# Date 2008-01-16 Time 05:13:58 PST -0800 (1200489238.37 s)
#phil __OFF__

Command line arguments: "../651.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29697
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 651

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 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: (70.25, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97109
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959916

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9711

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97109
Completeness in resolution range: 0.962888
Completeness with d_max=infinity: 0.959916

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2177 [2129/2157]  1918   211   9.9%
  bin  2:  4.2177 -  3.3602 [2051/2067]  1844   207  10.1%
  bin  3:  3.3602 -  2.9392 [2023/2042]  1819   204  10.1%
  bin  4:  2.9392 -  2.6721 [2016/2046]  1818   198   9.8%
  bin  5:  2.6721 -  2.4815 [1992/2011]  1792   200  10.0%
  bin  6:  2.4815 -  2.3358 [1980/2005]  1781   199  10.1%
  bin  7:  2.3358 -  2.2192 [1958/1991]  1765   193   9.9%
  bin  8:  2.2192 -  2.1229 [1975/2006]  1779   196   9.9%
  bin  9:  2.1229 -  2.0414 [1989/2031]  1787   202  10.2%
  bin 10:  2.0414 -  1.9711 [1476/1988]  1327   149  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/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: 25
        2.42 -     3.04: 2217
        3.04 -     3.66: 4738
        3.66 -     4.28: 9112
        4.28 -     4.90: 12468
  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 113 " - " O   HOH Z 350 "  2.038 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.049 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.125 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.163 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28555 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_651/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3026   r_free= 0.3029   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.986462                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7042 0.99   1385  154 0.2790 0.2768      6.3352      6.2883|
|  2:  4.7042 -  3.7534 0.99   1340  146 0.2393 0.2315      6.3735      6.3559|
|  3:  3.7534 -  3.2847 0.99   1305  147 0.2590 0.2652      6.2636      6.4007|
|  4:  3.2847 -  2.9870 0.99   1304  147 0.2617 0.2785      6.1425      6.1462|
|  5:  2.9870 -  2.7743 0.99   1291  142 0.2993 0.2809      6.0385      6.0007|
|  6:  2.7743 -  2.6117 0.99   1284  146 0.3158 0.3151      5.9811      5.9968|
|  7:  2.6117 -  2.4815 0.99   1282  138 0.3196 0.3066        5.96      5.9229|
|  8:  2.4815 -  2.3739 0.98   1267  146 0.3299 0.3249       5.925       5.924|
|  9:  2.3739 -  2.2829 0.98   1275  142 0.3243 0.3236      5.8689      5.8107|
| 10:  2.2829 -  2.2044 0.99   1261  135 0.3318 0.3696      5.8345      5.9506|
| 11:  2.2044 -  2.1356 0.99   1274  143 0.3534 0.3514      5.8188      5.8726|
| 12:  2.1356 -  2.0747 0.97   1244  138 0.3412 0.3482      5.7545      5.8065|
| 13:  2.0747 -  2.0203 0.99   1267  139 0.3483 0.3382      5.6586      5.6138|
| 14:  2.0203 -  1.9711 0.66    851   96 0.3855 0.3803      5.6855      5.5754|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7042  1385   154  0.80  25.47   0.87     0.81      40743.12|
|  2:  4.7042 -  3.7534  1340   146  0.85  21.15   0.99     0.93      42528.45|
|  3:  3.7534 -  3.2847  1305   147  0.82  24.27   1.01     0.98      40172.22|
|  4:  3.2847 -  2.9870  1304   147  0.80  26.62   1.02     0.97      34982.74|
|  5:  2.9870 -  2.7743  1291   142  0.75  30.72   1.00     0.95      29154.30|
|  6:  2.7743 -  2.6117  1284   146  0.74  31.82   1.01     0.94      26257.63|
|  7:  2.6117 -  2.4815  1282   138  0.75  31.24   1.02     0.96      23564.89|
|  8:  2.4815 -  2.3739  1267   146  0.73  32.97   1.02     0.96      22254.36|
|  9:  2.3739 -  2.2829  1275   142  0.74  32.46   1.05     0.95      20203.66|
| 10:  2.2829 -  2.2044  1261   135  0.71  34.96   1.06     0.95      20366.29|
| 11:  2.2044 -  2.1356  1274   143  0.70  36.18   1.08     0.96      19363.42|
| 12:  2.1356 -  2.0747  1244   138  0.71  35.41   1.08     0.98      18480.82|
| 13:  2.0747 -  2.0203  1267   139  0.68  37.31   1.07     0.95      15806.91|
| 14:  2.0203 -  1.9711   851    96  0.69  36.88   1.05     0.88      13188.21|
|alpha:            min =        0.81 max =            0.98 mean =         0.94|
|beta:             min =    13188.21 max =        42528.45 mean =     26748.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.98 mean =        31.00|
|phase err.(test): min =        0.00 max =           89.67 mean =        31.15|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.373988              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.411   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.598880              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.912   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      213 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2853 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4700 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4412 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5711 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6757 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.197 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3026   r_free= 0.3029   ksol= 0.00   Bsol= 0.00   scale= 0.988    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.986462                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2853   r_free= 0.2825   ksol= 0.33   Bsol= 31.77   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.13,1.22,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.962885                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.668717              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.481   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.290073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.876   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2853      final r-factor (work) = 0.1626          |
| start r-factor (free) = 0.2825      final r-factor (free) = 0.1862          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1213 = 3.67 * 0.50 * 5.9742 + 1.00 * 0.1625                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4373 = 3.67 * 0.50 * 5.6571 + 1.00 * 0.0602                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1626      final r-factor (work) = 0.1532          |
| start r-factor (free) = 0.1862      final r-factor (free) = 0.1884          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6476 = 0.29 * 1.00 * 5.6571 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6425 = 0.29 * 1.00 * 5.3808 + 1.00 * 0.0817                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.17   16.31    None  None   None       |
|    all(noH): 2823   0      0.00    84.17   16.31    None  None   None       |
|    Sol.    : 438    0      6.88    62.20   37.17    None  None   None       |
|    Mac.    : 2385   0      0.00    84.17   12.48    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 -   8.417:  530   |   5:    42.083 -  50.499:   98        |
|      1:     8.417 -  16.833: 1529   |   6:    50.499 -  58.916:   65        |
|      2:    16.833 -  25.250:  302   |   7:    58.916 -  67.333:    8        |
|      3:    25.250 -  33.666:  155   |   8:    67.333 -  75.749:    0        |
|      4:    33.666 -  42.083:  135   |   9:    75.749 -  84.166:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1532 r_free = 0.1884             target_work(ml) = 5.387         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1527 r_free = 0.1884             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1527   r_free= 0.1884   ksol= 0.33   Bsol= 31.77   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.14,-2.13,1.22,-0.00,0.00,0.00); trace/3= -1.35                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.384376                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1509   r_free= 0.1858   ksol= 0.32   Bsol= 39.93   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.70,-1.31,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.373345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.290822              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.963  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.483202              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1509      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1858      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9299 = 3.29 * 0.50 * 5.3906 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7123 = 3.29 * 0.50 * 5.2562 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5848 = 0.48 * 1.00 * 5.2562 + 1.00 * 0.0450                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4806 = 0.48 * 1.00 * 5.1172 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    79.01   16.98    None  None   None       |
|    all(noH): 2823   0      1.73    79.01   16.98    None  None   None       |
|    Sol.    : 438    0      3.98    74.65   39.06    None  None   None       |
|    Mac.    : 2385   0      1.73    79.01   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.731 -   9.459:  845   |   5:    40.370 -  48.098:  112        |
|      1:     9.459 -  17.187: 1206   |   6:    48.098 -  55.826:   87        |
|      2:    17.187 -  24.915:  274   |   7:    55.826 -  63.554:   45        |
|      3:    24.915 -  32.643:  123   |   8:    63.554 -  71.282:   18        |
|      4:    32.643 -  40.370:  108   |   9:    71.282 -  79.010:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1521             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1520             target_work(ml) = 5.114         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1520   ksol= 0.32   Bsol= 39.93   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.70,-1.31,-0.00,-0.00,-0.00); trace/3= -2.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.114264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1521   ksol= 0.32   Bsol= 41.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.49,-1.53,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.114437                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.414203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.995  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.281014              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.334  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6821 = 1.41 * 0.50 * 5.1172 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6669 = 1.41 * 0.50 * 5.1147 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1102      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4453 = 0.28 * 1.00 * 5.1147 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4451 = 0.28 * 1.00 * 5.1148 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    81.94   16.77    None  None   None       |
|    all(noH): 2823   0      1.37    81.94   16.77    None  None   None       |
|    Sol.    : 438    0      4.38    75.95   38.20    None  None   None       |
|    Mac.    : 2385   0      1.37    81.94   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.367 -   9.424:  870   |   5:    41.654 -  49.712:  109        |
|      1:     9.424 -  17.482: 1198   |   6:    49.712 -  57.769:   75        |
|      2:    17.482 -  25.539:  269   |   7:    57.769 -  65.827:   30        |
|      3:    25.539 -  33.597:  136   |   8:    65.827 -  73.885:    8        |
|      4:    33.597 -  41.654:  122   |   9:    73.885 -  81.942:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1523             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1096 r_free = 0.1523             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1523   ksol= 0.32   Bsol= 41.46   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.49,-1.53,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116959                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1523   ksol= 0.32   Bsol= 41.46   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.36,-1.55,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116875                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.340728              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.311  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.137520              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.755  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0366 = 2.34 * 0.50 * 5.1149 + 1.00 * 0.0503                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0296 = 2.34 * 0.50 * 5.0991 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1054      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1517      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7089 = 0.14 * 1.00 * 5.0991 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7079 = 0.14 * 1.00 * 5.0999 + 1.00 * 0.0065                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.95    78.48   16.26    None  None   None       |
|    all(noH): 2823   0      1.95    78.48   16.26    None  None   None       |
|    Sol.    : 438    0      5.66    74.99   36.09    None  None   None       |
|    Mac.    : 2385   0      1.95    78.48   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.954 -   9.606:  927   |   5:    40.216 -  47.869:   95        |
|      1:     9.606 -  17.259: 1143   |   6:    47.869 -  55.521:   73        |
|      2:    17.259 -  24.911:  271   |   7:    55.521 -  63.174:   21        |
|      3:    24.911 -  32.564:  135   |   8:    63.174 -  70.826:    6        |
|      4:    32.564 -  40.216:  146   |   9:    70.826 -  78.479:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1516             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1517             target_work(ml) = 5.100         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1517   ksol= 0.32   Bsol= 41.46   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.36,-1.55,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099605                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1518   ksol= 0.32   Bsol= 40.42   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.27,-1.46,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.099971                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.596467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.565  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.167158              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.684  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1518      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1330 = 1.60 * 0.50 * 5.1003 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1294 = 1.60 * 0.50 * 5.1077 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8603 = 0.17 * 1.00 * 5.1077 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8610 = 0.17 * 1.00 * 5.1109 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    78.38   16.19    None  None   None       |
|    all(noH): 2823   0      1.73    78.38   16.19    None  None   None       |
|    Sol.    : 438    0      6.12    74.89   36.09    None  None   None       |
|    Mac.    : 2385   0      1.73    78.38   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.727 -   9.392:  899   |   5:    40.052 -  47.717:  100        |
|      1:     9.392 -  17.057: 1160   |   6:    47.717 -  55.382:   74        |
|      2:    17.057 -  24.722:  281   |   7:    55.382 -  63.047:   21        |
|      3:    24.722 -  32.387:  135   |   8:    63.047 -  70.712:    6        |
|      4:    32.387 -  40.052:  141   |   9:    70.712 -  78.377:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1526             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1080 r_free = 0.1527             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1527   ksol= 0.32   Bsol= 40.42   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.27,-1.46,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112385                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7042 0.99   1385  154 0.0999 0.1252      5.3781      5.5092|
|  2:  4.7042 -  3.7534 0.99   1340  146 0.0866 0.1095      5.4408      5.6182|
|  3:  3.7534 -  3.2847 0.99   1305  147 0.1032 0.1494      5.4561      5.8461|
|  4:  3.2847 -  2.9870 0.99   1304  147 0.1173 0.1509      5.4328      5.5669|
|  5:  2.9870 -  2.7743 0.99   1291  142 0.1265 0.1675      5.2933      5.5153|
|  6:  2.7743 -  2.6117 0.99   1284  146 0.1144 0.1728      5.1707      5.3988|
|  7:  2.6117 -  2.4815 0.99   1282  138 0.1200 0.1553      5.1291      5.3473|
|  8:  2.4815 -  2.3739 0.98   1267  146 0.1121 0.1709      5.0189       5.292|
|  9:  2.3739 -  2.2829 0.98   1275  142 0.1114 0.1703      4.9903      5.2881|
| 10:  2.2829 -  2.2044 0.99   1261  135 0.1068 0.1690      4.9133      5.1517|
| 11:  2.2044 -  2.1356 0.99   1274  143 0.1092 0.1721      4.9044       5.255|
| 12:  2.1356 -  2.0747 0.97   1244  138 0.1053 0.1537      4.8409      5.0853|
| 13:  2.0747 -  2.0203 0.99   1267  139 0.1070 0.1709      4.7559      5.0727|
| 14:  2.0203 -  1.9711 0.66    851   96 0.0997 0.1625       4.613      4.8669|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7042  1385   154  0.94   8.66   0.98     0.96       6598.53|
|  2:  4.7042 -  3.7534  1340   146  0.96   7.65   1.02     1.01       8683.95|
|  3:  3.7534 -  3.2847  1305   147  0.94  11.12   1.02     1.01      10115.11|
|  4:  3.2847 -  2.9870  1304   147  0.92  13.29   1.01     0.99      10007.93|
|  5:  2.9870 -  2.7743  1291   142  0.90  15.45   0.99     0.96       7722.49|
|  6:  2.7743 -  2.6117  1284   146  0.91  14.97   0.98     0.95       6548.19|
|  7:  2.6117 -  2.4815  1282   138  0.91  14.57   0.99     0.96       5661.16|
|  8:  2.4815 -  2.3739  1267   146  0.92  14.27   0.99     0.98       4786.00|
|  9:  2.3739 -  2.2829  1275   142  0.92  14.22   1.01     0.99       4524.91|
| 10:  2.2829 -  2.2044  1261   135  0.91  14.39   1.00     0.96       3921.95|
| 11:  2.2044 -  2.1356  1274   143  0.90  15.78   1.00     0.96       4044.07|
| 12:  2.1356 -  2.0747  1244   138  0.92  14.02   1.01     1.00       3660.80|
| 13:  2.0747 -  2.0203  1267   139  0.91  15.23   1.01     1.01       3133.58|
| 14:  2.0203 -  1.9711   851    96  0.92  13.62   0.99     0.95       2259.49|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2259.49 max =        10115.11 mean =      5957.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.31|
|phase err.(test): min =        0.00 max =           89.62 mean =        12.92|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1527   ksol= 0.32   Bsol= 40.36   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.12,-1.31,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112423                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1080   r_free= 0.1527   ksol= 0.32   Bsol= 40.36   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.12,-1.31,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112423                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7042 0.99   1385  154 0.0999 0.1253      5.3786      5.5099|
|  2:  4.7042 -  3.7534 0.99   1340  146 0.0866 0.1095       5.441       5.618|
|  3:  3.7534 -  3.2847 0.99   1305  147 0.1032 0.1494      5.4561      5.8462|
|  4:  3.2847 -  2.9870 0.99   1304  147 0.1173 0.1509      5.4328      5.5669|
|  5:  2.9870 -  2.7743 0.99   1291  142 0.1265 0.1675      5.2933      5.5152|
|  6:  2.7743 -  2.6117 0.99   1284  146 0.1143 0.1728      5.1707      5.3988|
|  7:  2.6117 -  2.4815 0.99   1282  138 0.1200 0.1553      5.1291      5.3475|
|  8:  2.4815 -  2.3739 0.98   1267  146 0.1121 0.1709       5.019       5.292|
|  9:  2.3739 -  2.2829 0.98   1275  142 0.1114 0.1703      4.9903      5.2881|
| 10:  2.2829 -  2.2044 0.99   1261  135 0.1068 0.1690      4.9134      5.1516|
| 11:  2.2044 -  2.1356 0.99   1274  143 0.1092 0.1721      4.9044       5.255|
| 12:  2.1356 -  2.0747 0.97   1244  138 0.1053 0.1537      4.8408      5.0854|
| 13:  2.0747 -  2.0203 0.99   1267  139 0.1070 0.1709      4.7558      5.0724|
| 14:  2.0203 -  1.9711 0.66    851   96 0.0997 0.1625       4.613      4.8669|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7042  1385   154  0.94   8.66   0.99     0.96       6606.16|
|  2:  4.7042 -  3.7534  1340   146  0.96   7.66   1.02     1.01       8689.13|
|  3:  3.7534 -  3.2847  1305   147  0.94  11.12   1.02     1.02      10115.22|
|  4:  3.2847 -  2.9870  1304   147  0.92  13.29   1.01     0.99      10007.08|
|  5:  2.9870 -  2.7743  1291   142  0.90  15.45   0.99     0.96       7722.01|
|  6:  2.7743 -  2.6117  1284   146  0.91  14.97   0.98     0.95       6547.93|
|  7:  2.6117 -  2.4815  1282   138  0.91  14.57   0.99     0.96       5661.53|
|  8:  2.4815 -  2.3739  1267   146  0.92  14.27   1.00     0.98       4785.84|
|  9:  2.3739 -  2.2829  1275   142  0.92  14.23   1.01     0.99       4525.19|
| 10:  2.2829 -  2.2044  1261   135  0.91  14.39   1.00     0.97       3921.90|
| 11:  2.2044 -  2.1356  1274   143  0.90  15.78   1.00     0.96       4043.78|
| 12:  2.1356 -  2.0747  1244   138  0.92  14.02   1.01     1.00       3659.90|
| 13:  2.0747 -  2.0203  1267   139  0.91  15.23   1.02     1.02       3132.91|
| 14:  2.0203 -  1.9711   851    96  0.92  13.62   0.99     0.96       2259.44|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2259.44 max =        10115.22 mean =      5958.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.31|
|phase err.(test): min =        0.00 max =           89.62 mean =        12.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.697)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    78.32   16.12    None  None   None       |
|    all(noH): 2823   0      1.67    78.32   16.12    None  None   None       |
|    Sol.    : 438    0      6.06    74.83   36.03    None  None   None       |
|    Mac.    : 2385   0      1.67    78.32   12.47    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.666 -   9.331:  899   |   5:    39.990 -  47.655:  100        |
|      1:     9.331 -  16.995: 1160   |   6:    47.655 -  55.320:   74        |
|      2:    16.995 -  24.660:  281   |   7:    55.320 -  62.985:   21        |
|      3:    24.660 -  32.325:  135   |   8:    62.985 -  70.650:    6        |
|      4:    32.325 -  39.990:  141   |   9:    70.650 -  78.315:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 287         
Filter by distance & map next to the model:
   mapped sites are within: 0.515 - 4.577
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 287
   mapped sites are within: 0.710 - 4.577

peak=    5.911 closest distance to " NH2 ARG A  56 " =    2.211
peak=    5.812 closest distance to " O   HOH Z 126 " =    1.906
peak=    5.452 closest distance to " CG  PRO A  54 " =    1.288
peak=    5.420 closest distance to " CB  ARG A 275 " =    0.922
peak=    5.305 closest distance to " CB  SER A  63 " =    1.187
peak=    5.223 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.074 closest distance to " CB  GLN A 223 " =    1.416
peak=    5.024 closest distance to " O   HOH Z 142 " =    1.777
peak=    4.894 closest distance to " O   HOH Z 236 " =    1.910
peak=    4.836 closest distance to " C   PRO A 198 " =    1.498
peak=    4.750 closest distance to " CB  GLN A 183 " =    1.169
peak=    4.698 closest distance to " CG  PRO A  90 " =    1.131
peak=    4.690 closest distance to " O   HOH Z  78 " =    1.791
peak=    4.657 closest distance to " CB  GLU A 152 " =    1.177
peak=    4.645 closest distance to " CB  PRO A  54 " =    0.931
peak=    4.612 closest distance to " O   HOH Z 193 " =    1.916
peak=    4.498 closest distance to " O   HOH Z 232 " =    2.334
peak=    4.439 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.426 closest distance to " O   HOH Z  15 " =    2.293
peak=    4.414 closest distance to " O   HOH Z 234 " =    3.707
peak=    4.400 closest distance to " CB  SER A   3 " =    1.326
peak=    4.386 closest distance to " ND2 ASN A 187 " =    1.529
peak=    4.385 closest distance to " CB  ASN A 148 " =    1.401
peak=    4.359 closest distance to " OD1 ASN A  69 " =    2.585
peak=    4.352 closest distance to " O   HOH Z 298 " =    1.896
peak=    4.327 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.321 closest distance to " O   HOH Z 272 " =    1.815
peak=    4.316 closest distance to " O   HOH Z 427 " =    2.746
peak=    4.250 closest distance to " O   HOH Z 369 " =    2.044
peak=    4.242 closest distance to " CB  LEU A 228 " =    1.068
peak=    4.234 closest distance to " CG  PRO A 243 " =    1.075
peak=    4.214 closest distance to " CG2 VAL A 257 " =    0.915
peak=    4.205 closest distance to " CB  TYR A 169 " =    0.711
peak=    4.186 closest distance to " O   HOH Z 303 " =    2.017
peak=    4.183 closest distance to " O   HOH Z 344 " =    3.061
peak=    4.165 closest distance to " CG  PRO A 198 " =    1.302
peak=    4.113 closest distance to " CB  ARG A  79 " =    1.327
peak=    4.110 closest distance to " CG  PRO A 280 " =    0.728
peak=    4.098 closest distance to " CA  ASN A 215 " =    1.168
peak=    4.090 closest distance to " O   HOH Z  78 " =    2.103
peak=    4.049 closest distance to " O   HOH Z  44 " =    1.861
peak=    4.045 closest distance to " OD2 ASP A 286 " =    2.837
peak=    4.036 closest distance to " O   HOH Z  54 " =    1.700
peak=    4.024 closest distance to " O   HOH Z 346 " =    1.689
peak=    4.010 closest distance to " CB  VAL A 265 " =    1.254
peak=    4.007 closest distance to " O   HOH Z 316 " =    3.051
peak=    4.003 closest distance to " O   HOH Z  10 " =    1.854
peak=    4.000 closest distance to " O   HOH Z  61 " =    1.637
peak=    3.998 closest distance to " O   HOH Z 158 " =    2.997
peak=    3.995 closest distance to " O   HOH Z 368 " =    1.851
peak=    3.957 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.946 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.936 closest distance to " CB  TRP A 179 " =    1.282
peak=    3.931 closest distance to " O   HOH Z 144 " =    2.130
peak=    3.912 closest distance to " O   HOH Z 392 " =    3.140
peak=    3.906 closest distance to " O   SER A  87 " =    2.281
peak=    3.900 closest distance to " O   HOH Z 203 " =    1.831
peak=    3.896 closest distance to " O   HOH Z 403 " =    1.690
peak=    3.889 closest distance to " O   HOH Z 402 " =    1.456
peak=    3.889 closest distance to " O   HOH Z  40 " =    1.663
peak=    3.888 closest distance to " CA  THR A 264 " =    0.862
peak=    3.881 closest distance to " CB  TYR A 169 " =    0.784
peak=    3.866 closest distance to " NH1BARG A 145 " =    1.368
peak=    3.843 closest distance to " O   HOH Z 132 " =    2.469
peak=    3.837 closest distance to " O   HOH Z   9 " =    2.031
peak=    3.832 closest distance to " CB  SER A 216 " =    0.749
peak=    3.820 closest distance to " CA  ALA A  21 " =    1.156
peak=    3.816 closest distance to " O   HOH Z 207 " =    1.795
peak=    3.815 closest distance to " O   HOH Z 189 " =    2.032
peak=    3.770 closest distance to " O   HOH Z  43 " =    1.905
peak=    3.770 closest distance to " CG1 ILE A  33 " =    1.274
peak=    3.764 closest distance to " O   HOH Z 389 " =    1.852
peak=    3.764 closest distance to " NZ  LYS A 117 " =    3.279
peak=    3.756 closest distance to " CE  LYS A  76 " =    0.794
peak=    3.751 closest distance to " O   HOH Z 419 " =    1.942
peak=    3.747 closest distance to " O   HOH Z 250 " =    1.428
peak=    3.744 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.736 closest distance to " O   HOH Z 368 " =    3.573
peak=    3.732 closest distance to " O   HOH Z  61 " =    1.533
peak=    3.728 closest distance to " O   HOH Z  93 " =    2.360
peak=    3.711 closest distance to " O   HOH Z 128 " =    2.119
peak=    3.701 closest distance to " NH2BARG A 145 " =    2.002
peak=    3.700 closest distance to " O   HOH Z 128 " =    2.031
peak=    3.686 closest distance to " CG  ARG A  66 " =    2.490
peak=    3.683 closest distance to " CZ  PHE A 218 " =    1.011
peak=    3.679 closest distance to " CD2 TRP A 179 " =    1.357
peak=    3.672 closest distance to " CD1 LEU A 300 " =    1.262
peak=    3.671 closest distance to " NH1AARG A 145 " =    1.143
peak=    3.652 closest distance to " CD  ARG A 159 " =    0.711
peak=    3.649 closest distance to " O   HOH Z 219 " =    2.147
peak=    3.648 closest distance to " CG1BVAL A  72 " =    1.501
peak=    3.642 closest distance to " O   HOH Z 209 " =    2.269
peak=    3.638 closest distance to " O   HOH Z 425 " =    1.833
peak=    3.636 closest distance to " O   HOH Z   1 " =    1.944
peak=    3.634 closest distance to " O   HOH Z 245 " =    1.325
peak=    3.629 closest distance to " O   HOH Z 248 " =    1.678
peak=    3.624 closest distance to " CG2 ILE A 120 " =    1.197
peak=    3.609 closest distance to " CB  ARG A 190 " =    1.696
peak=    3.597 closest distance to " CB  SER A 212 " =    1.102
peak=    3.597 closest distance to " CD1 ILE A 106 " =    0.904
peak=    3.592 closest distance to " CB  ARG A 139 " =    0.970
peak=    3.590 closest distance to " O   HOH Z 407 " =    2.452
peak=    3.580 closest distance to " CB  VAL A 202 " =    1.580
peak=    3.579 closest distance to " CD2 LEU A 297 " =    0.873
peak=    3.570 closest distance to " O   HOH Z 214 " =    2.007
peak=    3.569 closest distance to " O   HOH Z 273 " =    2.672
peak=    3.561 closest distance to " CA  THR A 221 " =    0.969
peak=    3.560 closest distance to " CD BLYS A 290 " =    1.287
peak=    3.557 closest distance to " O   HOH Z 193 " =    1.982
peak=    3.556 closest distance to " CB  ALA A 291 " =    1.347
peak=    3.550 closest distance to " O   HOH Z  59 " =    1.885
peak=    3.550 closest distance to " O   HOH Z 147 " =    1.723
peak=    3.545 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.542 closest distance to " CD2 LEU A 255 " =    1.302
peak=    3.541 closest distance to " CB  LEU A 143 " =    1.096
peak=    3.541 closest distance to " O   HOH Z   3 " =    1.810
peak=    3.534 closest distance to " O   HOH Z 423 " =    1.858
peak=    3.526 closest distance to " O   HOH Z  89 " =    2.200
peak=    3.521 closest distance to " O   HOH Z 173 " =    1.895
peak=    3.515 closest distance to " O   HOH Z 371 " =    3.111
peak=    3.513 closest distance to " O   HOH Z 148 " =    3.247
peak=    3.505 closest distance to " CA  ALA A 233 " =    1.260
peak=    3.504 closest distance to " N   ARG A 156 " =    1.248
peak=    3.502 closest distance to " O   HOH Z 337 " =    3.642
peak=    3.496 closest distance to " CB  ILE A 120 " =    1.211
peak=    3.494 closest distance to " O   HOH Z 295 " =    1.506
peak=    3.493 closest distance to " O   HOH Z 286 " =    2.289
peak=    3.490 closest distance to " O   HOH Z 426 " =    1.540
peak=    3.481 closest distance to " O   HOH Z  64 " =    2.260
peak=    3.478 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.477 closest distance to " O   HOH Z 327 " =    1.743
peak=    3.472 closest distance to " N   ASN A  39 " =    1.169
peak=    3.472 closest distance to " CB  ASN A 224 " =    1.122
peak=    3.469 closest distance to " CB  SER A  26 " =    1.552
peak=    3.463 closest distance to " O   HOH Z 175 " =    2.134
peak=    3.462 closest distance to " O   HOH Z 345 " =    3.408
peak=    3.458 closest distance to " O   HOH Z 329 " =    3.697
peak=    3.454 closest distance to " OG BSER A 164 " =    2.391
peak=    3.443 closest distance to " O   HOH Z 193 " =    1.662
peak=    3.433 closest distance to " O   HOH Z 258 " =    1.788
peak=    3.429 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.425 closest distance to " CA  GLY A  80 " =    0.710
peak=    3.423 closest distance to " O   HOH Z 261 " =    2.144
peak=    3.416 closest distance to " CG  LYS A  76 " =    0.999
peak=    3.415 closest distance to " CG  GLN A  77 " =    1.988
peak=    3.412 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.400 closest distance to " CZ2 TRP A 179 " =    1.709
peak=    3.398 closest distance to " O   HOH Z 305 " =    3.638
peak=    3.382 closest distance to " O   HOH Z 133 " =    1.484
peak=    3.381 closest distance to " O   HOH Z 319 " =    2.208
peak=    3.379 closest distance to " O   HOH Z 280 " =    1.860
peak=    3.372 closest distance to " O   HOH Z 227 " =    1.591
peak=    3.371 closest distance to " O   HOH Z  88 " =    3.048
peak=    3.367 closest distance to " CA  ALA A  51 " =    0.892
peak=    3.365 closest distance to " O   HOH Z 163 " =    1.834
peak=    3.365 closest distance to " CB  ASP A 140 " =    0.860
peak=    3.362 closest distance to " CA  SER A  87 " =    0.960
peak=    3.361 closest distance to " O   HOH Z  19 " =    2.518
peak=    3.360 closest distance to " CB  GLU A 277 " =    3.483
peak=    3.359 closest distance to " CD  ARG A  66 " =    2.447
peak=    3.359 closest distance to " O   TRP A 274 " =    1.856
peak=    3.356 closest distance to " CG  GLU A 277 " =    2.237
peak=    3.352 closest distance to " CA  ASP A 140 " =    1.150
peak=    3.351 closest distance to " O   HOH Z 433 " =    1.803
peak=    3.347 closest distance to " O   HOH Z 234 " =    1.764
peak=    3.344 closest distance to " CB  GLN A 278 " =    0.847
peak=    3.344 closest distance to " O   HOH Z  71 " =    2.166
peak=    3.344 closest distance to " CA  ALA A 291 " =    0.923
peak=    3.343 closest distance to " O   HOH Z 353 " =    2.614
peak=    3.340 closest distance to " CA  ALA A  84 " =    1.268
peak=    3.340 closest distance to " CG  LEU A 167 " =    1.201
peak=    3.339 closest distance to " CA  MET A  40 " =    1.080
peak=    3.338 closest distance to " O   HOH Z 406 " =    1.639
peak=    3.338 closest distance to " O   HOH Z  97 " =    1.925
peak=    3.337 closest distance to " O   HOH Z 411 " =    3.819
peak=    3.337 closest distance to " CA  ASP A 162 " =    1.054
peak=    3.334 closest distance to " O   HOH Z 128 " =    2.058
peak=    3.331 closest distance to " OD1BASN A 224 " =    2.290
peak=    3.331 closest distance to " O   MET A 105 " =    1.753
peak=    3.331 closest distance to " OG  SER A  22 " =    2.649
peak=    3.323 closest distance to " OE1 GLU A   2 " =    2.174
peak=    3.322 closest distance to " CB  MET A  40 " =    0.858
peak=    3.319 closest distance to " CB  SER A  62 " =    1.249
peak=    3.316 closest distance to " O   HOH Z  85 " =    2.148
peak=    3.314 closest distance to " CA  ILE A 234 " =    0.904
peak=    3.307 closest distance to " O   HOH Z 281 " =    4.030
peak=    3.305 closest distance to " CB  ALA A  34 " =    1.088
peak=    3.304 closest distance to " CA  PHE A 283 " =    1.221
peak=    3.304 closest distance to " O   HOH Z  44 " =    3.279
peak=    3.303 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.301 closest distance to " NH2AARG A 190 " =    1.337
peak=    3.300 closest distance to " N   GLN A 278 " =    1.063
peak=    3.300 closest distance to " OG  SER A 206 " =    1.341
peak=    3.297 closest distance to " CB  THR A 157 " =    1.078
peak=    3.296 closest distance to " O   HOH Z 213 " =    1.612
peak=    3.293 closest distance to " CE1 TYR A 186 " =    1.357
peak=    3.292 closest distance to " CD  LYS A 119 " =    1.326
peak=    3.292 closest distance to " CD  PRO A 243 " =    1.561
peak=    3.292 closest distance to " CA  ILE A  33 " =    1.425
peak=    3.282 closest distance to " CE BLYS A 290 " =    1.134
peak=    3.280 closest distance to " CB  ALA A   1 " =    4.577
peak=    3.277 closest distance to " O   HOH Z 417 " =    3.219
peak=    3.276 closest distance to " ND1 HIS A  86 " =    1.599
peak=    3.276 closest distance to " O   HOH Z 172 " =    3.374
peak=    3.275 closest distance to " CD  ARG A 269 " =    0.943
peak=    3.273 closest distance to " O   HOH Z 366 " =    3.206
peak=    3.272 closest distance to " CG AARG A 275 " =    1.153
peak=    3.270 closest distance to " CA  VAL A 126 " =    1.014
peak=    3.270 closest distance to " OD1 ASP A 231 " =    1.889
peak=    3.268 closest distance to " CG  GLN A  89 " =    1.529
peak=    3.267 closest distance to " CB  ALA A 248 " =    1.337
peak=    3.263 closest distance to " O   HOH Z 124 " =    1.419
peak=    3.258 closest distance to " CG1 ILE A 151 " =    0.954
peak=    3.257 closest distance to " N   TRP A 177 " =    1.708
peak=    3.257 closest distance to " O   HOH Z 435 " =    1.929
peak=    3.256 closest distance to " NH2 ARG A 156 " =    1.123
peak=    3.252 closest distance to " O   HOH Z 411 " =    1.749
peak=    3.251 closest distance to " O   HOH Z 423 " =    2.923
peak=    3.251 closest distance to " O   HOH Z 144 " =    1.870
peak=    3.249 closest distance to " NE2 GLN A  73 " =    3.757
peak=    3.244 closest distance to " O   ALA A   1 " =    1.674
peak=    3.244 closest distance to " O   HOH Z   1 " =    1.714
peak=    3.243 closest distance to " O   HOH Z 125 " =    2.277
peak=    3.241 closest distance to " N   PHE A 130 " =    1.320
peak=    3.238 closest distance to " CA  ALA A  43 " =    1.180
peak=    3.235 closest distance to " CD  ARG A  36 " =    1.050
peak=    3.232 closest distance to " O   HOH Z 187 " =    2.268
peak=    3.232 closest distance to " O   HOH Z 263 " =    1.597
peak=    3.230 closest distance to " CB  HIS A 108 " =    0.819
peak=    3.226 closest distance to " CB  PRO A 198 " =    0.932
peak=    3.225 closest distance to " O   HOH Z 437 " =    1.590
peak=    3.222 closest distance to " OG  SER A  97 " =    3.537
peak=    3.221 closest distance to " O   HOH Z 357 " =    1.738
peak=    3.221 closest distance to " O   HOH Z 292 " =    1.752
peak=    3.218 closest distance to " CB  SER A 141 " =    1.005
peak=    3.217 closest distance to " O   HOH Z 171 " =    2.134
peak=    3.217 closest distance to " CB  ALA A 114 " =    1.186
peak=    3.211 closest distance to " O   ALA A   1 " =    1.423
peak=    3.209 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.207 closest distance to " CB  GLN A  88 " =    1.200
peak=    3.207 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.203 closest distance to " O   HOH Z 410 " =    1.892
peak=    3.200 closest distance to " O   HOH Z 374 " =    2.575
peak=    3.197 closest distance to " CG  MET A 113 " =    1.123
peak=    3.192 closest distance to " CB  ASN A 142 " =    0.992
peak=    3.191 closest distance to " CG1 VAL A 153 " =    0.916
peak=    3.188 closest distance to " O   HOH Z 108 " =    2.263
peak=    3.186 closest distance to " O  BHOH Z  74 " =    1.328
peak=    3.186 closest distance to " CB  SER A 273 " =    0.829
peak=    3.183 closest distance to " NZ  LYS A  76 " =    1.272
peak=    3.183 closest distance to " CD2 HIS A  81 " =    1.249
peak=    3.181 closest distance to " CD  LYS A 166 " =    1.216
peak=    3.175 closest distance to " ND1 HIS A  81 " =    1.640
peak=    3.173 closest distance to " CG2 ILE A  20 " =    1.467
peak=    3.167 closest distance to " CG  PRO A 213 " =    1.019
peak=    3.156 closest distance to " CG2BVAL A  41 " =    0.818
peak=    3.151 closest distance to " CE  MET A 188 " =    2.394
peak=    3.148 closest distance to " CB  LEU A 255 " =    0.777
peak=    3.145 closest distance to " CB  VAL A 268 " =    0.822
peak=    3.143 closest distance to " CB  ALA A  71 " =    1.377
peak=    3.139 closest distance to " O   HOH Z 336 " =    1.845
peak=    3.138 closest distance to " O   HOH Z 417 " =    1.943
peak=    3.137 closest distance to " O   HOH Z 409 " =    2.820
peak=    3.136 closest distance to " CG BARG A 275 " =    1.511
peak=    3.128 closest distance to " OG1 THR A 294 " =    1.667
peak=    3.128 closest distance to " O   HOH Z 391 " =    2.958
peak=    3.125 closest distance to " O   HOH Z 302 " =    1.941
peak=    3.117 closest distance to " CB  THR A  31 " =    1.685
peak=    3.116 closest distance to " O   HOH Z 216 " =    2.677
peak=    3.116 closest distance to " CB  TYR A 116 " =    0.822
peak=    3.113 closest distance to " O   HOH Z  40 " =    1.850
peak=    3.109 closest distance to " CZ3 TRP A 123 " =    1.259
peak=    3.099 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.099 closest distance to " CD  ARG A 219 " =    1.057
peak=    3.094 closest distance to " N   SER A  12 " =    1.548
peak=    3.090 closest distance to " CB  ASN A 215 " =    1.072
peak=    3.080 closest distance to " CB  LYS A 290 " =    1.329
peak=    3.079 closest distance to " O   SER A 164 " =    1.228
peak=    3.074 closest distance to " O   HOH Z  88 " =    1.981
peak=    3.074 closest distance to " CG BARG A 102 " =    1.772
peak=    3.066 closest distance to " O   HOH Z 325 " =    3.690
peak=    3.063 closest distance to " CA  ARG A  36 " =    0.990
peak=    3.054 closest distance to " O   GLY A 229 " =    1.628
peak=    3.045 closest distance to " O   HOH Z 371 " =    3.393
peak=    3.014 closest distance to " O   HOH Z 383 " =    1.624

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.509 - 5.561
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 204
   mapped sites are within: 0.764 - 5.561

peak=   -4.785 closest distance to " O   HOH Z 290 " =    1.014
peak=   -4.700 closest distance to " CB  PRO A 243 " =    2.621
peak=   -4.671 closest distance to " O   HOH Z 266 " =    4.533
peak=   -4.357 closest distance to " O   VAL A  67 " =    2.700
peak=   -4.244 closest distance to " O   HOH Z 372 " =    2.383
peak=   -4.199 closest distance to " C   HIS A 108 " =    1.108
peak=   -4.198 closest distance to " CG  GLN A 223 " =    1.666
peak=   -4.179 closest distance to " CG  ASP A 231 " =    0.778
peak=   -4.153 closest distance to " CD  ARG A 156 " =    1.999
peak=   -4.105 closest distance to " CA  VAL A  67 " =    2.666
peak=   -4.103 closest distance to " SG  CYS A 254 " =    3.301
peak=   -4.102 closest distance to " O   PRO A 198 " =    1.250
peak=   -4.081 closest distance to " O   HOH Z 435 " =    2.773
peak=   -4.068 closest distance to " O   ILE A 109 " =    2.578
peak=   -4.030 closest distance to " O   HOH Z 389 " =    1.833
peak=   -4.012 closest distance to " O   HOH Z 198 " =    2.101
peak=   -3.995 closest distance to " CG1 VAL A 112 " =    2.784
peak=   -3.975 closest distance to " N   GLN A  58 " =    1.724
peak=   -3.920 closest distance to " O   HOH Z 377 " =    2.003
peak=   -3.909 closest distance to " CE2 TYR A  30 " =    2.786
peak=   -3.871 closest distance to " CZ3 TRP A 179 " =    1.215
peak=   -3.870 closest distance to " C   ALA A 158 " =    1.304
peak=   -3.868 closest distance to " CD  ARG A 139 " =    1.478
peak=   -3.859 closest distance to " CG  PHE A 283 " =    2.737
peak=   -3.858 closest distance to " O   HOH Z 185 " =    2.269
peak=   -3.850 closest distance to " CB  CYS A 201 " =    2.672
peak=   -3.849 closest distance to " O   HOH Z 351 " =    1.454
peak=   -3.843 closest distance to " CD  GLN A  58 " =    1.016
peak=   -3.819 closest distance to " ND2 ASN A  45 " =    1.295
peak=   -3.801 closest distance to " OG BSER A 134 " =    1.212
peak=   -3.789 closest distance to " CE  MET A 105 " =    2.230
peak=   -3.781 closest distance to " O   ARG A 145 " =    1.604
peak=   -3.756 closest distance to " CE2 PHE A 218 " =    2.540
peak=   -3.755 closest distance to " O   HOH Z 353 " =    2.183
peak=   -3.735 closest distance to " OXT GLY A 302 " =    2.627
peak=   -3.734 closest distance to " CD1 PHE A  59 " =    1.777
peak=   -3.733 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.730 closest distance to " CZ  TYR A 169 " =    1.685
peak=   -3.723 closest distance to " NH1 ARG A 195 " =    2.514
peak=   -3.719 closest distance to " ND2 ASN A  45 " =    0.952
peak=   -3.711 closest distance to " CB  PRO A 163 " =    2.569
peak=   -3.692 closest distance to " O   HOH Z 211 " =    1.702
peak=   -3.684 closest distance to " O   HOH Z 114 " =    3.076
peak=   -3.684 closest distance to " O   HOH Z  43 " =    1.655
peak=   -3.682 closest distance to " O   HOH Z 407 " =    3.071
peak=   -3.682 closest distance to " CB  ASN A  39 " =    2.187
peak=   -3.677 closest distance to " N   SER A 212 " =    1.907
peak=   -3.673 closest distance to " O   HOH Z 231 " =    2.107
peak=   -3.663 closest distance to " CZ  PHE A  59 " =    1.502
peak=   -3.648 closest distance to " CD2 LEU A 300 " =    2.870
peak=   -3.646 closest distance to " CD1 LEU A 228 " =    2.193
peak=   -3.643 closest distance to " NH2AARG A 275 " =    5.245
peak=   -3.622 closest distance to " CD2 PHE A 192 " =    2.085
peak=   -3.621 closest distance to " N   ASP A 286 " =    2.394
peak=   -3.614 closest distance to " CG  MET A  93 " =    2.349
peak=   -3.611 closest distance to " O   PRO A 163 " =    1.983
peak=   -3.608 closest distance to " O   HOH Z 311 " =    3.536
peak=   -3.598 closest distance to " N   ALA A  43 " =    2.481
peak=   -3.587 closest distance to " OD1 ASP A 171 " =    1.612
peak=   -3.586 closest distance to " OG  SER A   3 " =    1.579
peak=   -3.578 closest distance to " O   ALA A 161 " =    1.510
peak=   -3.577 closest distance to " OG  SER A  97 " =    2.141
peak=   -3.574 closest distance to " CB  ALA A 291 " =    2.220
peak=   -3.560 closest distance to " CA  GLY A  98 " =    1.920
peak=   -3.551 closest distance to " O   HOH Z  10 " =    1.475
peak=   -3.527 closest distance to " CG  GLU A 152 " =    0.784
peak=   -3.526 closest distance to " CA  GLY A 203 " =    2.248
peak=   -3.521 closest distance to " CB  ALA A 248 " =    2.063
peak=   -3.517 closest distance to " O   HOH Z 196 " =    2.061
peak=   -3.514 closest distance to " C   LEU A 143 " =    1.082
peak=   -3.513 closest distance to " CG2 ILE A 263 " =    2.278
peak=   -3.511 closest distance to " N   ALA A 248 " =    1.571
peak=   -3.506 closest distance to " SG ACYS A 201 " =    1.905
peak=   -3.506 closest distance to " O   HOH Z 313 " =    1.929
peak=   -3.498 closest distance to " O   HOH Z 198 " =    1.295
peak=   -3.476 closest distance to " O   GLY A 196 " =    1.034
peak=   -3.465 closest distance to " CB  ALA A 291 " =    2.326
peak=   -3.462 closest distance to " CB  ASP A 286 " =    2.153
peak=   -3.454 closest distance to " CD1 ILE A 239 " =    2.059
peak=   -3.446 closest distance to " O   HOH Z 385 " =    2.056
peak=   -3.446 closest distance to " N   THR A 235 " =    1.314
peak=   -3.431 closest distance to " O   SER A 135 " =    1.455
peak=   -3.427 closest distance to " NH2 ARG A  79 " =    1.925
peak=   -3.418 closest distance to " CB  ASP A 132 " =    2.331
peak=   -3.417 closest distance to " C   MET A 188 " =    1.472
peak=   -3.414 closest distance to " CA  GLY A 241 " =    3.054
peak=   -3.410 closest distance to " OE1 GLN A  88 " =    1.150
peak=   -3.406 closest distance to " O   HOH Z  13 " =    1.407
peak=   -3.402 closest distance to " CD2 LEU A 300 " =    2.833
peak=   -3.398 closest distance to " NH2 ARG A  79 " =    1.659
peak=   -3.398 closest distance to " O   HOH Z 298 " =    1.236
peak=   -3.394 closest distance to " O   HOH Z  52 " =    1.256
peak=   -3.390 closest distance to " ND2 ASN A 187 " =    1.500
peak=   -3.390 closest distance to " O   HOH Z 377 " =    1.193
peak=   -3.383 closest distance to " CD2 LEU A 237 " =    2.778
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.703
peak=   -3.365 closest distance to " O   SER A  95 " =    1.445
peak=   -3.360 closest distance to " CE3 TRP A 123 " =    1.214
peak=   -3.360 closest distance to " CG  ARG A 269 " =    2.323
peak=   -3.353 closest distance to " CB  TYR A  15 " =    2.177
peak=   -3.351 closest distance to " O   HOH Z 388 " =    2.075
peak=   -3.351 closest distance to " O   HOH Z 111 " =    2.364
peak=   -3.349 closest distance to " CZ3 TRP A 274 " =    1.121
peak=   -3.349 closest distance to " O   HOH Z  44 " =    2.319
peak=   -3.346 closest distance to " CG1 VAL A 230 " =    2.027
peak=   -3.345 closest distance to " O   GLN A 240 " =    2.018
peak=   -3.340 closest distance to " CB  ASP A 132 " =    2.250
peak=   -3.337 closest distance to " CG  GLU A 277 " =    1.213
peak=   -3.336 closest distance to " CA  GLY A 133 " =    1.994
peak=   -3.332 closest distance to " O   HOH Z 193 " =    1.815
peak=   -3.329 closest distance to " CG  MET A 105 " =    0.946
peak=   -3.327 closest distance to " O   GLY A 211 " =    1.379
peak=   -3.323 closest distance to " OD1 ASN A 176 " =    1.292
peak=   -3.319 closest distance to " O   HOH Z  24 " =    1.484
peak=   -3.315 closest distance to " O   HOH Z  60 " =    2.437
peak=   -3.314 closest distance to " O   TRP A  70 " =    1.486
peak=   -3.310 closest distance to " O   HOH Z 210 " =    0.995
peak=   -3.310 closest distance to " CD  GLN A  88 " =    0.764
peak=   -3.307 closest distance to " OD1 ASP A 191 " =    1.497
peak=   -3.300 closest distance to " CB  PHE A 208 " =    2.227
peak=   -3.300 closest distance to " OG1 THR A 246 " =    1.467
peak=   -3.296 closest distance to " OE1 GLN A 223 " =    1.722
peak=   -3.287 closest distance to " CG  ARG A  66 " =    2.448
peak=   -3.284 closest distance to " N   GLN A 122 " =    1.436
peak=   -3.276 closest distance to " CE  LYS A  76 " =    2.718
peak=   -3.275 closest distance to " O   HOH Z  76 " =    1.862
peak=   -3.275 closest distance to " O   HOH Z 322 " =    1.526
peak=   -3.274 closest distance to " OXT GLY A 302 " =    3.432
peak=   -3.274 closest distance to " O   VAL A 189 " =    2.534
peak=   -3.269 closest distance to " OD2 ASP A 171 " =    2.324
peak=   -3.269 closest distance to " O   HOH Z  63 " =    1.561
peak=   -3.268 closest distance to " O   VAL A 174 " =    1.977
peak=   -3.263 closest distance to " O   HOH Z 395 " =    5.196
peak=   -3.261 closest distance to " OG1 THR A 178 " =    1.283
peak=   -3.259 closest distance to " CD1 LEU A 297 " =    2.346
peak=   -3.252 closest distance to " O   HOH Z 222 " =    1.286
peak=   -3.251 closest distance to " CA  TRP A 274 " =    1.521
peak=   -3.249 closest distance to " OG  SER A  62 " =    1.434
peak=   -3.248 closest distance to " O   HOH Z  11 " =    1.750
peak=   -3.241 closest distance to " O   HOH Z 385 " =    1.892
peak=   -3.236 closest distance to " CD  GLU A 152 " =    2.531
peak=   -3.235 closest distance to " C   PRO A  90 " =    1.426
peak=   -3.229 closest distance to " NE2 GLN A 278 " =    1.697
peak=   -3.224 closest distance to " O   MET A  40 " =    2.717
peak=   -3.224 closest distance to " O   HOH Z 417 " =    2.433
peak=   -3.222 closest distance to " O   VAL A 153 " =    2.263
peak=   -3.221 closest distance to " CE  LYS A  76 " =    2.842
peak=   -3.220 closest distance to " CZ  PHE A 130 " =    0.857
peak=   -3.218 closest distance to " CD1 ILE A 239 " =    2.468
peak=   -3.217 closest distance to " O   ALA A  51 " =    1.420
peak=   -3.215 closest distance to " N   ALA A 226 " =    2.030
peak=   -3.215 closest distance to " O   HOH Z  11 " =    2.078
peak=   -3.214 closest distance to " O   HOH Z 317 " =    2.449
peak=   -3.211 closest distance to " CD2 PHE A  61 " =    2.444
peak=   -3.209 closest distance to " C   GLN A 205 " =    1.973
peak=   -3.205 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.202 closest distance to " NZ  LYS A 119 " =    3.353
peak=   -3.191 closest distance to " CG1 VAL A  78 " =    3.171
peak=   -3.185 closest distance to " CD  GLU A 236 " =    0.990
peak=   -3.183 closest distance to " CG  LEU A  83 " =    1.825
peak=   -3.183 closest distance to " O   HOH Z 323 " =    1.263
peak=   -3.183 closest distance to " O   PRO A 198 " =    1.216
peak=   -3.181 closest distance to " O   HOH Z   6 " =    1.497
peak=   -3.176 closest distance to " OD1 ASP A 191 " =    1.658
peak=   -3.171 closest distance to " O   HOH Z  38 " =    1.642
peak=   -3.171 closest distance to " CZ  ARG A 259 " =    0.838
peak=   -3.164 closest distance to " O   HOH Z 250 " =    1.434
peak=   -3.161 closest distance to " O   HOH Z 166 " =    1.418
peak=   -3.159 closest distance to " CB  CYS A 254 " =    2.423
peak=   -3.159 closest distance to " O   LEU A 101 " =    2.773
peak=   -3.156 closest distance to " CG1 VAL A 197 " =    2.180
peak=   -3.151 closest distance to " O   SER A  22 " =    2.397
peak=   -3.144 closest distance to " O   HOH Z 262 " =    2.749
peak=   -3.144 closest distance to " O   HOH Z 282 " =    1.154
peak=   -3.140 closest distance to " CD  PRO A  90 " =    1.736
peak=   -3.132 closest distance to " CG  TRP A 266 " =    1.886
peak=   -3.123 closest distance to " OD2 ASP A  50 " =    2.298
peak=   -3.121 closest distance to " OD2 ASP A  50 " =    1.526
peak=   -3.120 closest distance to " O   TRP A  92 " =    1.610
peak=   -3.115 closest distance to " O   ASN A 249 " =    1.448
peak=   -3.111 closest distance to " O   HOH Z 241 " =    1.373
peak=   -3.107 closest distance to " OG  SER A 206 " =    1.725
peak=   -3.104 closest distance to " CE  MET A  93 " =    1.170
peak=   -3.101 closest distance to " O   HOH Z 390 " =    2.418
peak=   -3.101 closest distance to " O   PHE A 218 " =    1.643
peak=   -3.094 closest distance to " CD1 TYR A 247 " =    2.694
peak=   -3.092 closest distance to " OE2 GLU A   2 " =    1.880
peak=   -3.082 closest distance to " O   HOH Z 175 " =    4.363
peak=   -3.077 closest distance to " O   HOH Z 283 " =    5.561
peak=   -3.075 closest distance to " O   ALA A 292 " =    1.881
peak=   -3.066 closest distance to " O   HOH Z 429 " =    2.077
peak=   -3.055 closest distance to " O   HOH Z 137 " =    1.472
peak=   -3.054 closest distance to " O   HOH Z 361 " =    3.455
peak=   -3.053 closest distance to " O   HOH Z 281 " =    2.691
peak=   -3.053 closest distance to " O   HOH Z 436 " =    1.228
peak=   -3.041 closest distance to " O   LYS A 289 " =    2.932
peak=   -3.039 closest distance to " O   GLU A 152 " =    1.869
peak=   -3.032 closest distance to " N   GLN A  77 " =    1.602

================= 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    :  0.3026 0.3029   5.986462e+00   5.990679e+00
   1_bss:  0.2853 0.2825   5.962885e+00   5.946809e+00
   1_xyz:  0.1626 0.1862   5.425852e+00   5.539180e+00
   1_adp:  0.1532 0.1884   5.386950e+00   5.556891e+00
   1_occ:  0.1527 0.1884   5.384376e+00   5.555330e+00
   2_bss:  0.1509 0.1858   5.373345e+00   5.542289e+00
   2_xyz:  0.1175 0.1526   5.148121e+00   5.354918e+00
   2_adp:  0.1108 0.1521   5.114558e+00   5.345232e+00
   2_occ:  0.1107 0.1520   5.114264e+00   5.345109e+00
   3_bss:  0.1109 0.1521   5.114437e+00   5.345255e+00
   3_xyz:  0.1102 0.1519   5.117489e+00   5.350299e+00
   3_adp:  0.1096 0.1523   5.117087e+00   5.354439e+00
   3_occ:  0.1096 0.1523   5.116959e+00   5.354522e+00
   4_bss:  0.1095 0.1523   5.116875e+00   5.354516e+00
   4_xyz:  0.1054 0.1517   5.095315e+00   5.349101e+00
   4_adp:  0.1065 0.1516   5.099511e+00   5.348909e+00
   4_occ:  0.1065 0.1517   5.099605e+00   5.349238e+00
   5_bss:  0.1064 0.1518   5.099971e+00   5.349676e+00
   5_xyz:  0.1082 0.1525   5.112252e+00   5.358254e+00
   5_adp:  0.1080 0.1526   5.112343e+00   5.359925e+00
   5_occ:  0.1080 0.1527   5.112385e+00   5.360026e+00
   5_bss:  0.1080 0.1527   5.112423e+00   5.360057e+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:  0.326  31.775  -3.135  -2.126   1.218  -0.000   0.000   0.000
   1_xyz:  0.326  31.775  -3.135  -2.126   1.218  -0.000   0.000   0.000
   1_adp:  0.326  31.775  -3.135  -2.126   1.218  -0.000   0.000   0.000
   1_occ:  0.326  31.775  -3.135  -2.126   1.218  -0.000   0.000   0.000
   2_bss:  0.325  39.927  -3.100  -2.704  -1.310  -0.000  -0.000  -0.000
   2_xyz:  0.325  39.927  -3.100  -2.704  -1.310  -0.000  -0.000  -0.000
   2_adp:  0.325  39.927  -3.100  -2.704  -1.310  -0.000  -0.000  -0.000
   2_occ:  0.325  39.927  -3.100  -2.704  -1.310  -0.000  -0.000  -0.000
   3_bss:  0.321  41.456  -2.725  -2.486  -1.525  -0.000  -0.000  -0.000
   3_xyz:  0.321  41.456  -2.725  -2.486  -1.525  -0.000  -0.000  -0.000
   3_adp:  0.321  41.456  -2.725  -2.486  -1.525  -0.000  -0.000  -0.000
   3_occ:  0.321  41.456  -2.725  -2.486  -1.525  -0.000  -0.000  -0.000
   4_bss:  0.321  41.456  -2.553  -2.360  -1.551  -0.000  -0.000  -0.000
   4_xyz:  0.321  41.456  -2.553  -2.360  -1.551  -0.000  -0.000  -0.000
   4_adp:  0.321  41.456  -2.553  -2.360  -1.551  -0.000  -0.000  -0.000
   4_occ:  0.321  41.456  -2.553  -2.360  -1.551  -0.000  -0.000  -0.000
   5_bss:  0.324  40.422  -2.433  -2.266  -1.460  -0.000  -0.000  -0.000
   5_xyz:  0.324  40.422  -2.433  -2.266  -1.460  -0.000  -0.000  -0.000
   5_adp:  0.324  40.422  -2.433  -2.266  -1.460  -0.000  -0.000  -0.000
   5_occ:  0.324  40.422  -2.433  -2.266  -1.460  -0.000  -0.000  -0.000
   5_bss:  0.324  40.360  -2.276  -2.118  -1.313  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.019 0.7502  0.9413    26748.540
   1_bss:  29.262 0.7671  0.9166    22646.299
   1_xyz:  17.030 0.8906  1.0046     8793.572
   1_adp:  17.465 0.8864  1.0000     9052.124
   1_occ:  17.434 0.8866  0.9999     8996.452
   2_bss:  17.058 0.8899  0.9668     8722.015
   2_xyz:  13.298 0.9202  0.9816     5914.418
   2_adp:  13.181 0.9211  0.9801     5783.658
   2_occ:  13.179 0.9211  0.9801     5780.009
   3_bss:  13.179 0.9211  0.9845     5799.518
   3_xyz:  13.155 0.9218  0.9836     5827.351
   3_adp:  13.207 0.9215  0.9793     5870.595
   3_occ:  13.209 0.9214  0.9792     5871.856
   4_bss:  13.209 0.9214  0.9825     5874.103
   4_xyz:  13.129 0.9219  0.9829     5825.900
   4_adp:  13.091 0.9223  0.9794     5833.232
   4_occ:  13.099 0.9222  0.9793     5836.902
   5_bss:  13.108 0.9222  0.9829     5844.722
   5_xyz:  13.235 0.9213  0.9823     5939.449
   5_adp:  13.270 0.9210  0.9785     5956.757
   5_occ:  13.274 0.9210  0.9784     5958.543
   5_bss:  13.275 0.9210  0.9816     5959.324
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6252e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6252e-01
   1_xyz:   1.006  0.007  0.068 14.940  0.004  4.108   6.0159e-02
   1_adp:   1.006  0.007  0.068 14.940  0.004  4.108   6.0159e-02
   1_occ:   1.006  0.007  0.068 14.940  0.004  4.108   6.0159e-02
   2_bss:   1.006  0.007  0.068 14.940  0.004  4.108   6.0159e-02
   2_xyz:   1.041  0.007  0.076 15.005  0.004  4.111   6.3760e-02
   2_adp:   1.041  0.007  0.076 15.005  0.004  4.111   6.3760e-02
   2_occ:   1.041  0.007  0.076 15.005  0.004  4.111   6.3760e-02
   3_bss:   1.041  0.007  0.076 15.005  0.004  4.111   6.3760e-02
   3_xyz:   0.890  0.005  0.068 14.651  0.004  4.111   5.0250e-02
   3_adp:   0.890  0.005  0.068 14.651  0.004  4.111   5.0250e-02
   3_occ:   0.890  0.005  0.068 14.651  0.004  4.111   5.0250e-02
   4_bss:   0.890  0.005  0.068 14.651  0.004  4.111   5.0250e-02
   4_xyz:   1.015  0.007  0.075 14.960  0.004  4.112   6.1798e-02
   4_adp:   1.015  0.007  0.075 14.960  0.004  4.112   6.1798e-02
   4_occ:   1.015  0.007  0.075 14.960  0.004  4.112   6.1798e-02
   5_bss:   1.015  0.007  0.075 14.960  0.004  4.112   6.1798e-02
   5_xyz:   0.914  0.005  0.069 14.638  0.004  4.112   5.2238e-02
   5_adp:   0.914  0.005  0.069 14.638  0.004  4.112   5.2238e-02
   5_occ:   0.914  0.005  0.069 14.638  0.004  4.112   5.2238e-02
   5_bss:   0.914  0.005  0.069 14.638  0.004  4.112   5.2238e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3919e-01
   1_xyz:   7.785  0.048  0.331 85.894  0.036  2.323   5.5273e-02
   1_adp:   7.785  0.048  0.331 85.894  0.036  2.323   5.5273e-02
   1_occ:   7.785  0.048  0.331 85.894  0.036  2.323   5.5273e-02
   2_bss:   7.785  0.048  0.331 85.894  0.036  2.323   5.5273e-02
   2_xyz:   6.504  0.037  0.246 84.711  0.038  2.280   5.0694e-02
   2_adp:   6.504  0.037  0.246 84.711  0.038  2.280   5.0694e-02
   2_occ:   6.504  0.037  0.246 84.711  0.038  2.280   5.0694e-02
   3_bss:   6.504  0.037  0.246 84.711  0.038  2.280   5.0694e-02
   3_xyz:   6.539  0.038  0.208 83.395  0.040  2.368   3.2494e-02
   3_adp:   6.539  0.038  0.208 83.395  0.040  2.368   3.2494e-02
   3_occ:   6.539  0.038  0.208 83.395  0.040  2.368   3.2494e-02
   4_bss:   6.539  0.038  0.208 83.395  0.040  2.368   3.2494e-02
   4_xyz:   6.410  0.038  0.242 83.419  0.037  2.248   5.0874e-02
   4_adp:   6.410  0.038  0.242 83.419  0.037  2.248   5.0874e-02
   4_occ:   6.410  0.038  0.242 83.419  0.037  2.248   5.0874e-02
   5_bss:   6.410  0.038  0.242 83.419  0.037  2.248   5.0874e-02
   5_xyz:   6.327  0.037  0.214 83.833  0.038  2.336   3.2812e-02
   5_adp:   6.327  0.037  0.214 83.833  0.038  2.336   3.2812e-02
   5_occ:   6.327  0.037  0.214 83.833  0.038  2.336   3.2812e-02
   5_bss:   6.327  0.037  0.214 83.833  0.038  2.336   3.2812e-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:  84.17   0.00  16.31  84.17   0.00  12.48  62.20   6.88  37.17
   1_occ:  84.17   0.00  16.31  84.17   0.00  12.48  62.20   6.88  37.17
   2_bss:  84.17   0.00  16.31  84.17   0.00  12.48  62.20   6.88  37.17
   2_xyz:  84.17   0.00  16.31  84.17   0.00  12.48  62.20   6.88  37.17
   2_adp:  79.01   1.73  16.98  79.01   1.73  12.92  74.65   3.98  39.06
   2_occ:  79.01   1.73  16.98  79.01   1.73  12.92  74.65   3.98  39.06
   3_bss:  79.01   1.73  16.98  79.01   1.73  12.92  74.65   3.98  39.06
   3_xyz:  79.01   1.73  16.98  79.01   1.73  12.92  74.65   3.98  39.06
   3_adp:  81.94   1.37  16.77  81.94   1.37  12.84  75.95   4.38  38.20
   3_occ:  81.94   1.37  16.77  81.94   1.37  12.84  75.95   4.38  38.20
   4_bss:  81.94   1.37  16.77  81.94   1.37  12.84  75.95   4.38  38.20
   4_xyz:  81.94   1.37  16.77  81.94   1.37  12.84  75.95   4.38  38.20
   4_adp:  78.48   1.95  16.26  78.48   1.95  12.62  74.99   5.66  36.09
   4_occ:  78.48   1.95  16.26  78.48   1.95  12.62  74.99   5.66  36.09
   5_bss:  78.48   1.95  16.26  78.48   1.95  12.62  74.99   5.66  36.09
   5_xyz:  78.48   1.95  16.26  78.48   1.95  12.62  74.99   5.66  36.09
   5_adp:  78.38   1.73  16.19  78.38   1.73  12.53  74.89   6.12  36.09
   5_occ:  78.38   1.73  16.19  78.38   1.73  12.53  74.89   6.12  36.09
   5_bss:  78.32   1.67  16.12  78.32   1.67  12.47  74.83   6.06  36.03
------------------------------------------------------------------------
 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:    1.122    0.014    0.280
   1_adp:    1.122    0.014    0.280
   1_occ:    1.122    0.014    0.280
   2_bss:    1.122    0.014    0.280
   2_xyz:    0.743    0.023    0.330
   2_adp:    0.743    0.023    0.330
   2_occ:    0.743    0.023    0.330
   3_bss:    0.743    0.023    0.330
   3_xyz:    1.000    0.028    0.341
   3_adp:    1.000    0.028    0.341
   3_occ:    1.000    0.028    0.341
   4_bss:    1.000    0.028    0.341
   4_xyz:    0.955    0.024    0.355
   4_adp:    0.955    0.024    0.355
   4_occ:    0.955    0.024    0.355
   5_bss:    0.955    0.024    0.355
   5_xyz:    1.033    0.033    0.357
   5_adp:    1.033    0.033    0.357
   5_occ:    1.033    0.033    0.357
   5_bss:    1.033    0.033    0.357
------------------------------------------------------------------------

CPU time actual refinement: 333.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/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_651/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_651/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.74 
  Macro-tasks:
    bulk solvent and scale       = 37.68  
    individual site refinement   = 141.84 
    weights calculation          = 29.44  
    collect and process          = 6.64   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 215.73 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 106.42 
    alpha_beta                      = 8.06   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.82 
    fmodel                         = 6.89   
    r_factors                      = 0.19   
    phase_errors                   = 11.21  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 252.22 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.645 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    668 calls, 106.04 s
gradients_fft:          613 calls, 102.25 s

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

# Date 2008-01-16 Time 05:19:45 PST -0800 (1200489585.89 s)
Start R-work = 0.3026, R-free = 0.3029 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1735 (no bulk solvent and anisotropic scale)

Start R-work = 0.2853, R-free = 0.2825
Final R-work = 0.1080, R-free = 0.1527