# Date 2008-01-16 Time 06:05:33 PST -0800 (1200492333.32 s)
#phil __OFF__

Command line arguments: "../1003.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24195
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1003

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.4607, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97104
Completeness in resolution range: 0.953747
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9710

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97104
Completeness in resolution range: 0.953747
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2185 [2155/2181]  1943   212   9.8%
  bin  2:  4.2185 -  3.3605 [2080/2099]  1871   209  10.0%
  bin  3:  3.3605 -  2.9393 [2033/2052]  1827   206  10.1%
  bin  4:  2.9393 -  2.6721 [2025/2055]  1827   198   9.8%
  bin  5:  2.6721 -  2.4815 [2036/2055]  1830   206  10.1%
  bin  6:  2.4815 -  2.3358 [1990/2015]  1786   204  10.3%
  bin  7:  2.3358 -  2.2192 [1997/2025]  1800   197   9.9%
  bin  8:  2.2192 -  2.1228 [1984/2020]  1791   193   9.7%
  bin  9:  2.1228 -  2.0413 [1977/2019]  1778   199  10.1%
  bin 10:  2.0413 -  1.9710 [1312/2018]  1177   135  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 30
        2.42 -     3.04: 2203
        3.04 -     3.66: 4740
        3.66 -     4.28: 9088
        4.28 -     4.90: 12386
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.966 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.997 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.028 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.073 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28442 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_1003/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.4607 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3943   r_free= 0.3942   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.173437                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.3176 0.3192      6.4219      6.4076|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.3192 0.2998       6.614      6.5616|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.3516 0.3251      6.4844       6.582|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.3686 0.4075      6.3863      6.3753|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.4091 0.4171      6.2432      6.2493|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.4208 0.4358      6.1794       6.196|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.4257 0.3978      6.1552      6.0956|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.4511 0.4185       6.098       6.069|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.4267 0.4323      6.0337      6.0151|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.4471 0.4922      6.0212      6.0795|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.4620 0.4551      5.9878      6.0053|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.4613 0.5047      5.9261      5.9871|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.4576 0.4361       5.826      5.7536|
| 14:  2.0202 -  1.9710 0.53    686   74 0.4952 0.4703      5.8148      5.7697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.77  27.90   0.85     0.80      49091.86|
|  2:  4.7055 -  3.7538  1348   143  0.79  26.70   0.95     0.89      65068.49|
|  3:  3.7538 -  3.2849  1316   147  0.72  33.25   0.97     0.90      70073.29|
|  4:  3.2849 -  2.9871  1327   157  0.66  38.73   0.98     0.85      66187.47|
|  5:  2.9871 -  2.7744  1298   139  0.58  45.21   0.94     0.77      55601.21|
|  6:  2.7744 -  2.6117  1296   148  0.57  46.32   0.95     0.77      49326.36|
|  7:  2.6117 -  2.4815  1313   139  0.59  44.97   0.97     0.78      42536.60|
|  8:  2.4815 -  2.3739  1261   145  0.58  45.96   0.93     0.81      38580.73|
|  9:  2.3739 -  2.2829  1294   149  0.58  45.59   0.99     0.80      35559.10|
| 10:  2.2829 -  2.2043  1281   136  0.54  49.24   0.99     0.77      36331.55|
| 11:  2.2043 -  2.1356  1280   138  0.49  52.60   1.00     0.74      36210.22|
| 12:  2.1356 -  2.0747  1256   144  0.49  53.21   0.99     0.72      33458.14|
| 13:  2.0747 -  2.0202  1274   142  0.47  54.97   0.99     0.70      28838.03|
| 14:  2.0202 -  1.9710   686    74  0.47  54.83   0.96     0.66      24402.01|
|alpha:            min =        0.66 max =            0.90 mean =         0.79|
|beta:             min =    24402.01 max =        70073.29 mean =     46029.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.66|
|phase err.(test): min =        0.00 max =           89.93 mean =        43.92|
|-----------------------------------------------------------------------------|

============================== 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 = 8.401002              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.408   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.299896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.777   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      204 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1999 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1892 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2848 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4670 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4418 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5657 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6729 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.221 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3943   r_free= 0.3942   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.173437                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3846   r_free= 0.3854   ksol= 0.32   Bsol= 30.62   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.70,0.62,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.164462                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.992384              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.610   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.553   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3846      final r-factor (work) = 0.2117          |
| start r-factor (free) = 0.3854      final r-factor (free) = 0.2396          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.7093 = 6.99 * 0.50 * 6.1623 + 1.00 * 0.1647                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7717 = 6.99 * 0.50 * 5.9176 + 1.00 * 0.0827                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2117      final r-factor (work) = 0.1967          |
| start r-factor (free) = 0.2396      final r-factor (free) = 0.2470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7056 = 0.63 * 1.00 * 5.9176 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5625 = 0.63 * 1.00 * 5.6087 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.73   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    74.73   16.73    None  None   None       |
|    Sol.    : 438    0      5.42    61.72   38.30    None  None   None       |
|    Mac.    : 2385   0      0.00    74.73   12.77    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 -   7.473:  476   |   5:    37.366 -  44.840:  130        |
|      1:     7.473 -  14.947: 1265   |   6:    44.840 -  52.313:   79        |
|      2:    14.947 -  22.420:  503   |   7:    52.313 -  59.786:   62        |
|      3:    22.420 -  29.893:  175   |   8:    59.786 -  67.259:    7        |
|      4:    29.893 -  37.366:  125   |   9:    67.259 -  74.733:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1967 r_free = 0.2470             target_work(ml) = 5.623         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1961 r_free = 0.2471             target_work(ml) = 5.621         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1961   r_free= 0.2471   ksol= 0.32   Bsol= 30.62   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.70,0.62,-0.00,0.00,0.00); trace/3= -0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.621087                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1944   r_free= 0.2455   ksol= 0.33   Bsol= 50.41   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.52,-1.42,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.618955                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.200620              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.147   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.454   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1944      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2455      final r-factor (free) = 0.1861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0972 = 3.20 * 0.50 * 5.6330 + 1.00 * 0.0827                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8486 = 3.20 * 0.50 * 5.4946 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1410      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7095 = 0.48 * 1.00 * 5.4946 + 1.00 * 0.0447                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5745 = 0.48 * 1.00 * 5.2899 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.01    79.75   17.33    None  None   None       |
|    all(noH): 2823   0      1.01    79.75   17.33    None  None   None       |
|    Sol.    : 438    0      6.03    79.04   40.99    None  None   None       |
|    Mac.    : 2385   0      1.01    79.75   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.006 -   8.881:  732   |   5:    40.378 -  48.252:   97        |
|      1:     8.881 -  16.755: 1248   |   6:    48.252 -  56.127:   91        |
|      2:    16.755 -  24.629:  336   |   7:    56.127 -  64.001:   57        |
|      3:    24.629 -  32.504:  125   |   8:    64.001 -  71.875:   29        |
|      4:    32.504 -  40.378:   98   |   9:    71.875 -  79.750:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1733             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1284 r_free = 0.1733             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1733   ksol= 0.33   Bsol= 50.41   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.84,-2.52,-1.42,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.249870                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1736   ksol= 0.33   Bsol= 49.01   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.59,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.250384                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.781569              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.887  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.276304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.852  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1736      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0571 = 3.78 * 0.50 * 5.2896 + 1.00 * 0.0556                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8920 = 3.78 * 0.50 * 5.1943 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4442 = 0.28 * 1.00 * 5.1943 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4280 = 0.28 * 1.00 * 5.1390 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.24    85.26   17.00    None  None   None       |
|    all(noH): 2823   0      1.24    85.26   17.00    None  None   None       |
|    Sol.    : 438    0      3.59    81.96   39.37    None  None   None       |
|    Mac.    : 2385   0      1.24    85.26   12.89    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.240 -   9.642:  917   |   5:    43.251 -  51.653:  108        |
|      1:     9.642 -  18.044: 1173   |   6:    51.653 -  60.055:   55        |
|      2:    18.044 -  26.446:  262   |   7:    60.055 -  68.458:   33        |
|      3:    26.446 -  34.849:  131   |   8:    68.458 -  76.860:   13        |
|      4:    34.849 -  43.251:  126   |   9:    76.860 -  85.262:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1560             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1558             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1558   ksol= 0.33   Bsol= 49.01   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.59,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.126934                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1558   ksol= 0.33   Bsol= 49.01   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.59,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.126934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.989122              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.661  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.135569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.948  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1815 = 1.99 * 0.50 * 5.1387 + 1.00 * 0.0707                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1583 = 1.99 * 0.50 * 5.1299 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7035 = 0.14 * 1.00 * 5.1299 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7029 = 0.14 * 1.00 * 5.1342 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.11    83.95   16.57    None  None   None       |
|    all(noH): 2823   0      2.11    83.95   16.57    None  None   None       |
|    Sol.    : 438    0      5.70    81.63   37.35    None  None   None       |
|    Mac.    : 2385   0      2.11    83.95   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.111 -  10.295: 1081   |   5:    43.032 -  51.216:   90        |
|      1:    10.295 -  18.479: 1052   |   6:    51.216 -  59.401:   59        |
|      2:    18.479 -  26.663:  243   |   7:    59.401 -  67.585:   17        |
|      3:    26.663 -  34.848:  135   |   8:    67.585 -  75.769:   11        |
|      4:    34.848 -  43.032:  130   |   9:    75.769 -  83.954:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1552             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1552             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1552   ksol= 0.33   Bsol= 49.01   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-2.59,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133231                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1552   ksol= 0.33   Bsol= 49.01   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.60,-1.67,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.133235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.994884              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.585  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.317238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.355  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1552      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7440 = 2.99 * 0.50 * 5.1339 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7330 = 2.99 * 0.50 * 5.1169 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1060          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7470 = 1.32 * 1.00 * 5.1169 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7340 = 1.32 * 1.00 * 5.1054 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    94.23   16.97    None  None   None       |
|    all(noH): 2823   0      0.67    94.23   16.97    None  None   None       |
|    Sol.    : 438    0      6.40    84.35   39.68    None  None   None       |
|    Mac.    : 2385   0      0.67    94.23   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:     0.674 -  10.029: 1065   |   5:    47.450 -  56.805:   96        |
|      1:    10.029 -  19.384: 1103   |   6:    56.805 -  66.160:   53        |
|      2:    19.384 -  28.739:  220   |   7:    66.160 -  75.516:   13        |
|      3:    28.739 -  38.095:  139   |   8:    75.516 -  84.871:   12        |
|      4:    38.095 -  47.450:  120   |   9:    84.871 -  94.226:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1060 r_free = 0.1564             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1563             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1563   ksol= 0.33   Bsol= 49.01   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.60,-1.67,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111671                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.0978 0.1314      5.3759      5.5558|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.0824 0.1124      5.4155      5.6159|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.1043 0.1531      5.4596      5.8491|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.1154 0.1593      5.4295      5.5831|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.1259 0.1783      5.2941      5.5357|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.1135 0.1606      5.1686      5.3938|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.1176 0.1589      5.1278        5.31|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.1061 0.1774       4.982      5.3526|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.1083 0.1762      4.9848      5.3148|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.1029 0.1674      4.9018      5.1697|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.1088 0.1774       4.924      5.2998|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.1038 0.1544      4.8588      5.0512|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.1071 0.1802      4.7521      5.0696|
| 14:  2.0202 -  1.9710 0.53    686   74 0.0886 0.1552      4.5601      4.8674|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.94   8.63   0.98     0.95       6731.18|
|  2:  4.7055 -  3.7538  1348   143  0.95   7.87   1.02     1.01       8872.38|
|  3:  3.7538 -  3.2849  1316   147  0.93  11.25   1.03     1.02      10198.27|
|  4:  3.2849 -  2.9871  1327   157  0.92  13.53   1.00     0.98      10064.03|
|  5:  2.9871 -  2.7744  1298   139  0.90  15.76   0.99     0.97       8080.98|
|  6:  2.7744 -  2.6117  1296   148  0.90  15.45   0.98     0.95       6740.96|
|  7:  2.6117 -  2.4815  1313   139  0.91  14.78   0.99     0.97       5910.07|
|  8:  2.4815 -  2.3739  1261   145  0.91  14.67   0.98     0.95       4608.76|
|  9:  2.3739 -  2.2829  1294   149  0.92  14.34   1.00     0.97       4585.96|
| 10:  2.2829 -  2.2043  1281   136  0.91  14.71   0.99     0.96       4011.90|
| 11:  2.2043 -  2.1356  1280   138  0.90  16.45   0.99     0.95       4354.73|
| 12:  2.1356 -  2.0747  1256   144  0.92  14.89   1.00     0.99       3984.33|
| 13:  2.0747 -  2.0202  1274   142  0.91  15.82   1.00     0.98       3200.94|
| 14:  2.0202 -  1.9710   686    74  0.92  13.47   0.97     0.94       2192.11|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2192.11 max =        10198.27 mean =      6136.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.63|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1553   ksol= 0.32   Bsol= 49.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.40,-1.50,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110226                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1553   ksol= 0.32   Bsol= 49.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.40,-1.50,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110226                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.0961 0.1276      5.3578       5.543|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.0831 0.1103      5.4156        5.61|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.1043 0.1508      5.4569      5.8354|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.1160 0.1584      5.4275      5.5823|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.1263 0.1766      5.2941      5.5315|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.1138 0.1612      5.1696      5.3977|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.1176 0.1584      5.1284      5.3083|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.1058 0.1778      4.9832      5.3544|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.1085 0.1765      4.9858      5.3158|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.1028 0.1671      4.9016      5.1679|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.1088 0.1777      4.9238      5.3003|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.1039 0.1546      4.8586      5.0519|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.1070 0.1807      4.7528      5.0707|
| 14:  2.0202 -  1.9710 0.53    686   74 0.0885 0.1554      4.5615      4.8703|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.94   8.58   0.98     0.95       6543.96|
|  2:  4.7055 -  3.7538  1348   143  0.95   7.76   1.02     1.01       8684.70|
|  3:  3.7538 -  3.2849  1316   147  0.94  11.13   1.03     1.03      10060.06|
|  4:  3.2849 -  2.9871  1327   157  0.92  13.40   1.01     0.98       9949.43|
|  5:  2.9871 -  2.7744  1298   139  0.90  15.73   1.00     0.97       8036.88|
|  6:  2.7744 -  2.6117  1296   148  0.90  15.44   0.99     0.96       6730.61|
|  7:  2.6117 -  2.4815  1313   139  0.91  14.79   1.00     0.97       5921.83|
|  8:  2.4815 -  2.3739  1261   145  0.91  14.72   0.99     0.96       4636.63|
|  9:  2.3739 -  2.2829  1294   149  0.92  14.36   1.01     0.98       4600.17|
| 10:  2.2829 -  2.2043  1281   136  0.91  14.72   1.00     0.97       4017.02|
| 11:  2.2043 -  2.1356  1280   138  0.90  16.45   1.00     0.96       4351.99|
| 12:  2.1356 -  2.0747  1256   144  0.92  14.90   1.01     1.00       3984.56|
| 13:  2.0747 -  2.0202  1274   142  0.90  15.86   1.01     0.99       3213.10|
| 14:  2.0202 -  1.9710   686    74  0.92  13.52   0.98     0.95       2203.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2203.91 max =        10060.06 mean =      6089.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.61|
|phase err.(test): min =        0.00 max =           89.53 mean =        13.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.65    94.20   16.95    None  None   None       |
|    all(noH): 2823   0      0.65    94.20   16.95    None  None   None       |
|    Sol.    : 438    0      6.38    84.32   39.65    None  None   None       |
|    Mac.    : 2385   0      0.65    94.20   12.78    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:     0.651 -  10.007: 1065   |   5:    47.428 -  56.783:   96        |
|      1:    10.007 -  19.362: 1103   |   6:    56.783 -  66.138:   53        |
|      2:    19.362 -  28.717:  220   |   7:    66.138 -  75.493:   13        |
|      3:    28.717 -  38.072:  139   |   8:    75.493 -  84.849:   12        |
|      4:    38.072 -  47.428:  120   |   9:    84.849 -  94.204:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.443 - 4.571
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 288
   mapped sites are within: 0.727 - 4.571

peak=    5.858 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.812 closest distance to " NH2 ARG A  56 " =    2.192
peak=    5.365 closest distance to " O   HOH Z 126 " =    1.946
peak=    5.201 closest distance to " CB  GLN A 223 " =    1.503
peak=    5.105 closest distance to " O   HOH Z 232 " =    2.307
peak=    5.094 closest distance to " CG  PRO A  54 " =    1.134
peak=    5.033 closest distance to " CB  SER A  63 " =    1.256
peak=    4.864 closest distance to " CB  GLN A 183 " =    1.244
peak=    4.847 closest distance to " C   PRO A 198 " =    1.495
peak=    4.774 closest distance to " O   HOH Z 369 " =    2.156
peak=    4.772 closest distance to " O   HOH Z 144 " =    1.699
peak=    4.667 closest distance to " O   HOH Z 298 " =    1.842
peak=    4.611 closest distance to " CA  TYR A  30 " =    0.975
peak=    4.599 closest distance to " O   HOH Z  78 " =    1.804
peak=    4.574 closest distance to " O   HOH Z 427 " =    2.819
peak=    4.559 closest distance to " O   HOH Z 193 " =    1.852
peak=    4.469 closest distance to " CB  GLU A 152 " =    1.274
peak=    4.458 closest distance to " CB  ARG A 275 " =    0.907
peak=    4.414 closest distance to " OD1 ASN A  69 " =    2.630
peak=    4.395 closest distance to " CG  PRO A 213 " =    1.165
peak=    4.394 closest distance to " CB  ASN A 187 " =    1.428
peak=    4.361 closest distance to " CB  PRO A  54 " =    0.881
peak=    4.358 closest distance to " O   HOH Z  15 " =    2.232
peak=    4.355 closest distance to " CB  ASN A 148 " =    1.440
peak=    4.301 closest distance to " CB  ARG A  79 " =    1.466
peak=    4.300 closest distance to " CB  SER A   3 " =    1.458
peak=    4.294 closest distance to " CB  LEU A 228 " =    1.095
peak=    4.285 closest distance to " CB  GLU A 128 " =    1.047
peak=    4.230 closest distance to " O   HOH Z 193 " =    1.751
peak=    4.187 closest distance to " O   HOH Z  10 " =    1.839
peak=    4.156 closest distance to " OD2 ASP A 286 " =    2.816
peak=    4.149 closest distance to " O   HOH Z 203 " =    1.838
peak=    4.148 closest distance to " ND2 ASN A 187 " =    1.457
peak=    4.145 closest distance to " O   HOH Z 303 " =    2.130
peak=    4.122 closest distance to " O   HOH Z 236 " =    1.999
peak=    4.112 closest distance to " O   HOH Z 368 " =    2.055
peak=    4.102 closest distance to " O   HOH Z 217 " =    3.071
peak=    4.096 closest distance to " O   HOH Z  61 " =    1.608
peak=    4.054 closest distance to " O   HOH Z 344 " =    3.179
peak=    4.045 closest distance to " O   HOH Z 272 " =    1.842
peak=    4.014 closest distance to " CB  ARG A 139 " =    1.017
peak=    4.009 closest distance to " O   HOH Z 189 " =    2.180
peak=    3.977 closest distance to " O   HOH Z 132 " =    2.432
peak=    3.948 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.945 closest distance to " O   HOH Z 371 " =    2.914
peak=    3.908 closest distance to " CB  VAL A 265 " =    1.298
peak=    3.906 closest distance to " CA  ASN A 215 " =    1.237
peak=    3.903 closest distance to " CG2 VAL A 257 " =    0.962
peak=    3.902 closest distance to " O   HOH Z 234 " =    3.802
peak=    3.900 closest distance to " CD  ARG A  66 " =    2.305
peak=    3.896 closest distance to " O   HOH Z 316 " =    3.064
peak=    3.888 closest distance to " CD2 LEU A 255 " =    1.419
peak=    3.888 closest distance to " CA  MET A  40 " =    1.127
peak=    3.883 closest distance to " O   HOH Z 437 " =    1.625
peak=    3.880 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.880 closest distance to " CB  TYR A 169 " =    0.787
peak=    3.878 closest distance to " O   HOH Z 144 " =    2.357
peak=    3.869 closest distance to " O   HOH Z 180 " =    2.167
peak=    3.846 closest distance to " CB  ARG A 190 " =    1.702
peak=    3.814 closest distance to " CD  ARG A 159 " =    0.784
peak=    3.805 closest distance to " O   HOH Z 183 " =    1.336
peak=    3.801 closest distance to " CB  TRP A 266 " =    0.983
peak=    3.799 closest distance to " ND1 HIS A  86 " =    1.764
peak=    3.794 closest distance to " CD BLYS A 290 " =    1.241
peak=    3.793 closest distance to " OD1BASN A 224 " =    2.324
peak=    3.793 closest distance to " O   HOH Z 289 " =    1.717
peak=    3.782 closest distance to " O   HOH Z 158 " =    2.954
peak=    3.771 closest distance to " O   HOH Z   1 " =    1.895
peak=    3.761 closest distance to " CE  LYS A  76 " =    0.905
peak=    3.757 closest distance to " O   HOH Z 261 " =    1.643
peak=    3.757 closest distance to " CA  ASP A 124 " =    0.727
peak=    3.749 closest distance to " CA  THR A 264 " =    0.853
peak=    3.749 closest distance to " O   HOH Z 419 " =    1.930
peak=    3.734 closest distance to " O   MET A 105 " =    1.790
peak=    3.733 closest distance to " CG2 THR A 221 " =    1.038
peak=    3.730 closest distance to " CB  TRP A 179 " =    1.422
peak=    3.726 closest distance to " OE1 GLN A  11 " =    2.125
peak=    3.700 closest distance to " O   HOH Z 407 " =    2.245
peak=    3.694 closest distance to " O   HOH Z 133 " =    2.547
peak=    3.690 closest distance to " O   HOH Z   1 " =    1.723
peak=    3.689 closest distance to " O   HOH Z  66 " =    2.175
peak=    3.687 closest distance to " O   HOH Z 197 " =    3.154
peak=    3.686 closest distance to " CB  SER A 212 " =    1.135
peak=    3.675 closest distance to " O   HOH Z 214 " =    2.003
peak=    3.668 closest distance to " O   HOH Z  64 " =    2.316
peak=    3.668 closest distance to " O   HOH Z  88 " =    3.337
peak=    3.667 closest distance to " O   HOH Z  21 " =    1.647
peak=    3.666 closest distance to " O   HOH Z 163 " =    1.856
peak=    3.663 closest distance to " O   HOH Z 219 " =    2.160
peak=    3.659 closest distance to " O   HOH Z 108 " =    1.368
peak=    3.657 closest distance to " O   HOH Z 193 " =    2.047
peak=    3.643 closest distance to " O   HOH Z 213 " =    1.801
peak=    3.642 closest distance to " CB  SER A 216 " =    0.800
peak=    3.638 closest distance to " O   HOH Z  97 " =    1.935
peak=    3.625 closest distance to " O   HOH Z 403 " =    1.620
peak=    3.624 closest distance to " O   HOH Z 175 " =    2.158
peak=    3.615 closest distance to " N   PHE A 130 " =    1.309
peak=    3.614 closest distance to " O   HOH Z  44 " =    1.701
peak=    3.609 closest distance to " O   HOH Z 135 " =    1.651
peak=    3.599 closest distance to " CA  GLY A 241 " =    3.810
peak=    3.596 closest distance to " O   SER A  87 " =    2.132
peak=    3.590 closest distance to " O   HOH Z 403 " =    1.361
peak=    3.590 closest distance to " O   HOH Z 147 " =    1.768
peak=    3.589 closest distance to " O   HOH Z 374 " =    2.680
peak=    3.584 closest distance to " CB  GLU A 277 " =    3.552
peak=    3.582 closest distance to " O   HOH Z  63 " =    1.341
peak=    3.578 closest distance to " O   HOH Z 425 " =    2.075
peak=    3.571 closest distance to " O   HOH Z 284 " =    3.080
peak=    3.564 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.564 closest distance to " O   HOH Z  43 " =    1.807
peak=    3.560 closest distance to " O   HOH Z 217 " =    1.570
peak=    3.556 closest distance to " O   HOH Z 409 " =    2.719
peak=    3.552 closest distance to " O   HOH Z 153 " =    1.661
peak=    3.550 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.548 closest distance to " CB  VAL A 202 " =    1.658
peak=    3.545 closest distance to " O   HOH Z 133 " =    1.613
peak=    3.540 closest distance to " OG BSER A 164 " =    2.312
peak=    3.532 closest distance to " O   HOH Z 108 " =    2.085
peak=    3.530 closest distance to " O   HOH Z  44 " =    3.126
peak=    3.529 closest distance to " CB  MET A  47 " =    1.110
peak=    3.524 closest distance to " O   HOH Z 327 " =    1.686
peak=    3.522 closest distance to " O   HOH Z 391 " =    2.919
peak=    3.521 closest distance to " O   HOH Z 368 " =    3.640
peak=    3.516 closest distance to " O   HOH Z 250 " =    1.433
peak=    3.510 closest distance to " O   HOH Z 425 " =    1.230
peak=    3.510 closest distance to " OG  SER A  22 " =    2.770
peak=    3.508 closest distance to " CB  LEU A 143 " =    1.102
peak=    3.508 closest distance to " NH1BARG A 145 " =    1.226
peak=    3.507 closest distance to " O   HOH Z 271 " =    2.394
peak=    3.507 closest distance to " O   HOH Z 295 " =    1.571
peak=    3.506 closest distance to " CZ  PHE A 218 " =    1.031
peak=    3.502 closest distance to " CA  THR A 221 " =    0.990
peak=    3.497 closest distance to " CB  ALA A  34 " =    1.143
peak=    3.495 closest distance to " O   HOH Z 209 " =    2.344
peak=    3.494 closest distance to " NH1AARG A 145 " =    1.093
peak=    3.487 closest distance to " NH2BARG A 145 " =    1.966
peak=    3.481 closest distance to " O   HOH Z  40 " =    1.884
peak=    3.477 closest distance to " O   HOH Z 411 " =    1.829
peak=    3.476 closest distance to " O   HOH Z 207 " =    1.835
peak=    3.475 closest distance to " O   HOH Z 248 " =    1.671
peak=    3.472 closest distance to " CG  ARG A 159 " =    0.877
peak=    3.469 closest distance to " O   HOH Z 345 " =    3.558
peak=    3.467 closest distance to " CG  PRO A 198 " =    1.189
peak=    3.466 closest distance to " O   HOH Z 265 " =    2.394
peak=    3.464 closest distance to " O   HOH Z 281 " =    4.571
peak=    3.464 closest distance to " O   HOH Z 389 " =    1.872
peak=    3.461 closest distance to " OD1 ASN A 217 " =    1.665
peak=    3.458 closest distance to " O   HOH Z 188 " =    2.022
peak=    3.451 closest distance to " O   HOH Z 423 " =    1.456
peak=    3.448 closest distance to " CA  ALA A 233 " =    1.084
peak=    3.448 closest distance to " CD1 LEU A 300 " =    1.304
peak=    3.438 closest distance to " O   HOH Z 405 " =    1.081
peak=    3.432 closest distance to " CB  ALA A 291 " =    1.434
peak=    3.431 closest distance to " O   HOH Z 426 " =    1.663
peak=    3.424 closest distance to " O   THR A 220 " =    1.365
peak=    3.422 closest distance to " N   ARG A 156 " =    1.263
peak=    3.412 closest distance to " O   HOH Z  53 " =    2.581
peak=    3.412 closest distance to " CB  GLN A  88 " =    1.303
peak=    3.406 closest distance to " O   GLY A  57 " =    2.612
peak=    3.404 closest distance to " O   HOH Z  93 " =    2.559
peak=    3.403 closest distance to " N   SER A 134 " =    1.362
peak=    3.400 closest distance to " NE2 GLN A  73 " =    3.720
peak=    3.395 closest distance to " O   ALA A 165 " =    1.430
peak=    3.393 closest distance to " O   HOH Z  59 " =    1.762
peak=    3.387 closest distance to " O   HOH Z 172 " =    3.301
peak=    3.387 closest distance to " O   HOH Z 292 " =    1.647
peak=    3.386 closest distance to " CD1 LEU A 228 " =    2.072
peak=    3.374 closest distance to " O   HOH Z   3 " =    1.851
peak=    3.371 closest distance to " CB  THR A 157 " =    1.112
peak=    3.366 closest distance to " O   HOH Z 128 " =    2.194
peak=    3.358 closest distance to " O   HOH Z 303 " =    1.790
peak=    3.353 closest distance to " CB  LEU A 255 " =    0.757
peak=    3.352 closest distance to " O   HOH Z 371 " =    1.852
peak=    3.352 closest distance to " O   HOH Z  88 " =    3.777
peak=    3.350 closest distance to " O   HOH Z  20 " =    1.600
peak=    3.347 closest distance to " CB  TRP A 150 " =    1.353
peak=    3.342 closest distance to " O   HOH Z 365 " =    2.792
peak=    3.339 closest distance to " CG1 VAL A 153 " =    0.985
peak=    3.338 closest distance to " CB  THR A  82 " =    1.394
peak=    3.338 closest distance to " NH2AARG A 190 " =    1.193
peak=    3.336 closest distance to " CB  ASN A 142 " =    0.984
peak=    3.332 closest distance to " NH2 ARG A 156 " =    1.192
peak=    3.330 closest distance to " OE1 GLU A 236 " =    1.637
peak=    3.326 closest distance to " O   HOH Z 128 " =    2.220
peak=    3.326 closest distance to " NH2AARG A 190 " =    1.736
peak=    3.325 closest distance to " CA  ARG A 195 " =    1.239
peak=    3.324 closest distance to " CB  GLU A 236 " =    1.063
peak=    3.322 closest distance to " O   HOH Z 329 " =    3.705
peak=    3.322 closest distance to " CA  GLY A 267 " =    1.307
peak=    3.318 closest distance to " CG  LYS A  76 " =    1.003
peak=    3.315 closest distance to " O   HOH Z  54 " =    1.672
peak=    3.307 closest distance to " CB  ALA A 233 " =    1.320
peak=    3.306 closest distance to " CB  TYR A 116 " =    0.830
peak=    3.300 closest distance to " O   HOH Z 305 " =    3.549
peak=    3.299 closest distance to " O   HOH Z 211 " =    2.680
peak=    3.296 closest distance to " CD  LYS A 166 " =    1.190
peak=    3.295 closest distance to " O   ALA A 233 " =    1.736
peak=    3.294 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.293 closest distance to " O   HOH Z 291 " =    1.893
peak=    3.292 closest distance to " CB  ASP A 171 " =    0.944
peak=    3.290 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.289 closest distance to " O   GLY A 229 " =    1.720
peak=    3.288 closest distance to " ND1 HIS A  81 " =    1.590
peak=    3.287 closest distance to " CB  VAL A 126 " =    1.233
peak=    3.286 closest distance to " CA  ILE A 234 " =    0.987
peak=    3.286 closest distance to " CA  ALA A 291 " =    0.936
peak=    3.277 closest distance to " CE BLYS A 290 " =    1.192
peak=    3.275 closest distance to " N   TYR A  15 " =    0.791
peak=    3.271 closest distance to " N   ASN A 127 " =    1.261
peak=    3.271 closest distance to " O   HOH Z 245 " =    1.268
peak=    3.267 closest distance to " O   GLN A 278 " =    1.284
peak=    3.265 closest distance to " CB  SER A 276 " =    1.078
peak=    3.263 closest distance to " O   HOH Z 379 " =    1.883
peak=    3.260 closest distance to " O   HOH Z 227 " =    1.670
peak=    3.260 closest distance to " O   HOH Z 144 " =    1.854
peak=    3.248 closest distance to " CG BARG A 275 " =    1.506
peak=    3.247 closest distance to " NH2AARG A 275 " =    3.617
peak=    3.246 closest distance to " O   HOH Z 281 " =    4.135
peak=    3.245 closest distance to " O   HOH Z  50 " =    1.480
peak=    3.244 closest distance to " O   HOH Z 134 " =    1.210
peak=    3.242 closest distance to " O   HOH Z 227 " =    2.136
peak=    3.241 closest distance to " CG  PRO A 243 " =    1.147
peak=    3.238 closest distance to " CG  PRO A  90 " =    0.979
peak=    3.237 closest distance to " N   ASN A  39 " =    1.303
peak=    3.232 closest distance to " CA  TYR A 186 " =    1.489
peak=    3.222 closest distance to " O   HOH Z  64 " =    2.084
peak=    3.220 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.217 closest distance to " CG1BVAL A  72 " =    1.554
peak=    3.217 closest distance to " CA  LYS A 290 " =    1.312
peak=    3.214 closest distance to " CB  ILE A 120 " =    1.206
peak=    3.211 closest distance to " CB  VAL A 265 " =    2.097
peak=    3.209 closest distance to " CB  ARG A 138 " =    1.008
peak=    3.208 closest distance to " O  BHOH Z 338 " =    2.341
peak=    3.206 closest distance to " CD  PRO A 243 " =    1.666
peak=    3.204 closest distance to " O   HOH Z 213 " =    2.324
peak=    3.202 closest distance to " O   HOH Z 263 " =    1.731
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.200
peak=    3.183 closest distance to " O   HOH Z 184 " =    1.839
peak=    3.183 closest distance to " O   HOH Z 255 " =    1.730
peak=    3.178 closest distance to " CB  ASP A 140 " =    0.865
peak=    3.176 closest distance to " O   HOH Z 359 " =    1.418
peak=    3.174 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.174 closest distance to " CA  PHE A 283 " =    1.290
peak=    3.172 closest distance to " CD  ARG A 219 " =    1.092
peak=    3.169 closest distance to " CA  ALA A  84 " =    1.470
peak=    3.163 closest distance to " CA  LEU A 101 " =    1.427
peak=    3.159 closest distance to " CD2 TRP A 179 " =    1.323
peak=    3.159 closest distance to " CD2 HIS A  81 " =    1.178
peak=    3.157 closest distance to " O   ASN A 209 " =    1.300
peak=    3.155 closest distance to " CB  LYS A 117 " =    1.156
peak=    3.154 closest distance to " CG  MET A 185 " =    1.085
peak=    3.147 closest distance to " O   HOH Z 173 " =    1.791
peak=    3.146 closest distance to " CG  MET A 113 " =    1.387
peak=    3.146 closest distance to " NH2 ARG A 219 " =    1.823
peak=    3.146 closest distance to " O   HOH Z  88 " =    2.577
peak=    3.143 closest distance to " CB  ASN A 224 " =    0.994
peak=    3.141 closest distance to " CA  ARG A  36 " =    1.094
peak=    3.138 closest distance to " CB  ALA A  71 " =    1.413
peak=    3.138 closest distance to " O   HOH Z 302 " =    1.762
peak=    3.136 closest distance to " NE AARG A 275 " =    1.376
peak=    3.134 closest distance to " CB  ILE A 234 " =    1.135
peak=    3.132 closest distance to " O   TYR A 116 " =    1.334
peak=    3.131 closest distance to " CB  THR A 294 " =    1.643
peak=    3.129 closest distance to " O   HOH Z 383 " =    1.794
peak=    3.129 closest distance to " OG  SER A 206 " =    1.249
peak=    3.128 closest distance to " NH1 ARG A  56 " =    1.181
peak=    3.126 closest distance to " CG1 ILE A 151 " =    0.889
peak=    3.124 closest distance to " O   HOH Z 367 " =    2.125
peak=    3.118 closest distance to " OG  SER A  62 " =    3.071
peak=    3.112 closest distance to " O   HOH Z 116 " =    1.660
peak=    3.108 closest distance to " NE  ARG A  79 " =    1.124
peak=    3.106 closest distance to " O   HOH Z 151 " =    1.881
peak=    3.096 closest distance to " O   HOH Z 353 " =    2.746
peak=    3.090 closest distance to " N   SER A 135 " =    1.365
peak=    3.089 closest distance to " O   HOH Z 380 " =    1.910
peak=    3.088 closest distance to " O   HOH Z 406 " =    1.585
peak=    3.088 closest distance to " NZ  LYS A 119 " =    1.228
peak=    3.087 closest distance to " O   HOH Z 359 " =    4.020
peak=    3.080 closest distance to " O   ALA A 158 " =    1.324
peak=    3.077 closest distance to " O   HOH Z 325 " =    3.675
peak=    3.075 closest distance to " CB  TRP A 179 " =    1.680
peak=    3.075 closest distance to " CA  SER A  87 " =    1.001
peak=    3.069 closest distance to " O   HOH Z 213 " =    1.932
peak=    3.059 closest distance to " OG BSER A  99 " =    2.143
peak=    3.052 closest distance to " CA  THR A  82 " =    1.363

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.475
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 206
   mapped sites are within: 0.785 - 5.475

peak=   -4.608 closest distance to " CB  PRO A 280 " =    2.096
peak=   -4.548 closest distance to " O   HOH Z 266 " =    4.550
peak=   -4.467 closest distance to " CB  PRO A 243 " =    2.523
peak=   -4.392 closest distance to " CD  ARG A 156 " =    1.969
peak=   -4.266 closest distance to " O   HOH Z 372 " =    2.424
peak=   -4.262 closest distance to " CG  GLN A 223 " =    1.971
peak=   -4.146 closest distance to " SG  CYS A 254 " =    3.330
peak=   -4.097 closest distance to " O   VAL A  67 " =    2.677
peak=   -4.097 closest distance to " O   HOH Z 231 " =    2.126
peak=   -4.072 closest distance to " OG BSER A 134 " =    1.232
peak=   -4.035 closest distance to " O   HOH Z 198 " =    1.984
peak=   -3.955 closest distance to " CZ3 TRP A 179 " =    1.068
peak=   -3.955 closest distance to " ND2 ASN A  45 " =    1.357
peak=   -3.921 closest distance to " CA  GLY A 203 " =    2.192
peak=   -3.906 closest distance to " CG1 VAL A 112 " =    2.808
peak=   -3.903 closest distance to " C   HIS A 108 " =    1.066
peak=   -3.899 closest distance to " O   HOH Z 126 " =    1.869
peak=   -3.863 closest distance to " O   HOH Z  43 " =    1.623
peak=   -3.857 closest distance to " O   HOH Z 353 " =    2.158
peak=   -3.856 closest distance to " O   PRO A 198 " =    1.327
peak=   -3.849 closest distance to " CE2 TYR A  30 " =    2.828
peak=   -3.819 closest distance to " O   HOH Z 407 " =    3.197
peak=   -3.818 closest distance to " CE  MET A 105 " =    2.216
peak=   -3.812 closest distance to " O   HOH Z 389 " =    1.973
peak=   -3.812 closest distance to " C   ALA A 158 " =    1.308
peak=   -3.810 closest distance to " O   PRO A 163 " =    1.961
peak=   -3.798 closest distance to " CD  ARG A 139 " =    1.488
peak=   -3.783 closest distance to " OD1 ASN A 187 " =    1.591
peak=   -3.762 closest distance to " CD1 LEU A 101 " =    2.303
peak=   -3.755 closest distance to " O   HOH Z 435 " =    2.773
peak=   -3.753 closest distance to " O   HOH Z 290 " =    1.324
peak=   -3.747 closest distance to " O   HOH Z  10 " =    1.424
peak=   -3.736 closest distance to " O   HOH Z 313 " =    1.947
peak=   -3.732 closest distance to " CD1 PHE A  59 " =    1.850
peak=   -3.721 closest distance to " O   ILE A 109 " =    2.631
peak=   -3.714 closest distance to " C   ASN A 285 " =    2.468
peak=   -3.710 closest distance to " CD1 LEU A 228 " =    2.240
peak=   -3.704 closest distance to " N   GLN A  58 " =    1.726
peak=   -3.693 closest distance to " CZ BARG A 275 " =    1.825
peak=   -3.682 closest distance to " CB  PHE A 192 " =    1.924
peak=   -3.668 closest distance to " OG BSER A 134 " =    1.609
peak=   -3.667 closest distance to " O   HOH Z  11 " =    1.824
peak=   -3.660 closest distance to " O   SER A 135 " =    1.468
peak=   -3.656 closest distance to " CZ  PHE A  59 " =    1.537
peak=   -3.638 closest distance to " CG1 VAL A 197 " =    2.211
peak=   -3.637 closest distance to " NH2AARG A 275 " =    5.475
peak=   -3.637 closest distance to " O   HOH Z 185 " =    2.114
peak=   -3.635 closest distance to " CB  ALA A 291 " =    2.387
peak=   -3.635 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.633 closest distance to " CG  PHE A 283 " =    2.692
peak=   -3.631 closest distance to " O   HOH Z  38 " =    1.581
peak=   -3.631 closest distance to " CB  ASP A  27 " =    2.469
peak=   -3.612 closest distance to " O   HOH Z 152 " =    5.211
peak=   -3.612 closest distance to " CE2 PHE A 218 " =    2.479
peak=   -3.607 closest distance to " OXT GLY A 302 " =    3.345
peak=   -3.603 closest distance to " CZ  TYR A 169 " =    1.657
peak=   -3.598 closest distance to " O   HOH Z 316 " =    1.920
peak=   -3.588 closest distance to " CA  GLY A  98 " =    1.998
peak=   -3.586 closest distance to " OG  SER A  97 " =    2.122
peak=   -3.560 closest distance to " O   VAL A 153 " =    2.218
peak=   -3.559 closest distance to " CB  PRO A 163 " =    2.484
peak=   -3.557 closest distance to " O   HOH Z 388 " =    2.035
peak=   -3.553 closest distance to " O   HOH Z 118 " =    2.983
peak=   -3.535 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.524 closest distance to " O   HOH Z  13 " =    1.506
peak=   -3.511 closest distance to " CB  ASN A  39 " =    2.231
peak=   -3.510 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.509 closest distance to " OD1 ASN A 148 " =    1.634
peak=   -3.509 closest distance to " O   HOH Z 211 " =    1.633
peak=   -3.508 closest distance to " O   VAL A  67 " =    2.670
peak=   -3.502 closest distance to " CB  ALA A 291 " =    2.160
peak=   -3.501 closest distance to " CB  ALA A 248 " =    1.944
peak=   -3.498 closest distance to " O   HOH Z 351 " =    1.488
peak=   -3.494 closest distance to " O   HOH Z 385 " =    1.923
peak=   -3.483 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.482 closest distance to " CB  CYS A 254 " =    2.265
peak=   -3.480 closest distance to " O   HOH Z 198 " =    1.923
peak=   -3.480 closest distance to " O   HOH Z 311 " =    3.584
peak=   -3.477 closest distance to " O   ARG A 145 " =    1.495
peak=   -3.473 closest distance to " OG  SER A  87 " =    1.315
peak=   -3.471 closest distance to " C   LEU A 143 " =    1.280
peak=   -3.470 closest distance to " O   HOH Z 324 " =    2.204
peak=   -3.467 closest distance to " ND2 ASN A 249 " =    1.996
peak=   -3.461 closest distance to " O   HOH Z 417 " =    2.498
peak=   -3.459 closest distance to " NE2 GLN A  88 " =    1.901
peak=   -3.458 closest distance to " CG1 VAL A 250 " =    2.623
peak=   -3.456 closest distance to " OD1 ASP A 171 " =    1.585
peak=   -3.453 closest distance to " O   VAL A 189 " =    2.538
peak=   -3.444 closest distance to " CD2 LEU A 237 " =    2.784
peak=   -3.432 closest distance to " O   HOH Z 417 " =    2.995
peak=   -3.432 closest distance to " O   HOH Z  52 " =    1.249
peak=   -3.432 closest distance to " CD  GLN A  58 " =    1.110
peak=   -3.426 closest distance to " O   HOH Z 168 " =    1.785
peak=   -3.418 closest distance to " OXT GLY A 302 " =    2.873
peak=   -3.417 closest distance to " O   HOH Z 298 " =    1.243
peak=   -3.408 closest distance to " O   HOH Z 234 " =    4.098
peak=   -3.408 closest distance to " OG  SER A  26 " =    1.216
peak=   -3.406 closest distance to " OG  SER A  62 " =    1.614
peak=   -3.405 closest distance to " OD1 ASP A 191 " =    1.427
peak=   -3.404 closest distance to " NH2 ARG A  79 " =    1.856
peak=   -3.402 closest distance to " O   GLY A 211 " =    1.487
peak=   -3.394 closest distance to " CG  TRP A 266 " =    1.693
peak=   -3.388 closest distance to " O   HOH Z 198 " =    1.462
peak=   -3.381 closest distance to " CG  MET A 105 " =    0.990
peak=   -3.379 closest distance to " O   GLY A  80 " =    2.408
peak=   -3.376 closest distance to " O   ALA A 161 " =    1.560
peak=   -3.366 closest distance to " CD  GLN A  88 " =    0.877
peak=   -3.364 closest distance to " O   HOH Z 385 " =    1.910
peak=   -3.354 closest distance to " O   HOH Z 426 " =    1.644
peak=   -3.349 closest distance to " CG  PRO A 163 " =    2.457
peak=   -3.349 closest distance to " O   HOH Z 102 " =    1.674
peak=   -3.347 closest distance to " O   HOH Z 359 " =    3.074
peak=   -3.342 closest distance to " OH  TYR A 214 " =    1.247
peak=   -3.333 closest distance to " CB  ALA A  43 " =    2.404
peak=   -3.333 closest distance to " CD2 LEU A 300 " =    2.955
peak=   -3.329 closest distance to " CD1 LEU A 297 " =    2.407
peak=   -3.328 closest distance to " N   SER A 212 " =    1.909
peak=   -3.327 closest distance to " CB  TRP A  85 " =    2.413
peak=   -3.301 closest distance to " NH1 ARG A  36 " =    1.961
peak=   -3.297 closest distance to " N   ALA A 248 " =    1.526
peak=   -3.295 closest distance to " CB  ASP A 286 " =    2.248
peak=   -3.291 closest distance to " CG  GLU A 152 " =    1.295
peak=   -3.289 closest distance to " N   GLN A 122 " =    1.465
peak=   -3.282 closest distance to " O   HOH Z 166 " =    1.384
peak=   -3.281 closest distance to " O   HOH Z 137 " =    1.534
peak=   -3.281 closest distance to " OD1 ASN A 176 " =    1.170
peak=   -3.278 closest distance to " SG ACYS A 201 " =    1.908
peak=   -3.276 closest distance to " O   HOH Z 137 " =    1.415
peak=   -3.274 closest distance to " O   HOH Z 438 " =    1.302
peak=   -3.274 closest distance to " O   PRO A 243 " =    2.496
peak=   -3.274 closest distance to " O   HOH Z   6 " =    1.573
peak=   -3.274 closest distance to " O   VAL A 174 " =    2.145
peak=   -3.270 closest distance to " O   HOH Z 111 " =    1.238
peak=   -3.265 closest distance to " O   HOH Z  68 " =    2.122
peak=   -3.264 closest distance to " O   HOH Z 317 " =    2.431
peak=   -3.260 closest distance to " CB  ALA A 131 " =    1.931
peak=   -3.254 closest distance to " O   HOH Z  44 " =    2.100
peak=   -3.253 closest distance to " CA  SER A 146 " =    2.300
peak=   -3.246 closest distance to " O   HOH Z  63 " =    1.560
peak=   -3.245 closest distance to " O   HOH Z 352 " =    2.049
peak=   -3.243 closest distance to " CB  ALA A 248 " =    2.387
peak=   -3.235 closest distance to " O   HOH Z  90 " =    1.644
peak=   -3.234 closest distance to " CE  LYS A  76 " =    2.816
peak=   -3.234 closest distance to " OD2 ASP A 171 " =    1.753
peak=   -3.231 closest distance to " O   TYR A  30 " =    2.845
peak=   -3.228 closest distance to " O   SER A  22 " =    2.298
peak=   -3.222 closest distance to " CB  ASP A 132 " =    2.293
peak=   -3.220 closest distance to " CA  GLY A 241 " =    2.259
peak=   -3.218 closest distance to " CZ  PHE A 155 " =    1.353
peak=   -3.217 closest distance to " O   HOH Z  73 " =    2.279
peak=   -3.212 closest distance to " ND2 ASN A  60 " =    1.891
peak=   -3.212 closest distance to " CB  PRO A  54 " =    2.365
peak=   -3.212 closest distance to " O   HOH Z 207 " =    2.071
peak=   -3.210 closest distance to " CE3 TRP A 123 " =    1.316
peak=   -3.209 closest distance to " ND2 ASN A 249 " =    2.196
peak=   -3.207 closest distance to " O   HOH Z 210 " =    1.041
peak=   -3.189 closest distance to " N   GLY A  23 " =    2.190
peak=   -3.186 closest distance to " O   HOH Z  51 " =    1.198
peak=   -3.182 closest distance to " O   ASP A 162 " =    2.234
peak=   -3.182 closest distance to " N   ASP A 171 " =    2.410
peak=   -3.178 closest distance to " OG ASER A 216 " =    0.990
peak=   -3.162 closest distance to " N   THR A 235 " =    1.297
peak=   -3.160 closest distance to " O   ASN A 301 " =    1.506
peak=   -3.159 closest distance to " O   HOH Z 348 " =    1.890
peak=   -3.157 closest distance to " CE3 TRP A 274 " =    2.421
peak=   -3.155 closest distance to " CD  LYS A 289 " =    2.562
peak=   -3.145 closest distance to " ND2 ASN A  69 " =    1.666
peak=   -3.145 closest distance to " CG2 VAL A 189 " =    1.906
peak=   -3.143 closest distance to " CB  ALA A   7 " =    2.059
peak=   -3.135 closest distance to " O   HOH Z 322 " =    1.181
peak=   -3.127 closest distance to " CB  TYR A  15 " =    2.125
peak=   -3.124 closest distance to " O   SER A  12 " =    1.490
peak=   -3.122 closest distance to " CD  ARG A  36 " =    1.875
peak=   -3.121 closest distance to " O   HOH Z 423 " =    2.021
peak=   -3.117 closest distance to " CB  CYS A 201 " =    2.556
peak=   -3.112 closest distance to " O   PHE A 218 " =    1.584
peak=   -3.109 closest distance to " CG  GLU A   2 " =    1.981
peak=   -3.108 closest distance to " O   HOH Z  60 " =    1.993
peak=   -3.108 closest distance to " CG  ARG A 269 " =    2.599
peak=   -3.105 closest distance to " O   HOH Z 409 " =    4.529
peak=   -3.104 closest distance to " O   HOH Z 281 " =    2.734
peak=   -3.099 closest distance to " O   HOH Z 168 " =    1.783
peak=   -3.097 closest distance to " O   HOH Z 252 " =    4.306
peak=   -3.093 closest distance to " O   HOH Z 383 " =    1.045
peak=   -3.088 closest distance to " O   HOH Z 263 " =    3.015
peak=   -3.087 closest distance to " CD2 PHE A  61 " =    2.080
peak=   -3.081 closest distance to " CB  ASP A 132 " =    2.233
peak=   -3.080 closest distance to " CZ AARG A 102 " =    2.381
peak=   -3.075 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.073 closest distance to " C   LEU A 222 " =    0.796
peak=   -3.072 closest distance to " OD2 ASP A 171 " =    2.242
peak=   -3.071 closest distance to " OD1 ASN A 301 " =    1.881
peak=   -3.070 closest distance to " O   HOH Z 346 " =    1.661
peak=   -3.066 closest distance to " CA  TRP A 274 " =    1.544
peak=   -3.065 closest distance to " N   SER A 276 " =    1.189
peak=   -3.064 closest distance to " O   HOH Z  71 " =    1.265
peak=   -3.061 closest distance to " C   MET A 188 " =    1.407
peak=   -3.058 closest distance to " ND2 ASN A 252 " =    1.615
peak=   -3.053 closest distance to " O   HOH Z 150 " =    1.837
peak=   -3.053 closest distance to " SD  MET A 188 " =    2.306
peak=   -3.017 closest distance to " O   HOH Z 111 " =    2.259
peak=   -3.012 closest distance to " N   PHE A  59 " =    2.054
peak=   -3.007 closest distance to " CB  ASP A 286 " =    1.823
peak=   -3.001 closest distance to " O   HOH Z 350 " =    1.890

================= 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    :  0.3943 0.3942   6.173437e+00   6.171549e+00
   1_bss:  0.3846 0.3854   6.164462e+00   6.154859e+00
   1_xyz:  0.2117 0.2396   5.661556e+00   5.769582e+00
   1_adp:  0.1967 0.2470   5.622946e+00   5.802246e+00
   1_occ:  0.1961 0.2471   5.621087e+00   5.801033e+00
   2_bss:  0.1944 0.2455   5.618955e+00   5.798132e+00
   2_xyz:  0.1410 0.1861   5.331466e+00   5.544903e+00
   2_adp:  0.1285 0.1733   5.250338e+00   5.475054e+00
   2_occ:  0.1284 0.1733   5.249870e+00   5.474896e+00
   3_bss:  0.1285 0.1736   5.250384e+00   5.475468e+00
   3_xyz:  0.1125 0.1592   5.145609e+00   5.394353e+00
   3_adp:  0.1106 0.1560   5.127233e+00   5.375647e+00
   3_occ:  0.1104 0.1558   5.126934e+00   5.375646e+00
   4_bss:  0.1104 0.1558   5.126934e+00   5.375646e+00
   4_xyz:  0.1106 0.1555   5.130009e+00   5.375581e+00
   4_adp:  0.1114 0.1552   5.133483e+00   5.375449e+00
   4_occ:  0.1113 0.1552   5.133231e+00   5.375483e+00
   5_bss:  0.1113 0.1552   5.133235e+00   5.375452e+00
   5_xyz:  0.1075 0.1545   5.112967e+00   5.369368e+00
   5_adp:  0.1060 0.1564   5.111756e+00   5.376717e+00
   5_occ:  0.1060 0.1563   5.111671e+00   5.376740e+00
   5_bss:  0.1059 0.1553   5.110226e+00   5.374405e+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:  0.319  30.616  -0.275  -0.701   0.620  -0.000   0.000   0.000
   1_xyz:  0.319  30.616  -0.275  -0.701   0.620  -0.000   0.000   0.000
   1_adp:  0.319  30.616  -0.275  -0.701   0.620  -0.000   0.000   0.000
   1_occ:  0.319  30.616  -0.275  -0.701   0.620  -0.000   0.000   0.000
   2_bss:  0.335  50.411  -1.840  -2.522  -1.415  -0.000  -0.000  -0.000
   2_xyz:  0.335  50.411  -1.840  -2.522  -1.415  -0.000  -0.000  -0.000
   2_adp:  0.335  50.411  -1.840  -2.522  -1.415  -0.000  -0.000  -0.000
   2_occ:  0.335  50.411  -1.840  -2.522  -1.415  -0.000  -0.000  -0.000
   3_bss:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   3_xyz:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   3_adp:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   3_occ:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   4_bss:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   4_xyz:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   4_adp:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   4_occ:  0.326  49.014  -2.078  -2.588  -1.603  -0.000  -0.000  -0.000
   5_bss:  0.326  49.014  -2.170  -2.600  -1.673  -0.000  -0.000  -0.000
   5_xyz:  0.326  49.014  -2.170  -2.600  -1.673  -0.000  -0.000  -0.000
   5_adp:  0.326  49.014  -2.170  -2.600  -1.673  -0.000  -0.000  -0.000
   5_occ:  0.326  49.014  -2.170  -2.600  -1.673  -0.000  -0.000  -0.000
   5_bss:  0.323  49.755  -1.956  -2.396  -1.504  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.689 0.5999  0.7878    46032.814
   1_bss:  42.548 0.6117  0.8021    42803.616
   1_xyz:  23.027 0.8337  1.0110    14841.372
   1_adp:  24.262 0.8203  0.9985    15950.871
   1_occ:  24.238 0.8204  0.9982    15877.312
   2_bss:  24.114 0.8215  0.9373    15730.210
   2_xyz:  17.486 0.8849  0.9804     8784.378
   2_adp:  15.755 0.9005  0.9863     7657.303
   2_occ:  15.747 0.9005  0.9862     7648.142
   3_bss:  15.757 0.9005  0.9797     7663.042
   3_xyz:  14.136 0.9134  0.9853     6387.744
   3_adp:  13.672 0.9174  0.9837     6162.759
   3_occ:  13.668 0.9175  0.9836     6157.947
   4_bss:  13.668 0.9175  0.9836     6157.947
   4_xyz:  13.593 0.9184  0.9822     6135.159
   4_adp:  13.527 0.9191  0.9794     6151.535
   4_occ:  13.526 0.9191  0.9793     6149.030
   5_bss:  13.526 0.9191  0.9772     6148.347
   5_xyz:  13.419 0.9198  0.9781     6078.675
   5_adp:  13.598 0.9184  0.9724     6136.494
   5_occ:  13.598 0.9184  0.9723     6137.763
   5_bss:  13.578 0.9184  0.9786     6091.029
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6466e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6466e-01
   1_xyz:   1.206  0.009  0.081 15.327  0.006  4.109   8.2702e-02
   1_adp:   1.206  0.009  0.081 15.327  0.006  4.109   8.2702e-02
   1_occ:   1.206  0.009  0.081 15.327  0.006  4.109   8.2702e-02
   2_bss:   1.206  0.009  0.081 15.327  0.006  4.109   8.2702e-02
   2_xyz:   0.978  0.006  0.072 14.425  0.004  4.118   5.5560e-02
   2_adp:   0.978  0.006  0.072 14.425  0.004  4.118   5.5560e-02
   2_occ:   0.978  0.006  0.072 14.425  0.004  4.118   5.5560e-02
   3_bss:   0.978  0.006  0.072 14.425  0.004  4.118   5.5560e-02
   3_xyz:   1.096  0.009  0.080 14.970  0.005  4.120   7.0738e-02
   3_adp:   1.096  0.009  0.080 14.970  0.005  4.120   7.0738e-02
   3_occ:   1.096  0.009  0.080 14.970  0.005  4.120   7.0738e-02
   4_bss:   1.096  0.009  0.080 14.970  0.005  4.120   7.0738e-02
   4_xyz:   0.961  0.007  0.071 14.577  0.004  4.121   5.6288e-02
   4_adp:   0.961  0.007  0.071 14.577  0.004  4.121   5.6288e-02
   4_occ:   0.961  0.007  0.071 14.577  0.004  4.121   5.6288e-02
   5_bss:   0.961  0.007  0.071 14.577  0.004  4.121   5.6288e-02
   5_xyz:   1.092  0.009  0.080 15.016  0.005  4.111   7.0761e-02
   5_adp:   1.092  0.009  0.080 15.016  0.005  4.111   7.0761e-02
   5_occ:   1.092  0.009  0.080 15.016  0.005  4.111   7.0761e-02
   5_bss:   1.092  0.009  0.080 15.016  0.005  4.111   7.0761e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3997e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3997e-01
   1_xyz:   8.623  0.055  0.365 85.363  0.044  2.251   7.4900e-02
   1_adp:   8.623  0.055  0.365 85.363  0.044  2.251   7.4900e-02
   1_occ:   8.623  0.055  0.365 85.363  0.044  2.251   7.4900e-02
   2_bss:   8.623  0.055  0.365 85.363  0.044  2.251   7.4900e-02
   2_xyz:   8.022  0.034  0.222 83.248  0.037  2.331   4.3302e-02
   2_adp:   8.022  0.034  0.222 83.248  0.037  2.331   4.3302e-02
   2_occ:   8.022  0.034  0.222 83.248  0.037  2.331   4.3302e-02
   3_bss:   8.022  0.034  0.222 83.248  0.037  2.331   4.3302e-02
   3_xyz:   7.750  0.041  0.256 84.774  0.038  2.257   6.0003e-02
   3_adp:   7.750  0.041  0.256 84.774  0.038  2.257   6.0003e-02
   3_occ:   7.750  0.041  0.256 84.774  0.038  2.257   6.0003e-02
   4_bss:   7.750  0.041  0.256 84.774  0.038  2.257   6.0003e-02
   4_xyz:   7.417  0.039  0.214 83.693  0.038  2.337   3.9484e-02
   4_adp:   7.417  0.039  0.214 83.693  0.038  2.337   3.9484e-02
   4_occ:   7.417  0.039  0.214 83.693  0.038  2.337   3.9484e-02
   5_bss:   7.417  0.039  0.214 83.693  0.038  2.337   3.9484e-02
   5_xyz:   7.241  0.041  0.250 84.318  0.039  2.205   5.5682e-02
   5_adp:   7.241  0.041  0.250 84.318  0.039  2.205   5.5682e-02
   5_occ:   7.241  0.041  0.250 84.318  0.039  2.205   5.5682e-02
   5_bss:   7.241  0.041  0.250 84.318  0.039  2.205   5.5682e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  74.73   0.00  16.73  74.73   0.00  12.77  61.72   5.42  38.30
   1_occ:  74.73   0.00  16.73  74.73   0.00  12.77  61.72   5.42  38.30
   2_bss:  74.73   0.00  16.73  74.73   0.00  12.77  61.72   5.42  38.30
   2_xyz:  74.73   0.00  16.73  74.73   0.00  12.77  61.72   5.42  38.30
   2_adp:  79.75   1.01  17.33  79.75   1.01  12.99  79.04   6.03  40.99
   2_occ:  79.75   1.01  17.33  79.75   1.01  12.99  79.04   6.03  40.99
   3_bss:  79.75   1.01  17.33  79.75   1.01  12.99  79.04   6.03  40.99
   3_xyz:  79.75   1.01  17.33  79.75   1.01  12.99  79.04   6.03  40.99
   3_adp:  85.26   1.24  17.00  85.26   1.24  12.89  81.96   3.59  39.37
   3_occ:  85.26   1.24  17.00  85.26   1.24  12.89  81.96   3.59  39.37
   4_bss:  85.26   1.24  17.00  85.26   1.24  12.89  81.96   3.59  39.37
   4_xyz:  85.26   1.24  17.00  85.26   1.24  12.89  81.96   3.59  39.37
   4_adp:  83.95   2.11  16.57  83.95   2.11  12.75  81.63   5.70  37.35
   4_occ:  83.95   2.11  16.57  83.95   2.11  12.75  81.63   5.70  37.35
   5_bss:  83.95   2.11  16.57  83.95   2.11  12.75  81.63   5.70  37.35
   5_xyz:  83.95   2.11  16.57  83.95   2.11  12.75  81.63   5.70  37.35
   5_adp:  94.23   0.67  16.97  94.23   0.67  12.80  84.35   6.40  39.68
   5_occ:  94.23   0.67  16.97  94.23   0.67  12.80  84.35   6.40  39.68
   5_bss:  94.20   0.65  16.95  94.20   0.65  12.78  84.32   6.38  39.65
------------------------------------------------------------------------
 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:    1.447    0.016    0.395
   1_adp:    1.447    0.016    0.395
   1_occ:    1.447    0.016    0.395
   2_bss:    1.447    0.016    0.395
   2_xyz:    0.927    0.044    0.472
   2_adp:    0.927    0.044    0.472
   2_occ:    0.927    0.044    0.472
   3_bss:    0.927    0.044    0.472
   3_xyz:    0.941    0.032    0.513
   3_adp:    0.941    0.032    0.513
   3_occ:    0.941    0.032    0.513
   4_bss:    0.941    0.032    0.513
   4_xyz:    1.014    0.031    0.523
   4_adp:    1.014    0.031    0.523
   4_occ:    1.014    0.031    0.523
   5_bss:    1.014    0.031    0.523
   5_xyz:    1.102    0.057    0.534
   5_adp:    1.102    0.057    0.534
   5_occ:    1.102    0.057    0.534
   5_bss:    1.102    0.057    0.534
------------------------------------------------------------------------

CPU time actual refinement: 338.48


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/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_1003/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1003/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.34 
  Macro-tasks:
    bulk solvent and scale       = 35.95  
    individual site refinement   = 141.36 
    weights calculation          = 30.20  
    collect and process          = 6.60   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.23 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 110.89 
    alpha_beta                      = 8.08   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 118.88 
    fmodel                         = 6.53   
    r_factors                      = 0.19   
    phase_errors                   = 10.96  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 258.81 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.808 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    639 calls, 110.45 s
gradients_fft:          584 calls, 105.68 s

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

# Date 2008-01-16 Time 06:11:24 PST -0800 (1200492684.55 s)
Start R-work = 0.3943, R-free = 0.3942 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.3846, R-free = 0.3854
Final R-work = 0.1059, R-free = 0.1553