# Date 2008-01-16 Time 04:12:53 PST -0800 (1200485573.99 s)
#phil __OFF__

Command line arguments: "../218.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25902
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 218

-------------------------------------------------------------------------------
  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: (68.845, 47.6339, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


================================== 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: (68.845, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.96094
Completeness in resolution range: 0.917604
Completeness with d_max=infinity: 0.914861

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9376
                             d_min =   1.9609

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: (68.845, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.96094
Completeness in resolution range: 0.917604
Completeness with d_max=infinity: 0.914861

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9380 -  4.1964 [2236/2264]  2007   229  10.2%
  bin  2:  4.1964 -  3.3431 [2158/2181]  1943   215  10.0%
  bin  3:  3.3431 -  2.9241 [2132/2157]  1926   206   9.7%
  bin  4:  2.9241 -  2.6584 [2099/2115]  1883   216  10.3%
  bin  5:  2.6584 -  2.4688 [2081/2125]  1871   210  10.1%
  bin  6:  2.4688 -  2.3238 [2083/2111]  1881   202   9.7%
  bin  7:  2.3238 -  2.2078 [2060/2096]  1858   202   9.8%
  bin  8:  2.2078 -  2.1120 [2091/2133]  1882   209  10.0%
  bin  9:  2.1120 -  2.0309 [2012/2083]  1813   199   9.9%
  bin 10:  2.0309 -  1.9609 [ 637/2083]   566    71  11.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/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: 0.11 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.29 -     2.01: 14
        2.01 -     2.73: 229
        2.73 -     3.46: 4602
        3.46 -     4.18: 9312
        4.18 -     4.90: 14041
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.291 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.327 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.494 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.527 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.623 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28193 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_218/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/model_refine_001.geo

CPU time processing inputs: 7.85


============================ 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 = 68.845 47.63395 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4617   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.266883                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6807 0.99   1456  160 0.3513 0.3716      6.5231      6.5434|
|  2:  4.6807 -  3.7343 0.99   1414  156 0.3910 0.4106      6.7624      6.8073|
|  3:  3.7343 -  3.2679 0.99   1361  155 0.4413 0.4265      6.6445      6.6252|
|  4:  3.2679 -  2.9717 0.99   1373  145 0.4545 0.4462      6.4731      6.4703|
|  5:  2.9717 -  2.7601 0.98   1344  153 0.4885 0.4703       6.342      6.3704|
|  6:  2.7601 -  2.5983 0.99   1352  150 0.4911 0.5392      6.2582      6.1851|
|  7:  2.5983 -  2.4688 0.98   1330  157 0.4965 0.4332      6.2066      6.1195|
|  8:  2.4688 -  2.3617 0.99   1352  143 0.5255 0.5064      6.1679      6.1372|
|  9:  2.3617 -  2.2711 0.99   1336  148 0.5221 0.4921      6.1068      6.1881|
| 10:  2.2711 -  2.1930 0.98   1341  144 0.5210 0.5220      6.0873      6.0706|
| 11:  2.1930 -  2.1246 0.97   1310  156 0.5272 0.5290      6.0063      6.0303|
| 12:  2.1246 -  2.0641 0.99   1324  144 0.5261 0.5384      5.9446      5.9351|
| 13:  2.0641 -  2.0099 0.79   1088  115 0.5169 0.5431      5.8685      5.8358|
| 14:  2.0099 -  1.9609 0.19    249   33 0.4853 0.5053      5.9062      5.7138|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.6807  1456   160  0.72  32.96   0.83     0.73      65555.15|
|  2:  4.6807 -  3.7343  1414   156  0.71  33.96   0.92     0.80      99117.81|
|  3:  3.7343 -  3.2679  1361   155  0.61  42.87   0.89     0.79     105138.36|
|  4:  3.2679 -  2.9717  1373   145  0.52  50.23   0.90     0.71      93343.88|
|  5:  2.9717 -  2.7601  1344   153  0.46  55.37   0.89     0.63      74388.62|
|  6:  2.7601 -  2.5983  1352   150  0.43  57.69   0.89     0.59      65359.15|
|  7:  2.5983 -  2.4688  1330   157  0.43  57.28   0.90     0.59      58225.20|
|  8:  2.4688 -  2.3617  1352   143  0.42  58.59   0.91     0.60      52380.01|
|  9:  2.3617 -  2.2711  1336   148  0.42  58.12   0.90     0.63      48828.89|
| 10:  2.2711 -  2.1930  1341   144  0.41  59.07   0.91     0.59      44044.25|
| 11:  2.1930 -  2.1246  1310   156  0.33  65.23   0.91     0.52      46465.54|
| 12:  2.1246 -  2.0641  1324   144  0.26  70.74   0.93     0.42      45882.67|
| 13:  2.0641 -  2.0099  1088   115  0.23  73.01   0.92     0.38      41925.43|
| 14:  2.0099 -  1.9609   249    33  0.33  64.97   1.02     0.41      29849.75|
|alpha:            min =        0.38 max =            0.80 mean =         0.62|
|beta:             min =    29849.75 max =       105138.36 mean =     64799.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           89.98 mean =        54.61|
|phase err.(test): min =        0.00 max =           89.68 mean =        54.85|
|-----------------------------------------------------------------------------|

============================== 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 = 18.864162             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.667   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.089901              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.575   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.291 -  1.652:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.652 -  2.013:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.013 -  2.374:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.374 -  2.734:      211 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.734 -  3.095:     2322 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.095 -  3.456:     2280 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.456 -  3.817:     4183 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.817 -  4.178:     5129 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.178 -  4.539:     6283 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.539 -  4.900:     7758 |
|-----------------------------------------------------------------------------|
|-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 |        0.198 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.291 |       0.683 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    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: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4621   r_free= 0.4617   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.266883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4553   r_free= 0.4506   ksol= 0.31   Bsol= 37.95   scale= 0.943   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,1.52,2.93,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.261539                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.652238             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.206   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.145700              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.170   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4553      final r-factor (work) = 0.2822          |
| start r-factor (free) = 0.4506      final r-factor (free) = 0.3124          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.1916 = 15.65 * 0.50 * 6.2603 + 1.00 * 0.1975                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.7689 = 15.65 * 0.50 * 6.0852 + 1.00 * 0.1456                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2822      final r-factor (work) = 0.2543          |
| start r-factor (free) = 0.3124      final r-factor (free) = 0.3237          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9780 = 1.15 * 1.00 * 6.0852 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7101 = 1.15 * 1.00 * 5.8423 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.78   18.60    None  None   None       |
|    all(noH): 2823   0      0.00    94.78   18.60    None  None   None       |
|    Sol.    : 438    0      4.21    94.78   42.78    None  None   None       |
|    Mac.    : 2385   0      0.00    83.00   14.16    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:     0.000 -   9.478:  894   |   5:    47.392 -  56.870:   98        |
|      1:     9.478 -  18.957: 1011   |   6:    56.870 -  66.349:   63        |
|      2:    18.957 -  28.435:  375   |   7:    66.349 -  75.827:   32        |
|      3:    28.435 -  37.914:  188   |   8:    75.827 -  85.306:   16        |
|      4:    37.914 -  47.392:  139   |   9:    85.306 -  94.784:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2543 r_free = 0.3237             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2541 r_free = 0.3238             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2541   r_free= 0.3238   ksol= 0.31   Bsol= 37.95   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,1.52,2.93,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.855551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2502   r_free= 0.3215   ksol= 0.34   Bsol= 68.43   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.40,0.54,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.850224                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.753267              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.576   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.272790              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.168  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2502      final r-factor (work) = 0.1871          |
| start r-factor (free) = 0.3215      final r-factor (free) = 0.2380          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0421 = 4.75 * 0.50 * 5.8472 + 1.00 * 0.1455                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7417 = 4.75 * 0.50 * 5.7534 + 1.00 * 0.0680                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1871      final r-factor (work) = 0.1803          |
| start r-factor (free) = 0.2380      final r-factor (free) = 0.2265          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5860 = 0.27 * 1.00 * 5.7534 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5825 = 0.27 * 1.00 * 5.5690 + 1.00 * 0.0633                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.33   19.06    None  None   None       |
|    all(noH): 2823   0      0.00    93.33   19.06    None  None   None       |
|    Sol.    : 438    0      6.80    93.33   42.87    None  None   None       |
|    Mac.    : 2385   0      0.00    82.87   14.68    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 -   9.333:  695   |   5:    46.665 -  55.997:  100        |
|      1:     9.333 -  18.666: 1243   |   6:    55.997 -  65.330:   59        |
|      2:    18.666 -  27.999:  351   |   7:    65.330 -  74.663:   32        |
|      3:    27.999 -  37.332:  174   |   8:    74.663 -  83.996:   18        |
|      4:    37.332 -  46.665:  144   |   9:    83.996 -  93.329:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1803 r_free = 0.2265             target_work(ml) = 5.541         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1800 r_free = 0.2263             target_work(ml) = 5.540         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1800   r_free= 0.2263   ksol= 0.34   Bsol= 68.43   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-0.40,0.54,-0.00,0.00,0.00); trace/3= -0.68                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.540033                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1784   r_free= 0.2242   ksol= 0.33   Bsol= 68.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.87,-2.14,-1.09,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.538527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.612700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.809  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.491687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.141   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1784      final r-factor (work) = 0.1503          |
| start r-factor (free) = 0.2242      final r-factor (free) = 0.1958          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3384 = 2.61 * 0.50 * 5.5654 + 1.00 * 0.0680                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1960 = 2.61 * 0.50 * 5.4628 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1503      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.1958      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1802 = 1.49 * 1.00 * 5.4628 + 1.00 * 0.0314                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9894 = 1.49 * 1.00 * 5.3479 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.60    97.90   19.31    None  None   None       |
|    all(noH): 2823   0      0.60    97.90   19.31    None  None   None       |
|    Sol.    : 438    0      6.86    93.55   46.27    None  None   None       |
|    Mac.    : 2385   0      0.60    97.90   14.36    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:     0.597 -  10.328:  906   |   5:    49.249 -  58.980:   99        |
|      1:    10.328 -  20.058: 1196   |   6:    58.980 -  68.710:   73        |
|      2:    20.058 -  29.788:  245   |   7:    68.710 -  78.440:   44        |
|      3:    29.788 -  39.519:  125   |   8:    78.440 -  88.171:   23        |
|      4:    39.519 -  49.249:  103   |   9:    88.171 -  97.901:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1357 r_free = 0.1859             target_work(ml) = 5.317         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1356 r_free = 0.1860             target_work(ml) = 5.317         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1356   r_free= 0.1860   ksol= 0.33   Bsol= 68.43   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.87,-2.14,-1.09,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.317120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1360   r_free= 0.1861   ksol= 0.33   Bsol= 68.43   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-4.15,-2.44,-1.32,-0.00,-0.00,-0.00); trace/3= -2.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.318394                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.800874              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.863  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.761  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1861      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5510 = 2.80 * 0.50 * 5.3492 + 1.00 * 0.0597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4557 = 2.80 * 0.50 * 5.2763 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1732      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0943 = 0.21 * 1.00 * 5.2763 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0832 = 0.21 * 1.00 * 5.2352 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.13    95.00   18.45    None  None   None       |
|    all(noH): 2823   0      2.13    95.00   18.45    None  None   None       |
|    Sol.    : 438    0      3.61    88.07   42.96    None  None   None       |
|    Mac.    : 2385   0      2.13    95.00   13.94    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:     2.129 -  11.416: 1146   |   5:    48.562 -  57.849:   81        |
|      1:    11.416 -  20.702: 1030   |   6:    57.849 -  67.135:   60        |
|      2:    20.702 -  29.989:  216   |   7:    67.135 -  76.422:   41        |
|      3:    29.989 -  39.276:  114   |   8:    76.422 -  85.709:   11        |
|      4:    39.276 -  48.562:  116   |   9:    85.709 -  94.995:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1212 r_free = 0.1667             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1211 r_free = 0.1668             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1668   ksol= 0.33   Bsol= 68.43   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-4.15,-2.44,-1.32,-0.00,-0.00,-0.00); trace/3= -2.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.217952                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1211   r_free= 0.1668   ksol= 0.34   Bsol= 68.43   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-4.05,-2.59,-1.46,-0.00,-0.00,-0.00); trace/3= -2.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.947828              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.834  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.204713              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.052  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1211      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1649 = 1.95 * 0.50 * 5.2349 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1346 = 1.95 * 0.50 * 5.2120 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2880 = 1.20 * 1.00 * 5.2120 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2692 = 1.20 * 1.00 * 5.1953 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.52   18.47    None  None   None       |
|    all(noH): 2823   0      0.00    98.52   18.47    None  None   None       |
|    Sol.    : 438    0      0.00    94.19   43.60    None  None   None       |
|    Mac.    : 2385   0      1.45    98.52   13.85    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 -   9.852:  830   |   5:    49.261 -  59.113:   90        |
|      1:     9.852 -  19.704: 1301   |   6:    59.113 -  68.965:   63        |
|      2:    19.704 -  29.557:  245   |   7:    68.965 -  78.817:   35        |
|      3:    29.557 -  39.409:  122   |   8:    78.817 -  88.669:   18        |
|      4:    39.409 -  49.261:  115   |   9:    88.669 -  98.522:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1180 r_free = 0.1647             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1179 r_free = 0.1647             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1647   ksol= 0.34   Bsol= 68.43   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-4.05,-2.59,-1.46,-0.00,-0.00,-0.00); trace/3= -2.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6807 0.99   1456  160 0.0987 0.1283      5.3885      5.5745|
|  2:  4.6807 -  3.7343 0.99   1414  156 0.0847 0.1049      5.4256      5.6111|
|  3:  3.7343 -  3.2679 0.99   1361  155 0.1114 0.1548      5.4928      5.8284|
|  4:  3.2679 -  2.9717 0.99   1373  145 0.1330 0.1701      5.4848      5.6513|
|  5:  2.9717 -  2.7601 0.98   1344  153 0.1396 0.1747      5.3808      5.5649|
|  6:  2.7601 -  2.5983 0.99   1352  150 0.1350 0.2198      5.2736      5.5568|
|  7:  2.5983 -  2.4688 0.98   1330  157 0.1362 0.1741      5.2305      5.4016|
|  8:  2.4688 -  2.3617 0.99   1352  143 0.1274 0.1838      5.1566      5.3261|
|  9:  2.3617 -  2.2711 0.99   1336  148 0.1212 0.1851       5.061      5.3499|
| 10:  2.2711 -  2.1930 0.98   1341  144 0.1240 0.1929      5.0078      5.2355|
| 11:  2.1930 -  2.1246 0.97   1310  156 0.1224 0.1845       4.949      5.2802|
| 12:  2.1246 -  2.0641 0.99   1324  144 0.1171 0.1607      4.8884      5.0926|
| 13:  2.0641 -  2.0099 0.79   1088  115 0.1140 0.1990      4.8065      5.0915|
| 14:  2.0099 -  1.9609 0.19    249   33 0.1055 0.1637      4.7833      4.9268|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.6807  1456   160  0.94   9.21   0.97     0.94       7301.37|
|  2:  4.6807 -  3.7343  1414   156  0.95   8.07   1.01     0.99       8943.09|
|  3:  3.7343 -  3.2679  1361   155  0.93  11.72   1.02     1.02      10554.95|
|  4:  3.2679 -  2.9717  1373   145  0.91  14.91   1.01     0.99      10840.34|
|  5:  2.9717 -  2.7601  1344   153  0.89  16.94   1.00     0.98       9499.08|
|  6:  2.7601 -  2.5983  1352   150  0.88  17.82   0.98     0.94       8005.22|
|  7:  2.5983 -  2.4688  1330   157  0.89  17.05   0.98     0.95       7137.49|
|  8:  2.4688 -  2.3617  1352   143  0.89  17.46   0.99     0.95       6465.19|
|  9:  2.3617 -  2.2711  1336   148  0.90  16.76   0.98     0.94       5423.30|
| 10:  2.2711 -  2.1930  1341   144  0.89  16.98   0.98     0.95       4878.74|
| 11:  2.1930 -  2.1246  1310   156  0.90  16.93   0.98     0.93       4447.76|
| 12:  2.1246 -  2.0641  1324   144  0.90  16.68   0.99     0.99       4131.27|
| 13:  2.0641 -  2.0099  1088   115  0.89  17.32   0.97     0.95       3598.37|
| 14:  2.0099 -  1.9609   249    33  0.91  14.96   0.96     0.91       3198.89|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3198.89 max =        10840.34 mean =      7041.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.30 mean =        14.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1646   ksol= 0.33   Bsol= 68.43   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.87,-2.49,-1.34,-0.00,-0.00,-0.00); trace/3= -2.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1646   ksol= 0.33   Bsol= 68.43   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.87,-2.49,-1.34,-0.00,-0.00,-0.00); trace/3= -2.57                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199540                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.6807 0.99   1456  160 0.0986 0.1282      5.3878      5.5763|
|  2:  4.6807 -  3.7343 0.99   1414  156 0.0848 0.1050      5.4266      5.6118|
|  3:  3.7343 -  3.2679 0.99   1361  155 0.1114 0.1548      5.4933      5.8287|
|  4:  3.2679 -  2.9717 0.99   1373  145 0.1330 0.1701      5.4848      5.6515|
|  5:  2.9717 -  2.7601 0.98   1344  153 0.1396 0.1746      5.3806      5.5642|
|  6:  2.7601 -  2.5983 0.99   1352  150 0.1350 0.2198      5.2733      5.5568|
|  7:  2.5983 -  2.4688 0.98   1330  157 0.1362 0.1743      5.2305      5.4016|
|  8:  2.4688 -  2.3617 0.99   1352  143 0.1273 0.1838      5.1569      5.3262|
|  9:  2.3617 -  2.2711 0.99   1336  148 0.1212 0.1852      5.0611      5.3504|
| 10:  2.2711 -  2.1930 0.98   1341  144 0.1240 0.1928      5.0078      5.2353|
| 11:  2.1930 -  2.1246 0.97   1310  156 0.1224 0.1844       4.949      5.2801|
| 12:  2.1246 -  2.0641 0.99   1324  144 0.1172 0.1608      4.8884      5.0928|
| 13:  2.0641 -  2.0099 0.79   1088  115 0.1140 0.1988      4.8065      5.0902|
| 14:  2.0099 -  1.9609 0.19    249   33 0.1054 0.1637      4.7837      4.9275|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.6807  1456   160  0.94   9.21   0.97     0.94       7298.43|
|  2:  4.6807 -  3.7343  1414   156  0.95   8.08   1.01     1.00       8954.68|
|  3:  3.7343 -  3.2679  1361   155  0.93  11.73   1.02     1.02      10574.49|
|  4:  3.2679 -  2.9717  1373   145  0.91  14.91   1.01     1.00      10843.84|
|  5:  2.9717 -  2.7601  1344   153  0.89  16.94   1.00     0.99       9495.08|
|  6:  2.7601 -  2.5983  1352   150  0.88  17.81   0.98     0.95       8000.96|
|  7:  2.5983 -  2.4688  1330   157  0.89  17.05   0.99     0.96       7136.46|
|  8:  2.4688 -  2.3617  1352   143  0.89  17.47   1.00     0.95       6467.58|
|  9:  2.3617 -  2.2711  1336   148  0.90  16.77   0.99     0.95       5425.75|
| 10:  2.2711 -  2.1930  1341   144  0.89  16.98   0.99     0.95       4878.01|
| 11:  2.1930 -  2.1246  1310   156  0.90  16.93   0.99     0.94       4446.03|
| 12:  2.1246 -  2.0641  1324   144  0.90  16.68   1.00     1.00       4131.77|
| 13:  2.0641 -  2.0099  1088   115  0.89  17.32   0.98     0.96       3596.50|
| 14:  2.0099 -  1.9609   249    33  0.91  14.96   0.97     0.92       3195.34|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3195.34 max =        10843.84 mean =      7043.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.29 mean =        14.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.920)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.52   18.47    None  None   None       |
|    all(noH): 2823   0      0.00    98.52   18.47    None  None   None       |
|    Sol.    : 438    0      0.00    94.20   43.60    None  None   None       |
|    Mac.    : 2385   0      1.46    98.52   13.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.855:  830   |   5:    49.264 -  59.116:   90        |
|      1:     9.855 -  19.707: 1301   |   6:    59.116 -  68.968:   63        |
|      2:    19.707 -  29.559:  245   |   7:    68.968 -  78.820:   35        |
|      3:    29.559 -  39.412:  122   |   8:    78.820 -  88.672:   18        |
|      4:    39.412 -  49.264:  115   |   9:    88.672 -  98.525:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.659 - 4.683
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 311
   mapped sites are within: 0.701 - 4.683

peak=    5.329 closest distance to " O   HOH Z 210 " =    1.123
peak=    5.226 closest distance to " O   HOH Z 113 " =    2.055
peak=    5.019 closest distance to " CB  GLN A 223 " =    1.415
peak=    4.994 closest distance to " CG  PRO A  54 " =    1.383
peak=    4.969 closest distance to " CB  ARG A 275 " =    0.939
peak=    4.931 closest distance to " CA  ARG A  36 " =    1.072
peak=    4.899 closest distance to " O   HOH Z 403 " =    1.887
peak=    4.786 closest distance to " CG  PRO A 280 " =    0.875
peak=    4.756 closest distance to " O   HOH Z  49 " =    1.183
peak=    4.716 closest distance to " CG  PRO A 198 " =    1.212
peak=    4.654 closest distance to " CA  TYR A  30 " =    0.908
peak=    4.623 closest distance to " O   HOH Z 369 " =    2.340
peak=    4.607 closest distance to " CG  PRO A  90 " =    1.228
peak=    4.526 closest distance to " O   HOH Z  65 " =    0.994
peak=    4.502 closest distance to " CB  ARG A 190 " =    1.744
peak=    4.468 closest distance to " CD2 TRP A 179 " =    1.349
peak=    4.432 closest distance to " CB  PRO A  54 " =    1.024
peak=    4.420 closest distance to " CZ  PHE A 218 " =    1.147
peak=    4.410 closest distance to " O   HOH Z 188 " =    2.754
peak=    4.408 closest distance to " CB  GLU A 152 " =    1.103
peak=    4.402 closest distance to " O  BHOH Z  74 " =    1.198
peak=    4.398 closest distance to " O   HOH Z 248 " =    1.510
peak=    4.380 closest distance to " O   HOH Z 234 " =    3.694
peak=    4.334 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.314 closest distance to " O   PRO A 198 " =    1.539
peak=    4.280 closest distance to " O   GLY A  23 " =    2.420
peak=    4.280 closest distance to " O   HOH Z 142 " =    1.573
peak=    4.250 closest distance to " CZ3 TRP A 266 " =    1.096
peak=    4.225 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.192 closest distance to " CG  PRO A 243 " =    1.134
peak=    4.187 closest distance to " O   HOH Z  43 " =    1.727
peak=    4.136 closest distance to " O   HOH Z 287 " =    1.824
peak=    4.132 closest distance to " O   HOH Z 203 " =    1.423
peak=    4.126 closest distance to " CD  ARG A 269 " =    1.057
peak=    4.113 closest distance to " O   HOH Z 365 " =    2.565
peak=    4.107 closest distance to " CB  GLU A 277 " =    3.700
peak=    4.104 closest distance to " O   HOH Z 298 " =    1.843
peak=    4.082 closest distance to " CB  SER A  63 " =    1.060
peak=    4.064 closest distance to " CG  ARG A  66 " =    2.513
peak=    4.039 closest distance to " O   HOH Z 412 " =    3.798
peak=    4.038 closest distance to " O   HOH Z 346 " =    1.653
peak=    4.038 closest distance to " CB  ARG A  79 " =    1.494
peak=    4.009 closest distance to " CG  PRO A 213 " =    1.262
peak=    4.008 closest distance to " O   HOH Z 227 " =    1.633
peak=    3.998 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.996 closest distance to " CG  GLN A  58 " =    0.967
peak=    3.987 closest distance to " CA  ARG A 195 " =    1.301
peak=    3.982 closest distance to " CZ  PHE A  38 " =    1.184
peak=    3.974 closest distance to " NZ  LYS A 117 " =    3.049
peak=    3.967 closest distance to " O   HOH Z  63 " =    1.891
peak=    3.962 closest distance to " O   HOH Z 255 " =    0.957
peak=    3.940 closest distance to " NE2 GLN A  11 " =    1.039
peak=    3.940 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.931 closest distance to " CB  THR A  31 " =    1.522
peak=    3.930 closest distance to " N   ASN A  39 " =    1.261
peak=    3.900 closest distance to " CB  SER A 141 " =    1.114
peak=    3.886 closest distance to " O   SER A  87 " =    2.313
peak=    3.874 closest distance to " O   HOH Z  40 " =    2.051
peak=    3.872 closest distance to " O   HOH Z  97 " =    1.936
peak=    3.868 closest distance to " O   HOH Z 126 " =    1.903
peak=    3.864 closest distance to " O   HOH Z 380 " =    1.745
peak=    3.857 closest distance to " CD  LYS A  76 " =    1.877
peak=    3.848 closest distance to " ND2 ASN A 187 " =    1.625
peak=    3.847 closest distance to " O   HOH Z 361 " =    3.524
peak=    3.845 closest distance to " CB  ASN A 148 " =    1.439
peak=    3.843 closest distance to " O   HOH Z 261 " =    2.436
peak=    3.823 closest distance to " O   HOH Z 368 " =    2.199
peak=    3.823 closest distance to " CB  GLU A 128 " =    1.057
peak=    3.814 closest distance to " O   THR A 220 " =    1.154
peak=    3.801 closest distance to " O   HOH Z 209 " =    2.277
peak=    3.788 closest distance to " O   HOH Z 303 " =    2.202
peak=    3.773 closest distance to " CD  LYS A 166 " =    1.378
peak=    3.771 closest distance to " O   ALA A 165 " =    1.411
peak=    3.760 closest distance to " O   HOH Z 251 " =    1.585
peak=    3.750 closest distance to " O   HOH Z 406 " =    1.559
peak=    3.749 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.746 closest distance to " O   HOH Z 250 " =    1.406
peak=    3.742 closest distance to " CB  VAL A 202 " =    1.494
peak=    3.731 closest distance to " O   HOH Z 132 " =    1.157
peak=    3.716 closest distance to " CB  SER A  26 " =    1.858
peak=    3.714 closest distance to " O   HOH Z  44 " =    2.267
peak=    3.714 closest distance to " O   HOH Z  59 " =    2.214
peak=    3.708 closest distance to " CB  PRO A 198 " =    1.259
peak=    3.696 closest distance to " O   TYR A 116 " =    1.463
peak=    3.694 closest distance to " O   HOH Z  97 " =    2.047
peak=    3.693 closest distance to " O   HOH Z 193 " =    1.504
peak=    3.685 closest distance to " O   HOH Z 316 " =    3.021
peak=    3.680 closest distance to " O   ASN A  74 " =    1.434
peak=    3.679 closest distance to " O   HOH Z 185 " =    1.778
peak=    3.676 closest distance to " O   HOH Z 389 " =    1.906
peak=    3.672 closest distance to " CB  ASN A 285 " =    0.944
peak=    3.662 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.661 closest distance to " O   HOH Z 402 " =    1.391
peak=    3.660 closest distance to " O   HOH Z 427 " =    2.949
peak=    3.657 closest distance to " CB  SER A  62 " =    0.945
peak=    3.656 closest distance to " CB  PRO A  90 " =    1.107
peak=    3.655 closest distance to " O   HOH Z 423 " =    1.879
peak=    3.654 closest distance to " O   HOH Z 132 " =    2.283
peak=    3.652 closest distance to " CD1 LEU A  96 " =    0.748
peak=    3.649 closest distance to " CB  ARG A  79 " =    0.949
peak=    3.643 closest distance to " O   HOH Z 291 " =    1.461
peak=    3.641 closest distance to " CA  ASP A 162 " =    1.067
peak=    3.640 closest distance to " O   HOH Z 417 " =    2.989
peak=    3.638 closest distance to " CG  GLN A  11 " =    1.413
peak=    3.628 closest distance to " CB  TRP A 266 " =    1.112
peak=    3.624 closest distance to " O   HOH Z 117 " =    1.062
peak=    3.600 closest distance to " O   HOH Z 345 " =    1.652
peak=    3.600 closest distance to " NH1AARG A 145 " =    1.412
peak=    3.598 closest distance to " O   HOH Z 383 " =    2.081
peak=    3.589 closest distance to " CA  ALA A 160 " =    0.900
peak=    3.585 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.584 closest distance to " CG2 ILE A 120 " =    1.253
peak=    3.582 closest distance to " CD2 LEU A 297 " =    1.062
peak=    3.577 closest distance to " O   HOH Z  21 " =    1.845
peak=    3.573 closest distance to " CB  ALA A 248 " =    1.377
peak=    3.572 closest distance to " CB  PHE A 204 " =    0.734
peak=    3.570 closest distance to " O   HOH Z  80 " =    1.898
peak=    3.565 closest distance to " N   CYS A 260 " =    0.961
peak=    3.565 closest distance to " O   HOH Z 173 " =    2.095
peak=    3.563 closest distance to " O   HOH Z 353 " =    2.819
peak=    3.553 closest distance to " O   HOH Z  85 " =    1.457
peak=    3.546 closest distance to " N   TYR A 116 " =    1.610
peak=    3.545 closest distance to " O   HOH Z 359 " =    1.716
peak=    3.543 closest distance to " CE1 TYR A 186 " =    1.304
peak=    3.541 closest distance to " CB  TRP A 179 " =    1.326
peak=    3.540 closest distance to " O   HOH Z 126 " =    1.542
peak=    3.538 closest distance to " O   HOH Z 361 " =    2.480
peak=    3.537 closest distance to " O   HOH Z 285 " =    1.824
peak=    3.537 closest distance to " CG2BVAL A  41 " =    0.823
peak=    3.534 closest distance to " O   HOH Z   1 " =    2.462
peak=    3.528 closest distance to " O   HOH Z  76 " =    0.989
peak=    3.527 closest distance to " O   HOH Z 371 " =    2.908
peak=    3.518 closest distance to " O   HOH Z 214 " =    2.948
peak=    3.518 closest distance to " O   HOH Z  88 " =    2.728
peak=    3.514 closest distance to " O   HOH Z  15 " =    2.207
peak=    3.512 closest distance to " O   HOH Z 102 " =    1.328
peak=    3.512 closest distance to " O   HOH Z 404 " =    2.264
peak=    3.509 closest distance to " O   HOH Z 425 " =    1.326
peak=    3.504 closest distance to " O   HOH Z 180 " =    2.181
peak=    3.502 closest distance to " CB  ASN A  39 " =    0.823
peak=    3.499 closest distance to " O  BHOH Z 338 " =    2.207
peak=    3.498 closest distance to " CG2AVAL A 121 " =    2.158
peak=    3.497 closest distance to " O   HOH Z  78 " =    1.752
peak=    3.491 closest distance to " O   HOH Z  63 " =    2.160
peak=    3.490 closest distance to " CA  SER A  87 " =    1.055
peak=    3.483 closest distance to " O   HOH Z 371 " =    1.550
peak=    3.474 closest distance to " NH2BARG A 145 " =    2.190
peak=    3.473 closest distance to " CB  THR A  52 " =    0.778
peak=    3.469 closest distance to " CE  LYS A 119 " =    1.105
peak=    3.467 closest distance to " OG BSER A 164 " =    2.197
peak=    3.466 closest distance to " CB  GLU A  46 " =    1.079
peak=    3.461 closest distance to " CG2 ILE A  20 " =    1.382
peak=    3.461 closest distance to " O   HOH Z 146 " =    2.320
peak=    3.460 closest distance to " O   HOH Z  35 " =    2.426
peak=    3.450 closest distance to " O   HOH Z 124 " =    1.168
peak=    3.450 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.449 closest distance to " O   HOH Z  19 " =    1.467
peak=    3.449 closest distance to " O   HOH Z 272 " =    1.828
peak=    3.446 closest distance to " CA  VAL A 125 " =    1.252
peak=    3.446 closest distance to " O   HOH Z 219 " =    1.830
peak=    3.444 closest distance to " CA  ALA A 100 " =    1.048
peak=    3.443 closest distance to " O   HOH Z 325 " =    2.221
peak=    3.441 closest distance to " CD  PRO A  54 " =    0.933
peak=    3.440 closest distance to " O   THR A 182 " =    1.455
peak=    3.437 closest distance to " O   HOH Z 394 " =    1.617
peak=    3.435 closest distance to " O   ASP A 124 " =    1.557
peak=    3.434 closest distance to " O   HOH Z 298 " =    2.398
peak=    3.434 closest distance to " NE2 GLN A  77 " =    3.139
peak=    3.434 closest distance to " CD  LYS A 119 " =    1.720
peak=    3.432 closest distance to " N   HIS A 108 " =    1.711
peak=    3.430 closest distance to " OG BSER A 134 " =    2.820
peak=    3.430 closest distance to " O   HOH Z 285 " =    2.441
peak=    3.430 closest distance to " CB  ALA A 114 " =    0.795
peak=    3.428 closest distance to " CG1 ILE A  20 " =    1.246
peak=    3.427 closest distance to " O   HOH Z 265 " =    1.983
peak=    3.427 closest distance to " CA  ALA A 248 " =    1.190
peak=    3.423 closest distance to " CB  ASN A 110 " =    1.088
peak=    3.422 closest distance to " CB  PRO A 243 " =    1.251
peak=    3.421 closest distance to " O   HOH Z 258 " =    2.047
peak=    3.419 closest distance to " CA  GLU A 152 " =    0.857
peak=    3.418 closest distance to " CA  ALA A 295 " =    0.995
peak=    3.416 closest distance to " CA  TYR A 116 " =    1.315
peak=    3.416 closest distance to " O   HOH Z 327 " =    1.682
peak=    3.415 closest distance to " O   HOH Z 247 " =    1.319
peak=    3.415 closest distance to " CG  GLU A  37 " =    0.968
peak=    3.411 closest distance to " O   HOH Z 375 " =    2.090
peak=    3.407 closest distance to " CA  ASN A 176 " =    1.693
peak=    3.403 closest distance to " CB  SER A   3 " =    1.217
peak=    3.394 closest distance to " O   HOH Z 130 " =    2.259
peak=    3.390 closest distance to " N   ARG A 156 " =    1.486
peak=    3.390 closest distance to " O   HOH Z 357 " =    2.101
peak=    3.388 closest distance to " CG2 VAL A 257 " =    0.816
peak=    3.384 closest distance to " O   HOH Z 421 " =    2.083
peak=    3.373 closest distance to " OH  TYR A 116 " =    1.077
peak=    3.372 closest distance to " O   HOH Z 392 " =    2.367
peak=    3.369 closest distance to " O   HOH Z 134 " =    1.375
peak=    3.368 closest distance to " O   HOH Z 158 " =    3.032
peak=    3.364 closest distance to " O   HOH Z 214 " =    1.376
peak=    3.363 closest distance to " N   VAL A 265 " =    1.373
peak=    3.357 closest distance to " O   HOH Z 299 " =    4.307
peak=    3.351 closest distance to " CG2 THR A 221 " =    1.185
peak=    3.348 closest distance to " CA  ASN A 215 " =    0.950
peak=    3.335 closest distance to " O   ASP A 191 " =    1.639
peak=    3.335 closest distance to " CG2AVAL A  72 " =    1.803
peak=    3.335 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.331 closest distance to " O   HOH Z 139 " =    4.683
peak=    3.330 closest distance to " O   HOH Z 366 " =    2.349
peak=    3.327 closest distance to " CA  ILE A 106 " =    0.829
peak=    3.327 closest distance to " O   HOH Z 279 " =    2.189
peak=    3.326 closest distance to " O   HOH Z 116 " =    1.158
peak=    3.320 closest distance to " CG2 VAL A 197 " =    1.023
peak=    3.318 closest distance to " O   HOH Z  61 " =    1.648
peak=    3.315 closest distance to " CB  ASN A 142 " =    1.103
peak=    3.312 closest distance to " CG  LEU A 167 " =    1.150
peak=    3.310 closest distance to " CA  ILE A 234 " =    0.956
peak=    3.309 closest distance to " NE  ARG A  24 " =    0.945
peak=    3.306 closest distance to " CB  ALA A 291 " =    1.119
peak=    3.304 closest distance to " OG  SER A  28 " =    1.521
peak=    3.300 closest distance to " CA  ALA A  84 " =    1.160
peak=    3.298 closest distance to " N   ASP A 162 " =    1.251
peak=    3.295 closest distance to " CD1 ILE A 199 " =    1.237
peak=    3.295 closest distance to " CB  ASP A 124 " =    0.701
peak=    3.294 closest distance to " CG  MET A 185 " =    1.183
peak=    3.291 closest distance to " O   HOH Z  94 " =    2.667
peak=    3.288 closest distance to " CA  ASP A 140 " =    1.282
peak=    3.282 closest distance to " O   HOH Z 132 " =    2.616
peak=    3.276 closest distance to " CG1 ILE A  49 " =    1.587
peak=    3.271 closest distance to " CG1 VAL A 153 " =    1.036
peak=    3.270 closest distance to " CA  MET A 105 " =    1.079
peak=    3.269 closest distance to " CG AARG A 275 " =    1.259
peak=    3.268 closest distance to " CB  MET A  40 " =    1.075
peak=    3.268 closest distance to " CB  SER A 273 " =    0.916
peak=    3.264 closest distance to " OG1 THR A 264 " =    0.767
peak=    3.264 closest distance to " O   HOH Z  88 " =    3.319
peak=    3.255 closest distance to " O   HOH Z 290 " =    1.063
peak=    3.252 closest distance to " CB  LEU A 228 " =    1.154
peak=    3.249 closest distance to " O   HOH Z 148 " =    3.482
peak=    3.249 closest distance to " O   HOH Z 313 " =    1.937
peak=    3.243 closest distance to " O   HOH Z 130 " =    2.425
peak=    3.241 closest distance to " CA  ASN A 127 " =    1.130
peak=    3.239 closest distance to " NH2AARG A 275 " =    3.473
peak=    3.234 closest distance to " O   GLY A  91 " =    1.332
peak=    3.223 closest distance to " O   HOH Z 403 " =    1.471
peak=    3.219 closest distance to " NZ  LYS A  48 " =    1.041
peak=    3.215 closest distance to " CD  GLN A 194 " =    1.609
peak=    3.215 closest distance to " O   HOH Z 411 " =    1.705
peak=    3.211 closest distance to " O   HOH Z 259 " =    2.119
peak=    3.210 closest distance to " N   GLU A  44 " =    1.200
peak=    3.203 closest distance to " O   HOH Z 299 " =    4.422
peak=    3.197 closest distance to " CB  GLN A  88 " =    1.166
peak=    3.196 closest distance to " O   HOH Z 422 " =    2.689
peak=    3.193 closest distance to " CA  SER A  32 " =    1.680
peak=    3.193 closest distance to " O   HOH Z 120 " =    2.675
peak=    3.192 closest distance to " O   HOH Z 240 " =    2.745
peak=    3.186 closest distance to " CZ2 TRP A 179 " =    1.814
peak=    3.181 closest distance to " CB  TYR A 169 " =    0.864
peak=    3.181 closest distance to " CB  ILE A 120 " =    1.370
peak=    3.181 closest distance to " O   HOH Z 199 " =    1.636
peak=    3.178 closest distance to " O   HOH Z  20 " =    1.067
peak=    3.175 closest distance to " O   HOH Z 213 " =    2.202
peak=    3.174 closest distance to " OG  SER A 135 " =    1.284
peak=    3.173 closest distance to " O   HOH Z 426 " =    1.406
peak=    3.172 closest distance to " O   LEU A 228 " =    1.849
peak=    3.171 closest distance to " CD1AILE A 234 " =    0.776
peak=    3.168 closest distance to " OG  SER A  62 " =    2.774
peak=    3.159 closest distance to " O   HOH Z 154 " =    3.154
peak=    3.159 closest distance to " CG2 THR A 220 " =    0.852
peak=    3.159 closest distance to " ND2 ASN A 217 " =    1.121
peak=    3.158 closest distance to " CD  ARG A  66 " =    2.628
peak=    3.157 closest distance to " OG  SER A  22 " =    2.664
peak=    3.155 closest distance to " CB  ASP A 191 " =    1.207
peak=    3.153 closest distance to " CZ3 TRP A  85 " =    0.944
peak=    3.153 closest distance to " O   ASN A 284 " =    1.652
peak=    3.152 closest distance to " CB  HIS A 108 " =    0.838
peak=    3.152 closest distance to " O   HOH Z 305 " =    3.592
peak=    3.149 closest distance to " O   HOH Z 188 " =    1.414
peak=    3.148 closest distance to " O   HOH Z 404 " =    2.253
peak=    3.146 closest distance to " CA  ALA A  21 " =    1.229
peak=    3.143 closest distance to " OE1 GLN A  73 " =    2.534
peak=    3.140 closest distance to " CB  LEU A  83 " =    0.750
peak=    3.139 closest distance to " O   HOH Z 391 " =    3.033
peak=    3.136 closest distance to " O   HOH Z 345 " =    3.750
peak=    3.136 closest distance to " O   HOH Z 394 " =    3.906
peak=    3.130 closest distance to " NE2 GLN A  58 " =    3.214
peak=    3.128 closest distance to " CA  LEU A  83 " =    1.338
peak=    3.126 closest distance to " OD1 ASN A 301 " =    1.516
peak=    3.123 closest distance to " OD1 ASN A  69 " =    2.363
peak=    3.122 closest distance to " O   HOH Z 162 " =    1.666
peak=    3.122 closest distance to " NH2 ARG A 156 " =    1.115
peak=    3.107 closest distance to " O   HOH Z 327 " =    2.250
peak=    3.096 closest distance to " CB  ALA A 131 " =    1.111
peak=    3.085 closest distance to " CB  LYS A 117 " =    1.159
peak=    3.077 closest distance to " O   HOH Z 141 " =    1.642
peak=    3.070 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.068 closest distance to " O   HOH Z 298 " =    4.121
peak=    3.068 closest distance to " O   TRP A 274 " =    1.760
peak=    3.065 closest distance to " O   HOH Z 162 " =    1.906
peak=    3.062 closest distance to " O   HOH Z  47 " =    2.242
peak=    3.059 closest distance to " O   HOH Z 163 " =    1.475
peak=    3.052 closest distance to " O   HOH Z  48 " =    1.625
peak=    3.048 closest distance to " ND2AASN A 224 " =    0.923
peak=    3.048 closest distance to " OD2 ASP A 298 " =    3.821
peak=    3.047 closest distance to " CD2 TYR A 186 " =    1.109
peak=    3.043 closest distance to " CE1 TYR A  30 " =    1.002
peak=    3.043 closest distance to " CA  THR A 221 " =    1.411
peak=    3.035 closest distance to " O   THR A 251 " =    1.260
peak=    3.033 closest distance to " O   HOH Z 142 " =    1.841
peak=    3.026 closest distance to " CB  GLN A 240 " =    1.337

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.924 - 5.462
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.924 - 5.462

peak=   -4.728 closest distance to " SG  CYS A 254 " =    3.450
peak=   -4.522 closest distance to " O   PRO A 198 " =    1.323
peak=   -4.413 closest distance to " CG  GLN A  58 " =    0.998
peak=   -4.343 closest distance to " CG2 ILE A  49 " =    2.765
peak=   -4.213 closest distance to " O   HOH Z 377 " =    2.097
peak=   -4.130 closest distance to " CD2 TYR A 293 " =    1.879
peak=   -4.129 closest distance to " C   HIS A 108 " =    1.091
peak=   -4.107 closest distance to " CD  ARG A 156 " =    2.084
peak=   -4.092 closest distance to " O   HOH Z 266 " =    5.462
peak=   -4.092 closest distance to " CD2 LEU A 237 " =    2.653
peak=   -4.090 closest distance to " OXT GLY A 302 " =    2.972
peak=   -4.053 closest distance to " O   HOH Z 193 " =    1.161
peak=   -4.035 closest distance to " O   VAL A  67 " =    2.823
peak=   -4.030 closest distance to " CD1 LEU A 101 " =    2.426
peak=   -4.005 closest distance to " O   HOH Z 150 " =    2.114
peak=   -3.953 closest distance to " O   HOH Z  13 " =    1.740
peak=   -3.943 closest distance to " CB  ALA A  43 " =    2.536
peak=   -3.935 closest distance to " CG2 ILE A  20 " =    3.056
peak=   -3.893 closest distance to " OG BSER A 134 " =    1.454
peak=   -3.878 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.860 closest distance to " O   HOH Z 166 " =    1.797
peak=   -3.841 closest distance to " O   HOH Z 348 " =    2.241
peak=   -3.841 closest distance to " O   HOH Z 198 " =    1.461
peak=   -3.837 closest distance to " O   HOH Z 278 " =    1.140
peak=   -3.831 closest distance to " CE3 TRP A 150 " =    2.140
peak=   -3.821 closest distance to " CA  GLY A 241 " =    2.384
peak=   -3.821 closest distance to " O   ALA A  34 " =    2.396
peak=   -3.818 closest distance to " O   HOH Z 165 " =    1.833
peak=   -3.803 closest distance to " O   HOH Z 196 " =    2.029
peak=   -3.801 closest distance to " CE2 TYR A  30 " =    2.866
peak=   -3.783 closest distance to " CH2 TRP A 179 " =    1.277
peak=   -3.781 closest distance to " CB  PRO A 243 " =    2.747
peak=   -3.743 closest distance to " O   HOH Z 252 " =    3.862
peak=   -3.732 closest distance to " CD2 PHE A  61 " =    2.132
peak=   -3.729 closest distance to " CB  ALA A 184 " =    2.338
peak=   -3.707 closest distance to " OG  SER A  97 " =    2.159
peak=   -3.704 closest distance to " O   HOH Z 357 " =    2.153
peak=   -3.702 closest distance to " CG1AVAL A  41 " =    2.583
peak=   -3.697 closest distance to " O   HOH Z 102 " =    1.603
peak=   -3.687 closest distance to " O   HOH Z 214 " =    2.697
peak=   -3.682 closest distance to " O   HOH Z 374 " =    1.970
peak=   -3.658 closest distance to " OE1 GLN A 223 " =    2.157
peak=   -3.649 closest distance to " CZ  TYR A 169 " =    1.830
peak=   -3.646 closest distance to " CD2 PHE A 192 " =    2.171
peak=   -3.643 closest distance to " CG  PRO A 243 " =    1.693
peak=   -3.640 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.636 closest distance to " CD2 HIS A 207 " =    2.376
peak=   -3.635 closest distance to " O   HOH Z 366 " =    1.495
peak=   -3.635 closest distance to " CD  GLN A 223 " =    1.547
peak=   -3.629 closest distance to " O   HOH Z 394 " =    1.655
peak=   -3.618 closest distance to " CE  MET A 105 " =    2.921
peak=   -3.585 closest distance to " O   HOH Z 264 " =    1.726
peak=   -3.583 closest distance to " ND2 ASN A 249 " =    2.231
peak=   -3.577 closest distance to " O   HOH Z 285 " =    1.394
peak=   -3.577 closest distance to " O   HOH Z 210 " =    0.924
peak=   -3.574 closest distance to " CD1 PHE A  59 " =    1.973
peak=   -3.564 closest distance to " CG  GLU A  53 " =    1.540
peak=   -3.559 closest distance to " CD1 LEU A  25 " =    2.536
peak=   -3.545 closest distance to " NH2 ARG A  66 " =    1.171
peak=   -3.545 closest distance to " O   TRP A  92 " =    2.013
peak=   -3.544 closest distance to " O   PRO A 163 " =    2.118
peak=   -3.543 closest distance to " O   SER A   3 " =    1.041
peak=   -3.540 closest distance to " ND2BASN A 224 " =    1.834
peak=   -3.526 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -3.524 closest distance to " O   PHE A 218 " =    1.511
peak=   -3.515 closest distance to " O   HOH Z 174 " =    2.456
peak=   -3.505 closest distance to " O   HOH Z  10 " =    1.555
peak=   -3.501 closest distance to " O   SER A 210 " =    1.865
peak=   -3.499 closest distance to " CH2 TRP A 150 " =    1.170
peak=   -3.495 closest distance to " C   THR A 279 " =    1.177
peak=   -3.490 closest distance to " CG2 VAL A 189 " =    2.181
peak=   -3.481 closest distance to " CG  ASP A 132 " =    2.305
peak=   -3.480 closest distance to " O   HOH Z 154 " =    1.687
peak=   -3.478 closest distance to " CD2 TYR A 247 " =    2.422
peak=   -3.473 closest distance to " CG  GLU A 277 " =    1.348
peak=   -3.472 closest distance to " C   ASN A 285 " =    2.176
peak=   -3.470 closest distance to " CG  GLN A  11 " =    1.642
peak=   -3.465 closest distance to " N   ALA A  43 " =    2.557
peak=   -3.465 closest distance to " CB  ALA A  10 " =    2.246
peak=   -3.452 closest distance to " CZ  PHE A  38 " =    2.241
peak=   -3.450 closest distance to " CB  ALA A 161 " =    2.540
peak=   -3.447 closest distance to " O   HOH Z 185 " =    2.389
peak=   -3.444 closest distance to " O   HOH Z 171 " =    2.527
peak=   -3.440 closest distance to " CA  GLY A 241 " =    3.192
peak=   -3.436 closest distance to " OD1 ASP A 171 " =    1.545
peak=   -3.433 closest distance to " CD1 ILE A 106 " =    2.266
peak=   -3.432 closest distance to " NE2 GLN A  88 " =    1.089
peak=   -3.427 closest distance to " O   HOH Z 351 " =    1.615
peak=   -3.426 closest distance to " O   HOH Z 418 " =    1.357
peak=   -3.422 closest distance to " O   HOH Z 423 " =    2.415
peak=   -3.421 closest distance to " O   VAL A 174 " =    2.181
peak=   -3.418 closest distance to " O   HOH Z 113 " =    1.822
peak=   -3.416 closest distance to " CG1 VAL A  78 " =    2.590
peak=   -3.408 closest distance to " CA  GLY A 133 " =    2.051
peak=   -3.406 closest distance to " NE2 GLN A  88 " =    1.752
peak=   -3.406 closest distance to " O   HOH Z 395 " =    5.142
peak=   -3.406 closest distance to " O   HOH Z  71 " =    2.606
peak=   -3.403 closest distance to " CG  GLN A 103 " =    2.513
peak=   -3.401 closest distance to " OD2 ASP A 191 " =    1.492
peak=   -3.399 closest distance to " O   HOH Z 421 " =    4.073
peak=   -3.397 closest distance to " CG  LEU A  83 " =    2.109
peak=   -3.396 closest distance to " ND2 ASN A  45 " =    1.268
peak=   -3.395 closest distance to " O   ALA A 227 " =    1.348
peak=   -3.391 closest distance to " O   HOH Z 211 " =    1.357
peak=   -3.387 closest distance to " OD2 ASP A 171 " =    2.434
peak=   -3.381 closest distance to " CG  GLN A  58 " =    1.105
peak=   -3.371 closest distance to " ND2 ASN A  69 " =    1.894
peak=   -3.370 closest distance to " ND2 ASN A  45 " =    2.008
peak=   -3.367 closest distance to " CE BMET A  47 " =    1.520
peak=   -3.367 closest distance to " N   ALA A 248 " =    2.445
peak=   -3.354 closest distance to " OH  TYR A 172 " =    1.891
peak=   -3.354 closest distance to " O   HOH Z 283 " =    2.364
peak=   -3.352 closest distance to " O   HOH Z 174 " =    3.659
peak=   -3.346 closest distance to " CD2 LEU A 282 " =    2.141
peak=   -3.339 closest distance to " CG2BVAL A  41 " =    1.219
peak=   -3.327 closest distance to " CZ  PHE A 155 " =    1.110
peak=   -3.325 closest distance to " CG  ARG A 269 " =    2.232
peak=   -3.325 closest distance to " NE2 GLN A 223 " =    1.180
peak=   -3.322 closest distance to " N   SER A 276 " =    1.447
peak=   -3.321 closest distance to " O   ILE A  49 " =    1.751
peak=   -3.321 closest distance to " OG BSER A  99 " =    1.028
peak=   -3.319 closest distance to " C   LEU A 143 " =    1.038
peak=   -3.315 closest distance to " O   HOH Z  81 " =    2.002
peak=   -3.315 closest distance to " CE1 TYR A 247 " =    2.737
peak=   -3.309 closest distance to " O   GLU A 152 " =    1.383
peak=   -3.305 closest distance to " O   HOH Z 210 " =    1.939
peak=   -3.301 closest distance to " O   HOH Z  43 " =    1.466
peak=   -3.301 closest distance to " CB  TRP A  85 " =    2.575
peak=   -3.287 closest distance to " O   HOH Z 431 " =    4.218
peak=   -3.284 closest distance to " CA  SER A  62 " =    2.702
peak=   -3.278 closest distance to " O   ALA A  10 " =    1.881
peak=   -3.277 closest distance to " CB  ALA A 248 " =    2.246
peak=   -3.275 closest distance to " NE  ARG A  79 " =    1.309
peak=   -3.270 closest distance to " O   HOH Z  88 " =    2.246
peak=   -3.270 closest distance to " OE2 GLU A 152 " =    1.458
peak=   -3.266 closest distance to " O   HOH Z 166 " =    1.591
peak=   -3.266 closest distance to " O   HOH Z 111 " =    3.852
peak=   -3.262 closest distance to " CB  ALA A 291 " =    2.450
peak=   -3.262 closest distance to " O   HOH Z 287 " =    1.963
peak=   -3.261 closest distance to " CD  PRO A 243 " =    2.059
peak=   -3.261 closest distance to " CA  GLY A 203 " =    2.357
peak=   -3.261 closest distance to " CG  PHE A 283 " =    2.552
peak=   -3.254 closest distance to " CG1 VAL A  67 " =    2.864
peak=   -3.247 closest distance to " O   HOH Z 177 " =    1.553
peak=   -3.246 closest distance to " O   HOH Z 145 " =    3.111
peak=   -3.245 closest distance to " O   ALA A   1 " =    2.017
peak=   -3.245 closest distance to " CG  MET A 105 " =    1.007
peak=   -3.234 closest distance to " O   SER A 276 " =    1.678
peak=   -3.233 closest distance to " O   HOH Z 290 " =    0.977
peak=   -3.230 closest distance to " O   SER A 271 " =    2.083
peak=   -3.228 closest distance to " O   HOH Z 111 " =    2.038
peak=   -3.222 closest distance to " O   HOH Z 422 " =    1.362
peak=   -3.218 closest distance to " O   HOH Z 256 " =    2.313
peak=   -3.218 closest distance to " N   ALA A 248 " =    1.877
peak=   -3.216 closest distance to " O   HOH Z  19 " =    2.391
peak=   -3.216 closest distance to " O   SER A 273 " =    1.408
peak=   -3.213 closest distance to " O   HOH Z 197 " =    1.910
peak=   -3.212 closest distance to " O   HOH Z 252 " =    3.817
peak=   -3.211 closest distance to " O   HOH Z 407 " =    2.774
peak=   -3.206 closest distance to " O   TRP A  70 " =    1.704
peak=   -3.205 closest distance to " OD1 ASN A 148 " =    1.436
peak=   -3.194 closest distance to " CB  HIS A  86 " =    1.175
peak=   -3.188 closest distance to " O   VAL A 257 " =    1.324
peak=   -3.185 closest distance to " N   ALA A 226 " =    1.877
peak=   -3.184 closest distance to " CB  ALA A 129 " =    2.417
peak=   -3.183 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.182 closest distance to " CZ3 TRP A 274 " =    2.290
peak=   -3.181 closest distance to " O   HOH Z 301 " =    2.520
peak=   -3.179 closest distance to " CB  ALA A 291 " =    2.195
peak=   -3.179 closest distance to " NE2 GLN A 240 " =    1.725
peak=   -3.175 closest distance to " CD  LYS A 289 " =    2.373
peak=   -3.174 closest distance to " O   HOH Z  38 " =    1.709
peak=   -3.173 closest distance to " CB  ALA A   9 " =    2.493
peak=   -3.173 closest distance to " O   GLN A  11 " =    1.200
peak=   -3.170 closest distance to " O   HOH Z 106 " =    1.938
peak=   -3.169 closest distance to " O   HOH Z 156 " =    3.458
peak=   -3.167 closest distance to " CD  ARG A 139 " =    1.460
peak=   -3.163 closest distance to " O   ASP A 107 " =    1.900
peak=   -3.163 closest distance to " O   HOH Z  63 " =    1.342
peak=   -3.161 closest distance to " O   HOH Z 345 " =    2.833
peak=   -3.161 closest distance to " O   HOH Z 131 " =    4.125
peak=   -3.159 closest distance to " CB  PHE A  16 " =    2.388
peak=   -3.156 closest distance to " O   HOH Z 340 " =    2.081
peak=   -3.152 closest distance to " CA  GLY A  57 " =    2.088
peak=   -3.149 closest distance to " O   HOH Z 390 " =    1.447
peak=   -3.141 closest distance to " O   HOH Z 281 " =    2.496
peak=   -3.129 closest distance to " CD1 LEU A 222 " =    2.474
peak=   -3.125 closest distance to " O   HOH Z   6 " =    1.974
peak=   -3.120 closest distance to " O   ILE A 263 " =    2.272
peak=   -3.119 closest distance to " O   HOH Z 137 " =    1.504
peak=   -3.107 closest distance to " CZ  PHE A  38 " =    2.032
peak=   -3.103 closest distance to " O   HOH Z 392 " =    1.884
peak=   -3.100 closest distance to " O   GLY A 196 " =    1.098
peak=   -3.090 closest distance to " NH2 ARG A  66 " =    5.292
peak=   -3.089 closest distance to " CA  GLY A 133 " =    1.846
peak=   -3.087 closest distance to " ND2 ASN A 187 " =    1.659
peak=   -3.079 closest distance to " O   HOH Z  40 " =    2.111
peak=   -3.076 closest distance to " O   HOH Z 265 " =    2.455
peak=   -3.046 closest distance to " O   HOH Z 377 " =    1.827
peak=   -3.041 closest distance to " O   HOH Z 166 " =    1.669
peak=   -3.040 closest distance to " O   HOH Z 351 " =    1.465
peak=   -3.021 closest distance to " CB  ASN A  45 " =    1.997
peak=   -3.018 closest distance to " C   GLY A  17 " =    0.931

================= 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    :  0.4621 0.4617   6.266883e+00   6.258219e+00
   1_bss:  0.4553 0.4506   6.261539e+00   6.251117e+00
   1_xyz:  0.2822 0.3124   5.902589e+00   5.999243e+00
   1_adp:  0.2543 0.3237   5.855445e+00   6.023287e+00
   1_occ:  0.2541 0.3238   5.855551e+00   6.024481e+00
   2_bss:  0.2502 0.3215   5.850224e+00   6.018710e+00
   2_xyz:  0.1871 0.2380   5.579640e+00   5.774607e+00
   2_adp:  0.1803 0.2265   5.540761e+00   5.728017e+00
   2_occ:  0.1800 0.2263   5.540033e+00   5.727295e+00
   3_bss:  0.1784 0.2242   5.538527e+00   5.726063e+00
   3_xyz:  0.1503 0.1958   5.396141e+00   5.599285e+00
   3_adp:  0.1357 0.1859   5.317055e+00   5.542021e+00
   3_occ:  0.1356 0.1860   5.317120e+00   5.542219e+00
   4_bss:  0.1360 0.1861   5.318394e+00   5.541825e+00
   4_xyz:  0.1228 0.1732   5.237758e+00   5.474108e+00
   4_adp:  0.1212 0.1667   5.218177e+00   5.442206e+00
   4_occ:  0.1211 0.1668   5.217952e+00   5.442062e+00
   5_bss:  0.1211 0.1668   5.218046e+00   5.442265e+00
   5_xyz:  0.1192 0.1636   5.201118e+00   5.423641e+00
   5_adp:  0.1180 0.1647   5.199582e+00   5.429061e+00
   5_occ:  0.1179 0.1647   5.199476e+00   5.429090e+00
   5_bss:  0.1179 0.1646   5.199540e+00   5.429231e+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:  0.308  37.954  -1.195   1.517   2.927   0.000   0.000   0.000
   1_xyz:  0.308  37.954  -1.195   1.517   2.927   0.000   0.000   0.000
   1_adp:  0.308  37.954  -1.195   1.517   2.927   0.000   0.000   0.000
   1_occ:  0.308  37.954  -1.195   1.517   2.927   0.000   0.000   0.000
   2_bss:  0.335  68.431  -2.183  -0.399   0.537  -0.000   0.000   0.000
   2_xyz:  0.335  68.431  -2.183  -0.399   0.537  -0.000   0.000   0.000
   2_adp:  0.335  68.431  -2.183  -0.399   0.537  -0.000   0.000   0.000
   2_occ:  0.335  68.431  -2.183  -0.399   0.537  -0.000   0.000   0.000
   3_bss:  0.335  68.431  -3.866  -2.135  -1.090  -0.000  -0.000  -0.000
   3_xyz:  0.335  68.431  -3.866  -2.135  -1.090  -0.000  -0.000  -0.000
   3_adp:  0.335  68.431  -3.866  -2.135  -1.090  -0.000  -0.000  -0.000
   3_occ:  0.335  68.431  -3.866  -2.135  -1.090  -0.000  -0.000  -0.000
   4_bss:  0.335  68.431  -4.147  -2.438  -1.320  -0.000  -0.000  -0.000
   4_xyz:  0.335  68.431  -4.147  -2.438  -1.320  -0.000  -0.000  -0.000
   4_adp:  0.335  68.431  -4.147  -2.438  -1.320  -0.000  -0.000  -0.000
   4_occ:  0.335  68.431  -4.147  -2.438  -1.320  -0.000  -0.000  -0.000
   5_bss:  0.335  68.431  -4.055  -2.593  -1.463  -0.000  -0.000  -0.000
   5_xyz:  0.335  68.431  -4.055  -2.593  -1.463  -0.000  -0.000  -0.000
   5_adp:  0.335  68.431  -4.055  -2.593  -1.463  -0.000  -0.000  -0.000
   5_occ:  0.335  68.431  -4.055  -2.593  -1.463  -0.000  -0.000  -0.000
   5_bss:  0.331  68.434  -3.868  -2.493  -1.339  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.631 0.4624  0.6174    64794.119
   1_bss:  53.699 0.4727  0.6588    62057.384
   1_xyz:  32.894 0.7260  0.9558    26878.921
   1_adp:  34.409 0.7075  0.9390    28635.021
   1_occ:  34.466 0.7068  0.9382    28721.509
   2_bss:  34.127 0.7106  0.8887    28207.318
   2_xyz:  23.932 0.8212  0.9797    14632.988
   2_adp:  22.249 0.8395  1.0197    13275.848
   2_occ:  22.242 0.8396  1.0199    13267.845
   3_bss:  22.125 0.8406  0.9617    13172.009
   3_xyz:  18.833 0.8724  0.9794     9896.631
   3_adp:  17.469 0.8850  0.9779     8819.667
   3_occ:  17.473 0.8850  0.9778     8819.867
   4_bss:  17.477 0.8850  0.9684     8829.794
   4_xyz:  16.064 0.8975  0.9724     7653.081
   4_adp:  15.393 0.9034  0.9697     7265.358
   4_occ:  15.392 0.9034  0.9695     7261.227
   5_bss:  15.391 0.9034  0.9675     7265.963
   5_xyz:  14.969 0.9070  0.9701     6974.255
   5_adp:  15.061 0.9065  0.9637     7041.638
   5_occ:  15.061 0.9065  0.9636     7041.125
   5_bss:  15.064 0.9064  0.9683     7042.940
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.9754e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.9754e-01
   1_xyz:   1.682  0.013  0.101 15.812  0.006  4.105   1.4559e-01
   1_adp:   1.682  0.013  0.101 15.812  0.006  4.105   1.4559e-01
   1_occ:   1.682  0.013  0.101 15.812  0.006  4.105   1.4559e-01
   2_bss:   1.682  0.013  0.101 15.812  0.006  4.105   1.4559e-01
   2_xyz:   1.110  0.007  0.075 14.540  0.004  4.127   6.8021e-02
   2_adp:   1.110  0.007  0.075 14.540  0.004  4.127   6.8021e-02
   2_occ:   1.110  0.007  0.075 14.540  0.004  4.127   6.8021e-02
   3_bss:   1.110  0.007  0.075 14.540  0.004  4.127   6.8021e-02
   3_xyz:   1.028  0.007  0.072 14.416  0.004  4.112   5.9686e-02
   3_adp:   1.028  0.007  0.072 14.416  0.004  4.112   5.9686e-02
   3_occ:   1.028  0.007  0.072 14.416  0.004  4.112   5.9686e-02
   4_bss:   1.028  0.007  0.072 14.416  0.004  4.112   5.9686e-02
   4_xyz:   1.086  0.009  0.079 14.542  0.004  4.119   6.6619e-02
   4_adp:   1.086  0.009  0.079 14.542  0.004  4.119   6.6619e-02
   4_occ:   1.086  0.009  0.079 14.542  0.004  4.119   6.6619e-02
   5_bss:   1.086  0.009  0.079 14.542  0.004  4.119   6.6619e-02
   5_xyz:   1.003  0.007  0.076 14.291  0.004  4.113   5.8640e-02
   5_adp:   1.003  0.007  0.076 14.291  0.004  4.113   5.8640e-02
   5_occ:   1.003  0.007  0.076 14.291  0.004  4.113   5.8640e-02
   5_bss:   1.003  0.007  0.076 14.291  0.004  4.113   5.8640e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.291   2.4379e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.291   2.4379e-01
   1_xyz:  10.991  0.076  0.339 85.332  0.048  1.948   1.1830e-01
   1_adp:  10.991  0.076  0.339 85.332  0.048  1.948   1.1830e-01
   1_occ:  10.991  0.076  0.339 85.332  0.048  1.948   1.1830e-01
   2_bss:  10.991  0.076  0.339 85.332  0.048  1.948   1.1830e-01
   2_xyz:   7.215  0.044  0.222 80.551  0.048  2.344   9.3400e-02
   2_adp:   7.215  0.044  0.222 80.551  0.048  2.344   9.3400e-02
   2_occ:   7.215  0.044  0.222 80.551  0.048  2.344   9.3400e-02
   3_bss:   7.215  0.044  0.222 80.551  0.048  2.344   9.3400e-02
   3_xyz:   7.529  0.058  0.225 81.818  0.031  2.286   4.0560e-02
   3_adp:   7.529  0.058  0.225 81.818  0.031  2.286   4.0560e-02
   3_occ:   7.529  0.058  0.225 81.818  0.031  2.286   4.0560e-02
   4_bss:   7.529  0.058  0.225 81.818  0.031  2.286   4.0560e-02
   4_xyz:   7.871  0.044  0.267 82.511  0.033  2.275   6.0558e-02
   4_adp:   7.871  0.044  0.267 82.511  0.033  2.275   6.0558e-02
   4_occ:   7.871  0.044  0.267 82.511  0.033  2.275   6.0558e-02
   5_bss:   7.871  0.044  0.267 82.511  0.033  2.275   6.0558e-02
   5_xyz:   7.421  0.045  0.253 80.446  0.030  2.338   3.8357e-02
   5_adp:   7.421  0.045  0.253 80.446  0.030  2.338   3.8357e-02
   5_occ:   7.421  0.045  0.253 80.446  0.030  2.338   3.8357e-02
   5_bss:   7.421  0.045  0.253 80.446  0.030  2.338   3.8357e-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:  94.78   0.00  18.60  83.00   0.00  14.16  94.78   4.21  42.78
   1_occ:  94.78   0.00  18.60  83.00   0.00  14.16  94.78   4.21  42.78
   2_bss:  94.78   0.00  18.60  83.00   0.00  14.16  94.78   4.21  42.78
   2_xyz:  94.78   0.00  18.60  83.00   0.00  14.16  94.78   4.21  42.78
   2_adp:  93.33   0.00  19.06  82.87   0.00  14.68  93.33   6.80  42.87
   2_occ:  93.33   0.00  19.06  82.87   0.00  14.68  93.33   6.80  42.87
   3_bss:  93.33   0.00  19.06  82.87   0.00  14.68  93.33   6.80  42.87
   3_xyz:  93.33   0.00  19.06  82.87   0.00  14.68  93.33   6.80  42.87
   3_adp:  97.90   0.60  19.31  97.90   0.60  14.36  93.55   6.86  46.27
   3_occ:  97.90   0.60  19.31  97.90   0.60  14.36  93.55   6.86  46.27
   4_bss:  97.90   0.60  19.31  97.90   0.60  14.36  93.55   6.86  46.27
   4_xyz:  97.90   0.60  19.31  97.90   0.60  14.36  93.55   6.86  46.27
   4_adp:  95.00   2.13  18.45  95.00   2.13  13.94  88.07   3.61  42.96
   4_occ:  95.00   2.13  18.45  95.00   2.13  13.94  88.07   3.61  42.96
   5_bss:  95.00   2.13  18.45  95.00   2.13  13.94  88.07   3.61  42.96
   5_xyz:  95.00   2.13  18.45  95.00   2.13  13.94  88.07   3.61  42.96
   5_adp:  98.52   0.00  18.47  98.52   1.45  13.85  94.19   0.00  43.60
   5_occ:  98.52   0.00  18.47  98.52   1.45  13.85  94.19   0.00  43.60
   5_bss:  98.52   0.00  18.47  98.52   1.46  13.85  94.20   0.00  43.60
------------------------------------------------------------------------
 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:    2.074    0.011    0.546
   1_adp:    2.074    0.011    0.546
   1_occ:    2.074    0.011    0.546
   2_bss:    2.074    0.011    0.546
   2_xyz:    1.927    0.044    0.607
   2_adp:    1.927    0.044    0.607
   2_occ:    1.927    0.044    0.607
   3_bss:    1.927    0.044    0.607
   3_xyz:    1.851    0.055    0.678
   3_adp:    1.851    0.055    0.678
   3_occ:    1.851    0.055    0.678
   4_bss:    1.851    0.055    0.678
   4_xyz:    1.742    0.037    0.712
   4_adp:    1.742    0.037    0.712
   4_occ:    1.742    0.037    0.712
   5_bss:    1.742    0.037    0.712
   5_xyz:    1.644    0.076    0.722
   5_adp:    1.644    0.076    0.722
   5_occ:    1.644    0.076    0.722
   5_bss:    1.644    0.076    0.722
------------------------------------------------------------------------

CPU time actual refinement: 276.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/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_218/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_218/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 276.67 
  Macro-tasks:
    bulk solvent and scale       = 31.61  
    individual site refinement   = 115.24 
    weights calculation          = 24.59  
    collect and process          = 5.37   
    model show statistics        = 0.07   
    TOTAL for macro-tasks        = 176.88 
  Micro-tasks:
    mask                            = 1.47   
    f_calc                          = 88.96  
    alpha_beta                      = 6.69   
    target                          = 0.94   
    gradients_wrt_atomic_parameters = 96.55  
    fmodel                         = 5.14   
    r_factors                      = 0.18   
    phase_errors                   = 8.79   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 208.96 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.940 micro seconds
Total CPU time: 4.80 minutes
from_scatterers_fft:    639 calls, 88.74 s
gradients_fft:          584 calls, 85.03 s

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

# Date 2008-01-16 Time 04:17:40 PST -0800 (1200485860.95 s)
Start R-work = 0.4621, R-free = 0.4617 (no bulk solvent and anisotropic scale)
Final R-work = 0.1458, R-free = 0.1856 (no bulk solvent and anisotropic scale)

Start R-work = 0.4553, R-free = 0.4506
Final R-work = 0.1179, R-free = 0.1646