# Date 2008-01-16 Time 06:31:28 PST -0800 (1200493888.41 s)
#phil __OFF__

Command line arguments: "../1181.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8044
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1181

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.6339, 85.9581, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99125
Completeness in resolution range: 0.946054
Completeness with d_max=infinity: 0.943185

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9913

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99125
Completeness in resolution range: 0.946054
Completeness with d_max=infinity: 0.943185

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2614 [2179/2208]  1964   215   9.9%
  bin  2:  4.2614 -  3.3948 [2082/2101]  1872   210  10.1%
  bin  3:  3.3948 -  2.9693 [2055/2075]  1848   207  10.1%
  bin  4:  2.9693 -  2.6995 [2053/2078]  1854   199   9.7%
  bin  5:  2.6995 -  2.5069 [2047/2066]  1835   212  10.4%
  bin  6:  2.5069 -  2.3597 [2013/2059]  1815   198   9.8%
  bin  7:  2.3597 -  2.2419 [1999/2032]  1796   203  10.2%
  bin  8:  2.2419 -  2.1446 [2002/2037]  1803   199   9.9%
  bin  9:  2.1446 -  2.0623 [2000/2029]  1800   200  10.0%
  bin 10:  2.0623 -  1.9912 [1159/2021]  1043   116  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/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:
        1.39 -     2.09: 4
        2.09 -     2.80: 674
        2.80 -     3.50: 4410
        3.50 -     4.20: 9202
        4.20 -     4.90: 13643
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.393 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.911 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.032 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  2.183 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 27928 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_1181/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.63395 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4027   r_free= 0.3933   ksol= 0.00   Bsol= 0.00   scale= 0.921    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.196523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7532 0.99   1409  157 0.3203 0.3288      6.4362      6.4162|
|  2:  4.7532 -  3.7921 0.99   1362  146 0.3242 0.3351      6.6663       6.639|
|  3:  3.7921 -  3.3185 0.99   1329  156 0.3586 0.3285      6.5254      6.4921|
|  4:  3.3185 -  3.0176 0.99   1339  146 0.3880 0.3591      6.4141      6.3498|
|  5:  3.0176 -  2.8028 0.99   1312  146 0.4054 0.4204      6.2639      6.3493|
|  6:  2.8028 -  2.6385 0.98   1308  143 0.4443 0.4101      6.2027      6.1066|
|  7:  2.6385 -  2.5069 0.99   1314  149 0.4395 0.4165      6.1733      6.1355|
|  8:  2.5069 -  2.3982 0.98   1284  141 0.4537 0.4334      6.0965      6.1535|
|  9:  2.3982 -  2.3063 0.98   1304  149 0.4640 0.4366      6.0712      6.0588|
| 10:  2.3063 -  2.2269 0.98   1278  138 0.4543 0.4871      6.0406      6.0855|
| 11:  2.2269 -  2.1575 0.99   1292  143 0.4722 0.4414      6.0051      5.9997|
| 12:  2.1575 -  2.0960 0.98   1274  140 0.4696 0.4841      5.9269      5.9486|
| 13:  2.0960 -  2.0409 0.97   1278  143 0.4644 0.4242      5.8419       5.775|
| 14:  2.0409 -  1.9912 0.42    547   62 0.4376 0.4734      5.7639      5.7618|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7532  1409   157  0.76  28.66   0.84     0.79      51497.05|
|  2:  4.7532 -  3.7921  1362   146  0.79  26.97   0.94     0.85      65262.86|
|  3:  3.7921 -  3.3185  1329   156  0.72  33.56   0.93     0.86      69913.80|
|  4:  3.3185 -  3.0176  1339   146  0.66  38.57   0.93     0.82      64362.12|
|  5:  3.0176 -  2.8028  1312   146  0.59  45.06   0.93     0.76      55853.87|
|  6:  2.8028 -  2.6385  1308   143  0.56  47.16   0.94     0.74      48414.96|
|  7:  2.6385 -  2.5069  1314   149  0.56  47.16   0.94     0.73      44555.80|
|  8:  2.5069 -  2.3982  1284   141  0.52  50.78   0.92     0.72      43781.16|
|  9:  2.3982 -  2.3063  1304   149  0.49  53.22   0.95     0.68      42422.53|
| 10:  2.3063 -  2.2269  1278   138  0.48  53.54   0.96     0.68      40747.84|
| 11:  2.2269 -  2.1575  1292   143  0.48  53.51   0.96     0.69      37045.46|
| 12:  2.1575 -  2.0960  1274   140  0.49  53.00   0.95     0.73      33614.39|
| 13:  2.0960 -  2.0409  1278   143  0.49  52.99   0.93     0.71      28168.70|
| 14:  2.0409 -  1.9912   547    62  0.49  53.17   0.98     0.66      22846.43|
|alpha:            min =        0.66 max =            0.86 mean =         0.75|
|beta:             min =    22846.43 max =        69913.80 mean =     47560.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.58|
|phase err.(work): min =        0.00 max =           90.00 mean =        44.96|
|phase err.(test): min =        0.00 max =           89.64 mean =        44.89|
|-----------------------------------------------------------------------------|

============================== 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 = 7.472021              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.253   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.387968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.049   (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 |  1.393 -  1.744:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.744 -  2.094:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.094 -  2.445:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.445 -  2.796:      659 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.796 -  3.146:     2066 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.146 -  3.497:     2344 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.497 -  3.848:     4499 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.848 -  4.199:     4703 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.199 -  4.549:     6166 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7477 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.393 |       0.218 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4027   r_free= 0.3933   ksol= 0.00   Bsol= 0.00   scale= 0.921    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.196523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3927   r_free= 0.3826   ksol= 0.30   Bsol= 49.03   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,2.52,-1.86,0.00,-0.00,-0.00); trace/3= 0.49                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.185325                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.520915              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.734357              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.705   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3927      final r-factor (work) = 0.2526          |
| start r-factor (free) = 0.3826      final r-factor (free) = 0.2843          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.3328 = 6.52 * 0.50 * 6.1850 + 1.00 * 0.1669                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5680 = 6.52 * 0.50 * 5.9697 + 1.00 * 0.1040                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2526      final r-factor (work) = 0.2296          |
| start r-factor (free) = 0.2843      final r-factor (free) = 0.2866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3900 = 0.73 * 1.00 * 5.9697 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2431 = 0.73 * 1.00 * 5.7596 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.90   17.92    None  None   None       |
|    all(noH): 2823   0      0.00    96.90   17.92    None  None   None       |
|    Sol.    : 438    0      2.59    96.90   41.97    None  None   None       |
|    Mac.    : 2385   0      0.00    88.88   13.50    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 -   9.690:  945   |   5:    48.452 -  58.142:   85        |
|      1:     9.690 -  19.381: 1082   |   6:    58.142 -  67.833:   60        |
|      2:    19.381 -  29.071:  332   |   7:    67.833 -  77.523:   30        |
|      3:    29.071 -  38.762:  161   |   8:    77.523 -  87.214:    8        |
|      4:    38.762 -  48.452:  114   |   9:    87.214 -  96.904:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2296 r_free = 0.2866             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2292 r_free = 0.2862             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2292   r_free= 0.2862   ksol= 0.30   Bsol= 49.03   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,2.52,-1.86,0.00,-0.00,-0.00); trace/3= 0.49                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.762585                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2270   r_free= 0.2832   ksol= 0.33   Bsol= 69.97   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.08,-1.60,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.758508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.046626              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.185   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.354635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.108  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2270      final r-factor (work) = 0.1725          |
| start r-factor (free) = 0.2832      final r-factor (free) = 0.2165          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8824 = 3.05 * 0.50 * 5.7627 + 1.00 * 0.1040                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6654 = 3.05 * 0.50 * 5.6489 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1725      final r-factor (work) = 0.1617          |
| start r-factor (free) = 0.2165      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0167 = 0.35 * 1.00 * 5.6489 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9521 = 0.35 * 1.00 * 5.4756 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    95.73   17.66    None  None   None       |
|    all(noH): 2823   0      1.17    95.73   17.66    None  None   None       |
|    Sol.    : 438    0      4.63    95.73   42.08    None  None   None       |
|    Mac.    : 2385   0      1.17    92.54   13.18    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:     1.175 -  10.630: 1151   |   5:    48.454 -  57.910:   86        |
|      1:    10.630 -  20.086:  990   |   6:    57.910 -  67.365:   66        |
|      2:    20.086 -  29.542:  236   |   7:    67.365 -  76.821:   26        |
|      3:    29.542 -  38.998:  135   |   8:    76.821 -  86.277:   11        |
|      4:    38.998 -  48.454:  117   |   9:    86.277 -  95.733:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1617 r_free = 0.2026             target_work(ml) = 5.449         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1615 r_free = 0.2025             target_work(ml) = 5.448         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1615   r_free= 0.2025   ksol= 0.33   Bsol= 69.97   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.08,-1.60,-0.00,-0.00,-0.00); trace/3= -0.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.448380                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1615   r_free= 0.2027   ksol= 0.33   Bsol= 71.18   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.09,-1.49,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.449001                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.993109              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.773  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.435271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.692  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1615      final r-factor (work) = 0.1309          |
| start r-factor (free) = 0.2027      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2571 = 2.99 * 0.50 * 5.4768 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0820 = 2.99 * 0.50 * 5.3551 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1309      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1732      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6964 = 1.44 * 1.00 * 5.3551 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5437 = 1.44 * 1.00 * 5.2476 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    105.66  17.84    None  None   None       |
|    all(noH): 2823   0      0.37    105.66  17.84    None  None   None       |
|    Sol.    : 438    0      4.92    100.06  43.96    None  None   None       |
|    Mac.    : 2385   0      0.37    105.66  13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.373 -  10.901: 1265   |   5:    53.015 -  63.544:   90        |
|      1:    10.901 -  21.430:  953   |   6:    63.544 -  74.072:   58        |
|      2:    21.430 -  31.958:  187   |   7:    74.072 -  84.601:   19        |
|      3:    31.958 -  42.487:  139   |   8:    84.601 -  95.129:   11        |
|      4:    42.487 -  53.015:   96   |   9:    95.129 - 105.658:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1705             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1241 r_free = 0.1705             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1241   r_free= 0.1705   ksol= 0.33   Bsol= 71.18   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-1.09,-1.49,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1703   ksol= 0.33   Bsol= 69.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.50,-1.39,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.237858                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.455486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.959  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.501465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.874  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1367 = 3.46 * 0.50 * 5.2490 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0710 = 3.46 * 0.50 * 5.2048 + 1.00 * 0.0785                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6219 = 0.50 * 1.00 * 5.2048 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6096 = 0.50 * 1.00 * 5.1822 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.21    106.24  17.43    None  None   None       |
|    all(noH): 2823   0      0.21    106.24  17.43    None  None   None       |
|    Sol.    : 438    0      4.24    99.14   42.66    None  None   None       |
|    Mac.    : 2385   0      0.21    106.24  12.80    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:     0.205 -  10.809: 1277   |   5:    53.221 -  63.824:   79        |
|      1:    10.809 -  21.412:  960   |   6:    63.824 -  74.427:   49        |
|      2:    21.412 -  32.015:  201   |   7:    74.427 -  85.030:   13        |
|      3:    32.015 -  42.618:  120   |   8:    85.030 -  95.633:    9        |
|      4:    42.618 -  53.221:  110   |   9:    95.633 - 106.237:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1643             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1643             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1643   ksol= 0.33   Bsol= 69.89   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.50,-1.39,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1642   ksol= 0.32   Bsol= 65.58   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.53,-1.20,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176370                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.006192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.300  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.135954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.349  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1642      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2767 = 2.01 * 0.50 * 5.1822 + 1.00 * 0.0785                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2626 = 2.01 * 0.50 * 5.1842 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8998 = 1.14 * 1.00 * 5.1842 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9008 = 1.14 * 1.00 * 5.1846 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.70  17.25    None  None   None       |
|    all(noH): 2823   0      0.00    110.70  17.25    None  None   None       |
|    Sol.    : 438    0      5.12    99.87   42.23    None  None   None       |
|    Mac.    : 2385   0      0.00    110.70  12.67    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 -  11.070: 1363   |   5:    55.350 -  66.420:   76        |
|      1:    11.070 -  22.140:  889   |   6:    66.420 -  77.490:   38        |
|      2:    22.140 -  33.210:  196   |   7:    77.490 -  88.560:   13        |
|      3:    33.210 -  44.280:  129   |   8:    88.560 -  99.630:    6        |
|      4:    44.280 -  55.350:  109   |   9:    99.630 - 110.700:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1656             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1657             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1657   ksol= 0.32   Bsol= 65.58   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,-1.53,-1.20,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.188089                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7532 0.99   1409  157 0.0988 0.1318      5.3836       5.544|
|  2:  4.7532 -  3.7921 0.99   1362  146 0.0839 0.1053      5.4141      5.6021|
|  3:  3.7921 -  3.3185 0.99   1329  156 0.1048 0.1564      5.4654      5.8651|
|  4:  3.3185 -  3.0176 0.99   1339  146 0.1249 0.1619      5.4849      5.6375|
|  5:  3.0176 -  2.8028 0.99   1312  146 0.1399 0.1853      5.3832      5.5791|
|  6:  2.8028 -  2.6385 0.98   1308  143 0.1318 0.2029      5.2772      5.5079|
|  7:  2.6385 -  2.5069 0.99   1314  149 0.1283 0.1811      5.2106      5.4461|
|  8:  2.5069 -  2.3982 0.98   1284  141 0.1232 0.1789      5.1154      5.3506|
|  9:  2.3982 -  2.3063 0.98   1304  149 0.1216 0.1915      5.0755        5.37|
| 10:  2.3063 -  2.2269 0.98   1278  138 0.1190 0.1835      5.0246      5.2657|
| 11:  2.2269 -  2.1575 0.99   1292  143 0.1188 0.1920      4.9879      5.3404|
| 12:  2.1575 -  2.0960 0.98   1274  140 0.1143 0.1727      4.9259      5.1495|
| 13:  2.0960 -  2.0409 0.97   1278  143 0.1224 0.1830       4.843      5.0956|
| 14:  2.0409 -  1.9912 0.42    547   62 0.1055 0.1911      4.6971      5.0641|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7532  1409   157  0.94   9.01   0.96     0.94       7120.23|
|  2:  4.7532 -  3.7921  1362   146  0.95   7.86   1.00     0.98       8631.69|
|  3:  3.7921 -  3.3185  1329   156  0.93  11.44   1.02     1.01      10371.17|
|  4:  3.3185 -  3.0176  1339   146  0.91  14.53   1.00     0.98      11242.15|
|  5:  3.0176 -  2.8028  1312   146  0.89  17.47   0.99     0.97       9565.31|
|  6:  2.8028 -  2.6385  1308   143  0.89  17.49   0.98     0.95       8195.61|
|  7:  2.6385 -  2.5069  1314   149  0.90  16.40   0.98     0.95       6966.50|
|  8:  2.5069 -  2.3982  1284   141  0.89  16.88   0.98     0.95       6110.13|
|  9:  2.3982 -  2.3063  1304   149  0.90  16.74   0.98     0.94       5573.56|
| 10:  2.3063 -  2.2269  1278   138  0.89  16.76   0.97     0.93       5063.64|
| 11:  2.2269 -  2.1575  1292   143  0.89  17.31   0.97     0.93       4833.24|
| 12:  2.1575 -  2.0960  1274   140  0.90  16.33   0.98     0.96       4512.31|
| 13:  2.0960 -  2.0409  1278   143  0.89  17.77   0.97     0.96       3842.65|
| 14:  2.0409 -  1.9912   547    62  0.90  16.44   0.96     0.92       2895.02|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2895.02 max =        11242.15 mean =      6983.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.04|
|phase err.(test): min =        0.00 max =           89.49 mean =        14.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1656   ksol= 0.32   Bsol= 65.58   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.42,-1.02,-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: 5.188187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1656   ksol= 0.32   Bsol= 65.58   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,-1.42,-1.02,-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: 5.188187                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7532 0.99   1409  157 0.0988 0.1319      5.3843       5.545|
|  2:  4.7532 -  3.7921 0.99   1362  146 0.0840 0.1053      5.4145      5.6021|
|  3:  3.7921 -  3.3185 0.99   1329  156 0.1048 0.1564      5.4655      5.8652|
|  4:  3.3185 -  3.0176 0.99   1339  146 0.1248 0.1619      5.4849      5.6375|
|  5:  3.0176 -  2.8028 0.99   1312  146 0.1399 0.1853      5.3831      5.5791|
|  6:  2.8028 -  2.6385 0.98   1308  143 0.1318 0.2027       5.277      5.5074|
|  7:  2.6385 -  2.5069 0.99   1314  149 0.1283 0.1812      5.2105      5.4462|
|  8:  2.5069 -  2.3982 0.98   1284  141 0.1232 0.1789      5.1154      5.3504|
|  9:  2.3982 -  2.3063 0.98   1304  149 0.1216 0.1914      5.0756        5.37|
| 10:  2.3063 -  2.2269 0.98   1278  138 0.1190 0.1836       5.025      5.2664|
| 11:  2.2269 -  2.1575 0.99   1292  143 0.1188 0.1920       4.988      5.3405|
| 12:  2.1575 -  2.0960 0.98   1274  140 0.1143 0.1729       4.926      5.1502|
| 13:  2.0960 -  2.0409 0.97   1278  143 0.1224 0.1831      4.8429      5.0955|
| 14:  2.0409 -  1.9912 0.42    547   62 0.1055 0.1907      4.6969      5.0625|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7532  1409   157  0.94   9.02   0.96     0.94       7130.56|
|  2:  4.7532 -  3.7921  1362   146  0.95   7.87   1.00     0.98       8638.25|
|  3:  3.7921 -  3.3185  1329   156  0.93  11.44   1.02     1.02      10374.08|
|  4:  3.3185 -  3.0176  1339   146  0.91  14.53   1.00     0.98      11243.02|
|  5:  3.0176 -  2.8028  1312   146  0.89  17.47   1.00     0.97       9561.06|
|  6:  2.8028 -  2.6385  1308   143  0.89  17.49   0.99     0.96       8190.89|
|  7:  2.6385 -  2.5069  1314   149  0.90  16.39   0.99     0.96       6962.89|
|  8:  2.5069 -  2.3982  1284   141  0.89  16.88   0.99     0.96       6109.34|
|  9:  2.3982 -  2.3063  1304   149  0.90  16.74   0.99     0.94       5573.86|
| 10:  2.3063 -  2.2269  1278   138  0.89  16.77   0.98     0.94       5066.59|
| 11:  2.2269 -  2.1575  1292   143  0.89  17.32   0.98     0.94       4835.16|
| 12:  2.1575 -  2.0960  1274   140  0.90  16.33   0.99     0.97       4515.26|
| 13:  2.0960 -  2.0409  1278   143  0.89  17.77   0.98     0.97       3840.92|
| 14:  2.0409 -  1.9912   547    62  0.90  16.41   0.97     0.93       2891.81|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2891.81 max =        11243.02 mean =      6984.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.04|
|phase err.(test): min =        0.00 max =           89.49 mean =        14.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.253)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.70  17.25    None  None   None       |
|    all(noH): 2823   0      0.00    110.70  17.25    None  None   None       |
|    Sol.    : 438    0      5.12    99.87   42.23    None  None   None       |
|    Mac.    : 2385   0      0.00    110.70  12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.073: 1363   |   5:    55.353 -  66.423:   76        |
|      1:    11.073 -  22.143:  889   |   6:    66.423 -  77.493:   38        |
|      2:    22.143 -  33.213:  196   |   7:    77.493 -  88.563:   13        |
|      3:    33.213 -  44.283:  129   |   8:    88.563 -  99.633:    6        |
|      4:    44.283 -  55.353:  109   |   9:    99.633 - 110.703:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 4.591
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 306
   mapped sites are within: 0.702 - 4.591

peak=    6.074 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.835 closest distance to " O   HOH Z 111 " =    2.005
peak=    5.241 closest distance to " CB  SER A  63 " =    1.323
peak=    5.149 closest distance to " O   HOH Z 232 " =    2.323
peak=    4.905 closest distance to " CG  PRO A 213 " =    1.223
peak=    4.767 closest distance to " CB  GLU A 128 " =    1.108
peak=    4.677 closest distance to " C   PRO A 198 " =    1.539
peak=    4.666 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.621 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.595 closest distance to " CG  PRO A 198 " =    1.255
peak=    4.594 closest distance to " O   HOH Z 298 " =    1.996
peak=    4.556 closest distance to " CG  PRO A  90 " =    1.128
peak=    4.538 closest distance to " CA  TYR A  30 " =    0.980
peak=    4.388 closest distance to " CB  ARG A 190 " =    1.707
peak=    4.358 closest distance to " O   HOH Z  68 " =    1.934
peak=    4.329 closest distance to " CG1 ILE A  33 " =    1.298
peak=    4.288 closest distance to " CB  TRP A 266 " =    0.976
peak=    4.285 closest distance to " CB  LEU A 228 " =    1.072
peak=    4.285 closest distance to " CZ  PHE A 218 " =    1.076
peak=    4.261 closest distance to " NH2 ARG A 156 " =    1.171
peak=    4.259 closest distance to " O   HOH Z 134 " =    1.442
peak=    4.245 closest distance to " OD1 ASN A  69 " =    2.684
peak=    4.239 closest distance to " CD  ARG A 269 " =    0.956
peak=    4.235 closest distance to " CG  PRO A 243 " =    1.161
peak=    4.234 closest distance to " C   ILE A 106 " =    1.902
peak=    4.167 closest distance to " CB  ASN A 148 " =    1.384
peak=    4.159 closest distance to " CZ  PHE A 192 " =    0.948
peak=    4.149 closest distance to " CA  ALA A  21 " =    1.313
peak=    4.130 closest distance to " CB  GLU A 152 " =    1.118
peak=    4.130 closest distance to " O   HOH Z 133 " =    2.382
peak=    4.123 closest distance to " O   HOH Z 369 " =    2.160
peak=    4.108 closest distance to " O   HOH Z 236 " =    2.050
peak=    4.108 closest distance to " O   HOH Z  21 " =    1.774
peak=    4.101 closest distance to " O   HOH Z 126 " =    2.062
peak=    4.096 closest distance to " O   HOH Z  20 " =    1.987
peak=    4.080 closest distance to " CB  VAL A 202 " =    1.615
peak=    4.079 closest distance to " CG2 THR A 221 " =    1.023
peak=    4.074 closest distance to " O   HOH Z 261 " =    2.083
peak=    4.053 closest distance to " O   HOH Z 108 " =    2.720
peak=    4.049 closest distance to " CD BLYS A 290 " =    0.996
peak=    4.036 closest distance to " O   HOH Z  15 " =    2.125
peak=    4.029 closest distance to " O   HOH Z 234 " =    3.838
peak=    4.025 closest distance to " O   HOH Z  54 " =    2.243
peak=    4.008 closest distance to " O   HOH Z  40 " =    1.732
peak=    3.996 closest distance to " CD1 LEU A 300 " =    1.210
peak=    3.982 closest distance to " O   HOH Z 403 " =    1.738
peak=    3.936 closest distance to " CB  SER A   3 " =    1.401
peak=    3.931 closest distance to " O   HOH Z  78 " =    2.056
peak=    3.930 closest distance to " O   HOH Z 411 " =    3.742
peak=    3.927 closest distance to " CB  TRP A 179 " =    1.474
peak=    3.920 closest distance to " CA  ALA A 160 " =    0.869
peak=    3.920 closest distance to " CA  ARG A 195 " =    1.202
peak=    3.919 closest distance to " O   HOH Z 189 " =    2.552
peak=    3.916 closest distance to " O   HOH Z 180 " =    2.209
peak=    3.907 closest distance to " O   HOH Z 247 " =    1.394
peak=    3.899 closest distance to " O   HOH Z 209 " =    2.325
peak=    3.899 closest distance to " O   HOH Z 427 " =    3.207
peak=    3.899 closest distance to " CA  THR A 221 " =    0.924
peak=    3.897 closest distance to " CB  ARG A  79 " =    1.355
peak=    3.895 closest distance to " CD  ARG A 159 " =    0.845
peak=    3.880 closest distance to " CA  ASP A 191 " =    0.817
peak=    3.879 closest distance to " N   ASN A  39 " =    1.339
peak=    3.863 closest distance to " O   HOH Z  80 " =    1.720
peak=    3.861 closest distance to " CA  ASN A 176 " =    1.827
peak=    3.850 closest distance to " O   HOH Z 368 " =    2.101
peak=    3.847 closest distance to " O   HOH Z  47 " =    1.423
peak=    3.844 closest distance to " CG2BVAL A  41 " =    0.894
peak=    3.843 closest distance to " O   HOH Z 426 " =    1.516
peak=    3.839 closest distance to " CA  ARG A  36 " =    1.219
peak=    3.834 closest distance to " O   ALA A 165 " =    1.440
peak=    3.834 closest distance to " NE2 GLN A  11 " =    0.998
peak=    3.830 closest distance to " CB  GLU A 277 " =    3.778
peak=    3.820 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.819 closest distance to " CB  TYR A 169 " =    0.778
peak=    3.811 closest distance to " CA  MET A  40 " =    1.147
peak=    3.809 closest distance to " O   HOH Z 303 " =    2.109
peak=    3.804 closest distance to " O   HOH Z 193 " =    1.979
peak=    3.802 closest distance to " O   HOH Z  49 " =    1.977
peak=    3.801 closest distance to " CB  ASP A 124 " =    0.745
peak=    3.801 closest distance to " O   HOH Z 316 " =    3.104
peak=    3.796 closest distance to " CD2 LEU A 297 " =    0.919
peak=    3.791 closest distance to " CB  VAL A 265 " =    1.193
peak=    3.788 closest distance to " O   HOH Z 214 " =    2.190
peak=    3.785 closest distance to " NZ  LYS A 117 " =    3.256
peak=    3.772 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.770 closest distance to " O   HOH Z 132 " =    2.672
peak=    3.754 closest distance to " O   THR A 251 " =    1.258
peak=    3.743 closest distance to " O   SER A  87 " =    2.343
peak=    3.743 closest distance to " CA  ALA A  51 " =    0.990
peak=    3.739 closest distance to " CD  ARG A  66 " =    2.412
peak=    3.737 closest distance to " O   HOH Z 272 " =    1.905
peak=    3.731 closest distance to " NH1AARG A 145 " =    1.173
peak=    3.727 closest distance to " O   HOH Z 163 " =    1.641
peak=    3.725 closest distance to " O   HOH Z 423 " =    1.862
peak=    3.711 closest distance to " O   HOH Z 374 " =    2.884
peak=    3.708 closest distance to " O   HOH Z  19 " =    2.279
peak=    3.705 closest distance to " O   HOH Z 383 " =    2.095
peak=    3.704 closest distance to " O   HOH Z  88 " =    3.608
peak=    3.703 closest distance to " ND2 ASN A 187 " =    1.390
peak=    3.701 closest distance to " CD1 ILE A 106 " =    0.849
peak=    3.688 closest distance to " NE2 HIS A 115 " =    1.006
peak=    3.682 closest distance to " O   HOH Z  97 " =    2.053
peak=    3.677 closest distance to " CB  ASP A 140 " =    0.869
peak=    3.668 closest distance to " CA  ASP A 124 " =    0.734
peak=    3.664 closest distance to " CD  LYS A 166 " =    1.343
peak=    3.663 closest distance to " O   HOH Z 391 " =    3.018
peak=    3.658 closest distance to " CB  SER A 212 " =    1.105
peak=    3.633 closest distance to " OD2 ASP A 286 " =    2.971
peak=    3.621 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.620 closest distance to " NH2BARG A 145 " =    2.185
peak=    3.620 closest distance to " NZ  LYS A 166 " =    3.061
peak=    3.619 closest distance to " O   HOH Z 368 " =    3.655
peak=    3.618 closest distance to " O   HOH Z 352 " =    1.888
peak=    3.612 closest distance to " CB  SER A 216 " =    0.885
peak=    3.610 closest distance to " CG1 VAL A 153 " =    0.995
peak=    3.602 closest distance to " CB  MET A  47 " =    0.943
peak=    3.599 closest distance to " O   HOH Z 389 " =    1.982
peak=    3.595 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.591 closest distance to " ND1 HIS A  81 " =    1.669
peak=    3.589 closest distance to " CA  GLU A 152 " =    0.870
peak=    3.584 closest distance to " O   TRP A 274 " =    1.808
peak=    3.575 closest distance to " O   HOH Z  43 " =    1.823
peak=    3.570 closest distance to " O   HOH Z 158 " =    2.920
peak=    3.569 closest distance to " O   HOH Z 145 " =    2.398
peak=    3.565 closest distance to " CA  ALA A 295 " =    1.120
peak=    3.557 closest distance to " O   HOH Z 437 " =    1.356
peak=    3.554 closest distance to " CD2 LEU A 255 " =    1.554
peak=    3.543 closest distance to " CB  TYR A 116 " =    1.115
peak=    3.538 closest distance to " CB  ILE A 120 " =    1.304
peak=    3.536 closest distance to " O   HOH Z 128 " =    2.221
peak=    3.534 closest distance to " CG2 VAL A  78 " =    0.990
peak=    3.526 closest distance to " O   HOH Z 250 " =    1.512
peak=    3.526 closest distance to " CG2 VAL A 257 " =    0.919
peak=    3.525 closest distance to " CG2 VAL A 197 " =    1.174
peak=    3.525 closest distance to " O   HOH Z 279 " =    2.380
peak=    3.523 closest distance to " N   ILE A  33 " =    1.088
peak=    3.517 closest distance to " CE  LYS A  76 " =    0.815
peak=    3.512 closest distance to " O   ASN A  74 " =    1.595
peak=    3.506 closest distance to " CB  ALA A 248 " =    1.111
peak=    3.504 closest distance to " CG1 ILE A 151 " =    1.008
peak=    3.477 closest distance to " O   HOH Z 284 " =    2.996
peak=    3.477 closest distance to " CB  ARG A  79 " =    0.911
peak=    3.473 closest distance to " CB  ALA A 291 " =    1.207
peak=    3.471 closest distance to " O   HOH Z 344 " =    3.204
peak=    3.466 closest distance to " O   HOH Z 371 " =    3.372
peak=    3.461 closest distance to " O   HOH Z 142 " =    1.511
peak=    3.456 closest distance to " ND2 ASN A 110 " =    1.621
peak=    3.456 closest distance to " CD1 TRP A 266 " =    1.154
peak=    3.454 closest distance to " CB  ASN A 187 " =    1.181
peak=    3.449 closest distance to " O   HOH Z 281 " =    4.591
peak=    3.448 closest distance to " CA  ASP A 140 " =    1.228
peak=    3.446 closest distance to " CG  GLU A  37 " =    0.883
peak=    3.441 closest distance to " CD1 LEU A  96 " =    0.744
peak=    3.439 closest distance to " CB  SER A 141 " =    1.000
peak=    3.438 closest distance to " O   HOH Z 345 " =    1.821
peak=    3.431 closest distance to " CG  GLN A  58 " =    2.628
peak=    3.418 closest distance to " O   HOH Z 402 " =    1.483
peak=    3.418 closest distance to " CE1 TYR A 186 " =    1.248
peak=    3.415 closest distance to " N   TYR A  15 " =    0.803
peak=    3.414 closest distance to " ND1 HIS A  86 " =    1.737
peak=    3.414 closest distance to " O   HOH Z 346 " =    1.636
peak=    3.413 closest distance to " CD  ARG A 219 " =    1.067
peak=    3.413 closest distance to " O   HOH Z 298 " =    2.538
peak=    3.412 closest distance to " O   HOH Z 357 " =    2.040
peak=    3.407 closest distance to " CB  ALA A 100 " =    1.353
peak=    3.400 closest distance to " O   HOH Z 406 " =    1.578
peak=    3.398 closest distance to " O   HOH Z 193 " =    2.341
peak=    3.396 closest distance to " N   ASN A 127 " =    1.257
peak=    3.392 closest distance to " CD  LYS A 119 " =    1.359
peak=    3.392 closest distance to " O   HOH Z 155 " =    3.305
peak=    3.388 closest distance to " CA  VAL A 125 " =    1.187
peak=    3.382 closest distance to " O   HOH Z 295 " =    1.492
peak=    3.382 closest distance to " CB  SER A  62 " =    0.702
peak=    3.379 closest distance to " CZ  PHE A  38 " =    1.292
peak=    3.379 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.378 closest distance to " O   HOH Z 174 " =    2.331
peak=    3.373 closest distance to " CG AARG A 275 " =    1.195
peak=    3.370 closest distance to " O   THR A 220 " =    1.134
peak=    3.368 closest distance to " CD1AILE A 234 " =    0.911
peak=    3.366 closest distance to " O   HOH Z  59 " =    2.297
peak=    3.366 closest distance to " O   ALA A 158 " =    1.275
peak=    3.364 closest distance to " CA  SER A  87 " =    1.012
peak=    3.364 closest distance to " OG BSER A 164 " =    2.422
peak=    3.361 closest distance to " O   HOH Z 112 " =    1.552
peak=    3.360 closest distance to " O   HOH Z 102 " =    1.281
peak=    3.360 closest distance to " O   HOH Z 197 " =    2.057
peak=    3.357 closest distance to " CB  PHE A  16 " =    0.997
peak=    3.354 closest distance to " CG BARG A 275 " =    1.418
peak=    3.350 closest distance to " O   HOH Z 313 " =    1.937
peak=    3.346 closest distance to " O   HOH Z 245 " =    1.285
peak=    3.342 closest distance to " O   HOH Z 227 " =    1.653
peak=    3.337 closest distance to " OE1 GLU A 152 " =    0.880
peak=    3.329 closest distance to " CA  MET A 105 " =    1.127
peak=    3.319 closest distance to " O   HOH Z 387 " =    2.819
peak=    3.318 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.317 closest distance to " O   HOH Z 305 " =    3.709
peak=    3.316 closest distance to " O   HOH Z 109 " =    2.643
peak=    3.311 closest distance to " CA  LYS A 117 " =    1.242
peak=    3.310 closest distance to " O   HOH Z 327 " =    2.076
peak=    3.306 closest distance to " CG  ARG A 219 " =    1.201
peak=    3.303 closest distance to " O   HOH Z  63 " =    1.830
peak=    3.302 closest distance to " CB  PRO A 198 " =    1.040
peak=    3.300 closest distance to " CD  ARG A  66 " =    2.375
peak=    3.296 closest distance to " O   HOH Z  66 " =    2.068
peak=    3.294 closest distance to " O   HOH Z 183 " =    1.507
peak=    3.294 closest distance to " O   HOH Z  61 " =    1.532
peak=    3.291 closest distance to " CB  GLN A  89 " =    1.279
peak=    3.287 closest distance to " O   HOH Z 271 " =    2.665
peak=    3.283 closest distance to " O   HOH Z 403 " =    1.367
peak=    3.282 closest distance to " N   VAL A 126 " =    1.452
peak=    3.280 closest distance to " O   HOH Z 171 " =    3.897
peak=    3.278 closest distance to " O   HOH Z   6 " =    2.141
peak=    3.275 closest distance to " OE1 GLN A  11 " =    1.952
peak=    3.271 closest distance to " CA  THR A 264 " =    0.875
peak=    3.261 closest distance to " CB  MET A  40 " =    0.793
peak=    3.257 closest distance to " CG2 ILE A 106 " =    1.009
peak=    3.252 closest distance to " N   ARG A 156 " =    1.447
peak=    3.251 closest distance to " CA  ARG A 102 " =    1.197
peak=    3.249 closest distance to " OD2 ASP A 298 " =    4.051
peak=    3.246 closest distance to " CA  LEU A 282 " =    1.109
peak=    3.241 closest distance to " O   HOH Z 359 " =    1.478
peak=    3.236 closest distance to " CG1BVAL A  72 " =    1.748
peak=    3.235 closest distance to " CA  GLN A  88 " =    1.429
peak=    3.235 closest distance to " CB  ALA A  34 " =    0.970
peak=    3.233 closest distance to " CA  ALA A 154 " =    0.999
peak=    3.231 closest distance to " OG  SER A  97 " =    3.480
peak=    3.230 closest distance to " O   HOH Z   1 " =    2.429
peak=    3.229 closest distance to " CA  ALA A 100 " =    1.033
peak=    3.228 closest distance to " CB  ASN A 285 " =    0.864
peak=    3.227 closest distance to " O   HOH Z 419 " =    3.058
peak=    3.227 closest distance to " O   HOH Z 250 " =    1.542
peak=    3.224 closest distance to " N   GLN A 278 " =    1.006
peak=    3.223 closest distance to " O   HOH Z 176 " =    1.376
peak=    3.217 closest distance to " OG  SER A 245 " =    1.675
peak=    3.216 closest distance to " C   TYR A 214 " =    1.522
peak=    3.214 closest distance to " CB  ASN A 142 " =    1.006
peak=    3.210 closest distance to " CA  ASN A 127 " =    1.120
peak=    3.209 closest distance to " CG  LEU A 167 " =    1.118
peak=    3.207 closest distance to " CA  LEU A  83 " =    1.506
peak=    3.205 closest distance to " CA  GLN A 223 " =    0.948
peak=    3.203 closest distance to " CB  ASN A 215 " =    1.200
peak=    3.202 closest distance to " O   HOH Z 345 " =    3.398
peak=    3.201 closest distance to " CA  GLU A  46 " =    0.725
peak=    3.201 closest distance to " O   HOH Z 193 " =    1.647
peak=    3.199 closest distance to " O   HOH Z 422 " =    2.624
peak=    3.198 closest distance to " CB  ALA A   9 " =    1.563
peak=    3.195 closest distance to " O   HOH Z  10 " =    1.817
peak=    3.193 closest distance to " O   HOH Z 291 " =    1.480
peak=    3.192 closest distance to " CG2AVAL A 121 " =    2.283
peak=    3.192 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.188 closest distance to " O   HOH Z 353 " =    2.824
peak=    3.183 closest distance to " CZ  PHE A 208 " =    1.092
peak=    3.183 closest distance to " CD  ARG A  14 " =    1.278
peak=    3.182 closest distance to " O   HOH Z 197 " =    2.564
peak=    3.182 closest distance to " CG  MET A 185 " =    1.231
peak=    3.173 closest distance to " O   HOH Z 296 " =    1.597
peak=    3.169 closest distance to " O   HOH Z 134 " =    2.472
peak=    3.164 closest distance to " CB  ARG A 139 " =    0.782
peak=    3.164 closest distance to " C   GLY A  80 " =    1.065
peak=    3.163 closest distance to " O   HOH Z 355 " =    1.581
peak=    3.163 closest distance to " O   HOH Z 128 " =    2.233
peak=    3.159 closest distance to " CB  TYR A  30 " =    1.420
peak=    3.158 closest distance to " CB  SER A  28 " =    1.090
peak=    3.157 closest distance to " CE2 TYR A 186 " =    0.885
peak=    3.157 closest distance to " O  BHOH Z 338 " =    2.283
peak=    3.152 closest distance to " CA  LYS A 290 " =    1.271
peak=    3.150 closest distance to " O   HOH Z 116 " =    1.856
peak=    3.146 closest distance to " O   GLY A  57 " =    2.643
peak=    3.143 closest distance to " NE1 TRP A 266 " =    1.402
peak=    3.141 closest distance to " O   HOH Z  63 " =    2.278
peak=    3.139 closest distance to " CG BARG A 102 " =    1.950
peak=    3.138 closest distance to " OG  SER A  22 " =    2.808
peak=    3.137 closest distance to " N   GLU A  44 " =    0.960
peak=    3.136 closest distance to " OD1 ASP A 238 " =    0.866
peak=    3.133 closest distance to " NZ ALYS A 290 " =    1.068
peak=    3.119 closest distance to " CB  SER A 273 " =    0.865
peak=    3.111 closest distance to " O   HOH Z 432 " =    1.577
peak=    3.106 closest distance to " O   HOH Z 394 " =    1.662
peak=    3.103 closest distance to " CG2 ILE A 151 " =    0.777
peak=    3.103 closest distance to " NH2BARG A 190 " =    1.781
peak=    3.101 closest distance to " CE  MET A 113 " =    1.858
peak=    3.100 closest distance to " CG  GLN A  11 " =    1.336
peak=    3.089 closest distance to " CB  ALA A 248 " =    1.265
peak=    3.087 closest distance to " NE2 GLN A  58 " =    3.664
peak=    3.085 closest distance to " OD2 ASP A 200 " =    1.308
peak=    3.081 closest distance to " O   HOH Z  50 " =    3.592
peak=    3.077 closest distance to " CG2 ILE A 120 " =    1.002
peak=    3.076 closest distance to " CB  GLU A 152 " =    1.527
peak=    3.076 closest distance to " O   HOH Z  32 " =    1.692
peak=    3.074 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.067 closest distance to " O   HOH Z 409 " =    3.329
peak=    3.062 closest distance to " O   HOH Z 302 " =    1.956
peak=    3.059 closest distance to " O   HOH Z 213 " =    1.756
peak=    3.057 closest distance to " CA  ALA A 248 " =    1.204
peak=    3.052 closest distance to " CB  ALA A  43 " =    0.864
peak=    3.051 closest distance to " O   HOH Z  44 " =    1.732
peak=    3.051 closest distance to " CG  MET A 185 " =    1.027
peak=    3.045 closest distance to " O   TYR A 116 " =    1.277
peak=    3.039 closest distance to " O   GLN A 278 " =    1.558
peak=    3.035 closest distance to " O   HOH Z 371 " =    3.412
peak=    3.022 closest distance to " CB  PRO A  54 " =    1.250

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.840 - 5.550
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.840 - 5.550

peak=   -4.678 closest distance to " O   HOH Z 266 " =    4.863
peak=   -4.278 closest distance to " CD  ARG A 156 " =    2.044
peak=   -4.177 closest distance to " O   HOH Z  10 " =    1.639
peak=   -4.169 closest distance to " O   VAL A  67 " =    2.685
peak=   -4.122 closest distance to " CG1 VAL A 250 " =    2.677
peak=   -4.072 closest distance to " O   HOH Z  52 " =    1.596
peak=   -4.018 closest distance to " O   HOH Z 377 " =    1.923
peak=   -4.002 closest distance to " O   HOH Z  38 " =    1.142
peak=   -3.969 closest distance to " CB  PRO A 243 " =    2.652
peak=   -3.968 closest distance to " N   ALA A  43 " =    2.638
peak=   -3.908 closest distance to " OE1 GLN A 223 " =    1.961
peak=   -3.875 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.874 closest distance to " O   PRO A 198 " =    1.311
peak=   -3.869 closest distance to " OG  SER A  97 " =    2.252
peak=   -3.866 closest distance to " ND2 ASN A  45 " =    1.657
peak=   -3.860 closest distance to " CD  GLN A 223 " =    1.344
peak=   -3.858 closest distance to " CB  ALA A 161 " =    2.713
peak=   -3.857 closest distance to " NH2 ARG A  66 " =    1.767
peak=   -3.826 closest distance to " CZ3 TRP A 179 " =    1.171
peak=   -3.788 closest distance to " CG  GLU A  53 " =    1.421
peak=   -3.787 closest distance to " O   HOH Z 185 " =    2.489
peak=   -3.787 closest distance to " OD1 ASN A 148 " =    1.553
peak=   -3.786 closest distance to " O   HOH Z 292 " =    4.607
peak=   -3.775 closest distance to " CB  ASN A  39 " =    2.217
peak=   -3.771 closest distance to " CD1 PHE A  59 " =    1.907
peak=   -3.766 closest distance to " CD2 LEU A 300 " =    2.923
peak=   -3.765 closest distance to " O   HOH Z  13 " =    1.575
peak=   -3.759 closest distance to " O   HOH Z  43 " =    1.521
peak=   -3.748 closest distance to " CD1 PHE A 130 " =    2.332
peak=   -3.748 closest distance to " O   HOH Z  73 " =    2.269
peak=   -3.743 closest distance to " O   PRO A 163 " =    2.145
peak=   -3.742 closest distance to " O   HOH Z 198 " =    2.404
peak=   -3.741 closest distance to " O   HOH Z 353 " =    2.284
peak=   -3.709 closest distance to " O   HOH Z 290 " =    1.228
peak=   -3.705 closest distance to " CB  ASP A 132 " =    2.361
peak=   -3.699 closest distance to " O   HOH Z  19 " =    2.151
peak=   -3.684 closest distance to " CD2 TYR A 293 " =    2.041
peak=   -3.681 closest distance to " CG1 VAL A 112 " =    2.579
peak=   -3.675 closest distance to " O   HOH Z 407 " =    3.681
peak=   -3.674 closest distance to " C   ASN A 285 " =    2.486
peak=   -3.674 closest distance to " ND2 ASN A  60 " =    1.448
peak=   -3.673 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.670 closest distance to " C   ALA A 158 " =    1.292
peak=   -3.670 closest distance to " O   HOH Z 196 " =    2.354
peak=   -3.669 closest distance to " O   HOH Z 372 " =    2.564
peak=   -3.665 closest distance to " C   HIS A 108 " =    1.070
peak=   -3.660 closest distance to " CG  MET A  93 " =    2.536
peak=   -3.658 closest distance to " O   HOH Z 393 " =    1.485
peak=   -3.656 closest distance to " C   ASN A 187 " =    1.857
peak=   -3.644 closest distance to " OXT GLY A 302 " =    2.983
peak=   -3.626 closest distance to " OD1 ASP A 191 " =    1.639
peak=   -3.606 closest distance to " CD1 LEU A 228 " =    2.413
peak=   -3.599 closest distance to " O   HOH Z 394 " =    1.620
peak=   -3.592 closest distance to " CD  ARG A  14 " =    3.445
peak=   -3.581 closest distance to " O   HOH Z 426 " =    1.775
peak=   -3.559 closest distance to " O   HOH Z 377 " =    1.290
peak=   -3.558 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.556 closest distance to " OG BSER A 134 " =    1.922
peak=   -3.553 closest distance to " CD2 PHE A  59 " =    2.534
peak=   -3.550 closest distance to " N   ALA A 226 " =    2.081
peak=   -3.546 closest distance to " O   HOH Z 128 " =    2.488
peak=   -3.544 closest distance to " CA  GLY A 241 " =    3.084
peak=   -3.534 closest distance to " CA  GLY A 241 " =    2.273
peak=   -3.531 closest distance to " O   HOH Z 103 " =    1.843
peak=   -3.523 closest distance to " CE  MET A  93 " =    1.338
peak=   -3.523 closest distance to " CG2 ILE A 263 " =    2.392
peak=   -3.520 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.519 closest distance to " CH2 TRP A 177 " =    2.104
peak=   -3.513 closest distance to " OG ASER A 134 " =    1.273
peak=   -3.509 closest distance to " CG  ARG A  66 " =    2.359
peak=   -3.508 closest distance to " O   HOH Z 275 " =    1.592
peak=   -3.501 closest distance to " CG  ARG A 269 " =    2.358
peak=   -3.497 closest distance to " CD  GLN A  88 " =    0.907
peak=   -3.495 closest distance to " C   SER A 206 " =    1.501
peak=   -3.493 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.486 closest distance to " CD2 LEU A 167 " =    1.880
peak=   -3.479 closest distance to " O   HOH Z 389 " =    1.846
peak=   -3.476 closest distance to " O   HOH Z 348 " =    2.233
peak=   -3.468 closest distance to " NH2AARG A 275 " =    5.550
peak=   -3.466 closest distance to " NE2 GLN A  88 " =    1.986
peak=   -3.463 closest distance to " O   HOH Z 166 " =    1.785
peak=   -3.463 closest distance to " N   SER A 276 " =    1.431
peak=   -3.463 closest distance to " O   HOH Z 118 " =    3.248
peak=   -3.461 closest distance to " O   HOH Z 177 " =    1.678
peak=   -3.457 closest distance to " CG1 VAL A 125 " =    2.020
peak=   -3.456 closest distance to " O   HOH Z 252 " =    4.209
peak=   -3.445 closest distance to " SG ACYS A 201 " =    1.131
peak=   -3.445 closest distance to " OD2 ASP A 171 " =    1.829
peak=   -3.444 closest distance to " O   HOH Z  71 " =    1.564
peak=   -3.444 closest distance to " CE3 TRP A 150 " =    2.042
peak=   -3.434 closest distance to " CG  MET A 105 " =    0.944
peak=   -3.429 closest distance to " C   LEU A 143 " =    1.163
peak=   -3.424 closest distance to " O   ALA A  34 " =    2.579
peak=   -3.424 closest distance to " O   HOH Z 166 " =    1.686
peak=   -3.423 closest distance to " CZ  TYR A 169 " =    1.872
peak=   -3.419 closest distance to " O   HOH Z 111 " =    1.937
peak=   -3.413 closest distance to " CB  ALA A 291 " =    2.298
peak=   -3.410 closest distance to " O   VAL A 125 " =    2.190
peak=   -3.406 closest distance to " CD2 PHE A 225 " =    1.284
peak=   -3.403 closest distance to " CD  LYS A 289 " =    2.422
peak=   -3.390 closest distance to " ND2 ASN A 249 " =    2.356
peak=   -3.385 closest distance to " CD1 ILE A 151 " =    2.366
peak=   -3.380 closest distance to " CD  PRO A 213 " =    2.237
peak=   -3.380 closest distance to " CB  PHE A  16 " =    2.611
peak=   -3.377 closest distance to " O   ALA A  10 " =    1.776
peak=   -3.374 closest distance to " O   HOH Z 252 " =    4.024
peak=   -3.372 closest distance to " CD  ARG A 195 " =    5.105
peak=   -3.371 closest distance to " CA  GLY A 203 " =    2.377
peak=   -3.365 closest distance to " O   HOH Z  11 " =    2.130
peak=   -3.364 closest distance to " O   HOH Z 232 " =    1.656
peak=   -3.363 closest distance to " CE2 PHE A  61 " =    2.572
peak=   -3.363 closest distance to " O   HOH Z 311 " =    3.735
peak=   -3.361 closest distance to " CA  GLY A 133 " =    2.328
peak=   -3.360 closest distance to " O   HOH Z 243 " =    2.042
peak=   -3.358 closest distance to " CG  ASP A 231 " =    0.840
peak=   -3.357 closest distance to " OE1 GLN A  58 " =    1.134
peak=   -3.353 closest distance to " O   HOH Z 165 " =    1.913
peak=   -3.351 closest distance to " OD1 ASN A 187 " =    1.611
peak=   -3.348 closest distance to " O   SER A 210 " =    2.090
peak=   -3.345 closest distance to " OG BSER A 134 " =    1.354
peak=   -3.343 closest distance to " CB  ALA A  10 " =    2.106
peak=   -3.339 closest distance to " O   HOH Z 351 " =    1.567
peak=   -3.338 closest distance to " CB  ALA A 248 " =    2.069
peak=   -3.332 closest distance to " CB  ALA A 291 " =    2.329
peak=   -3.331 closest distance to " OH  TYR A 169 " =    1.022
peak=   -3.329 closest distance to " OE1 GLN A  88 " =    1.090
peak=   -3.324 closest distance to " CG2 VAL A 189 " =    2.207
peak=   -3.324 closest distance to " CD2 LEU A 237 " =    2.877
peak=   -3.320 closest distance to " CA  VAL A  67 " =    2.855
peak=   -3.320 closest distance to " NE1 TRP A 266 " =    2.283
peak=   -3.313 closest distance to " O   HOH Z  11 " =    1.865
peak=   -3.312 closest distance to " CB  TRP A  85 " =    2.423
peak=   -3.308 closest distance to " C   GLY A  17 " =    1.255
peak=   -3.303 closest distance to " O   HOH Z 396 " =    1.676
peak=   -3.301 closest distance to " CE  MET A 105 " =    2.062
peak=   -3.299 closest distance to " O   HOH Z 350 " =    1.758
peak=   -3.297 closest distance to " O   HOH Z 308 " =    1.679
peak=   -3.296 closest distance to " O   GLY A 211 " =    1.476
peak=   -3.293 closest distance to " CE BMET A  47 " =    2.321
peak=   -3.292 closest distance to " CG  GLU A 277 " =    1.189
peak=   -3.291 closest distance to " O   HOH Z 418 " =    1.341
peak=   -3.282 closest distance to " ND2BASN A 224 " =    1.774
peak=   -3.280 closest distance to " O   HOH Z  90 " =    1.827
peak=   -3.278 closest distance to " O   HOH Z 234 " =    4.317
peak=   -3.275 closest distance to " N   SER A   3 " =    2.246
peak=   -3.274 closest distance to " O   HOH Z 117 " =    4.422
peak=   -3.271 closest distance to " O   HOH Z 189 " =    1.808
peak=   -3.270 closest distance to " O   PHE A 218 " =    1.588
peak=   -3.265 closest distance to " C   ALA A   8 " =    1.650
peak=   -3.264 closest distance to " CB  ASP A 286 " =    2.237
peak=   -3.258 closest distance to " O   HOH Z  93 " =    2.313
peak=   -3.253 closest distance to " NH1 ARG A 195 " =    2.674
peak=   -3.250 closest distance to " O   LEU A 167 " =    1.618
peak=   -3.244 closest distance to " CD1 ILE A 239 " =    2.064
peak=   -3.243 closest distance to " O   HOH Z 241 " =    1.170
peak=   -3.243 closest distance to " O   ASN A 187 " =    1.590
peak=   -3.243 closest distance to " CG  TRP A 266 " =    1.891
peak=   -3.238 closest distance to " OG  SER A  62 " =    1.661
peak=   -3.237 closest distance to " NE2 GLN A 103 " =    1.803
peak=   -3.237 closest distance to " O   HOH Z  51 " =    1.622
peak=   -3.234 closest distance to " CG1 VAL A 112 " =    2.943
peak=   -3.230 closest distance to " O   HOH Z 380 " =    4.859
peak=   -3.228 closest distance to " ND2 ASN A  60 " =    1.895
peak=   -3.225 closest distance to " O   HOH Z   6 " =    1.623
peak=   -3.222 closest distance to " O   HOH Z 388 " =    1.967
peak=   -3.219 closest distance to " O   HOH Z 298 " =    2.698
peak=   -3.219 closest distance to " O   VAL A 189 " =    2.602
peak=   -3.218 closest distance to " O   HOH Z 436 " =    1.502
peak=   -3.217 closest distance to " NE  ARG A  79 " =    1.232
peak=   -3.215 closest distance to " O   HOH Z 423 " =    2.283
peak=   -3.211 closest distance to " O   ASN A 301 " =    1.469
peak=   -3.202 closest distance to " O   ALA A 160 " =    1.589
peak=   -3.198 closest distance to " CD1 ILE A 263 " =    2.043
peak=   -3.198 closest distance to " OD2 ASP A  65 " =    1.860
peak=   -3.197 closest distance to " OE2 GLU A   2 " =    1.749
peak=   -3.194 closest distance to " N   GLN A  58 " =    1.670
peak=   -3.193 closest distance to " CG1 VAL A 197 " =    2.365
peak=   -3.191 closest distance to " O   HOH Z 431 " =    1.890
peak=   -3.189 closest distance to " O   HOH Z 222 " =    1.343
peak=   -3.188 closest distance to " O   GLY A 196 " =    1.214
peak=   -3.186 closest distance to " O   HOH Z 417 " =    2.689
peak=   -3.186 closest distance to " C   ILE A 234 " =    1.243
peak=   -3.185 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.184 closest distance to " O   GLY A 203 " =    2.511
peak=   -3.179 closest distance to " O   HOH Z 357 " =    2.091
peak=   -3.179 closest distance to " CA  ASN A 127 " =    1.041
peak=   -3.168 closest distance to " CB  ALA A   9 " =    2.678
peak=   -3.166 closest distance to " CG1 VAL A  78 " =    2.699
peak=   -3.165 closest distance to " CB  CYS A 254 " =    2.478
peak=   -3.164 closest distance to " CG  LEU A 101 " =    2.385
peak=   -3.163 closest distance to " CG2 THR A 221 " =    2.257
peak=   -3.162 closest distance to " CA  GLY A  98 " =    2.190
peak=   -3.162 closest distance to " O   ALA A   1 " =    2.034
peak=   -3.159 closest distance to " CB  ALA A 291 " =    2.188
peak=   -3.159 closest distance to " O   HOH Z 251 " =    1.867
peak=   -3.157 closest distance to " CE3 TRP A 274 " =    2.545
peak=   -3.153 closest distance to " CD1 TRP A 179 " =    1.101
peak=   -3.150 closest distance to " CB  PRO A 163 " =    2.638
peak=   -3.146 closest distance to " O   HOH Z  88 " =    2.315
peak=   -3.138 closest distance to " CD2 PHE A  61 " =    2.000
peak=   -3.137 closest distance to " O   GLY A 118 " =    2.224
peak=   -3.131 closest distance to " O   HOH Z  61 " =    1.557
peak=   -3.130 closest distance to " O   HOH Z  91 " =    1.881
peak=   -3.127 closest distance to " OD2 ASP A  50 " =    2.311
peak=   -3.123 closest distance to " CD1 LEU A 167 " =    2.176
peak=   -3.122 closest distance to " O   HOH Z 422 " =    1.559
peak=   -3.094 closest distance to " CZ  PHE A  38 " =    2.376
peak=   -3.079 closest distance to " O   HOH Z 421 " =    3.414
peak=   -3.036 closest distance to " O   HOH Z 259 " =    2.134
peak=   -3.018 closest distance to " O   HOH Z 184 " =    1.617

================= 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    :  0.4027 0.3933   6.196523e+00   6.184228e+00
   1_bss:  0.3927 0.3826   6.185325e+00   6.166790e+00
   1_xyz:  0.2526 0.2843   5.820737e+00   5.912726e+00
   1_adp:  0.2296 0.2866   5.763749e+00   5.926265e+00
   1_occ:  0.2292 0.2862   5.762585e+00   5.925306e+00
   2_bss:  0.2270 0.2832   5.758508e+00   5.920719e+00
   2_xyz:  0.1725 0.2165   5.504273e+00   5.692941e+00
   2_adp:  0.1617 0.2026   5.449201e+00   5.638219e+00
   2_occ:  0.1615 0.2025   5.448380e+00   5.637521e+00
   3_bss:  0.1615 0.2027   5.449001e+00   5.636705e+00
   3_xyz:  0.1309 0.1732   5.270985e+00   5.489316e+00
   3_adp:  0.1242 0.1705   5.237328e+00   5.469931e+00
   3_occ:  0.1241 0.1705   5.237124e+00   5.469788e+00
   4_bss:  0.1246 0.1703   5.237858e+00   5.468437e+00
   4_xyz:  0.1147 0.1660   5.186557e+00   5.436088e+00
   4_adp:  0.1134 0.1643   5.176348e+00   5.425463e+00
   4_occ:  0.1134 0.1643   5.176400e+00   5.425841e+00
   5_bss:  0.1133 0.1642   5.176370e+00   5.425801e+00
   5_xyz:  0.1153 0.1648   5.187096e+00   5.430607e+00
   5_adp:  0.1150 0.1656   5.188050e+00   5.435446e+00
   5_occ:  0.1150 0.1657   5.188089e+00   5.435671e+00
   5_bss:  0.1149 0.1656   5.188187e+00   5.435757e+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:  0.297  49.027   0.810   2.521  -1.863   0.000  -0.000  -0.000
   1_xyz:  0.297  49.027   0.810   2.521  -1.863   0.000  -0.000  -0.000
   1_adp:  0.297  49.027   0.810   2.521  -1.863   0.000  -0.000  -0.000
   1_occ:  0.297  49.027   0.810   2.521  -1.863   0.000  -0.000  -0.000
   2_bss:  0.328  69.971  -1.097  -0.084  -1.597  -0.000  -0.000  -0.000
   2_xyz:  0.328  69.971  -1.097  -0.084  -1.597  -0.000  -0.000  -0.000
   2_adp:  0.328  69.971  -1.097  -0.084  -1.597  -0.000  -0.000  -0.000
   2_occ:  0.328  69.971  -1.097  -0.084  -1.597  -0.000  -0.000  -0.000
   3_bss:  0.328  71.184  -1.749  -1.085  -1.493  -0.000  -0.000  -0.000
   3_xyz:  0.328  71.184  -1.749  -1.085  -1.493  -0.000  -0.000  -0.000
   3_adp:  0.328  71.184  -1.749  -1.085  -1.493  -0.000  -0.000  -0.000
   3_occ:  0.328  71.184  -1.749  -1.085  -1.493  -0.000  -0.000  -0.000
   4_bss:  0.326  69.892  -1.881  -1.499  -1.393  -0.000  -0.000  -0.000
   4_xyz:  0.326  69.892  -1.881  -1.499  -1.393  -0.000  -0.000  -0.000
   4_adp:  0.326  69.892  -1.881  -1.499  -1.393  -0.000  -0.000  -0.000
   4_occ:  0.326  69.892  -1.881  -1.499  -1.393  -0.000  -0.000  -0.000
   5_bss:  0.321  65.577  -1.756  -1.526  -1.199  -0.000  -0.000  -0.000
   5_xyz:  0.321  65.577  -1.756  -1.526  -1.199  -0.000  -0.000  -0.000
   5_adp:  0.321  65.577  -1.756  -1.526  -1.199  -0.000  -0.000  -0.000
   5_occ:  0.321  65.577  -1.756  -1.526  -1.199  -0.000  -0.000  -0.000
   5_bss:  0.321  65.580  -1.607  -1.422  -1.017  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.952 0.5841  0.7486    47561.893
   1_bss:  43.999 0.5940  0.7767    44655.087
   1_xyz:  28.971 0.7696  0.9575    21068.095
   1_adp:  29.563 0.7623  0.9463    21809.382
   1_occ:  29.524 0.7626  0.9463    21749.359
   2_bss:  29.241 0.7658  0.9065    21455.380
   2_xyz:  21.389 0.8474  0.9680    12166.169
   2_adp:  19.612 0.8655  0.9726    10750.067
   2_occ:  19.598 0.8656  0.9727    10737.034
   3_bss:  19.597 0.8656  0.9552    10730.448
   3_xyz:  16.271 0.8956  0.9733     7798.474
   3_adp:  15.741 0.9006  0.9698     7495.466
   3_occ:  15.737 0.9006  0.9698     7491.049
   4_bss:  15.720 0.9007  0.9648     7463.680
   4_xyz:  15.058 0.9062  0.9673     6987.333
   4_adp:  14.824 0.9084  0.9617     6885.639
   4_occ:  14.829 0.9083  0.9616     6888.045
   5_bss:  14.829 0.9083  0.9650     6885.411
   5_xyz:  14.881 0.9080  0.9647     6915.533
   5_adp:  14.983 0.9071  0.9577     6982.220
   5_occ:  14.987 0.9071  0.9577     6983.903
   5_bss:  14.990 0.9070  0.9626     6984.893
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6692e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6692e-01
   1_xyz:   1.416  0.011  0.086 15.598  0.005  4.120   1.0398e-01
   1_adp:   1.416  0.011  0.086 15.598  0.005  4.120   1.0398e-01
   1_occ:   1.416  0.011  0.086 15.598  0.005  4.120   1.0398e-01
   2_bss:   1.416  0.011  0.086 15.598  0.005  4.120   1.0398e-01
   2_xyz:   1.032  0.007  0.071 14.627  0.004  4.134   6.0367e-02
   2_adp:   1.032  0.007  0.071 14.627  0.004  4.134   6.0367e-02
   2_occ:   1.032  0.007  0.071 14.627  0.004  4.134   6.0367e-02
   3_bss:   1.032  0.007  0.071 14.627  0.004  4.134   6.0367e-02
   3_xyz:   1.070  0.009  0.076 14.945  0.004  4.132   6.7791e-02
   3_adp:   1.070  0.009  0.076 14.945  0.004  4.132   6.7791e-02
   3_occ:   1.070  0.009  0.076 14.945  0.004  4.132   6.7791e-02
   4_bss:   1.070  0.009  0.076 14.945  0.004  4.132   6.7791e-02
   4_xyz:   1.148  0.011  0.083 15.208  0.005  4.140   7.8456e-02
   4_adp:   1.148  0.011  0.083 15.208  0.005  4.140   7.8456e-02
   4_occ:   1.148  0.011  0.083 15.208  0.005  4.140   7.8456e-02
   5_bss:   1.148  0.011  0.083 15.208  0.005  4.140   7.8456e-02
   5_xyz:   1.023  0.008  0.076 14.862  0.004  4.139   6.2343e-02
   5_adp:   1.023  0.008  0.076 14.862  0.004  4.139   6.2343e-02
   5_occ:   1.023  0.008  0.076 14.862  0.004  4.139   6.2343e-02
   5_bss:   1.023  0.008  0.076 14.862  0.004  4.139   6.2343e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.393   2.4372e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.393   2.4372e-01
   1_xyz:   9.225  0.061  0.320 86.249  0.016  2.155   1.1822e-01
   1_adp:   9.225  0.061  0.320 86.249  0.016  2.155   1.1822e-01
   1_occ:   9.225  0.061  0.320 86.249  0.016  2.155   1.1822e-01
   2_bss:   9.225  0.061  0.320 86.249  0.016  2.155   1.1822e-01
   2_xyz:   8.077  0.039  0.228 87.329  0.044  2.410   8.6885e-02
   2_adp:   8.077  0.039  0.228 87.329  0.044  2.410   8.6885e-02
   2_occ:   8.077  0.039  0.228 87.329  0.044  2.410   8.6885e-02
   3_bss:   8.077  0.039  0.228 87.329  0.044  2.410   8.6885e-02
   3_xyz:   7.822  0.052  0.222 80.461  0.041  2.264   5.0928e-02
   3_adp:   7.822  0.052  0.222 80.461  0.041  2.264   5.0928e-02
   3_occ:   7.822  0.052  0.222 80.461  0.041  2.264   5.0928e-02
   4_bss:   7.822  0.052  0.222 80.461  0.041  2.264   5.0928e-02
   4_xyz:   7.950  0.051  0.269 82.527  0.044  2.290   5.6990e-02
   4_adp:   7.950  0.051  0.269 82.527  0.044  2.290   5.6990e-02
   4_occ:   7.950  0.051  0.269 82.527  0.044  2.290   5.6990e-02
   5_bss:   7.950  0.051  0.269 82.527  0.044  2.290   5.6990e-02
   5_xyz:   8.037  0.043  0.244 81.844  0.041  2.363   4.1020e-02
   5_adp:   8.037  0.043  0.244 81.844  0.041  2.363   4.1020e-02
   5_occ:   8.037  0.043  0.244 81.844  0.041  2.363   4.1020e-02
   5_bss:   8.037  0.043  0.244 81.844  0.041  2.363   4.1020e-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:  96.90   0.00  17.92  88.88   0.00  13.50  96.90   2.59  41.97
   1_occ:  96.90   0.00  17.92  88.88   0.00  13.50  96.90   2.59  41.97
   2_bss:  96.90   0.00  17.92  88.88   0.00  13.50  96.90   2.59  41.97
   2_xyz:  96.90   0.00  17.92  88.88   0.00  13.50  96.90   2.59  41.97
   2_adp:  95.73   1.17  17.66  92.54   1.17  13.18  95.73   4.63  42.08
   2_occ:  95.73   1.17  17.66  92.54   1.17  13.18  95.73   4.63  42.08
   3_bss:  95.73   1.17  17.66  92.54   1.17  13.18  95.73   4.63  42.08
   3_xyz:  95.73   1.17  17.66  92.54   1.17  13.18  95.73   4.63  42.08
   3_adp: 105.66   0.37  17.84 105.66   0.37  13.05 100.06   4.92  43.96
   3_occ: 105.66   0.37  17.84 105.66   0.37  13.05 100.06   4.92  43.96
   4_bss: 105.66   0.37  17.84 105.66   0.37  13.05 100.06   4.92  43.96
   4_xyz: 105.66   0.37  17.84 105.66   0.37  13.05 100.06   4.92  43.96
   4_adp: 106.24   0.21  17.43 106.24   0.21  12.80  99.14   4.24  42.66
   4_occ: 106.24   0.21  17.43 106.24   0.21  12.80  99.14   4.24  42.66
   5_bss: 106.24   0.21  17.43 106.24   0.21  12.80  99.14   4.24  42.66
   5_xyz: 106.24   0.21  17.43 106.24   0.21  12.80  99.14   4.24  42.66
   5_adp: 110.70   0.00  17.25 110.70   0.00  12.67  99.87   5.12  42.23
   5_occ: 110.70   0.00  17.25 110.70   0.00  12.67  99.87   5.12  42.23
   5_bss: 110.70   0.00  17.25 110.70   0.00  12.67  99.87   5.12  42.23
------------------------------------------------------------------------
 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:    1.830    0.031    0.406
   1_adp:    1.830    0.031    0.406
   1_occ:    1.830    0.031    0.406
   2_bss:    1.830    0.031    0.406
   2_xyz:    1.190    0.028    0.476
   2_adp:    1.190    0.028    0.476
   2_occ:    1.190    0.028    0.476
   3_bss:    1.190    0.028    0.476
   3_xyz:    1.071    0.011    0.567
   3_adp:    1.071    0.011    0.567
   3_occ:    1.071    0.011    0.567
   4_bss:    1.071    0.011    0.567
   4_xyz:    1.155    0.040    0.597
   4_adp:    1.155    0.040    0.597
   4_occ:    1.155    0.040    0.597
   5_bss:    1.155    0.040    0.597
   5_xyz:    1.125    0.067    0.604
   5_adp:    1.125    0.067    0.604
   5_occ:    1.125    0.067    0.604
   5_bss:    1.125    0.067    0.604
------------------------------------------------------------------------

CPU time actual refinement: 323.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/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_1181/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1181/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.35 
  Macro-tasks:
    bulk solvent and scale       = 38.23  
    individual site refinement   = 129.67 
    weights calculation          = 29.42  
    collect and process          = 6.62   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 204.07 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 102.23 
    alpha_beta                      = 8.32   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 110.93 
    fmodel                         = 6.37   
    r_factors                      = 0.19   
    phase_errors                   = 11.02  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 242.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.597 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    654 calls, 101.90 s
gradients_fft:          599 calls,  97.42 s

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

# Date 2008-01-16 Time 06:37:03 PST -0800 (1200494223.93 s)
Start R-work = 0.4027, R-free = 0.3933 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1822 (no bulk solvent and anisotropic scale)

Start R-work = 0.3927, R-free = 0.3826
Final R-work = 0.1149, R-free = 0.1656