# Date 2008-01-16 Time 05:16:25 PST -0800 (1200489385.26 s)
#phil __OFF__

Command line arguments: "../662.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15274
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 662

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97116
Completeness in resolution range: 0.958132
Completeness with d_max=infinity: 0.955188

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9712

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: (70.25, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97116
Completeness in resolution range: 0.958132
Completeness with d_max=infinity: 0.955188

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2178 [2141/2169]  1929   212   9.9%
  bin  2:  4.2178 -  3.3604 [2056/2072]  1848   208  10.1%
  bin  3:  3.3604 -  2.9393 [2035/2054]  1831   204  10.0%
  bin  4:  2.9393 -  2.6722 [2023/2053]  1826   197   9.7%
  bin  5:  2.6722 -  2.4816 [2010/2029]  1808   202  10.0%
  bin  6:  2.4816 -  2.3359 [1980/2016]  1782   198  10.0%
  bin  7:  2.3359 -  2.2193 [1970/2003]  1770   200  10.2%
  bin  8:  2.2193 -  2.1230 [1991/2025]  1792   199  10.0%
  bin  9:  2.1230 -  2.0414 [1980/2008]  1783   197   9.9%
  bin 10:  2.0414 -  1.9712 [1403/2016]  1261   142  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2211
        3.04 -     3.66: 4728
        3.66 -     4.28: 9067
        4.28 -     4.90: 12453
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.970 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.996 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.149 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.153 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28475 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_662/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 70.25 46.93 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2758   r_free= 0.2781   ksol= 0.00   Bsol= 0.00   scale= 0.994    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.924344                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.2686 0.2669      6.3132      6.2695|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.2161 0.2046      6.2992      6.2875|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.2351 0.2329      6.1885      6.3084|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.2364 0.2627      6.0633      6.0785|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.2670 0.2358      5.9593      5.9098|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.2855 0.2970      5.9124      5.9254|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.2837 0.2574      5.8977      5.8333|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.2964 0.2903      5.8526      5.8695|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.2980 0.3065      5.8134      5.8042|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.3023 0.3661      5.7841      5.9489|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.3083 0.3233      5.7441      5.8393|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.3032 0.3213      5.6926      5.7405|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.3127 0.3120      5.5933      5.5661|
| 14:  2.0203 -  1.9712 0.59    769   85 0.3535 0.3679       5.642      5.5624|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7043  1386   154  0.80  24.94   0.88     0.81      39273.74|
|  2:  4.7043 -  3.7535  1353   147  0.86  19.90   0.99     0.93      37584.67|
|  3:  3.7535 -  3.2848  1307   150  0.84  22.44   1.01     0.99      33879.14|
|  4:  3.2848 -  2.9871  1309   145  0.83  23.90   1.03     0.99      28700.69|
|  5:  2.9871 -  2.7744  1306   143  0.79  27.70   1.01     0.97      23956.22|
|  6:  2.7744 -  2.6118  1286   145  0.78  28.86   1.02     0.97      21378.97|
|  7:  2.6118 -  2.4816  1295   139  0.79  28.11   1.02     0.98      19526.97|
|  8:  2.4816 -  2.3740  1273   149  0.76  30.46   1.03     0.98      19003.89|
|  9:  2.3740 -  2.2830  1278   142  0.76  30.83   1.07     0.96      17794.69|
| 10:  2.2830 -  2.2044  1270   134  0.73  33.22   1.07     0.96      18247.68|
| 11:  2.2044 -  2.1357  1267   146  0.73  33.33   1.09     0.97      16846.71|
| 12:  2.1357 -  2.0748  1264   135  0.74  32.68   1.09     1.01      16219.75|
| 13:  2.0748 -  2.0203  1267   145  0.70  35.61   1.08     0.97      14444.38|
| 14:  2.0203 -  1.9712   769    85  0.68  37.61   1.06     0.87      13728.81|
|alpha:            min =        0.81 max =            1.01 mean =         0.96|
|beta:             min =    13728.81 max =        39273.74 mean =     23370.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           89.98 mean =        28.91|
|phase err.(test): min =        0.00 max =           89.99 mean =        28.92|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.370308              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.382   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.538104              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.698   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2012 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1881 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2847 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4394 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5704 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6749 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.194 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2758   r_free= 0.2781   ksol= 0.00   Bsol= 0.00   scale= 0.994    |
|                                                                             |
| 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:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.924344                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.2575   ksol= 0.32   Bsol= 34.36   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.82,1.32,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.895582                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.732273              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.404   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.630   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2559      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2575      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1969 = 3.73 * 0.50 * 5.9128 + 1.00 * 0.1627                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5015 = 3.73 * 0.50 * 5.5950 + 1.00 * 0.0603                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1514      final r-factor (work) = 0.1384          |
| start r-factor (free) = 0.1754      final r-factor (free) = 0.1784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4820 = 0.26 * 1.00 * 5.5950 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4056 = 0.26 * 1.00 * 5.3001 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    71.75   16.85    None  None   None       |
|    all(noH): 2823   0      0.92    71.75   16.85    None  None   None       |
|    Sol.    : 438    0      7.33    65.90   37.78    None  None   None       |
|    Mac.    : 2385   0      0.92    71.75   13.01    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:     0.922 -   8.004:  478   |   5:    36.336 -  43.419:  112        |
|      1:     8.004 -  15.087: 1362   |   6:    43.419 -  50.501:  113        |
|      2:    15.087 -  22.170:  425   |   7:    50.501 -  57.584:   58        |
|      3:    22.170 -  29.253:  130   |   8:    57.584 -  64.667:   24        |
|      4:    29.253 -  36.336:  116   |   9:    64.667 -  71.750:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1384 r_free = 0.1784             target_work(ml) = 5.309         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1783             target_work(ml) = 5.308         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1783   ksol= 0.32   Bsol= 34.36   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.16,-2.82,1.32,-0.00,0.00,0.00); trace/3= -1.55                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.307833                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1739   ksol= 0.32   Bsol= 40.70   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.76,-1.14,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.290328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.497404              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.544  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.164075              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1739      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0285 = 1.50 * 0.50 * 5.3000 + 1.00 * 0.0603                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9628 = 1.50 * 0.50 * 5.2238 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8646 = 0.16 * 1.00 * 5.2238 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8521 = 0.16 * 1.00 * 5.1519 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.98    72.07   16.70    None  None   None       |
|    all(noH): 2823   0      1.98    72.07   16.70    None  None   None       |
|    Sol.    : 438    0      5.84    68.72   37.19    None  None   None       |
|    Mac.    : 2385   0      1.98    72.07   12.94    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:     1.984 -   8.993:  691   |   5:    37.028 -  44.037:  120        |
|      1:     8.993 -  16.002: 1243   |   6:    44.037 -  51.046:  103        |
|      2:    16.002 -  23.011:  360   |   7:    51.046 -  58.055:   46        |
|      3:    23.011 -  30.020:  125   |   8:    58.055 -  65.064:   19        |
|      4:    30.020 -  37.028:  109   |   9:    65.064 -  72.073:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1156 r_free = 0.1525             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1524             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1524   ksol= 0.32   Bsol= 40.70   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-2.76,-1.14,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144333                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1521   ksol= 0.32   Bsol= 40.70   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.49,-1.57,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142385                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.704788              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.079  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.781  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1499          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4420 = 1.70 * 0.50 * 5.1505 + 1.00 * 0.0517                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4195 = 1.70 * 0.50 * 5.1194 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1499      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5354 = 0.30 * 1.00 * 5.1194 + 1.00 * 0.0068                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5323 = 0.30 * 1.00 * 5.1074 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.67    72.86   16.66    None  None   None       |
|    all(noH): 2823   0      1.67    72.86   16.66    None  None   None       |
|    Sol.    : 438    0      6.14    69.14   37.41    None  None   None       |
|    Mac.    : 2385   0      1.67    72.86   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.669 -   8.788:  673   |   5:    37.263 -  44.382:  120        |
|      1:     8.788 -  15.907: 1261   |   6:    44.382 -  51.501:   99        |
|      2:    15.907 -  23.025:  363   |   7:    51.501 -  58.620:   48        |
|      3:    23.025 -  30.144:  122   |   8:    58.620 -  65.739:   21        |
|      4:    30.144 -  37.263:  110   |   9:    65.739 -  72.857:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1506             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1506             target_work(ml) = 5.110         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1506   ksol= 0.32   Bsol= 40.70   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-2.49,-1.57,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110479                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1505   ksol= 0.32   Bsol= 41.20   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.33,-1.60,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110136                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.449595              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.446  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732339              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.074  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7577 = 1.45 * 0.50 * 5.1074 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7563 = 1.45 * 0.50 * 5.1127 + 1.00 * 0.0506                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7515 = 0.73 * 1.00 * 5.1127 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7531 = 0.73 * 1.00 * 5.1131 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.87    81.30   16.88    None  None   None       |
|    all(noH): 2823   0      0.87    81.30   16.88    None  None   None       |
|    Sol.    : 438    0      5.96    71.73   38.82    None  None   None       |
|    Mac.    : 2385   0      0.87    81.30   12.85    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:     0.873 -   8.916:  760   |   5:    41.089 -  49.132:  126        |
|      1:     8.916 -  16.959: 1254   |   6:    49.132 -  57.175:   79        |
|      2:    16.959 -  25.002:  317   |   7:    57.175 -  65.218:   40        |
|      3:    25.002 -  33.046:  127   |   8:    65.218 -  73.261:   15        |
|      4:    33.046 -  41.089:  100   |   9:    73.261 -  81.305:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1527             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1528             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1528   ksol= 0.32   Bsol= 41.20   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.63,-2.33,-1.60,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.118566                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1530   ksol= 0.32   Bsol= 41.20   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.14,-1.48,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.120626                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.298617              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.780  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.922925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.320  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1084      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1530      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3715 = 1.30 * 0.50 * 5.1145 + 1.00 * 0.0506                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3732 = 1.30 * 0.50 * 5.1204 + 1.00 * 0.0485                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1084          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7343 = 0.92 * 1.00 * 5.1204 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7379 = 0.92 * 1.00 * 5.1239 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.31    82.14   16.75    None  None   None       |
|    all(noH): 2823   0      0.31    82.14   16.75    None  None   None       |
|    Sol.    : 438    0      5.80    71.99   38.80    None  None   None       |
|    Mac.    : 2385   0      0.31    82.14   12.70    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:     0.313 -   8.495:  697   |   5:    41.225 -  49.408:  124        |
|      1:     8.495 -  16.678: 1306   |   6:    49.408 -  57.590:   79        |
|      2:    16.678 -  24.860:  328   |   7:    57.590 -  65.773:   36        |
|      3:    24.860 -  33.043:  128   |   8:    65.773 -  73.955:   15        |
|      4:    33.043 -  41.225:  105   |   9:    73.955 -  82.138:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1084 r_free = 0.1551             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1083 r_free = 0.1551             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1551   ksol= 0.32   Bsol= 41.20   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.43,-2.14,-1.48,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127215                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.0992 0.1257      5.3834      5.5143|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.0841 0.1048      5.4198      5.5898|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.1020 0.1468      5.4414      5.8337|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.1166 0.1527      5.4358       5.576|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.1250 0.1745       5.295      5.5287|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.1180 0.1753      5.1902      5.4246|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.1186 0.1613      5.1284      5.3658|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.1114 0.1702      5.0358      5.2871|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.1132 0.1835      5.0097      5.3342|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.1081 0.1728      4.9417      5.1986|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.1111 0.1656      4.9301      5.2505|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.1065 0.1651      4.8576      5.1389|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.1122 0.1774      4.7945      5.0924|
| 14:  2.0203 -  1.9712 0.59    769   85 0.1056 0.1661      4.6679      4.9157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7043  1386   154  0.94   8.92   0.98     0.95       6902.11|
|  2:  4.7043 -  3.7535  1353   147  0.96   7.60   1.02     1.01       8493.84|
|  3:  3.7535 -  3.2848  1307   150  0.94  10.92   1.03     1.02       9769.83|
|  4:  3.2848 -  2.9871  1309   145  0.92  13.58   1.01     1.00      10221.08|
|  5:  2.9871 -  2.7744  1306   143  0.90  15.44   0.99     0.96       7880.03|
|  6:  2.7744 -  2.6118  1286   145  0.90  15.70   0.99     0.96       6925.08|
|  7:  2.6118 -  2.4816  1295   139  0.91  14.67   0.99     0.96       5778.90|
|  8:  2.4816 -  2.3740  1273   149  0.91  14.87   0.99     0.97       5090.38|
|  9:  2.3740 -  2.2830  1278   142  0.92  14.66   1.00     0.98       4799.12|
| 10:  2.2830 -  2.2044  1270   134  0.91  15.27   0.99     0.95       4254.81|
| 11:  2.2044 -  2.1357  1267   146  0.90  16.48   0.99     0.96       4369.27|
| 12:  2.1357 -  2.0748  1264   135  0.92  14.57   1.00     0.97       3830.52|
| 13:  2.0748 -  2.0203  1267   145  0.90  16.19   1.00     1.00       3427.13|
| 14:  2.0203 -  1.9712   769    85  0.91  14.82   0.98     0.94       2566.12|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2566.12 max =        10221.08 mean =      6159.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.74|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1550   ksol= 0.32   Bsol= 43.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.94,-1.33,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126758                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1083   r_free= 0.1550   ksol= 0.32   Bsol= 43.35   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.94,-1.33,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126758                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.0992 0.1259      5.3819      5.5138|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.0844 0.1049      5.4215      5.5912|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.1022 0.1468      5.4422      5.8341|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.1165 0.1526      5.4352      5.5754|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.1248 0.1743      5.2938      5.5274|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.1178 0.1751      5.1892      5.4236|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.1186 0.1610      5.1275      5.3648|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.1113 0.1698      5.0351      5.2857|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.1132 0.1837      5.0093      5.3349|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.1081 0.1726      4.9413      5.1969|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.1110 0.1654      4.9296      5.2501|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.1065 0.1650      4.8571      5.1381|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.1122 0.1773      4.7939      5.0915|
| 14:  2.0203 -  1.9712 0.59    769   85 0.1056 0.1662      4.6675      4.9159|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9324 -  4.7043  1386   154  0.94   8.90   0.98     0.95       6875.16|
|  2:  4.7043 -  3.7535  1353   147  0.96   7.59   1.02     1.01       8493.09|
|  3:  3.7535 -  3.2848  1307   150  0.94  10.94   1.03     1.03       9782.43|
|  4:  3.2848 -  2.9871  1309   145  0.92  13.56   1.02     1.00      10212.08|
|  5:  2.9871 -  2.7744  1306   143  0.90  15.43   1.00     0.97       7869.08|
|  6:  2.7744 -  2.6118  1286   145  0.90  15.68   0.99     0.97       6910.60|
|  7:  2.6118 -  2.4816  1295   139  0.91  14.65   1.00     0.96       5766.06|
|  8:  2.4816 -  2.3740  1273   149  0.91  14.86   1.00     0.97       5079.79|
|  9:  2.3740 -  2.2830  1278   142  0.92  14.66   1.01     0.98       4791.72|
| 10:  2.2830 -  2.2044  1270   134  0.91  15.26   1.00     0.96       4250.67|
| 11:  2.2044 -  2.1357  1267   146  0.90  16.46   1.00     0.97       4362.17|
| 12:  2.1357 -  2.0748  1264   135  0.92  14.56   1.01     0.98       3823.84|
| 13:  2.0748 -  2.0203  1267   145  0.90  16.18   1.01     1.01       3421.43|
| 14:  2.0203 -  1.9712   769    85  0.91  14.81   0.99     0.95       2563.98|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2563.98 max =        10212.08 mean =      6152.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.73|
|phase err.(test): min =        0.00 max =           89.11 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.30    82.13   16.74    None  None   None       |
|    all(noH): 2823   0      0.30    82.13   16.74    None  None   None       |
|    Sol.    : 438    0      5.79    71.98   38.79    None  None   None       |
|    Mac.    : 2385   0      0.30    82.13   12.69    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:     0.304 -   8.487:  697   |   5:    41.217 -  49.399:  124        |
|      1:     8.487 -  16.669: 1306   |   6:    49.399 -  57.581:   79        |
|      2:    16.669 -  24.852:  328   |   7:    57.581 -  65.764:   36        |
|      3:    24.852 -  33.034:  128   |   8:    65.764 -  73.946:   15        |
|      4:    33.034 -  41.217:  105   |   9:    73.946 -  82.129:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 293         
Filter by distance & map next to the model:
   mapped sites are within: 0.584 - 4.587
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 293
   mapped sites are within: 0.731 - 4.587

peak=    5.690 closest distance to " NH2 ARG A  56 " =    2.189
peak=    5.638 closest distance to " CG  PRO A  54 " =    1.255
peak=    5.474 closest distance to " CB  GLN A 223 " =    1.445
peak=    5.362 closest distance to " O   HOH Z 126 " =    1.875
peak=    5.340 closest distance to " CG  PRO A  90 " =    1.123
peak=    5.333 closest distance to " CB  ARG A 275 " =    0.906
peak=    5.329 closest distance to " CB  SER A  63 " =    1.202
peak=    4.884 closest distance to " NE2 GLN A  11 " =    1.086
peak=    4.836 closest distance to " O   HOH Z  78 " =    1.701
peak=    4.787 closest distance to " O   HOH Z 142 " =    1.705
peak=    4.778 closest distance to " CB  PRO A  54 " =    0.983
peak=    4.746 closest distance to " CB  GLN A 183 " =    1.262
peak=    4.629 closest distance to " O   HOH Z 298 " =    1.847
peak=    4.593 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.580 closest distance to " CG  PRO A 198 " =    1.228
peak=    4.517 closest distance to " C   PRO A 198 " =    1.523
peak=    4.488 closest distance to " O   HOH Z 427 " =    2.870
peak=    4.478 closest distance to " O   HOH Z  15 " =    2.230
peak=    4.474 closest distance to " CB  LEU A 228 " =    1.106
peak=    4.467 closest distance to " CB  ASN A 148 " =    1.385
peak=    4.467 closest distance to " CB  GLU A 128 " =    1.081
peak=    4.433 closest distance to " O   HOH Z 232 " =    2.369
peak=    4.425 closest distance to " OD1 ASN A  69 " =    2.565
peak=    4.410 closest distance to " O   HOH Z 236 " =    2.102
peak=    4.405 closest distance to " O   HOH Z 234 " =    3.683
peak=    4.359 closest distance to " O   HOH Z 193 " =    1.799
peak=    4.332 closest distance to " CB  TYR A 169 " =    0.731
peak=    4.268 closest distance to " ND2 ASN A 187 " =    1.430
peak=    4.267 closest distance to " O   HOH Z 316 " =    3.037
peak=    4.267 closest distance to " CB  TRP A 179 " =    1.279
peak=    4.255 closest distance to " O   HOH Z 203 " =    1.848
peak=    4.254 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.235 closest distance to " O   HOH Z 369 " =    2.084
peak=    4.221 closest distance to " O   HOH Z  40 " =    1.653
peak=    4.183 closest distance to " CG  PRO A 243 " =    1.094
peak=    4.162 closest distance to " O   HOH Z 272 " =    1.817
peak=    4.156 closest distance to " O   HOH Z  43 " =    1.936
peak=    4.131 closest distance to " OD2 ASP A 286 " =    2.845
peak=    4.131 closest distance to " O   HOH Z 303 " =    1.992
peak=    4.095 closest distance to " CB  SER A   3 " =    1.306
peak=    4.085 closest distance to " CB  VAL A 265 " =    1.210
peak=    4.083 closest distance to " O   HOH Z 344 " =    3.031
peak=    4.041 closest distance to " O   HOH Z 368 " =    1.937
peak=    3.999 closest distance to " CA  ALA A  21 " =    1.155
peak=    3.988 closest distance to " NZ  LYS A 117 " =    3.261
peak=    3.975 closest distance to " O   HOH Z 144 " =    2.290
peak=    3.973 closest distance to " O   HOH Z 402 " =    1.406
peak=    3.956 closest distance to " CG2 VAL A 257 " =    0.875
peak=    3.948 closest distance to " CG1 ILE A  33 " =    1.273
peak=    3.939 closest distance to " CB  ARG A 190 " =    1.714
peak=    3.936 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.929 closest distance to " O   HOH Z 403 " =    1.718
peak=    3.916 closest distance to " O   HOH Z  54 " =    1.710
peak=    3.896 closest distance to " CG  ARG A  66 " =    2.458
peak=    3.896 closest distance to " O   HOH Z  66 " =    2.077
peak=    3.892 closest distance to " CA  ASN A 215 " =    1.184
peak=    3.871 closest distance to " O   HOH Z  59 " =    1.985
peak=    3.863 closest distance to " O   HOH Z  44 " =    1.838
peak=    3.852 closest distance to " O   HOH Z 189 " =    2.024
peak=    3.844 closest distance to " CB  TRP A 266 " =    0.970
peak=    3.841 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.837 closest distance to " CB  ARG A  79 " =    1.401
peak=    3.830 closest distance to " O   HOH Z 158 " =    3.018
peak=    3.815 closest distance to " CD2 LEU A 297 " =    0.905
peak=    3.812 closest distance to " O   HOH Z 346 " =    1.669
peak=    3.797 closest distance to " O   MET A 105 " =    1.815
peak=    3.796 closest distance to " O   HOH Z  97 " =    1.950
peak=    3.765 closest distance to " O   HOH Z 132 " =    2.548
peak=    3.761 closest distance to " O   HOH Z 389 " =    1.875
peak=    3.742 closest distance to " CA  THR A 264 " =    0.867
peak=    3.733 closest distance to " CD  ARG A 159 " =    0.734
peak=    3.732 closest distance to " O   HOH Z  93 " =    2.497
peak=    3.731 closest distance to " O   SER A  87 " =    2.355
peak=    3.729 closest distance to " CZ  PHE A 218 " =    1.023
peak=    3.727 closest distance to " O   HOH Z 214 " =    2.061
peak=    3.724 closest distance to " NH1AARG A 145 " =    1.113
peak=    3.721 closest distance to " O   HOH Z 128 " =    2.034
peak=    3.717 closest distance to " O   HOH Z 368 " =    3.614
peak=    3.712 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.712 closest distance to " CA  THR A 221 " =    0.983
peak=    3.701 closest distance to " CD BLYS A 290 " =    1.209
peak=    3.698 closest distance to " N   ARG A 156 " =    1.312
peak=    3.689 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.683 closest distance to " O   HOH Z 392 " =    3.077
peak=    3.680 closest distance to " O   HOH Z 209 " =    2.241
peak=    3.677 closest distance to " CD  ARG A 269 " =    0.982
peak=    3.676 closest distance to " CB  GLU A 277 " =    3.544
peak=    3.675 closest distance to " O   HOH Z 207 " =    1.789
peak=    3.667 closest distance to " O   HOH Z 426 " =    1.542
peak=    3.665 closest distance to " O   HOH Z 126 " =    2.134
peak=    3.664 closest distance to " CB  SER A 216 " =    0.802
peak=    3.661 closest distance to " O   HOH Z  10 " =    1.866
peak=    3.660 closest distance to " CG1BVAL A  72 " =    1.525
peak=    3.645 closest distance to " CG  LEU A 167 " =    1.141
peak=    3.641 closest distance to " O   HOH Z 108 " =    2.227
peak=    3.633 closest distance to " O   HOH Z   9 " =    2.090
peak=    3.633 closest distance to " CB  GLN A  89 " =    1.293
peak=    3.631 closest distance to " O   HOH Z 273 " =    2.686
peak=    3.622 closest distance to " NH2BARG A 145 " =    2.032
peak=    3.611 closest distance to " O   HOH Z 245 " =    1.312
peak=    3.609 closest distance to " O   HOH Z  88 " =    3.211
peak=    3.607 closest distance to " OE1 GLU A   2 " =    2.155
peak=    3.597 closest distance to " O   HOH Z 407 " =    2.616
peak=    3.592 closest distance to " CD1 ILE A 106 " =    0.872
peak=    3.591 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.591 closest distance to " CG2 ILE A 120 " =    1.252
peak=    3.582 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.574 closest distance to " O   HOH Z  19 " =    2.449
peak=    3.571 closest distance to " CA  ASP A 140 " =    1.133
peak=    3.564 closest distance to " OG BSER A 164 " =    2.305
peak=    3.560 closest distance to " CB  VAL A 202 " =    1.596
peak=    3.549 closest distance to " CG2 THR A 221 " =    1.161
peak=    3.548 closest distance to " O   HOH Z  21 " =    1.727
peak=    3.546 closest distance to " O   HOH Z 135 " =    1.618
peak=    3.541 closest distance to " CA  ALA A 291 " =    0.878
peak=    3.536 closest distance to " CD  LYS A 119 " =    1.194
peak=    3.533 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.532 closest distance to " NH2 ARG A 156 " =    1.151
peak=    3.531 closest distance to " NH1BARG A 145 " =    1.133
peak=    3.531 closest distance to " O   HOH Z 128 " =    2.196
peak=    3.525 closest distance to " CB  PRO A 198 " =    1.022
peak=    3.524 closest distance to " O   HOH Z 425 " =    2.016
peak=    3.515 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.514 closest distance to " O   HOH Z 371 " =    3.247
peak=    3.513 closest distance to " O   HOH Z  61 " =    1.557
peak=    3.509 closest distance to " CB  SER A  62 " =    1.248
peak=    3.509 closest distance to " CB  LEU A 143 " =    1.100
peak=    3.505 closest distance to " O   HOH Z 227 " =    1.599
peak=    3.501 closest distance to " CE1 TYR A 186 " =    1.315
peak=    3.494 closest distance to " CB  ARG A 139 " =    0.876
peak=    3.494 closest distance to " O   HOH Z 133 " =    1.496
peak=    3.479 closest distance to " CA  GLY A  80 " =    0.920
peak=    3.473 closest distance to " O   HOH Z 327 " =    1.619
peak=    3.473 closest distance to " O   HOH Z 345 " =    3.301
peak=    3.472 closest distance to " O   HOH Z 173 " =    1.830
peak=    3.472 closest distance to " O   HOH Z 147 " =    1.714
peak=    3.468 closest distance to " CB  ALA A 248 " =    1.362
peak=    3.461 closest distance to " CB  MET A  47 " =    1.003
peak=    3.461 closest distance to " CB  ASN A  39 " =    0.933
peak=    3.457 closest distance to " CB  SER A  26 " =    1.573
peak=    3.456 closest distance to " O   HOH Z 291 " =    1.488
peak=    3.452 closest distance to " CA  ASN A 176 " =    1.183
peak=    3.451 closest distance to " O   HOH Z 172 " =    3.609
peak=    3.451 closest distance to " O   HOH Z 183 " =    1.426
peak=    3.444 closest distance to " O   HOH Z 423 " =    1.860
peak=    3.442 closest distance to " CB  ALA A 291 " =    1.328
peak=    3.439 closest distance to " O   HOH Z 411 " =    3.808
peak=    3.434 closest distance to " CB  TRP A 179 " =    1.409
peak=    3.432 closest distance to " O   HOH Z 295 " =    1.486
peak=    3.428 closest distance to " O   HOH Z 329 " =    3.682
peak=    3.428 closest distance to " NZ  LYS A  76 " =    1.251
peak=    3.423 closest distance to " O   HOH Z   1 " =    1.842
peak=    3.421 closest distance to " CZ2 TRP A 179 " =    1.667
peak=    3.418 closest distance to " CA  ALA A  43 " =    1.222
peak=    3.415 closest distance to " O   HOH Z 250 " =    1.858
peak=    3.414 closest distance to " O   HOH Z 353 " =    2.734
peak=    3.412 closest distance to " O   HOH Z 337 " =    3.672
peak=    3.411 closest distance to " O   TRP A 274 " =    1.864
peak=    3.406 closest distance to " O   HOH Z   3 " =    1.638
peak=    3.404 closest distance to " CA  MET A  40 " =    1.083
peak=    3.401 closest distance to " CG2BVAL A  41 " =    0.822
peak=    3.397 closest distance to " CD  ARG A  66 " =    2.492
peak=    3.392 closest distance to " CB  ASP A 140 " =    0.878
peak=    3.391 closest distance to " CA  ALA A  51 " =    0.934
peak=    3.389 closest distance to " CB  SER A 212 " =    1.060
peak=    3.381 closest distance to " CA  ARG A 195 " =    1.246
peak=    3.377 closest distance to " O   HOH Z 175 " =    2.109
peak=    3.375 closest distance to " O   HOH Z 279 " =    2.134
peak=    3.374 closest distance to " O   HOH Z 425 " =    1.240
peak=    3.372 closest distance to " O   HOH Z 299 " =    4.366
peak=    3.370 closest distance to " O   HOH Z 419 " =    1.924
peak=    3.370 closest distance to " O   HOH Z 366 " =    3.141
peak=    3.369 closest distance to " O   HOH Z 211 " =    2.747
peak=    3.368 closest distance to " CA  PHE A 283 " =    1.298
peak=    3.363 closest distance to " N   ASN A  39 " =    1.249
peak=    3.363 closest distance to " CD2 HIS A  81 " =    1.146
peak=    3.360 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.356 closest distance to " O   HOH Z 134 " =    1.244
peak=    3.355 closest distance to " O   HOH Z 193 " =    2.068
peak=    3.354 closest distance to " OD1 ASN A 217 " =    1.724
peak=    3.345 closest distance to " O   HOH Z 406 " =    1.628
peak=    3.344 closest distance to " O   HOH Z 227 " =    2.194
peak=    3.341 closest distance to " CB  ALA A  34 " =    1.034
peak=    3.339 closest distance to " C   TYR A 214 " =    1.528
peak=    3.335 closest distance to " O   HOH Z  64 " =    2.288
peak=    3.329 closest distance to " CA  ALA A 158 " =    1.145
peak=    3.328 closest distance to " OD1BASN A 224 " =    2.307
peak=    3.328 closest distance to " O   HOH Z 125 " =    2.352
peak=    3.327 closest distance to " CA  ILE A 234 " =    0.918
peak=    3.324 closest distance to " CG1 ILE A 151 " =    0.959
peak=    3.318 closest distance to " CG  MET A 113 " =    1.168
peak=    3.317 closest distance to " CB  PHE A  16 " =    0.967
peak=    3.314 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.303 closest distance to " O   HOH Z 409 " =    2.994
peak=    3.298 closest distance to " CD  LYS A 166 " =    1.261
peak=    3.297 closest distance to " CB  ARG A  79 " =    0.860
peak=    3.288 closest distance to " CB  SER A 141 " =    1.076
peak=    3.286 closest distance to " N   GLN A 278 " =    1.045
peak=    3.282 closest distance to " CA  ASP A 162 " =    1.120
peak=    3.281 closest distance to " CB  GLN A 278 " =    0.858
peak=    3.278 closest distance to " CD2 LEU A 255 " =    1.340
peak=    3.276 closest distance to " CG2 ILE A  20 " =    1.423
peak=    3.276 closest distance to " O   HOH Z 148 " =    3.211
peak=    3.273 closest distance to " O   HOH Z 193 " =    1.648
peak=    3.268 closest distance to " O   ALA A   1 " =    1.661
peak=    3.267 closest distance to " O   HOH Z 261 " =    1.457
peak=    3.265 closest distance to " O   HOH Z  49 " =    2.121
peak=    3.265 closest distance to " CA  ALA A  84 " =    1.314
peak=    3.265 closest distance to " CG AARG A 275 " =    1.058
peak=    3.260 closest distance to " ND2 ASN A 209 " =    1.629
peak=    3.253 closest distance to " CA  ALA A 233 " =    1.440
peak=    3.251 closest distance to " CB  LEU A 255 " =    0.760
peak=    3.250 closest distance to " CG  GLU A 277 " =    2.123
peak=    3.245 closest distance to " O   THR A 220 " =    1.308
peak=    3.245 closest distance to " O   HOH Z  44 " =    3.382
peak=    3.244 closest distance to " CB  VAL A 268 " =    0.826
peak=    3.243 closest distance to " N   ASN A 127 " =    1.249
peak=    3.241 closest distance to " CB  THR A 157 " =    1.076
peak=    3.240 closest distance to " CD  ARG A  36 " =    1.038
peak=    3.239 closest distance to " O   HOH Z 437 " =    1.502
peak=    3.239 closest distance to " O   HOH Z 234 " =    1.763
peak=    3.239 closest distance to " ND1 HIS A  86 " =    1.759
peak=    3.237 closest distance to " OD1 ASP A 238 " =    1.002
peak=    3.236 closest distance to " CB  VAL A 126 " =    1.116
peak=    3.230 closest distance to " CB  THR A  31 " =    1.745
peak=    3.229 closest distance to " CG  LYS A  76 " =    1.046
peak=    3.228 closest distance to " O   HOH Z 421 " =    1.669
peak=    3.225 closest distance to " O   HOH Z 305 " =    3.614
peak=    3.224 closest distance to " O   HOH Z 133 " =    2.478
peak=    3.224 closest distance to " ND1 HIS A  81 " =    1.598
peak=    3.220 closest distance to " O   HOH Z 374 " =    2.543
peak=    3.218 closest distance to " CG  MET A 185 " =    1.175
peak=    3.217 closest distance to " O   HOH Z 180 " =    2.153
peak=    3.216 closest distance to " CG  PRO A 213 " =    1.042
peak=    3.214 closest distance to " O   HOH Z 336 " =    1.775
peak=    3.207 closest distance to " O   HOH Z 403 " =    1.298
peak=    3.206 closest distance to " CA  ARG A 102 " =    1.128
peak=    3.206 closest distance to " CD1 LEU A  96 " =    0.762
peak=    3.206 closest distance to " NE2 GLN A  73 " =    3.787
peak=    3.204 closest distance to " CA  SER A  87 " =    1.060
peak=    3.203 closest distance to " O   HOH Z 281 " =    4.587
peak=    3.203 closest distance to " N   TYR A 116 " =    1.667
peak=    3.203 closest distance to " CB  TYR A 116 " =    0.792
peak=    3.193 closest distance to " CA  MET A 105 " =    1.005
peak=    3.192 closest distance to " N   VAL A 126 " =    1.247
peak=    3.188 closest distance to " CG1 ILE A 120 " =    1.103
peak=    3.187 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.187 closest distance to " O   HOH Z 391 " =    2.957
peak=    3.186 closest distance to " CB  ALA A  71 " =    1.351
peak=    3.178 closest distance to " NZ  LYS A 119 " =    1.174
peak=    3.176 closest distance to " CA  LYS A 290 " =    1.269
peak=    3.173 closest distance to " CA  SER A 146 " =    1.761
peak=    3.171 closest distance to " CA  ASN A 217 " =    1.273
peak=    3.169 closest distance to " O   HOH Z 417 " =    3.125
peak=    3.164 closest distance to " N   TYR A  15 " =    0.765
peak=    3.162 closest distance to " CB  ALA A 114 " =    1.151
peak=    3.162 closest distance to " N   ASN A 252 " =    1.377
peak=    3.162 closest distance to " OG1 THR A 294 " =    2.419
peak=    3.158 closest distance to " O   HOH Z 219 " =    1.940
peak=    3.155 closest distance to " O   HOH Z 286 " =    2.253
peak=    3.148 closest distance to " O   ALA A   1 " =    1.465
peak=    3.135 closest distance to " OD1 ASP A 231 " =    1.893
peak=    3.133 closest distance to " O   HOH Z 248 " =    1.749
peak=    3.131 closest distance to " OD2 ASP A 200 " =    1.266
peak=    3.128 closest distance to " O   HOH Z 359 " =    1.384
peak=    3.128 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.127 closest distance to " O   HOH Z 433 " =    1.768
peak=    3.123 closest distance to " CB  GLU A 152 " =    1.423
peak=    3.121 closest distance to " OG  SER A 206 " =    1.288
peak=    3.120 closest distance to " N   ALA A 154 " =    0.997
peak=    3.118 closest distance to " O   SER A 164 " =    1.234
peak=    3.116 closest distance to " CA  ASP A 191 " =    0.835
peak=    3.114 closest distance to " N   SER A 135 " =    1.261
peak=    3.112 closest distance to " CA  ALA A 154 " =    0.944
peak=    3.111 closest distance to " CG BARG A 102 " =    1.836
peak=    3.108 closest distance to " CB  GLN A 205 " =    1.112
peak=    3.104 closest distance to " O   HOH Z  30 " =    2.160
peak=    3.100 closest distance to " O   HOH Z  66 " =    1.897
peak=    3.092 closest distance to " O   HOH Z 124 " =    1.289
peak=    3.090 closest distance to " O   ALA A 158 " =    1.270
peak=    3.087 closest distance to " O   HOH Z 261 " =    2.102
peak=    3.085 closest distance to " O   HOH Z 411 " =    1.783
peak=    3.085 closest distance to " CG2 VAL A 202 " =    1.165
peak=    3.076 closest distance to " CD1AILE A 234 " =    1.020
peak=    3.075 closest distance to " O   HOH Z 327 " =    2.310
peak=    3.065 closest distance to " O   HOH Z 383 " =    1.763
peak=    3.059 closest distance to " O   HOH Z 423 " =    3.072
peak=    3.035 closest distance to " CG  GLN A  89 " =    1.540
peak=    3.028 closest distance to " O   HOH Z 334 " =    1.593
peak=    3.017 closest distance to " O   HOH Z 392 " =    1.967

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.824 - 5.581
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.824 - 5.581

peak=   -4.827 closest distance to " O   HOH Z 266 " =    4.536
peak=   -4.366 closest distance to " O   HOH Z 372 " =    2.266
peak=   -4.317 closest distance to " O   VAL A  67 " =    2.655
peak=   -4.294 closest distance to " CD  ARG A 156 " =    2.002
peak=   -4.278 closest distance to " O   HOH Z 198 " =    2.090
peak=   -4.277 closest distance to " CB  PRO A 243 " =    2.601
peak=   -4.252 closest distance to " CG  GLN A 223 " =    1.859
peak=   -4.223 closest distance to " O   ILE A 109 " =    2.598
peak=   -4.217 closest distance to " O   HOH Z 377 " =    1.987
peak=   -4.217 closest distance to " O   HOH Z 290 " =    1.039
peak=   -4.200 closest distance to " C   HIS A 108 " =    1.084
peak=   -4.149 closest distance to " SG  CYS A 254 " =    3.277
peak=   -4.119 closest distance to " O   HOH Z 231 " =    2.177
peak=   -4.064 closest distance to " N   ALA A  43 " =    2.548
peak=   -4.061 closest distance to " OG BSER A 134 " =    1.156
peak=   -4.023 closest distance to " O   HOH Z  43 " =    1.657
peak=   -4.019 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.014 closest distance to " CG1 VAL A 112 " =    2.806
peak=   -3.983 closest distance to " ND2 ASN A  45 " =    0.965
peak=   -3.975 closest distance to " O   HOH Z 126 " =    1.886
peak=   -3.915 closest distance to " OXT GLY A 302 " =    2.767
peak=   -3.913 closest distance to " CZ3 TRP A 179 " =    1.221
peak=   -3.883 closest distance to " O   HOH Z 353 " =    2.156
peak=   -3.877 closest distance to " CE2 TYR A  30 " =    2.792
peak=   -3.866 closest distance to " CD2 LEU A 300 " =    2.871
peak=   -3.855 closest distance to " O   HOH Z 114 " =    3.117
peak=   -3.855 closest distance to " CD1 LEU A 228 " =    2.193
peak=   -3.845 closest distance to " CG  PHE A 283 " =    2.724
peak=   -3.811 closest distance to " O   HOH Z  10 " =    1.489
peak=   -3.810 closest distance to " OG  SER A  97 " =    2.121
peak=   -3.806 closest distance to " CD  ARG A 139 " =    1.465
peak=   -3.801 closest distance to " NH2AARG A 275 " =    5.247
peak=   -3.796 closest distance to " C   ALA A 158 " =    1.271
peak=   -3.788 closest distance to " ND2 ASN A  45 " =    1.421
peak=   -3.751 closest distance to " O   HOH Z  13 " =    1.475
peak=   -3.747 closest distance to " O   SER A 210 " =    1.950
peak=   -3.741 closest distance to " O   PRO A 163 " =    1.990
peak=   -3.737 closest distance to " O   HOH Z 389 " =    1.789
peak=   -3.726 closest distance to " O   HOH Z 351 " =    1.513
peak=   -3.721 closest distance to " N   GLN A  58 " =    1.649
peak=   -3.721 closest distance to " CB  ALA A 291 " =    2.226
peak=   -3.719 closest distance to " O   HOH Z 185 " =    2.261
peak=   -3.713 closest distance to " O   HOH Z 196 " =    2.097
peak=   -3.709 closest distance to " O   HOH Z  47 " =    1.556
peak=   -3.705 closest distance to " CG  ASP A 231 " =    0.824
peak=   -3.693 closest distance to " CA  VAL A  67 " =    2.873
peak=   -3.677 closest distance to " CB  TYR A  15 " =    2.212
peak=   -3.660 closest distance to " O   HOH Z 102 " =    1.636
peak=   -3.660 closest distance to " CG2 ILE A 263 " =    2.285
peak=   -3.659 closest distance to " O   SER A 135 " =    1.485
peak=   -3.653 closest distance to " CD  GLN A  58 " =    1.104
peak=   -3.647 closest distance to " N   ASP A 286 " =    2.446
peak=   -3.643 closest distance to " OD1 ASN A 187 " =    1.647
peak=   -3.641 closest distance to " CE  MET A 105 " =    2.182
peak=   -3.641 closest distance to " CB  ASN A  39 " =    2.236
peak=   -3.640 closest distance to " O   HOH Z 435 " =    2.790
peak=   -3.638 closest distance to " CB  CYS A 201 " =    2.625
peak=   -3.630 closest distance to " CZ  TYR A 169 " =    1.709
peak=   -3.628 closest distance to " N   ALA A 248 " =    1.594
peak=   -3.623 closest distance to " O   HOH Z  11 " =    2.067
peak=   -3.612 closest distance to " CB  PHE A 192 " =    1.997
peak=   -3.599 closest distance to " O   HOH Z 407 " =    3.043
peak=   -3.587 closest distance to " CA  GLY A  98 " =    1.985
peak=   -3.582 closest distance to " CD1 PHE A  59 " =    1.806
peak=   -3.576 closest distance to " CD1 LEU A 101 " =    2.423
peak=   -3.564 closest distance to " CZ  PHE A  59 " =    1.590
peak=   -3.559 closest distance to " O   HOH Z  52 " =    1.327
peak=   -3.543 closest distance to " OE1 GLN A  88 " =    1.137
peak=   -3.539 closest distance to " O   HOH Z 198 " =    1.443
peak=   -3.529 closest distance to " NH1 ARG A 195 " =    2.606
peak=   -3.510 closest distance to " CB  ALA A 291 " =    2.382
peak=   -3.497 closest distance to " O   HOH Z 311 " =    3.504
peak=   -3.491 closest distance to " O   GLY A 196 " =    1.015
peak=   -3.491 closest distance to " O   HOH Z 211 " =    1.691
peak=   -3.490 closest distance to " C   LEU A 143 " =    1.143
peak=   -3.486 closest distance to " CA  GLY A 203 " =    2.240
peak=   -3.481 closest distance to " CA  ASP A 298 " =    1.028
peak=   -3.480 closest distance to " OD1 ASP A 191 " =    1.674
peak=   -3.465 closest distance to " CG  ARG A 269 " =    2.370
peak=   -3.445 closest distance to " OG  SER A  62 " =    1.619
peak=   -3.440 closest distance to " SG ACYS A 201 " =    2.063
peak=   -3.432 closest distance to " O   HOH Z 244 " =    2.120
peak=   -3.430 closest distance to " OD2 ASP A  50 " =    1.565
peak=   -3.429 closest distance to " O   TRP A  92 " =    1.642
peak=   -3.423 closest distance to " O   HOH Z 313 " =    1.994
peak=   -3.417 closest distance to " O   MET A  40 " =    2.636
peak=   -3.394 closest distance to " CB  ALA A 248 " =    1.964
peak=   -3.388 closest distance to " CD  LYS A 289 " =    2.429
peak=   -3.385 closest distance to " OD1 ASP A 171 " =    1.598
peak=   -3.382 closest distance to " OD2 ASP A 171 " =    2.298
peak=   -3.380 closest distance to " N   THR A 235 " =    1.375
peak=   -3.378 closest distance to " O   VAL A 174 " =    1.934
peak=   -3.373 closest distance to " OD1 ASP A 191 " =    1.511
peak=   -3.371 closest distance to " CA  GLY A 133 " =    1.931
peak=   -3.369 closest distance to " N   ALA A 226 " =    2.040
peak=   -3.368 closest distance to " CD1 ILE A 239 " =    2.184
peak=   -3.367 closest distance to " CB  ALA A 131 " =    2.121
peak=   -3.366 closest distance to " O   HOH Z 166 " =    1.495
peak=   -3.361 closest distance to " O   HOH Z 298 " =    1.244
peak=   -3.359 closest distance to " CG  GLU A   2 " =    1.970
peak=   -3.357 closest distance to " OG BSER A 134 " =    1.756
peak=   -3.357 closest distance to " C   MET A 188 " =    1.506
peak=   -3.356 closest distance to " O   TRP A  70 " =    1.491
peak=   -3.356 closest distance to " O   ALA A  34 " =    2.449
peak=   -3.355 closest distance to " O   HOH Z 395 " =    5.187
peak=   -3.354 closest distance to " O   HOH Z 292 " =    4.481
peak=   -3.351 closest distance to " NH2 ARG A  79 " =    1.969
peak=   -3.349 closest distance to " O   HOH Z  63 " =    1.485
peak=   -3.345 closest distance to " CG  GLU A 277 " =    1.193
peak=   -3.345 closest distance to " CD1 LEU A  25 " =    2.458
peak=   -3.343 closest distance to " OD2 ASP A 191 " =    1.514
peak=   -3.339 closest distance to " O   ALA A 161 " =    1.594
peak=   -3.336 closest distance to " O   PHE A 218 " =    1.515
peak=   -3.334 closest distance to " O   HOH Z 322 " =    1.574
peak=   -3.333 closest distance to " O   HOH Z 193 " =    1.847
peak=   -3.331 closest distance to " CD2 LEU A 300 " =    2.867
peak=   -3.329 closest distance to " O   HOH Z  11 " =    1.770
peak=   -3.329 closest distance to " CE2 PHE A 218 " =    2.550
peak=   -3.326 closest distance to " CD1 ILE A 199 " =    2.471
peak=   -3.324 closest distance to " ND2 ASN A 187 " =    1.507
peak=   -3.318 closest distance to " CG1 VAL A 250 " =    2.613
peak=   -3.318 closest distance to " CE3 TRP A 150 " =    2.014
peak=   -3.316 closest distance to " CG  MET A 105 " =    0.928
peak=   -3.304 closest distance to " CB  ASP A 132 " =    2.279
peak=   -3.295 closest distance to " O   HOH Z 222 " =    1.233
peak=   -3.292 closest distance to " O   HOH Z  93 " =    1.831
peak=   -3.292 closest distance to " O   HOH Z 417 " =    2.436
peak=   -3.288 closest distance to " O   HOH Z 388 " =    1.981
peak=   -3.286 closest distance to " CB  PHE A 208 " =    2.221
peak=   -3.286 closest distance to " O   ALA A  51 " =    1.370
peak=   -3.285 closest distance to " O   SER A  95 " =    1.510
peak=   -3.284 closest distance to " O   HOH Z  38 " =    1.597
peak=   -3.284 closest distance to " O   HOH Z 385 " =    2.053
peak=   -3.272 closest distance to " O   HOH Z  44 " =    2.162
peak=   -3.271 closest distance to " CB  ASP A 286 " =    2.267
peak=   -3.269 closest distance to " O   HOH Z 166 " =    1.900
peak=   -3.268 closest distance to " O   HOH Z 385 " =    1.964
peak=   -3.262 closest distance to " CD  GLU A 236 " =    1.070
peak=   -3.259 closest distance to " O   HOH Z 414 " =    1.659
peak=   -3.255 closest distance to " CD2 PHE A  61 " =    2.552
peak=   -3.253 closest distance to " O   ALA A 180 " =    1.278
peak=   -3.241 closest distance to " CZ3 TRP A 274 " =    2.359
peak=   -3.231 closest distance to " O   HOH Z  37 " =    1.869
peak=   -3.228 closest distance to " O   HOH Z  24 " =    1.553
peak=   -3.226 closest distance to " O   HOH Z  19 " =    2.369
peak=   -3.220 closest distance to " O   ASN A 249 " =    1.507
peak=   -3.215 closest distance to " O   HOH Z 252 " =    3.776
peak=   -3.214 closest distance to " CB  PRO A 163 " =    2.497
peak=   -3.203 closest distance to " O   HOH Z 148 " =    3.633
peak=   -3.198 closest distance to " O   HOH Z 283 " =    2.281
peak=   -3.194 closest distance to " CA  TYR A  68 " =    2.879
peak=   -3.192 closest distance to " O   HOH Z  76 " =    1.861
peak=   -3.190 closest distance to " NE2 GLN A  58 " =    1.177
peak=   -3.184 closest distance to " O   HOH Z 427 " =    1.405
peak=   -3.181 closest distance to " NH2 ARG A  79 " =    1.545
peak=   -3.181 closest distance to " N   SER A 206 " =    1.982
peak=   -3.181 closest distance to " O   HOH Z 234 " =    4.014
peak=   -3.180 closest distance to " CD2 LEU A 237 " =    2.632
peak=   -3.175 closest distance to " CB  ASP A 132 " =    2.328
peak=   -3.170 closest distance to " CG  GLU A 152 " =    0.965
peak=   -3.170 closest distance to " OXT GLY A 302 " =    3.377
peak=   -3.167 closest distance to " O   GLY A  80 " =    2.490
peak=   -3.167 closest distance to " OD1 ASP A 200 " =    1.332
peak=   -3.164 closest distance to " O   HOH Z 191 " =    5.581
peak=   -3.162 closest distance to " O   HOH Z 250 " =    1.454
peak=   -3.161 closest distance to " CE2 PHE A 192 " =    2.101
peak=   -3.160 closest distance to " CA  GLY A 241 " =    3.114
peak=   -3.157 closest distance to " OD2 ASP A 171 " =    1.753
peak=   -3.156 closest distance to " O   HOH Z 361 " =    3.388
peak=   -3.154 closest distance to " ND2 ASN A 249 " =    2.283
peak=   -3.148 closest distance to " CB  GLN A  11 " =    1.648
peak=   -3.148 closest distance to " NE2 GLN A  88 " =    1.878
peak=   -3.148 closest distance to " CZ  ARG A 259 " =    0.854
peak=   -3.146 closest distance to " O   HOH Z 263 " =    2.938
peak=   -3.146 closest distance to " OG ASER A 134 " =    1.089
peak=   -3.146 closest distance to " CG  TRP A 266 " =    1.825
peak=   -3.144 closest distance to " OG  SER A 206 " =    1.732
peak=   -3.127 closest distance to " O   ALA A   1 " =    1.866
peak=   -3.117 closest distance to " O   ALA A  10 " =    1.709
peak=   -3.116 closest distance to " O   HOH Z   9 " =    2.166
peak=   -3.116 closest distance to " CZ  PHE A 130 " =    0.937
peak=   -3.115 closest distance to " CB  ALA A  51 " =    1.871
peak=   -3.112 closest distance to " O   PRO A 198 " =    1.288
peak=   -3.110 closest distance to " O   HOH Z  51 " =    1.370
peak=   -3.105 closest distance to " O   GLY A  80 " =    2.321
peak=   -3.105 closest distance to " CB  ASN A  69 " =    1.131
peak=   -3.097 closest distance to " CD2 TYR A 293 " =    1.998
peak=   -3.097 closest distance to " O   HOH Z 324 " =    2.052
peak=   -3.088 closest distance to " CE  MET A  93 " =    1.245
peak=   -3.087 closest distance to " O   HOH Z 298 " =    2.503
peak=   -3.084 closest distance to " O   LEU A 167 " =    1.462
peak=   -3.074 closest distance to " O   HOH Z 184 " =    1.789
peak=   -3.073 closest distance to " CD1 TYR A 247 " =    2.617
peak=   -3.067 closest distance to " O   HOH Z 128 " =    2.463
peak=   -3.064 closest distance to " O   HOH Z 351 " =    1.675
peak=   -3.063 closest distance to " O   HOH Z 111 " =    2.543
peak=   -3.053 closest distance to " O   HOH Z  60 " =    2.457
peak=   -3.041 closest distance to " OD2 ASP A  50 " =    2.289
peak=   -3.040 closest distance to " ND2 ASN A  60 " =    1.505
peak=   -3.040 closest distance to " O   PRO A 243 " =    2.533
peak=   -3.040 closest distance to " N   ALA A 248 " =    2.625
peak=   -3.028 closest distance to " CG  ASN A 301 " =    1.992
peak=   -3.011 closest distance to " O   GLY A 211 " =    1.504

================= 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    :  0.2758 0.2781   5.924344e+00   5.939675e+00
   1_bss:  0.2559 0.2575   5.895582e+00   5.890248e+00
   1_xyz:  0.1514 0.1754   5.363846e+00   5.482870e+00
   1_adp:  0.1384 0.1784   5.309490e+00   5.506900e+00
   1_occ:  0.1380 0.1783   5.307833e+00   5.505707e+00
   2_bss:  0.1361 0.1739   5.290328e+00   5.484471e+00
   2_xyz:  0.1180 0.1542   5.162559e+00   5.372234e+00
   2_adp:  0.1156 0.1525   5.145034e+00   5.356857e+00
   2_occ:  0.1154 0.1524   5.144333e+00   5.356314e+00
   3_bss:  0.1152 0.1521   5.142385e+00   5.354733e+00
   3_xyz:  0.1098 0.1499   5.112231e+00   5.341977e+00
   3_adp:  0.1089 0.1506   5.110409e+00   5.346130e+00
   3_occ:  0.1088 0.1506   5.110479e+00   5.346423e+00
   4_bss:  0.1088 0.1505   5.110136e+00   5.346124e+00
   4_xyz:  0.1092 0.1516   5.117770e+00   5.356046e+00
   4_adp:  0.1083 0.1527   5.118439e+00   5.363041e+00
   4_occ:  0.1083 0.1528   5.118566e+00   5.363425e+00
   5_bss:  0.1084 0.1530   5.120626e+00   5.364300e+00
   5_xyz:  0.1085 0.1543   5.125671e+00   5.373392e+00
   5_adp:  0.1084 0.1551   5.127235e+00   5.378151e+00
   5_occ:  0.1083 0.1551   5.127215e+00   5.378203e+00
   5_bss:  0.1083 0.1550   5.126758e+00   5.377702e+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:  0.323  34.357  -3.158  -2.821   1.323  -0.000   0.000   0.000
   1_xyz:  0.323  34.357  -3.158  -2.821   1.323  -0.000   0.000   0.000
   1_adp:  0.323  34.357  -3.158  -2.821   1.323  -0.000   0.000   0.000
   1_occ:  0.323  34.357  -3.158  -2.821   1.323  -0.000   0.000   0.000
   2_bss:  0.323  40.702  -3.008  -2.764  -1.138  -0.000  -0.000  -0.000
   2_xyz:  0.323  40.702  -3.008  -2.764  -1.138  -0.000  -0.000  -0.000
   2_adp:  0.323  40.702  -3.008  -2.764  -1.138  -0.000  -0.000  -0.000
   2_occ:  0.323  40.702  -3.008  -2.764  -1.138  -0.000  -0.000  -0.000
   3_bss:  0.323  40.702  -2.796  -2.489  -1.573  -0.000  -0.000  -0.000
   3_xyz:  0.323  40.702  -2.796  -2.489  -1.573  -0.000  -0.000  -0.000
   3_adp:  0.323  40.702  -2.796  -2.489  -1.573  -0.000  -0.000  -0.000
   3_occ:  0.323  40.702  -2.796  -2.489  -1.573  -0.000  -0.000  -0.000
   4_bss:  0.322  41.195  -2.625  -2.332  -1.600  -0.000  -0.000  -0.000
   4_xyz:  0.322  41.195  -2.625  -2.332  -1.600  -0.000  -0.000  -0.000
   4_adp:  0.322  41.195  -2.625  -2.332  -1.600  -0.000  -0.000  -0.000
   4_occ:  0.322  41.195  -2.625  -2.332  -1.600  -0.000  -0.000  -0.000
   5_bss:  0.322  41.195  -2.425  -2.137  -1.478  -0.000  -0.000  -0.000
   5_xyz:  0.322  41.195  -2.425  -2.137  -1.478  -0.000  -0.000  -0.000
   5_adp:  0.322  41.195  -2.425  -2.137  -1.478  -0.000  -0.000  -0.000
   5_occ:  0.322  41.195  -2.425  -2.137  -1.478  -0.000  -0.000  -0.000
   5_bss:  0.319  43.346  -2.234  -1.940  -1.328  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.915 0.7732  0.9565    23369.556
   1_bss:  27.058 0.7909  0.9257    19373.287
   1_xyz:  15.827 0.9009  1.0007     7807.199
   1_adp:  16.435 0.8951  0.9983     8089.330
   1_occ:  16.413 0.8952  0.9982     8054.911
   2_bss:  15.874 0.8998  0.9756     7688.167
   2_xyz:  13.686 0.9174  0.9835     6086.981
   2_adp:  13.366 0.9201  0.9825     5928.037
   2_occ:  13.354 0.9202  0.9824     5913.641
   3_bss:  13.320 0.9204  0.9830     5900.487
   3_xyz:  13.070 0.9224  0.9834     5750.363
   3_adp:  13.121 0.9220  0.9788     5788.266
   3_occ:  13.126 0.9220  0.9787     5790.530
   4_bss:  13.121 0.9221  0.9823     5788.181
   4_xyz:  13.271 0.9210  0.9815     5900.636
   4_adp:  13.424 0.9198  0.9760     5965.456
   4_occ:  13.429 0.9198  0.9760     5969.729
   5_bss:  13.457 0.9196  0.9818     5990.310
   5_xyz:  13.627 0.9183  0.9810     6111.397
   5_adp:  13.710 0.9176  0.9747     6159.368
   5_occ:  13.712 0.9176  0.9746     6160.155
   5_bss:  13.701 0.9177  0.9808     6152.344
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6272e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6272e-01
   1_xyz:   1.014  0.007  0.070 15.038  0.004  4.110   6.0337e-02
   1_adp:   1.014  0.007  0.070 15.038  0.004  4.110   6.0337e-02
   1_occ:   1.014  0.007  0.070 15.038  0.004  4.110   6.0337e-02
   2_bss:   1.014  0.007  0.070 15.038  0.004  4.110   6.0337e-02
   2_xyz:   0.910  0.005  0.067 14.695  0.004  4.114   5.1714e-02
   2_adp:   0.910  0.005  0.067 14.695  0.004  4.114   5.1714e-02
   2_occ:   0.910  0.005  0.067 14.695  0.004  4.114   5.1714e-02
   3_bss:   0.910  0.005  0.067 14.695  0.004  4.114   5.1714e-02
   3_xyz:   0.957  0.006  0.072 14.888  0.004  4.114   5.5836e-02
   3_adp:   0.957  0.006  0.072 14.888  0.004  4.114   5.5836e-02
   3_occ:   0.957  0.006  0.072 14.888  0.004  4.114   5.5836e-02
   4_bss:   0.957  0.006  0.072 14.888  0.004  4.114   5.5836e-02
   4_xyz:   0.897  0.005  0.069 14.701  0.004  4.114   5.0647e-02
   4_adp:   0.897  0.005  0.069 14.701  0.004  4.114   5.0647e-02
   4_occ:   0.897  0.005  0.069 14.701  0.004  4.114   5.0647e-02
   5_bss:   0.897  0.005  0.069 14.701  0.004  4.114   5.0647e-02
   5_xyz:   0.875  0.005  0.067 14.639  0.003  4.114   4.8517e-02
   5_adp:   0.875  0.005  0.067 14.639  0.003  4.114   4.8517e-02
   5_occ:   0.875  0.005  0.067 14.639  0.003  4.114   4.8517e-02
   5_bss:   0.875  0.005  0.067 14.639  0.003  4.114   4.8517e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3975e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3975e-01
   1_xyz:   6.814  0.049  0.317 84.010  0.037  2.352   5.9573e-02
   1_adp:   6.814  0.049  0.317 84.010  0.037  2.352   5.9573e-02
   1_occ:   6.814  0.049  0.317 84.010  0.037  2.352   5.9573e-02
   2_bss:   6.814  0.049  0.317 84.010  0.037  2.352   5.9573e-02
   2_xyz:   6.857  0.032  0.207 84.600  0.037  2.391   6.8971e-02
   2_adp:   6.857  0.032  0.207 84.600  0.037  2.391   6.8971e-02
   2_occ:   6.857  0.032  0.207 84.600  0.037  2.391   6.8971e-02
   3_bss:   6.857  0.032  0.207 84.600  0.037  2.391   6.8971e-02
   3_xyz:   6.655  0.035  0.223 83.709  0.035  2.327   3.6581e-02
   3_adp:   6.655  0.035  0.223 83.709  0.035  2.327   3.6581e-02
   3_occ:   6.655  0.035  0.223 83.709  0.035  2.327   3.6581e-02
   4_bss:   6.655  0.035  0.223 83.709  0.035  2.327   3.6581e-02
   4_xyz:   6.353  0.037  0.215 83.574  0.035  2.379   3.0736e-02
   4_adp:   6.353  0.037  0.215 83.574  0.035  2.379   3.0736e-02
   4_occ:   6.353  0.037  0.215 83.574  0.035  2.379   3.0736e-02
   5_bss:   6.353  0.037  0.215 83.574  0.035  2.379   3.0736e-02
   5_xyz:   6.291  0.036  0.211 83.368  0.031  2.375   2.7683e-02
   5_adp:   6.291  0.036  0.211 83.368  0.031  2.375   2.7683e-02
   5_occ:   6.291  0.036  0.211 83.368  0.031  2.375   2.7683e-02
   5_bss:   6.291  0.036  0.211 83.368  0.031  2.375   2.7683e-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:  71.75   0.92  16.85  71.75   0.92  13.01  65.90   7.33  37.78
   1_occ:  71.75   0.92  16.85  71.75   0.92  13.01  65.90   7.33  37.78
   2_bss:  71.75   0.92  16.85  71.75   0.92  13.01  65.90   7.33  37.78
   2_xyz:  71.75   0.92  16.85  71.75   0.92  13.01  65.90   7.33  37.78
   2_adp:  72.07   1.98  16.70  72.07   1.98  12.94  68.72   5.84  37.19
   2_occ:  72.07   1.98  16.70  72.07   1.98  12.94  68.72   5.84  37.19
   3_bss:  72.07   1.98  16.70  72.07   1.98  12.94  68.72   5.84  37.19
   3_xyz:  72.07   1.98  16.70  72.07   1.98  12.94  68.72   5.84  37.19
   3_adp:  72.86   1.67  16.66  72.86   1.67  12.84  69.14   6.14  37.41
   3_occ:  72.86   1.67  16.66  72.86   1.67  12.84  69.14   6.14  37.41
   4_bss:  72.86   1.67  16.66  72.86   1.67  12.84  69.14   6.14  37.41
   4_xyz:  72.86   1.67  16.66  72.86   1.67  12.84  69.14   6.14  37.41
   4_adp:  81.30   0.87  16.88  81.30   0.87  12.85  71.73   5.96  38.82
   4_occ:  81.30   0.87  16.88  81.30   0.87  12.85  71.73   5.96  38.82
   5_bss:  81.30   0.87  16.88  81.30   0.87  12.85  71.73   5.96  38.82
   5_xyz:  81.30   0.87  16.88  81.30   0.87  12.85  71.73   5.96  38.82
   5_adp:  82.14   0.31  16.75  82.14   0.31  12.70  71.99   5.80  38.80
   5_occ:  82.14   0.31  16.75  82.14   0.31  12.70  71.99   5.80  38.80
   5_bss:  82.13   0.30  16.74  82.13   0.30  12.69  71.98   5.79  38.79
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.009    0.009    0.250
   1_adp:    1.009    0.009    0.250
   1_occ:    1.009    0.009    0.250
   2_bss:    1.009    0.009    0.250
   2_xyz:    0.922    0.015    0.277
   2_adp:    0.922    0.015    0.277
   2_occ:    0.922    0.015    0.277
   3_bss:    0.922    0.015    0.277
   3_xyz:    0.989    0.005    0.294
   3_adp:    0.989    0.005    0.294
   3_occ:    0.989    0.005    0.294
   4_bss:    0.989    0.005    0.294
   4_xyz:    1.058    0.006    0.302
   4_adp:    1.058    0.006    0.302
   4_occ:    1.058    0.006    0.302
   5_bss:    1.058    0.006    0.302
   5_xyz:    1.055    0.013    0.309
   5_adp:    1.055    0.013    0.309
   5_occ:    1.055    0.013    0.309
   5_bss:    1.055    0.013    0.309
------------------------------------------------------------------------

CPU time actual refinement: 323.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/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_662/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_662/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.77 
  Macro-tasks:
    bulk solvent and scale       = 36.88  
    individual site refinement   = 133.54 
    weights calculation          = 29.77  
    collect and process          = 6.64   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.94 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 102.90 
    alpha_beta                      = 7.92   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 111.82 
    fmodel                         = 6.84   
    r_factors                      = 0.15   
    phase_errors                   = 11.43  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 243.54 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.587 micro seconds
Total CPU time: 5.62 minutes
from_scatterers_fft:    647 calls, 102.51 s
gradients_fft:          592 calls,  98.20 s

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

# Date 2008-01-16 Time 05:22:01 PST -0800 (1200489721.69 s)
Start R-work = 0.2758, R-free = 0.2781 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.2559, R-free = 0.2575
Final R-work = 0.1083, R-free = 0.1550