# Date 2008-01-16 Time 04:37:05 PST -0800 (1200487025.46 s)
#phil __OFF__

Command line arguments: "../388.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28239
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 388

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.2261, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.97157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9716

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.97157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2182 [2103/2127]  1893   210  10.0%
  bin  2:  4.2182 -  3.3609 [2026/2046]  1822   204  10.1%
  bin  3:  3.3609 -  2.9398 [1993/2012]  1794   199  10.0%
  bin  4:  2.9398 -  2.6727 [1963/1993]  1766   197  10.0%
  bin  5:  2.6727 -  2.4821 [1976/1995]  1781   195   9.9%
  bin  6:  2.4821 -  2.3363 [1958/1983]  1758   200  10.2%
  bin  7:  2.3363 -  2.2197 [1940/1968]  1748   192   9.9%
  bin  8:  2.2197 -  2.1234 [1934/1970]  1741   193  10.0%
  bin  9:  2.1234 -  2.0419 [1916/1958]  1725   191  10.0%
  bin 10:  2.0419 -  1.9716 [1780/1973]  1602   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/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: 0.14 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:
        1.67 -     2.31: 25
        2.31 -     2.96: 1740
        2.96 -     3.61: 4652
        3.61 -     4.25: 9349
        4.25 -     4.90: 13033
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.666 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.950 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.983 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28794 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_388/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/model_refine_001.geo

CPU time processing inputs: 9.13


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3900   r_free= 0.3866   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.173587                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.3192 0.3144      6.4347      6.4058|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.3187 0.2929      6.6156       6.554|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.3463 0.3259      6.5304      6.5983|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.3595 0.3929      6.3847      6.4278|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.4068 0.3734      6.2624       6.197|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.4095 0.4222      6.1874      6.1537|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.4173 0.4142      6.1393       6.077|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.4304 0.4451       6.111      6.1628|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.4370 0.4410      6.0616      6.0503|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.4329 0.4482      6.0259      6.0198|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.4407 0.4482      5.9627       6.018|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.4560 0.4446      5.9521      5.9435|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.4439 0.4338       5.829      5.8064|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.4693 0.4304      5.8239       5.694|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.76  29.19   0.85     0.79      53024.83|
|  2:  4.7045 -  3.7540  1303   146  0.79  26.83   0.96     0.90      67012.19|
|  3:  3.7540 -  3.2853  1287   144  0.73  32.43   0.99     0.92      70535.64|
|  4:  3.2853 -  2.9876  1284   143  0.68  37.35   0.98     0.88      64846.62|
|  5:  2.9876 -  2.7750  1267   138  0.62  42.48   0.95     0.83      52448.07|
|  6:  2.7750 -  2.6123  1272   143  0.61  43.04   0.96     0.82      45698.77|
|  7:  2.6123 -  2.4821  1269   139  0.60  44.32   0.97     0.81      41880.48|
|  8:  2.4821 -  2.3745  1248   141  0.57  46.23   1.00     0.80      40314.15|
|  9:  2.3745 -  2.2834  1258   138  0.57  46.82   0.97     0.77      37168.98|
| 10:  2.2834 -  2.2049  1234   141  0.56  47.62   1.02     0.78      34501.55|
| 11:  2.2049 -  2.1361  1255   135  0.54  48.58   1.01     0.80      32137.99|
| 12:  2.1361 -  2.0753  1245   140  0.55  48.06   1.03     0.81      28616.96|
| 13:  2.0753 -  2.0208  1245   136  0.55  48.28   1.01     0.80      24338.90|
| 14:  2.0208 -  1.9716  1089   123  0.57  47.12   1.01     0.77      19830.02|
|alpha:            min =        0.77 max =            0.92 mean =         0.82|
|beta:             min =    19830.02 max =        70535.64 mean =     44211.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.81|
|phase err.(test): min =        0.00 max =           89.47 mean =        41.70|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.066519              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.647   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.192668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.826   (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 |  1.666 -  1.989:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.989 -  2.313:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.313 -  2.636:       75 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.636 -  2.959:     1665 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.959 -  3.283:     1958 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.283 -  3.606:     2694 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.606 -  3.930:     4809 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.930 -  4.253:     4540 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.253 -  4.577:     5932 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.577 -  4.900:     7101 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.666 |       0.320 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3900   r_free= 0.3866   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.173587                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3777   r_free= 0.3733   ksol= 0.33   Bsol= 22.66   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,2.00,-0.66,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.159719                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.158353              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.522   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.639180              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.715   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3777      final r-factor (work) = 0.2277          |
| start r-factor (free) = 0.3733      final r-factor (free) = 0.2549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0559 = 5.16 * 0.50 * 6.1594 + 1.00 * 0.1698                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3355 = 5.16 * 0.50 * 5.9127 + 1.00 * 0.0856                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2277      final r-factor (work) = 0.2083          |
| start r-factor (free) = 0.2549      final r-factor (free) = 0.2678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7853 = 0.64 * 1.00 * 5.9127 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6355 = 0.64 * 1.00 * 5.6696 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.64   17.64    None  None   None       |
|    all(noH): 2823   0      0.00    82.64   17.64    None  None   None       |
|    Sol.    : 438    0      6.89    82.64   40.31    None  None   None       |
|    Mac.    : 2385   0      0.00    78.71   13.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.264:  662   |   5:    41.318 -  49.582:  118        |
|      1:     8.264 -  16.527: 1198   |   6:    49.582 -  57.845:   86        |
|      2:    16.527 -  24.791:  406   |   7:    57.845 -  66.109:   51        |
|      3:    24.791 -  33.054:  158   |   8:    66.109 -  74.372:   10        |
|      4:    33.054 -  41.318:  129   |   9:    74.372 -  82.636:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2083 r_free = 0.2678             target_work(ml) = 5.686         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2080 r_free = 0.2674             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2080   r_free= 0.2674   ksol= 0.33   Bsol= 22.66   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,2.00,-0.66,0.00,-0.00,-0.00); trace/3= -0.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.684946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2051   r_free= 0.2635   ksol= 0.33   Bsol= 37.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.15,-1.40,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.674532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.617588              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.656   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.156345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.330  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2051      final r-factor (work) = 0.1509          |
| start r-factor (free) = 0.2635      final r-factor (free) = 0.1991          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5134 = 2.62 * 0.50 * 5.6753 + 1.00 * 0.0856                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3135 = 2.62 * 0.50 * 5.5481 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1509      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.1991      final r-factor (free) = 0.1848          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8790 = 0.16 * 1.00 * 5.5481 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8460 = 0.16 * 1.00 * 5.3657 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    78.47   16.97    None  None   None       |
|    all(noH): 2823   0      1.48    78.47   16.97    None  None   None       |
|    Sol.    : 438    0      6.71    78.47   38.47    None  None   None       |
|    Mac.    : 2385   0      1.48    78.40   13.02    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:     1.476 -   9.175:  762   |   5:    39.973 -  47.672:  105        |
|      1:     9.175 -  16.875: 1236   |   6:    47.672 -  55.372:   89        |
|      2:    16.875 -  24.574:  314   |   7:    55.372 -  63.071:   42        |
|      3:    24.574 -  32.273:  127   |   8:    63.071 -  70.770:   11        |
|      4:    32.273 -  39.973:  133   |   9:    70.770 -  78.470:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1410 r_free = 0.1848             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1407 r_free = 0.1848             target_work(ml) = 5.329         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1848   ksol= 0.33   Bsol= 37.82   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.69,-1.15,-1.40,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.328745                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1408   r_free= 0.1844   ksol= 0.32   Bsol= 38.47   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.03,-1.31,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.325815                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.150564              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.245  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.523732              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.492  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1408      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1844      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5035 = 3.15 * 0.50 * 5.3649 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3157 = 3.15 * 0.50 * 5.2401 + 1.00 * 0.0611                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7515 = 0.52 * 1.00 * 5.2401 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7006 = 0.52 * 1.00 * 5.1409 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    82.98   17.05    None  None   None       |
|    all(noH): 2823   0      0.49    82.98   17.05    None  None   None       |
|    Sol.    : 438    0      3.70    81.17   39.73    None  None   None       |
|    Mac.    : 2385   0      0.49    82.98   12.89    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:     0.494 -   8.742:  696   |   5:    41.736 -  49.985:  107        |
|      1:     8.742 -  16.991: 1320   |   6:    49.985 -  58.233:   82        |
|      2:    16.991 -  25.239:  312   |   7:    58.233 -  66.482:   45        |
|      3:    25.239 -  33.488:  120   |   8:    66.482 -  74.731:    8        |
|      4:    33.488 -  41.736:  129   |   9:    74.731 -  82.979:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1562             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1561             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1561   ksol= 0.32   Bsol= 38.47   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-2.03,-1.31,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128586                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1562   ksol= 0.32   Bsol= 40.78   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.43,-1.49,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.129048                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.264447              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.027162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.143  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.3123 = 1.26 * 0.50 * 5.1426 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2905 = 1.26 * 0.50 * 5.1311 + 1.00 * 0.0465                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4099 = 2.03 * 1.00 * 5.1311 + 1.00 * 0.0082                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3976 = 2.03 * 1.00 * 5.1244 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.80   17.26    None  None   None       |
|    all(noH): 2823   0      0.00    91.80   17.26    None  None   None       |
|    Sol.    : 438    0      4.98    85.73   40.90    None  None   None       |
|    Mac.    : 2385   0      0.00    91.80   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.180:  859   |   5:    45.899 -  55.079:  109        |
|      1:     9.180 -  18.360: 1242   |   6:    55.079 -  64.259:   60        |
|      2:    18.360 -  27.539:  262   |   7:    64.259 -  73.438:   30        |
|      3:    27.539 -  36.719:  125   |   8:    73.438 -  82.618:   15        |
|      4:    36.719 -  45.899:  118   |   9:    82.618 -  91.798:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1563             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1109 r_free = 0.1564             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1564   ksol= 0.32   Bsol= 40.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.43,-1.49,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128620                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1563   ksol= 0.32   Bsol= 42.54   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.31,-1.30,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.128328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.070721              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.266  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.624705              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.073   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3526 = 2.07 * 0.50 * 5.1250 + 1.00 * 0.0465                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3468 = 2.07 * 0.50 * 5.1095 + 1.00 * 0.0566                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.4206 = 2.62 * 1.00 * 5.1095 + 1.00 * 0.0096                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3972 = 2.62 * 1.00 * 5.1005 + 1.00 * 0.0098                              |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.30   17.09    None  None   None       |
|    all(noH): 2823   0      0.00    95.30   17.09    None  None   None       |
|    Sol.    : 438    0      5.97    87.88   40.65    None  None   None       |
|    Mac.    : 2385   0      0.00    95.30   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.530:  973   |   5:    47.650 -  57.180:   98        |
|      1:     9.530 -  19.060: 1176   |   6:    57.180 -  66.710:   47        |
|      2:    19.060 -  28.590:  232   |   7:    66.710 -  76.240:   23        |
|      3:    28.590 -  38.120:  128   |   8:    76.240 -  85.770:   15        |
|      4:    38.120 -  47.650:  128   |   9:    85.770 -  95.300:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1061 r_free = 0.1545             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1061 r_free = 0.1545             target_work(ml) = 5.101         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1061   r_free= 0.1545   ksol= 0.32   Bsol= 42.54   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.60,-2.31,-1.30,-0.00,-0.00,-0.00); trace/3= -2.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101252                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.0947 0.1229      5.3423      5.4908|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.0811 0.1122      5.4035      5.6152|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.1022 0.1510      5.4559      5.8405|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.1164 0.1533      5.4277       5.565|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.1214 0.1710      5.2781      5.5119|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.1111 0.1747      5.1582      5.4084|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.1176 0.1534      5.1079      5.3143|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.1107 0.1722      5.0323      5.3575|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.1111 0.1621      4.9962      5.2155|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.1039 0.1768       4.924      5.2389|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.1074 0.1604      4.9057      5.1954|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.1087 0.1763      4.8581       5.237|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.1063 0.1636      4.7701      5.0238|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.0989 0.1736      4.6346      4.9332|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.94   8.76   0.98     0.96       6558.46|
|  2:  4.7045 -  3.7540  1303   146  0.95   7.65   1.03     1.02       8636.09|
|  3:  3.7540 -  3.2853  1287   144  0.94  10.78   1.04     1.03       9990.34|
|  4:  3.2853 -  2.9876  1284   143  0.93  12.87   1.02     1.01       9820.52|
|  5:  2.9876 -  2.7750  1267   138  0.91  14.91   1.01     0.98       7715.76|
|  6:  2.7750 -  2.6123  1272   143  0.91  14.96   0.99     0.97       6465.32|
|  7:  2.6123 -  2.4821  1269   139  0.91  14.99   0.99     0.96       5652.15|
|  8:  2.4821 -  2.3745  1248   141  0.92  14.07   1.00     0.97       4860.58|
|  9:  2.3745 -  2.2834  1258   138  0.91  14.60   1.01     0.99       4704.29|
| 10:  2.2834 -  2.2049  1234   141  0.91  14.50   1.00     0.96       4055.81|
| 11:  2.2049 -  2.1361  1255   135  0.90  15.79   1.00     0.97       4201.58|
| 12:  2.1361 -  2.0753  1245   140  0.91  15.03   1.01     1.00       3798.57|
| 13:  2.0753 -  2.0208  1245   136  0.91  15.00   1.00     1.00       3226.89|
| 14:  2.0208 -  1.9716  1089   123  0.92  13.80   0.99     0.95       2422.50|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2422.50 max =         9990.34 mean =      5930.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.35|
|phase err.(test): min =        0.00 max =           88.64 mean =        12.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1545   ksol= 0.32   Bsol= 43.27   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.16,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101297                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1545   ksol= 0.32   Bsol= 43.27   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.16,-1.10,-0.00,-0.00,-0.00); trace/3= -1.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.101297                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.0948 0.1232      5.3441      5.4929|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.0812 0.1121      5.4045      5.6153|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.1023 0.1510      5.4561      5.8411|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.1164 0.1532      5.4275      5.5649|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.1213 0.1708      5.2776      5.5113|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.1111 0.1745      5.1577      5.4076|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.1176 0.1534      5.1076      5.3142|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.1106 0.1720      5.0321       5.357|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.1111 0.1621      4.9962      5.2153|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.1039 0.1770      4.9241      5.2397|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.1074 0.1604      4.9058      5.1955|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.1087 0.1764      4.8579      5.2368|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.1063 0.1635      4.7698      5.0233|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.0989 0.1734      4.6341      4.9325|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.94   8.79   0.98     0.96       6590.17|
|  2:  4.7045 -  3.7540  1303   146  0.95   7.67   1.03     1.02       8657.20|
|  3:  3.7540 -  3.2853  1287   144  0.94  10.79   1.04     1.03       9993.01|
|  4:  3.2853 -  2.9876  1284   143  0.93  12.87   1.02     1.01       9814.90|
|  5:  2.9876 -  2.7750  1267   138  0.91  14.90   1.01     0.98       7705.42|
|  6:  2.7750 -  2.6123  1272   143  0.91  14.95   1.00     0.98       6457.44|
|  7:  2.6123 -  2.4821  1269   139  0.91  14.99   1.00     0.97       5646.51|
|  8:  2.4821 -  2.3745  1248   141  0.92  14.07   1.00     0.98       4856.56|
|  9:  2.3745 -  2.2834  1258   138  0.91  14.60   1.02     1.00       4704.21|
| 10:  2.2834 -  2.2049  1234   141  0.91  14.51   1.01     0.97       4055.82|
| 11:  2.2049 -  2.1361  1255   135  0.90  15.79   1.01     0.98       4203.11|
| 12:  2.1361 -  2.0753  1245   140  0.91  15.02   1.02     1.01       3797.19|
| 13:  2.0753 -  2.0208  1245   136  0.91  14.99   1.02     1.01       3223.69|
| 14:  2.0208 -  1.9716  1089   123  0.92  13.78   1.00     0.96       2418.38|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2418.38 max =         9993.01 mean =      5931.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.35|
|phase err.(test): min =        0.00 max =           88.65 mean =        12.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.30   17.09    None  None   None       |
|    all(noH): 2823   0      0.00    95.30   17.09    None  None   None       |
|    Sol.    : 438    0      5.97    87.89   40.66    None  None   None       |
|    Mac.    : 2385   0      0.00    95.30   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.533:  973   |   5:    47.653 -  57.183:   98        |
|      1:     9.533 -  19.063: 1176   |   6:    57.183 -  66.713:   47        |
|      2:    19.063 -  28.593:  232   |   7:    66.713 -  76.243:   23        |
|      3:    28.593 -  38.123:  128   |   8:    76.243 -  85.773:   15        |
|      4:    38.123 -  47.653:  128   |   9:    85.773 -  95.303:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 4.584
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 294
   mapped sites are within: 0.757 - 4.584

peak=    6.399 closest distance to " NE2 GLN A  11 " =    1.220
peak=    6.066 closest distance to " O   HOH Z 144 " =    1.804
peak=    5.998 closest distance to " O   HOH Z 126 " =    1.889
peak=    5.609 closest distance to " CG  PRO A  54 " =    1.257
peak=    5.348 closest distance to " NH2 ARG A  56 " =    2.125
peak=    5.105 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.078 closest distance to " CG  PRO A 213 " =    1.269
peak=    4.969 closest distance to " O   HOH Z 427 " =    2.638
peak=    4.880 closest distance to " O   HOH Z 236 " =    1.416
peak=    4.815 closest distance to " CB  SER A  63 " =    1.164
peak=    4.799 closest distance to " O   HOH Z  78 " =    1.748
peak=    4.749 closest distance to " CB  GLN A 183 " =    1.202
peak=    4.645 closest distance to " CB  GLN A 223 " =    1.555
peak=    4.620 closest distance to " O   HOH Z 209 " =    2.206
peak=    4.609 closest distance to " O   HOH Z 193 " =    1.774
peak=    4.574 closest distance to " O   HOH Z 369 " =    2.178
peak=    4.558 closest distance to " C   PRO A 198 " =    1.455
peak=    4.518 closest distance to " O   HOH Z 371 " =    1.829
peak=    4.494 closest distance to " CB  PRO A  54 " =    0.964
peak=    4.461 closest distance to " O   HOH Z 287 " =    1.905
peak=    4.456 closest distance to " O   HOH Z   9 " =    2.264
peak=    4.444 closest distance to " O   HOH Z 298 " =    1.851
peak=    4.394 closest distance to " CB  ASN A 148 " =    1.375
peak=    4.383 closest distance to " O   HOH Z 232 " =    2.357
peak=    4.379 closest distance to " O   HOH Z 203 " =    1.818
peak=    4.362 closest distance to " OG ASER A 258 " =    3.055
peak=    4.356 closest distance to " O   HOH Z  44 " =    1.768
peak=    4.350 closest distance to " OG BSER A 164 " =    2.257
peak=    4.336 closest distance to " ND2 ASN A 187 " =    1.392
peak=    4.329 closest distance to " CG  ARG A  66 " =    2.443
peak=    4.298 closest distance to " O   HOH Z 303 " =    2.244
peak=    4.288 closest distance to " O   HOH Z 234 " =    3.532
peak=    4.288 closest distance to " CB  GLU A 152 " =    1.303
peak=    4.272 closest distance to " O   HOH Z 112 " =    1.163
peak=    4.271 closest distance to " CA  TYR A  30 " =    0.919
peak=    4.233 closest distance to " CG2 VAL A 257 " =    0.819
peak=    4.230 closest distance to " O   HOH Z 272 " =    1.806
peak=    4.193 closest distance to " NZ  LYS A 117 " =    2.976
peak=    4.171 closest distance to " CG  PRO A  90 " =    1.111
peak=    4.168 closest distance to " O   HOH Z  78 " =    2.085
peak=    4.103 closest distance to " CB  SER A   3 " =    1.296
peak=    4.082 closest distance to " CB  GLU A 128 " =    1.072
peak=    4.074 closest distance to " O   HOH Z  61 " =    1.711
peak=    4.036 closest distance to " O   HOH Z   1 " =    1.876
peak=    4.034 closest distance to " O   HOH Z 289 " =    1.651
peak=    4.031 closest distance to " CB  VAL A 265 " =    1.346
peak=    4.031 closest distance to " O   HOH Z 425 " =    2.026
peak=    4.013 closest distance to " O   HOH Z 144 " =    2.132
peak=    4.003 closest distance to " CG1 ILE A  33 " =    1.239
peak=    3.999 closest distance to " CB  ARG A  79 " =    1.428
peak=    3.989 closest distance to " O   HOH Z 132 " =    2.212
peak=    3.985 closest distance to " O   HOH Z 419 " =    2.206
peak=    3.984 closest distance to " CG  PRO A 198 " =    1.221
peak=    3.981 closest distance to " O   HOH Z 368 " =    3.603
peak=    3.977 closest distance to " OD1 ASN A  69 " =    2.619
peak=    3.975 closest distance to " O   HOH Z 344 " =    3.181
peak=    3.972 closest distance to " O   SER A  87 " =    2.210
peak=    3.958 closest distance to " CD2 TRP A 179 " =    1.377
peak=    3.956 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.922 closest distance to " O   HOH Z 158 " =    2.943
peak=    3.921 closest distance to " CB  ARG A 139 " =    1.023
peak=    3.917 closest distance to " O   HOH Z 423 " =    1.329
peak=    3.897 closest distance to " O   HOH Z 189 " =    2.000
peak=    3.896 closest distance to " O   HOH Z 362 " =    2.524
peak=    3.876 closest distance to " O   HOH Z 405 " =    1.189
peak=    3.874 closest distance to " O   HOH Z  59 " =    1.565
peak=    3.871 closest distance to " O   HOH Z 368 " =    1.958
peak=    3.868 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.860 closest distance to " O   HOH Z 128 " =    2.088
peak=    3.830 closest distance to " O   HOH Z  43 " =    1.890
peak=    3.829 closest distance to " O   HOH Z 425 " =    1.269
peak=    3.829 closest distance to " CB  ARG A 190 " =    1.632
peak=    3.826 closest distance to " O   HOH Z   1 " =    1.652
peak=    3.820 closest distance to " CG  PRO A 243 " =    1.138
peak=    3.802 closest distance to " CB  LEU A 228 " =    1.097
peak=    3.798 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.797 closest distance to " CB  TYR A 169 " =    0.839
peak=    3.785 closest distance to " O   HOH Z  63 " =    1.430
peak=    3.781 closest distance to " CB  TRP A 179 " =    1.315
peak=    3.773 closest distance to " O   HOH Z 380 " =    1.581
peak=    3.766 closest distance to " O   HOH Z 403 " =    1.658
peak=    3.765 closest distance to " O   HOH Z  64 " =    2.443
peak=    3.760 closest distance to " O   HOH Z 250 " =    1.476
peak=    3.757 closest distance to " O   HOH Z 392 " =    3.052
peak=    3.730 closest distance to " O   HOH Z  93 " =    2.149
peak=    3.721 closest distance to " O   HOH Z 407 " =    2.299
peak=    3.717 closest distance to " NH1BARG A 145 " =    1.303
peak=    3.712 closest distance to " O   HOH Z 286 " =    2.345
peak=    3.707 closest distance to " O   HOH Z   3 " =    1.930
peak=    3.701 closest distance to " O   HOH Z 437 " =    1.629
peak=    3.698 closest distance to " N   PHE A 130 " =    1.253
peak=    3.696 closest distance to " CB  THR A 157 " =    1.092
peak=    3.692 closest distance to " O   HOH Z 175 " =    2.295
peak=    3.687 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.684 closest distance to " CB  SER A  26 " =    1.631
peak=    3.678 closest distance to " O   HOH Z 402 " =    1.395
peak=    3.668 closest distance to " O   HOH Z 327 " =    1.632
peak=    3.658 closest distance to " O   HOH Z 298 " =    2.507
peak=    3.656 closest distance to " CD2 LEU A 297 " =    0.984
peak=    3.650 closest distance to " O   HOH Z 214 " =    2.247
peak=    3.647 closest distance to " CA  ASN A 215 " =    1.195
peak=    3.644 closest distance to " CG2 ILE A 120 " =    1.112
peak=    3.627 closest distance to " CG AARG A 275 " =    1.034
peak=    3.622 closest distance to " O   HOH Z 357 " =    1.848
peak=    3.618 closest distance to " NH2BARG A 145 " =    2.057
peak=    3.614 closest distance to " O   HOH Z  97 " =    1.992
peak=    3.612 closest distance to " O   HOH Z 207 " =    1.635
peak=    3.607 closest distance to " CB  THR A  31 " =    1.738
peak=    3.605 closest distance to " O   HOH Z 124 " =    1.333
peak=    3.603 closest distance to " O   HOH Z 365 " =    2.732
peak=    3.591 closest distance to " O   HOH Z 172 " =    3.085
peak=    3.586 closest distance to " OD1BASN A 224 " =    2.218
peak=    3.583 closest distance to " O   HOH Z  40 " =    1.991
peak=    3.582 closest distance to " O   HOH Z 371 " =    2.960
peak=    3.574 closest distance to " O  BHOH Z 338 " =    2.330
peak=    3.574 closest distance to " CB  ALA A  34 " =    1.139
peak=    3.572 closest distance to " O   HOH Z 305 " =    3.530
peak=    3.567 closest distance to " O   HOH Z   6 " =    2.064
peak=    3.565 closest distance to " O   HOH Z 423 " =    2.389
peak=    3.562 closest distance to " O   HOH Z  10 " =    1.756
peak=    3.556 closest distance to " O   HOH Z 128 " =    2.044
peak=    3.555 closest distance to " CD BLYS A 290 " =    1.215
peak=    3.551 closest distance to " O   HOH Z 389 " =    1.697
peak=    3.547 closest distance to " ND1 HIS A  86 " =    1.828
peak=    3.532 closest distance to " CB  VAL A 202 " =    1.586
peak=    3.522 closest distance to " O   HOH Z 133 " =    2.675
peak=    3.514 closest distance to " NH1AARG A 145 " =    1.172
peak=    3.514 closest distance to " CG  GLN A  77 " =    2.388
peak=    3.513 closest distance to " O   HOH Z 193 " =    1.834
peak=    3.510 closest distance to " CD  PRO A 243 " =    1.551
peak=    3.507 closest distance to " CA  ALA A 233 " =    0.931
peak=    3.500 closest distance to " O   HOH Z  88 " =    2.479
peak=    3.498 closest distance to " CB  GLN A  89 " =    1.406
peak=    3.497 closest distance to " O   HOH Z 283 " =    2.324
peak=    3.494 closest distance to " CG2 THR A 221 " =    1.158
peak=    3.483 closest distance to " CA  ALA A  21 " =    1.080
peak=    3.479 closest distance to " O   HOH Z 173 " =    1.934
peak=    3.473 closest distance to " O   HOH Z 336 " =    1.926
peak=    3.469 closest distance to " O   HOH Z  71 " =    2.016
peak=    3.467 closest distance to " CD  ARG A 159 " =    0.757
peak=    3.467 closest distance to " O   HOH Z 126 " =    1.482
peak=    3.463 closest distance to " OD2 ASP A 286 " =    2.706
peak=    3.458 closest distance to " O   HOH Z 245 " =    1.306
peak=    3.456 closest distance to " O   HOH Z 345 " =    3.329
peak=    3.452 closest distance to " CA  MET A  40 " =    1.058
peak=    3.447 closest distance to " O   HOH Z  40 " =    2.026
peak=    3.446 closest distance to " O   HOH Z 417 " =    1.064
peak=    3.444 closest distance to " OG  SER A  62 " =    2.869
peak=    3.443 closest distance to " NE2 GLN A  73 " =    3.568
peak=    3.440 closest distance to " O   HOH Z 146 " =    1.670
peak=    3.440 closest distance to " CA  PHE A 283 " =    1.279
peak=    3.438 closest distance to " CB  TRP A 266 " =    1.061
peak=    3.438 closest distance to " O   HOH Z 180 " =    2.205
peak=    3.437 closest distance to " CE1 TYR A 186 " =    1.303
peak=    3.431 closest distance to " OE2 GLU A  53 " =    2.076
peak=    3.428 closest distance to " CB  ASP A 140 " =    0.886
peak=    3.425 closest distance to " CB  ALA A 291 " =    1.469
peak=    3.425 closest distance to " CB  ALA A   1 " =    4.584
peak=    3.423 closest distance to " O   HOH Z 415 " =    3.538
peak=    3.420 closest distance to " O   HOH Z  64 " =    2.106
peak=    3.418 closest distance to " CB  TYR A 116 " =    0.828
peak=    3.400 closest distance to " CA  THR A 264 " =    0.834
peak=    3.397 closest distance to " CB  SER A  62 " =    1.309
peak=    3.394 closest distance to " O   HOH Z 189 " =    2.187
peak=    3.393 closest distance to " O   HOH Z 227 " =    1.786
peak=    3.391 closest distance to " CA  ALA A 299 " =    0.935
peak=    3.387 closest distance to " CG  MET A 113 " =    1.096
peak=    3.381 closest distance to " O   HOH Z 261 " =    2.230
peak=    3.379 closest distance to " O   HOH Z 284 " =    2.805
peak=    3.376 closest distance to " O   HOH Z 426 " =    1.824
peak=    3.375 closest distance to " CB  LYS A 117 " =    1.191
peak=    3.372 closest distance to " O   HOH Z 147 " =    1.700
peak=    3.370 closest distance to " OG  SER A  22 " =    2.701
peak=    3.367 closest distance to " O   HOH Z 153 " =    1.616
peak=    3.360 closest distance to " NE  ARG A  24 " =    1.957
peak=    3.350 closest distance to " O   HOH Z 292 " =    1.721
peak=    3.348 closest distance to " O   HOH Z 290 " =    0.937
peak=    3.345 closest distance to " CA  ALA A  84 " =    1.362
peak=    3.344 closest distance to " O   HOH Z 394 " =    1.583
peak=    3.343 closest distance to " O   HOH Z 286 " =    2.357
peak=    3.341 closest distance to " O   HOH Z 337 " =    3.602
peak=    3.337 closest distance to " O   HOH Z 409 " =    2.498
peak=    3.331 closest distance to " O   HOH Z  88 " =    2.447
peak=    3.328 closest distance to " CA  ASP A 162 " =    1.094
peak=    3.328 closest distance to " N   ASN A  39 " =    1.238
peak=    3.327 closest distance to " CB  ALA A 114 " =    1.482
peak=    3.323 closest distance to " O   HOH Z 271 " =    2.245
peak=    3.321 closest distance to " NH2AARG A 190 " =    1.948
peak=    3.320 closest distance to " ND1 HIS A  81 " =    1.509
peak=    3.320 closest distance to " O  BHOH Z  74 " =    1.415
peak=    3.318 closest distance to " OG BSER A  99 " =    2.273
peak=    3.314 closest distance to " O   HOH Z 213 " =    2.008
peak=    3.313 closest distance to " O   HOH Z 227 " =    2.126
peak=    3.313 closest distance to " N   ASN A 127 " =    1.324
peak=    3.311 closest distance to " CB  LEU A 255 " =    0.794
peak=    3.308 closest distance to " CG  MET A 185 " =    1.292
peak=    3.308 closest distance to " CA  LYS A 290 " =    1.430
peak=    3.308 closest distance to " CZ  PHE A 218 " =    1.014
peak=    3.302 closest distance to " O   HOH Z 291 " =    1.559
peak=    3.301 closest distance to " C   ILE A 106 " =    1.869
peak=    3.301 closest distance to " O   HOH Z 411 " =    3.699
peak=    3.299 closest distance to " CD  ARG A  79 " =    2.344
peak=    3.298 closest distance to " CG  GLU A 277 " =    2.004
peak=    3.293 closest distance to " O   HOH Z  47 " =    1.769
peak=    3.291 closest distance to " CA  SER A 146 " =    1.789
peak=    3.290 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.289 closest distance to " N   SER A 134 " =    1.422
peak=    3.284 closest distance to " O   HOH Z 128 " =    1.999
peak=    3.284 closest distance to " CA  ALA A 158 " =    1.166
peak=    3.279 closest distance to " O   HOH Z 108 " =    2.310
peak=    3.278 closest distance to " CA  ASN A  74 " =    1.257
peak=    3.276 closest distance to " O   HOH Z  21 " =    1.742
peak=    3.275 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.272 closest distance to " O   HOH Z 422 " =    2.612
peak=    3.269 closest distance to " N   GLN A 278 " =    1.101
peak=    3.267 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.262 closest distance to " O   HOH Z 135 " =    1.678
peak=    3.258 closest distance to " O   HOH Z 391 " =    2.936
peak=    3.258 closest distance to " CB  ILE A 120 " =    1.383
peak=    3.256 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.253 closest distance to " O   HOH Z 279 " =    2.210
peak=    3.251 closest distance to " CB  ASN A  39 " =    0.827
peak=    3.251 closest distance to " CB  THR A 279 " =    1.757
peak=    3.250 closest distance to " CA  ILE A 234 " =    1.072
peak=    3.249 closest distance to " O   HOH Z 281 " =    1.774
peak=    3.248 closest distance to " O   HOH Z 433 " =    1.807
peak=    3.247 closest distance to " CG1BVAL A  72 " =    1.329
peak=    3.244 closest distance to " CE AMET A  47 " =    1.396
peak=    3.240 closest distance to " NH1 ARG A  14 " =    1.235
peak=    3.238 closest distance to " N   ARG A 156 " =    1.276
peak=    3.236 closest distance to " CB  VAL A 265 " =    2.306
peak=    3.232 closest distance to " O   HOH Z  44 " =    3.002
peak=    3.222 closest distance to " O   HOH Z  55 " =    2.242
peak=    3.220 closest distance to " O   HOH Z  30 " =    1.589
peak=    3.220 closest distance to " CA  LEU A 300 " =    1.027
peak=    3.217 closest distance to " O   HOH Z 248 " =    1.608
peak=    3.217 closest distance to " CB  ASN A 110 " =    1.079
peak=    3.215 closest distance to " OH  TYR A 116 " =    0.998
peak=    3.212 closest distance to " OG BSER A 134 " =    2.800
peak=    3.212 closest distance to " CB  SER A 212 " =    0.963
peak=    3.211 closest distance to " O   HOH Z 423 " =    1.735
peak=    3.211 closest distance to " CB  SER A 276 " =    1.113
peak=    3.203 closest distance to " N   GLU A   2 " =    1.412
peak=    3.202 closest distance to " O   HOH Z 291 " =    1.801
peak=    3.201 closest distance to " CB  SER A 216 " =    0.787
peak=    3.200 closest distance to " CB  GLN A  88 " =    1.248
peak=    3.196 closest distance to " O   HOH Z 435 " =    1.849
peak=    3.195 closest distance to " O   HOH Z 325 " =    3.685
peak=    3.188 closest distance to " CG2 VAL A 197 " =    1.083
peak=    3.188 closest distance to " O   HOH Z 432 " =    1.781
peak=    3.187 closest distance to " NH2 ARG A 219 " =    1.889
peak=    3.185 closest distance to " CB  TRP A 179 " =    1.398
peak=    3.178 closest distance to " O   HOH Z 266 " =    3.111
peak=    3.173 closest distance to " CA  ALA A 291 " =    0.860
peak=    3.173 closest distance to " CB  MET A  47 " =    1.275
peak=    3.168 closest distance to " N   ASP A 162 " =    1.242
peak=    3.167 closest distance to " CD2 LEU A 255 " =    1.434
peak=    3.165 closest distance to " CG1 ILE A 120 " =    1.212
peak=    3.162 closest distance to " O   HOH Z  59 " =    1.907
peak=    3.158 closest distance to " CG2 THR A 294 " =    1.626
peak=    3.149 closest distance to " CD1 ILE A 106 " =    0.969
peak=    3.142 closest distance to " O   HOH Z 119 " =    4.383
peak=    3.142 closest distance to " O   HOH Z  80 " =    1.901
peak=    3.141 closest distance to " O   HOH Z 261 " =    1.485
peak=    3.141 closest distance to " CB  VAL A 126 " =    1.160
peak=    3.141 closest distance to " O   HOH Z 329 " =    3.698
peak=    3.139 closest distance to " O   HOH Z  15 " =    1.473
peak=    3.138 closest distance to " CG1 VAL A 189 " =    1.889
peak=    3.135 closest distance to " O   HOH Z 148 " =    3.337
peak=    3.135 closest distance to " O   HOH Z 109 " =    2.538
peak=    3.133 closest distance to " O   HOH Z  43 " =    2.658
peak=    3.122 closest distance to " CB  VAL A 268 " =    0.822
peak=    3.120 closest distance to " CA  MET A 105 " =    0.948
peak=    3.118 closest distance to " CB  MET A 188 " =    1.566
peak=    3.116 closest distance to " CB  SER A  62 " =    0.859
peak=    3.113 closest distance to " O   ASN A  74 " =    1.591
peak=    3.090 closest distance to " O   HOH Z 374 " =    2.470
peak=    3.086 closest distance to " CG  LYS A  76 " =    0.991
peak=    3.086 closest distance to " O   HOH Z 218 " =    2.154
peak=    3.085 closest distance to " CB  ALA A 248 " =    0.904
peak=    3.076 closest distance to " CA  ALA A 248 " =    1.201
peak=    3.068 closest distance to " O   HOH Z 421 " =    1.882
peak=    3.067 closest distance to " CA  ARG A  36 " =    0.979
peak=    3.065 closest distance to " CA  LEU A 101 " =    1.575
peak=    3.062 closest distance to " O   HOH Z 151 " =    1.373
peak=    3.058 closest distance to " O   HOH Z  85 " =    2.269
peak=    3.043 closest distance to " CD  LYS A 166 " =    1.276
peak=    3.013 closest distance to " O   HOH Z 153 " =    3.756
peak=    3.010 closest distance to " O   HOH Z  88 " =    3.104
peak=    3.003 closest distance to " O   HOH Z  66 " =    1.903

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.992
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 213
   mapped sites are within: 0.779 - 5.992

peak=   -4.666 closest distance to " O   HOH Z 266 " =    4.694
peak=   -4.633 closest distance to " O   HOH Z 377 " =    2.037
peak=   -4.604 closest distance to " CD  ARG A 156 " =    2.046
peak=   -4.560 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.330 closest distance to " CG  GLN A 223 " =    1.829
peak=   -4.327 closest distance to " CB  PRO A 243 " =    2.566
peak=   -4.296 closest distance to " SG  CYS A 254 " =    3.333
peak=   -4.212 closest distance to " OG BSER A 134 " =    1.255
peak=   -4.120 closest distance to " CG1 VAL A 112 " =    2.868
peak=   -4.105 closest distance to " O   HOH Z 231 " =    2.247
peak=   -4.101 closest distance to " O   HOH Z 372 " =    2.471
peak=   -4.100 closest distance to " O   VAL A  67 " =    2.623
peak=   -4.070 closest distance to " N   GLN A  58 " =    1.571
peak=   -4.017 closest distance to " O   PRO A 198 " =    1.329
peak=   -4.007 closest distance to " CA  VAL A  67 " =    2.801
peak=   -3.996 closest distance to " O   HOH Z 198 " =    2.021
peak=   -3.944 closest distance to " OD2 ASP A 191 " =    1.407
peak=   -3.937 closest distance to " O   HOH Z 313 " =    1.871
peak=   -3.935 closest distance to " CB  ALA A 291 " =    2.130
peak=   -3.933 closest distance to " CB  ASN A  39 " =    2.291
peak=   -3.931 closest distance to " CB  TYR A  15 " =    2.136
peak=   -3.925 closest distance to " CD1 LEU A 255 " =    2.871
peak=   -3.918 closest distance to " CG  PHE A 283 " =    2.602
peak=   -3.910 closest distance to " ND2 ASN A  45 " =    1.725
peak=   -3.895 closest distance to " O   HOH Z 351 " =    1.586
peak=   -3.887 closest distance to " O   ARG A 145 " =    1.531
peak=   -3.884 closest distance to " O   HOH Z 385 " =    1.966
peak=   -3.880 closest distance to " OD1 ASN A 187 " =    1.632
peak=   -3.878 closest distance to " CA  GLY A  98 " =    1.832
peak=   -3.869 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.867 closest distance to " O   ALA A 161 " =    1.569
peak=   -3.860 closest distance to " O   HOH Z 389 " =    1.841
peak=   -3.859 closest distance to " O   HOH Z 290 " =    1.162
peak=   -3.843 closest distance to " CE  MET A 105 " =    2.245
peak=   -3.839 closest distance to " O   HOH Z  13 " =    1.498
peak=   -3.836 closest distance to " ND2 ASN A  45 " =    1.046
peak=   -3.829 closest distance to " O   HOH Z 263 " =    2.914
peak=   -3.824 closest distance to " CZ  PHE A  59 " =    1.461
peak=   -3.792 closest distance to " O   SER A 135 " =    1.464
peak=   -3.738 closest distance to " O   HOH Z 407 " =    2.955
peak=   -3.724 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.708 closest distance to " O   SER A  95 " =    1.415
peak=   -3.694 closest distance to " CZ  TYR A 169 " =    1.624
peak=   -3.671 closest distance to " CB  ALA A 291 " =    2.252
peak=   -3.668 closest distance to " O   HOH Z  52 " =    1.369
peak=   -3.660 closest distance to " O   PRO A 163 " =    1.931
peak=   -3.657 closest distance to " CG  GLN A  58 " =    1.134
peak=   -3.642 closest distance to " CB  PHE A 192 " =    1.892
peak=   -3.638 closest distance to " CD1 LEU A 228 " =    2.048
peak=   -3.638 closest distance to " O   PRO A 243 " =    2.541
peak=   -3.637 closest distance to " O   HOH Z 152 " =    5.122
peak=   -3.634 closest distance to " O   HOH Z 185 " =    2.047
peak=   -3.629 closest distance to " OD2 ASP A 171 " =    2.192
peak=   -3.626 closest distance to " O   HOH Z  43 " =    1.771
peak=   -3.616 closest distance to " OXT GLY A 302 " =    2.853
peak=   -3.614 closest distance to " OD1 ASP A 191 " =    1.935
peak=   -3.614 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.611 closest distance to " N   ALA A 248 " =    1.537
peak=   -3.610 closest distance to " CB  ALA A 248 " =    2.025
peak=   -3.601 closest distance to " O   VAL A 189 " =    2.492
peak=   -3.596 closest distance to " O   PHE A 218 " =    1.502
peak=   -3.591 closest distance to " CB  ALA A 161 " =    2.446
peak=   -3.585 closest distance to " O   HOH Z 362 " =    5.992
peak=   -3.581 closest distance to " CE2 PHE A 218 " =    2.423
peak=   -3.572 closest distance to " O   HOH Z 388 " =    2.040
peak=   -3.565 closest distance to " N   ASP A 286 " =    2.354
peak=   -3.564 closest distance to " OD1 ASP A 191 " =    1.448
peak=   -3.556 closest distance to " CZ3 TRP A 179 " =    1.245
peak=   -3.554 closest distance to " O   HOH Z 211 " =    1.537
peak=   -3.535 closest distance to " O   SER A 146 " =    1.028
peak=   -3.524 closest distance to " O   HOH Z 126 " =    1.893
peak=   -3.518 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.508 closest distance to " O   HOH Z  24 " =    1.262
peak=   -3.502 closest distance to " O   HOH Z 298 " =    1.257
peak=   -3.498 closest distance to " CA  ASP A  27 " =    2.405
peak=   -3.490 closest distance to " OD1 ASN A 148 " =    1.608
peak=   -3.488 closest distance to " CG1 VAL A 268 " =    2.408
peak=   -3.478 closest distance to " CB  ALA A 248 " =    2.271
peak=   -3.476 closest distance to " O   HOH Z 198 " =    1.587
peak=   -3.474 closest distance to " O   HOH Z  63 " =    1.849
peak=   -3.471 closest distance to " CB  ALA A   7 " =    2.025
peak=   -3.467 closest distance to " O   HOH Z  60 " =    2.113
peak=   -3.466 closest distance to " O   HOH Z 193 " =    1.991
peak=   -3.463 closest distance to " O   HOH Z 131 " =    4.043
peak=   -3.457 closest distance to " CB  ILE A  33 " =    2.832
peak=   -3.456 closest distance to " O   SER A  22 " =    2.446
peak=   -3.454 closest distance to " NH1 ARG A 195 " =    2.644
peak=   -3.453 closest distance to " CG  ASP A 231 " =    0.779
peak=   -3.451 closest distance to " NH2 ARG A  79 " =    1.983
peak=   -3.446 closest distance to " O   HOH Z 393 " =    3.437
peak=   -3.440 closest distance to " O   ALA A  51 " =    1.235
peak=   -3.439 closest distance to " OD1 ASP A 171 " =    1.561
peak=   -3.434 closest distance to " N   HIS A 115 " =    2.198
peak=   -3.431 closest distance to " CG2 THR A 178 " =    2.199
peak=   -3.427 closest distance to " CD  ARG A 139 " =    1.552
peak=   -3.425 closest distance to " O   HOH Z 266 " =    4.452
peak=   -3.424 closest distance to " CE3 TRP A 274 " =    2.248
peak=   -3.422 closest distance to " OG  SER A  97 " =    2.072
peak=   -3.419 closest distance to " CA  GLY A 203 " =    2.159
peak=   -3.412 closest distance to " C   LEU A 143 " =    1.069
peak=   -3.403 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.401 closest distance to " CG1 VAL A 230 " =    1.926
peak=   -3.400 closest distance to " C   ALA A 158 " =    1.263
peak=   -3.392 closest distance to " NE  ARG A  36 " =    1.874
peak=   -3.391 closest distance to " O   HOH Z  90 " =    2.361
peak=   -3.389 closest distance to " CA  GLY A 133 " =    1.938
peak=   -3.389 closest distance to " ND2 ASN A  39 " =    1.406
peak=   -3.381 closest distance to " O   HOH Z 103 " =    1.705
peak=   -3.377 closest distance to " NH1AARG A 275 " =    1.813
peak=   -3.377 closest distance to " OG  SER A  87 " =    1.290
peak=   -3.373 closest distance to " O   HOH Z 191 " =    5.535
peak=   -3.364 closest distance to " CG2 VAL A 189 " =    1.986
peak=   -3.359 closest distance to " NH2BARG A 275 " =    1.795
peak=   -3.358 closest distance to " O   HOH Z 114 " =    2.945
peak=   -3.358 closest distance to " O   HOH Z 250 " =    1.393
peak=   -3.357 closest distance to " CB  ASP A 286 " =    2.263
peak=   -3.354 closest distance to " CB  ASP A 132 " =    2.360
peak=   -3.352 closest distance to " CZ2 TRP A 274 " =    0.971
peak=   -3.352 closest distance to " O   HOH Z 165 " =    2.191
peak=   -3.346 closest distance to " CD2 LEU A 237 " =    2.631
peak=   -3.346 closest distance to " NE2 GLN A 278 " =    1.690
peak=   -3.343 closest distance to " O   MET A  40 " =    2.697
peak=   -3.343 closest distance to " N   THR A 235 " =    1.363
peak=   -3.342 closest distance to " O   HOH Z 140 " =    1.842
peak=   -3.342 closest distance to " CA  GLY A  57 " =    2.129
peak=   -3.334 closest distance to " CB  PHE A 208 " =    2.183
peak=   -3.333 closest distance to " O   HOH Z 166 " =    1.294
peak=   -3.333 closest distance to " CD2 LEU A 237 " =    2.290
peak=   -3.328 closest distance to " CD1 LEU A 101 " =    2.253
peak=   -3.318 closest distance to " O   TRP A  70 " =    1.452
peak=   -3.317 closest distance to " O   ALA A  10 " =    1.709
peak=   -3.317 closest distance to " CD2 PHE A 225 " =    1.110
peak=   -3.315 closest distance to " CG  MET A 105 " =    0.945
peak=   -3.315 closest distance to " N   SER A 276 " =    1.151
peak=   -3.303 closest distance to " O   VAL A 174 " =    2.195
peak=   -3.302 closest distance to " CG2 ILE A 263 " =    2.250
peak=   -3.298 closest distance to " C   PRO A  90 " =    1.534
peak=   -3.290 closest distance to " CB  PRO A 163 " =    2.408
peak=   -3.289 closest distance to " ND2 ASN A  69 " =    1.520
peak=   -3.289 closest distance to " CE  MET A  93 " =    1.215
peak=   -3.288 closest distance to " OE1 GLN A 223 " =    1.983
peak=   -3.288 closest distance to " O   ALA A 292 " =    1.912
peak=   -3.286 closest distance to " N   ALA A  43 " =    2.550
peak=   -3.281 closest distance to " CG  GLU A   2 " =    2.086
peak=   -3.279 closest distance to " O   HOH Z 359 " =    3.293
peak=   -3.278 closest distance to " O   HOH Z  60 " =    1.908
peak=   -3.278 closest distance to " CB  ALA A 244 " =    2.035
peak=   -3.276 closest distance to " CB  CYS A 254 " =    2.256
peak=   -3.270 closest distance to " O   PRO A 198 " =    1.597
peak=   -3.267 closest distance to " O   HOH Z 166 " =    2.031
peak=   -3.266 closest distance to " O   HOH Z 137 " =    1.468
peak=   -3.264 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.263 closest distance to " O   HOH Z 213 " =    1.355
peak=   -3.261 closest distance to " O   HOH Z  51 " =    1.197
peak=   -3.255 closest distance to " OG  SER A 245 " =    1.337
peak=   -3.253 closest distance to " N   SER A 212 " =    1.957
peak=   -3.246 closest distance to " OE2 GLU A 152 " =    1.141
peak=   -3.246 closest distance to " CB  CYS A 201 " =    2.545
peak=   -3.245 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.242 closest distance to " CD  LYS A 289 " =    2.339
peak=   -3.239 closest distance to " CG  PRO A 243 " =    1.594
peak=   -3.236 closest distance to " O   HOH Z 326 " =    1.641
peak=   -3.234 closest distance to " O   HOH Z  38 " =    1.805
peak=   -3.231 closest distance to " C   LYS A  76 " =    1.628
peak=   -3.221 closest distance to " CE1 TYR A 169 " =    2.488
peak=   -3.221 closest distance to " O   HOH Z  93 " =    1.962
peak=   -3.219 closest distance to " O   HOH Z 111 " =    2.438
peak=   -3.217 closest distance to " N   THR A 157 " =    1.466
peak=   -3.212 closest distance to " O   ALA A 180 " =    1.188
peak=   -3.212 closest distance to " OH  TYR A 214 " =    1.249
peak=   -3.211 closest distance to " O   HOH Z 282 " =    1.352
peak=   -3.202 closest distance to " O   ASN A 249 " =    1.433
peak=   -3.201 closest distance to " CG  ARG A 269 " =    2.358
peak=   -3.194 closest distance to " OD2 ASP A  50 " =    1.519
peak=   -3.191 closest distance to " OD1 ASN A 176 " =    1.289
peak=   -3.191 closest distance to " O   ILE A 120 " =    1.509
peak=   -3.189 closest distance to " O   GLY A  80 " =    2.378
peak=   -3.185 closest distance to " O   HOH Z 234 " =    3.785
peak=   -3.185 closest distance to " O   ASP A 162 " =    2.115
peak=   -3.183 closest distance to " O   HOH Z 298 " =    2.380
peak=   -3.182 closest distance to " CB  ASP A 132 " =    2.232
peak=   -3.181 closest distance to " CE3 TRP A 123 " =    1.328
peak=   -3.175 closest distance to " OG1 THR A 178 " =    1.183
peak=   -3.174 closest distance to " O   HOH Z 137 " =    1.399
peak=   -3.168 closest distance to " O   HOH Z 418 " =    1.616
peak=   -3.168 closest distance to " O   HOH Z 281 " =    2.739
peak=   -3.167 closest distance to " OE1 GLN A 183 " =    1.401
peak=   -3.164 closest distance to " O   HOH Z 236 " =    2.001
peak=   -3.159 closest distance to " CD2 PHE A  61 " =    2.252
peak=   -3.158 closest distance to " O   HOH Z 111 " =    4.680
peak=   -3.150 closest distance to " N   PHE A  59 " =    1.802
peak=   -3.150 closest distance to " CB  ASP A 286 " =    1.761
peak=   -3.149 closest distance to " CG  TRP A 266 " =    1.883
peak=   -3.144 closest distance to " CB  ALA A 131 " =    1.909
peak=   -3.137 closest distance to " CG  GLN A  88 " =    0.810
peak=   -3.132 closest distance to " CD2 TYR A 293 " =    1.956
peak=   -3.129 closest distance to " CE  LYS A  76 " =    2.846
peak=   -3.128 closest distance to " OG ASER A 134 " =    1.056
peak=   -3.113 closest distance to " OD1 ASP A 200 " =    1.416
peak=   -3.113 closest distance to " O   THR A 220 " =    1.818
peak=   -3.105 closest distance to " O   HOH Z 414 " =    1.933
peak=   -3.104 closest distance to " CG1 VAL A 197 " =    2.087
peak=   -3.103 closest distance to " O   ALA A  34 " =    2.475
peak=   -3.102 closest distance to " CG  GLN A  58 " =    1.278
peak=   -3.083 closest distance to " O   HOH Z 394 " =    1.398
peak=   -3.080 closest distance to " CD2 LEU A 300 " =    2.805
peak=   -3.080 closest distance to " OE1 GLN A 194 " =    1.589
peak=   -3.076 closest distance to " O   HOH Z 357 " =    2.048
peak=   -3.073 closest distance to " CB  TRP A  85 " =    2.417
peak=   -3.051 closest distance to " O   HOH Z 288 " =    1.363
peak=   -3.030 closest distance to " OG  SER A  87 " =    1.652
peak=   -3.021 closest distance to " CB  ASN A  39 " =    2.034
peak=   -3.017 closest distance to " C   MET A 188 " =    1.486

================= 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    :  0.3900 0.3866   6.173587e+00   6.159770e+00
   1_bss:  0.3777 0.3733   6.159719e+00   6.134114e+00
   1_xyz:  0.2277 0.2549   5.735210e+00   5.829032e+00
   1_adp:  0.2083 0.2678   5.686303e+00   5.869430e+00
   1_occ:  0.2080 0.2674   5.684946e+00   5.868259e+00
   2_bss:  0.2051 0.2635   5.674532e+00   5.858035e+00
   2_xyz:  0.1509 0.1991   5.393359e+00   5.610047e+00
   2_adp:  0.1410 0.1848   5.329589e+00   5.538193e+00
   2_occ:  0.1407 0.1848   5.328745e+00   5.537753e+00
   3_bss:  0.1408 0.1844   5.325815e+00   5.532860e+00
   3_xyz:  0.1166 0.1602   5.162148e+00   5.390659e+00
   3_adp:  0.1119 0.1562   5.128601e+00   5.368282e+00
   3_occ:  0.1118 0.1561   5.128586e+00   5.368430e+00
   4_bss:  0.1121 0.1562   5.129048e+00   5.368677e+00
   4_xyz:  0.1121 0.1553   5.129627e+00   5.365482e+00
   4_adp:  0.1110 0.1563   5.128603e+00   5.372006e+00
   4_occ:  0.1109 0.1564   5.128620e+00   5.372148e+00
   5_bss:  0.1109 0.1563   5.128328e+00   5.371788e+00
   5_xyz:  0.1064 0.1544   5.102666e+00   5.360846e+00
   5_adp:  0.1061 0.1545   5.101217e+00   5.360947e+00
   5_occ:  0.1061 0.1545   5.101252e+00   5.361096e+00
   5_bss:  0.1060 0.1545   5.101297e+00   5.361102e+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:  0.329  22.656  -2.362   2.004  -0.662   0.000  -0.000  -0.000
   1_xyz:  0.329  22.656  -2.362   2.004  -0.662   0.000  -0.000  -0.000
   1_adp:  0.329  22.656  -2.362   2.004  -0.662   0.000  -0.000  -0.000
   1_occ:  0.329  22.656  -2.362   2.004  -0.662   0.000  -0.000  -0.000
   2_bss:  0.325  37.817  -2.688  -1.155  -1.402  -0.000  -0.000  -0.000
   2_xyz:  0.325  37.817  -2.688  -1.155  -1.402  -0.000  -0.000  -0.000
   2_adp:  0.325  37.817  -2.688  -1.155  -1.402  -0.000  -0.000  -0.000
   2_occ:  0.325  37.817  -2.688  -1.155  -1.402  -0.000  -0.000  -0.000
   3_bss:  0.321  38.466  -2.654  -2.031  -1.313  -0.000  -0.000  -0.000
   3_xyz:  0.321  38.466  -2.654  -2.031  -1.313  -0.000  -0.000  -0.000
   3_adp:  0.321  38.466  -2.654  -2.031  -1.313  -0.000  -0.000  -0.000
   3_occ:  0.321  38.466  -2.654  -2.031  -1.313  -0.000  -0.000  -0.000
   4_bss:  0.321  40.779  -2.814  -2.429  -1.493  -0.000  -0.000  -0.000
   4_xyz:  0.321  40.779  -2.814  -2.429  -1.493  -0.000  -0.000  -0.000
   4_adp:  0.321  40.779  -2.814  -2.429  -1.493  -0.000  -0.000  -0.000
   4_occ:  0.321  40.779  -2.814  -2.429  -1.493  -0.000  -0.000  -0.000
   5_bss:  0.320  42.535  -2.597  -2.306  -1.299  -0.000  -0.000  -0.000
   5_xyz:  0.320  42.535  -2.597  -2.306  -1.299  -0.000  -0.000  -0.000
   5_adp:  0.320  42.535  -2.597  -2.306  -1.299  -0.000  -0.000  -0.000
   5_occ:  0.320  42.535  -2.597  -2.306  -1.299  -0.000  -0.000  -0.000
   5_bss:  0.321  43.265  -2.395  -2.161  -1.095  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.801 0.6239  0.8203    44212.894
   1_bss:  40.470 0.6377  0.8251    40141.696
   1_xyz:  24.720 0.8164  0.9984    16908.512
   1_adp:  26.153 0.8004  0.9845    18337.007
   1_occ:  26.112 0.8008  0.9845    18262.099
   2_bss:  25.572 0.8062  0.9438    17604.979
   2_xyz:  18.845 0.8724  0.9917     9860.716
   2_adp:  16.964 0.8904  0.9996     8627.673
   2_occ:  16.951 0.8905  0.9994     8606.059
   3_bss:  16.843 0.8913  0.9910     8489.965
   3_xyz:  14.102 0.9135  1.0003     6317.211
   3_adp:  13.609 0.9177  0.9972     6071.676
   3_occ:  13.611 0.9176  0.9970     6068.866
   4_bss:  13.598 0.9177  0.9883     6078.406
   4_xyz:  13.450 0.9193  0.9876     6004.685
   4_adp:  13.523 0.9190  0.9818     6065.596
   4_occ:  13.525 0.9190  0.9817     6067.436
   5_bss:  13.515 0.9190  0.9884     6062.013
   5_xyz:  13.313 0.9205  0.9889     5933.899
   5_adp:  13.309 0.9205  0.9827     5927.935
   5_occ:  13.312 0.9205  0.9826     5930.274
   5_bss:  13.312 0.9205  0.9896     5931.616
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.6976e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.6976e-01
   1_xyz:   1.207  0.009  0.079 14.880  0.006  4.105   8.5584e-02
   1_adp:   1.207  0.009  0.079 14.880  0.006  4.105   8.5584e-02
   1_occ:   1.207  0.009  0.079 14.880  0.006  4.105   8.5584e-02
   2_bss:   1.207  0.009  0.079 14.880  0.006  4.105   8.5584e-02
   2_xyz:   0.946  0.005  0.067 14.243  0.004  4.109   5.2231e-02
   2_adp:   0.946  0.005  0.067 14.243  0.004  4.109   5.2231e-02
   2_occ:   0.946  0.005  0.067 14.243  0.004  4.109   5.2231e-02
   3_bss:   0.946  0.005  0.067 14.243  0.004  4.109   5.2231e-02
   3_xyz:   1.019  0.006  0.074 14.797  0.004  4.107   6.1071e-02
   3_adp:   1.019  0.006  0.074 14.797  0.004  4.107   6.1071e-02
   3_occ:   1.019  0.006  0.074 14.797  0.004  4.107   6.1071e-02
   4_bss:   1.019  0.006  0.074 14.797  0.004  4.107   6.1071e-02
   4_xyz:   0.854  0.004  0.065 14.258  0.004  4.107   4.6451e-02
   4_adp:   0.854  0.004  0.065 14.258  0.004  4.107   4.6451e-02
   4_occ:   0.854  0.004  0.065 14.258  0.004  4.107   4.6451e-02
   5_bss:   0.854  0.004  0.065 14.258  0.004  4.107   4.6451e-02
   5_xyz:   0.973  0.006  0.071 14.566  0.004  4.107   5.6559e-02
   5_adp:   0.973  0.006  0.071 14.566  0.004  4.107   5.6559e-02
   5_occ:   0.973  0.006  0.071 14.566  0.004  4.107   5.6559e-02
   5_bss:   0.973  0.006  0.071 14.566  0.004  4.107   5.6559e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.666   2.3779e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.666   2.3779e-01
   1_xyz:   7.885  0.067  0.350 88.537  0.052  2.153   7.7018e-02
   1_adp:   7.885  0.067  0.350 88.537  0.052  2.153   7.7018e-02
   1_occ:   7.885  0.067  0.350 88.537  0.052  2.153   7.7018e-02
   2_bss:   7.885  0.067  0.350 88.537  0.052  2.153   7.7018e-02
   2_xyz:   6.179  0.040  0.193 81.834  0.039  2.370   4.8647e-02
   2_adp:   6.179  0.040  0.193 81.834  0.039  2.370   4.8647e-02
   2_occ:   6.179  0.040  0.193 81.834  0.039  2.370   4.8647e-02
   3_bss:   6.179  0.040  0.193 81.834  0.039  2.370   4.8647e-02
   3_xyz:   6.547  0.040  0.234 84.904  0.034  2.281   4.9969e-02
   3_adp:   6.547  0.040  0.234 84.904  0.034  2.281   4.9969e-02
   3_occ:   6.547  0.040  0.234 84.904  0.034  2.281   4.9969e-02
   4_bss:   6.547  0.040  0.234 84.904  0.034  2.281   4.9969e-02
   4_xyz:   6.060  0.040  0.195 83.994  0.041  2.369   3.0451e-02
   4_adp:   6.060  0.040  0.195 83.994  0.041  2.369   3.0451e-02
   4_occ:   6.060  0.040  0.195 83.994  0.041  2.369   3.0451e-02
   5_bss:   6.060  0.040  0.195 83.994  0.041  2.369   3.0451e-02
   5_xyz:   6.458  0.036  0.230 84.061  0.036  2.278   5.1344e-02
   5_adp:   6.458  0.036  0.230 84.061  0.036  2.278   5.1344e-02
   5_occ:   6.458  0.036  0.230 84.061  0.036  2.278   5.1344e-02
   5_bss:   6.458  0.036  0.230 84.061  0.036  2.278   5.1344e-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:  82.64   0.00  17.64  78.71   0.00  13.48  82.64   6.89  40.31
   1_occ:  82.64   0.00  17.64  78.71   0.00  13.48  82.64   6.89  40.31
   2_bss:  82.64   0.00  17.64  78.71   0.00  13.48  82.64   6.89  40.31
   2_xyz:  82.64   0.00  17.64  78.71   0.00  13.48  82.64   6.89  40.31
   2_adp:  78.47   1.48  16.97  78.40   1.48  13.02  78.47   6.71  38.47
   2_occ:  78.47   1.48  16.97  78.40   1.48  13.02  78.47   6.71  38.47
   3_bss:  78.47   1.48  16.97  78.40   1.48  13.02  78.47   6.71  38.47
   3_xyz:  78.47   1.48  16.97  78.40   1.48  13.02  78.47   6.71  38.47
   3_adp:  82.98   0.49  17.05  82.98   0.49  12.89  81.17   3.70  39.73
   3_occ:  82.98   0.49  17.05  82.98   0.49  12.89  81.17   3.70  39.73
   4_bss:  82.98   0.49  17.05  82.98   0.49  12.89  81.17   3.70  39.73
   4_xyz:  82.98   0.49  17.05  82.98   0.49  12.89  81.17   3.70  39.73
   4_adp:  91.80   0.00  17.26  91.80   0.00  12.91  85.73   4.98  40.90
   4_occ:  91.80   0.00  17.26  91.80   0.00  12.91  85.73   4.98  40.90
   5_bss:  91.80   0.00  17.26  91.80   0.00  12.91  85.73   4.98  40.90
   5_xyz:  91.80   0.00  17.26  91.80   0.00  12.91  85.73   4.98  40.90
   5_adp:  95.30   0.00  17.09  95.30   0.00  12.76  87.88   5.97  40.65
   5_occ:  95.30   0.00  17.09  95.30   0.00  12.76  87.88   5.97  40.65
   5_bss:  95.30   0.00  17.09  95.30   0.00  12.77  87.89   5.97  40.66
------------------------------------------------------------------------
 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:    1.585    0.019    0.389
   1_adp:    1.585    0.019    0.389
   1_occ:    1.585    0.019    0.389
   2_bss:    1.585    0.019    0.389
   2_xyz:    0.986    0.023    0.456
   2_adp:    0.986    0.023    0.456
   2_occ:    0.986    0.023    0.456
   3_bss:    0.986    0.023    0.456
   3_xyz:    1.010    0.070    0.526
   3_adp:    1.010    0.070    0.526
   3_occ:    1.010    0.070    0.526
   4_bss:    1.010    0.070    0.526
   4_xyz:    1.086    0.090    0.534
   4_adp:    1.086    0.090    0.534
   4_occ:    1.086    0.090    0.534
   5_bss:    1.086    0.090    0.534
   5_xyz:    1.141    0.089    0.549
   5_adp:    1.141    0.089    0.549
   5_occ:    1.141    0.089    0.549
   5_bss:    1.141    0.089    0.549
------------------------------------------------------------------------

CPU time actual refinement: 340.07


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/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_388/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_388/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.92 
  Macro-tasks:
    bulk solvent and scale       = 44.13  
    individual site refinement   = 142.41 
    weights calculation          = 28.74  
    collect and process          = 6.52   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 221.92 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 107.06 
    alpha_beta                      = 8.28   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 117.38 
    fmodel                         = 7.26   
    r_factors                      = 0.28   
    phase_errors                   = 11.01  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 254.44 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.722 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    661 calls, 106.65 s
gradients_fft:          606 calls, 103.15 s

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

# Date 2008-01-16 Time 04:42:59 PST -0800 (1200487379.41 s)
Start R-work = 0.3900, R-free = 0.3866 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1737 (no bulk solvent and anisotropic scale)

Start R-work = 0.3777, R-free = 0.3733
Final R-work = 0.1060, R-free = 0.1545