# Date 2008-01-16 Time 06:11:29 PST -0800 (1200492689.50 s)
#phil __OFF__

Command line arguments: "../1042.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26588
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1042

-------------------------------------------------------------------------------
  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, 47.1647, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


================================== 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, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.01224
Completeness in resolution range: 0.969752
Completeness with d_max=infinity: 0.966737

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   2.0122

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, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 2.01224
Completeness in resolution range: 0.969752
Completeness with d_max=infinity: 0.966737

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.3056 [2118/2142]  1905   213  10.1%
  bin  2:  4.3056 -  3.4303 [2036/2056]  1833   203  10.0%
  bin  3:  3.4303 -  3.0005 [2014/2033]  1814   200   9.9%
  bin  4:  3.0005 -  2.7279 [1998/2028]  1798   200  10.0%
  bin  5:  2.7279 -  2.5333 [1988/2007]  1788   200  10.1%
  bin  6:  2.5333 -  2.3846 [1957/1982]  1759   198  10.1%
  bin  7:  2.3846 -  2.2655 [1954/1982]  1761   193   9.9%
  bin  8:  2.2655 -  2.1672 [1965/2001]  1770   195   9.9%
  bin  9:  2.1672 -  2.0840 [1942/1984]  1749   193   9.9%
  bin 10:  2.0840 -  2.0122 [1617/1985]  1453   164  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/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: 2165
        3.04 -     3.66: 4570
        3.66 -     4.28: 8859
        4.28 -     4.90: 12212
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.877 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.285 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27811 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_1042/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/model_refine_001.geo

CPU time processing inputs: 9.22


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


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


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


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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3576   r_free= 0.3470   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.106643                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.2924 0.2749      6.3704      6.2726|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.2776 0.2679      6.5137       6.491|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.3145 0.2769      6.4309      6.3965|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.3252 0.3508       6.299      6.2831|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.3708 0.3497      6.1843      6.1905|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.3736 0.3720      6.1015       6.036|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.3942 0.3836      6.0754      6.1331|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.4021 0.3767      6.0598      6.0137|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.3969 0.3779      5.9779      5.9869|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.4127 0.3727      5.9897      5.9383|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.4285 0.4287      5.9474      5.9821|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.4267 0.4454      5.8728       5.946|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.4258 0.4036      5.7897       5.726|
| 14:  2.0624 -  2.0122 0.74    929  103 0.4094 0.4312      5.7197      5.7237|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.80  25.49   0.85     0.81      40820.85|
|  2:  4.8022 -  3.8316  1325   149  0.84  22.65   0.95     0.89      48617.80|
|  3:  3.8316 -  3.3532  1298   142  0.79  27.62   0.96     0.90      49943.88|
|  4:  3.3532 -  3.0493  1287   145  0.75  31.35   0.96     0.86      45911.88|
|  5:  3.0493 -  2.8322  1281   143  0.67  37.84   0.96     0.83      39520.14|
|  6:  2.8322 -  2.6662  1295   140  0.67  38.51   0.96     0.81      35560.23|
|  7:  2.6662 -  2.5333  1272   144  0.64  40.74   0.96     0.81      33478.31|
|  8:  2.5333 -  2.4235  1257   137  0.65  40.39   0.97     0.83      31376.37|
|  9:  2.4235 -  2.3305  1263   142  0.64  40.56   0.98     0.83      29070.74|
| 10:  2.3305 -  2.2504  1262   143  0.62  42.48   1.02     0.82      27111.78|
| 11:  2.2504 -  2.1802  1264   136  0.60  43.95   0.98     0.81      27067.09|
| 12:  2.1802 -  2.1181  1236   140  0.60  44.56   0.97     0.82      25952.03|
| 13:  2.1181 -  2.0624  1281   142  0.59  45.47   0.99     0.82      22450.07|
| 14:  2.0624 -  2.0122   929   103  0.62  42.49   0.99     0.78      16930.45|
|alpha:            min =        0.78 max =            0.90 mean =         0.83|
|beta:             min =    16930.45 max =        49943.88 mean =     34320.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.99 mean =        37.18|
|phase err.(test): min =        0.00 max =           89.38 mean =        36.66|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.460415              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.120   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.858899              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.974   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      173 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1992 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1802 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2768 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4578 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4281 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5564 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6648 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.141 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3576   r_free= 0.3470   ksol= 0.00   Bsol= 0.00   scale= 0.942    |
|                                                                             |
| 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:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.106643                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3467   r_free= 0.3381   ksol= 0.30   Bsol= 80.00   scale= 0.963   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-2.26,2.15,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.089110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.135331              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.050   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.488644              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.687   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3467      final r-factor (work) = 0.2192          |
| start r-factor (free) = 0.3381      final r-factor (free) = 0.2377          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7110 = 3.14 * 0.50 * 6.0912 + 1.00 * 0.1621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2369 = 3.14 * 0.50 * 5.8478 + 1.00 * 0.0695                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2192      final r-factor (work) = 0.1991          |
| start r-factor (free) = 0.2377      final r-factor (free) = 0.2457          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8638 = 0.49 * 1.00 * 5.8478 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7573 = 0.49 * 1.00 * 5.6199 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.74   17.69    None  None   None       |
|    all(noH): 2823   0      0.00    80.74   17.69    None  None   None       |
|    Sol.    : 438    0      3.91    80.74   40.91    None  None   None       |
|    Mac.    : 2385   0      0.00    76.27   13.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.074:  594   |   5:    40.371 -  48.445:   89        |
|      1:     8.074 -  16.148: 1244   |   6:    48.445 -  56.519:   98        |
|      2:    16.148 -  24.222:  421   |   7:    56.519 -  64.593:   50        |
|      3:    24.222 -  32.297:  178   |   8:    64.593 -  72.667:   30        |
|      4:    32.297 -  40.371:  108   |   9:    72.667 -  80.741:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1991 r_free = 0.2457             target_work(ml) = 5.629         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1986 r_free = 0.2455             target_work(ml) = 5.628         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1986   r_free= 0.2455   ksol= 0.30   Bsol= 80.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.55,-2.26,2.15,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.628200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1970   r_free= 0.2443   ksol= 0.34   Bsol= 82.28   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.53,-0.34,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.626577                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.215656              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.913   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.390  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1970      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2443      final r-factor (free) = 0.1854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1216 = 3.22 * 0.50 * 5.6300 + 1.00 * 0.0695                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8921 = 3.22 * 0.50 * 5.4914 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.1854      final r-factor (free) = 0.1734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6527 = 0.30 * 1.00 * 5.4914 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5954 = 0.30 * 1.00 * 5.3055 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    80.25   17.37    None  None   None       |
|    all(noH): 2823   0      0.86    80.25   17.37    None  None   None       |
|    Sol.    : 438    0      5.43    80.25   40.88    None  None   None       |
|    Mac.    : 2385   0      0.86    76.04   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:     0.864 -   8.802:  718   |   5:    40.557 -  48.495:   90        |
|      1:     8.802 -  16.741: 1249   |   6:    48.495 -  56.434:   94        |
|      2:    16.741 -  24.680:  335   |   7:    56.434 -  64.373:   55        |
|      3:    24.680 -  32.618:  142   |   8:    64.373 -  72.311:   28        |
|      4:    32.618 -  40.557:  101   |   9:    72.311 -  80.250:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1325 r_free = 0.1734             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1324 r_free = 0.1735             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1324   r_free= 0.1735   ksol= 0.34   Bsol= 82.28   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.53,-0.34,-0.00,-0.00,-0.00); trace/3= -1.60                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1732   ksol= 0.33   Bsol= 72.53   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.27,-0.53,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272416                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.165627              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.863  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.642410              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.706  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1732      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8079 = 2.17 * 0.50 * 5.3056 + 1.00 * 0.0629                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7266 = 2.17 * 0.50 * 5.2302 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1202      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3691 = 0.64 * 1.00 * 5.2302 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3430 = 0.64 * 1.00 * 5.1882 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.39    82.21   17.23    None  None   None       |
|    all(noH): 2823   0      0.39    82.21   17.23    None  None   None       |
|    Sol.    : 438    0      5.85    82.21   41.03    None  None   None       |
|    Mac.    : 2385   0      0.39    79.74   12.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.394 -   8.576:  740   |   5:    41.303 -  49.485:   87        |
|      1:     8.576 -  16.758: 1253   |   6:    49.485 -  57.667:   87        |
|      2:    16.758 -  24.940:  316   |   7:    57.667 -  65.849:   57        |
|      3:    24.940 -  33.121:  130   |   8:    65.849 -  74.031:   27        |
|      4:    33.121 -  41.303:  117   |   9:    74.031 -  82.213:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1179 r_free = 0.1634             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1178 r_free = 0.1633             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1633   ksol= 0.33   Bsol= 72.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-2.27,-0.53,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1178   r_free= 0.1634   ksol= 0.32   Bsol= 66.78   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.13,-0.64,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.847322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.566  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.725313              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.619  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8551 = 1.85 * 0.50 * 5.1880 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8503 = 1.85 * 0.50 * 5.1817 + 1.00 * 0.0641                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7684 = 0.73 * 1.00 * 5.1817 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7657 = 0.73 * 1.00 * 5.1775 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    84.52   17.06    None  None   None       |
|    all(noH): 2823   0      0.22    84.52   17.06    None  None   None       |
|    Sol.    : 438    0      5.71    84.52   41.00    None  None   None       |
|    Mac.    : 2385   0      0.22    83.84   12.66    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:     0.220 -   8.650:  806   |   5:    42.368 -  50.798:   83        |
|      1:     8.650 -  17.079: 1231   |   6:    50.798 -  59.227:   81        |
|      2:    17.079 -  25.509:  289   |   7:    59.227 -  67.657:   50        |
|      3:    25.509 -  33.938:  128   |   8:    67.657 -  76.086:   23        |
|      4:    33.938 -  42.368:  122   |   9:    76.086 -  84.516:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1630             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1630             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1630   ksol= 0.32   Bsol= 66.78   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.13,-0.64,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1629   ksol= 0.32   Bsol= 66.78   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.85,-0.44,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.178109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.474495              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.879  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.492599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.353  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0607 = 3.47 * 0.50 * 5.1787 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0406 = 3.47 * 0.50 * 5.1561 + 1.00 * 0.0832                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8624 = 2.49 * 1.00 * 5.1561 + 1.00 * 0.0103                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8461 = 2.49 * 1.00 * 5.1492 + 1.00 * 0.0112                              |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.54   16.95    None  None   None       |
|    all(noH): 2823   0      0.00    88.54   16.95    None  None   None       |
|    Sol.    : 438    0      3.98    87.47   41.17    None  None   None       |
|    Mac.    : 2385   0      0.00    88.54   12.51    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 -   8.854:  911   |   5:    44.271 -  53.125:   80        |
|      1:     8.854 -  17.709: 1171   |   6:    53.125 -  61.980:   86        |
|      2:    17.709 -  26.563:  268   |   7:    61.980 -  70.834:   38        |
|      3:    26.563 -  35.417:  130   |   8:    70.834 -  79.688:   19        |
|      4:    35.417 -  44.271:  111   |   9:    79.688 -  88.542:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1620             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1621             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1621   ksol= 0.32   Bsol= 66.78   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.85,-0.44,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150805                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.0983 0.1352      5.4018      5.5566|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.0822 0.1093      5.4194      5.6214|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.1030 0.1486      5.4615      5.8442|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.1196 0.1632      5.4558      5.6107|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.1345 0.1817      5.3506      5.6016|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.1205 0.2027        5.24      5.5063|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.1286 0.1636      5.1838      5.3685|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.1151 0.1691      5.0773      5.3478|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.1141 0.1729      5.0353      5.2873|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.1104 0.1835      4.9687      5.2724|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.1130 0.1789      4.9517      5.2498|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.1118 0.1793      4.9058      5.2499|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.1113 0.1854      4.8084      5.0996|
| 14:  2.0624 -  2.0122 0.74    929  103 0.1009 0.1729      4.6661      4.9548|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.94   9.66   0.97     0.94       7873.43|
|  2:  4.8022 -  3.8316  1325   149  0.95   8.05   1.00     0.99       9149.39|
|  3:  3.8316 -  3.3532  1298   142  0.94  10.93   1.01     1.01      10109.76|
|  4:  3.3532 -  3.0493  1287   145  0.92  13.86   1.00     0.98      10575.15|
|  5:  3.0493 -  2.8322  1281   143  0.90  16.20   0.99     0.96       8847.73|
|  6:  2.8322 -  2.6662  1295   140  0.89  16.63   0.98     0.95       7742.21|
|  7:  2.6662 -  2.5333  1272   144  0.90  16.22   0.98     0.96       6560.52|
|  8:  2.5333 -  2.4235  1257   137  0.91  15.37   0.98     0.96       5473.37|
|  9:  2.4235 -  2.3305  1263   142  0.91  15.27   0.98     0.94       5092.49|
| 10:  2.3305 -  2.2504  1262   143  0.90  15.70   0.98     0.94       4539.19|
| 11:  2.2504 -  2.1802  1264   136  0.89  16.88   0.97     0.93       4558.28|
| 12:  2.1802 -  2.1181  1236   140  0.91  15.67   0.99     0.98       4245.00|
| 13:  2.1181 -  2.0624  1281   142  0.90  16.53   0.97     0.94       3555.52|
| 14:  2.0624 -  2.0122   929   103  0.92  14.39   0.94     0.91       2642.20|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2642.20 max =        10575.15 mean =      6607.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.33|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1619   ksol= 0.32   Bsol= 66.78   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-1.55,-0.18,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150942                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1619   ksol= 0.32   Bsol= 66.78   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-1.55,-0.18,-0.00,-0.00,-0.00); trace/3= -1.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.150942                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.8022 0.99   1380  153 0.0983 0.1353      5.4025       5.558|
|  2:  4.8022 -  3.8316 0.99   1325  149 0.0822 0.1093      5.4199      5.6212|
|  3:  3.8316 -  3.3532 0.99   1298  142 0.1030 0.1486      5.4614      5.8445|
|  4:  3.3532 -  3.0493 0.99   1287  145 0.1196 0.1633      5.4558      5.6108|
|  5:  3.0493 -  2.8322 0.99   1281  143 0.1344 0.1816      5.3505      5.6013|
|  6:  2.8322 -  2.6662 0.99   1295  140 0.1205 0.2029        5.24      5.5066|
|  7:  2.6662 -  2.5333 0.99   1272  144 0.1286 0.1636      5.1839      5.3688|
|  8:  2.5333 -  2.4235 0.98   1257  137 0.1152 0.1691      5.0774      5.3476|
|  9:  2.4235 -  2.3305 0.98   1263  142 0.1140 0.1730      5.0355      5.2876|
| 10:  2.3305 -  2.2504 1.00   1262  143 0.1104 0.1834      4.9689       5.272|
| 11:  2.2504 -  2.1802 0.97   1264  136 0.1130 0.1788      4.9517      5.2497|
| 12:  2.1802 -  2.1181 0.98   1236  140 0.1118 0.1793      4.9057      5.2497|
| 13:  2.1181 -  2.0624 0.99   1281  142 0.1113 0.1854      4.8085      5.0995|
| 14:  2.0624 -  2.0122 0.74    929  103 0.1009 0.1729      4.6665      4.9553|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.8022  1380   153  0.94   9.67   0.97     0.94       7890.32|
|  2:  4.8022 -  3.8316  1325   149  0.95   8.06   1.00     0.99       9158.97|
|  3:  3.8316 -  3.3532  1298   142  0.94  10.94   1.02     1.02      10109.98|
|  4:  3.3532 -  3.0493  1287   145  0.92  13.86   1.01     0.99      10574.59|
|  5:  3.0493 -  2.8322  1281   143  0.90  16.20   1.00     0.97       8848.38|
|  6:  2.8322 -  2.6662  1295   140  0.89  16.63   0.99     0.96       7742.01|
|  7:  2.6662 -  2.5333  1272   144  0.90  16.22   0.99     0.97       6561.42|
|  8:  2.5333 -  2.4235  1257   137  0.91  15.37   0.99     0.97       5474.37|
|  9:  2.4235 -  2.3305  1263   142  0.91  15.28   1.00     0.95       5093.22|
| 10:  2.3305 -  2.2504  1262   143  0.90  15.70   0.99     0.95       4539.14|
| 11:  2.2504 -  2.1802  1264   136  0.89  16.87   0.98     0.94       4556.36|
| 12:  2.1802 -  2.1181  1236   140  0.91  15.67   1.00     1.00       4243.69|
| 13:  2.1181 -  2.0624  1281   142  0.90  16.54   0.99     0.96       3555.86|
| 14:  2.0624 -  2.0122   929   103  0.92  14.40   0.96     0.93       2644.96|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2644.96 max =        10574.59 mean =      6609.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.33|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.83|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.319)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.55   16.96    None  None   None       |
|    all(noH): 2823   0      0.00    88.55   16.96    None  None   None       |
|    Sol.    : 438    0      3.98    87.47   41.17    None  None   None       |
|    Mac.    : 2385   0      0.00    88.55   12.51    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 -   8.857:  911   |   5:    44.274 -  53.128:   80        |
|      1:     8.857 -  17.711: 1171   |   6:    53.128 -  61.983:   86        |
|      2:    17.711 -  26.566:  268   |   7:    61.983 -  70.837:   38        |
|      3:    26.566 -  35.420:  130   |   8:    70.837 -  79.691:   19        |
|      4:    35.420 -  44.274:  111   |   9:    79.691 -  88.545:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.489 - 4.848
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 281
   mapped sites are within: 0.716 - 4.848

peak=    5.674 closest distance to " O   HOH Z 111 " =    2.188
peak=    5.649 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.070 closest distance to " CG  PRO A  54 " =    1.287
peak=    4.951 closest distance to " O   HOH Z 232 " =    2.268
peak=    4.894 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.837 closest distance to " CB  ARG A 190 " =    1.583
peak=    4.730 closest distance to " NE2 GLN A  11 " =    1.028
peak=    4.689 closest distance to " O   HOH Z 369 " =    2.160
peak=    4.666 closest distance to " CB  ARG A  79 " =    1.433
peak=    4.644 closest distance to " CB  SER A  63 " =    1.201
peak=    4.579 closest distance to " O   HOH Z 298 " =    2.018
peak=    4.459 closest distance to " CZ  PHE A 218 " =    1.093
peak=    4.419 closest distance to " O   HOH Z  78 " =    1.692
peak=    4.350 closest distance to " O   HOH Z  15 " =    2.184
peak=    4.326 closest distance to " O   HOH Z 126 " =    1.985
peak=    4.317 closest distance to " CB  LEU A 228 " =    1.121
peak=    4.305 closest distance to " CB  ARG A 275 " =    0.958
peak=    4.267 closest distance to " O   HOH Z  19 " =    2.515
peak=    4.252 closest distance to " C   PRO A 198 " =    1.502
peak=    4.240 closest distance to " CG  PRO A 213 " =    1.142
peak=    4.211 closest distance to " NH1AARG A 145 " =    1.303
peak=    4.146 closest distance to " O   HOH Z 368 " =    2.178
peak=    4.133 closest distance to " CA  TYR A  30 " =    1.043
peak=    4.129 closest distance to " O   HOH Z 287 " =    2.099
peak=    4.079 closest distance to " CB  PRO A  54 " =    0.927
peak=    4.076 closest distance to " O   HOH Z 180 " =    2.110
peak=    4.068 closest distance to " CD  ARG A 159 " =    0.785
peak=    4.065 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.044 closest distance to " O   HOH Z 392 " =    2.928
peak=    4.042 closest distance to " CB  GLU A 277 " =    3.742
peak=    4.038 closest distance to " CB  TYR A 169 " =    0.830
peak=    4.024 closest distance to " CD  ARG A 269 " =    0.903
peak=    4.018 closest distance to " CB  VAL A 202 " =    1.648
peak=    4.018 closest distance to " CA  ARG A 195 " =    1.230
peak=    4.011 closest distance to " O   HOH Z 427 " =    3.152
peak=    4.005 closest distance to " CB  ASP A 140 " =    1.046
peak=    3.999 closest distance to " O   HOH Z 142 " =    1.657
peak=    3.981 closest distance to " ND2 ASN A 187 " =    1.395
peak=    3.979 closest distance to " CE  LYS A  76 " =    0.836
peak=    3.979 closest distance to " O   HOH Z 303 " =    2.144
peak=    3.978 closest distance to " O   HOH Z 234 " =    3.870
peak=    3.967 closest distance to " CA  ALA A  51 " =    0.905
peak=    3.959 closest distance to " O   HOH Z 189 " =    2.971
peak=    3.954 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.924 closest distance to " O   HOH Z 158 " =    3.050
peak=    3.922 closest distance to " CD1 LEU A 300 " =    1.201
peak=    3.896 closest distance to " O   HOH Z 265 " =    2.264
peak=    3.887 closest distance to " CB  ASN A 148 " =    1.487
peak=    3.882 closest distance to " NZ  LYS A 117 " =    3.228
peak=    3.881 closest distance to " O   HOH Z  78 " =    2.133
peak=    3.877 closest distance to " O   HOH Z 133 " =    2.576
peak=    3.864 closest distance to " CB  SER A 212 " =    1.067
peak=    3.859 closest distance to " OD1 ASN A  69 " =    2.631
peak=    3.859 closest distance to " O  BHOH Z 338 " =    2.405
peak=    3.858 closest distance to " O   HOH Z 316 " =    3.143
peak=    3.850 closest distance to " CD ALYS A 290 " =    0.961
peak=    3.841 closest distance to " C   ILE A 106 " =    1.915
peak=    3.836 closest distance to " O   HOH Z  63 " =    1.935
peak=    3.828 closest distance to " O   HOH Z 346 " =    1.627
peak=    3.817 closest distance to " O   HOH Z  61 " =    1.670
peak=    3.817 closest distance to " CB  TYR A 116 " =    0.776
peak=    3.793 closest distance to " CB  GLU A 152 " =    1.147
peak=    3.777 closest distance to " CD  LYS A 166 " =    1.288
peak=    3.771 closest distance to " CG2 THR A 221 " =    1.085
peak=    3.766 closest distance to " CD  ARG A  66 " =    2.401
peak=    3.756 closest distance to " CB  GLU A 128 " =    0.945
peak=    3.756 closest distance to " O   HOH Z  40 " =    1.960
peak=    3.736 closest distance to " O   HOH Z 285 " =    2.436
peak=    3.734 closest distance to " O   HOH Z 411 " =    3.807
peak=    3.732 closest distance to " O   HOH Z 214 " =    2.189
peak=    3.730 closest distance to " O   HOH Z 250 " =    1.483
peak=    3.730 closest distance to " CB  GLU A  46 " =    1.031
peak=    3.730 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.728 closest distance to " O   HOH Z 261 " =    1.770
peak=    3.725 closest distance to " O   HOH Z 272 " =    1.871
peak=    3.725 closest distance to " CG2 VAL A 257 " =    0.843
peak=    3.721 closest distance to " O   HOH Z 193 " =    1.965
peak=    3.714 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.709 closest distance to " CA  MET A 105 " =    1.038
peak=    3.702 closest distance to " CA  ARG A  36 " =    1.126
peak=    3.691 closest distance to " O   HOH Z   1 " =    2.189
peak=    3.673 closest distance to " O   HOH Z  21 " =    1.804
peak=    3.672 closest distance to " O   HOH Z 313 " =    1.873
peak=    3.667 closest distance to " CA  MET A  40 " =    1.198
peak=    3.667 closest distance to " CB  ASN A 142 " =    1.015
peak=    3.659 closest distance to " NH2 ARG A 156 " =    1.214
peak=    3.658 closest distance to " CZ3 TRP A 266 " =    1.139
peak=    3.657 closest distance to " O   HOH Z 406 " =    1.592
peak=    3.651 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.646 closest distance to " O   HOH Z 425 " =    1.324
peak=    3.645 closest distance to " CA  ASN A 215 " =    1.170
peak=    3.643 closest distance to " CA  VAL A 125 " =    1.261
peak=    3.639 closest distance to " CA  ALA A 158 " =    1.197
peak=    3.626 closest distance to " CA  ALA A 160 " =    0.937
peak=    3.616 closest distance to " O   HOH Z 371 " =    3.271
peak=    3.608 closest distance to " O   HOH Z 422 " =    2.709
peak=    3.606 closest distance to " O   HOH Z 403 " =    1.603
peak=    3.601 closest distance to " O   SER A  87 " =    2.217
peak=    3.598 closest distance to " O   TYR A 116 " =    1.315
peak=    3.596 closest distance to " O   HOH Z 227 " =    1.793
peak=    3.594 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.593 closest distance to " CA  PRO A  54 " =    1.375
peak=    3.591 closest distance to " N   ASN A 127 " =    1.336
peak=    3.589 closest distance to " CD2 LEU A 297 " =    0.890
peak=    3.572 closest distance to " O   HOH Z 325 " =    2.399
peak=    3.563 closest distance to " O   HOH Z 193 " =    1.789
peak=    3.562 closest distance to " OG BSER A 164 " =    2.351
peak=    3.560 closest distance to " O   HOH Z 368 " =    3.745
peak=    3.555 closest distance to " CG  LEU A 167 " =    1.270
peak=    3.545 closest distance to " O   HOH Z 185 " =    1.962
peak=    3.543 closest distance to " O   HOH Z 213 " =    2.023
peak=    3.541 closest distance to " CA  THR A 221 " =    1.000
peak=    3.541 closest distance to " O   HOH Z  44 " =    2.272
peak=    3.540 closest distance to " CA  ALA A 295 " =    1.067
peak=    3.539 closest distance to " CB  THR A  82 " =    1.405
peak=    3.531 closest distance to " NE  ARG A  79 " =    1.110
peak=    3.527 closest distance to " CG1 VAL A 153 " =    0.978
peak=    3.526 closest distance to " O   HOH Z 403 " =    1.459
peak=    3.525 closest distance to " O   HOH Z 147 " =    1.825
peak=    3.522 closest distance to " O   HOH Z 391 " =    2.925
peak=    3.515 closest distance to " O   HOH Z 280 " =    2.983
peak=    3.512 closest distance to " O   HOH Z 126 " =    1.630
peak=    3.509 closest distance to " CB  PRO A  90 " =    1.188
peak=    3.502 closest distance to " CG2 ILE A 234 " =    0.854
peak=    3.501 closest distance to " O   HOH Z 423 " =    1.842
peak=    3.501 closest distance to " CB  MET A  40 " =    0.809
peak=    3.494 closest distance to " O   HOH Z 106 " =    4.127
peak=    3.494 closest distance to " CB  TRP A 179 " =    1.550
peak=    3.493 closest distance to " CG BARG A 275 " =    1.430
peak=    3.487 closest distance to " ND2 ASN A 249 " =    1.928
peak=    3.481 closest distance to " O   HOH Z 271 " =    2.793
peak=    3.475 closest distance to " O   HOH Z 359 " =    1.477
peak=    3.466 closest distance to " CB  GLN A  88 " =    1.210
peak=    3.461 closest distance to " CA  GLU A  46 " =    0.791
peak=    3.457 closest distance to " CG  PRO A 243 " =    1.038
peak=    3.456 closest distance to " CB  ASN A 187 " =    1.227
peak=    3.456 closest distance to " O   HOH Z 172 " =    3.698
peak=    3.455 closest distance to " O   HOH Z 171 " =    3.955
peak=    3.449 closest distance to " O   HOH Z  59 " =    2.340
peak=    3.447 closest distance to " CE1 TYR A 186 " =    1.295
peak=    3.439 closest distance to " O   HOH Z  80 " =    1.628
peak=    3.438 closest distance to " O   HOH Z  10 " =    1.758
peak=    3.437 closest distance to " CA  GLY A 241 " =    0.781
peak=    3.435 closest distance to " CB  ALA A   9 " =    1.620
peak=    3.434 closest distance to " O   ALA A 158 " =    1.281
peak=    3.432 closest distance to " O   HOH Z 167 " =    1.737
peak=    3.432 closest distance to " CG2AVAL A  72 " =    1.791
peak=    3.430 closest distance to " CB  GLN A  89 " =    1.246
peak=    3.429 closest distance to " CA  ALA A 154 " =    1.022
peak=    3.426 closest distance to " CB  SER A   3 " =    1.433
peak=    3.424 closest distance to " O   HOH Z  66 " =    2.174
peak=    3.424 closest distance to " CG2 ILE A 120 " =    1.084
peak=    3.423 closest distance to " O   HOH Z 353 " =    2.700
peak=    3.415 closest distance to " CB  ALA A 248 " =    0.975
peak=    3.413 closest distance to " O   HOH Z 290 " =    0.989
peak=    3.413 closest distance to " O   THR A 251 " =    1.298
peak=    3.410 closest distance to " O   HOH Z 305 " =    3.636
peak=    3.407 closest distance to " NH2BARG A 145 " =    2.222
peak=    3.407 closest distance to " CB  LYS A 117 " =    1.135
peak=    3.405 closest distance to " OG  SER A  22 " =    2.823
peak=    3.404 closest distance to " O   HOH Z 291 " =    1.598
peak=    3.401 closest distance to " O   HOH Z 203 " =    1.715
peak=    3.398 closest distance to " CG  MET A 185 " =    1.236
peak=    3.398 closest distance to " N   ARG A 156 " =    1.386
peak=    3.394 closest distance to " NE2 HIS A 207 " =    1.269
peak=    3.391 closest distance to " ND2 ASN A 249 " =    0.812
peak=    3.386 closest distance to " CB  ALA A  34 " =    0.971
peak=    3.383 closest distance to " O   HOH Z 294 " =    1.525
peak=    3.381 closest distance to " O   HOH Z  88 " =    3.824
peak=    3.381 closest distance to " N   ASN A  39 " =    1.375
peak=    3.379 closest distance to " CA  ASN A 217 " =    1.214
peak=    3.379 closest distance to " O   HOH Z 148 " =    3.354
peak=    3.372 closest distance to " CB  ARG A 138 " =    0.991
peak=    3.368 closest distance to " OG BSER A 134 " =    2.914
peak=    3.365 closest distance to " CB  MET A  47 " =    1.013
peak=    3.361 closest distance to " O   HOH Z 365 " =    2.963
peak=    3.360 closest distance to " O   HOH Z  43 " =    1.890
peak=    3.360 closest distance to " CB  ASN A 110 " =    1.196
peak=    3.355 closest distance to " CG1 ILE A  33 " =    1.167
peak=    3.353 closest distance to " O   HOH Z  98 " =    1.723
peak=    3.353 closest distance to " CB  ALA A 104 " =    0.765
peak=    3.351 closest distance to " CA  THR A 264 " =    0.888
peak=    3.345 closest distance to " CA  SER A  87 " =    1.051
peak=    3.342 closest distance to " O   HOH Z 166 " =    3.775
peak=    3.342 closest distance to " O   HOH Z 344 " =    3.197
peak=    3.341 closest distance to " CB  THR A  31 " =    1.676
peak=    3.340 closest distance to " CA  ASP A 124 " =    0.716
peak=    3.334 closest distance to " O   HOH Z 383 " =    2.231
peak=    3.327 closest distance to " ND1 HIS A  81 " =    1.662
peak=    3.326 closest distance to " CB  LEU A  96 " =    1.305
peak=    3.315 closest distance to " CB  ASP A 298 " =    1.223
peak=    3.312 closest distance to " CA  ALA A 291 " =    0.808
peak=    3.311 closest distance to " CB  LEU A  83 " =    0.805
peak=    3.307 closest distance to " NH2AARG A 275 " =    3.557
peak=    3.307 closest distance to " O   HOH Z  29 " =    2.664
peak=    3.306 closest distance to " O   THR A 220 " =    1.222
peak=    3.298 closest distance to " O   ALA A 165 " =    1.541
peak=    3.298 closest distance to " CG  GLU A  37 " =    0.907
peak=    3.295 closest distance to " O   HOH Z 299 " =    4.482
peak=    3.288 closest distance to " O   HOH Z 128 " =    2.510
peak=    3.288 closest distance to " O   HOH Z 135 " =    1.733
peak=    3.287 closest distance to " O   HOH Z 245 " =    1.226
peak=    3.286 closest distance to " O   THR A 251 " =    1.904
peak=    3.283 closest distance to " CB  ALA A  43 " =    0.856
peak=    3.279 closest distance to " CB  ILE A 120 " =    1.264
peak=    3.278 closest distance to " CB  ALA A   1 " =    4.848
peak=    3.275 closest distance to " CA  ALA A 100 " =    1.092
peak=    3.274 closest distance to " O   ASN A  74 " =    1.572
peak=    3.272 closest distance to " O   HOH Z 285 " =    1.821
peak=    3.272 closest distance to " O   HOH Z 426 " =    1.707
peak=    3.269 closest distance to " CB  ALA A 248 " =    1.190
peak=    3.263 closest distance to " CB  ARG A 139 " =    0.955
peak=    3.262 closest distance to " CD2 LEU A 255 " =    1.713
peak=    3.260 closest distance to " O   HOH Z 132 " =    2.747
peak=    3.258 closest distance to " O   HOH Z 273 " =    2.824
peak=    3.257 closest distance to " O   HOH Z 193 " =    2.167
peak=    3.254 closest distance to " CA  ALA A 233 " =    1.452
peak=    3.251 closest distance to " O   HOH Z 128 " =    2.193
peak=    3.249 closest distance to " CA  ARG A 139 " =    1.064
peak=    3.249 closest distance to " NZ  LYS A  48 " =    1.346
peak=    3.246 closest distance to " CA  TYR A  30 " =    1.045
peak=    3.244 closest distance to " CZ  PHE A  38 " =    1.241
peak=    3.243 closest distance to " CG1 ILE A 151 " =    1.034
peak=    3.241 closest distance to " N   GLY A  98 " =    1.130
peak=    3.239 closest distance to " O   HOH Z  97 " =    2.025
peak=    3.238 closest distance to " O   HOH Z 282 " =    1.861
peak=    3.237 closest distance to " O   HOH Z 248 " =    1.620
peak=    3.236 closest distance to " OD1 ASN A 217 " =    1.744
peak=    3.236 closest distance to " CA  ALA A  21 " =    1.239
peak=    3.235 closest distance to " O   HOH Z 313 " =    1.551
peak=    3.234 closest distance to " CB  GLN A 103 " =    0.829
peak=    3.232 closest distance to " CB  ALA A 227 " =    1.068
peak=    3.220 closest distance to " CG2 ILE A  20 " =    1.275
peak=    3.219 closest distance to " CA  TYR A 116 " =    1.360
peak=    3.214 closest distance to " OE2 GLU A  53 " =    2.015
peak=    3.210 closest distance to " O   HOH Z 430 " =    1.522
peak=    3.205 closest distance to " O   HOH Z 124 " =    1.924
peak=    3.203 closest distance to " CB  ALA A 242 " =    0.880
peak=    3.202 closest distance to " OG  SER A 245 " =    1.753
peak=    3.179 closest distance to " O   HOH Z 258 " =    1.644
peak=    3.176 closest distance to " O   HOH Z 174 " =    2.509
peak=    3.175 closest distance to " CD1 ILE A 106 " =    0.768
peak=    3.171 closest distance to " O   HOH Z 409 " =    3.061
peak=    3.169 closest distance to " N   PHE A 130 " =    1.242
peak=    3.167 closest distance to " CB  ASN A 215 " =    1.157
peak=    3.166 closest distance to " O   HOH Z  88 " =    1.923
peak=    3.166 closest distance to " CG  GLN A  11 " =    1.494
peak=    3.164 closest distance to " CZ2 TRP A 179 " =    1.716
peak=    3.164 closest distance to " CA  ASP A 191 " =    0.896
peak=    3.163 closest distance to " CG  ARG A 159 " =    0.900
peak=    3.161 closest distance to " CE  LYS A  48 " =    1.037
peak=    3.153 closest distance to " CA  ARG A 102 " =    1.139
peak=    3.148 closest distance to " O   HOH Z 163 " =    1.788
peak=    3.147 closest distance to " CA  ARG A 159 " =    1.252
peak=    3.146 closest distance to " O   THR A 182 " =    1.449
peak=    3.145 closest distance to " CG1 ILE A  49 " =    1.560
peak=    3.140 closest distance to " O   ASP A 124 " =    1.115
peak=    3.137 closest distance to " CB  ALA A 100 " =    1.236
peak=    3.132 closest distance to " O   HOH Z 116 " =    1.799
peak=    3.126 closest distance to " N   TYR A 247 " =    1.110
peak=    3.126 closest distance to " CA  LYS A 117 " =    1.268
peak=    3.125 closest distance to " O   HOH Z 302 " =    2.000
peak=    3.122 closest distance to " O   HOH Z 234 " =    1.812
peak=    3.119 closest distance to " O   HOH Z 425 " =    2.067
peak=    3.116 closest distance to " CB  SER A 216 " =    0.923
peak=    3.113 closest distance to " CB  MET A 113 " =    1.899
peak=    3.104 closest distance to " CE1 HIS A 115 " =    0.998
peak=    3.104 closest distance to " O   HOH Z 248 " =    1.686
peak=    3.096 closest distance to " CA  GLY A 211 " =    1.290
peak=    3.094 closest distance to " CB  PHE A 204 " =    0.998
peak=    3.080 closest distance to " O   HOH Z 327 " =    1.721
peak=    3.079 closest distance to " O   GLU A   2 " =    1.652
peak=    3.036 closest distance to " CG BARG A 102 " =    1.866
peak=    3.026 closest distance to " CB  VAL A 265 " =    1.992
peak=    3.024 closest distance to " OD2 ASP A 200 " =    1.242
peak=    3.019 closest distance to " CE  MET A 113 " =    1.768

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.819 - 5.896
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 217
   mapped sites are within: 0.819 - 5.896

peak=   -4.618 closest distance to " CG1 VAL A 112 " =    2.639
peak=   -4.598 closest distance to " CB  PRO A 243 " =    2.644
peak=   -4.597 closest distance to " CD  ARG A 156 " =    2.116
peak=   -4.422 closest distance to " CD  ARG A  14 " =    3.504
peak=   -4.393 closest distance to " O   HOH Z 231 " =    2.290
peak=   -4.373 closest distance to " N   ALA A  43 " =    2.767
peak=   -4.306 closest distance to " O   HOH Z 266 " =    5.560
peak=   -4.267 closest distance to " CD  GLN A  58 " =    0.944
peak=   -4.220 closest distance to " O   HOH Z  73 " =    2.268
peak=   -4.216 closest distance to " O   HOH Z 377 " =    1.968
peak=   -4.212 closest distance to " OE1 GLN A 223 " =    2.103
peak=   -4.184 closest distance to " O   VAL A  67 " =    2.765
peak=   -4.108 closest distance to " CD1 PHE A  59 " =    1.969
peak=   -4.052 closest distance to " O   PRO A 198 " =    1.343
peak=   -4.044 closest distance to " CG1 VAL A 250 " =    2.709
peak=   -4.010 closest distance to " CE2 TYR A  30 " =    2.769
peak=   -4.008 closest distance to " O   HOH Z  10 " =    1.569
peak=   -3.983 closest distance to " C   HIS A 108 " =    1.064
peak=   -3.952 closest distance to " OG BSER A 134 " =    1.330
peak=   -3.952 closest distance to " CE2 PHE A  61 " =    2.652
peak=   -3.927 closest distance to " CD2 TYR A 293 " =    2.049
peak=   -3.918 closest distance to " O   HOH Z 198 " =    2.224
peak=   -3.880 closest distance to " CD1 ILE A 151 " =    2.459
peak=   -3.878 closest distance to " CB  ALA A 161 " =    2.655
peak=   -3.876 closest distance to " O   HOH Z 211 " =    1.359
peak=   -3.866 closest distance to " CZ3 TRP A 179 " =    1.146
peak=   -3.858 closest distance to " CA  GLY A 241 " =    3.280
peak=   -3.830 closest distance to " OD1 ASN A 148 " =    1.525
peak=   -3.822 closest distance to " O   HOH Z 196 " =    2.072
peak=   -3.789 closest distance to " CG2 ILE A  49 " =    2.754
peak=   -3.782 closest distance to " O   HOH Z 394 " =    1.558
peak=   -3.770 closest distance to " O   HOH Z  38 " =    1.277
peak=   -3.763 closest distance to " ND2 ASN A  45 " =    1.990
peak=   -3.760 closest distance to " O   HOH Z  51 " =    1.635
peak=   -3.737 closest distance to " O   HOH Z 216 " =    1.359
peak=   -3.735 closest distance to " O   HOH Z 290 " =    1.327
peak=   -3.724 closest distance to " CG1 VAL A 112 " =    2.859
peak=   -3.721 closest distance to " OG  SER A  97 " =    2.267
peak=   -3.706 closest distance to " ND2 ASN A 249 " =    2.419
peak=   -3.693 closest distance to " O   HOH Z 128 " =    2.743
peak=   -3.692 closest distance to " OXT GLY A 302 " =    3.114
peak=   -3.686 closest distance to " NH2AARG A 275 " =    5.512
peak=   -3.679 closest distance to " ND2BASN A 224 " =    1.783
peak=   -3.679 closest distance to " CB  ALA A  43 " =    2.671
peak=   -3.676 closest distance to " O   HOH Z 389 " =    2.035
peak=   -3.675 closest distance to " CA  VAL A  67 " =    2.889
peak=   -3.674 closest distance to " CE  MET A 105 " =    2.415
peak=   -3.658 closest distance to " CG  ARG A 269 " =    2.466
peak=   -3.641 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.622 closest distance to " CD1 LEU A 101 " =    2.429
peak=   -3.608 closest distance to " CB  ALA A 291 " =    2.352
peak=   -3.605 closest distance to " CG  HIS A  86 " =    1.089
peak=   -3.603 closest distance to " O   HOH Z 407 " =    3.407
peak=   -3.595 closest distance to " C   LEU A 143 " =    1.177
peak=   -3.568 closest distance to " O   HOH Z  60 " =    2.482
peak=   -3.568 closest distance to " NE2 GLN A 194 " =    1.842
peak=   -3.565 closest distance to " O   HOH Z 232 " =    1.718
peak=   -3.565 closest distance to " O   HOH Z  43 " =    1.613
peak=   -3.556 closest distance to " OD1 ASP A 171 " =    1.641
peak=   -3.554 closest distance to " CA  GLY A 203 " =    2.427
peak=   -3.550 closest distance to " O   VAL A 189 " =    2.614
peak=   -3.536 closest distance to " CE3 TRP A 150 " =    2.186
peak=   -3.531 closest distance to " O   HOH Z 185 " =    2.271
peak=   -3.521 closest distance to " C   ASN A 285 " =    2.517
peak=   -3.516 closest distance to " CB  ALA A   9 " =    2.529
peak=   -3.516 closest distance to " O   HOH Z   6 " =    2.381
peak=   -3.515 closest distance to " O   HOH Z  52 " =    1.438
peak=   -3.512 closest distance to " O   HOH Z 166 " =    1.827
peak=   -3.506 closest distance to " CB  ASN A  39 " =    2.340
peak=   -3.499 closest distance to " ND2 ASN A  45 " =    1.187
peak=   -3.495 closest distance to " CG  ARG A  66 " =    2.294
peak=   -3.494 closest distance to " O   HOH Z 111 " =    1.518
peak=   -3.492 closest distance to " C   GLY A  17 " =    1.163
peak=   -3.492 closest distance to " CA  GLY A 241 " =    2.343
peak=   -3.483 closest distance to " O   HOH Z 426 " =    1.641
peak=   -3.483 closest distance to " O   HOH Z 114 " =    1.268
peak=   -3.476 closest distance to " CG2 VAL A 189 " =    2.217
peak=   -3.475 closest distance to " CG2 ILE A 263 " =    2.354
peak=   -3.470 closest distance to " O   PRO A 163 " =    2.181
peak=   -3.468 closest distance to " CB  ALA A 291 " =    2.274
peak=   -3.457 closest distance to " O   HOH Z 114 " =    3.500
peak=   -3.457 closest distance to " O   HOH Z  44 " =    2.320
peak=   -3.456 closest distance to " CG1 VAL A 125 " =    1.927
peak=   -3.453 closest distance to " O   HOH Z 372 " =    2.435
peak=   -3.442 closest distance to " O   HOH Z 357 " =    2.081
peak=   -3.438 closest distance to " NE2 GLN A  88 " =    2.009
peak=   -3.421 closest distance to " O   HOH Z 353 " =    2.160
peak=   -3.417 closest distance to " OE1 GLN A  88 " =    1.104
peak=   -3.412 closest distance to " ND2 ASN A  60 " =    1.400
peak=   -3.411 closest distance to " O   PHE A 218 " =    1.495
peak=   -3.410 closest distance to " O   HOH Z 393 " =    1.285
peak=   -3.404 closest distance to " O   ALA A  10 " =    1.689
peak=   -3.400 closest distance to " O   HOH Z  37 " =    1.864
peak=   -3.395 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.394 closest distance to " O   HOH Z 275 " =    1.882
peak=   -3.384 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.383 closest distance to " O   HOH Z 264 " =    1.741
peak=   -3.382 closest distance to " C   ALA A 158 " =    1.359
peak=   -3.374 closest distance to " O   HOH Z 189 " =    2.079
peak=   -3.371 closest distance to " O   HOH Z 106 " =    1.942
peak=   -3.369 closest distance to " N   THR A 264 " =    1.361
peak=   -3.361 closest distance to " OD2 ASP A 171 " =    1.891
peak=   -3.358 closest distance to " O   HOH Z 174 " =    3.055
peak=   -3.352 closest distance to " O   HOH Z 243 " =    2.069
peak=   -3.351 closest distance to " O   HOH Z   6 " =    1.481
peak=   -3.349 closest distance to " N   ALA A 248 " =    1.665
peak=   -3.349 closest distance to " O   HOH Z 295 " =    1.573
peak=   -3.345 closest distance to " CD2 PHE A 225 " =    1.152
peak=   -3.344 closest distance to " CG  GLN A  11 " =    1.713
peak=   -3.343 closest distance to " O   HOH Z  19 " =    2.453
peak=   -3.343 closest distance to " CE BMET A  47 " =    1.833
peak=   -3.341 closest distance to " O   HOH Z 435 " =    2.809
peak=   -3.339 closest distance to " O   HOH Z  70 " =    2.197
peak=   -3.338 closest distance to " NH2 ARG A  79 " =    1.527
peak=   -3.335 closest distance to " O   HOH Z 311 " =    3.881
peak=   -3.334 closest distance to " CD1 LEU A  83 " =    2.641
peak=   -3.331 closest distance to " CD2 PHE A 192 " =    2.062
peak=   -3.328 closest distance to " O   HOH Z 234 " =    4.503
peak=   -3.326 closest distance to " CB  ALA A 100 " =    2.087
peak=   -3.325 closest distance to " O   HOH Z 275 " =    1.582
peak=   -3.323 closest distance to " O   HOH Z 396 " =    1.863
peak=   -3.321 closest distance to " O   HOH Z 409 " =    4.641
peak=   -3.317 closest distance to " CG  GLU A 277 " =    1.162
peak=   -3.315 closest distance to " CB  ASP A 286 " =    2.230
peak=   -3.314 closest distance to " C   ASN A 187 " =    1.911
peak=   -3.311 closest distance to " CG  PRO A 163 " =    2.307
peak=   -3.311 closest distance to " CA  GLY A 241 " =    2.899
peak=   -3.311 closest distance to " O   HOH Z 351 " =    1.557
peak=   -3.310 closest distance to " O   GLY A 211 " =    1.409
peak=   -3.310 closest distance to " O   HOH Z 350 " =    2.151
peak=   -3.309 closest distance to " CB  PRO A  54 " =    2.488
peak=   -3.307 closest distance to " O   HOH Z 193 " =    1.570
peak=   -3.299 closest distance to " O   HOH Z 359 " =    2.986
peak=   -3.297 closest distance to " O   HOH Z 236 " =    1.383
peak=   -3.296 closest distance to " OD1 ASP A 191 " =    1.678
peak=   -3.288 closest distance to " ND2 ASN A  69 " =    1.779
peak=   -3.285 closest distance to " O   HOH Z  71 " =    2.150
peak=   -3.285 closest distance to " CG  PHE A 283 " =    2.610
peak=   -3.284 closest distance to " N   ASP A 171 " =    2.422
peak=   -3.282 closest distance to " CD1 LEU A 228 " =    2.401
peak=   -3.274 closest distance to " CD  ARG A 139 " =    1.547
peak=   -3.271 closest distance to " CG  PRO A 243 " =    1.846
peak=   -3.269 closest distance to " CD2 PHE A  59 " =    2.440
peak=   -3.259 closest distance to " O   HOH Z 253 " =    4.198
peak=   -3.254 closest distance to " CG1BVAL A  41 " =    2.771
peak=   -3.253 closest distance to " OH  TYR A 247 " =    2.136
peak=   -3.253 closest distance to " O   SER A 210 " =    1.985
peak=   -3.250 closest distance to " O   HOH Z 348 " =    2.219
peak=   -3.249 closest distance to " O   HOH Z  90 " =    1.667
peak=   -3.249 closest distance to " O   HOH Z 421 " =    3.217
peak=   -3.242 closest distance to " CG1 VAL A 197 " =    2.290
peak=   -3.241 closest distance to " O   HOH Z 111 " =    1.921
peak=   -3.240 closest distance to " O   HOH Z 175 " =    4.023
peak=   -3.236 closest distance to " CG  LEU A  83 " =    2.035
peak=   -3.234 closest distance to " OH  TYR A 247 " =    1.822
peak=   -3.233 closest distance to " OD1 ASN A 187 " =    1.521
peak=   -3.233 closest distance to " O   HOH Z 252 " =    4.093
peak=   -3.230 closest distance to " O   SER A 135 " =    1.468
peak=   -3.229 closest distance to " CA  GLY A 133 " =    2.283
peak=   -3.224 closest distance to " CB  TRP A  85 " =    2.508
peak=   -3.220 closest distance to " OE1 GLN A 223 " =    2.160
peak=   -3.219 closest distance to " OD2 ASP A 191 " =    1.528
peak=   -3.213 closest distance to " SG ACYS A 201 " =    2.029
peak=   -3.212 closest distance to " O   GLN A 240 " =    2.541
peak=   -3.211 closest distance to " CD  ARG A 195 " =    5.123
peak=   -3.209 closest distance to " O   HOH Z 113 " =    2.358
peak=   -3.207 closest distance to " NE2 GLN A 103 " =    1.783
peak=   -3.203 closest distance to " CG1AVAL A  41 " =    2.834
peak=   -3.202 closest distance to " CB  ALA A  10 " =    2.216
peak=   -3.200 closest distance to " ND2 ASN A  60 " =    4.105
peak=   -3.195 closest distance to " CG  GLU A  53 " =    1.540
peak=   -3.193 closest distance to " O   HOH Z 414 " =    1.730
peak=   -3.193 closest distance to " O   HOH Z 322 " =    1.331
peak=   -3.192 closest distance to " O   HOH Z 298 " =    2.555
peak=   -3.184 closest distance to " O   HOH Z 176 " =    0.819
peak=   -3.183 closest distance to " NH2 ARG A 159 " =    2.367
peak=   -3.178 closest distance to " OG BSER A 134 " =    1.835
peak=   -3.177 closest distance to " O   HOH Z 134 " =    2.837
peak=   -3.174 closest distance to " O   GLY A  80 " =    2.680
peak=   -3.169 closest distance to " O   HOH Z  60 " =    1.730
peak=   -3.163 closest distance to " NH2 ARG A  66 " =    2.217
peak=   -3.162 closest distance to " O   TYR A 186 " =    1.766
peak=   -3.161 closest distance to " CZ  PHE A  59 " =    1.711
peak=   -3.158 closest distance to " O   ALA A  34 " =    2.552
peak=   -3.155 closest distance to " CE3 TRP A 274 " =    2.490
peak=   -3.149 closest distance to " OD1 ASN A 173 " =    1.332
peak=   -3.145 closest distance to " N   SER A 276 " =    1.421
peak=   -3.145 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.138 closest distance to " O   LEU A 101 " =    2.710
peak=   -3.138 closest distance to " CE3 TRP A  70 " =    1.797
peak=   -3.131 closest distance to " C   MET A 188 " =    1.408
peak=   -3.128 closest distance to " CD2 PHE A  61 " =    2.135
peak=   -3.128 closest distance to " O   ASP A  27 " =    2.141
peak=   -3.125 closest distance to " C   SER A 206 " =    1.417
peak=   -3.123 closest distance to " CG  TRP A 266 " =    1.822
peak=   -3.122 closest distance to " CB  PHE A  16 " =    2.565
peak=   -3.122 closest distance to " O   HOH Z 191 " =    5.896
peak=   -3.117 closest distance to " O   HOH Z 323 " =    1.494
peak=   -3.117 closest distance to " N   LYS A 166 " =    2.038
peak=   -3.115 closest distance to " O   HOH Z  11 " =    1.702
peak=   -3.114 closest distance to " CZ  PHE A  38 " =    1.967
peak=   -3.108 closest distance to " CB  ALA A 248 " =    2.422
peak=   -3.107 closest distance to " O   HOH Z 317 " =    2.221
peak=   -3.101 closest distance to " O   HOH Z  13 " =    1.591
peak=   -3.100 closest distance to " O   HOH Z 198 " =    1.683
peak=   -3.098 closest distance to " CD2 TYR A 293 " =    2.147
peak=   -3.097 closest distance to " CA  SER A 135 " =    1.294
peak=   -3.089 closest distance to " SD  MET A 188 " =    2.260
peak=   -3.087 closest distance to " O   HOH Z 139 " =    2.979
peak=   -3.083 closest distance to " CB  PRO A 163 " =    2.525
peak=   -3.073 closest distance to " CD2 TYR A 247 " =    2.390
peak=   -3.064 closest distance to " CA  GLY A  98 " =    2.203
peak=   -3.062 closest distance to " O   HOH Z 266 " =    5.318
peak=   -3.053 closest distance to " O   HOH Z 304 " =    1.493
peak=   -3.046 closest distance to " CG2AVAL A  72 " =    2.942
peak=   -3.040 closest distance to " OD1 ASN A 301 " =    1.973
peak=   -3.038 closest distance to " O   HOH Z 166 " =    1.660

================= 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    :  0.3576 0.3470   6.106643e+00   6.090611e+00
   1_bss:  0.3467 0.3381   6.089110e+00   6.069423e+00
   1_xyz:  0.2192 0.2377   5.689497e+00   5.761939e+00
   1_adp:  0.1991 0.2457   5.629477e+00   5.791163e+00
   1_occ:  0.1986 0.2455   5.628200e+00   5.791114e+00
   2_bss:  0.1970 0.2443   5.626577e+00   5.789628e+00
   2_xyz:  0.1421 0.1854   5.337188e+00   5.543666e+00
   2_adp:  0.1325 0.1734   5.273161e+00   5.483449e+00
   2_occ:  0.1324 0.1735   5.272830e+00   5.483539e+00
   3_bss:  0.1327 0.1732   5.272416e+00   5.481574e+00
   3_xyz:  0.1202 0.1641   5.198364e+00   5.425106e+00
   3_adp:  0.1179 0.1634   5.186115e+00   5.419433e+00
   3_occ:  0.1178 0.1633   5.186058e+00   5.419445e+00
   4_bss:  0.1178 0.1634   5.186059e+00   5.419533e+00
   4_xyz:  0.1167 0.1630   5.179978e+00   5.415611e+00
   4_adp:  0.1166 0.1630   5.177880e+00   5.414163e+00
   4_occ:  0.1166 0.1630   5.177958e+00   5.414340e+00
   5_bss:  0.1164 0.1629   5.178109e+00   5.414453e+00
   5_xyz:  0.1110 0.1618   5.152242e+00   5.408566e+00
   5_adp:  0.1107 0.1620   5.150597e+00   5.408997e+00
   5_occ:  0.1107 0.1621   5.150805e+00   5.409389e+00
   5_bss:  0.1105 0.1619   5.150942e+00   5.409511e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  80.000  -0.553  -2.256   2.150  -0.000   0.000   0.000
   1_xyz:  0.300  80.000  -0.553  -2.256   2.150  -0.000   0.000   0.000
   1_adp:  0.300  80.000  -0.553  -2.256   2.150  -0.000   0.000   0.000
   1_occ:  0.300  80.000  -0.553  -2.256   2.150  -0.000   0.000   0.000
   2_bss:  0.336  82.276  -1.923  -2.525  -0.342  -0.000  -0.000  -0.000
   2_xyz:  0.336  82.276  -1.923  -2.525  -0.342  -0.000  -0.000  -0.000
   2_adp:  0.336  82.276  -1.923  -2.525  -0.342  -0.000  -0.000  -0.000
   2_occ:  0.336  82.276  -1.923  -2.525  -0.342  -0.000  -0.000  -0.000
   3_bss:  0.332  72.529  -2.054  -2.273  -0.532  -0.000  -0.000  -0.000
   3_xyz:  0.332  72.529  -2.054  -2.273  -0.532  -0.000  -0.000  -0.000
   3_adp:  0.332  72.529  -2.054  -2.273  -0.532  -0.000  -0.000  -0.000
   3_occ:  0.332  72.529  -2.054  -2.273  -0.532  -0.000  -0.000  -0.000
   4_bss:  0.324  66.777  -2.073  -2.129  -0.640  -0.000  -0.000  -0.000
   4_xyz:  0.324  66.777  -2.073  -2.129  -0.640  -0.000  -0.000  -0.000
   4_adp:  0.324  66.777  -2.073  -2.129  -0.640  -0.000  -0.000  -0.000
   4_occ:  0.324  66.777  -2.073  -2.129  -0.640  -0.000  -0.000  -0.000
   5_bss:  0.324  66.777  -1.850  -1.846  -0.436  -0.000  -0.000  -0.000
   5_xyz:  0.324  66.777  -1.850  -1.846  -0.436  -0.000  -0.000  -0.000
   5_adp:  0.324  66.777  -1.850  -1.846  -0.436  -0.000  -0.000  -0.000
   5_occ:  0.324  66.777  -1.850  -1.846  -0.436  -0.000  -0.000  -0.000
   5_bss:  0.324  66.780  -1.560  -1.552  -0.176  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.129 0.6790  0.8313    34321.026
   1_bss:  36.209 0.6885  0.8437    32165.932
   1_xyz:  22.864 0.8353  0.9813    14444.450
   1_adp:  23.888 0.8240  0.9734    15377.804
   1_occ:  23.881 0.8241  0.9729    15353.769
   2_bss:  23.774 0.8253  0.9280    15306.106
   2_xyz:  17.516 0.8845  0.9684     8732.446
   2_adp:  15.976 0.8986  0.9675     7709.853
   2_occ:  15.976 0.8986  0.9674     7711.454
   3_bss:  15.955 0.8987  0.9664     7659.895
   3_xyz:  14.641 0.9100  0.9710     6820.574
   3_adp:  14.474 0.9116  0.9628     6747.689
   3_occ:  14.474 0.9116  0.9627     6746.513
   4_bss:  14.479 0.9115  0.9627     6746.683
   4_xyz:  14.403 0.9122  0.9632     6694.179
   4_adp:  14.366 0.9125  0.9549     6681.871
   4_occ:  14.370 0.9125  0.9548     6683.007
   5_bss:  14.373 0.9124  0.9628     6684.957
   5_xyz:  14.268 0.9131  0.9654     6616.280
   5_adp:  14.272 0.9132  0.9578     6604.693
   5_occ:  14.278 0.9131  0.9576     6607.184
   5_bss:  14.282 0.9131  0.9673     6609.360
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6208e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6208e-01
   1_xyz:   1.116  0.008  0.071 15.118  0.005  4.115   6.9487e-02
   1_adp:   1.116  0.008  0.071 15.118  0.005  4.115   6.9487e-02
   1_occ:   1.116  0.008  0.071 15.118  0.005  4.115   6.9487e-02
   2_bss:   1.116  0.008  0.071 15.118  0.005  4.115   6.9487e-02
   2_xyz:   1.052  0.008  0.078 14.829  0.004  4.134   6.2916e-02
   2_adp:   1.052  0.008  0.078 14.829  0.004  4.134   6.2916e-02
   2_occ:   1.052  0.008  0.078 14.829  0.004  4.134   6.2916e-02
   3_bss:   1.052  0.008  0.078 14.829  0.004  4.134   6.2916e-02
   3_xyz:   1.022  0.009  0.076 14.822  0.003  4.142   6.3202e-02
   3_adp:   1.022  0.009  0.076 14.822  0.003  4.142   6.3202e-02
   3_occ:   1.022  0.009  0.076 14.822  0.003  4.142   6.3202e-02
   4_bss:   1.022  0.009  0.076 14.822  0.003  4.142   6.3202e-02
   4_xyz:   1.022  0.009  0.078 14.786  0.004  4.115   6.4087e-02
   4_adp:   1.022  0.009  0.078 14.786  0.004  4.115   6.4087e-02
   4_occ:   1.022  0.009  0.078 14.786  0.004  4.115   6.4087e-02
   5_bss:   1.022  0.009  0.078 14.786  0.004  4.115   6.4087e-02
   5_xyz:   1.148  0.012  0.087 15.021  0.004  4.119   8.3167e-02
   5_adp:   1.148  0.012  0.087 15.021  0.004  4.119   8.3167e-02
   5_occ:   1.148  0.012  0.087 15.021  0.004  4.119   8.3167e-02
   5_bss:   1.148  0.012  0.087 15.021  0.004  4.119   8.3167e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4418e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4418e-01
   1_xyz:   8.097  0.044  0.259 85.680  0.045  2.221   7.1515e-02
   1_adp:   8.097  0.044  0.259 85.680  0.045  2.221   7.1515e-02
   1_occ:   8.097  0.044  0.259 85.680  0.045  2.221   7.1515e-02
   2_bss:   8.097  0.044  0.259 85.680  0.045  2.221   7.1515e-02
   2_xyz:   7.167  0.044  0.237 84.278  0.040  2.332   4.3868e-02
   2_adp:   7.167  0.044  0.237 84.278  0.040  2.332   4.3868e-02
   2_occ:   7.167  0.044  0.237 84.278  0.040  2.332   4.3868e-02
   3_bss:   7.167  0.044  0.237 84.278  0.040  2.332   4.3868e-02
   3_xyz:   7.585  0.042  0.234 84.070  0.035  2.400   4.1214e-02
   3_adp:   7.585  0.042  0.234 84.070  0.035  2.400   4.1214e-02
   3_occ:   7.585  0.042  0.234 84.070  0.035  2.400   4.1214e-02
   4_bss:   7.585  0.042  0.234 84.070  0.035  2.400   4.1214e-02
   4_xyz:   7.601  0.043  0.231 83.307  0.037  2.404   4.1844e-02
   4_adp:   7.601  0.043  0.231 83.307  0.037  2.404   4.1844e-02
   4_occ:   7.601  0.043  0.231 83.307  0.037  2.404   4.1844e-02
   5_bss:   7.601  0.043  0.231 83.307  0.037  2.404   4.1844e-02
   5_xyz:   7.645  0.054  0.285 82.910  0.039  2.332   6.2377e-02
   5_adp:   7.645  0.054  0.285 82.910  0.039  2.332   6.2377e-02
   5_occ:   7.645  0.054  0.285 82.910  0.039  2.332   6.2377e-02
   5_bss:   7.645  0.054  0.285 82.910  0.039  2.332   6.2377e-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:  80.74   0.00  17.69  76.27   0.00  13.42  80.74   3.91  40.91
   1_occ:  80.74   0.00  17.69  76.27   0.00  13.42  80.74   3.91  40.91
   2_bss:  80.74   0.00  17.69  76.27   0.00  13.42  80.74   3.91  40.91
   2_xyz:  80.74   0.00  17.69  76.27   0.00  13.42  80.74   3.91  40.91
   2_adp:  80.25   0.86  17.37  76.04   0.86  13.05  80.25   5.43  40.88
   2_occ:  80.25   0.86  17.37  76.04   0.86  13.05  80.25   5.43  40.88
   3_bss:  80.25   0.86  17.37  76.04   0.86  13.05  80.25   5.43  40.88
   3_xyz:  80.25   0.86  17.37  76.04   0.86  13.05  80.25   5.43  40.88
   3_adp:  82.21   0.39  17.23  79.74   0.39  12.86  82.21   5.85  41.03
   3_occ:  82.21   0.39  17.23  79.74   0.39  12.86  82.21   5.85  41.03
   4_bss:  82.21   0.39  17.23  79.74   0.39  12.86  82.21   5.85  41.03
   4_xyz:  82.21   0.39  17.23  79.74   0.39  12.86  82.21   5.85  41.03
   4_adp:  84.52   0.22  17.06  83.84   0.22  12.66  84.52   5.71  41.00
   4_occ:  84.52   0.22  17.06  83.84   0.22  12.66  84.52   5.71  41.00
   5_bss:  84.52   0.22  17.06  83.84   0.22  12.66  84.52   5.71  41.00
   5_xyz:  84.52   0.22  17.06  83.84   0.22  12.66  84.52   5.71  41.00
   5_adp:  88.54   0.00  16.95  88.54   0.00  12.51  87.47   3.98  41.17
   5_occ:  88.54   0.00  16.95  88.54   0.00  12.51  87.47   3.98  41.17
   5_bss:  88.55   0.00  16.96  88.55   0.00  12.51  87.47   3.98  41.17
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.425    0.016    0.281
   1_adp:    1.425    0.016    0.281
   1_occ:    1.425    0.016    0.281
   2_bss:    1.425    0.016    0.281
   2_xyz:    1.121    0.023    0.386
   2_adp:    1.121    0.023    0.386
   2_occ:    1.121    0.023    0.386
   3_bss:    1.121    0.023    0.386
   3_xyz:    1.061    0.038    0.427
   3_adp:    1.061    0.038    0.427
   3_occ:    1.061    0.038    0.427
   4_bss:    1.061    0.038    0.427
   4_xyz:    1.055    0.040    0.428
   4_adp:    1.055    0.040    0.428
   4_occ:    1.055    0.040    0.428
   5_bss:    1.055    0.040    0.428
   5_xyz:    1.141    0.055    0.443
   5_adp:    1.141    0.055    0.443
   5_occ:    1.141    0.055    0.443
   5_bss:    1.141    0.055    0.443
------------------------------------------------------------------------

CPU time actual refinement: 338.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/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_1042/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1042/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.32 
  Macro-tasks:
    bulk solvent and scale       = 49.62  
    individual site refinement   = 136.17 
    weights calculation          = 29.28  
    collect and process          = 6.68   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.86 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 103.72 
    alpha_beta                      = 8.35   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 112.94 
    fmodel                         = 8.20   
    r_factors                      = 0.30   
    phase_errors                   = 11.19  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 247.31 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.738 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    649 calls, 103.42 s
gradients_fft:          594 calls,  99.17 s

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

# Date 2008-01-16 Time 06:17:20 PST -0800 (1200493040.90 s)
Start R-work = 0.3576, R-free = 0.3470 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1778 (no bulk solvent and anisotropic scale)

Start R-work = 0.3467, R-free = 0.3381
Final R-work = 0.1105, R-free = 0.1619