# Date 2008-01-16 Time 04:56:19 PST -0800 (1200488179.17 s)
#phil __OFF__

Command line arguments: "../526.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17271
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 526

-------------------------------------------------------------------------------
  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: (69.8988, 46.4607, 88.1178, 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: (69.8988, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.98226
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9823

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: (69.8988, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.98226
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2416 [2156/2180]  1937   219  10.2%
  bin  2:  4.2416 -  3.3793 [2063/2083]  1858   205   9.9%
  bin  3:  3.3793 -  2.9558 [2047/2066]  1845   202   9.9%
  bin  4:  2.9558 -  2.6872 [2020/2050]  1817   203  10.0%
  bin  5:  2.6872 -  2.4956 [2000/2019]  1797   203  10.2%
  bin  6:  2.4956 -  2.3490 [2018/2043]  1814   204  10.1%
  bin  7:  2.3490 -  2.2318 [1992/2020]  1794   198   9.9%
  bin  8:  2.2318 -  2.1349 [1977/2013]  1781   196   9.9%
  bin  9:  2.1349 -  2.0529 [1967/2009]  1772   195   9.9%
  bin 10:  2.0529 -  1.9823 [1349/2037]  1215   134   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/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: 0.15 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:
        1.50 -     2.18: 11
        2.18 -     2.86: 1151
        2.86 -     3.54: 4414
        3.54 -     4.22: 9216
        4.22 -     4.90: 13456
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.498 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.647 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.721 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.947 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28243 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_526/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/model_refine_001.geo

CPU time processing inputs: 9.02


============================ 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 = 69.89875 46.4607 88.1178 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: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3871   r_free= 0.3834   ksol= 0.00   Bsol= 0.00   scale= 0.939    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.174473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.3110 0.2972      6.4411      6.3325|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.3029 0.3330        6.58      6.6159|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.3432 0.3140      6.5224      6.4884|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.3688 0.4047       6.391      6.4471|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.4088 0.3348      6.2474      6.1686|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.3994 0.4591      6.1415      6.1183|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.4082 0.3835      6.1245      6.0272|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.4412 0.4385      6.1234      6.1303|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.4291 0.4520      6.0332      6.0799|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.4571 0.4099      6.0476      5.9706|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.4622 0.4586       5.994      6.0034|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.4614 0.3846       5.928      5.9182|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.4467 0.4861      5.8198      5.7874|
| 14:  2.0317 -  1.9823 0.54    703   83 0.4459 0.4297      5.8245      5.7165|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7308  1402   154  0.79  25.88   0.85     0.82      43661.84|
|  2:  4.7308 -  3.7746  1349   152  0.81  25.66   0.95     0.90      62031.47|
|  3:  3.7746 -  3.3033  1304   144  0.74  31.52   0.96     0.90      65972.87|
|  4:  3.3033 -  3.0039  1321   149  0.69  36.64   0.95     0.85      59978.40|
|  5:  3.0039 -  2.7901  1298   146  0.63  41.79   0.96     0.80      47361.84|
|  6:  2.7901 -  2.6265  1304   139  0.61  43.27   0.95     0.78      42026.62|
|  7:  2.6265 -  2.4956  1276   148  0.60  43.88   0.97     0.77      39042.76|
|  8:  2.4956 -  2.3874  1297   142  0.59  45.30   0.94     0.77      36839.63|
|  9:  2.3874 -  2.2958  1265   139  0.58  45.99   0.99     0.77      34803.25|
| 10:  2.2958 -  2.2168  1309   145  0.56  47.27   0.98     0.78      32562.49|
| 11:  2.2168 -  2.1477  1257   143  0.54  48.74   0.96     0.81      33040.51|
| 12:  2.1477 -  2.0865  1277   141  0.53  49.62   0.99     0.79      30307.28|
| 13:  2.0865 -  2.0317  1268   134  0.51  51.34   0.97     0.75      26917.69|
| 14:  2.0317 -  1.9823   703    83  0.53  49.93   1.03     0.71      22048.73|
|alpha:            min =        0.71 max =            0.90 mean =         0.80|
|beta:             min =    22048.73 max =        65972.87 mean =     42005.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.96 mean =        41.45|
|phase err.(test): min =        0.00 max =           89.96 mean =        41.54|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.093810              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.138   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.989300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.861   (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 |  1.498 -  1.838:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.838 -  2.179:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.179 -  2.519:       31 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.519 -  2.859:     1120 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.859 -  3.199:     1925 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.199 -  3.539:     2489 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.539 -  3.879:     4642 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.879 -  4.220:     4574 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.220 -  4.560:     6133 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.560 -  4.900:     7323 |
|-----------------------------------------------------------------------------|
|-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 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.498 |       0.292 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    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: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3871   r_free= 0.3834   ksol= 0.00   Bsol= 0.00   scale= 0.939    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.174473                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3728   r_free= 0.3700   ksol= 0.32   Bsol= 41.94   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-0.39,4.11,-0.00,0.00,0.00); trace/3= 0.21                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.156725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.890072              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.992   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.556409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.678   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3728      final r-factor (work) = 0.2187          |
| start r-factor (free) = 0.3700      final r-factor (free) = 0.2494          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2906 = 5.89 * 0.50 * 6.1528 + 1.00 * 0.1705                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4503 = 5.89 * 0.50 * 5.8947 + 1.00 * 0.0901                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2187      final r-factor (work) = 0.1979          |
| start r-factor (free) = 0.2494      final r-factor (free) = 0.2576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2862 = 0.56 * 1.00 * 5.8947 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1398 = 0.56 * 1.00 * 5.6223 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.91   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    86.91   17.55    None  None   None       |
|    Sol.    : 438    0      2.31    86.91   41.14    None  None   None       |
|    Mac.    : 2385   0      0.00    70.91   13.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.691:  721   |   5:    43.456 -  52.147:  108        |
|      1:     8.691 -  17.382: 1223   |   6:    52.147 -  60.838:   76        |
|      2:    17.382 -  26.074:  374   |   7:    60.838 -  69.530:   43        |
|      3:    26.074 -  34.765:  149   |   8:    69.530 -  78.221:   10        |
|      4:    34.765 -  43.456:  115   |   9:    78.221 -  86.912:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1979 r_free = 0.2576             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1978 r_free = 0.2571             target_work(ml) = 5.639         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1978   r_free= 0.2571   ksol= 0.32   Bsol= 41.94   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-0.39,4.11,-0.00,0.00,0.00); trace/3= 0.21                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.639014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1946   r_free= 0.2544   ksol= 0.33   Bsol= 63.22   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.00,0.64,-0.00,0.00,0.00); trace/3= -1.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.631425                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.509838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.955   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.210994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.548  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1946      final r-factor (work) = 0.1488          |
| start r-factor (free) = 0.2544      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1583 = 2.51 * 0.50 * 5.6326 + 1.00 * 0.0899                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9875 = 2.51 * 0.50 * 5.5241 + 1.00 * 0.0552                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1488      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1770 = 0.21 * 1.00 * 5.5241 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1415 = 0.21 * 1.00 * 5.3697 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.39   17.13    None  None   None       |
|    all(noH): 2823   0      0.00    84.39   17.13    None  None   None       |
|    Sol.    : 438    0      5.10    84.39   40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    68.94   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.439:  641   |   5:    42.195 -  50.633:  101        |
|      1:     8.439 -  16.878: 1350   |   6:    50.633 -  59.072:   87        |
|      2:    16.878 -  25.317:  341   |   7:    59.072 -  67.511:   34        |
|      3:    25.317 -  33.756:  129   |   8:    67.511 -  75.950:   13        |
|      4:    33.756 -  42.195:  123   |   9:    75.950 -  84.389:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1883             target_work(ml) = 5.338         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1419 r_free = 0.1882             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1882   ksol= 0.33   Bsol= 63.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.08,-2.00,0.64,-0.00,0.00,0.00); trace/3= -1.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.336600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1418   r_free= 0.1877   ksol= 0.33   Bsol= 60.58   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.25,-0.08,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.334080                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.337831              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.499  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.341400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.451  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1877      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0143 = 3.34 * 0.50 * 5.3682 + 1.00 * 0.0552                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8461 = 3.34 * 0.50 * 5.2602 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8042 = 0.34 * 1.00 * 5.2602 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7756 = 0.34 * 1.00 * 5.1753 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    82.37   17.03    None  None   None       |
|    all(noH): 2823   0      0.78    82.37   17.03    None  None   None       |
|    Sol.    : 438    0      5.78    82.37   40.19    None  None   None       |
|    Mac.    : 2385   0      0.78    75.51   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:     0.782 -   8.941:  791   |   5:    41.575 -  49.734:   91        |
|      1:     8.941 -  17.099: 1237   |   6:    49.734 -  57.893:   92        |
|      2:    17.099 -  25.258:  295   |   7:    57.893 -  66.051:   44        |
|      3:    25.258 -  33.417:  137   |   8:    66.051 -  74.210:   17        |
|      4:    33.417 -  41.575:  112   |   9:    74.210 -  82.369:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1595             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1155 r_free = 0.1595             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1155   r_free= 0.1595   ksol= 0.33   Bsol= 60.58   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.25,-0.08,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1596   ksol= 0.33   Bsol= 60.58   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.36,-0.35,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164911                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.580919              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.782  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.461056              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.146  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7460 = 2.58 * 0.50 * 5.1754 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7110 = 2.58 * 0.50 * 5.1505 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3833 = 0.46 * 1.00 * 5.1505 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3783 = 0.46 * 1.00 * 5.1389 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    81.02   16.87    None  None   None       |
|    all(noH): 2823   0      0.68    81.02   16.87    None  None   None       |
|    Sol.    : 438    0      5.23    80.38   39.74    None  None   None       |
|    Mac.    : 2385   0      0.68    81.02   12.66    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.682 -   8.716:  782   |   5:    40.851 -  48.885:   95        |
|      1:     8.716 -  16.750: 1232   |   6:    48.885 -  56.919:   81        |
|      2:    16.750 -  24.784:  297   |   7:    56.919 -  64.953:   54        |
|      3:    24.784 -  32.817:  146   |   8:    64.953 -  72.986:   18        |
|      4:    32.817 -  40.851:  108   |   9:    72.986 -  81.020:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1568             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1568             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1568   ksol= 0.33   Bsol= 60.58   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-2.36,-0.35,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138573                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1567   ksol= 0.33   Bsol= 60.58   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.23,-0.27,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138563                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.532107              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.974  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.942760              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.084  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5712 = 2.53 * 0.50 * 5.1393 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5644 = 2.53 * 0.50 * 5.1331 + 1.00 * 0.0657                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1091      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8482 = 0.94 * 1.00 * 5.1331 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8466 = 0.94 * 1.00 * 5.1306 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.44    86.86   16.80    None  None   None       |
|    all(noH): 2823   0      0.44    86.86   16.80    None  None   None       |
|    Sol.    : 438    0      5.57    81.92   39.96    None  None   None       |
|    Mac.    : 2385   0      0.44    86.86   12.55    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:     0.441 -   9.083:  927   |   5:    43.653 -  52.295:   99        |
|      1:     9.083 -  17.726: 1168   |   6:    52.295 -  60.938:   71        |
|      2:    17.726 -  26.368:  261   |   7:    60.938 -  69.580:   42        |
|      3:    26.368 -  35.010:  124   |   8:    69.580 -  78.222:   13        |
|      4:    35.010 -  43.653:  112   |   9:    78.222 -  86.865:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1571             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1570             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1570   ksol= 0.33   Bsol= 60.58   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.23,-0.27,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132783                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.0988 0.1277      5.4003      5.5523|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.0841 0.1124       5.433       5.631|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.1029 0.1516      5.4599      5.8522|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.1171 0.1657      5.4245      5.5942|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.1280 0.1600      5.3066      5.5317|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.1178 0.2014      5.1975      5.5149|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.1256 0.1612      5.1672      5.3107|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.1107 0.1602      5.0583      5.3071|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.1122 0.1869      5.0115      5.3274|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.1103 0.1649      4.9388      5.1737|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.1074 0.1823      4.9188      5.2605|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.1156 0.1663      4.8976      5.2231|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.1036 0.1776      4.7475      5.0161|
| 14:  2.0317 -  1.9823 0.54    703   83 0.0883 0.1591      4.5862      4.8824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7308  1402   154  0.94   9.56   0.97     0.94       7661.97|
|  2:  4.7308 -  3.7746  1349   152  0.95   7.97   1.01     1.00       9293.90|
|  3:  3.7746 -  3.3033  1304   144  0.93  11.17   1.02     1.02      10126.81|
|  4:  3.3033 -  3.0039  1321   149  0.92  13.34   1.01     0.98       9902.72|
|  5:  3.0039 -  2.7901  1298   146  0.91  15.44   1.00     0.98       8150.68|
|  6:  2.7901 -  2.6265  1304   139  0.90  16.39   0.98     0.95       7130.06|
|  7:  2.6265 -  2.4956  1276   148  0.90  15.63   0.98     0.95       6287.16|
|  8:  2.4956 -  2.3874  1297   142  0.91  15.08   0.99     0.96       5365.61|
|  9:  2.3874 -  2.2958  1265   139  0.91  14.97   0.99     0.95       4827.68|
| 10:  2.2958 -  2.2168  1309   145  0.90  15.80   1.00     0.96       4355.35|
| 11:  2.2168 -  2.1477  1257   143  0.90  15.97   0.98     0.95       4320.94|
| 12:  2.1477 -  2.0865  1277   141  0.90  16.23   1.00     0.99       4138.96|
| 13:  2.0865 -  2.0317  1268   134  0.91  15.71   0.98     0.95       3191.92|
| 14:  2.0317 -  1.9823   703    83  0.93  12.41   0.97     0.94       2250.70|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2250.70 max =        10126.81 mean =      6385.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1570   ksol= 0.33   Bsol= 60.57   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.06,-0.11,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132629                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1570   ksol= 0.33   Bsol= 60.57   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.06,-0.11,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132629                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.0985 0.1277      5.3982      5.5521|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.0842 0.1125      5.4338      5.6316|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.1029 0.1517      5.4604      5.8525|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.1171 0.1656      5.4244      5.5941|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.1280 0.1599      5.3062       5.531|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.1177 0.2014      5.1973      5.5148|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.1256 0.1612      5.1671      5.3106|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.1107 0.1602      5.0584      5.3071|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.1121 0.1869      5.0115      5.3276|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.1103 0.1648      4.9388      5.1738|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.1074 0.1822      4.9187        5.26|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.1156 0.1661      4.8975      5.2227|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.1035 0.1777      4.7473      5.0165|
| 14:  2.0317 -  1.9823 0.54    703   83 0.0883 0.1590      4.5861       4.882|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.7308  1402   154  0.94   9.53   0.97     0.94       7633.71|
|  2:  4.7308 -  3.7746  1349   152  0.95   7.98   1.01     1.00       9292.55|
|  3:  3.7746 -  3.3033  1304   144  0.93  11.18   1.03     1.02      10137.05|
|  4:  3.3033 -  3.0039  1321   149  0.92  13.34   1.01     0.99       9899.87|
|  5:  3.0039 -  2.7901  1298   146  0.91  15.44   1.00     0.98       8146.27|
|  6:  2.7901 -  2.6265  1304   139  0.90  16.39   0.98     0.96       7125.37|
|  7:  2.6265 -  2.4956  1276   148  0.90  15.63   0.99     0.96       6285.96|
|  8:  2.4956 -  2.3874  1297   142  0.91  15.09   1.00     0.97       5366.21|
|  9:  2.3874 -  2.2958  1265   139  0.91  14.97   1.00     0.96       4828.48|
| 10:  2.2958 -  2.2168  1309   145  0.90  15.80   1.00     0.97       4354.63|
| 11:  2.2168 -  2.1477  1257   143  0.90  15.97   0.99     0.95       4318.93|
| 12:  2.1477 -  2.0865  1277   141  0.90  16.23   1.01     1.00       4138.36|
| 13:  2.0865 -  2.0317  1268   134  0.91  15.70   0.99     0.96       3189.84|
| 14:  2.0317 -  1.9823   703    83  0.93  12.40   0.98     0.95       2248.06|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2248.06 max =        10137.05 mean =      6382.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.97|
|phase err.(test): min =        0.00 max =           89.91 mean =        13.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.43    86.85   16.79    None  None   None       |
|    all(noH): 2823   0      0.43    86.85   16.79    None  None   None       |
|    Sol.    : 438    0      5.55    81.90   39.94    None  None   None       |
|    Mac.    : 2385   0      0.43    86.85   12.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.427 -   9.070:  927   |   5:    43.639 -  52.282:   99        |
|      1:     9.070 -  17.712: 1168   |   6:    52.282 -  60.924:   71        |
|      2:    17.712 -  26.354:  261   |   7:    60.924 -  69.566:   42        |
|      3:    26.354 -  34.997:  124   |   8:    69.566 -  78.209:   13        |
|      4:    34.997 -  43.639:  112   |   9:    78.209 -  86.851:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.439 - 4.816
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 289
   mapped sites are within: 0.721 - 4.816

peak=    5.608 closest distance to " NE2 GLN A  11 " =    1.170
peak=    5.556 closest distance to " NH2 ARG A  56 " =    2.184
peak=    5.544 closest distance to " O   HOH Z 142 " =    1.871
peak=    5.315 closest distance to " CG  PRO A  54 " =    1.310
peak=    4.929 closest distance to " CB  ARG A 275 " =    0.937
peak=    4.914 closest distance to " O   HOH Z 126 " =    1.884
peak=    4.861 closest distance to " CB  GLN A 223 " =    1.441
peak=    4.824 closest distance to " CB  GLN A 183 " =    1.227
peak=    4.796 closest distance to " O   HOH Z 232 " =    2.336
peak=    4.739 closest distance to " CB  ARG A  79 " =    1.446
peak=    4.686 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.638 closest distance to " O   HOH Z 369 " =    2.192
peak=    4.636 closest distance to " CB  ARG A 190 " =    1.660
peak=    4.579 closest distance to " O   HOH Z 287 " =    2.226
peak=    4.551 closest distance to " O   HOH Z  78 " =    1.805
peak=    4.540 closest distance to " CB  PRO A  54 " =    0.956
peak=    4.495 closest distance to " ND2 ASN A 187 " =    1.512
peak=    4.488 closest distance to " O   HOH Z 298 " =    1.931
peak=    4.484 closest distance to " CZ  PHE A 218 " =    1.077
peak=    4.388 closest distance to " CB  VAL A 265 " =    1.286
peak=    4.368 closest distance to " O   HOH Z 427 " =    2.963
peak=    4.352 closest distance to " CG  TRP A 179 " =    2.176
peak=    4.302 closest distance to " O   HOH Z 188 " =    2.899
peak=    4.300 closest distance to " O   HOH Z  15 " =    2.121
peak=    4.235 closest distance to " CG2 VAL A 257 " =    0.854
peak=    4.187 closest distance to " O   HOH Z 158 " =    3.134
peak=    4.173 closest distance to " CB  ASN A 148 " =    1.429
peak=    4.133 closest distance to " CD  ARG A 159 " =    0.735
peak=    4.118 closest distance to " CB  SER A  63 " =    1.162
peak=    4.117 closest distance to " CG  PRO A 198 " =    1.249
peak=    4.108 closest distance to " CA  TYR A  30 " =    0.944
peak=    4.095 closest distance to " C   PRO A 198 " =    1.481
peak=    4.091 closest distance to " CD2 TRP A 179 " =    1.307
peak=    4.085 closest distance to " O   HOH Z 133 " =    2.766
peak=    4.079 closest distance to " O   HOH Z 406 " =    1.683
peak=    4.077 closest distance to " O   SER A  87 " =    2.236
peak=    4.077 closest distance to " O   HOH Z 313 " =    2.049
peak=    4.076 closest distance to " CB  GLU A 152 " =    1.235
peak=    4.067 closest distance to " O   HOH Z  61 " =    1.683
peak=    4.061 closest distance to " O   HOH Z 272 " =    1.818
peak=    4.020 closest distance to " OD1 ASN A  69 " =    2.590
peak=    3.972 closest distance to " CB  TRP A 266 " =    1.079
peak=    3.966 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.930 closest distance to " CA  ASN A 215 " =    1.082
peak=    3.925 closest distance to " NZ  LYS A 117 " =    3.198
peak=    3.925 closest distance to " CB  TYR A 169 " =    0.792
peak=    3.922 closest distance to " O   HOH Z 346 " =    1.632
peak=    3.909 closest distance to " O   HOH Z 265 " =    2.205
peak=    3.907 closest distance to " O   HOH Z   1 " =    1.999
peak=    3.906 closest distance to " O   HOH Z 419 " =    2.186
peak=    3.888 closest distance to " O   HOH Z 180 " =    2.190
peak=    3.887 closest distance to " O   HOH Z 250 " =    1.470
peak=    3.878 closest distance to " CB  GLU A 277 " =    3.622
peak=    3.878 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.877 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.873 closest distance to " OG ASER A 258 " =    3.110
peak=    3.865 closest distance to " CB  ASP A 140 " =    1.039
peak=    3.859 closest distance to " O   HOH Z 353 " =    2.634
peak=    3.849 closest distance to " CB  ASN A 142 " =    1.011
peak=    3.836 closest distance to " O   HOH Z 214 " =    2.170
peak=    3.823 closest distance to " O   HOH Z 234 " =    3.650
peak=    3.822 closest distance to " OG BSER A 164 " =    2.311
peak=    3.816 closest distance to " O   HOH Z 327 " =    1.512
peak=    3.801 closest distance to " CB  ASN A 110 " =    1.103
peak=    3.797 closest distance to " NH1AARG A 145 " =    1.250
peak=    3.792 closest distance to " O   HOH Z 371 " =    1.851
peak=    3.791 closest distance to " ND2 ASN A 249 " =    0.872
peak=    3.778 closest distance to " CA  ARG A 195 " =    1.186
peak=    3.773 closest distance to " CG  PRO A 243 " =    1.045
peak=    3.772 closest distance to " O   HOH Z 203 " =    1.787
peak=    3.769 closest distance to " O   HOH Z  53 " =    2.539
peak=    3.761 closest distance to " O   HOH Z 368 " =    2.159
peak=    3.755 closest distance to " CB  SER A 212 " =    1.158
peak=    3.740 closest distance to " CZ3 TRP A 266 " =    1.136
peak=    3.711 closest distance to " O   HOH Z 172 " =    3.037
peak=    3.705 closest distance to " O   HOH Z 392 " =    3.054
peak=    3.684 closest distance to " CA  SER A  87 " =    1.039
peak=    3.681 closest distance to " O   HOH Z 389 " =    1.847
peak=    3.679 closest distance to " CB  ASN A  39 " =    0.913
peak=    3.678 closest distance to " CG  LEU A 167 " =    1.284
peak=    3.673 closest distance to " O   ASN A  74 " =    1.438
peak=    3.668 closest distance to " N   ASN A  39 " =    1.288
peak=    3.665 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.662 closest distance to " CB  GLU A  46 " =    0.992
peak=    3.661 closest distance to " CD  ARG A  66 " =    2.421
peak=    3.656 closest distance to " CA  ARG A  36 " =    1.026
peak=    3.641 closest distance to " CG2 ILE A 120 " =    1.184
peak=    3.638 closest distance to " O   HOH Z 394 " =    3.927
peak=    3.631 closest distance to " O   HOH Z  10 " =    1.811
peak=    3.629 closest distance to " O   HOH Z 411 " =    3.829
peak=    3.625 closest distance to " CB  GLU A 128 " =    0.936
peak=    3.624 closest distance to " O   HOH Z  40 " =    1.701
peak=    3.621 closest distance to " O   HOH Z 294 " =    1.502
peak=    3.621 closest distance to " O   HOH Z 359 " =    1.559
peak=    3.621 closest distance to " CB  PRO A  90 " =    1.141
peak=    3.618 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.616 closest distance to " CB  TYR A 116 " =    0.798
peak=    3.601 closest distance to " O   HOH Z 337 " =    3.580
peak=    3.596 closest distance to " O   HOH Z 248 " =    1.552
peak=    3.586 closest distance to " O   HOH Z 423 " =    1.853
peak=    3.577 closest distance to " CB  GLN A  88 " =    1.205
peak=    3.572 closest distance to " O  BHOH Z 338 " =    2.326
peak=    3.572 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.572 closest distance to " CZ  PHE A  38 " =    1.239
peak=    3.571 closest distance to " CB  SER A   3 " =    1.309
peak=    3.570 closest distance to " O   HOH Z 132 " =    2.500
peak=    3.567 closest distance to " CB  ARG A 139 " =    1.018
peak=    3.567 closest distance to " O   HOH Z 425 " =    1.976
peak=    3.559 closest distance to " CD  ARG A 269 " =    0.904
peak=    3.559 closest distance to " O   HOH Z 209 " =    2.275
peak=    3.554 closest distance to " O   HOH Z   3 " =    1.933
peak=    3.548 closest distance to " O   HOH Z 261 " =    1.926
peak=    3.546 closest distance to " O   HOH Z 285 " =    2.173
peak=    3.537 closest distance to " O   HOH Z 193 " =    2.045
peak=    3.535 closest distance to " CD2 LEU A 297 " =    0.894
peak=    3.529 closest distance to " N   TYR A 116 " =    1.573
peak=    3.527 closest distance to " CA  ASP A 124 " =    0.724
peak=    3.525 closest distance to " N   PHE A 130 " =    1.276
peak=    3.525 closest distance to " CA  ALA A 233 " =    1.023
peak=    3.518 closest distance to " CA  THR A 264 " =    0.906
peak=    3.515 closest distance to " O   HOH Z 371 " =    2.963
peak=    3.513 closest distance to " NE2 HIS A 207 " =    1.244
peak=    3.511 closest distance to " O   HOH Z 261 " =    1.731
peak=    3.508 closest distance to " O   HOH Z 193 " =    1.767
peak=    3.503 closest distance to " CA  ALA A 158 " =    1.237
peak=    3.501 closest distance to " CB  THR A  31 " =    1.602
peak=    3.491 closest distance to " O   HOH Z 128 " =    2.213
peak=    3.481 closest distance to " O   HOH Z 403 " =    1.511
peak=    3.476 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.473 closest distance to " O   HOH Z 402 " =    1.395
peak=    3.472 closest distance to " CB  ASN A 215 " =    1.107
peak=    3.466 closest distance to " O   HOH Z 421 " =    2.096
peak=    3.459 closest distance to " CD  ARG A  66 " =    2.361
peak=    3.453 closest distance to " ND1 HIS A  86 " =    1.794
peak=    3.441 closest distance to " O   HOH Z 258 " =    2.208
peak=    3.439 closest distance to " CG2AVAL A  72 " =    1.618
peak=    3.428 closest distance to " CG  MET A 185 " =    1.158
peak=    3.428 closest distance to " O   HOH Z 365 " =    2.808
peak=    3.426 closest distance to " CG  GLU A  37 " =    0.948
peak=    3.424 closest distance to " O   HOH Z  66 " =    2.010
peak=    3.422 closest distance to " O   HOH Z 329 " =    4.096
peak=    3.418 closest distance to " CA  ARG A 159 " =    1.246
peak=    3.416 closest distance to " O   HOH Z 245 " =    1.298
peak=    3.415 closest distance to " O   HOH Z 213 " =    2.054
peak=    3.413 closest distance to " OG BSER A  99 " =    2.308
peak=    3.409 closest distance to " CB  SER A  26 " =    1.747
peak=    3.408 closest distance to " O   HOH Z  21 " =    1.753
peak=    3.405 closest distance to " CB  ALA A  34 " =    1.024
peak=    3.403 closest distance to " O   HOH Z 286 " =    2.345
peak=    3.390 closest distance to " O   HOH Z 380 " =    1.679
peak=    3.381 closest distance to " O   HOH Z 116 " =    1.771
peak=    3.381 closest distance to " O   HOH Z 280 " =    2.998
peak=    3.380 closest distance to " CG2 THR A 221 " =    1.088
peak=    3.379 closest distance to " O   HOH Z 147 " =    1.808
peak=    3.372 closest distance to " O   HOH Z 126 " =    1.540
peak=    3.368 closest distance to " CG1 VAL A 153 " =    1.013
peak=    3.362 closest distance to " O   HOH Z 405 " =    1.133
peak=    3.360 closest distance to " O   HOH Z 171 " =    4.101
peak=    3.359 closest distance to " CB  GLN A  89 " =    1.398
peak=    3.355 closest distance to " CA  VAL A 125 " =    1.106
peak=    3.351 closest distance to " O   HOH Z   9 " =    1.264
peak=    3.351 closest distance to " CB  ALA A   1 " =    4.816
peak=    3.349 closest distance to " NH2BARG A 145 " =    2.115
peak=    3.346 closest distance to " CD1 LEU A 300 " =    1.148
peak=    3.343 closest distance to " O   HOH Z  40 " =    2.076
peak=    3.337 closest distance to " CA  TYR A 116 " =    1.315
peak=    3.334 closest distance to " N   GLN A 278 " =    1.423
peak=    3.333 closest distance to " CD  LYS A 166 " =    1.251
peak=    3.333 closest distance to " O   HOH Z 305 " =    3.517
peak=    3.332 closest distance to " OG BSER A 134 " =    3.124
peak=    3.331 closest distance to " O   HOH Z 417 " =    3.505
peak=    3.317 closest distance to " O   HOH Z 291 " =    1.500
peak=    3.316 closest distance to " CE1 TYR A 186 " =    1.340
peak=    3.315 closest distance to " O   HOH Z  59 " =    1.691
peak=    3.314 closest distance to " O   HOH Z  44 " =    2.796
peak=    3.313 closest distance to " CD1 ILE A 106 " =    0.857
peak=    3.310 closest distance to " O   HOH Z 325 " =    2.432
peak=    3.310 closest distance to " O   HOH Z   9 " =    3.296
peak=    3.309 closest distance to " CA  GLU A  46 " =    0.854
peak=    3.306 closest distance to " CB  TRP A 179 " =    1.408
peak=    3.305 closest distance to " O   HOH Z  61 " =    1.435
peak=    3.305 closest distance to " CB  LEU A  83 " =    0.745
peak=    3.304 closest distance to " CD  LYS A  76 " =    1.977
peak=    3.300 closest distance to " CA  ASN A 127 " =    1.109
peak=    3.297 closest distance to " O   HOH Z   1 " =    1.626
peak=    3.293 closest distance to " CG AARG A 275 " =    1.140
peak=    3.292 closest distance to " O   HOH Z  44 " =    1.680
peak=    3.291 closest distance to " O   HOH Z 345 " =    1.690
peak=    3.290 closest distance to " O   HOH Z 273 " =    2.863
peak=    3.289 closest distance to " CA  THR A 221 " =    1.051
peak=    3.287 closest distance to " O   HOH Z 336 " =    1.775
peak=    3.286 closest distance to " CA  ASN A 217 " =    1.189
peak=    3.283 closest distance to " CA  ALA A 160 " =    0.973
peak=    3.275 closest distance to " O   HOH Z 148 " =    3.443
peak=    3.272 closest distance to " CA  ALA A 291 " =    0.799
peak=    3.271 closest distance to " CG2 ILE A  20 " =    1.439
peak=    3.271 closest distance to " CD1 LEU A  96 " =    0.738
peak=    3.270 closest distance to " O   SER A 164 " =    1.307
peak=    3.268 closest distance to " O   HOH Z 287 " =    2.268
peak=    3.267 closest distance to " CG2 VAL A 197 " =    1.113
peak=    3.267 closest distance to " O   HOH Z 116 " =    3.083
peak=    3.265 closest distance to " CA  PHE A  59 " =    0.991
peak=    3.265 closest distance to " O   HOH Z 407 " =    2.414
peak=    3.261 closest distance to " O   THR A 220 " =    1.311
peak=    3.260 closest distance to " O   HOH Z 391 " =    2.901
peak=    3.254 closest distance to " O   HOH Z 185 " =    1.891
peak=    3.252 closest distance to " CG1 ILE A  49 " =    1.489
peak=    3.251 closest distance to " O   HOH Z  97 " =    2.657
peak=    3.250 closest distance to " O   HOH Z 345 " =    3.346
peak=    3.246 closest distance to " O   HOH Z 426 " =    1.999
peak=    3.243 closest distance to " O   HOH Z 340 " =    2.134
peak=    3.241 closest distance to " N   ASN A 127 " =    1.311
peak=    3.239 closest distance to " CB  SER A 210 " =    0.721
peak=    3.239 closest distance to " CB  MET A  47 " =    1.191
peak=    3.239 closest distance to " NZ  LYS A  48 " =    1.174
peak=    3.238 closest distance to " CD1 ILE A 263 " =    1.310
peak=    3.235 closest distance to " O   PHE A 192 " =    1.416
peak=    3.233 closest distance to " OG  SER A  22 " =    2.702
peak=    3.233 closest distance to " N   ARG A 156 " =    1.330
peak=    3.229 closest distance to " OD2 ASP A 286 " =    3.249
peak=    3.225 closest distance to " O   HOH Z 373 " =    1.526
peak=    3.218 closest distance to " O   HOH Z 380 " =    1.896
peak=    3.216 closest distance to " CB  ASP A 171 " =    1.389
peak=    3.215 closest distance to " O   HOH Z 227 " =    1.868
peak=    3.215 closest distance to " CB  MET A  40 " =    0.783
peak=    3.213 closest distance to " O   HOH Z 188 " =    1.908
peak=    3.213 closest distance to " CB  ILE A 120 " =    1.348
peak=    3.211 closest distance to " O   HOH Z 233 " =    1.956
peak=    3.211 closest distance to " CB  SER A  62 " =    1.219
peak=    3.206 closest distance to " O   HOH Z 173 " =    1.810
peak=    3.200 closest distance to " CA  ALA A 100 " =    0.957
peak=    3.198 closest distance to " CA  ALA A 129 " =    1.354
peak=    3.198 closest distance to " O   HOH Z  97 " =    2.028
peak=    3.195 closest distance to " O   HOH Z 128 " =    2.165
peak=    3.193 closest distance to " O   HOH Z  88 " =    2.549
peak=    3.192 closest distance to " CB  ASN A 187 " =    1.012
peak=    3.191 closest distance to " CB  ARG A 138 " =    0.934
peak=    3.186 closest distance to " O   HOH Z 357 " =    2.023
peak=    3.186 closest distance to " CA  ALA A  84 " =    1.290
peak=    3.180 closest distance to " O   ALA A   1 " =    1.662
peak=    3.180 closest distance to " CB  THR A 157 " =    1.109
peak=    3.179 closest distance to " N   ASP A 162 " =    1.167
peak=    3.175 closest distance to " CB  PHE A 204 " =    0.767
peak=    3.174 closest distance to " OE2 GLU A  53 " =    1.998
peak=    3.170 closest distance to " CA  LEU A  83 " =    1.180
peak=    3.167 closest distance to " CB  ALA A 114 " =    1.419
peak=    3.167 closest distance to " CB  VAL A 268 " =    0.809
peak=    3.167 closest distance to " CG1 ILE A  33 " =    1.199
peak=    3.164 closest distance to " O   HOH Z 194 " =    2.410
peak=    3.163 closest distance to " O   HOH Z  43 " =    1.955
peak=    3.163 closest distance to " CG2 ILE A 234 " =    0.863
peak=    3.152 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.147 closest distance to " O   HOH Z  28 " =    1.761
peak=    3.146 closest distance to " O   HOH Z  88 " =    2.521
peak=    3.135 closest distance to " CA  ALA A 154 " =    1.043
peak=    3.130 closest distance to " CZ2 TRP A 179 " =    1.685
peak=    3.129 closest distance to " O   HOH Z 193 " =    1.686
peak=    3.127 closest distance to " O   HOH Z 227 " =    2.049
peak=    3.120 closest distance to " O   HOH Z 234 " =    2.244
peak=    3.116 closest distance to " CA  PRO A 280 " =    1.303
peak=    3.111 closest distance to " CD1 ILE A 199 " =    1.100
peak=    3.106 closest distance to " NH1 ARG A 138 " =    1.122
peak=    3.105 closest distance to " O   HOH Z  88 " =    3.820
peak=    3.103 closest distance to " CB  ASP A 200 " =    0.843
peak=    3.101 closest distance to " OG  SER A  62 " =    2.885
peak=    3.092 closest distance to " CB  LEU A 300 " =    0.894
peak=    3.092 closest distance to " CB  ASP A 191 " =    1.270
peak=    3.091 closest distance to " CG  MET A 113 " =    1.175
peak=    3.083 closest distance to " CB  ALA A 248 " =    0.924
peak=    3.083 closest distance to " CA  LYS A 117 " =    1.221
peak=    3.081 closest distance to " O   HOH Z 433 " =    1.840
peak=    3.076 closest distance to " O   HOH Z 342 " =    1.555
peak=    3.072 closest distance to " CB  ALA A   9 " =    1.603
peak=    3.072 closest distance to " CG  GLN A  89 " =    1.560
peak=    3.070 closest distance to " O   PRO A  90 " =    1.548
peak=    3.069 closest distance to " CA  ALA A 299 " =    0.849
peak=    3.065 closest distance to " CG  LYS A  76 " =    0.947
peak=    3.058 closest distance to " O   HOH Z 188 " =    2.394
peak=    3.056 closest distance to " CB  ALA A 114 " =    0.928
peak=    3.052 closest distance to " O   HOH Z 175 " =    2.156
peak=    3.046 closest distance to " O   HOH Z 286 " =    2.494
peak=    3.033 closest distance to " CA  ALA A 233 " =    1.009
peak=    3.030 closest distance to " O   HOH Z 423 " =    2.752
peak=    3.014 closest distance to " CB  SER A 216 " =    0.843

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.746 - 5.670
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.746 - 5.670

peak=   -4.693 closest distance to " O   HOH Z 377 " =    2.115
peak=   -4.661 closest distance to " CD  ARG A  14 " =    3.469
peak=   -4.470 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.456 closest distance to " CB  PRO A 243 " =    2.694
peak=   -4.433 closest distance to " OG BSER A 134 " =    1.338
peak=   -4.392 closest distance to " O   HOH Z 231 " =    2.276
peak=   -4.343 closest distance to " CD  GLN A  58 " =    1.032
peak=   -4.264 closest distance to " O   HOH Z 266 " =    5.383
peak=   -4.203 closest distance to " CD2 PHE A 192 " =    1.996
peak=   -4.201 closest distance to " O   VAL A  67 " =    2.678
peak=   -4.190 closest distance to " O   PRO A 198 " =    1.276
peak=   -4.184 closest distance to " CE  MET A 105 " =    2.487
peak=   -4.121 closest distance to " C   HIS A 108 " =    1.107
peak=   -4.042 closest distance to " CG1 VAL A 112 " =    2.897
peak=   -4.030 closest distance to " O   HOH Z  73 " =    2.257
peak=   -3.958 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.955 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.935 closest distance to " CG  GLN A 223 " =    2.076
peak=   -3.933 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -3.932 closest distance to " CB  ALA A  43 " =    2.544
peak=   -3.906 closest distance to " CG1 VAL A  67 " =    2.989
peak=   -3.903 closest distance to " O   HOH Z 198 " =    1.744
peak=   -3.863 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.858 closest distance to " CE BMET A  47 " =    1.338
peak=   -3.834 closest distance to " CE2 TYR A  30 " =    2.762
peak=   -3.828 closest distance to " ND2 ASN A 249 " =    2.351
peak=   -3.827 closest distance to " O   HOH Z 372 " =    2.434
peak=   -3.820 closest distance to " OD1 ASP A 171 " =    1.633
peak=   -3.812 closest distance to " CG2 ILE A 263 " =    2.247
peak=   -3.793 closest distance to " CB  ASN A  39 " =    2.327
peak=   -3.768 closest distance to " O   HOH Z 389 " =    2.012
peak=   -3.763 closest distance to " CD1 LEU A 255 " =    2.858
peak=   -3.717 closest distance to " CB  ALA A 291 " =    2.044
peak=   -3.714 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.707 closest distance to " CB  ALA A 248 " =    2.329
peak=   -3.706 closest distance to " ND2 ASN A  45 " =    1.876
peak=   -3.705 closest distance to " OXT GLY A 302 " =    2.938
peak=   -3.699 closest distance to " CD2 TYR A 293 " =    1.904
peak=   -3.675 closest distance to " CD2 PHE A  61 " =    2.042
peak=   -3.669 closest distance to " CG2 THR A 178 " =    2.341
peak=   -3.667 closest distance to " CA  ASP A 298 " =    1.098
peak=   -3.652 closest distance to " O   HOH Z 407 " =    3.047
peak=   -3.650 closest distance to " O   HOH Z 290 " =    1.206
peak=   -3.641 closest distance to " N   ALA A  43 " =    2.604
peak=   -3.636 closest distance to " O   HOH Z 211 " =    1.432
peak=   -3.634 closest distance to " OD1 ASN A 148 " =    1.509
peak=   -3.632 closest distance to " O   PHE A 218 " =    1.531
peak=   -3.630 closest distance to " O   HOH Z 313 " =    1.810
peak=   -3.629 closest distance to " O   SER A 210 " =    1.968
peak=   -3.615 closest distance to " N   THR A 157 " =    1.541
peak=   -3.613 closest distance to " O   HOH Z 348 " =    2.219
peak=   -3.598 closest distance to " CD2 TYR A 247 " =    2.477
peak=   -3.595 closest distance to " CD2 LEU A 237 " =    2.861
peak=   -3.588 closest distance to " O   HOH Z  38 " =    1.619
peak=   -3.587 closest distance to " O   SER A 135 " =    1.428
peak=   -3.584 closest distance to " CD1 PHE A  59 " =    2.053
peak=   -3.562 closest distance to " OG  SER A  97 " =    2.214
peak=   -3.556 closest distance to " CB  ALA A 161 " =    2.463
peak=   -3.554 closest distance to " CE2 PHE A 218 " =    2.392
peak=   -3.542 closest distance to " O   HOH Z  60 " =    2.185
peak=   -3.538 closest distance to " ND2 ASN A 187 " =    1.486
peak=   -3.523 closest distance to " O   VAL A 189 " =    2.600
peak=   -3.520 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.518 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.506 closest distance to " CZ  TYR A 169 " =    1.793
peak=   -3.505 closest distance to " CG1 VAL A 250 " =    2.624
peak=   -3.501 closest distance to " ND2 ASN A  45 " =    1.229
peak=   -3.501 closest distance to " NH2BARG A 275 " =    1.893
peak=   -3.500 closest distance to " OD2 ASP A 191 " =    1.344
peak=   -3.493 closest distance to " O   HOH Z 429 " =    1.931
peak=   -3.488 closest distance to " O   HOH Z  10 " =    1.468
peak=   -3.488 closest distance to " CD1 LEU A 101 " =    2.265
peak=   -3.486 closest distance to " NH2AARG A 275 " =    5.310
peak=   -3.477 closest distance to " O   HOH Z 196 " =    2.130
peak=   -3.473 closest distance to " O   HOH Z 174 " =    2.621
peak=   -3.472 closest distance to " O   HOH Z 394 " =    1.459
peak=   -3.472 closest distance to " O   HOH Z 357 " =    2.095
peak=   -3.446 closest distance to " O   PRO A 163 " =    2.019
peak=   -3.442 closest distance to " O   HOH Z  52 " =    1.307
peak=   -3.429 closest distance to " ND2 ASN A  60 " =    4.122
peak=   -3.427 closest distance to " O   HOH Z 114 " =    2.918
peak=   -3.420 closest distance to " O   HOH Z 253 " =    3.842
peak=   -3.419 closest distance to " O   HOH Z 298 " =    1.326
peak=   -3.417 closest distance to " O   PRO A 198 " =    1.310
peak=   -3.416 closest distance to " CB  TRP A  85 " =    2.498
peak=   -3.414 closest distance to " O   HOH Z  13 " =    1.890
peak=   -3.407 closest distance to " N   ALA A 248 " =    1.573
peak=   -3.401 closest distance to " O   VAL A 189 " =    1.696
peak=   -3.398 closest distance to " O   HOH Z 166 " =    2.058
peak=   -3.391 closest distance to " NE2 GLN A 278 " =    1.616
peak=   -3.389 closest distance to " O   SER A  22 " =    2.518
peak=   -3.385 closest distance to " O   HOH Z 395 " =    5.148
peak=   -3.384 closest distance to " O   TRP A  70 " =    1.430
peak=   -3.378 closest distance to " O   HOH Z   9 " =    1.643
peak=   -3.378 closest distance to " CE2 PHE A  61 " =    2.595
peak=   -3.368 closest distance to " O   ALA A  10 " =    1.630
peak=   -3.366 closest distance to " N   THR A  52 " =    1.773
peak=   -3.362 closest distance to " O   HOH Z 191 " =    5.610
peak=   -3.358 closest distance to " O   HOH Z  11 " =    1.772
peak=   -3.358 closest distance to " CA  GLY A  57 " =    2.202
peak=   -3.358 closest distance to " O   HOH Z 102 " =    1.568
peak=   -3.352 closest distance to " CA  GLY A 241 " =    3.211
peak=   -3.351 closest distance to " O   HOH Z 131 " =    4.075
peak=   -3.350 closest distance to " CB  TYR A  15 " =    2.308
peak=   -3.347 closest distance to " CB  GLN A  11 " =    1.824
peak=   -3.346 closest distance to " O   HOH Z 298 " =    2.445
peak=   -3.340 closest distance to " O   ALA A  51 " =    1.299
peak=   -3.330 closest distance to " CB  ASP A 171 " =    2.338
peak=   -3.326 closest distance to " O   MET A  40 " =    2.848
peak=   -3.318 closest distance to " O   HOH Z 140 " =    1.674
peak=   -3.318 closest distance to " CB  ASP A 132 " =    2.414
peak=   -3.316 closest distance to " O   HOH Z 359 " =    3.220
peak=   -3.315 closest distance to " OD1 ASN A 187 " =    1.624
peak=   -3.314 closest distance to " CB  ASP A 286 " =    1.730
peak=   -3.313 closest distance to " CE3 TRP A 274 " =    2.340
peak=   -3.306 closest distance to " CZ  PHE A  59 " =    1.605
peak=   -3.300 closest distance to " CE3 TRP A 150 " =    2.257
peak=   -3.295 closest distance to " O   HOH Z 243 " =    2.000
peak=   -3.294 closest distance to " OE1 GLN A  88 " =    1.117
peak=   -3.289 closest distance to " OH  TYR A 172 " =    1.839
peak=   -3.287 closest distance to " OD1 ASP A 191 " =    1.722
peak=   -3.280 closest distance to " O   HOH Z  15 " =    1.541
peak=   -3.279 closest distance to " O   HOH Z 134 " =    3.330
peak=   -3.275 closest distance to " O   ARG A 145 " =    1.512
peak=   -3.270 closest distance to " CG  PHE A 283 " =    2.636
peak=   -3.254 closest distance to " CG  MET A 105 " =    0.985
peak=   -3.252 closest distance to " CG  LEU A  83 " =    1.928
peak=   -3.252 closest distance to " CA  GLY A 133 " =    2.020
peak=   -3.249 closest distance to " CB  ASP A 132 " =    2.262
peak=   -3.247 closest distance to " NE  ARG A  36 " =    2.010
peak=   -3.247 closest distance to " O   SER A  95 " =    1.561
peak=   -3.240 closest distance to " O   HOH Z  51 " =    1.640
peak=   -3.238 closest distance to " O   SER A 276 " =    1.697
peak=   -3.238 closest distance to " CB  ALA A 100 " =    2.191
peak=   -3.233 closest distance to " CG1 VAL A 125 " =    1.875
peak=   -3.230 closest distance to " O   GLN A 240 " =    2.451
peak=   -3.227 closest distance to " CB  ALA A  10 " =    2.313
peak=   -3.227 closest distance to " CG2 THR A 221 " =    2.670
peak=   -3.226 closest distance to " CG  GLU A 277 " =    1.327
peak=   -3.224 closest distance to " O   ALA A 161 " =    1.706
peak=   -3.223 closest distance to " O   HOH Z 216 " =    1.367
peak=   -3.222 closest distance to " O   HOH Z 275 " =    1.485
peak=   -3.216 closest distance to " O   HOH Z 421 " =    3.063
peak=   -3.215 closest distance to " CD  GLU A 236 " =    1.101
peak=   -3.208 closest distance to " CD  ARG A 139 " =    1.686
peak=   -3.207 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.205 closest distance to " ND2 ASN A  60 " =    1.370
peak=   -3.204 closest distance to " O   GLN A 240 " =    2.045
peak=   -3.204 closest distance to " O   HOH Z  71 " =    2.270
peak=   -3.203 closest distance to " CB  PHE A  16 " =    2.623
peak=   -3.202 closest distance to " N   SER A 276 " =    1.311
peak=   -3.202 closest distance to " O   HOH Z 100 " =    1.181
peak=   -3.197 closest distance to " O   HOH Z 123 " =    2.545
peak=   -3.192 closest distance to " C   ASP A 272 " =    2.344
peak=   -3.192 closest distance to " O   HOH Z  37 " =    1.811
peak=   -3.192 closest distance to " O   HOH Z 353 " =    2.281
peak=   -3.184 closest distance to " ND2 ASN A  69 " =    1.802
peak=   -3.182 closest distance to " OD1AASN A 224 " =    1.824
peak=   -3.181 closest distance to " O   HOH Z 174 " =    4.055
peak=   -3.180 closest distance to " OG BSER A 134 " =    1.767
peak=   -3.178 closest distance to " O   ALA A 292 " =    2.126
peak=   -3.176 closest distance to " O   HOH Z 426 " =    1.586
peak=   -3.174 closest distance to " O   HOH Z 165 " =    2.089
peak=   -3.174 closest distance to " CG2 VAL A 189 " =    1.978
peak=   -3.171 closest distance to " CA  ASP A  27 " =    2.458
peak=   -3.171 closest distance to " O   HOH Z 252 " =    4.223
peak=   -3.164 closest distance to " O   HOH Z 318 " =    1.931
peak=   -3.160 closest distance to " O   HOH Z 281 " =    2.733
peak=   -3.159 closest distance to " O   GLU A 152 " =    1.363
peak=   -3.157 closest distance to " O   HOH Z 200 " =    2.832
peak=   -3.156 closest distance to " OG  SER A  87 " =    1.389
peak=   -3.154 closest distance to " CD2 PHE A 225 " =    1.143
peak=   -3.148 closest distance to " O   HOH Z 283 " =    5.670
peak=   -3.144 closest distance to " CG  TRP A 266 " =    1.928
peak=   -3.143 closest distance to " CG1 VAL A 197 " =    2.187
peak=   -3.135 closest distance to " O   ALA A 180 " =    1.072
peak=   -3.131 closest distance to " OD2 ASP A 171 " =    1.796
peak=   -3.120 closest distance to " O   GLY A  17 " =    1.123
peak=   -3.119 closest distance to " O   HOH Z 412 " =    4.183
peak=   -3.115 closest distance to " CA  GLY A 241 " =    2.872
peak=   -3.115 closest distance to " O   HOH Z   6 " =    1.424
peak=   -3.113 closest distance to " OE1 GLN A 183 " =    1.562
peak=   -3.101 closest distance to " O   HOH Z 244 " =    1.889
peak=   -3.099 closest distance to " CG  ASP A 231 " =    0.746
peak=   -3.096 closest distance to " O   HOH Z 134 " =    3.602
peak=   -3.094 closest distance to " CD  GLN A  77 " =    1.560
peak=   -3.092 closest distance to " O   HOH Z   9 " =    2.342
peak=   -3.086 closest distance to " O   HOH Z 108 " =    2.295
peak=   -3.083 closest distance to " CG1 VAL A 197 " =    2.283
peak=   -3.078 closest distance to " OE2 GLU A 152 " =    1.269
peak=   -3.070 closest distance to " CD1 LEU A   5 " =    2.468
peak=   -3.065 closest distance to " CG  ARG A 269 " =    2.016
peak=   -3.058 closest distance to " C   MET A 188 " =    1.425
peak=   -3.042 closest distance to " C   ALA A 114 " =    2.274

================= 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    :  0.3871 0.3834   6.174473e+00   6.147597e+00
   1_bss:  0.3728 0.3700   6.156725e+00   6.123940e+00
   1_xyz:  0.2187 0.2494   5.689688e+00   5.779045e+00
   1_adp:  0.1979 0.2576   5.639717e+00   5.819964e+00
   1_occ:  0.1978 0.2571   5.639014e+00   5.819196e+00
   2_bss:  0.1946 0.2544   5.631425e+00   5.814568e+00
   2_xyz:  0.1488 0.2006   5.389382e+00   5.598925e+00
   2_adp:  0.1422 0.1883   5.337518e+00   5.539473e+00
   2_occ:  0.1419 0.1882   5.336600e+00   5.539355e+00
   3_bss:  0.1418 0.1877   5.334080e+00   5.537222e+00
   3_xyz:  0.1196 0.1627   5.190968e+00   5.418160e+00
   3_adp:  0.1156 0.1595   5.164735e+00   5.398795e+00
   3_occ:  0.1155 0.1595   5.164662e+00   5.399004e+00
   4_bss:  0.1158 0.1596   5.164911e+00   5.398580e+00
   4_xyz:  0.1118 0.1575   5.143320e+00   5.387761e+00
   4_adp:  0.1107 0.1568   5.138576e+00   5.385379e+00
   4_occ:  0.1106 0.1568   5.138573e+00   5.385587e+00
   5_bss:  0.1106 0.1567   5.138563e+00   5.385683e+00
   5_xyz:  0.1091 0.1567   5.133354e+00   5.387259e+00
   5_adp:  0.1087 0.1571   5.132864e+00   5.389389e+00
   5_occ:  0.1086 0.1570   5.132783e+00   5.389393e+00
   5_bss:  0.1086 0.1570   5.132629e+00   5.389327e+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:  0.322  41.935  -3.098  -0.392   4.110  -0.000   0.000   0.000
   1_xyz:  0.322  41.935  -3.098  -0.392   4.110  -0.000   0.000   0.000
   1_adp:  0.322  41.935  -3.098  -0.392   4.110  -0.000   0.000   0.000
   1_occ:  0.322  41.935  -3.098  -0.392   4.110  -0.000   0.000   0.000
   2_bss:  0.333  63.219  -3.078  -2.001   0.640  -0.000   0.000   0.000
   2_xyz:  0.333  63.219  -3.078  -2.001   0.640  -0.000   0.000   0.000
   2_adp:  0.333  63.219  -3.078  -2.001   0.640  -0.000   0.000   0.000
   2_occ:  0.333  63.219  -3.078  -2.001   0.640  -0.000   0.000   0.000
   3_bss:  0.332  60.584  -2.869  -2.247  -0.080  -0.000  -0.000  -0.000
   3_xyz:  0.332  60.584  -2.869  -2.247  -0.080  -0.000  -0.000  -0.000
   3_adp:  0.332  60.584  -2.869  -2.247  -0.080  -0.000  -0.000  -0.000
   3_occ:  0.332  60.584  -2.869  -2.247  -0.080  -0.000  -0.000  -0.000
   4_bss:  0.332  60.584  -2.759  -2.359  -0.348  -0.000  -0.000  -0.000
   4_xyz:  0.332  60.584  -2.759  -2.359  -0.348  -0.000  -0.000  -0.000
   4_adp:  0.332  60.584  -2.759  -2.359  -0.348  -0.000  -0.000  -0.000
   4_occ:  0.332  60.584  -2.759  -2.359  -0.348  -0.000  -0.000  -0.000
   5_bss:  0.332  60.584  -2.534  -2.233  -0.267  -0.000  -0.000  -0.000
   5_xyz:  0.332  60.584  -2.534  -2.233  -0.267  -0.000  -0.000  -0.000
   5_adp:  0.332  60.584  -2.534  -2.233  -0.267  -0.000  -0.000  -0.000
   5_occ:  0.332  60.584  -2.534  -2.233  -0.267  -0.000  -0.000  -0.000
   5_bss:  0.325  60.570  -2.321  -2.057  -0.109  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.456 0.6274  0.8029    42008.219
   1_bss:  40.093 0.6420  0.8285    38576.352
   1_xyz:  23.831 0.8246  1.0006    15275.525
   1_adp:  25.207 0.8096  0.9876    16714.159
   1_occ:  25.194 0.8097  0.9875    16678.438
   2_bss:  24.775 0.8143  0.9380    16395.641
   2_xyz:  18.873 0.8721  0.9770     9945.309
   2_adp:  17.317 0.8870  0.9791     8898.714
   2_occ:  17.314 0.8870  0.9788     8887.812
   3_bss:  17.229 0.8877  0.9708     8823.287
   3_xyz:  14.753 0.9085  0.9819     6843.270
   3_adp:  14.284 0.9125  0.9774     6563.683
   3_occ:  14.288 0.9125  0.9773     6563.983
   4_bss:  14.277 0.9126  0.9742     6566.430
   4_xyz:  13.950 0.9155  0.9754     6394.249
   4_adp:  13.884 0.9162  0.9695     6348.825
   4_occ:  13.889 0.9161  0.9694     6348.431
   5_bss:  13.888 0.9161  0.9745     6350.198
   5_xyz:  13.899 0.9160  0.9749     6382.094
   5_adp:  13.931 0.9158  0.9678     6387.796
   5_occ:  13.930 0.9158  0.9677     6386.150
   5_bss:  13.928 0.9158  0.9736     6383.194
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7048e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7048e-01
   1_xyz:   1.258  0.010  0.085 15.790  0.005  4.111   9.0104e-02
   1_adp:   1.258  0.010  0.085 15.790  0.005  4.111   9.0104e-02
   1_occ:   1.258  0.010  0.085 15.790  0.005  4.111   9.0104e-02
   2_bss:   1.258  0.010  0.085 15.790  0.005  4.111   9.0104e-02
   2_xyz:   0.974  0.006  0.070 15.077  0.003  4.123   5.5173e-02
   2_adp:   0.974  0.006  0.070 15.077  0.003  4.123   5.5173e-02
   2_occ:   0.974  0.006  0.070 15.077  0.003  4.123   5.5173e-02
   3_bss:   0.974  0.006  0.070 15.077  0.003  4.123   5.5173e-02
   3_xyz:   1.057  0.009  0.078 15.169  0.004  4.115   6.7296e-02
   3_adp:   1.057  0.009  0.078 15.169  0.004  4.115   6.7296e-02
   3_occ:   1.057  0.009  0.078 15.169  0.004  4.115   6.7296e-02
   4_bss:   1.057  0.009  0.078 15.169  0.004  4.115   6.7296e-02
   4_xyz:   1.029  0.008  0.079 14.931  0.004  4.119   6.4523e-02
   4_adp:   1.029  0.008  0.079 14.931  0.004  4.119   6.4523e-02
   4_occ:   1.029  0.008  0.079 14.931  0.004  4.119   6.4523e-02
   5_bss:   1.029  0.008  0.079 14.931  0.004  4.119   6.4523e-02
   5_xyz:   1.038  0.009  0.080 14.910  0.004  4.120   6.5657e-02
   5_adp:   1.038  0.009  0.080 14.910  0.004  4.120   6.5657e-02
   5_occ:   1.038  0.009  0.080 14.910  0.004  4.120   6.5657e-02
   5_bss:   1.038  0.009  0.080 14.910  0.004  4.120   6.5657e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.498   2.4162e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.498   2.4162e-01
   1_xyz:   7.967  0.048  0.300 82.451  0.044  2.069   8.8936e-02
   1_adp:   7.967  0.048  0.300 82.451  0.044  2.069   8.8936e-02
   1_occ:   7.967  0.048  0.300 82.451  0.044  2.069   8.8936e-02
   2_bss:   7.967  0.048  0.300 82.451  0.044  2.069   8.8936e-02
   2_xyz:   6.299  0.042  0.207 82.593  0.030  2.385   3.6981e-02
   2_adp:   6.299  0.042  0.207 82.593  0.030  2.385   3.6981e-02
   2_occ:   6.299  0.042  0.207 82.593  0.030  2.385   3.6981e-02
   3_bss:   6.299  0.042  0.207 82.593  0.030  2.385   3.6981e-02
   3_xyz:   6.446  0.051  0.280 83.790  0.033  2.335   4.8588e-02
   3_adp:   6.446  0.051  0.280 83.790  0.033  2.335   4.8588e-02
   3_occ:   6.446  0.051  0.280 83.790  0.033  2.335   4.8588e-02
   4_bss:   6.446  0.051  0.280 83.790  0.033  2.335   4.8588e-02
   4_xyz:   6.434  0.048  0.262 83.007  0.035  2.314   4.7360e-02
   4_adp:   6.434  0.048  0.262 83.007  0.035  2.314   4.7360e-02
   4_occ:   6.434  0.048  0.262 83.007  0.035  2.314   4.7360e-02
   5_bss:   6.434  0.048  0.262 83.007  0.035  2.314   4.7360e-02
   5_xyz:   6.474  0.051  0.267 83.844  0.033  2.332   4.9097e-02
   5_adp:   6.474  0.051  0.267 83.844  0.033  2.332   4.9097e-02
   5_occ:   6.474  0.051  0.267 83.844  0.033  2.332   4.9097e-02
   5_bss:   6.474  0.051  0.267 83.844  0.033  2.332   4.9097e-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:  86.91   0.00  17.55  70.91   0.00  13.22  86.91   2.31  41.14
   1_occ:  86.91   0.00  17.55  70.91   0.00  13.22  86.91   2.31  41.14
   2_bss:  86.91   0.00  17.55  70.91   0.00  13.22  86.91   2.31  41.14
   2_xyz:  86.91   0.00  17.55  70.91   0.00  13.22  86.91   2.31  41.14
   2_adp:  84.39   0.00  17.13  68.94   0.00  12.90  84.39   5.10  40.13
   2_occ:  84.39   0.00  17.13  68.94   0.00  12.90  84.39   5.10  40.13
   3_bss:  84.39   0.00  17.13  68.94   0.00  12.90  84.39   5.10  40.13
   3_xyz:  84.39   0.00  17.13  68.94   0.00  12.90  84.39   5.10  40.13
   3_adp:  82.37   0.78  17.03  75.51   0.78  12.78  82.37   5.78  40.19
   3_occ:  82.37   0.78  17.03  75.51   0.78  12.78  82.37   5.78  40.19
   4_bss:  82.37   0.78  17.03  75.51   0.78  12.78  82.37   5.78  40.19
   4_xyz:  82.37   0.78  17.03  75.51   0.78  12.78  82.37   5.78  40.19
   4_adp:  81.02   0.68  16.87  81.02   0.68  12.66  80.38   5.23  39.74
   4_occ:  81.02   0.68  16.87  81.02   0.68  12.66  80.38   5.23  39.74
   5_bss:  81.02   0.68  16.87  81.02   0.68  12.66  80.38   5.23  39.74
   5_xyz:  81.02   0.68  16.87  81.02   0.68  12.66  80.38   5.23  39.74
   5_adp:  86.86   0.44  16.80  86.86   0.44  12.55  81.92   5.57  39.96
   5_occ:  86.86   0.44  16.80  86.86   0.44  12.55  81.92   5.57  39.96
   5_bss:  86.85   0.43  16.79  86.85   0.43  12.53  81.90   5.55  39.94
------------------------------------------------------------------------
 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:    1.643    0.028    0.393
   1_adp:    1.643    0.028    0.393
   1_occ:    1.643    0.028    0.393
   2_bss:    1.643    0.028    0.393
   2_xyz:    1.310    0.031    0.444
   2_adp:    1.310    0.031    0.444
   2_occ:    1.310    0.031    0.444
   3_bss:    1.310    0.031    0.444
   3_xyz:    1.176    0.021    0.508
   3_adp:    1.176    0.021    0.508
   3_occ:    1.176    0.021    0.508
   4_bss:    1.176    0.021    0.508
   4_xyz:    1.457    0.056    0.525
   4_adp:    1.457    0.056    0.525
   4_occ:    1.457    0.056    0.525
   5_bss:    1.457    0.056    0.525
   5_xyz:    1.506    0.055    0.535
   5_adp:    1.506    0.055    0.535
   5_occ:    1.506    0.055    0.535
   5_bss:    1.506    0.055    0.535
------------------------------------------------------------------------

CPU time actual refinement: 316.06


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/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_526/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_526/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.90 
  Macro-tasks:
    bulk solvent and scale       = 36.00  
    individual site refinement   = 128.11 
    weights calculation          = 28.77  
    collect and process          = 6.49   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 199.47 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 100.45 
    alpha_beta                      = 8.00   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 108.70 
    fmodel                         = 6.11   
    r_factors                      = 0.25   
    phase_errors                   = 11.14  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 237.77 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.520 micro seconds
Total CPU time: 5.49 minutes
from_scatterers_fft:    641 calls, 100.16 s
gradients_fft:          586 calls,  95.67 s

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

# Date 2008-01-16 Time 05:01:48 PST -0800 (1200488508.18 s)
Start R-work = 0.3871, R-free = 0.3834 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.3728, R-free = 0.3700
Final R-work = 0.1086, R-free = 0.1570