# Date 2008-01-16 Time 03:48:40 PST -0800 (1200484120.99 s)
#phil __OFF__

Command line arguments: "../55.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31738
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 55

-------------------------------------------------------------------------------
  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: (68.4938, 46.93, 84.2302, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (68.4938, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6644 1.9505
Completeness in resolution range: 0.962179
Completeness with d_max=infinity: 0.959164

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6644
                             d_min =   1.9505

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: (68.4938, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6644 1.9505
Completeness in resolution range: 0.962179
Completeness with d_max=infinity: 0.959164

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6648 -  4.1730 [2139/2167]  1924   215  10.1%
  bin  2:  4.1730 -  3.3249 [2042/2065]  1839   203   9.9%
  bin  3:  3.3249 -  2.9083 [2031/2053]  1826   205  10.1%
  bin  4:  2.9083 -  2.6441 [1997/2016]  1802   195   9.8%
  bin  5:  2.6441 -  2.4555 [2002/2032]  1796   206  10.3%
  bin  6:  2.4555 -  2.3114 [1975/2016]  1783   192   9.7%
  bin  7:  2.3114 -  2.1960 [1969/2005]  1773   196  10.0%
  bin  8:  2.1960 -  2.1007 [1979/2016]  1777   202  10.2%
  bin  9:  2.1007 -  2.0200 [1942/1974]  1751   191   9.8%
  bin 10:  2.0200 -  1.9505 [1513/2015]  1359   154  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/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:
        0.92 -     1.72: 13
        1.72 -     2.51: 98
        2.51 -     3.31: 3861
        3.31 -     4.10: 9686
        4.10 -     4.90: 15471
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.919 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.141 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.323 3.440 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.342 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.376 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29124 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_55/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/model_refine_001.geo

CPU time processing inputs: 9.57


============================ 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 = 68.49375 46.93 84.23025 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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4448   r_free= 0.4463   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.251904                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6648 -  4.6540 0.99   1385  156 0.3571 0.3698      6.5312      6.5681|
|  2:  4.6540 -  3.7138 0.99   1340  145 0.3817 0.3593      6.7416      6.7419|
|  3:  3.7138 -  3.2502 0.99   1312  152 0.4017 0.4186        6.63      6.7526|
|  4:  3.2502 -  2.9556 0.99   1300  134 0.4246 0.4556        6.48      6.5176|
|  5:  2.9556 -  2.7453 0.98   1276  146 0.4590 0.4632      6.3492      6.3502|
|  6:  2.7453 -  2.5843 0.98   1292  142 0.4728 0.4884       6.249      6.1953|
|  7:  2.5843 -  2.4555 0.99   1282  149 0.4796 0.4213      6.2301      6.1575|
|  8:  2.4555 -  2.3491 0.99   1281  136 0.4865 0.4996      6.1669      6.1859|
|  9:  2.3491 -  2.2590 0.98   1285  146 0.5098 0.4781      6.1114      6.1295|
| 10:  2.2590 -  2.1813 0.97   1246  139 0.4867 0.5447      6.0926      6.1029|
| 11:  2.1813 -  2.1133 0.98   1259  144 0.5098 0.4849      6.0312      6.0736|
| 12:  2.1133 -  2.0531 0.99   1279  133 0.4969 0.4825      5.9719       5.986|
| 13:  2.0531 -  1.9992 0.97   1248  135 0.4957 0.5566      5.8794      5.8901|
| 14:  1.9992 -  1.9505 0.66    845  102 0.5169 0.5105      5.8506      5.7358|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6648 -  4.6540  1385   156  0.69  34.93   0.84     0.72      70966.56|
|  2:  4.6540 -  3.7138  1340   145  0.69  35.71   0.93     0.81     105668.80|
|  3:  3.7138 -  3.2502  1312   152  0.60  43.48   0.95     0.80     113431.04|
|  4:  3.2502 -  2.9556  1300   134  0.52  50.26   0.97     0.74      99851.65|
|  5:  2.9556 -  2.7453  1276   146  0.46  54.81   0.92     0.67      79060.45|
|  6:  2.7453 -  2.5843  1292   142  0.44  56.85   0.91     0.62      66084.30|
|  7:  2.5843 -  2.4555  1282   149  0.45  56.01   0.93     0.63      59488.18|
|  8:  2.4555 -  2.3491  1281   136  0.44  57.17   0.95     0.63      53165.36|
|  9:  2.3491 -  2.2590  1285   146  0.41  59.20   0.94     0.62      49877.06|
| 10:  2.2590 -  2.1813  1246   139  0.42  58.61   1.00     0.61      45183.31|
| 11:  2.1813 -  2.1133  1259   144  0.39  60.89   0.96     0.59      42713.25|
| 12:  2.1133 -  2.0531  1279   133  0.38  61.56   1.00     0.60      40307.99|
| 13:  2.0531 -  1.9992  1248   135  0.34  64.69   0.97     0.53      36820.00|
| 14:  1.9992 -  1.9505   845   102  0.30  67.85   0.95     0.41      30689.05|
|alpha:            min =        0.41 max =            0.81 mean =         0.65|
|beta:             min =    30689.05 max =       113431.04 mean =     65045.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.86|
|phase err.(test): min =        0.00 max =           89.93 mean =        53.90|
|-----------------------------------------------------------------------------|

============================== 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 = 9.154530              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.771   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.279932              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.249   (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 |  0.919 -  1.318:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.318 -  1.716:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.716 -  2.114:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.114 -  2.512:       72 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.512 -  2.910:     1481 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.910 -  3.308:     2380 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.308 -  3.706:     3800 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.706 -  4.104:     5886 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.104 -  4.502:     6813 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.502 -  4.900:     8658 |
|-----------------------------------------------------------------------------|
|-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 |        0.264 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  0.919 |       1.751 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4448   r_free= 0.4463   ksol= 0.00   Bsol= 0.00   scale= 0.925    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.251904                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4349   r_free= 0.4361   ksol= 0.30   Bsol= 20.00   scale= 0.949   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,-3.03,2.55,-0.00,0.00,0.00); trace/3= -0.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.243133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.466372              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.036344              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.956   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4349      final r-factor (work) = 0.3148          |
| start r-factor (free) = 0.4361      final r-factor (free) = 0.3413          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5720 = 7.47 * 0.50 * 6.2435 + 1.00 * 0.2638                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9530 = 7.47 * 0.50 * 6.1058 + 1.00 * 0.1588                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3148      final r-factor (work) = 0.2839          |
| start r-factor (free) = 0.3413      final r-factor (free) = 0.3433          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3339 = 1.04 * 1.00 * 6.1058 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1732 = 1.04 * 1.00 * 5.9383 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.64   19.49    None  None   None       |
|    all(noH): 2823   0      0.00    95.64   19.49    None  None   None       |
|    Sol.    : 438    0      2.92    95.64   42.39    None  None   None       |
|    Mac.    : 2385   0      0.00    85.65   15.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.564:  881   |   5:    47.820 -  57.384:  102        |
|      1:     9.564 -  19.128:  944   |   6:    57.384 -  66.948:   67        |
|      2:    19.128 -  28.692:  400   |   7:    66.948 -  76.512:   36        |
|      3:    28.692 -  38.256:  219   |   8:    76.512 -  86.076:   20        |
|      4:    38.256 -  47.820:  152   |   9:    86.076 -  95.640:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2839 r_free = 0.3433             target_work(ml) = 5.942         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2836 r_free = 0.3433             target_work(ml) = 5.941         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2836   r_free= 0.3433   ksol= 0.30   Bsol= 20.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,-3.03,2.55,-0.00,0.00,0.00); trace/3= -0.06                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.941037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2793   r_free= 0.3393   ksol= 0.32   Bsol= 34.06   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-2.07,0.48,-0.00,0.00,0.00); trace/3= -1.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.932150                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.581602              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.114   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415798              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.368  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2793      final r-factor (work) = 0.2169          |
| start r-factor (free) = 0.3393      final r-factor (free) = 0.2682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7852 = 3.58 * 0.50 * 5.9341 + 1.00 * 0.1584                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5038 = 3.58 * 0.50 * 5.8284 + 1.00 * 0.0663                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2169      final r-factor (work) = 0.2008          |
| start r-factor (free) = 0.2682      final r-factor (free) = 0.2561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4411 = 0.42 * 1.00 * 5.8284 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3721 = 0.42 * 1.00 * 5.6783 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.81  18.55    None  None   None       |
|    all(noH): 2823   0      0.00    100.81  18.55    None  None   None       |
|    Sol.    : 438    0      5.29    88.88   41.51    None  None   None       |
|    Mac.    : 2385   0      0.00    100.81  14.33    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 -  10.081: 1017   |   5:    50.406 -  60.488:   81        |
|      1:    10.081 -  20.163:  975   |   6:    60.488 -  70.569:   53        |
|      2:    20.163 -  30.244:  338   |   7:    70.569 -  80.650:   18        |
|      3:    30.244 -  40.325:  178   |   8:    80.650 -  90.731:    7        |
|      4:    40.325 -  50.406:  154   |   9:    90.731 - 100.813:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2008 r_free = 0.2561             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2004 r_free = 0.2559             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2004   r_free= 0.2559   ksol= 0.32   Bsol= 34.06   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.56,-2.07,0.48,-0.00,0.00,0.00); trace/3= -1.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.651233                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1999   r_free= 0.2541   ksol= 0.31   Bsol= 26.29   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.94,-0.71,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.647759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.265179              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.133  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216786              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.615  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1999      final r-factor (work) = 0.1527          |
| start r-factor (free) = 0.2541      final r-factor (free) = 0.2028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3367 = 3.27 * 0.50 * 5.6784 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0877 = 3.27 * 0.50 * 5.5291 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1527      final r-factor (work) = 0.1428          |
| start r-factor (free) = 0.2028      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2107 = 0.22 * 1.00 * 5.5291 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1788 = 0.22 * 1.00 * 5.3814 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.09   17.69    None  None   None       |
|    all(noH): 2823   0      0.00    98.09   17.69    None  None   None       |
|    Sol.    : 438    0      2.28    85.98   40.61    None  None   None       |
|    Mac.    : 2385   0      0.00    98.09   13.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.809:  931   |   5:    49.045 -  58.854:   96        |
|      1:     9.809 -  19.618: 1190   |   6:    58.854 -  68.663:   41        |
|      2:    19.618 -  29.427:  256   |   7:    68.663 -  78.471:   15        |
|      3:    29.427 -  39.236:  142   |   8:    78.471 -  88.280:    8        |
|      4:    39.236 -  49.045:  143   |   9:    88.280 -  98.089:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1428 r_free = 0.1883             target_work(ml) = 5.339         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1882             target_work(ml) = 5.338         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1882   ksol= 0.31   Bsol= 26.29   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.94,-0.71,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.337528                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1866   ksol= 0.31   Bsol= 28.83   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.33,-1.84,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.334416                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.109758              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.792  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.818   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1423      final r-factor (work) = 0.1211          |
| start r-factor (free) = 0.1866      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4375 = 3.11 * 0.50 * 5.3872 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2477 = 3.11 * 0.50 * 5.2623 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4572 = 0.27 * 1.00 * 5.2623 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4275 = 0.27 * 1.00 * 5.1844 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.46    99.77   17.58    None  None   None       |
|    all(noH): 2823   0      2.46    99.77   17.58    None  None   None       |
|    Sol.    : 438    0      2.46    85.69   40.91    None  None   None       |
|    Mac.    : 2385   0      2.67    99.77   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.461 -  12.192: 1451   |   5:    51.117 -  60.848:   94        |
|      1:    12.192 -  21.923:  798   |   6:    60.848 -  70.579:   38        |
|      2:    21.923 -  31.654:  170   |   7:    70.579 -  80.311:   12        |
|      3:    31.654 -  41.386:  129   |   8:    80.311 -  90.042:    6        |
|      4:    41.386 -  51.117:  124   |   9:    90.042 -  99.773:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1630             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1628             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1628   ksol= 0.31   Bsol= 28.83   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.18,-2.33,-1.84,-0.00,-0.00,-0.00); trace/3= -2.45                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.173522                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1626   ksol= 0.31   Bsol= 32.21   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.36,-2.05,-0.00,-0.00,-0.00); trace/3= -2.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172537                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.167480              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.568  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303772              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.880  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6834 = 2.17 * 0.50 * 5.1838 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6503 = 2.17 * 0.50 * 5.1587 + 1.00 * 0.0596                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1113          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5749 = 0.30 * 1.00 * 5.1587 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5696 = 0.30 * 1.00 * 5.1411 + 1.00 * 0.0079                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.78    100.89  17.38    None  None   None       |
|    all(noH): 2823   0      2.78    100.89  17.38    None  None   None       |
|    Sol.    : 438    0      3.43    89.17   40.37    None  None   None       |
|    Mac.    : 2385   0      2.78    100.89  13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.779 -  12.590: 1542   |   5:    51.834 -  61.645:   78        |
|      1:    12.590 -  22.401:  730   |   6:    61.645 -  71.456:   36        |
|      2:    22.401 -  32.212:  163   |   7:    71.456 -  81.267:    8        |
|      3:    32.212 -  42.023:  132   |   8:    81.267 -  91.078:    8        |
|      4:    42.023 -  51.834:  125   |   9:    91.078 - 100.889:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1113 r_free = 0.1591             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1590             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1590   ksol= 0.31   Bsol= 32.21   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.36,-2.05,-0.00,-0.00,-0.00); trace/3= -2.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6648 -  4.6540 0.99   1385  156 0.1040 0.1302      5.4234      5.5744|
|  2:  4.6540 -  3.7138 0.99   1340  145 0.0861 0.1104      5.4401      5.6055|
|  3:  3.7138 -  3.2502 0.99   1312  152 0.1038 0.1491       5.449       5.821|
|  4:  3.2502 -  2.9556 0.99   1300  134 0.1204 0.1648       5.448      5.6399|
|  5:  2.9556 -  2.7453 0.98   1276  146 0.1256 0.1581      5.3028      5.4699|
|  6:  2.7453 -  2.5843 0.98   1292  142 0.1256 0.1888      5.2179      5.4435|
|  7:  2.5843 -  2.4555 0.99   1282  149 0.1148 0.1616      5.1088      5.3554|
|  8:  2.4555 -  2.3491 0.99   1281  136 0.1150 0.1778      5.0694      5.3327|
|  9:  2.3491 -  2.2590 0.98   1285  146 0.1187 0.1916      5.0356      5.3409|
| 10:  2.2590 -  2.1813 0.97   1246  139 0.1132 0.1877      4.9777      5.2043|
| 11:  2.1813 -  2.1133 0.98   1259  144 0.1119 0.1622      4.9119      5.2408|
| 12:  2.1133 -  2.0531 0.99   1279  133 0.1100 0.1755      4.8559      5.1411|
| 13:  2.0531 -  1.9992 0.97   1248  135 0.1094 0.1778      4.7898      5.0615|
| 14:  1.9992 -  1.9505 0.66    845  102 0.1083 0.1791      4.7082      4.9505|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6648 -  4.6540  1385   156  0.94   9.28   0.99     0.97       7477.41|
|  2:  4.6540 -  3.7138  1340   145  0.95   8.13   1.03     1.02       8957.93|
|  3:  3.7138 -  3.2502  1312   152  0.94  10.79   1.04     1.03       9683.52|
|  4:  3.2502 -  2.9556  1300   134  0.92  13.44   1.02     1.02      10193.53|
|  5:  2.9556 -  2.7453  1276   146  0.91  15.17   1.00     0.97       7942.14|
|  6:  2.7453 -  2.5843  1292   142  0.90  15.92   0.99     0.95       7037.30|
|  7:  2.5843 -  2.4555  1282   149  0.91  14.89   0.99     0.96       5688.05|
|  8:  2.4555 -  2.3491  1281   136  0.91  14.89   1.01     0.99       5423.62|
|  9:  2.3491 -  2.2590  1285   146  0.91  15.60   1.01     0.99       5018.89|
| 10:  2.2590 -  2.1813  1246   139  0.90  15.60   1.01     0.97       4584.07|
| 11:  2.1813 -  2.1133  1259   144  0.91  15.43   1.01     0.98       4077.42|
| 12:  2.1133 -  2.0531  1279   133  0.91  15.14   1.02     1.01       3790.27|
| 13:  2.0531 -  1.9992  1248   135  0.91  15.74   1.01     1.00       3364.73|
| 14:  1.9992 -  1.9505   845   102  0.91  15.39   1.00     0.97       2774.31|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2774.31 max =        10193.53 mean =      6265.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.86|
|phase err.(test): min =        0.00 max =           88.45 mean =        13.46|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1590   ksol= 0.31   Bsol= 32.96   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.14,-1.90,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1590   ksol= 0.31   Bsol= 32.96   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.14,-1.90,-0.00,-0.00,-0.00); trace/3= -2.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140542                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6648 -  4.6540 0.99   1385  156 0.1028 0.1311      5.4163      5.5712|
|  2:  4.6540 -  3.7138 0.99   1340  145 0.0872 0.1117       5.453      5.6215|
|  3:  3.7138 -  3.2502 0.99   1312  152 0.1044 0.1483      5.4577       5.814|
|  4:  3.2502 -  2.9556 0.99   1300  134 0.1213 0.1635      5.4519       5.637|
|  5:  2.9556 -  2.7453 0.98   1276  146 0.1259 0.1592      5.3047      5.4787|
|  6:  2.7453 -  2.5843 0.98   1292  142 0.1260 0.1885      5.2197      5.4402|
|  7:  2.5843 -  2.4555 0.99   1282  149 0.1145 0.1627      5.1087      5.3586|
|  8:  2.4555 -  2.3491 0.99   1281  136 0.1151 0.1778      5.0701      5.3341|
|  9:  2.3491 -  2.2590 0.98   1285  146 0.1185 0.1909      5.0333      5.3396|
| 10:  2.2590 -  2.1813 0.97   1246  139 0.1129 0.1880      4.9759       5.204|
| 11:  2.1813 -  2.1133 0.98   1259  144 0.1120 0.1616      4.9111      5.2387|
| 12:  2.1133 -  2.0531 0.99   1279  133 0.1098 0.1760      4.8548      5.1465|
| 13:  2.0531 -  1.9992 0.97   1248  135 0.1090 0.1770      4.7889      5.0571|
| 14:  1.9992 -  1.9505 0.66    845  102 0.1084 0.1780      4.7075      4.9483|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6648 -  4.6540  1385   156  0.94   9.30   0.99     0.97       7606.93|
|  2:  4.6540 -  3.7138  1340   145  0.95   8.31   1.04     1.02       9190.21|
|  3:  3.7138 -  3.2502  1312   152  0.94  10.92   1.04     1.03       9877.75|
|  4:  3.2502 -  2.9556  1300   134  0.92  13.44   1.02     1.02      10189.25|
|  5:  2.9556 -  2.7453  1276   146  0.91  15.17   1.00     0.98       7936.58|
|  6:  2.7453 -  2.5843  1292   142  0.90  16.04   0.99     0.96       7083.56|
|  7:  2.5843 -  2.4555  1282   149  0.91  14.89   0.99     0.97       5693.78|
|  8:  2.4555 -  2.3491  1281   136  0.91  14.94   1.01     1.00       5447.36|
|  9:  2.3491 -  2.2590  1285   146  0.91  15.61   1.02     1.00       5007.30|
| 10:  2.2590 -  2.1813  1246   139  0.90  15.59   1.01     0.98       4564.70|
| 11:  2.1813 -  2.1133  1259   144  0.91  15.43   1.02     0.98       4075.01|
| 12:  2.1133 -  2.0531  1279   133  0.91  15.15   1.03     1.02       3792.24|
| 13:  2.0531 -  1.9992  1248   135  0.90  15.78   1.02     1.01       3370.58|
| 14:  1.9992 -  1.9505   845   102  0.91  15.31   1.01     0.97       2757.55|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2757.55 max =        10189.25 mean =      6310.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.90|
|phase err.(test): min =        0.00 max =           88.98 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.243)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.68    100.79  17.28    None  None   None       |
|    all(noH): 2823   0      2.68    100.79  17.28    None  None   None       |
|    Sol.    : 438    0      3.32    89.07   40.27    None  None   None       |
|    Mac.    : 2385   0      2.68    100.79  13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.677 -  12.488: 1542   |   5:    51.733 -  61.544:   78        |
|      1:    12.488 -  22.299:  730   |   6:    61.544 -  71.355:   36        |
|      2:    22.299 -  32.110:  163   |   7:    71.355 -  81.166:    8        |
|      3:    32.110 -  41.922:  132   |   8:    81.166 -  90.977:    8        |
|      4:    41.922 -  51.733:  125   |   9:    90.977 - 100.788:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.756 - 5.893
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 295 from: 295
   mapped sites are within: 0.756 - 5.893

peak=    6.792 closest distance to " O   HOH Z 199 " =    1.238
peak=    6.230 closest distance to " O   HOH Z 126 " =    2.034
peak=    6.224 closest distance to " O   HOH Z 142 " =    1.814
peak=    5.824 closest distance to " NH2 ARG A  56 " =    2.109
peak=    5.813 closest distance to " O   HOH Z 416 " =    1.172
peak=    5.754 closest distance to " O   HOH Z 124 " =    1.559
peak=    5.748 closest distance to " O   HOH Z 193 " =    1.775
peak=    5.614 closest distance to " CB  ARG A 275 " =    0.955
peak=    5.409 closest distance to " O   HOH Z 236 " =    1.461
peak=    5.407 closest distance to " NE2 GLN A  11 " =    1.123
peak=    5.269 closest distance to " O   HOH Z 102 " =    1.092
peak=    5.179 closest distance to " O   HOH Z 278 " =    1.301
peak=    5.055 closest distance to " O   HOH Z 272 " =    1.907
peak=    4.997 closest distance to " O   HOH Z  97 " =    1.992
peak=    4.897 closest distance to " CB  ASN A 148 " =    1.826
peak=    4.897 closest distance to " CG  PRO A 213 " =    1.227
peak=    4.884 closest distance to " C   PRO A 198 " =    1.577
peak=    4.786 closest distance to " O   HOH Z  42 " =    2.248
peak=    4.782 closest distance to " O   HOH Z 132 " =    1.346
peak=    4.738 closest distance to " NZ  LYS A 119 " =    2.035
peak=    4.713 closest distance to " O   HOH Z 108 " =    1.317
peak=    4.669 closest distance to " CG  PRO A  54 " =    1.178
peak=    4.650 closest distance to " O   HOH Z  54 " =    1.665
peak=    4.646 closest distance to " O   HOH Z 109 " =    1.510
peak=    4.569 closest distance to " O   HOH Z 427 " =    2.810
peak=    4.567 closest distance to " O   HOH Z 402 " =    1.503
peak=    4.555 closest distance to " O   HOH Z 188 " =    1.189
peak=    4.529 closest distance to " O   HOH Z 368 " =    2.028
peak=    4.517 closest distance to " CB  SER A  63 " =    1.118
peak=    4.484 closest distance to " O   HOH Z 234 " =    3.613
peak=    4.476 closest distance to " O   SER A  87 " =    2.345
peak=    4.468 closest distance to " O   HOH Z  61 " =    1.587
peak=    4.461 closest distance to " O   HOH Z  95 " =    1.642
peak=    4.455 closest distance to " O   HOH Z 209 " =    2.378
peak=    4.445 closest distance to " O   HOH Z 207 " =    1.840
peak=    4.442 closest distance to " O   HOH Z  92 " =    1.235
peak=    4.417 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.400 closest distance to " CB  GLN A 183 " =    1.252
peak=    4.386 closest distance to " O   HOH Z 403 " =    1.929
peak=    4.380 closest distance to " O   HOH Z  44 " =    1.854
peak=    4.368 closest distance to " O   HOH Z 232 " =    2.242
peak=    4.350 closest distance to " O   HOH Z 134 " =    1.530
peak=    4.331 closest distance to " CA  TYR A  30 " =    1.029
peak=    4.286 closest distance to " O   HOH Z  85 " =    1.540
peak=    4.277 closest distance to " O   HOH Z   6 " =    2.246
peak=    4.228 closest distance to " O   HOH Z 260 " =    1.256
peak=    4.222 closest distance to " CG1 ILE A  33 " =    1.207
peak=    4.198 closest distance to " O   HOH Z 346 " =    1.654
peak=    4.178 closest distance to " CB  GLU A 152 " =    1.198
peak=    4.175 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.165 closest distance to " CG  ARG A  66 " =    1.051
peak=    4.157 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.149 closest distance to " O   HOH Z 389 " =    1.781
peak=    4.147 closest distance to " O   HOH Z  47 " =    1.704
peak=    4.126 closest distance to " O   HOH Z 406 " =    1.634
peak=    4.101 closest distance to " O   HOH Z 250 " =    1.410
peak=    4.100 closest distance to " O   HOH Z 112 " =    1.023
peak=    4.090 closest distance to " O   HOH Z 298 " =    1.848
peak=    4.087 closest distance to " CB  SER A   3 " =    1.201
peak=    4.082 closest distance to " NZ  LYS A 117 " =    3.113
peak=    4.078 closest distance to " O   HOH Z 261 " =    1.856
peak=    4.058 closest distance to " O  BHOH Z  74 " =    1.462
peak=    4.056 closest distance to " OD2 ASP A 286 " =    2.523
peak=    4.052 closest distance to " O   HOH Z 203 " =    1.823
peak=    4.042 closest distance to " O   HOH Z 425 " =    1.406
peak=    4.012 closest distance to " CG AARG A 275 " =    0.998
peak=    4.011 closest distance to " O   HOH Z 128 " =    1.938
peak=    4.009 closest distance to " O   HOH Z  15 " =    2.246
peak=    3.994 closest distance to " O   HOH Z 423 " =    2.022
peak=    3.982 closest distance to " O   HOH Z 132 " =    2.239
peak=    3.976 closest distance to " O   HOH Z  59 " =    2.052
peak=    3.962 closest distance to " CG  ARG A  66 " =    2.981
peak=    3.945 closest distance to " O   HOH Z 411 " =    3.399
peak=    3.940 closest distance to " O   HOH Z 118 " =    1.334
peak=    3.935 closest distance to " NH2BARG A 145 " =    2.144
peak=    3.935 closest distance to " O   HOH Z 173 " =    2.005
peak=    3.933 closest distance to " CD  ARG A 269 " =    1.023
peak=    3.926 closest distance to " O   HOH Z 344 " =    2.900
peak=    3.921 closest distance to " CG  PRO A 243 " =    1.176
peak=    3.920 closest distance to " O   HOH Z 194 " =    1.995
peak=    3.912 closest distance to " O   HOH Z 156 " =    3.142
peak=    3.908 closest distance to " CG  GLN A  77 " =    2.002
peak=    3.891 closest distance to " O   HOH Z 192 " =    1.553
peak=    3.885 closest distance to " O   HOH Z 163 " =    2.051
peak=    3.870 closest distance to " O   HOH Z 426 " =    1.430
peak=    3.869 closest distance to " O   HOH Z 326 " =    1.438
peak=    3.853 closest distance to " O   HOH Z 345 " =    2.897
peak=    3.852 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.847 closest distance to " O   HOH Z  97 " =    2.290
peak=    3.847 closest distance to " O   HOH Z 316 " =    2.897
peak=    3.840 closest distance to " O   HOH Z 407 " =    2.641
peak=    3.830 closest distance to " CA  ALA A  21 " =    1.094
peak=    3.825 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.824 closest distance to " O   HOH Z  43 " =    2.102
peak=    3.823 closest distance to " O   HOH Z   3 " =    1.754
peak=    3.802 closest distance to " CB  VAL A 265 " =    1.196
peak=    3.799 closest distance to " O   HOH Z 111 " =    1.857
peak=    3.784 closest distance to " ND2 ASN A 187 " =    1.514
peak=    3.776 closest distance to " CD BLYS A 290 " =    1.236
peak=    3.771 closest distance to " CB  PRO A  54 " =    0.958
peak=    3.765 closest distance to " NH1BARG A 145 " =    1.374
peak=    3.753 closest distance to " O   HOH Z  63 " =    1.908
peak=    3.746 closest distance to " CG2BVAL A  41 " =    0.825
peak=    3.745 closest distance to " CA  ALA A  51 " =    0.921
peak=    3.729 closest distance to " O   HOH Z 303 " =    2.095
peak=    3.704 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.702 closest distance to " O   HOH Z 369 " =    1.870
peak=    3.697 closest distance to " O   HOH Z 287 " =    1.721
peak=    3.690 closest distance to " O   HOH Z  21 " =    1.909
peak=    3.689 closest distance to " CE  LYS A 119 " =    1.105
peak=    3.683 closest distance to " O   HOH Z 286 " =    2.236
peak=    3.682 closest distance to " O   HOH Z 365 " =    2.681
peak=    3.673 closest distance to " CG AARG A 275 " =    1.109
peak=    3.661 closest distance to " O   HOH Z  49 " =    2.138
peak=    3.658 closest distance to " O   HOH Z  19 " =    2.083
peak=    3.657 closest distance to " O   HOH Z 118 " =    1.369
peak=    3.654 closest distance to " O   HOH Z  40 " =    1.484
peak=    3.646 closest distance to " CB  SER A 216 " =    0.941
peak=    3.644 closest distance to " O   HOH Z 421 " =    1.564
peak=    3.643 closest distance to " CB  SER A  26 " =    1.613
peak=    3.641 closest distance to " CB  TRP A 179 " =    1.068
peak=    3.637 closest distance to " O   MET A 105 " =    1.884
peak=    3.636 closest distance to " CB  ARG A 139 " =    1.260
peak=    3.634 closest distance to " N   ASN A  39 " =    1.227
peak=    3.634 closest distance to " O   HOH Z  85 " =    2.355
peak=    3.632 closest distance to " O   HOH Z 108 " =    1.957
peak=    3.629 closest distance to " O   HOH Z 255 " =    1.626
peak=    3.625 closest distance to " O   SER A  26 " =    1.584
peak=    3.621 closest distance to " O   HOH Z 191 " =    1.508
peak=    3.617 closest distance to " O   HOH Z  73 " =    1.673
peak=    3.616 closest distance to " CB  ALA A   9 " =    1.502
peak=    3.613 closest distance to " O   HOH Z 343 " =    1.557
peak=    3.598 closest distance to " OG BSER A 210 " =    1.438
peak=    3.592 closest distance to " CB  SER A 141 " =    1.108
peak=    3.590 closest distance to " O   HOH Z 392 " =    2.511
peak=    3.580 closest distance to " CG2 THR A 221 " =    1.135
peak=    3.578 closest distance to " O   HOH Z  88 " =    2.961
peak=    3.573 closest distance to " C   ALA A   1 " =    1.601
peak=    3.572 closest distance to " CG2 ILE A 120 " =    1.196
peak=    3.556 closest distance to " CA  ASN A 176 " =    1.068
peak=    3.552 closest distance to " O   HOH Z  66 " =    2.099
peak=    3.549 closest distance to " OG BSER A 164 " =    2.346
peak=    3.540 closest distance to " O   HOH Z 273 " =    2.737
peak=    3.538 closest distance to " CB  LEU A 228 " =    1.155
peak=    3.538 closest distance to " CG  MET A 185 " =    1.254
peak=    3.521 closest distance to " O   HOH Z 381 " =    1.726
peak=    3.518 closest distance to " CB  ARG A  79 " =    1.475
peak=    3.518 closest distance to " O   HOH Z 408 " =    1.623
peak=    3.516 closest distance to " O   HOH Z 250 " =    1.788
peak=    3.513 closest distance to " NH2 ARG A 219 " =    1.969
peak=    3.513 closest distance to " OG ASER A 216 " =    2.345
peak=    3.512 closest distance to " O   HOH Z 183 " =    1.742
peak=    3.497 closest distance to " O   HOH Z   9 " =    2.093
peak=    3.486 closest distance to " O   HOH Z 417 " =    2.072
peak=    3.481 closest distance to " O   HOH Z 427 " =    3.080
peak=    3.476 closest distance to " CB  GLU A 128 " =    1.102
peak=    3.473 closest distance to " CA  THR A 221 " =    0.928
peak=    3.469 closest distance to " CB  GLU A 277 " =    3.428
peak=    3.469 closest distance to " CZ2 TRP A 274 " =    1.783
peak=    3.466 closest distance to " O   HOH Z 247 " =    1.240
peak=    3.459 closest distance to " O   HOH Z 430 " =    5.753
peak=    3.459 closest distance to " O   HOH Z 327 " =    1.781
peak=    3.450 closest distance to " O   HOH Z  89 " =    1.579
peak=    3.450 closest distance to " NE2 GLN A  55 " =    1.320
peak=    3.447 closest distance to " O   ALA A 165 " =    1.397
peak=    3.446 closest distance to " CD2 TRP A 179 " =    1.440
peak=    3.445 closest distance to " O   HOH Z 214 " =    2.388
peak=    3.439 closest distance to " O   HOH Z 180 " =    2.206
peak=    3.438 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.435 closest distance to " CD  GLN A  58 " =    5.893
peak=    3.423 closest distance to " O   HOH Z  71 " =    1.561
peak=    3.419 closest distance to " O   HOH Z 156 " =    2.669
peak=    3.416 closest distance to " O   HOH Z 357 " =    1.704
peak=    3.416 closest distance to " CB  ALA A  34 " =    1.002
peak=    3.414 closest distance to " O   HOH Z 193 " =    2.140
peak=    3.410 closest distance to " CD2 HIS A  81 " =    1.147
peak=    3.408 closest distance to " N   ARG A 156 " =    1.280
peak=    3.407 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.402 closest distance to " O   HOH Z 380 " =    1.996
peak=    3.397 closest distance to " O   HOH Z 417 " =    2.974
peak=    3.397 closest distance to " NE  ARG A  14 " =    1.241
peak=    3.396 closest distance to " O   HOH Z 359 " =    1.418
peak=    3.390 closest distance to " OG  SER A  62 " =    2.809
peak=    3.385 closest distance to " O   HOH Z 222 " =    2.293
peak=    3.381 closest distance to " O   HOH Z 172 " =    3.720
peak=    3.381 closest distance to " O   HOH Z 313 " =    1.684
peak=    3.379 closest distance to " O   HOH Z 334 " =    1.299
peak=    3.378 closest distance to " CB  SER A  62 " =    1.411
peak=    3.378 closest distance to " CG2 THR A 294 " =    1.607
peak=    3.377 closest distance to " CB  THR A  31 " =    1.690
peak=    3.376 closest distance to " O   HOH Z 170 " =    1.963
peak=    3.375 closest distance to " O   HOH Z 261 " =    1.931
peak=    3.373 closest distance to " O   HOH Z 353 " =    2.533
peak=    3.367 closest distance to " CA  ILE A  33 " =    1.276
peak=    3.367 closest distance to " CA  ALA A 233 " =    1.187
peak=    3.366 closest distance to " O   HOH Z 241 " =    1.699
peak=    3.365 closest distance to " O   HOH Z 281 " =    1.724
peak=    3.357 closest distance to " O   HOH Z 189 " =    1.620
peak=    3.355 closest distance to " O   HOH Z 214 " =    2.354
peak=    3.355 closest distance to " CA  MET A  40 " =    1.052
peak=    3.352 closest distance to " O   GLY A  91 " =    1.496
peak=    3.348 closest distance to " O   HOH Z 279 " =    2.121
peak=    3.346 closest distance to " CA  GLY A  80 " =    0.756
peak=    3.342 closest distance to " O   HOH Z 189 " =    1.458
peak=    3.341 closest distance to " CB  ARG A 102 " =    0.820
peak=    3.340 closest distance to " O   HOH Z 369 " =    2.622
peak=    3.337 closest distance to " O   HOH Z 299 " =    2.299
peak=    3.336 closest distance to " CB  VAL A 202 " =    1.607
peak=    3.334 closest distance to " CB  TRP A 266 " =    1.211
peak=    3.325 closest distance to " CE1 TYR A 186 " =    1.272
peak=    3.319 closest distance to " CD  GLN A 194 " =    1.467
peak=    3.318 closest distance to " CA  LEU A 282 " =    1.336
peak=    3.314 closest distance to " O   HOH Z 365 " =    2.546
peak=    3.311 closest distance to " CD  LYS A 119 " =    2.151
peak=    3.311 closest distance to " O   HOH Z 219 " =    1.884
peak=    3.310 closest distance to " O   HOH Z  80 " =    1.679
peak=    3.306 closest distance to " OE1 GLN A  11 " =    1.827
peak=    3.305 closest distance to " NE2 GLN A 223 " =    1.831
peak=    3.303 closest distance to " CB  ALA A 291 " =    1.296
peak=    3.300 closest distance to " O   HOH Z 249 " =    1.152
peak=    3.297 closest distance to " CB  SER A  62 " =    0.966
peak=    3.293 closest distance to " CG2 ILE A  20 " =    1.512
peak=    3.293 closest distance to " O   HOH Z 303 " =    1.636
peak=    3.293 closest distance to " CG  LYS A 166 " =    1.617
peak=    3.290 closest distance to " CD2 LEU A 297 " =    1.015
peak=    3.287 closest distance to " N   ASP A 162 " =    1.320
peak=    3.284 closest distance to " CA  ALA A  84 " =    1.284
peak=    3.283 closest distance to " O   HOH Z  35 " =    2.312
peak=    3.283 closest distance to " O   HOH Z 251 " =    1.608
peak=    3.280 closest distance to " O   HOH Z 227 " =    1.515
peak=    3.274 closest distance to " CG  GLN A 240 " =    3.391
peak=    3.272 closest distance to " OD1 ASN A  69 " =    2.596
peak=    3.271 closest distance to " O   HOH Z 374 " =    2.439
peak=    3.268 closest distance to " O   HOH Z 435 " =    1.874
peak=    3.268 closest distance to " C   ALA A 299 " =    0.981
peak=    3.265 closest distance to " CG  MET A  93 " =    0.930
peak=    3.260 closest distance to " O   HOH Z 361 " =    3.020
peak=    3.260 closest distance to " O   HOH Z 411 " =    1.677
peak=    3.254 closest distance to " O   HOH Z 261 " =    1.965
peak=    3.250 closest distance to " CG2 VAL A  67 " =    1.018
peak=    3.249 closest distance to " O   HOH Z 257 " =    2.203
peak=    3.242 closest distance to " CG1BVAL A  72 " =    1.417
peak=    3.240 closest distance to " CG  PRO A 280 " =    0.764
peak=    3.240 closest distance to " O   HOH Z 227 " =    1.738
peak=    3.239 closest distance to " CA  ARG A  36 " =    1.024
peak=    3.235 closest distance to " CE3 TRP A 274 " =    2.407
peak=    3.233 closest distance to " N   TRP A 150 " =    1.535
peak=    3.232 closest distance to " OG BSER A 258 " =    2.806
peak=    3.230 closest distance to " CG  GLU A 277 " =    2.145
peak=    3.228 closest distance to " CA  THR A 264 " =    0.820
peak=    3.228 closest distance to " O   HOH Z 394 " =    1.589
peak=    3.224 closest distance to " CA  ASN A 215 " =    1.167
peak=    3.218 closest distance to " N   ASN A  39 " =    1.599
peak=    3.217 closest distance to " CA  ARG A  66 " =    1.182
peak=    3.209 closest distance to " CG  LYS A  76 " =    1.022
peak=    3.204 closest distance to " OG ASER A 216 " =    2.218
peak=    3.204 closest distance to " CD2 LEU A 255 " =    0.968
peak=    3.200 closest distance to " CA  ILE A  20 " =    0.863
peak=    3.189 closest distance to " O   HOH Z  89 " =    2.188
peak=    3.188 closest distance to " O   HOH Z 367 " =    3.397
peak=    3.187 closest distance to " O   HOH Z 428 " =    3.633
peak=    3.187 closest distance to " CE BLYS A 290 " =    1.039
peak=    3.179 closest distance to " CG2 VAL A 257 " =    0.843
peak=    3.171 closest distance to " CG  GLN A  77 " =    1.861
peak=    3.169 closest distance to " CB  ALA A 248 " =    1.334
peak=    3.166 closest distance to " O   HOH Z 296 " =    1.283
peak=    3.166 closest distance to " CA  ASP A 140 " =    1.042
peak=    3.164 closest distance to " CB  THR A 279 " =    1.639
peak=    3.162 closest distance to " O   HOH Z 291 " =    1.755
peak=    3.162 closest distance to " O   HOH Z 211 " =    2.480
peak=    3.160 closest distance to " O   HOH Z 234 " =    2.193
peak=    3.159 closest distance to " O   HOH Z 106 " =    2.185
peak=    3.155 closest distance to " O   TRP A 274 " =    1.860
peak=    3.153 closest distance to " CD  LYS A 166 " =    1.272
peak=    3.147 closest distance to " CB  GLN A 205 " =    1.162
peak=    3.139 closest distance to " CB  ASN A 110 " =    1.018
peak=    3.132 closest distance to " CB  ARG A  79 " =    0.835
peak=    3.126 closest distance to " CG  MET A 185 " =    0.984
peak=    3.121 closest distance to " O   HOH Z  37 " =    1.287
peak=    3.110 closest distance to " O   HOH Z 383 " =    1.873
peak=    3.109 closest distance to " CB  ASN A 215 " =    0.998
peak=    3.104 closest distance to " O   HOH Z  15 " =    1.493
peak=    3.104 closest distance to " NH1 ARG A 138 " =    1.353
peak=    3.103 closest distance to " O   HOH Z  64 " =    2.373
peak=    3.098 closest distance to " CA  ALA A 291 " =    0.885
peak=    3.080 closest distance to " CB  VAL A 268 " =    0.839
peak=    3.074 closest distance to " CB  ARG A 269 " =    0.762
peak=    3.072 closest distance to " CB  ASN A  39 " =    0.799
peak=    3.071 closest distance to " CA  LEU A 300 " =    1.032
peak=    3.061 closest distance to " CG  LYS A  76 " =    1.601
peak=    3.058 closest distance to " O   HOH Z 334 " =    1.506
peak=    3.058 closest distance to " O   HOH Z 284 " =    2.730
peak=    3.045 closest distance to " O   HOH Z  68 " =    1.581
peak=    3.039 closest distance to " O   HOH Z 119 " =    4.570
peak=    3.009 closest distance to " O   HOH Z 102 " =    1.436

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.655 - 5.070
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.744 - 5.070

peak=   -4.877 closest distance to " C   HIS A 108 " =    1.099
peak=   -4.631 closest distance to " OXT GLY A 302 " =    2.697
peak=   -4.374 closest distance to " N   ALA A 248 " =    1.744
peak=   -4.339 closest distance to " O   HOH Z  52 " =    0.752
peak=   -4.213 closest distance to " SG  CYS A 254 " =    3.156
peak=   -4.162 closest distance to " O   HOH Z 266 " =    4.342
peak=   -4.132 closest distance to " O   HOH Z 407 " =    2.671
peak=   -4.089 closest distance to " CG  LYS A 193 " =    2.243
peak=   -4.048 closest distance to " O   HOH Z 290 " =    0.955
peak=   -4.044 closest distance to " O   PRO A 163 " =    1.826
peak=   -4.042 closest distance to " O   HOH Z  13 " =    1.370
peak=   -3.983 closest distance to " C   ALA A 158 " =    1.093
peak=   -3.948 closest distance to " CD1 LEU A 101 " =    2.400
peak=   -3.941 closest distance to " NH2 ARG A  79 " =    1.914
peak=   -3.926 closest distance to " O   HOH Z  11 " =    1.952
peak=   -3.920 closest distance to " N   GLN A  58 " =    1.628
peak=   -3.914 closest distance to " O   HOH Z  97 " =    1.321
peak=   -3.895 closest distance to " O   HOH Z  92 " =    1.816
peak=   -3.892 closest distance to " N   SER A 206 " =    1.811
peak=   -3.881 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.871 closest distance to " O   HOH Z 416 " =    1.415
peak=   -3.862 closest distance to " N   ASP A 286 " =    2.165
peak=   -3.855 closest distance to " N   GLN A 122 " =    1.484
peak=   -3.850 closest distance to " OG  SER A   3 " =    1.421
peak=   -3.836 closest distance to " OG BSER A 134 " =    1.287
peak=   -3.835 closest distance to " O   HOH Z 234 " =    3.976
peak=   -3.815 closest distance to " CD  ARG A 156 " =    1.981
peak=   -3.800 closest distance to " OD1 ASN A  39 " =    2.191
peak=   -3.799 closest distance to " O   HOH Z 250 " =    1.403
peak=   -3.785 closest distance to " O   SER A 146 " =    0.793
peak=   -3.780 closest distance to " N   SER A 276 " =    1.165
peak=   -3.779 closest distance to " O   HOH Z 377 " =    2.060
peak=   -3.768 closest distance to " O   TRP A  92 " =    1.756
peak=   -3.752 closest distance to " CB  ASN A  39 " =    2.252
peak=   -3.749 closest distance to " CZ  TYR A 169 " =    1.785
peak=   -3.736 closest distance to " C   ASP A 231 " =    2.427
peak=   -3.712 closest distance to " O   VAL A  67 " =    2.653
peak=   -3.712 closest distance to " CE1 HIS A  81 " =    1.525
peak=   -3.704 closest distance to " CB  ALA A 291 " =    2.261
peak=   -3.698 closest distance to " O   VAL A 174 " =    1.878
peak=   -3.688 closest distance to " O   HOH Z   3 " =    1.596
peak=   -3.680 closest distance to " OD2 ASP A 171 " =    2.338
peak=   -3.675 closest distance to " CD1 PHE A 130 " =    2.118
peak=   -3.639 closest distance to " O   HOH Z 126 " =    1.832
peak=   -3.638 closest distance to " O   ALA A 161 " =    1.605
peak=   -3.636 closest distance to " O   MET A  40 " =    2.631
peak=   -3.629 closest distance to " O   HOH Z 435 " =    2.624
peak=   -3.629 closest distance to " ND2 ASN A  45 " =    1.098
peak=   -3.618 closest distance to " N   HIS A 115 " =    1.901
peak=   -3.611 closest distance to " O   HOH Z 351 " =    1.486
peak=   -3.610 closest distance to " CD  ARG A 139 " =    1.481
peak=   -3.602 closest distance to " CA  GLY A 133 " =    1.823
peak=   -3.600 closest distance to " O   SER A 135 " =    1.506
peak=   -3.587 closest distance to " CD1 PHE A  59 " =    1.932
peak=   -3.586 closest distance to " CB  ALA A  51 " =    1.819
peak=   -3.581 closest distance to " O   HOH Z  11 " =    1.690
peak=   -3.577 closest distance to " O   HOH Z 427 " =    1.480
peak=   -3.576 closest distance to " ND2 ASN A  45 " =    0.888
peak=   -3.559 closest distance to " OD2 ASP A  50 " =    1.300
peak=   -3.556 closest distance to " O   HOH Z  56 " =    1.407
peak=   -3.555 closest distance to " OXT GLY A 302 " =    3.394
peak=   -3.553 closest distance to " N   ALA A 248 " =    2.182
peak=   -3.553 closest distance to " CB  PRO A 243 " =    2.587
peak=   -3.548 closest distance to " O   HOH Z 166 " =    1.602
peak=   -3.544 closest distance to " O   HOH Z 109 " =    5.070
peak=   -3.538 closest distance to " O   HOH Z 263 " =    3.040
peak=   -3.528 closest distance to " ND2 ASN A  39 " =    1.229
peak=   -3.524 closest distance to " O   PRO A 163 " =    1.419
peak=   -3.522 closest distance to " CG1 VAL A  78 " =    3.155
peak=   -3.516 closest distance to " CD2 LEU A 300 " =    2.798
peak=   -3.512 closest distance to " CB  ALA A 244 " =    1.977
peak=   -3.503 closest distance to " OH  TYR A 172 " =    1.684
peak=   -3.498 closest distance to " O   HOH Z  60 " =    1.839
peak=   -3.496 closest distance to " CD  GLN A  88 " =    0.941
peak=   -3.494 closest distance to " O   HOH Z 198 " =    1.476
peak=   -3.494 closest distance to " OD2 ASP A 191 " =    1.363
peak=   -3.468 closest distance to " O   PHE A 218 " =    1.458
peak=   -3.462 closest distance to " O   HOH Z  47 " =    1.512
peak=   -3.455 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.454 closest distance to " CA  ALA A 299 " =    2.306
peak=   -3.452 closest distance to " CG  PHE A 283 " =    2.547
peak=   -3.439 closest distance to " NH2 ARG A  66 " =    4.314
peak=   -3.434 closest distance to " CG  GLN A 223 " =    2.174
peak=   -3.427 closest distance to " CB  GLN A  11 " =    1.636
peak=   -3.417 closest distance to " O   HOH Z  44 " =    2.004
peak=   -3.416 closest distance to " CB  PHE A 192 " =    1.877
peak=   -3.413 closest distance to " O   LEU A 222 " =    1.336
peak=   -3.411 closest distance to " CZ  TYR A 214 " =    1.324
peak=   -3.407 closest distance to " ND2 ASN A  69 " =    1.440
peak=   -3.406 closest distance to " O   HOH Z 309 " =    2.519
peak=   -3.399 closest distance to " CB  PHE A 208 " =    2.163
peak=   -3.393 closest distance to " OG  SER A  97 " =    1.660
peak=   -3.389 closest distance to " OD1 ASP A 200 " =    1.179
peak=   -3.378 closest distance to " ND2 ASN A 209 " =    1.758
peak=   -3.375 closest distance to " ND2 ASN A 187 " =    1.401
peak=   -3.368 closest distance to " CD2 LEU A 237 " =    2.695
peak=   -3.363 closest distance to " CB  ALA A 161 " =    2.456
peak=   -3.354 closest distance to " CB  PRO A 163 " =    2.646
peak=   -3.354 closest distance to " O   MET A 188 " =    1.782
peak=   -3.352 closest distance to " O   HOH Z 185 " =    2.116
peak=   -3.351 closest distance to " O   HOH Z 198 " =    1.463
peak=   -3.349 closest distance to " OG  SER A  87 " =    1.276
peak=   -3.345 closest distance to " OD1 ASP A 191 " =    1.724
peak=   -3.341 closest distance to " OG BSER A 134 " =    1.592
peak=   -3.341 closest distance to " CD1 LEU A 228 " =    2.082
peak=   -3.340 closest distance to " O   ARG A  56 " =    1.441
peak=   -3.334 closest distance to " O   HOH Z 422 " =    1.361
peak=   -3.328 closest distance to " O   HOH Z 197 " =    4.899
peak=   -3.327 closest distance to " OG1 THR A 178 " =    1.223
peak=   -3.318 closest distance to " O   SER A  26 " =    1.105
peak=   -3.318 closest distance to " CD1 LEU A  25 " =    2.433
peak=   -3.316 closest distance to " N   PRO A 163 " =    1.462
peak=   -3.315 closest distance to " N   SER A 210 " =    1.363
peak=   -3.313 closest distance to " O   HOH Z 377 " =    1.254
peak=   -3.312 closest distance to " OG  SER A  97 " =    1.922
peak=   -3.301 closest distance to " O   HOH Z 423 " =    2.167
peak=   -3.299 closest distance to " O   HOH Z 165 " =    2.137
peak=   -3.289 closest distance to " O   ALA A 256 " =    1.475
peak=   -3.286 closest distance to " O   HOH Z 385 " =    2.011
peak=   -3.281 closest distance to " O   HOH Z 251 " =    1.253
peak=   -3.279 closest distance to " O   GLY A  75 " =    1.515
peak=   -3.269 closest distance to " C   PRO A  90 " =    1.472
peak=   -3.266 closest distance to " O   HOH Z 105 " =    3.267
peak=   -3.266 closest distance to " NE2 GLN A  58 " =    1.050
peak=   -3.263 closest distance to " SG ACYS A 201 " =    1.933
peak=   -3.262 closest distance to " O   TRP A  70 " =    1.553
peak=   -3.260 closest distance to " CE2 TYR A  30 " =    2.984
peak=   -3.260 closest distance to " O   HOH Z 193 " =    1.725
peak=   -3.259 closest distance to " OD1 ASP A 191 " =    1.474
peak=   -3.258 closest distance to " O   ASN A 249 " =    1.453
peak=   -3.257 closest distance to " CE3 TRP A 150 " =    1.906
peak=   -3.256 closest distance to " C   THR A 264 " =    1.459
peak=   -3.253 closest distance to " CB  GLN A  55 " =    1.383
peak=   -3.251 closest distance to " O   VAL A  67 " =    2.691
peak=   -3.247 closest distance to " N   ALA A  43 " =    2.304
peak=   -3.239 closest distance to " ND2 ASN A 142 " =    1.870
peak=   -3.236 closest distance to " O   ALA A  51 " =    1.325
peak=   -3.236 closest distance to " O   HOH Z 360 " =    2.427
peak=   -3.236 closest distance to " CG  GLU A 152 " =    1.021
peak=   -3.234 closest distance to " N   GLN A  77 " =    1.573
peak=   -3.232 closest distance to " O   ALA A  34 " =    2.490
peak=   -3.228 closest distance to " OD1 ASP A 171 " =    1.666
peak=   -3.219 closest distance to " CZ  PHE A 130 " =    0.806
peak=   -3.216 closest distance to " O   HOH Z 417 " =    2.418
peak=   -3.215 closest distance to " CD1 ILE A 239 " =    2.442
peak=   -3.205 closest distance to " CB  ASP A 132 " =    2.235
peak=   -3.202 closest distance to " C   LEU A 143 " =    1.127
peak=   -3.199 closest distance to " O   HOH Z  43 " =    1.714
peak=   -3.197 closest distance to " OG ASER A 134 " =    1.148
peak=   -3.192 closest distance to " O   HOH Z 199 " =    0.905
peak=   -3.189 closest distance to " O   HOH Z 424 " =    2.996
peak=   -3.188 closest distance to " CG  ASP A  50 " =    2.419
peak=   -3.188 closest distance to " O   HOH Z 385 " =    1.906
peak=   -3.188 closest distance to " CD2 TYR A 293 " =    2.036
peak=   -3.186 closest distance to " O   HOH Z 114 " =    2.892
peak=   -3.185 closest distance to " O   HOH Z  33 " =    2.376
peak=   -3.184 closest distance to " O   HOH Z 198 " =    1.314
peak=   -3.182 closest distance to " O   HOH Z 113 " =    1.616
peak=   -3.179 closest distance to " O   HIS A 207 " =    2.596
peak=   -3.175 closest distance to " O   VAL A 125 " =    1.917
peak=   -3.174 closest distance to " OG  SER A  22 " =    4.238
peak=   -3.172 closest distance to " O   GLY A 196 " =    0.896
peak=   -3.172 closest distance to " O   HOH Z 326 " =    1.612
peak=   -3.171 closest distance to " O   THR A 182 " =    1.151
peak=   -3.170 closest distance to " O   HOH Z 346 " =    1.845
peak=   -3.167 closest distance to " O   HOH Z  88 " =    2.263
peak=   -3.166 closest distance to " O   HOH Z 436 " =    1.348
peak=   -3.165 closest distance to " CG  ASN A 110 " =    1.168
peak=   -3.164 closest distance to " ND2 ASN A 173 " =    1.322
peak=   -3.163 closest distance to " CG  ASP A 231 " =    0.744
peak=   -3.154 closest distance to " OD1 ASN A 249 " =    1.154
peak=   -3.152 closest distance to " O   HOH Z  98 " =    1.796
peak=   -3.146 closest distance to " O   HOH Z 313 " =    1.807
peak=   -3.142 closest distance to " OE1 GLN A 205 " =    1.264
peak=   -3.140 closest distance to " O   GLY A 118 " =    2.291
peak=   -3.139 closest distance to " O   HOH Z 388 " =    1.899
peak=   -3.137 closest distance to " CG1AVAL A  41 " =    2.679
peak=   -3.137 closest distance to " O   HOH Z  93 " =    1.491
peak=   -3.136 closest distance to " CB  ALA A 248 " =    2.018
peak=   -3.131 closest distance to " N   ALA A 226 " =    1.826
peak=   -3.129 closest distance to " CD1 TYR A 247 " =    2.202
peak=   -3.128 closest distance to " CB  ASP A 286 " =    2.175
peak=   -3.125 closest distance to " OD1 ASN A 301 " =    1.980
peak=   -3.124 closest distance to " OG  SER A  62 " =    1.428
peak=   -3.117 closest distance to " N   SER A 245 " =    2.234
peak=   -3.117 closest distance to " O   HOH Z 281 " =    2.877
peak=   -3.113 closest distance to " CG BARG A 275 " =    1.044
peak=   -3.113 closest distance to " O   HOH Z 421 " =    3.426
peak=   -3.111 closest distance to " O   ALA A   1 " =    1.774
peak=   -3.110 closest distance to " O   HOH Z  24 " =    1.393
peak=   -3.105 closest distance to " OG  SER A 273 " =    2.111
peak=   -3.105 closest distance to " N   THR A 220 " =    2.186
peak=   -3.103 closest distance to " O   HOH Z 137 " =    1.413
peak=   -3.091 closest distance to " ND2 ASN A  60 " =    1.451
peak=   -3.077 closest distance to " CG  ARG A 269 " =    2.172
peak=   -3.076 closest distance to " O   HOH Z 429 " =    1.771
peak=   -3.075 closest distance to " O   ALA A 292 " =    2.005
peak=   -3.067 closest distance to " N   VAL A 189 " =    1.611
peak=   -3.059 closest distance to " OE1 GLN A  88 " =    1.230
peak=   -3.058 closest distance to " CE  LYS A 166 " =    2.925
peak=   -3.047 closest distance to " CD2 LEU A 300 " =    2.685
peak=   -3.032 closest distance to " CG  GLU A 152 " =    2.152
peak=   -3.028 closest distance to " O   HOH Z 226 " =    1.954

================= 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    :  0.4448 0.4463   6.251904e+00   6.259165e+00
   1_bss:  0.4349 0.4361   6.243133e+00   6.242064e+00
   1_xyz:  0.3148 0.3413   6.007199e+00   6.070525e+00
   1_adp:  0.2839 0.3433   5.941619e+00   6.076624e+00
   1_occ:  0.2836 0.3433   5.941037e+00   6.076579e+00
   2_bss:  0.2793 0.3393   5.932150e+00   6.070200e+00
   2_xyz:  0.2169 0.2682   5.709130e+00   5.879929e+00
   2_adp:  0.2008 0.2561   5.652177e+00   5.836100e+00
   2_occ:  0.2004 0.2559   5.651233e+00   5.835428e+00
   3_bss:  0.1999 0.2541   5.647759e+00   5.829249e+00
   3_xyz:  0.1527 0.2028   5.413157e+00   5.625025e+00
   3_adp:  0.1428 0.1883   5.338921e+00   5.545762e+00
   3_occ:  0.1425 0.1882   5.337528e+00   5.543942e+00
   4_bss:  0.1423 0.1866   5.334416e+00   5.538348e+00
   4_xyz:  0.1211 0.1650   5.199605e+00   5.426468e+00
   4_adp:  0.1170 0.1630   5.174321e+00   5.407465e+00
   4_occ:  0.1168 0.1628   5.173522e+00   5.406934e+00
   5_bss:  0.1167 0.1626   5.172537e+00   5.406011e+00
   5_xyz:  0.1125 0.1592   5.145721e+00   5.385721e+00
   5_adp:  0.1113 0.1591   5.139930e+00   5.384331e+00
   5_occ:  0.1112 0.1590   5.139397e+00   5.384171e+00
   5_bss:  0.1113 0.1590   5.140542e+00   5.384799e+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:  0.300  20.000   0.293  -3.027   2.554  -0.000   0.000   0.000
   1_xyz:  0.300  20.000   0.293  -3.027   2.554  -0.000   0.000   0.000
   1_adp:  0.300  20.000   0.293  -3.027   2.554  -0.000   0.000   0.000
   1_occ:  0.300  20.000   0.293  -3.027   2.554  -0.000   0.000   0.000
   2_bss:  0.321  34.061  -1.556  -2.067   0.481  -0.000   0.000   0.000
   2_xyz:  0.321  34.061  -1.556  -2.067   0.481  -0.000   0.000   0.000
   2_adp:  0.321  34.061  -1.556  -2.067   0.481  -0.000   0.000   0.000
   2_occ:  0.321  34.061  -1.556  -2.067   0.481  -0.000   0.000   0.000
   3_bss:  0.313  26.291  -2.343  -1.935  -0.711  -0.000  -0.000  -0.000
   3_xyz:  0.313  26.291  -2.343  -1.935  -0.711  -0.000  -0.000  -0.000
   3_adp:  0.313  26.291  -2.343  -1.935  -0.711  -0.000  -0.000  -0.000
   3_occ:  0.313  26.291  -2.343  -1.935  -0.711  -0.000  -0.000  -0.000
   4_bss:  0.311  28.834  -3.179  -2.326  -1.841  -0.000  -0.000  -0.000
   4_xyz:  0.311  28.834  -3.179  -2.326  -1.841  -0.000  -0.000  -0.000
   4_adp:  0.311  28.834  -3.179  -2.326  -1.841  -0.000  -0.000  -0.000
   4_occ:  0.311  28.834  -3.179  -2.326  -1.841  -0.000  -0.000  -0.000
   5_bss:  0.310  32.210  -3.281  -2.356  -2.052  -0.000  -0.000  -0.000
   5_xyz:  0.310  32.210  -3.281  -2.356  -2.052  -0.000  -0.000  -0.000
   5_adp:  0.310  32.210  -3.281  -2.356  -2.052  -0.000  -0.000  -0.000
   5_occ:  0.310  32.210  -3.281  -2.356  -2.052  -0.000  -0.000  -0.000
   5_bss:  0.314  32.963  -3.102  -2.144  -1.902  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.867 0.4730  0.6484    65034.397
   1_bss:  52.084 0.4941  0.6797    60397.815
   1_xyz:  35.999 0.6905  0.9115    32084.009
   1_adp:  36.778 0.6805  0.9024    32559.764
   1_occ:  36.747 0.6808  0.9026    32525.885
   2_bss:  36.264 0.6860  0.8784    31586.517
   2_xyz:  27.454 0.7845  0.9772    18814.093
   2_adp:  25.047 0.8116  0.9959    16823.179
   2_occ:  25.016 0.8119  0.9959    16789.442
   3_bss:  24.767 0.8141  0.9727    16429.609
   3_xyz:  19.320 0.8681  1.0098    10385.164
   3_adp:  17.251 0.8880  1.0197     8946.497
   3_occ:  17.216 0.8883  1.0196     8904.453
   4_bss:  17.060 0.8895  0.9906     8735.838
   4_xyz:  14.889 0.9075  0.9970     6857.265
   4_adp:  14.440 0.9115  0.9959     6656.052
   4_occ:  14.422 0.9117  0.9958     6638.472
   5_bss:  14.402 0.9118  0.9917     6628.678
   5_xyz:  13.903 0.9159  0.9927     6286.228
   5_adp:  13.832 0.9167  0.9894     6272.970
   5_occ:  13.822 0.9167  0.9893     6264.415
   5_bss:  13.863 0.9164  0.9923     6308.891
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.6382e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.6382e-01
   1_xyz:   1.552  0.013  0.091 16.194  0.007  4.104   1.5880e-01
   1_adp:   1.552  0.013  0.091 16.194  0.007  4.104   1.5880e-01
   1_occ:   1.552  0.013  0.091 16.194  0.007  4.104   1.5880e-01
   2_bss:   1.552  0.013  0.091 16.194  0.007  4.104   1.5880e-01
   2_xyz:   1.105  0.007  0.074 14.616  0.005  4.105   6.6270e-02
   2_adp:   1.105  0.007  0.074 14.616  0.005  4.105   6.6270e-02
   2_occ:   1.105  0.007  0.074 14.616  0.005  4.105   6.6270e-02
   3_bss:   1.105  0.007  0.074 14.616  0.005  4.105   6.6270e-02
   3_xyz:   1.019  0.006  0.067 14.800  0.004  4.106   6.0969e-02
   3_adp:   1.019  0.006  0.067 14.800  0.004  4.106   6.0969e-02
   3_occ:   1.019  0.006  0.067 14.800  0.004  4.106   6.0969e-02
   4_bss:   1.019  0.006  0.067 14.800  0.004  4.106   6.0969e-02
   4_xyz:   1.078  0.007  0.073 15.106  0.004  4.105   6.5473e-02
   4_adp:   1.078  0.007  0.073 15.106  0.004  4.105   6.5473e-02
   4_occ:   1.078  0.007  0.073 15.106  0.004  4.105   6.5473e-02
   5_bss:   1.078  0.007  0.073 15.106  0.004  4.105   6.5473e-02
   5_xyz:   1.015  0.006  0.069 14.926  0.004  4.104   5.9593e-02
   5_adp:   1.015  0.006  0.069 14.926  0.004  4.104   5.9593e-02
   5_occ:   1.015  0.006  0.069 14.926  0.004  4.104   5.9593e-02
   5_bss:   1.015  0.006  0.069 14.926  0.004  4.104   5.9593e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.919   2.4457e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.919   2.4457e-01
   1_xyz:  11.051  0.100  0.336 85.318  0.074  1.726   2.7479e-01
   1_adp:  11.051  0.100  0.336 85.318  0.074  1.726   2.7479e-01
   1_occ:  11.051  0.100  0.336 85.318  0.074  1.726   2.7479e-01
   2_bss:  11.051  0.100  0.336 85.318  0.074  1.726   2.7479e-01
   2_xyz:   8.264  0.040  0.229 83.644  0.042  2.060   5.1212e-02
   2_adp:   8.264  0.040  0.229 83.644  0.042  2.060   5.1212e-02
   2_occ:   8.264  0.040  0.229 83.644  0.042  2.060   5.1212e-02
   3_bss:   8.264  0.040  0.229 83.644  0.042  2.060   5.1212e-02
   3_xyz:   7.596  0.045  0.263 81.614  0.030  2.262   5.1828e-02
   3_adp:   7.596  0.045  0.263 81.614  0.030  2.262   5.1828e-02
   3_occ:   7.596  0.045  0.263 81.614  0.030  2.262   5.1828e-02
   4_bss:   7.596  0.045  0.263 81.614  0.030  2.262   5.1828e-02
   4_xyz:   7.026  0.042  0.219 83.068  0.032  2.306   5.2784e-02
   4_adp:   7.026  0.042  0.219 83.068  0.032  2.306   5.2784e-02
   4_occ:   7.026  0.042  0.219 83.068  0.032  2.306   5.2784e-02
   5_bss:   7.026  0.042  0.219 83.068  0.032  2.306   5.2784e-02
   5_xyz:   6.817  0.045  0.228 82.451  0.032  2.325   5.4375e-02
   5_adp:   6.817  0.045  0.228 82.451  0.032  2.325   5.4375e-02
   5_occ:   6.817  0.045  0.228 82.451  0.032  2.325   5.4375e-02
   5_bss:   6.817  0.045  0.228 82.451  0.032  2.325   5.4375e-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:  95.64   0.00  19.49  85.65   0.00  15.29  95.64   2.92  42.39
   1_occ:  95.64   0.00  19.49  85.65   0.00  15.29  95.64   2.92  42.39
   2_bss:  95.64   0.00  19.49  85.65   0.00  15.29  95.64   2.92  42.39
   2_xyz:  95.64   0.00  19.49  85.65   0.00  15.29  95.64   2.92  42.39
   2_adp: 100.81   0.00  18.55 100.81   0.00  14.33  88.88   5.29  41.51
   2_occ: 100.81   0.00  18.55 100.81   0.00  14.33  88.88   5.29  41.51
   3_bss: 100.81   0.00  18.55 100.81   0.00  14.33  88.88   5.29  41.51
   3_xyz: 100.81   0.00  18.55 100.81   0.00  14.33  88.88   5.29  41.51
   3_adp:  98.09   0.00  17.69  98.09   0.00  13.48  85.98   2.28  40.61
   3_occ:  98.09   0.00  17.69  98.09   0.00  13.48  85.98   2.28  40.61
   4_bss:  98.09   0.00  17.69  98.09   0.00  13.48  85.98   2.28  40.61
   4_xyz:  98.09   0.00  17.69  98.09   0.00  13.48  85.98   2.28  40.61
   4_adp:  99.77   2.46  17.58  99.77   2.67  13.29  85.69   2.46  40.91
   4_occ:  99.77   2.46  17.58  99.77   2.67  13.29  85.69   2.46  40.91
   5_bss:  99.77   2.46  17.58  99.77   2.67  13.29  85.69   2.46  40.91
   5_xyz:  99.77   2.46  17.58  99.77   2.67  13.29  85.69   2.46  40.91
   5_adp: 100.89   2.78  17.38 100.89   2.78  13.16  89.17   3.43  40.37
   5_occ: 100.89   2.78  17.38 100.89   2.78  13.16  89.17   3.43  40.37
   5_bss: 100.79   2.68  17.28 100.79   2.68  13.06  89.07   3.32  40.27
------------------------------------------------------------------------
 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:    3.715    0.024    0.391
   1_adp:    3.715    0.024    0.391
   1_occ:    3.715    0.024    0.391
   2_bss:    3.715    0.024    0.391
   2_xyz:    2.498    0.041    0.500
   2_adp:    2.498    0.041    0.500
   2_occ:    2.498    0.041    0.500
   3_bss:    2.498    0.041    0.500
   3_xyz:    2.511    0.029    0.612
   3_adp:    2.511    0.029    0.612
   3_occ:    2.511    0.029    0.612
   4_bss:    2.511    0.029    0.612
   4_xyz:    2.524    0.053    0.651
   4_adp:    2.524    0.053    0.651
   4_occ:    2.524    0.053    0.651
   5_bss:    2.524    0.053    0.651
   5_xyz:    2.560    0.065    0.667
   5_adp:    2.560    0.065    0.667
   5_occ:    2.560    0.065    0.667
   5_bss:    2.560    0.065    0.667
------------------------------------------------------------------------

CPU time actual refinement: 351.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/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_55/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_55/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.64 
  Macro-tasks:
    bulk solvent and scale       = 45.27  
    individual site refinement   = 138.76 
    weights calculation          = 31.39  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.13 
  Micro-tasks:
    mask                            = 2.52   
    f_calc                          = 112.01 
    alpha_beta                      = 8.53   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 118.36 
    fmodel                         = 7.13   
    r_factors                      = 0.20   
    phase_errors                   = 10.37  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 260.56 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.052 micro seconds
Total CPU time: 6.09 minutes
from_scatterers_fft:    636 calls, 111.69 s
gradients_fft:          581 calls, 105.76 s

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

# Date 2008-01-16 Time 03:54:45 PST -0800 (1200484485.32 s)
Start R-work = 0.4448, R-free = 0.4463 (no bulk solvent and anisotropic scale)
Final R-work = 0.1390, R-free = 0.1817 (no bulk solvent and anisotropic scale)

Start R-work = 0.4349, R-free = 0.4361
Final R-work = 0.1113, R-free = 0.1590