# Date 2008-01-16 Time 04:46:08 PST -0800 (1200487568.40 s)
#phil __OFF__

Command line arguments: "../454.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11773
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 454

-------------------------------------------------------------------------------
  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: (69.5475, 47.6339, 85.5261, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (69.5475, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.9805
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8850
                             d_min =   1.9805

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: (69.5475, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.9805
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8855 -  4.2371 [2137/2165]  1923   214  10.0%
  bin  2:  4.2371 -  3.3760 [2041/2064]  1837   204  10.0%
  bin  3:  3.3760 -  2.9531 [2031/2053]  1827   204  10.0%
  bin  4:  2.9531 -  2.6848 [2000/2019]  1804   196   9.8%
  bin  5:  2.6848 -  2.4933 [1999/2028]  1793   206  10.3%
  bin  6:  2.4933 -  2.3469 [1969/2010]  1777   192   9.8%
  bin  7:  2.3469 -  2.2298 [1973/2009]  1778   195   9.9%
  bin  8:  2.2298 -  2.1330 [1978/2016]  1775   203  10.3%
  bin  9:  2.1330 -  2.0511 [1946/1978]  1755   191   9.8%
  bin 10:  2.0511 -  1.9805 [1515/2005]  1361   154  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2202
        3.04 -     3.66: 4726
        3.66 -     4.28: 9029
        4.28 -     4.90: 12399
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.883 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.899 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.986 3.040 -x+1,y+1/2,-z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  2.008 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28379 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_454/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/model_refine_001.geo

CPU time processing inputs: 8.99


============================ 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 = 69.5475 47.63395 85.5261 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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3808   r_free= 0.3749   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.162412                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.3106 0.3285      6.4175      6.4325|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.3110 0.3053       6.599      6.5984|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.3323 0.3158      6.4902      6.4783|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.3513 0.3377      6.3505      6.2537|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.3820 0.3459      6.2354      6.1778|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.4076 0.3809      6.1697      6.0586|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.4098 0.3543      6.1458      6.0108|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.4170 0.4633      6.0878      6.1434|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.4462 0.4430      6.0554       6.069|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.4385 0.4797      6.0305      6.0786|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.4335 0.4088      5.9639      5.9914|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.4368 0.4670      5.9146      5.9649|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.4624 0.4433      5.8451      5.8181|
| 14:  2.0299 -  1.9805 0.67    851  103 0.4473 0.4434      5.7714      5.6899|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7256  1385   155  0.74  30.51   0.86     0.76      56791.64|
|  2:  4.7256 -  3.7709  1339   146  0.80  26.25   0.96     0.88      62419.34|
|  3:  3.7709 -  3.3001  1308   152  0.76  30.00   0.97     0.92      59828.32|
|  4:  3.3001 -  3.0011  1301   133  0.73  33.05   0.97     0.91      50276.86|
|  5:  3.0011 -  2.7875  1279   146  0.69  36.47   0.96     0.88      41174.03|
|  6:  2.7875 -  2.6241  1293   143  0.67  38.36   0.96     0.87      35853.20|
|  7:  2.6241 -  2.4933  1279   149  0.66  38.88   0.96     0.85      34042.07|
|  8:  2.4933 -  2.3852  1279   136  0.61  43.64   0.98     0.80      36321.64|
|  9:  2.3852 -  2.2938  1285   146  0.55  48.36   0.97     0.76      36727.29|
| 10:  2.2938 -  2.2149  1245   139  0.53  49.67   0.99     0.73      36287.00|
| 11:  2.2149 -  2.1458  1260   143  0.53  50.08   1.00     0.75      33259.95|
| 12:  2.1458 -  2.0847  1278   134  0.53  49.75   1.01     0.77      30457.19|
| 13:  2.0847 -  2.0299  1248   134  0.53  50.17   0.98     0.77      26105.36|
| 14:  2.0299 -  1.9805   851   103  0.54  49.08   1.00     0.74      21397.26|
|alpha:            min =        0.73 max =            0.92 mean =         0.82|
|beta:             min =    21397.26 max =        62419.34 mean =     40777.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           89.97 mean =        40.64|
|phase err.(test): min =        0.00 max =           89.57 mean =        40.70|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.430892              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.919   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.013708              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.359   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2007 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1879 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2847 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4627 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4402 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5653 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6746 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| 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  1.806 |       0.261 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3808   r_free= 0.3749   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| 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:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.162412                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3696   r_free= 0.3611   ksol= 0.30   Bsol= 27.18   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,2.98,-0.67,0.00,-0.00,-0.00); trace/3= -0.06                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.145119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.142498              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.757   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.563288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.176   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3696      final r-factor (work) = 0.2508          |
| start r-factor (free) = 0.3611      final r-factor (free) = 0.2709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8306 = 3.14 * 0.50 * 6.1498 + 1.00 * 0.1677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4030 = 3.14 * 0.50 * 5.9280 + 1.00 * 0.0887                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2508      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.2709      final r-factor (free) = 0.2825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3451 = 0.56 * 1.00 * 5.9280 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2565 = 0.56 * 1.00 * 5.7570 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.82   17.23    None  None   None       |
|    all(noH): 2823   0      0.00    65.82   17.23    None  None   None       |
|    Sol.    : 438    0      3.51    65.82   37.49    None  None   None       |
|    Mac.    : 2385   0      0.00    59.05   13.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.582:  451   |   5:    32.909 -  39.491:  118        |
|      1:     6.582 -  13.164:  980   |   6:    39.491 -  46.073:  103        |
|      2:    13.164 -  19.746:  583   |   7:    46.073 -  52.655:   81        |
|      3:    19.746 -  26.327:  271   |   8:    52.655 -  59.237:   59        |
|      4:    26.327 -  32.909:  160   |   9:    59.237 -  65.818:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2285 r_free = 0.2825             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2281 r_free = 0.2830             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2281   r_free= 0.2830   ksol= 0.30   Bsol= 27.18   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,2.98,-0.67,0.00,-0.00,-0.00); trace/3= -0.06                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.770378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2269   r_free= 0.2817   ksol= 0.30   Bsol= 44.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,0.48,-1.19,0.00,-0.00,-0.00); trace/3= -1.16                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.767176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.994507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.325   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.225486              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.304  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2269      final r-factor (work) = 0.1604          |
| start r-factor (free) = 0.2817      final r-factor (free) = 0.2011          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5890 = 3.99 * 0.50 * 5.7581 + 1.00 * 0.0887                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3084 = 3.99 * 0.50 * 5.6283 + 1.00 * 0.0672                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1604      final r-factor (work) = 0.1466          |
| start r-factor (free) = 0.2011      final r-factor (free) = 0.1853          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2830 = 0.23 * 1.00 * 5.6283 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2246 = 0.23 * 1.00 * 5.3962 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    66.50   16.68    None  None   None       |
|    all(noH): 2823   0      1.23    66.50   16.68    None  None   None       |
|    Sol.    : 438    0      5.51    65.99   37.64    None  None   None       |
|    Mac.    : 2385   0      1.23    66.50   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.234 -   7.761:  544   |   5:    33.867 -  40.393:  119        |
|      1:     7.761 -  14.287: 1217   |   6:    40.393 -  46.920:   92        |
|      2:    14.287 -  20.814:  434   |   7:    46.920 -  53.446:   73        |
|      3:    20.814 -  27.340:  170   |   8:    53.446 -  59.973:   59        |
|      4:    27.340 -  33.867:   98   |   9:    59.973 -  66.499:   17        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1466 r_free = 0.1853             target_work(ml) = 5.358         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1465 r_free = 0.1853             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1853   ksol= 0.30   Bsol= 44.80   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,0.48,-1.19,0.00,-0.00,-0.00); trace/3= -1.16                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.357202                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1842   ksol= 0.32   Bsol= 49.30   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.78,-1.23,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.354943                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.590159              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.582  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.661066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1464      final r-factor (work) = 0.1270          |
| start r-factor (free) = 0.1842      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3581 = 1.59 * 0.50 * 5.3968 + 1.00 * 0.0672                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2532 = 1.59 * 0.50 * 5.2877 + 1.00 * 0.0491                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5034 = 0.66 * 1.00 * 5.2877 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4550 = 0.66 * 1.00 * 5.2121 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.17    86.66   16.98    None  None   None       |
|    all(noH): 2823   0      1.17    86.66   16.98    None  None   None       |
|    Sol.    : 438    0      5.28    75.93   40.12    None  None   None       |
|    Mac.    : 2385   0      1.17    86.66   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.167 -   9.716: 1017   |   5:    43.914 -  52.464:  113        |
|      1:     9.716 -  18.266: 1091   |   6:    52.464 -  61.013:   77        |
|      2:    18.266 -  26.815:  240   |   7:    61.013 -  69.563:   37        |
|      3:    26.815 -  35.365:  120   |   8:    69.563 -  78.112:   12        |
|      4:    35.365 -  43.914:  113   |   9:    78.112 -  86.662:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1637             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1637             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1637   ksol= 0.32   Bsol= 49.30   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-0.78,-1.23,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.206145                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1637   ksol= 0.32   Bsol= 50.36   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.11,-1.13,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.205830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.859709              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.750  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.405638              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.915  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8953 = 1.86 * 0.50 * 5.2119 + 1.00 * 0.0491                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8663 = 1.86 * 0.50 * 5.1734 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1079 = 0.41 * 1.00 * 5.1734 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0969 = 0.41 * 1.00 * 5.1471 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    89.05   16.67    None  None   None       |
|    all(noH): 2823   0      0.87    89.05   16.67    None  None   None       |
|    Sol.    : 438    0      4.39    77.38   39.43    None  None   None       |
|    Mac.    : 2385   0      0.87    89.05   12.49    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:     0.870 -   9.688: 1050   |   5:    44.962 -  53.780:  113        |
|      1:     9.688 -  18.507: 1103   |   6:    53.780 -  62.598:   64        |
|      2:    18.507 -  27.325:  216   |   7:    62.598 -  71.417:   29        |
|      3:    27.325 -  36.143:  127   |   8:    71.417 -  80.235:    9        |
|      4:    36.143 -  44.962:  108   |   9:    80.235 -  89.053:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1569             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1569             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1569   ksol= 0.32   Bsol= 50.36   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-1.11,-1.13,-0.00,-0.00,-0.00); trace/3= -1.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144083                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1569   ksol= 0.32   Bsol= 50.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.14,-1.00,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.408807              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.868613              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.629  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6818 = 1.41 * 0.50 * 5.1476 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6740 = 1.41 * 0.50 * 5.1468 + 1.00 * 0.0486                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6264 = 1.87 * 1.00 * 5.1468 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6270 = 1.87 * 1.00 * 5.1464 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.52  16.71    None  None   None       |
|    all(noH): 2823   0      0.00    103.52  16.71    None  None   None       |
|    Sol.    : 438    0      5.05    88.93   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    103.52  12.43    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 -  10.352: 1255   |   5:    51.761 -  62.114:   83        |
|      1:    10.352 -  20.705:  974   |   6:    62.114 -  72.466:   37        |
|      2:    20.705 -  31.057:  196   |   7:    72.466 -  82.818:   10        |
|      3:    31.057 -  41.409:  130   |   8:    82.818 -  93.170:    5        |
|      4:    41.409 -  51.761:  130   |   9:    93.170 - 103.522:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1589             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1590             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1590   ksol= 0.32   Bsol= 50.36   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-1.14,-1.00,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.0977 0.1295      5.3747      5.5304|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.0855 0.1068      5.4289      5.6099|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.1037 0.1474       5.459      5.8274|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.1224 0.1571      5.4578      5.6193|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.1295 0.1694      5.3248      5.5143|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.1278 0.1924      5.2467      5.4659|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.1214 0.1667      5.1499      5.3768|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.1188 0.1812      5.0988      5.3459|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.1184 0.1871      5.0373       5.341|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.1133 0.1824      4.9881       5.216|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.1154 0.1718      4.9411      5.2693|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.1111 0.1779      4.8801      5.1727|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.1137 0.1685      4.8127      5.0622|
| 14:  2.0299 -  1.9805 0.67    851  103 0.1090 0.1845      4.7252       4.984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7256  1385   155  0.94   9.11   0.97     0.95       7089.27|
|  2:  4.7256 -  3.7709  1339   146  0.95   7.96   1.01     1.00       8782.36|
|  3:  3.7709 -  3.3001  1308   152  0.94  10.79   1.03     1.02       9964.32|
|  4:  3.3001 -  3.0011  1301   133  0.92  13.63   1.01     1.00      10250.00|
|  5:  3.0011 -  2.7875  1279   146  0.90  15.62   1.00     0.97       8279.96|
|  6:  2.7875 -  2.6241  1293   143  0.90  16.35   0.98     0.95       7385.77|
|  7:  2.6241 -  2.4933  1279   149  0.91  15.42   0.98     0.96       6067.21|
|  8:  2.4933 -  2.3852  1279   136  0.91  15.36   0.99     0.96       5676.16|
|  9:  2.3852 -  2.2938  1285   146  0.90  15.91   0.99     0.96       5082.25|
| 10:  2.2938 -  2.2149  1245   139  0.90  15.94   0.99     0.95       4715.30|
| 11:  2.2149 -  2.1458  1260   143  0.90  15.86   0.99     0.95       4292.80|
| 12:  2.1458 -  2.0847  1278   134  0.91  15.26   0.99     0.99       3972.20|
| 13:  2.0847 -  2.0299  1248   134  0.90  16.21   0.98     0.97       3543.94|
| 14:  2.0299 -  1.9805   851   103  0.90  16.06   0.97     0.92       2917.02|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2917.02 max =        10250.00 mean =      6403.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.75|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1590   ksol= 0.32   Bsol= 50.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.00,-0.80,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1590   ksol= 0.32   Bsol= 50.36   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-1.00,-0.80,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152143                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.0978 0.1297      5.3759      5.5319|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.0855 0.1068      5.4295      5.6098|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.1038 0.1475      5.4591      5.8278|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.1224 0.1571      5.4578      5.6194|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.1295 0.1693      5.3246       5.514|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.1278 0.1923      5.2465      5.4652|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.1214 0.1668      5.1498      5.3769|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.1188 0.1812      5.0989      5.3459|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.1184 0.1871      5.0374       5.341|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.1134 0.1825      4.9884      5.2166|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.1154 0.1717      4.9412      5.2695|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.1111 0.1780        4.88      5.1729|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.1137 0.1685      4.8127       5.062|
| 14:  2.0299 -  1.9805 0.67    851  103 0.1090 0.1845      4.7251      4.9837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7256  1385   155  0.94   9.12   0.97     0.95       7108.86|
|  2:  4.7256 -  3.7709  1339   146  0.95   7.96   1.02     1.00       8794.96|
|  3:  3.7709 -  3.3001  1308   152  0.94  10.80   1.03     1.02       9968.90|
|  4:  3.3001 -  3.0011  1301   133  0.92  13.63   1.01     1.00      10250.83|
|  5:  3.0011 -  2.7875  1279   146  0.90  15.61   1.00     0.97       8274.12|
|  6:  2.7875 -  2.6241  1293   143  0.90  16.35   0.99     0.95       7380.12|
|  7:  2.6241 -  2.4933  1279   149  0.91  15.42   0.99     0.97       6064.50|
|  8:  2.4933 -  2.3852  1279   136  0.91  15.37   1.00     0.97       5677.32|
|  9:  2.3852 -  2.2938  1285   146  0.90  15.91   1.00     0.97       5085.03|
| 10:  2.2938 -  2.2149  1245   139  0.90  15.94   1.00     0.96       4717.07|
| 11:  2.2149 -  2.1458  1260   143  0.90  15.86   1.00     0.96       4292.95|
| 12:  2.1458 -  2.0847  1278   134  0.91  15.26   1.00     1.00       3971.98|
| 13:  2.0847 -  2.0299  1248   134  0.90  16.20   1.00     0.98       3542.04|
| 14:  2.0299 -  1.9805   851   103  0.90  16.05   0.98     0.93       2914.94|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2914.94 max =        10250.83 mean =      6405.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.53  16.72    None  None   None       |
|    all(noH): 2823   0      0.00    103.53  16.72    None  None   None       |
|    Sol.    : 438    0      5.05    88.93   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    103.53  12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.355: 1255   |   5:    51.764 -  62.116:   83        |
|      1:    10.355 -  20.708:  974   |   6:    62.116 -  72.469:   37        |
|      2:    20.708 -  31.060:  196   |   7:    72.469 -  82.821:   10        |
|      3:    31.060 -  41.412:  130   |   8:    82.821 -  93.173:    5        |
|      4:    41.412 -  51.764:  130   |   9:    93.173 - 103.525:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 296         
Filter by distance & map next to the model:
   mapped sites are within: 0.568 - 4.512
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 296
   mapped sites are within: 0.709 - 4.512

peak=    5.800 closest distance to " CB  GLN A 223 " =    1.391
peak=    5.659 closest distance to " CB  ARG A 275 " =    0.932
peak=    5.467 closest distance to " NH2 ARG A  56 " =    2.309
peak=    5.376 closest distance to " CG  PRO A  54 " =    1.306
peak=    5.142 closest distance to " CG  PRO A 213 " =    1.262
peak=    5.061 closest distance to " CG  PRO A  90 " =    1.210
peak=    4.995 closest distance to " CB  SER A  63 " =    1.178
peak=    4.926 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.898 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.800 closest distance to " O   HOH Z 403 " =    1.756
peak=    4.733 closest distance to " O   HOH Z 402 " =    1.517
peak=    4.624 closest distance to " CB  GLN A 183 " =    1.296
peak=    4.596 closest distance to " O   HOH Z 209 " =    2.256
peak=    4.590 closest distance to " O   HOH Z  15 " =    2.159
peak=    4.590 closest distance to " C   PRO A 198 " =    1.511
peak=    4.588 closest distance to " O   HOH Z  97 " =    1.948
peak=    4.573 closest distance to " O   HOH Z 298 " =    1.863
peak=    4.556 closest distance to " CB  PRO A  54 " =    0.917
peak=    4.508 closest distance to " O   HOH Z 234 " =    3.776
peak=    4.455 closest distance to " CB  ARG A 190 " =    1.699
peak=    4.435 closest distance to " O   HOH Z 232 " =    2.392
peak=    4.358 closest distance to " CB  GLU A 128 " =    1.183
peak=    4.347 closest distance to " O   HOH Z 272 " =    1.860
peak=    4.323 closest distance to " CB  TYR A 169 " =    0.782
peak=    4.319 closest distance to " CG1 ILE A  33 " =    1.291
peak=    4.311 closest distance to " CD  ARG A 269 " =    0.999
peak=    4.306 closest distance to " NZ  LYS A 117 " =    3.162
peak=    4.270 closest distance to " O   HOH Z 193 " =    1.707
peak=    4.268 closest distance to " NH2BARG A 145 " =    2.100
peak=    4.251 closest distance to " CG  PRO A 243 " =    1.133
peak=    4.209 closest distance to " O   HOH Z  43 " =    2.160
peak=    4.205 closest distance to " O   HOH Z 142 " =    1.571
peak=    4.195 closest distance to " CB  ASN A 148 " =    1.390
peak=    4.164 closest distance to " O   HOH Z  40 " =    1.905
peak=    4.133 closest distance to " O   HOH Z 189 " =    2.169
peak=    4.132 closest distance to " O   HOH Z 203 " =    1.792
peak=    4.130 closest distance to " O   SER A  87 " =    2.180
peak=    4.122 closest distance to " O   HOH Z 247 " =    1.369
peak=    4.116 closest distance to " O  BHOH Z  74 " =    1.268
peak=    4.102 closest distance to " O   HOH Z 126 " =    1.893
peak=    4.096 closest distance to " O   HOH Z  78 " =    1.703
peak=    4.092 closest distance to " CA  ALA A  21 " =    1.229
peak=    4.082 closest distance to " O   HOH Z 369 " =    2.362
peak=    4.061 closest distance to " CB  GLU A 152 " =    1.127
peak=    4.059 closest distance to " CG  ARG A  66 " =    0.972
peak=    4.058 closest distance to " O   HOH Z 389 " =    1.950
peak=    4.051 closest distance to " O   HOH Z  59 " =    2.272
peak=    4.035 closest distance to " CB  GLU A 277 " =    3.580
peak=    4.026 closest distance to " CB  LEU A 228 " =    1.116
peak=    4.024 closest distance to " CB  SER A  62 " =    0.864
peak=    4.015 closest distance to " CG  ARG A  66 " =    2.745
peak=    4.010 closest distance to " CA  ASN A 176 " =    1.127
peak=    4.008 closest distance to " O   HOH Z 368 " =    2.060
peak=    4.006 closest distance to " O   HOH Z 102 " =    1.251
peak=    3.992 closest distance to " O   HOH Z  80 " =    1.720
peak=    3.984 closest distance to " O   HOH Z  44 " =    1.962
peak=    3.977 closest distance to " OD1 ASN A  69 " =    2.540
peak=    3.971 closest distance to " CB  ARG A  79 " =    1.292
peak=    3.968 closest distance to " CB  SER A   3 " =    1.222
peak=    3.957 closest distance to " O   HOH Z  54 " =    2.195
peak=    3.937 closest distance to " NE2 GLN A  11 " =    0.942
peak=    3.933 closest distance to " CA  ARG A 195 " =    1.263
peak=    3.921 closest distance to " O   HOH Z 421 " =    1.815
peak=    3.910 closest distance to " O   HOH Z 316 " =    2.976
peak=    3.904 closest distance to " O   HOH Z 128 " =    2.008
peak=    3.904 closest distance to " O   HOH Z 287 " =    1.923
peak=    3.898 closest distance to " O   HOH Z 134 " =    1.368
peak=    3.886 closest distance to " CA  ARG A  36 " =    1.047
peak=    3.883 closest distance to " O   HOH Z 227 " =    1.709
peak=    3.881 closest distance to " O   HOH Z 284 " =    2.914
peak=    3.874 closest distance to " O   HOH Z 426 " =    1.529
peak=    3.871 closest distance to " NH2 ARG A 156 " =    1.142
peak=    3.867 closest distance to " O   HOH Z 346 " =    1.618
peak=    3.862 closest distance to " O   HOH Z  63 " =    1.934
peak=    3.854 closest distance to " O   HOH Z 303 " =    2.072
peak=    3.853 closest distance to " O   HOH Z 250 " =    1.447
peak=    3.842 closest distance to " O   HOH Z 245 " =    1.330
peak=    3.829 closest distance to " CG2 VAL A 257 " =    0.863
peak=    3.817 closest distance to " CB  TRP A 179 " =    1.268
peak=    3.816 closest distance to " ND2 ASN A 187 " =    1.595
peak=    3.816 closest distance to " CZ  PHE A 218 " =    1.052
peak=    3.814 closest distance to " O   HOH Z 345 " =    2.924
peak=    3.814 closest distance to " O   HOH Z 427 " =    2.897
peak=    3.807 closest distance to " O   HOH Z 158 " =    2.974
peak=    3.797 closest distance to " O   HOH Z 423 " =    1.914
peak=    3.793 closest distance to " O   HOH Z 411 " =    3.510
peak=    3.790 closest distance to " CB  PRO A  54 " =    1.371
peak=    3.789 closest distance to " O   HOH Z  61 " =    1.609
peak=    3.789 closest distance to " CG  GLN A  58 " =    2.540
peak=    3.787 closest distance to " O   HOH Z 124 " =    1.349
peak=    3.784 closest distance to " N   ASN A  39 " =    1.283
peak=    3.773 closest distance to " CB  PRO A 198 " =    1.096
peak=    3.758 closest distance to " O   HOH Z  49 " =    2.298
peak=    3.758 closest distance to " O   HOH Z 279 " =    2.137
peak=    3.758 closest distance to " OD2 ASP A 286 " =    2.798
peak=    3.757 closest distance to " CG2 ILE A  20 " =    1.338
peak=    3.744 closest distance to " CB  VAL A 265 " =    1.213
peak=    3.731 closest distance to " O   HOH Z 357 " =    1.913
peak=    3.728 closest distance to " O   HOH Z 261 " =    1.654
peak=    3.724 closest distance to " O   HOH Z 214 " =    2.266
peak=    3.719 closest distance to " O   HOH Z 371 " =    3.345
peak=    3.718 closest distance to " O   HOH Z 406 " =    1.561
peak=    3.714 closest distance to " O   HOH Z  21 " =    1.776
peak=    3.713 closest distance to " CD2 TRP A 179 " =    1.429
peak=    3.710 closest distance to " CA  ASP A 140 " =    1.112
peak=    3.709 closest distance to " OE1 GLU A   2 " =    2.124
peak=    3.703 closest distance to " O   HOH Z 365 " =    2.794
peak=    3.702 closest distance to " CD1 LEU A  96 " =    0.732
peak=    3.693 closest distance to " CD2 LEU A 297 " =    0.926
peak=    3.692 closest distance to " CG2BVAL A  41 " =    0.840
peak=    3.685 closest distance to " O   HOH Z 147 " =    1.781
peak=    3.684 closest distance to " CG AARG A 275 " =    1.129
peak=    3.682 closest distance to " OD2 ASP A 298 " =    3.938
peak=    3.671 closest distance to " CB  ARG A  79 " =    0.873
peak=    3.655 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.647 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.638 closest distance to " CB  SER A 141 " =    1.035
peak=    3.635 closest distance to " CG2 VAL A  78 " =    0.887
peak=    3.632 closest distance to " O   HOH Z 132 " =    2.670
peak=    3.631 closest distance to " C   GLY A  80 " =    1.128
peak=    3.628 closest distance to " CA  ALA A  51 " =    0.966
peak=    3.619 closest distance to " N   HIS A 108 " =    1.861
peak=    3.618 closest distance to " O   HOH Z 327 " =    1.589
peak=    3.615 closest distance to " O   HOH Z  68 " =    1.879
peak=    3.614 closest distance to " O   HOH Z 344 " =    3.104
peak=    3.613 closest distance to " CG1BVAL A  72 " =    1.743
peak=    3.613 closest distance to " CA  ALA A 160 " =    0.847
peak=    3.612 closest distance to " O   HOH Z  54 " =    1.696
peak=    3.606 closest distance to " OG BSER A 164 " =    2.312
peak=    3.606 closest distance to " CA  THR A 221 " =    0.939
peak=    3.604 closest distance to " O   HOH Z 402 " =    2.875
peak=    3.598 closest distance to " CG2 ILE A 120 " =    1.147
peak=    3.593 closest distance to " CG2 VAL A 197 " =    1.130
peak=    3.590 closest distance to " O   HOH Z 132 " =    2.496
peak=    3.579 closest distance to " CB  ASN A  39 " =    0.816
peak=    3.579 closest distance to " O   HOH Z  66 " =    2.111
peak=    3.579 closest distance to " CB  ALA A 291 " =    1.262
peak=    3.576 closest distance to " CB  ARG A 269 " =    0.757
peak=    3.572 closest distance to " O   HOH Z 361 " =    3.611
peak=    3.556 closest distance to " O   HOH Z 298 " =    2.340
peak=    3.548 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.537 closest distance to " O   HOH Z  97 " =    2.512
peak=    3.536 closest distance to " CB  VAL A 202 " =    1.455
peak=    3.522 closest distance to " O   HOH Z  19 " =    1.652
peak=    3.519 closest distance to " O   HOH Z 185 " =    1.717
peak=    3.513 closest distance to " CB  TRP A 266 " =    0.980
peak=    3.507 closest distance to " O   HOH Z 374 " =    2.634
peak=    3.503 closest distance to " CA  VAL A  41 " =    0.913
peak=    3.502 closest distance to " O   HOH Z 345 " =    1.581
peak=    3.502 closest distance to " O   HOH Z 108 " =    2.565
peak=    3.499 closest distance to " O   THR A 220 " =    1.197
peak=    3.497 closest distance to " O   HOH Z 183 " =    1.493
peak=    3.497 closest distance to " CB  ARG A 139 " =    0.785
peak=    3.487 closest distance to " O   HOH Z 163 " =    1.522
peak=    3.485 closest distance to " CB  TYR A 169 " =    0.853
peak=    3.484 closest distance to " CA  LYS A 117 " =    1.286
peak=    3.476 closest distance to " C   SER A  32 " =    1.075
peak=    3.470 closest distance to " CE1 TYR A 186 " =    1.276
peak=    3.459 closest distance to " CB  MET A  47 " =    0.955
peak=    3.457 closest distance to " CB  ASP A 140 " =    0.955
peak=    3.455 closest distance to " O   HOH Z 417 " =    3.049
peak=    3.432 closest distance to " O   HOH Z 295 " =    1.468
peak=    3.427 closest distance to " CA  ASP A 162 " =    1.175
peak=    3.425 closest distance to " O   THR A 251 " =    1.183
peak=    3.425 closest distance to " NH2AARG A 145 " =    2.313
peak=    3.424 closest distance to " O   HOH Z 427 " =    3.043
peak=    3.420 closest distance to " OE1 GLN A  11 " =    1.812
peak=    3.420 closest distance to " CE  LYS A  76 " =    0.858
peak=    3.418 closest distance to " O   HOH Z 257 " =    2.285
peak=    3.418 closest distance to " N   TYR A 116 " =    1.590
peak=    3.417 closest distance to " CA  ALA A 248 " =    1.218
peak=    3.416 closest distance to " CA  ALA A  84 " =    1.195
peak=    3.412 closest distance to " CD BLYS A 290 " =    1.105
peak=    3.407 closest distance to " O   HOH Z 337 " =    3.728
peak=    3.404 closest distance to " O   HOH Z 291 " =    1.496
peak=    3.400 closest distance to " CA  MET A 105 " =    1.121
peak=    3.400 closest distance to " O   HOH Z 383 " =    2.119
peak=    3.399 closest distance to " OG1 THR A 294 " =    2.327
peak=    3.397 closest distance to " NZ  LYS A  76 " =    1.547
peak=    3.396 closest distance to " CG1 VAL A 153 " =    1.015
peak=    3.395 closest distance to " OG  SER A  62 " =    2.835
peak=    3.395 closest distance to " CG2AVAL A 121 " =    2.150
peak=    3.393 closest distance to " O   TRP A 274 " =    1.908
peak=    3.386 closest distance to " O   HOH Z 380 " =    1.995
peak=    3.381 closest distance to " CD1 LEU A 300 " =    1.246
peak=    3.379 closest distance to " O   HOH Z 173 " =    2.171
peak=    3.375 closest distance to " NZ  LYS A 119 " =    1.496
peak=    3.367 closest distance to " CA  ALA A 291 " =    0.833
peak=    3.364 closest distance to " NH1AARG A 145 " =    1.198
peak=    3.364 closest distance to " CA  VAL A 125 " =    1.310
peak=    3.357 closest distance to " O   HOH Z 419 " =    1.490
peak=    3.357 closest distance to " O   HOH Z 193 " =    2.176
peak=    3.350 closest distance to " N   TRP A 150 " =    1.104
peak=    3.343 closest distance to " CA  ASP A 191 " =    0.851
peak=    3.338 closest distance to " CD  LYS A 166 " =    1.335
peak=    3.336 closest distance to " O   HOH Z 148 " =    3.177
peak=    3.336 closest distance to " CB  SER A 273 " =    0.823
peak=    3.336 closest distance to " O   HOH Z 261 " =    2.048
peak=    3.326 closest distance to " OH  TYR A 116 " =    1.106
peak=    3.321 closest distance to " CD2 LEU A 255 " =    1.263
peak=    3.312 closest distance to " O   SER A  26 " =    1.728
peak=    3.308 closest distance to " O   HOH Z 299 " =    4.510
peak=    3.306 closest distance to " CE1 HIS A 108 " =    1.132
peak=    3.304 closest distance to " CG2 THR A 221 " =    1.149
peak=    3.304 closest distance to " ND2 ASN A 110 " =    1.592
peak=    3.302 closest distance to " CA  ASP A 191 " =    1.133
peak=    3.297 closest distance to " CD1 ILE A 106 " =    0.863
peak=    3.293 closest distance to " O   HOH Z  89 " =    2.213
peak=    3.291 closest distance to " O   HOH Z 437 " =    1.372
peak=    3.282 closest distance to " O   HOH Z 336 " =    1.693
peak=    3.282 closest distance to " CB  GLU A  46 " =    1.006
peak=    3.279 closest distance to " CB  ASN A 285 " =    0.958
peak=    3.277 closest distance to " O   HOH Z 250 " =    1.728
peak=    3.277 closest distance to " O   HOH Z 408 " =    1.454
peak=    3.275 closest distance to " O   HOH Z 261 " =    2.130
peak=    3.275 closest distance to " CB  ALA A  71 " =    1.258
peak=    3.270 closest distance to " O   HOH Z  20 " =    1.388
peak=    3.268 closest distance to " C   PHE A  59 " =    0.807
peak=    3.265 closest distance to " O   HOH Z 435 " =    1.842
peak=    3.264 closest distance to " O   HOH Z 273 " =    2.888
peak=    3.260 closest distance to " O   HOH Z 422 " =    2.607
peak=    3.257 closest distance to " CZ  PHE A  38 " =    1.369
peak=    3.254 closest distance to " CB  SER A  26 " =    1.691
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.659
peak=    3.250 closest distance to " O   HOH Z 334 " =    1.573
peak=    3.249 closest distance to " O   HOH Z 234 " =    1.784
peak=    3.245 closest distance to " CA  MET A  40 " =    1.076
peak=    3.243 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.235 closest distance to " OG BSER A 134 " =    2.837
peak=    3.231 closest distance to " O   HOH Z 409 " =    3.404
peak=    3.228 closest distance to " CA  SER A  87 " =    1.046
peak=    3.226 closest distance to " O   ALA A 242 " =    1.041
peak=    3.225 closest distance to " CG  MET A 185 " =    1.152
peak=    3.223 closest distance to " NZ  LYS A 117 " =    2.254
peak=    3.223 closest distance to " O   HOH Z 126 " =    1.520
peak=    3.222 closest distance to " O   HOH Z 392 " =    2.681
peak=    3.219 closest distance to " O   HOH Z   1 " =    2.253
peak=    3.218 closest distance to " CB  PHE A  16 " =    1.001
peak=    3.218 closest distance to " O   HOH Z 353 " =    2.803
peak=    3.218 closest distance to " CG  GLN A  11 " =    1.306
peak=    3.213 closest distance to " CB  THR A 157 " =    1.079
peak=    3.211 closest distance to " CD  PRO A  54 " =    1.249
peak=    3.211 closest distance to " O   ALA A 165 " =    1.450
peak=    3.204 closest distance to " CE  LYS A 119 " =    1.120
peak=    3.204 closest distance to " O   HOH Z 414 " =    1.671
peak=    3.203 closest distance to " CB  GLN A 278 " =    0.902
peak=    3.202 closest distance to " O   HOH Z 135 " =    1.776
peak=    3.201 closest distance to " CD1 LEU A 222 " =    0.709
peak=    3.198 closest distance to " CB  SER A 216 " =    0.839
peak=    3.193 closest distance to " O   HOH Z 423 " =    3.433
peak=    3.192 closest distance to " O   HOH Z 425 " =    2.056
peak=    3.185 closest distance to " CG1 ILE A 120 " =    1.131
peak=    3.183 closest distance to " CG2 ILE A 106 " =    0.877
peak=    3.182 closest distance to " CA  GLU A 152 " =    0.865
peak=    3.175 closest distance to " O   HOH Z 417 " =    2.412
peak=    3.172 closest distance to " O   HOH Z 305 " =    3.699
peak=    3.169 closest distance to " OH  TYR A  30 " =    1.145
peak=    3.169 closest distance to " O   HOH Z  88 " =    3.227
peak=    3.166 closest distance to " O   HOH Z 281 " =    4.512
peak=    3.159 closest distance to " N   ARG A 156 " =    1.418
peak=    3.159 closest distance to " CA  SER A  32 " =    1.582
peak=    3.159 closest distance to " NE1 TRP A 274 " =    0.873
peak=    3.152 closest distance to " O   HOH Z  10 " =    1.741
peak=    3.150 closest distance to " CG  ARG A 219 " =    1.261
peak=    3.149 closest distance to " O   HOH Z 267 " =    1.974
peak=    3.145 closest distance to " CG  LEU A 167 " =    1.146
peak=    3.144 closest distance to " CB  ILE A 120 " =    1.280
peak=    3.143 closest distance to " O   HOH Z 367 " =    3.566
peak=    3.135 closest distance to " NH2AARG A 190 " =    1.857
peak=    3.128 closest distance to " NZ  LYS A 166 " =    2.971
peak=    3.127 closest distance to " O   HOH Z 359 " =    1.361
peak=    3.124 closest distance to " CD  LYS A 119 " =    1.309
peak=    3.118 closest distance to " CZ2 TRP A 179 " =    1.733
peak=    3.114 closest distance to " O   HOH Z 156 " =    2.630
peak=    3.114 closest distance to " C   TYR A 214 " =    1.479
peak=    3.110 closest distance to " O   HOH Z  63 " =    2.248
peak=    3.110 closest distance to " CA  ARG A  66 " =    1.035
peak=    3.104 closest distance to " CD2 TYR A  30 " =    0.965
peak=    3.101 closest distance to " CB  ALA A 242 " =    0.967
peak=    3.099 closest distance to " CB  ALA A   9 " =    1.554
peak=    3.095 closest distance to " O   HOH Z  48 " =    1.747
peak=    3.095 closest distance to " CG  GLN A  77 " =    2.020
peak=    3.082 closest distance to " O   ASP A 238 " =    0.752
peak=    3.076 closest distance to " O   HOH Z 393 " =    3.443
peak=    3.074 closest distance to " N   ARG A 190 " =    0.936
peak=    3.073 closest distance to " O   HOH Z 163 " =    1.572
peak=    3.071 closest distance to " CG2 VAL A 202 " =    1.098
peak=    3.070 closest distance to " CB  PRO A 243 " =    1.488
peak=    3.067 closest distance to " OD1 ASP A 238 " =    1.009
peak=    3.066 closest distance to " CB  VAL A 126 " =    1.167
peak=    3.063 closest distance to " CB  LYS A 289 " =    1.041
peak=    3.059 closest distance to " O   HOH Z 403 " =    1.327
peak=    3.053 closest distance to " CB  ASN A 215 " =    1.114
peak=    3.048 closest distance to " CB  GLN A 103 " =    0.831

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.882 - 5.807
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.882 - 5.807

peak=   -4.867 closest distance to " O   HOH Z 266 " =    4.560
peak=   -4.535 closest distance to " C   HIS A 108 " =    1.062
peak=   -4.454 closest distance to " CD  ARG A 156 " =    2.032
peak=   -4.244 closest distance to " O   HOH Z  13 " =    1.655
peak=   -4.180 closest distance to " O   HOH Z 165 " =    1.912
peak=   -4.166 closest distance to " OXT GLY A 302 " =    2.829
peak=   -4.136 closest distance to " SG  CYS A 254 " =    3.302
peak=   -4.118 closest distance to " O   HOH Z 372 " =    2.286
peak=   -4.109 closest distance to " O   PRO A 163 " =    2.035
peak=   -4.055 closest distance to " CD  GLN A  58 " =    1.150
peak=   -4.011 closest distance to " O   HOH Z 377 " =    1.972
peak=   -4.005 closest distance to " O   HOH Z 353 " =    2.226
peak=   -3.986 closest distance to " O   HOH Z 231 " =    2.324
peak=   -3.963 closest distance to " ND2 ASN A  45 " =    0.968
peak=   -3.957 closest distance to " O   ALA A 256 " =    1.514
peak=   -3.952 closest distance to " CD1 LEU A 101 " =    2.455
peak=   -3.921 closest distance to " CE2 TYR A  30 " =    2.795
peak=   -3.919 closest distance to " O   ILE A 109 " =    2.596
peak=   -3.911 closest distance to " CA  VAL A  67 " =    2.918
peak=   -3.894 closest distance to " O   VAL A  67 " =    2.672
peak=   -3.881 closest distance to " OG BSER A 134 " =    1.253
peak=   -3.876 closest distance to " CB  PHE A 192 " =    1.912
peak=   -3.823 closest distance to " N   ALA A 248 " =    1.720
peak=   -3.822 closest distance to " O   SER A 210 " =    1.912
peak=   -3.814 closest distance to " OE1 GLN A 223 " =    2.074
peak=   -3.812 closest distance to " C   THR A 279 " =    1.210
peak=   -3.802 closest distance to " O   HOH Z 196 " =    1.929
peak=   -3.801 closest distance to " CB  PRO A 243 " =    2.665
peak=   -3.798 closest distance to " O   HOH Z 407 " =    3.065
peak=   -3.794 closest distance to " OG  SER A   3 " =    1.702
peak=   -3.779 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.771 closest distance to " O   HOH Z  10 " =    1.562
peak=   -3.768 closest distance to " CG  ASP A 132 " =    2.288
peak=   -3.765 closest distance to " O   ALA A  34 " =    2.255
peak=   -3.741 closest distance to " CD1 LEU A  25 " =    2.447
peak=   -3.740 closest distance to " OG  SER A  97 " =    2.156
peak=   -3.736 closest distance to " O   PHE A 218 " =    1.544
peak=   -3.736 closest distance to " O   HOH Z 351 " =    1.415
peak=   -3.727 closest distance to " O   HOH Z 198 " =    1.928
peak=   -3.717 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.715 closest distance to " O   HOH Z  11 " =    1.967
peak=   -3.690 closest distance to " N   GLN A  58 " =    1.651
peak=   -3.687 closest distance to " CD  ARG A 139 " =    1.586
peak=   -3.686 closest distance to " O   HOH Z 234 " =    4.151
peak=   -3.675 closest distance to " O   HOH Z 292 " =    4.520
peak=   -3.660 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.650 closest distance to " O   TRP A  92 " =    1.830
peak=   -3.642 closest distance to " CB  ASN A  39 " =    2.286
peak=   -3.625 closest distance to " OD2 ASP A 171 " =    2.437
peak=   -3.619 closest distance to " CG  GLU A  53 " =    1.281
peak=   -3.602 closest distance to " O   HOH Z 166 " =    1.930
peak=   -3.597 closest distance to " O   HOH Z  52 " =    1.690
peak=   -3.591 closest distance to " O   HOH Z 290 " =    1.063
peak=   -3.588 closest distance to " ND2 ASN A 187 " =    1.522
peak=   -3.577 closest distance to " CD1 PHE A  59 " =    1.907
peak=   -3.575 closest distance to " CG2 ILE A 263 " =    2.295
peak=   -3.572 closest distance to " CZ  PHE A  59 " =    1.632
peak=   -3.561 closest distance to " O   HOH Z 126 " =    1.906
peak=   -3.557 closest distance to " CG  ASP A 231 " =    0.882
peak=   -3.553 closest distance to " O   HOH Z 414 " =    1.687
peak=   -3.550 closest distance to " CD1 TYR A 247 " =    2.461
peak=   -3.536 closest distance to " N   ALA A  43 " =    2.582
peak=   -3.536 closest distance to " O   HOH Z 418 " =    1.351
peak=   -3.535 closest distance to " CG  PRO A 243 " =    1.686
peak=   -3.531 closest distance to " CH2 TRP A 179 " =    1.313
peak=   -3.528 closest distance to " CB  PHE A 208 " =    2.247
peak=   -3.527 closest distance to " O   HOH Z 114 " =    3.441
peak=   -3.499 closest distance to " O   HOH Z 197 " =    1.938
peak=   -3.497 closest distance to " CD  GLN A 223 " =    1.390
peak=   -3.494 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.493 closest distance to " OD1 ASP A 191 " =    1.472
peak=   -3.493 closest distance to " O   GLY A  75 " =    1.843
peak=   -3.490 closest distance to " NE2 GLN A  88 " =    1.805
peak=   -3.490 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.483 closest distance to " CE  MET A 105 " =    2.108
peak=   -3.481 closest distance to " OD1 ASN A  39 " =    2.225
peak=   -3.474 closest distance to " C   GLY A  80 " =    2.382
peak=   -3.469 closest distance to " O   ALA A 160 " =    1.488
peak=   -3.468 closest distance to " O   HOH Z  71 " =    1.628
peak=   -3.467 closest distance to " O  BHOH Z 338 " =    1.354
peak=   -3.464 closest distance to " O   HOH Z 102 " =    1.671
peak=   -3.463 closest distance to " N   ALA A 226 " =    1.907
peak=   -3.458 closest distance to " O   GLN A  11 " =    1.319
peak=   -3.455 closest distance to " CD  ARG A 195 " =    5.051
peak=   -3.450 closest distance to " OG BSER A 134 " =    1.793
peak=   -3.445 closest distance to " C   ALA A 158 " =    1.274
peak=   -3.440 closest distance to " O   GLY A 196 " =    0.968
peak=   -3.433 closest distance to " O   HOH Z 435 " =    2.602
peak=   -3.432 closest distance to " CD1 LEU A 228 " =    2.181
peak=   -3.423 closest distance to " OG  SER A  62 " =    1.560
peak=   -3.422 closest distance to " CD2 LEU A 300 " =    2.789
peak=   -3.415 closest distance to " CD  LYS A 289 " =    2.433
peak=   -3.414 closest distance to " C   LEU A 143 " =    1.085
peak=   -3.412 closest distance to " O   HOH Z 243 " =    2.143
peak=   -3.411 closest distance to " OE2 GLU A   2 " =    1.605
peak=   -3.401 closest distance to " CG  GLU A 277 " =    1.200
peak=   -3.399 closest distance to " O   HOH Z 311 " =    3.496
peak=   -3.399 closest distance to " O   LEU A 167 " =    1.587
peak=   -3.396 closest distance to " CE3 TRP A 150 " =    2.169
peak=   -3.394 closest distance to " O   ALA A  10 " =    1.823
peak=   -3.384 closest distance to " CB  ALA A  10 " =    2.242
peak=   -3.380 closest distance to " C   ASN A 285 " =    2.363
peak=   -3.376 closest distance to " O   HOH Z  15 " =    1.520
peak=   -3.372 closest distance to " CG  GLN A  58 " =    1.047
peak=   -3.371 closest distance to " CG1 VAL A 112 " =    2.753
peak=   -3.366 closest distance to " O   HOH Z 251 " =    1.578
peak=   -3.363 closest distance to " OD2 ASP A 191 " =    1.511
peak=   -3.359 closest distance to " C   SER A 206 " =    1.636
peak=   -3.354 closest distance to " O   MET A  40 " =    2.571
peak=   -3.351 closest distance to " O   HOH Z 377 " =    1.855
peak=   -3.348 closest distance to " NH2 ARG A  66 " =    5.315
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    2.059
peak=   -3.347 closest distance to " N   THR A  52 " =    1.685
peak=   -3.347 closest distance to " CD2 LEU A 237 " =    2.231
peak=   -3.342 closest distance to " CB  ASP A 286 " =    1.905
peak=   -3.333 closest distance to " N   GLY A 133 " =    1.858
peak=   -3.331 closest distance to " O   HOH Z 389 " =    1.698
peak=   -3.329 closest distance to " O   HOH Z 250 " =    1.379
peak=   -3.328 closest distance to " O   HOH Z 265 " =    2.168
peak=   -3.327 closest distance to " NE2 GLN A 103 " =    1.771
peak=   -3.322 closest distance to " NH1 ARG A  66 " =    1.120
peak=   -3.313 closest distance to " CG  ASP A  50 " =    2.391
peak=   -3.312 closest distance to " CA  TYR A  68 " =    2.997
peak=   -3.311 closest distance to " NH1 ARG A 195 " =    2.600
peak=   -3.307 closest distance to " O   HOH Z 422 " =    1.558
peak=   -3.305 closest distance to " CB  GLN A  11 " =    1.724
peak=   -3.300 closest distance to " O   HOH Z  38 " =    1.578
peak=   -3.294 closest distance to " CD2 LEU A 237 " =    2.457
peak=   -3.292 closest distance to " O   HOH Z  60 " =    2.264
peak=   -3.289 closest distance to " O   HOH Z  43 " =    1.571
peak=   -3.286 closest distance to " OD1 ASN A 148 " =    1.555
peak=   -3.286 closest distance to " O   HOH Z 427 " =    1.351
peak=   -3.280 closest distance to " O   HOH Z 171 " =    2.092
peak=   -3.273 closest distance to " O   VAL A 174 " =    2.028
peak=   -3.272 closest distance to " O   HOH Z  11 " =    1.826
peak=   -3.271 closest distance to " CA  GLY A 203 " =    2.254
peak=   -3.269 closest distance to " CA  GLY A 241 " =    2.328
peak=   -3.268 closest distance to " CD  PRO A 198 " =    1.246
peak=   -3.263 closest distance to " OG BSER A 210 " =    2.083
peak=   -3.260 closest distance to " O   HOH Z 222 " =    1.318
peak=   -3.258 closest distance to " O   HOH Z 185 " =    2.360
peak=   -3.254 closest distance to " O   HOH Z  63 " =    1.270
peak=   -3.250 closest distance to " O   HOH Z 283 " =    1.933
peak=   -3.249 closest distance to " NH2 ARG A  66 " =    1.782
peak=   -3.241 closest distance to " O   HOH Z  19 " =    2.032
peak=   -3.241 closest distance to " OH  TYR A 169 " =    0.966
peak=   -3.240 closest distance to " CD1 ILE A 239 " =    2.133
peak=   -3.235 closest distance to " CB  ALA A 248 " =    2.238
peak=   -3.233 closest distance to " CB  PHE A  16 " =    2.600
peak=   -3.231 closest distance to " O   HOH Z 377 " =    1.576
peak=   -3.230 closest distance to " O   HOH Z 111 " =    3.767
peak=   -3.227 closest distance to " N   VAL A 189 " =    1.701
peak=   -3.227 closest distance to " CG2 THR A 178 " =    2.167
peak=   -3.223 closest distance to " CD2 TYR A 247 " =    2.419
peak=   -3.220 closest distance to " OD1 ASP A 171 " =    1.448
peak=   -3.219 closest distance to " CD2 PHE A 225 " =    1.301
peak=   -3.217 closest distance to " N   SER A 276 " =    1.453
peak=   -3.208 closest distance to " O   HOH Z 351 " =    1.410
peak=   -3.203 closest distance to " O   HOH Z   9 " =    2.008
peak=   -3.197 closest distance to " O   SER A   3 " =    1.095
peak=   -3.194 closest distance to " NE2 GLN A 194 " =    1.742
peak=   -3.193 closest distance to " CG1 VAL A 112 " =    2.559
peak=   -3.192 closest distance to " ND2 ASN A  69 " =    1.560
peak=   -3.190 closest distance to " ND2BASN A 224 " =    1.774
peak=   -3.188 closest distance to " CE  LYS A 166 " =    2.869
peak=   -3.187 closest distance to " O   ALA A 161 " =    1.455
peak=   -3.184 closest distance to " O   VAL A 125 " =    2.370
peak=   -3.175 closest distance to " CE  MET A  93 " =    1.149
peak=   -3.169 closest distance to " O   HOH Z  37 " =    1.694
peak=   -3.160 closest distance to " O   HOH Z 326 " =    1.744
peak=   -3.158 closest distance to " CD1 TRP A 179 " =    1.176
peak=   -3.151 closest distance to " O   HOH Z 111 " =    1.935
peak=   -3.150 closest distance to " O   HOH Z 252 " =    4.225
peak=   -3.146 closest distance to " CG1AVAL A  41 " =    2.668
peak=   -3.145 closest distance to " NH1 ARG A  66 " =    3.298
peak=   -3.143 closest distance to " CD  GLU A 236 " =    1.080
peak=   -3.139 closest distance to " O   HOH Z  91 " =    2.181
peak=   -3.137 closest distance to " O   ASN A  45 " =    1.884
peak=   -3.135 closest distance to " O   HOH Z 123 " =    2.236
peak=   -3.135 closest distance to " O   HOH Z  61 " =    1.575
peak=   -3.126 closest distance to " CZ  PHE A 130 " =    0.937
peak=   -3.125 closest distance to " CG1 VAL A  78 " =    2.569
peak=   -3.123 closest distance to " CG  PHE A 283 " =    2.660
peak=   -3.121 closest distance to " CG  ARG A 269 " =    2.272
peak=   -3.120 closest distance to " O   HOH Z   6 " =    1.728
peak=   -3.117 closest distance to " CB  PRO A 213 " =    1.561
peak=   -3.114 closest distance to " OD2 ASP A 171 " =    1.797
peak=   -3.110 closest distance to " O   GLU A 152 " =    1.697
peak=   -3.109 closest distance to " O   HOH Z 111 " =    3.516
peak=   -3.107 closest distance to " O   PRO A 198 " =    1.300
peak=   -3.104 closest distance to " O   HOH Z 396 " =    1.716
peak=   -3.099 closest distance to " O   SER A 135 " =    1.530
peak=   -3.098 closest distance to " O   HOH Z 423 " =    2.302
peak=   -3.098 closest distance to " CG2 VAL A 189 " =    2.212
peak=   -3.090 closest distance to " OG ASER A 134 " =    1.244
peak=   -3.077 closest distance to " O   HOH Z  41 " =    2.222
peak=   -3.076 closest distance to " O   HOH Z 280 " =    2.288
peak=   -3.075 closest distance to " OD1 ASP A 200 " =    1.331
peak=   -3.069 closest distance to " O   HOH Z 191 " =    5.807
peak=   -3.061 closest distance to " O   HOH Z 384 " =    2.097
peak=   -3.028 closest distance to " O   HOH Z 361 " =    3.402
peak=   -3.021 closest distance to " O   HOH Z 193 " =    1.898
peak=   -3.016 closest distance to " O   HOH Z 414 " =    2.162

================= 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    :  0.3808 0.3749   6.162412e+00   6.140401e+00
   1_bss:  0.3696 0.3611   6.145119e+00   6.114847e+00
   1_xyz:  0.2508 0.2709   5.821154e+00   5.887967e+00
   1_adp:  0.2285 0.2825   5.770962e+00   5.921897e+00
   1_occ:  0.2281 0.2830   5.770378e+00   5.922345e+00
   2_bss:  0.2269 0.2817   5.767176e+00   5.919106e+00
   2_xyz:  0.1604 0.2011   5.440698e+00   5.625469e+00
   2_adp:  0.1466 0.1853   5.357915e+00   5.542759e+00
   2_occ:  0.1465 0.1853   5.357202e+00   5.542076e+00
   3_bss:  0.1464 0.1842   5.354943e+00   5.536919e+00
   3_xyz:  0.1270 0.1660   5.233908e+00   5.437471e+00
   3_adp:  0.1216 0.1637   5.206183e+00   5.423295e+00
   3_occ:  0.1216 0.1637   5.206145e+00   5.423245e+00
   4_bss:  0.1216 0.1637   5.205830e+00   5.423216e+00
   4_xyz:  0.1131 0.1577   5.151003e+00   5.385679e+00
   4_adp:  0.1124 0.1569   5.144145e+00   5.379839e+00
   4_occ:  0.1124 0.1569   5.144083e+00   5.380110e+00
   5_bss:  0.1126 0.1569   5.144907e+00   5.380438e+00
   5_xyz:  0.1126 0.1575   5.149909e+00   5.386378e+00
   5_adp:  0.1121 0.1589   5.152037e+00   5.394109e+00
   5_occ:  0.1121 0.1590   5.152018e+00   5.394285e+00
   5_bss:  0.1120 0.1590   5.152143e+00   5.394411e+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:  0.304  27.182  -2.504   2.980  -0.669   0.000  -0.000  -0.000
   1_xyz:  0.304  27.182  -2.504   2.980  -0.669   0.000  -0.000  -0.000
   1_adp:  0.304  27.182  -2.504   2.980  -0.669   0.000  -0.000  -0.000
   1_occ:  0.304  27.182  -2.504   2.980  -0.669   0.000  -0.000  -0.000
   2_bss:  0.304  44.797  -2.769   0.484  -1.189   0.000  -0.000  -0.000
   2_xyz:  0.304  44.797  -2.769   0.484  -1.189   0.000  -0.000  -0.000
   2_adp:  0.304  44.797  -2.769   0.484  -1.189   0.000  -0.000  -0.000
   2_occ:  0.304  44.797  -2.769   0.484  -1.189   0.000  -0.000  -0.000
   3_bss:  0.321  49.298  -2.596  -0.785  -1.230  -0.000  -0.000  -0.000
   3_xyz:  0.321  49.298  -2.596  -0.785  -1.230  -0.000  -0.000  -0.000
   3_adp:  0.321  49.298  -2.596  -0.785  -1.230  -0.000  -0.000  -0.000
   3_occ:  0.321  49.298  -2.596  -0.785  -1.230  -0.000  -0.000  -0.000
   4_bss:  0.322  50.360  -2.477  -1.105  -1.131  -0.000  -0.000  -0.000
   4_xyz:  0.322  50.360  -2.477  -1.105  -1.131  -0.000  -0.000  -0.000
   4_adp:  0.322  50.360  -2.477  -1.105  -1.131  -0.000  -0.000  -0.000
   4_occ:  0.322  50.360  -2.477  -1.105  -1.131  -0.000  -0.000  -0.000
   5_bss:  0.322  50.360  -2.327  -1.138  -1.000  -0.000  -0.000  -0.000
   5_xyz:  0.322  50.360  -2.327  -1.138  -1.000  -0.000  -0.000  -0.000
   5_adp:  0.322  50.360  -2.327  -1.138  -1.000  -0.000  -0.000  -0.000
   5_occ:  0.322  50.360  -2.327  -1.138  -1.000  -0.000  -0.000  -0.000
   5_bss:  0.322  50.363  -2.126  -1.002  -0.803  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.645 0.6372  0.8171    40772.955
   1_bss:  39.460 0.6494  0.8276    36952.842
   1_xyz:  27.577 0.7853  0.9588    19518.173
   1_adp:  29.153 0.7672  0.9354    21273.006
   1_occ:  29.189 0.7667  0.9347    21297.774
   2_bss:  28.903 0.7700  0.9063    21013.575
   2_xyz:  19.718 0.8635  0.9803    10347.975
   2_adp:  17.582 0.8842  0.9832     8737.053
   2_occ:  17.579 0.8842  0.9830     8727.120
   3_bss:  17.418 0.8856  0.9719     8591.103
   3_xyz:  15.143 0.9055  0.9819     6976.581
   3_adp:  14.797 0.9087  0.9767     6823.632
   3_occ:  14.797 0.9087  0.9766     6823.286
   4_bss:  14.788 0.9088  0.9759     6823.146
   4_xyz:  14.049 0.9146  0.9785     6305.537
   4_adp:  13.897 0.9159  0.9730     6248.056
   4_occ:  13.901 0.9159  0.9729     6250.967
   5_bss:  13.908 0.9158  0.9758     6256.702
   5_xyz:  13.957 0.9156  0.9760     6310.632
   5_adp:  14.099 0.9145  0.9689     6401.062
   5_occ:  14.100 0.9145  0.9688     6402.426
   5_bss:  14.101 0.9145  0.9752     6404.459
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6769e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6769e-01
   1_xyz:   1.258  0.010  0.074 15.036  0.005  4.111   8.8681e-02
   1_adp:   1.258  0.010  0.074 15.036  0.005  4.111   8.8681e-02
   1_occ:   1.258  0.010  0.074 15.036  0.005  4.111   8.8681e-02
   2_bss:   1.258  0.010  0.074 15.036  0.005  4.111   8.8681e-02
   2_xyz:   1.131  0.007  0.075 14.520  0.005  4.122   6.7231e-02
   2_adp:   1.131  0.007  0.075 14.520  0.005  4.122   6.7231e-02
   2_occ:   1.131  0.007  0.075 14.520  0.005  4.122   6.7231e-02
   3_bss:   1.131  0.007  0.075 14.520  0.005  4.122   6.7231e-02
   3_xyz:   0.895  0.005  0.064 14.383  0.004  4.117   4.9071e-02
   3_adp:   0.895  0.005  0.064 14.383  0.004  4.117   4.9071e-02
   3_occ:   0.895  0.005  0.064 14.383  0.004  4.117   4.9071e-02
   4_bss:   0.895  0.005  0.064 14.383  0.004  4.117   4.9071e-02
   4_xyz:   0.978  0.006  0.072 14.557  0.004  4.120   5.5840e-02
   4_adp:   0.978  0.006  0.072 14.557  0.004  4.120   5.5840e-02
   4_occ:   0.978  0.006  0.072 14.557  0.004  4.120   5.5840e-02
   5_bss:   0.978  0.006  0.072 14.557  0.004  4.120   5.5840e-02
   5_xyz:   0.892  0.005  0.067 14.335  0.003  4.121   4.8624e-02
   5_adp:   0.892  0.005  0.067 14.335  0.003  4.121   4.8624e-02
   5_occ:   0.892  0.005  0.067 14.335  0.003  4.121   4.8624e-02
   5_bss:   0.892  0.005  0.067 14.335  0.003  4.121   4.8624e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4058e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4058e-01
   1_xyz:   7.958  0.061  0.403 86.964  0.032  2.187   1.7217e-01
   1_adp:   7.958  0.061  0.403 86.964  0.032  2.187   1.7217e-01
   1_occ:   7.958  0.061  0.403 86.964  0.032  2.187   1.7217e-01
   2_bss:   7.958  0.061  0.403 86.964  0.032  2.187   1.7217e-01
   2_xyz:   7.197  0.051  0.252 81.589  0.042  2.252   5.8115e-02
   2_adp:   7.197  0.051  0.252 81.589  0.042  2.252   5.8115e-02
   2_occ:   7.197  0.051  0.252 81.589  0.042  2.252   5.8115e-02
   3_bss:   7.197  0.051  0.252 81.589  0.042  2.252   5.8115e-02
   3_xyz:   6.552  0.037  0.205 79.936  0.036  2.373   3.7667e-02
   3_adp:   6.552  0.037  0.205 79.936  0.036  2.373   3.7667e-02
   3_occ:   6.552  0.037  0.205 79.936  0.036  2.373   3.7667e-02
   4_bss:   6.552  0.037  0.205 79.936  0.036  2.373   3.7667e-02
   4_xyz:   7.133  0.044  0.233 82.837  0.035  2.335   3.6248e-02
   4_adp:   7.133  0.044  0.233 82.837  0.035  2.335   3.6248e-02
   4_occ:   7.133  0.044  0.233 82.837  0.035  2.335   3.6248e-02
   5_bss:   7.133  0.044  0.233 82.837  0.035  2.335   3.6248e-02
   5_xyz:   6.734  0.041  0.220 81.000  0.033  2.412   2.9120e-02
   5_adp:   6.734  0.041  0.220 81.000  0.033  2.412   2.9120e-02
   5_occ:   6.734  0.041  0.220 81.000  0.033  2.412   2.9120e-02
   5_bss:   6.734  0.041  0.220 81.000  0.033  2.412   2.9120e-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:  65.82   0.00  17.23  59.05   0.00  13.51  65.82   3.51  37.49
   1_occ:  65.82   0.00  17.23  59.05   0.00  13.51  65.82   3.51  37.49
   2_bss:  65.82   0.00  17.23  59.05   0.00  13.51  65.82   3.51  37.49
   2_xyz:  65.82   0.00  17.23  59.05   0.00  13.51  65.82   3.51  37.49
   2_adp:  66.50   1.23  16.68  66.50   1.23  12.83  65.99   5.51  37.64
   2_occ:  66.50   1.23  16.68  66.50   1.23  12.83  65.99   5.51  37.64
   3_bss:  66.50   1.23  16.68  66.50   1.23  12.83  65.99   5.51  37.64
   3_xyz:  66.50   1.23  16.68  66.50   1.23  12.83  65.99   5.51  37.64
   3_adp:  86.66   1.17  16.98  86.66   1.17  12.73  75.93   5.28  40.12
   3_occ:  86.66   1.17  16.98  86.66   1.17  12.73  75.93   5.28  40.12
   4_bss:  86.66   1.17  16.98  86.66   1.17  12.73  75.93   5.28  40.12
   4_xyz:  86.66   1.17  16.98  86.66   1.17  12.73  75.93   5.28  40.12
   4_adp:  89.05   0.87  16.67  89.05   0.87  12.49  77.38   4.39  39.43
   4_occ:  89.05   0.87  16.67  89.05   0.87  12.49  77.38   4.39  39.43
   5_bss:  89.05   0.87  16.67  89.05   0.87  12.49  77.38   4.39  39.43
   5_xyz:  89.05   0.87  16.67  89.05   0.87  12.49  77.38   4.39  39.43
   5_adp: 103.52   0.00  16.71 103.52   0.00  12.43  88.93   5.05  40.06
   5_occ: 103.52   0.00  16.71 103.52   0.00  12.43  88.93   5.05  40.06
   5_bss: 103.53   0.00  16.72 103.53   0.00  12.43  88.93   5.05  40.06
------------------------------------------------------------------------
 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:    1.879    0.021    0.308
   1_adp:    1.879    0.021    0.308
   1_occ:    1.879    0.021    0.308
   2_bss:    1.879    0.021    0.308
   2_xyz:    1.053    0.026    0.446
   2_adp:    1.053    0.026    0.446
   2_occ:    1.053    0.026    0.446
   3_bss:    1.053    0.026    0.446
   3_xyz:    1.148    0.059    0.502
   3_adp:    1.148    0.059    0.502
   3_occ:    1.148    0.059    0.502
   4_bss:    1.148    0.059    0.502
   4_xyz:    1.187    0.067    0.531
   4_adp:    1.187    0.067    0.531
   4_occ:    1.187    0.067    0.531
   5_bss:    1.187    0.067    0.531
   5_xyz:    1.228    0.038    0.541
   5_adp:    1.228    0.038    0.541
   5_occ:    1.228    0.038    0.541
   5_bss:    1.228    0.038    0.541
------------------------------------------------------------------------

CPU time actual refinement: 345.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/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_454/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_454/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.92 
  Macro-tasks:
    bulk solvent and scale       = 40.60  
    individual site refinement   = 144.64 
    weights calculation          = 30.18  
    collect and process          = 6.79   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 222.29 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 112.39 
    alpha_beta                      = 8.48   
    target                          = 1.25   
    gradients_wrt_atomic_parameters = 116.95 
    fmodel                         = 6.93   
    r_factors                      = 0.18   
    phase_errors                   = 12.00  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 260.09 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.801 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    665 calls, 111.92 s
gradients_fft:          610 calls, 104.79 s

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

# Date 2008-01-16 Time 04:52:07 PST -0800 (1200487927.02 s)
Start R-work = 0.3808, R-free = 0.3749 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1767 (no bulk solvent and anisotropic scale)

Start R-work = 0.3696, R-free = 0.3611
Final R-work = 0.1120, R-free = 0.1590