BSER A  99 " =    2.241
peak=    3.155 closest distance to " O   HOH Z 171 " =    4.042
peak=    3.155 closest distance to " CA  ARG A 159 " =    1.252
peak=    3.150 closest distance to " O   HOH Z 285 " =    1.784
peak=    3.149 closest distance to " O   HOH Z 175 " =    2.197
peak=    3.149 closest distance to " O   ASN A 209 " =    1.298
peak=    3.148 closest distance to " CB  TRP A 150 " =    1.203
peak=    3.142 closest distance to " CA  PRO A 280 " =    1.321
peak=    3.136 closest distance to " O   HOH Z 302 " =    1.898
peak=    3.128 closest distance to " O   HOH Z 124 " =    1.839
peak=    3.124 closest distance to " CB  LEU A  96 " =    1.288
peak=    3.122 closest distance to " CD1 LEU A  96 " =    0.704
peak=    3.120 closest distance to " CA  SER A  32 " =    1.627
peak=    3.118 closest distance to " CD  ARG A 195 " =    3.418
peak=    3.114 closest distance to " CB  LEU A 255 " =    0.775
peak=    3.111 closest distance to " CB  ASN A 285 " =    0.833
peak=    3.111 closest distance to " O   HOH Z 325 " =    2.421
peak=    3.107 closest distance to " CB  ASN A 215 " =    1.146
peak=    3.105 closest distance to " O   HOH Z  97 " =    2.895
peak=    3.097 closest distance to " O   HOH Z 319 " =    2.224
peak=    3.096 closest distance to " CB  LYS A 193 " =    0.990
peak=    3.093 closest distance to " O   HOH Z 345 " =    3.553
peak=    3.093 closest distance to " CB  ASN A 224 " =    0.952
peak=    3.093 closest distance to " O   HOH Z 287 " =    2.163
peak=    3.089 closest distance to " CB  GLN A 103 " =    0.870
peak=    3.081 closest distance to " N   CYS A 260 " =    0.893
peak=    3.080 closest distance to " O   HOH Z  88 " =    2.915
peak=    3.072 closest distance to " O   HOH Z 116 " =    1.805
peak=    3.072 closest distance to " CB  ALA A  43 " =    0.807
peak=    3.068 closest distance to " OD1 ASN A 217 " =    1.787
peak=    3.066 closest distance to " CA  ALA A 100 " =    1.201
peak=    3.064 closest distance to " CG  LYS A  76 " =    0.990
peak=    3.056 closest distance to " CG BARG A 102 " =    1.850
peak=    3.047 closest distance to " O   HOH Z 271 " =    2.420
peak=    3.045 closest distance to " O   HOH Z 423 " =    2.780
peak=    3.039 closest distance to " O   HOH Z 128 " =    2.692
peak=    3.038 closest distance to " OE2 GLU A  53 " =    2.099
peak=    3.013 closest distance to " O   HOH Z 356 " =    3.004

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.741 - 5.731
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.741 - 5.731

peak=   -4.617 closest distance to " O   HOH Z 377 " =    2.102
peak=   -4.578 closest distance to " CD  ARG A  14 " =    3.512
peak=   -4.521 closest distance to " CB  PRO A 243 " =    2.600
peak=   -4.407 closest distance to " CD  ARG A 156 " =    2.065
peak=   -4.318 closest distance to " O   HOH Z 266 " =    5.283
peak=   -4.316 closest distance to " CG  GLN A 223 " =    2.124
peak=   -4.313 closest distance to " O   HOH Z 231 " =    2.253
peak=   -4.275 closest distance to " O   VAL A  67 " =    2.783
peak=   -4.209 closest distance to " OG BSER A 134 " =    1.296
peak=   -4.157 closest distance to " CG1 VAL A 112 " =    2.935
peak=   -4.073 closest distance to " N   ALA A  43 " =    2.694
peak=   -4.054 closest distance to " O   HOH Z 389 " =    2.016
peak=   -4.018 closest distance to " O   PRO A 198 " =    1.318
peak=   -4.012 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -4.003 closest distance to " O   HOH Z 198 " =    2.101
peak=   -3.957 closest distance to " O   HOH Z  73 " =    2.105
peak=   -3.946 closest distance to " CE2 TYR A  30 " =    2.768
peak=   -3.926 closest distance to " CD  GLN A  58 " =    0.974
peak=   -3.921 closest distance to " CB  ALA A  43 " =    2.609
peak=   -3.908 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.887 closest distance to " CE  MET A 105 " =    2.421
peak=   -3.873 closest distance to " CD1 PHE A  59 " =    1.846
peak=   -3.840 closest distance to " CB  ALA A 291 " =    2.227
peak=   -3.818 closest distance to " O   HOH Z  38 " =    1.350
peak=   -3.802 closest distance to " O   HOH Z 435 " =    2.850
peak=   -3.788 closest distance to " OD1 ASP A 171 " =    1.699
peak=   -3.774 closest distance to " NH2AARG A 275 " =    5.522
peak=   -3.768 closest distance to " O   PRO A 163 " =    2.090
peak=   -3.761 closest distance to " O   HOH Z  10 " =    1.518
peak=   -3.756 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.752 closest distance to " O   HOH Z 185 " =    2.266
peak=   -3.741 closest distance to " O   HOH Z 372 " =    2.464
peak=   -3.740 closest distance to " CA  GLY A 203 " =    2.416
peak=   -3.726 closest distance to " OXT GLY A 302 " =    3.033
peak=   -3.722 closest distance to " O   HOH Z 394 " =    1.497
peak=   -3.722 closest distance to " O   HOH Z 114 " =    3.244
peak=   -3.720 closest distance to " O   HOH Z  43 " =    1.617
peak=   -3.718 closest distance to " CG1 VAL A 250 " =    2.621
peak=   -3.700 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -3.699 closest distance to " C   ASN A 285 " =    2.503
peak=   -3.678 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.665 closest distance to " O   HOH Z  52 " =    1.397
peak=   -3.664 closest distance to " ND2 ASN A  45 " =    1.863
peak=   -3.651 closest distance to " O   HOH Z 313 " =    1.864
peak=   -3.650 closest distance to " CG2 ILE A  49 " =    2.719
peak=   -3.642 closest distance to " ND2 ASN A 249 " =    2.415
peak=   -3.629 closest distance to " CE2 PHE A  61 " =    2.636
peak=   -3.619 closest distance to " O   HOH Z 290 " =    1.359
peak=   -3.608 closest distance to " OD1 ASN A 148 " =    1.517
peak=   -3.604 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.600 closest distance to " O   HOH Z  60 " =    2.474
peak=   -3.595 closest distance to " CD2 PHE A 192 " =    2.064
peak=   -3.590 closest distance to " O   HOH Z 407 " =    3.253
peak=   -3.585 closest distance to " CG  MET A 105 " =    0.958
peak=   -3.580 closest distance to " C   GLY A  17 " =    1.158
peak=   -3.576 closest distance to " CD  ARG A 195 " =    5.230
peak=   -3.567 closest distance to " N   THR A 157 " =    1.529
peak=   -3.565 closest distance to " CD2 LEU A 237 " =    2.891
peak=   -3.562 closest distance to " O   HOH Z 126 " =    1.898
peak=   -3.561 closest distance to " CB  TRP A  85 " =    2.509
peak=   -3.559 closest distance to " O   HOH Z 198 " =    1.501
peak=   -3.558 closest distance to " O   HOH Z 253 " =    4.009
peak=   -3.555 closest distance to " CG  ARG A 269 " =    2.587
peak=   -3.555 closest distance to " O   PHE A 218 " =    1.568
peak=   -3.553 closest distance to " O   HOH Z 353 " =    2.153
peak=   -3.551 closest distance to " O   HOH Z  51 " =    1.628
peak=   -3.546 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.541 closest distance to " CG2 THR A 178 " =    2.287
peak=   -3.528 closest distance to " CD2 TYR A 293 " =    1.978
peak=   -3.528 closest distance to " CG  PHE A 283 " =    2.706
peak=   -3.527 closest distance to " CD1 LEU A 101 " =    2.340
peak=   -3.525 closest distance to " C   LEU A 222 " =    0.741
peak=   -3.524 closest distance to " CA  GLY A 241 " =    3.140
peak=   -3.521 closest distance to " CD1 LEU A 228 " =    2.409
peak=   -3.517 closest distance to " CB  ASN A  39 " =    2.301
peak=   -3.512 closest distance to " O   HOH Z 196 " =    2.129
peak=   -3.509 closest distance to " CB  ASP A 286 " =    2.204
peak=   -3.502 closest distance to " NH2BARG A 275 " =    1.815
peak=   -3.500 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.485 closest distance to " O   ILE A 109 " =    2.608
peak=   -3.484 closest distance to " O   VAL A  67 " =    2.943
peak=   -3.476 closest distance to " ND2 ASN A  45 " =    1.228
peak=   -3.475 closest distance to " CE BMET A  47 " =    1.555
peak=   -3.474 closest distance to " ND2BASN A 224 " =    1.704
peak=   -3.471 closest distance to " CG2 ILE A 263 " =    2.303
peak=   -3.466 closest distance to " CD  ARG A 139 " =    1.567
peak=   -3.464 closest distance to " CD2 PHE A 225 " =    1.150
peak=   -3.462 closest distance to " NE2 GLN A 194 " =    1.780
peak=   -3.454 closest distance to " N   ASP A 171 " =    2.407
peak=   -3.453 closest distance to " OD1 ASN A 187 " =    1.599
peak=   -3.422 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.417 closest distance to " ND2 ASN A  60 " =    1.450
peak=   -3.415 closest distance to " CG1 VAL A 197 " =    2.254
peak=   -3.411 closest distance to " O   GLY A 211 " =    1.424
peak=   -3.405 closest distance to " O   HOH Z 295 " =    1.604
peak=   -3.402 closest distance to " CE3 TRP A 150 " =    2.146
peak=   -3.401 closest distance to " CD2 TYR A 247 " =    2.434
peak=   -3.401 closest distance to " CZ  PHE A  59 " =    1.625
peak=   -3.396 closest distance to " CG  TRP A 266 " =    1.682
peak=   -3.386 closest distance to " O   HOH Z 111 " =    1.787
peak=   -3.385 closest distance to " O   HOH Z  11 " =    1.753
peak=   -3.382 closest distance to " O   HOH Z 281 " =    2.656
peak=   -3.382 closest distance to " CD2 PHE A  61 " =    2.061
peak=   -3.378 closest distance to " O   HOH Z 350 " =    1.806
peak=   -3.377 closest distance to " CB  ALA A 100 " =    2.148
peak=   -3.377 closest distance to " CA  SER A 135 " =    1.350
peak=   -3.369 closest distance to " O   HOH Z 189 " =    1.984
peak=   -3.369 closest distance to " O   HOH Z 311 " =    3.818
peak=   -3.368 closest distance to " CG1 VAL A 125 " =    1.910
peak=   -3.366 closest distance to " O   PRO A 198 " =    1.395
peak=   -3.362 closest distance to " CB  PRO A  54 " =    2.471
peak=   -3.355 closest distance to " O   HOH Z 359 " =    3.145
peak=   -3.348 closest distance to " OD1 ASP A 191 " =    1.886
peak=   -3.347 closest distance to " CA  GLY A 241 " =    2.296
peak=   -3.347 closest distance to " NE2 GLN A  88 " =    1.943
peak=   -3.346 closest distance to " O   HOH Z 298 " =    1.281
peak=   -3.345 closest distance to " N   ALA A 248 " =    1.595
peak=   -3.345 closest distance to " CB  PRO A 163 " =    2.505
peak=   -3.343 closest distance to " O   HOH Z 102 " =    1.586
peak=   -3.339 closest distance to " C   LEU A 143 " =    1.244
peak=   -3.329 closest distance to " O   SER A 135 " =    1.434
peak=   -3.327 closest distance to " O   HOH Z   6 " =    1.513
peak=   -3.323 closest distance to " O   HOH Z 166 " =    1.927
peak=   -3.320 closest distance to " CB  ALA A 248 " =    2.428
peak=   -3.317 closest distance to " O   HOH Z 243 " =    2.006
peak=   -3.317 closest distance to " SD  MET A 188 " =    2.255
peak=   -3.313 closest distance to " CE2 PHE A 218 " =    2.401
peak=   -3.309 closest distance to " O   HOH Z 103 " =    1.885
peak=   -3.308 closest distance to " O   HOH Z  90 " =    1.656
peak=   -3.302 closest distance to " CG  PRO A 163 " =    2.352
peak=   -3.300 closest distance to " O   HOH Z 132 " =    1.547
peak=   -3.296 closest distance to " O   HOH Z 111 " =    1.415
peak=   -3.293 closest distance to " O   TRP A  70 " =    1.435
peak=   -3.292 closest distance to " CB  ALA A 129 " =    2.457
peak=   -3.291 closest distance to " N   SER A 276 " =    1.314
peak=   -3.284 closest distance to " CG2 ILE A  20 " =    2.807
peak=   -3.283 closest distance to " CG2 VAL A 189 " =    2.061
peak=   -3.280 closest distance to " O   HOH Z 211 " =    1.493
peak=   -3.279 closest distance to " O   HOH Z 348 " =    2.251
peak=   -3.277 closest distance to " NH2 ARG A  79 " =    1.535
peak=   -3.275 closest distance to " CB  TYR A  15 " =    2.216
peak=   -3.271 closest distance to " O   ALA A  10 " =    1.675
peak=   -3.264 closest distance to " O   HOH Z 298 " =    2.490
peak=   -3.259 closest distance to " O   ALA A  34 " =    2.493
peak=   -3.252 closest distance to " O   HOH Z 174 " =    2.946
peak=   -3.251 closest distance to " O   ARG A 145 " =    1.604
peak=   -3.244 closest distance to " OG  SER A  87 " =    1.383
peak=   -3.244 closest distance to " NH2 ARG A 159 " =    2.394
peak=   -3.243 closest distance to " OH  TYR A 247 " =    1.845
peak=   -3.243 closest distance to " O   GLN A 240 " =    2.489
peak=   -3.238 closest distance to " O   HOH Z 128 " =    2.688
peak=   -3.238 closest distance to " CB  ASP A 132 " =    2.277
peak=   -3.238 closest distance to " C   ALA A 158 " =    1.480
peak=   -3.237 closest distance to " OD2 ASP A 171 " =    1.853
peak=   -3.236 closest distance to " O   HOH Z 275 " =    1.826
peak=   -3.231 closest distance to " CA  GLY A  98 " =    1.925
peak=   -3.223 closest distance to " O   HOH Z 114 " =    1.511
peak=   -3.222 closest distance to " CD1 LEU A 297 " =    2.512
peak=   -3.222 closest distance to " O   HOH Z  13 " =    1.700
peak=   -3.217 closest distance to " O   HOH Z 191 " =    5.731
peak=   -3.214 closest distance to " OG BSER A 134 " =    1.774
peak=   -3.212 closest distance to " O   HOH Z 396 " =    1.675
peak=   -3.211 closest distance to " O   ALA A  34 " =    2.162
peak=   -3.206 closest distance to " O   HOH Z 174 " =    2.585
peak=   -3.204 closest distance to " O   HOH Z 193 " =    1.643
peak=   -3.200 closest distance to " OH  TYR A 172 " =    1.778
peak=   -3.196 closest distance to " O   HOH Z 176 " =    0.899
peak=   -3.195 closest distance to " OD1AASN A 224 " =    1.792
peak=   -3.193 closest distance to " NE2 GLN A 278 " =    1.734
peak=   -3.193 closest distance to " O   SER A 210 " =    1.837
peak=   -3.179 closest distance to " O   HOH Z 322 " =    1.300
peak=   -3.174 closest distance to " NH2 ARG A 219 " =    1.705
peak=   -3.174 closest distance to " CA  GLY A 133 " =    2.262
peak=   -3.170 closest distance to " NH1 ARG A 195 " =    2.645
peak=   -3.167 closest distance to " O   HOH Z  70 " =    2.195
peak=   -3.164 closest distance to " CG  GLU A   2 " =    1.968
peak=   -3.163 closest distance to " C   MET A 188 " =    1.352
peak=   -3.158 closest distance to " CB  GLN A  11 " =    1.803
peak=   -3.156 closest distance to " CZ  TYR A 169 " =    1.690
peak=   -3.154 closest distance to " NE  ARG A  36 " =    1.904
peak=   -3.149 closest distance to " OE1 GLN A  88 " =    1.177
peak=   -3.146 closest distance to " ND2 ASN A 187 " =    1.584
peak=   -3.143 closest distance to " C   GLY A  13 " =    0.987
peak=   -3.142 closest distance to " OD2 ASP A 191 " =    1.513
peak=   -3.141 closest distance to " O   HOH Z 292 " =    1.832
peak=   -3.135 closest distance to " O   HOH Z 348 " =    1.932
peak=   -3.130 closest distance to " O   HOH Z 393 " =    1.408
peak=   -3.126 closest distance to " N   LYS A 166 " =    1.970
peak=   -3.125 closest distance to " CG1BVAL A  41 " =    2.871
peak=   -3.118 closest distance to " NH1 ARG A  36 " =    1.941
peak=   -3.105 closest distance to " SG ACYS A 201 " =    1.914
peak=   -3.102 closest distance to " O   HOH Z 266 " =    5.102
peak=   -3.101 closest distance to " CD  GLN A  77 " =    1.697
peak=   -3.101 closest distance to " CG  PRO A 243 " =    1.816
peak=   -3.097 closest distance to " CA  ASP A  27 " =    2.514
peak=   -3.094 closest distance to " CB  ALA A  10 " =    2.299
peak=   -3.090 closest distance to " O   HOH Z 184 " =    1.710
peak=   -3.090 closest distance to " O   HOH Z 106 " =    1.950
peak=   -3.078 closest distance to " CB  ASP A 132 " =    2.368
peak=   -3.075 closest distance to " OG  SER A 206 " =    1.822
peak=   -3.072 closest distance to " O   HOH Z 123 " =    2.500
peak=   -3.067 closest distance to " NH2 ARG A  24 " =    1.843
peak=   -3.058 closest distance to " O   SER A  62 " =    2.324
peak=   -3.031 closest distance to " O   ASP A  27 " =    2.007
peak=   -3.027 closest distance to " O   HOH Z 234 " =    4.292

================= 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    :  0.3262 0.3194   6.036562e+00   6.025360e+00
   1_bss:  0.3139 0.3099   6.015778e+00   6.002268e+00
   1_xyz:  0.1693 0.1915   5.457582e+00   5.554190e+00
   1_adp:  0.1533 0.1982   5.400886e+00   5.587218e+00
   1_occ:  0.1529 0.1978   5.399069e+00   5.586141e+00
   2_bss:  0.1517 0.1956   5.398579e+00   5.585414e+00
   2_xyz:  0.1250 0.1675   5.230920e+00   5.447657e+00
   2_adp:  0.1218 0.1623   5.202372e+00   5.415916e+00
   2_occ:  0.1217 0.1622   5.201849e+00   5.415823e+00
   3_bss:  0.1216 0.1619   5.200307e+00   5.413140e+00
   3_xyz:  0.1140 0.1574   5.158017e+00   5.389560e+00
   3_adp:  0.1131 0.1565   5.150270e+00   5.383137e+00
   3_occ:  0.1130 0.1565   5.150259e+00   5.383339e+00
   4_bss:  0.1130 0.1566   5.150326e+00   5.383481e+00
   4_xyz:  0.1152 0.1583   5.166720e+00   5.396602e+00
   4_adp:  0.1143 0.1595   5.165188e+00   5.402713e+00
   4_occ:  0.1142 0.1594   5.165171e+00   5.402830e+00
   5_bss:  0.1142 0.1593   5.165132e+00   5.402791e+00
   5_xyz:  0.1083 0.1587   5.136329e+00   5.394999e+00
   5_adp:  0.1079 0.1596   5.134793e+00   5.395743e+00
   5_occ:  0.1079 0.1596   5.134775e+00   5.395823e+00
   5_bss:  0.1077 0.1595   5.134872e+00   5.395818e+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:  0.330  63.795  -0.165  -2.586   0.270  -0.000   0.000   0.000
   1_xyz:  0.330  63.795  -0.165  -2.586   0.270  -0.000   0.000   0.000
   1_adp:  0.330  63.795  -0.165  -2.586   0.270  -0.000   0.000   0.000
   1_occ:  0.330  63.795  -0.165  -2.586   0.270  -0.000   0.000   0.000
   2_bss:  0.331  63.795  -1.966  -3.077  -1.091  -0.000  -0.000  -0.000
   2_xyz:  0.331  63.795  -1.966  -3.077  -1.091  -0.000  -0.000  -0.000
   2_adp:  0.331  63.795  -1.966  -3.077  -1.091  -0.000  -0.000  -0.000
   2_occ:  0.331  63.795  -1.966  -3.077  -1.091  -0.000  -0.000  -0.000
   3_bss:  0.332  63.795  -2.405  -2.937  -1.234  -0.000  -0.000  -0.000
   3_xyz:  0.332  63.795  -2.405  -2.937  -1.234  -0.000  -0.000  -0.000
   3_adp:  0.332  63.795  -2.405  -2.937  -1.234  -0.000  -0.000  -0.000
   3_occ:  0.332  63.795  -2.405  -2.937  -1.234  -0.000  -0.000  -0.000
   4_bss:  0.324  57.147  -2.426  -2.781  -1.184  -0.000  -0.000  -0.000
   4_xyz:  0.324  57.147  -2.426  -2.781  -1.184  -0.000  -0.000  -0.000
   4_adp:  0.324  57.147  -2.426  -2.781  -1.184  -0.000  -0.000  -0.000
   4_occ:  0.324  57.147  -2.426  -2.781  -1.184  -0.000  -0.000  -0.000
   5_bss:  0.319  57.147  -2.296  -2.595  -1.033  -0.000  -0.000  -0.000
   5_xyz:  0.319  57.147  -2.296  -2.595  -1.033  -0.000  -0.000  -0.000
   5_adp:  0.319  57.147  -2.296  -2.595  -1.033  -0.000  -0.000  -0.000
   5_occ:  0.319  57.147  -2.296  -2.595  -1.033  -0.000  -0.000  -0.000
   5_bss:  0.318  57.757  -1.972  -2.267  -0.745  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.814 0.7295  0.8902    28437.511
   1_bss:  31.841 0.7389  0.8807    26170.398
   1_xyz:  17.567 0.8855  1.0035     9158.072
   1_adp:  18.371 0.8775  1.0047     9695.212
   1_occ:  18.331 0.8778  1.0043     9646.956
   2_bss:  18.292 0.8783  0.9618     9649.784
   2_xyz:  15.314 0.9040  0.9741     7171.451
   2_adp:  14.561 0.9106  0.9737     6755.208
   2_occ:  14.556 0.9106  0.9736     6747.638
   3_bss:  14.524 0.9108  0.9682     6697.049
   3_xyz:  14.003 0.9151  0.9709     6391.157
   3_adp:  13.856 0.9165  0.9681     6303.246
   3_occ:  13.861 0.9164  0.9680     6304.030
   4_bss:  13.865 0.9164  0.9699     6299.859
   4_xyz:  14.080 0.9148  0.9681     6478.161
   4_adp:  14.210 0.9137  0.9617     6536.159
   4_occ:  14.212 0.9137  0.9616     6537.471
   5_bss:  14.212 0.9137  0.9668     6535.943
   5_xyz:  14.083 0.9146  0.9682     6474.300
   5_adp:  14.111 0.9143  0.9605     6463.359
   5_occ:  14.112 0.9143  0.9605     6464.880
   5_bss:  14.116 0.9143  0.9712     6466.260
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6089e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6089e-01
   1_xyz:   1.063  0.008  0.074 15.317  0.004  4.123   6.6177e-02
   1_adp:   1.063  0.008  0.074 15.317  0.004  4.123   6.6177e-02
   1_occ:   1.063  0.008  0.074 15.317  0.004  4.123   6.6177e-02
   2_bss:   1.063  0.008  0.074 15.317  0.004  4.123   6.6177e-02
   2_xyz:   0.986  0.007  0.075 14.765  0.003  4.126   5.8646e-02
   2_adp:   0.986  0.007  0.075 14.765  0.003  4.126   5.8646e-02
   2_occ:   0.986  0.007  0.075 14.765  0.003  4.126   5.8646e-02
   3_bss:   0.986  0.007  0.075 14.765  0.003  4.126   5.8646e-02
   3_xyz:   1.023  0.009  0.078 14.880  0.004  4.131   6.3983e-02
   3_adp:   1.023  0.009  0.078 14.880  0.004  4.131   6.3983e-02
   3_occ:   1.023  0.009  0.078 14.880  0.004  4.131   6.3983e-02
   4_bss:   1.023  0.009  0.078 14.880  0.004  4.131   6.3983e-02
   4_xyz:   0.919  0.007  0.071 14.623  0.003  4.131   5.2622e-02
   4_adp:   0.919  0.007  0.071 14.623  0.003  4.131   5.2622e-02
   4_occ:   0.919  0.007  0.071 14.623  0.003  4.131   5.2622e-02
   5_bss:   0.919  0.007  0.071 14.623  0.003  4.131   5.2622e-02
   5_xyz:   1.115  0.011  0.085 14.997  0.004  4.135   7.6588e-02
   5_adp:   1.115  0.011  0.085 14.997  0.004  4.135   7.6588e-02
   5_occ:   1.115  0.011  0.085 14.997  0.004  4.135   7.6588e-02
   5_bss:   1.115  0.011  0.085 14.997  0.004  4.135   7.6588e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4265e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4265e-01
   1_xyz:   9.028  0.042  0.235 83.859  0.041  2.344   6.4361e-02
   1_adp:   9.028  0.042  0.235 83.859  0.041  2.344   6.4361e-02
   1_occ:   9.028  0.042  0.235 83.859  0.041  2.344   6.4361e-02
   2_bss:   9.028  0.042  0.235 83.859  0.041  2.344   6.4361e-02
   2_xyz:   7.150  0.038  0.230 81.071  0.032  2.359   6.3239e-02
   2_adp:   7.150  0.038  0.230 81.071  0.032  2.359   6.3239e-02
   2_occ:   7.150  0.038  0.230 81.071  0.032  2.359   6.3239e-02
   3_bss:   7.150  0.038  0.230 81.071  0.032  2.359   6.3239e-02
   3_xyz:   7.959  0.043  0.244 83.968  0.034  2.324   4.3269e-02
   3_adp:   7.959  0.043  0.244 83.968  0.034  2.324   4.3269e-02
   3_occ:   7.959  0.043  0.244 83.968  0.034  2.324   4.3269e-02
   4_bss:   7.959  0.043  0.244 83.968  0.034  2.324   4.3269e-02
   4_xyz:   7.554  0.040  0.209 83.004  0.034  2.401   3.0906e-02
   4_adp:   7.554  0.040  0.209 83.004  0.034  2.401   3.0906e-02
   4_occ:   7.554  0.040  0.209 83.004  0.034  2.401   3.0906e-02
   5_bss:   7.554  0.040  0.209 83.004  0.034  2.401   3.0906e-02
   5_xyz:   7.391  0.053  0.276 83.412  0.038  2.290   6.2670e-02
   5_adp:   7.391  0.053  0.276 83.412  0.038  2.290   6.2670e-02
   5_occ:   7.391  0.053  0.276 83.412  0.038  2.290   6.2670e-02
   5_bss:   7.391  0.053  0.276 83.412  0.038  2.290   6.2670e-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:  74.20   0.87  17.30  67.72   0.87  13.13  74.20   4.15  39.99
   1_occ:  74.20   0.87  17.30  67.72   0.87  13.13  74.20   4.15  39.99
   2_bss:  74.20   0.87  17.30  67.72   0.87  13.13  74.20   4.15  39.99
   2_xyz:  74.20   0.87  17.30  67.72   0.87  13.13  74.20   4.15  39.99
   2_adp:  75.39   1.61  17.00  70.34   1.61  13.05  75.39   6.50  38.46
   2_occ:  75.39   1.61  17.00  70.34   1.61  13.05  75.39   6.50  38.46
   3_bss:  75.39   1.61  17.00  70.34   1.61  13.05  75.39   6.50  38.46
   3_xyz:  75.39   1.61  17.00  70.34   1.61  13.05  75.39   6.50  38.46
   3_adp:  75.95   1.46  16.91  71.35   1.46  12.99  75.95   6.51  38.30
   3_occ:  75.95   1.46  16.91  71.35   1.46  12.99  75.95   6.51  38.30
   4_bss:  75.95   1.46  16.91  71.35   1.46  12.99  75.95   6.51  38.30
   4_xyz:  75.95   1.46  16.91  71.35   1.46  12.99  75.95   6.51  38.30
   4_adp:  78.32   0.50  17.10  77.46   0.50  12.98  78.32   6.11  39.49
   4_occ:  78.32   0.50  17.10  77.46   0.50  12.98  78.32   6.11  39.49
   5_bss:  78.32   0.50  17.10  77.46   0.50  12.98  78.32   6.11  39.49
   5_xyz:  78.32   0.50  17.10  77.46   0.50  12.98  78.32   6.11  39.49
   5_adp:  87.41   0.00  17.24  87.41   0.00  12.92  85.99   5.85  40.79
   5_occ:  87.41   0.00  17.24  87.41   0.00  12.92  85.99   5.85  40.79
   5_bss:  87.41   0.00  17.25  87.41   0.00  12.92  85.99   5.85  40.79
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.860    0.010    0.314
   1_adp:    0.860    0.010    0.314
   1_occ:    0.860    0.010    0.314
   2_bss:    0.860    0.010    0.314
   2_xyz:    0.850    0.029    0.346
   2_adp:    0.850    0.029    0.346
   2_occ:    0.850    0.029    0.346
   3_bss:    0.850    0.029    0.346
   3_xyz:    1.010    0.038    0.375
   3_adp:    1.010    0.038    0.375
   3_occ:    1.010    0.038    0.375
   4_bss:    1.010    0.038    0.375
   4_xyz:    1.147    0.028    0.380
   4_adp:    1.147    0.028    0.380
   4_occ:    1.147    0.028    0.380
   5_bss:    1.147    0.028    0.380
   5_xyz:    1.169    0.056    0.387
   5_adp:    1.169    0.056    0.387
   5_occ:    1.169    0.056    0.387
   5_bss:    1.169    0.056    0.387
------------------------------------------------------------------------

CPU time actual refinement: 331.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/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_1019/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1019/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.26 
  Macro-tasks:
    bulk solvent and scale       = 36.71  
    individual site refinement   = 145.46 
    weights calculation          = 30.02  
    collect and process          = 6.79   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 219.11 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 104.97 
    alpha_beta                      = 8.35   
    target                          = 1.23   
    gradients_wrt_atomic_parameters = 116.32 
    fmodel                         = 6.79   
    r_factors                      = 0.23   
    phase_errors                   = 11.48  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 250.86 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.575 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    657 calls, 104.50 s
gradients_fft:          602 calls, 101.59 s

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

# Date 2008-01-16 Time 06:13:23 PST -0800 (1200492803.52 s)
Start R-work = 0.3262, R-free = 0.3194 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1776 (no bulk solvent and anisotropic scale)

Start R-work = 0.3139, R-free = 0.3099
Final R-work = 0.1077, R-free = 0.1595