# Date 2008-01-16 Time 05:31:47 PST -0800 (1200490307.40 s)
#phil __OFF__

Command line arguments: "../774.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6922
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 774

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99038
Completeness in resolution range: 0.976472
Completeness with d_max=infinity: 0.973463

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.99038
Completeness in resolution range: 0.976472
Completeness with d_max=infinity: 0.973463

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2587 [2099/2124]  1889   210  10.0%
  bin  2:  4.2587 -  3.3930 [2031/2051]  1828   203  10.0%
  bin  3:  3.3930 -  2.9679 [1998/2017]  1796   202  10.1%
  bin  4:  2.9679 -  2.6982 [1971/2001]  1777   194   9.8%
  bin  5:  2.6982 -  2.5058 [1980/1999]  1783   197   9.9%
  bin  6:  2.5058 -  2.3586 [1955/1980]  1760   195  10.0%
  bin  7:  2.3586 -  2.2409 [1945/1973]  1745   200  10.3%
  bin  8:  2.2409 -  2.1437 [1944/1980]  1751   193   9.9%
  bin  9:  2.1437 -  2.0613 [1933/1975]  1745   188   9.7%
  bin 10:  2.0613 -  1.9904 [1733/1961]  1556   177  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/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:
        1.81 -     2.42: 9
        2.42 -     3.04: 2207
        3.04 -     3.66: 4677
        3.66 -     4.28: 9087
        4.28 -     4.90: 12349
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.377 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 341 " - " O   HOH Z 207 "  2.377 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28324 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_774/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 85.95805 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: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2307   r_free= 0.2308   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.721157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7497 0.99   1372  152 0.2540 0.2465      6.2586      6.1889|
|  2:  4.7497 -  3.7899 0.99   1316  146 0.1796 0.1825      6.1073      6.1068|
|  3:  3.7899 -  3.3167 0.99   1286  144 0.1848 0.1856      5.9617         6.1|
|  4:  3.3167 -  3.0161 0.99   1279  144 0.1967 0.2060      5.8619      5.8679|
|  5:  3.0161 -  2.8015 0.99   1279  141 0.2208 0.2108      5.7502      5.7738|
|  6:  2.8015 -  2.6372 0.99   1269  139 0.2282 0.2400       5.698      5.6696|
|  7:  2.6372 -  2.5058 0.99   1272  140 0.2387 0.2270      5.6705      5.6571|
|  8:  2.5058 -  2.3972 0.98   1253  143 0.2460 0.2392      5.6546       5.645|
|  9:  2.3972 -  2.3052 0.98   1243  134 0.2358 0.2464      5.5598      5.5541|
| 10:  2.3052 -  2.2259 1.00   1250  144 0.2447 0.2344      5.5665      5.4974|
| 11:  2.2259 -  2.1565 0.97   1259  136 0.2521 0.2473      5.5421      5.5517|
| 12:  2.1565 -  2.0951 0.98   1231  138 0.2527 0.2529      5.4916      5.5525|
| 13:  2.0951 -  2.0400 0.99   1246  142 0.2622 0.2684      5.4377      5.4334|
| 14:  2.0400 -  1.9904 0.84   1075  116 0.2633 0.2662      5.4052      5.3019|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7497  1372   152  0.82  23.10   0.87     0.83      33774.32|
|  2:  4.7497 -  3.7899  1316   146  0.89  16.73   1.00     0.95      27328.70|
|  3:  3.7899 -  3.3167  1286   144  0.89  17.54   1.03     1.01      22071.28|
|  4:  3.3167 -  3.0161  1279   144  0.89  17.90   1.03     1.02      17677.29|
|  5:  3.0161 -  2.8015  1279   141  0.86  20.50   1.03     1.01      14065.86|
|  6:  2.8015 -  2.6372  1269   139  0.87  20.27   1.04     1.01      11728.51|
|  7:  2.6372 -  2.5058  1272   140  0.86  20.92   1.05     1.03      10689.32|
|  8:  2.5058 -  2.3972  1253   143  0.86  21.18   1.06     1.04      10062.00|
|  9:  2.3972 -  2.3052  1243   134  0.86  21.02   1.08     1.05       9297.94|
| 10:  2.3052 -  2.2259  1250   144  0.85  21.83   1.10     1.07       9004.78|
| 11:  2.2259 -  2.1565  1259   136  0.84  23.14   1.11     1.07       8873.17|
| 12:  2.1565 -  2.0951  1231   138  0.84  23.24   1.11     1.08       8549.43|
| 13:  2.0951 -  2.0400  1246   142  0.83  24.28   1.11     1.06       7413.69|
| 14:  2.0400 -  1.9904  1075   116  0.84  22.72   1.10     1.03       5661.82|
|alpha:            min =        0.83 max =            1.08 mean =         1.02|
|beta:             min =     5661.82 max =        33774.32 mean =     14305.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.98 mean =        20.99|
|phase err.(test): min =        0.00 max =           89.92 mean =        20.76|
|-----------------------------------------------------------------------------|

============================== 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 = 2.761093              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.470   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.367301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.337   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      207 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2000 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1842 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2835 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4683 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4404 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5608 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6741 |
|-----------------------------------------------------------------------------|
|-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 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.139 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    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: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2307   r_free= 0.2308   ksol= 0.00   Bsol= 0.00   scale= 1.007    |
|                                                                             |
| 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:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.721157                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2125   r_free= 0.2124   ksol= 0.33   Bsol= 45.96   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.06,-1.45,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.683636                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.507133              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.700   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.215   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.2124      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3630 = 2.51 * 0.50 * 5.7463 + 1.00 * 0.1596                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8048 = 2.51 * 0.50 * 5.3828 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9803 = 0.18 * 1.00 * 5.3828 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9937 = 0.18 * 1.00 * 5.1859 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.07   16.23    None  None   None       |
|    all(noH): 2823   0      0.00    73.07   16.23    None  None   None       |
|    Sol.    : 438    0      6.65    62.44   36.90    None  None   None       |
|    Mac.    : 2385   0      0.00    73.07   12.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.307:  247   |   5:    36.537 -  43.844:  116        |
|      1:     7.307 -  14.615: 1618   |   6:    43.844 -  51.151:   80        |
|      2:    14.615 -  21.922:  441   |   7:    51.151 -  58.459:   55        |
|      3:    21.922 -  29.229:  143   |   8:    58.459 -  65.766:   10        |
|      4:    29.229 -  36.537:  112   |   9:    65.766 -  73.073:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1248 r_free = 0.1523             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1523             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1523   ksol= 0.33   Bsol= 45.96   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-2.06,-1.45,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.185002                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1248   r_free= 0.1520   ksol= 0.32   Bsol= 47.63   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.69,-1.73,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.187295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.685885              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.314935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.560   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1477          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0278 = 2.69 * 0.50 * 5.1907 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9590 = 2.69 * 0.50 * 5.1299 + 1.00 * 0.0698                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1125      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1477      final r-factor (free) = 0.1483          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6570 = 0.31 * 1.00 * 5.1299 + 1.00 * 0.0414                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6088 = 0.31 * 1.00 * 5.0849 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    71.76   16.71    None  None   None       |
|    all(noH): 2823   0      1.68    71.76   16.71    None  None   None       |
|    Sol.    : 438    0      4.81    69.93   37.93    None  None   None       |
|    Mac.    : 2385   0      1.68    71.76   12.82    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:     1.677 -   8.685:  649   |   5:    36.716 -  43.724:  115        |
|      1:     8.685 -  15.693: 1290   |   6:    43.724 -  50.732:   77        |
|      2:    15.693 -  22.701:  356   |   7:    50.732 -  57.740:   76        |
|      3:    22.701 -  29.709:  117   |   8:    57.740 -  64.748:   28        |
|      4:    29.709 -  36.716:  108   |   9:    64.748 -  71.755:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1483             target_work(ml) = 5.090         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1074 r_free = 0.1484             target_work(ml) = 5.090         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1074   r_free= 0.1484   ksol= 0.32   Bsol= 47.63   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-2.69,-1.73,-0.00,-0.00,-0.00); trace/3= -2.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.090282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1483   ksol= 0.32   Bsol= 47.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.48,-1.47,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.090359                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.408757              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.920  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268053              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1073      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1483      final r-factor (free) = 0.1497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1959 = 2.41 * 0.50 * 5.0866 + 1.00 * 0.0698                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1917 = 2.41 * 0.50 * 5.0871 + 1.00 * 0.0649                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1503          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3710 = 0.27 * 1.00 * 5.0871 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3718 = 0.27 * 1.00 * 5.0894 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    74.23   16.59    None  None   None       |
|    all(noH): 2823   0      1.50    74.23   16.59    None  None   None       |
|    Sol.    : 438    0      5.98    70.54   37.62    None  None   None       |
|    Mac.    : 2385   0      1.50    74.23   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.503 -   8.775:  708   |   5:    37.864 -  45.136:  111        |
|      1:     8.775 -  16.047: 1251   |   6:    45.136 -  52.409:   83        |
|      2:    16.047 -  23.320:  349   |   7:    52.409 -  59.681:   61        |
|      3:    23.320 -  30.592:  124   |   8:    59.681 -  66.953:   19        |
|      4:    30.592 -  37.864:  111   |   9:    66.953 -  74.225:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1061 r_free = 0.1503             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1060 r_free = 0.1504             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1060   r_free= 0.1504   ksol= 0.32   Bsol= 47.63   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.48,-1.47,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1059   r_free= 0.1505   ksol= 0.32   Bsol= 47.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.32,-1.28,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.950964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.929  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265632              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.011  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0305 = 1.95 * 0.50 * 5.0904 + 1.00 * 0.0649                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0311 = 1.95 * 0.50 * 5.0982 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1072      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1521      final r-factor (free) = 0.1521          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3618 = 0.27 * 1.00 * 5.0982 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3633 = 0.27 * 1.00 * 5.1036 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    74.96   16.45    None  None   None       |
|    all(noH): 2823   0      1.30    74.96   16.45    None  None   None       |
|    Sol.    : 438    0      6.41    70.59   37.44    None  None   None       |
|    Mac.    : 2385   0      1.30    74.96   12.60    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:     1.300 -   8.667:  729   |   5:    38.132 -  45.499:  113        |
|      1:     8.667 -  16.033: 1242   |   6:    45.499 -  52.865:   83        |
|      2:    16.033 -  23.400:  343   |   7:    52.865 -  60.232:   55        |
|      3:    23.400 -  30.766:  124   |   8:    60.232 -  67.598:   19        |
|      4:    30.766 -  38.132:  109   |   9:    67.598 -  74.965:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1071 r_free = 0.1521             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1071 r_free = 0.1522             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1522   ksol= 0.32   Bsol= 47.63   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,-2.32,-1.28,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1522   ksol= 0.32   Bsol= 47.63   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.20,-1.14,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105233                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.865570              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 169.801  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.180038              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.186  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1047          |
| start r-factor (free) = 0.1522      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3707 = 2.87 * 0.50 * 5.1042 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3688 = 2.87 * 0.50 * 5.0955 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1047      final r-factor (work) = 0.1053          |
| start r-factor (free) = 0.1524      final r-factor (free) = 0.1524          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9250 = 0.18 * 1.00 * 5.0955 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9244 = 0.18 * 1.00 * 5.0955 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.51    75.63   16.14    None  None   None       |
|    all(noH): 2823   0      1.51    75.63   16.14    None  None   None       |
|    Sol.    : 438    0      6.30    69.70   36.41    None  None   None       |
|    Mac.    : 2385   0      1.51    75.63   12.42    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:     1.509 -   8.921:  813   |   5:    38.568 -  45.980:  108        |
|      1:     8.921 -  16.332: 1199   |   6:    45.980 -  53.392:   83        |
|      2:    16.332 -  23.744:  313   |   7:    53.392 -  60.804:   38        |
|      3:    23.744 -  31.156:  130   |   8:    60.804 -  68.216:   12        |
|      4:    31.156 -  38.568:  123   |   9:    68.216 -  75.628:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1053 r_free = 0.1524             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1052 r_free = 0.1525             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1525   ksol= 0.32   Bsol= 47.63   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-2.20,-1.14,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095650                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7497 0.99   1372  152 0.0980 0.1275      5.3743      5.5093|
|  2:  4.7497 -  3.7899 0.99   1316  146 0.0844 0.1144       5.432      5.6375|
|  3:  3.7899 -  3.3167 0.99   1286  144 0.1018 0.1486      5.4541       5.848|
|  4:  3.3167 -  3.0161 0.99   1279  144 0.1155 0.1498      5.4258      5.5605|
|  5:  3.0161 -  2.8015 0.99   1279  141 0.1243 0.1703      5.2884      5.5424|
|  6:  2.8015 -  2.6372 0.99   1269  139 0.1116 0.1745        5.17      5.3747|
|  7:  2.6372 -  2.5058 0.99   1272  140 0.1189 0.1575      5.1182      5.3655|
|  8:  2.5058 -  2.3972 0.98   1253  143 0.1067 0.1656      5.0018      5.3079|
|  9:  2.3972 -  2.3052 0.98   1243  134 0.1057 0.1545      4.9644      5.1702|
| 10:  2.3052 -  2.2259 1.00   1250  144 0.1014 0.1752      4.9012      5.2546|
| 11:  2.2259 -  2.1565 0.97   1259  136 0.1065 0.1660       4.895      5.2022|
| 12:  2.1565 -  2.0951 0.98   1231  138 0.1029 0.1691      4.8251      5.1938|
| 13:  2.0951 -  2.0400 0.99   1246  142 0.1016 0.1614      4.7383      5.0316|
| 14:  2.0400 -  1.9904 0.84   1075  116 0.0993 0.1627      4.6091      4.8591|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7497  1372   152  0.94   9.07   0.98     0.95       6982.80|
|  2:  4.7497 -  3.7899  1316   146  0.95   7.85   1.01     1.00       8999.80|
|  3:  3.7899 -  3.3167  1286   144  0.94  10.84   1.02     1.01      10051.14|
|  4:  3.3167 -  3.0161  1279   144  0.92  13.05   1.00     0.99       9882.37|
|  5:  3.0161 -  2.8015  1279   141  0.91  15.23   0.99     0.96       7813.02|
|  6:  2.8015 -  2.6372  1269   139  0.91  14.98   0.98     0.96       6623.87|
|  7:  2.6372 -  2.5058  1272   140  0.91  15.02   0.98     0.96       5723.02|
|  8:  2.5058 -  2.3972  1253   143  0.92  13.81   0.99     0.97       4618.11|
|  9:  2.3972 -  2.3052  1243   134  0.92  13.91   1.00     0.97       4399.19|
| 10:  2.3052 -  2.2259  1250   144  0.92  13.91   1.00     0.96       3869.55|
| 11:  2.2259 -  2.1565  1259   136  0.90  15.92   1.00     0.96       4096.34|
| 12:  2.1565 -  2.0951  1231   138  0.92  14.00   1.00     0.99       3565.54|
| 13:  2.0951 -  2.0400  1246   142  0.92  14.41   1.00     1.00       3038.62|
| 14:  2.0400 -  1.9904  1075   116  0.92  13.37   0.97     0.94       2256.91|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2256.91 max =        10051.14 mean =      5928.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.19|
|phase err.(test): min =        0.00 max =           88.24 mean =        12.72|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1526   ksol= 0.32   Bsol= 47.57   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.02,-0.94,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095774                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1052   r_free= 0.1526   ksol= 0.32   Bsol= 47.57   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-2.02,-0.94,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095774                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7497 0.99   1372  152 0.0981 0.1277      5.3756      5.5108|
|  2:  4.7497 -  3.7899 0.99   1316  146 0.0843 0.1143      5.4322      5.6371|
|  3:  3.7899 -  3.3167 0.99   1286  144 0.1018 0.1487       5.454      5.8482|
|  4:  3.3167 -  3.0161 0.99   1279  144 0.1155 0.1499      5.4258      5.5606|
|  5:  3.0161 -  2.8015 0.99   1279  141 0.1243 0.1702      5.2884      5.5423|
|  6:  2.8015 -  2.6372 0.99   1269  139 0.1116 0.1745        5.17      5.3745|
|  7:  2.6372 -  2.5058 0.99   1272  140 0.1189 0.1576      5.1183      5.3656|
|  8:  2.5058 -  2.3972 0.98   1253  143 0.1067 0.1656      5.0019      5.3077|
|  9:  2.3972 -  2.3052 0.98   1243  134 0.1057 0.1545      4.9645      5.1702|
| 10:  2.3052 -  2.2259 1.00   1250  144 0.1014 0.1753      4.9013      5.2548|
| 11:  2.2259 -  2.1565 0.97   1259  136 0.1065 0.1661      4.8951      5.2023|
| 12:  2.1565 -  2.0951 0.98   1231  138 0.1029 0.1691      4.8251      5.1939|
| 13:  2.0951 -  2.0400 0.99   1246  142 0.1016 0.1613      4.7383      5.0314|
| 14:  2.0400 -  1.9904 0.84   1075  116 0.0993 0.1627      4.6091      4.8589|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7497  1372   152  0.94   9.08   0.98     0.95       7005.55|
|  2:  4.7497 -  3.7899  1316   146  0.95   7.87   1.02     1.00       9011.52|
|  3:  3.7899 -  3.3167  1286   144  0.94  10.84   1.02     1.01      10049.35|
|  4:  3.3167 -  3.0161  1279   144  0.92  13.05   1.01     0.99       9881.82|
|  5:  3.0161 -  2.8015  1279   141  0.91  15.23   0.99     0.96       7811.84|
|  6:  2.8015 -  2.6372  1269   139  0.91  14.98   0.99     0.96       6623.64|
|  7:  2.6372 -  2.5058  1272   140  0.91  15.02   0.99     0.96       5723.12|
|  8:  2.5058 -  2.3972  1253   143  0.92  13.81   1.00     0.98       4617.99|
|  9:  2.3972 -  2.3052  1243   134  0.92  13.92   1.01     0.98       4399.68|
| 10:  2.3052 -  2.2259  1250   144  0.92  13.91   1.00     0.97       3870.28|
| 11:  2.2259 -  2.1565  1259   136  0.90  15.92   1.00     0.97       4097.61|
| 12:  2.1565 -  2.0951  1231   138  0.92  14.00   1.01     1.00       3565.63|
| 13:  2.0951 -  2.0400  1246   142  0.92  14.41   1.01     1.00       3038.21|
| 14:  2.0400 -  1.9904  1075   116  0.92  13.37   0.98     0.95       2256.41|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2256.41 max =        10049.35 mean =      5930.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.20|
|phase err.(test): min =        0.00 max =           88.23 mean =        12.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.870)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.46    75.57   16.09    None  None   None       |
|    all(noH): 2823   0      1.46    75.57   16.09    None  None   None       |
|    Sol.    : 438    0      6.24    69.65   36.36    None  None   None       |
|    Mac.    : 2385   0      1.46    75.57   12.37    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:     1.455 -   8.867:  813   |   5:    38.514 -  45.926:  108        |
|      1:     8.867 -  16.279: 1199   |   6:    45.926 -  53.338:   83        |
|      2:    16.279 -  23.691:  313   |   7:    53.338 -  60.750:   38        |
|      3:    23.691 -  31.103:  130   |   8:    60.750 -  68.162:   12        |
|      4:    31.103 -  38.514:  123   |   9:    68.162 -  75.574:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 274         
Filter by distance & map next to the model:
   mapped sites are within: 0.560 - 4.710
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 274
   mapped sites are within: 0.701 - 4.710

peak=    5.491 closest distance to " NH2 ARG A  56 " =    2.180
peak=    5.473 closest distance to " O   HOH Z 126 " =    1.871
peak=    5.461 closest distance to " CG  PRO A  54 " =    1.277
peak=    5.272 closest distance to " CB  SER A  63 " =    1.185
peak=    5.054 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.987 closest distance to " NE2 GLN A  11 " =    1.130
peak=    4.925 closest distance to " O   HOH Z 232 " =    2.370
peak=    4.897 closest distance to " C   PRO A 198 " =    1.460
peak=    4.856 closest distance to " O   HOH Z 236 " =    1.948
peak=    4.822 closest distance to " CB  GLN A 223 " =    1.433
peak=    4.780 closest distance to " CB  GLN A 183 " =    1.140
peak=    4.741 closest distance to " CB  GLU A 152 " =    1.173
peak=    4.719 closest distance to " O   HOH Z 144 " =    1.731
peak=    4.577 closest distance to " O   HOH Z  15 " =    2.232
peak=    4.553 closest distance to " O   HOH Z  78 " =    1.765
peak=    4.541 closest distance to " CB  ARG A  79 " =    1.335
peak=    4.452 closest distance to " ND2 ASN A 187 " =    1.504
peak=    4.450 closest distance to " O   HOH Z 298 " =    1.898
peak=    4.436 closest distance to " O   HOH Z 193 " =    1.925
peak=    4.394 closest distance to " O   HOH Z 369 " =    2.053
peak=    4.351 closest distance to " OD1 ASN A  69 " =    2.614
peak=    4.330 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.310 closest distance to " O   HOH Z 234 " =    3.683
peak=    4.303 closest distance to " O   HOH Z 303 " =    2.082
peak=    4.295 closest distance to " CB  PRO A  54 " =    0.917
peak=    4.252 closest distance to " CB  ASN A 148 " =    1.587
peak=    4.238 closest distance to " O   HOH Z 158 " =    3.012
peak=    4.189 closest distance to " O   HOH Z 427 " =    2.850
peak=    4.151 closest distance to " CB  TYR A 169 " =    0.701
peak=    4.142 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.060 closest distance to " CB  SER A   3 " =    1.342
peak=    4.053 closest distance to " O   HOH Z 197 " =    3.197
peak=    4.041 closest distance to " O   HOH Z 261 " =    2.196
peak=    4.040 closest distance to " O   HOH Z 250 " =    1.497
peak=    4.033 closest distance to " O   HOH Z 346 " =    1.646
peak=    4.027 closest distance to " O   HOH Z 193 " =    1.708
peak=    4.027 closest distance to " O   HOH Z  61 " =    1.624
peak=    4.024 closest distance to " O   HOH Z 403 " =    1.642
peak=    4.010 closest distance to " CB  ARG A 190 " =    1.576
peak=    4.003 closest distance to " O   HOH Z 203 " =    1.737
peak=    3.993 closest distance to " O   HOH Z 209 " =    2.366
peak=    3.988 closest distance to " CA  ASN A 215 " =    1.196
peak=    3.972 closest distance to " O   HOH Z  10 " =    1.847
peak=    3.970 closest distance to " O   HOH Z 189 " =    2.272
peak=    3.965 closest distance to " O   HOH Z 389 " =    1.902
peak=    3.958 closest distance to " O   HOH Z  78 " =    2.127
peak=    3.938 closest distance to " O   SER A  87 " =    2.227
peak=    3.936 closest distance to " O   HOH Z 316 " =    3.104
peak=    3.932 closest distance to " CG2 VAL A 257 " =    0.945
peak=    3.908 closest distance to " O   HOH Z 344 " =    3.208
peak=    3.885 closest distance to " O   HOH Z 272 " =    1.835
peak=    3.865 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.855 closest distance to " NZ  LYS A 117 " =    3.300
peak=    3.838 closest distance to " O   HOH Z  40 " =    1.702
peak=    3.838 closest distance to " CG  PRO A 243 " =    1.061
peak=    3.834 closest distance to " O   HOH Z   1 " =    1.988
peak=    3.833 closest distance to " CD2 TRP A 179 " =    1.334
peak=    3.832 closest distance to " O   HOH Z 248 " =    1.647
peak=    3.814 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.812 closest distance to " O   HOH Z 426 " =    1.598
peak=    3.807 closest distance to " CB  TRP A 266 " =    0.925
peak=    3.802 closest distance to " CE  LYS A  76 " =    0.901
peak=    3.789 closest distance to " O   HOH Z  66 " =    2.146
peak=    3.789 closest distance to " O   HOH Z 214 " =    2.017
peak=    3.780 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.776 closest distance to " CB  GLU A 128 " =    1.013
peak=    3.775 closest distance to " O   HOH Z   9 " =    2.043
peak=    3.775 closest distance to " O   HOH Z  21 " =    1.772
peak=    3.772 closest distance to " NH1AARG A 145 " =    1.185
peak=    3.771 closest distance to " O   HOH Z 291 " =    1.576
peak=    3.765 closest distance to " O   HOH Z 368 " =    1.996
peak=    3.764 closest distance to " CB  TYR A 169 " =    0.797
peak=    3.760 closest distance to " O   HOH Z 219 " =    2.113
peak=    3.746 closest distance to " O   HOH Z 213 " =    1.754
peak=    3.742 closest distance to " OD2 ASP A 286 " =    2.864
peak=    3.706 closest distance to " O   HOH Z 402 " =    1.457
peak=    3.694 closest distance to " O   HOH Z 425 " =    2.090
peak=    3.693 closest distance to " O   HOH Z  61 " =    1.507
peak=    3.692 closest distance to " CA  THR A 264 " =    0.896
peak=    3.691 closest distance to " O   HOH Z 265 " =    2.375
peak=    3.684 closest distance to " O   HOH Z 423 " =    1.861
peak=    3.683 closest distance to " CD  ARG A  66 " =    2.422
peak=    3.669 closest distance to " O   HOH Z 133 " =    1.574
peak=    3.667 closest distance to " CB  SER A 212 " =    1.110
peak=    3.665 closest distance to " O   HOH Z 305 " =    3.525
peak=    3.654 closest distance to " O   HOH Z 132 " =    2.484
peak=    3.652 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.650 closest distance to " O   HOH Z 128 " =    2.219
peak=    3.638 closest distance to " CG  PRO A 198 " =    1.289
peak=    3.637 closest distance to " CA  ALA A  51 " =    0.888
peak=    3.636 closest distance to " CB  TRP A 179 " =    1.359
peak=    3.632 closest distance to " CB  VAL A 202 " =    1.557
peak=    3.630 closest distance to " O   HOH Z 128 " =    2.133
peak=    3.630 closest distance to " O   HOH Z  43 " =    1.879
peak=    3.616 closest distance to " CZ  PHE A 218 " =    1.020
peak=    3.613 closest distance to " ND2 ASN A 110 " =    1.807
peak=    3.608 closest distance to " CG1BVAL A  72 " =    1.617
peak=    3.607 closest distance to " CD  ARG A 159 " =    0.732
peak=    3.605 closest distance to " CD1 LEU A 300 " =    1.281
peak=    3.601 closest distance to " CB  ASN A 142 " =    0.968
peak=    3.595 closest distance to " O   HOH Z 147 " =    1.791
peak=    3.593 closest distance to " CG2 THR A 221 " =    1.101
peak=    3.589 closest distance to " CA  ALA A  21 " =    1.165
peak=    3.589 closest distance to " O   HOH Z 368 " =    3.594
peak=    3.582 closest distance to " CD  ARG A  66 " =    2.350
peak=    3.581 closest distance to " CA  THR A 221 " =    0.988
peak=    3.580 closest distance to " CD2 LEU A 255 " =    1.445
peak=    3.577 closest distance to " O   HOH Z 371 " =    3.006
peak=    3.568 closest distance to " O   HOH Z 419 " =    1.960
peak=    3.566 closest distance to " CB  GLU A 277 " =    3.525
peak=    3.566 closest distance to " CB  ASN A 224 " =    1.044
peak=    3.560 closest distance to " NH2BARG A 145 " =    2.122
peak=    3.555 closest distance to " CG1 ILE A  33 " =    1.226
peak=    3.554 closest distance to " CB  MET A  40 " =    0.849
peak=    3.552 closest distance to " O   HOH Z 172 " =    3.243
peak=    3.549 closest distance to " O   HOH Z 175 " =    2.204
peak=    3.542 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.540 closest distance to " CB  ALA A  34 " =    0.980
peak=    3.534 closest distance to " CG2 ILE A 120 " =    1.253
peak=    3.532 closest distance to " O   HOH Z 234 " =    1.773
peak=    3.528 closest distance to " O   HOH Z  93 " =    2.571
peak=    3.523 closest distance to " O   HOH Z  54 " =    1.643
peak=    3.523 closest distance to " CD1 ILE A 106 " =    0.836
peak=    3.518 closest distance to " O   HOH Z 417 " =    3.185
peak=    3.517 closest distance to " CB  ARG A 139 " =    0.979
peak=    3.516 closest distance to " O   HOH Z 407 " =    2.343
peak=    3.510 closest distance to " N   ARG A 156 " =    1.279
peak=    3.505 closest distance to " O   HOH Z  44 " =    1.764
peak=    3.500 closest distance to " O   HOH Z  19 " =    2.487
peak=    3.494 closest distance to " O   HOH Z 280 " =    3.027
peak=    3.486 closest distance to " O   HOH Z 148 " =    3.307
peak=    3.484 closest distance to " O   HOH Z 173 " =    1.843
peak=    3.482 closest distance to " CB  SER A 141 " =    1.049
peak=    3.481 closest distance to " O   HOH Z 273 " =    2.691
peak=    3.471 closest distance to " O   HOH Z 199 " =    1.581
peak=    3.470 closest distance to " CA  ALA A 233 " =    1.201
peak=    3.467 closest distance to " CB  ALA A 291 " =    1.424
peak=    3.465 closest distance to " CB  THR A 157 " =    1.094
peak=    3.462 closest distance to " CA  ALA A  84 " =    1.324
peak=    3.461 closest distance to " CD2 LEU A 297 " =    0.842
peak=    3.460 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.457 closest distance to " ND1 HIS A  86 " =    1.672
peak=    3.452 closest distance to " CB  LEU A 143 " =    1.103
peak=    3.452 closest distance to " O   HOH Z 166 " =    3.805
peak=    3.444 closest distance to " CB  SER A 216 " =    0.792
peak=    3.442 closest distance to " O   HOH Z 313 " =    1.974
peak=    3.429 closest distance to " NH2 ARG A 156 " =    1.130
peak=    3.428 closest distance to " O   MET A 105 " =    1.810
peak=    3.426 closest distance to " CA  SER A  87 " =    0.995
peak=    3.425 closest distance to " O   HOH Z  64 " =    2.182
peak=    3.420 closest distance to " O   HOH Z  40 " =    1.800
peak=    3.417 closest distance to " CB  ILE A 120 " =    1.206
peak=    3.416 closest distance to " O   HOH Z 188 " =    2.107
peak=    3.401 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.399 closest distance to " CB  GLN A 278 " =    0.855
peak=    3.397 closest distance to " O   HOH Z 263 " =    1.727
peak=    3.395 closest distance to " OE1 GLU A   2 " =    2.171
peak=    3.391 closest distance to " O   HOH Z  88 " =    3.130
peak=    3.390 closest distance to " OG BSER A 164 " =    2.337
peak=    3.384 closest distance to " CD BLYS A 290 " =    1.273
peak=    3.381 closest distance to " CG  LYS A  76 " =    0.970
peak=    3.378 closest distance to " O   HOH Z 261 " =    2.273
peak=    3.376 closest distance to " O   HOH Z 133 " =    2.456
peak=    3.368 closest distance to " O   HOH Z 295 " =    1.562
peak=    3.366 closest distance to " O   HOH Z 286 " =    2.285
peak=    3.365 closest distance to " OG  SER A 206 " =    1.313
peak=    3.358 closest distance to " CA  ALA A  43 " =    1.224
peak=    3.351 closest distance to " CA  ALA A 248 " =    1.245
peak=    3.348 closest distance to " N   PHE A 130 " =    1.281
peak=    3.347 closest distance to " CG  GLN A  77 " =    2.052
peak=    3.343 closest distance to " O   HOH Z 345 " =    3.433
peak=    3.338 closest distance to " O   HOH Z 281 " =    4.135
peak=    3.338 closest distance to " O  BHOH Z 338 " =    2.338
peak=    3.336 closest distance to " CD  LYS A 166 " =    1.203
peak=    3.336 closest distance to " O   HOH Z 329 " =    3.814
peak=    3.328 closest distance to " OG  SER A  97 " =    3.665
peak=    3.326 closest distance to " CB  GLN A  88 " =    1.219
peak=    3.322 closest distance to " O   HOH Z 227 " =    1.710
peak=    3.320 closest distance to " CB  ALA A   1 " =    4.710
peak=    3.319 closest distance to " CG1 VAL A 153 " =    0.934
peak=    3.318 closest distance to " OG  SER A  22 " =    2.709
peak=    3.317 closest distance to " CZ2 TRP A 179 " =    1.755
peak=    3.314 closest distance to " O   HOH Z 337 " =    3.677
peak=    3.313 closest distance to " ND1 HIS A  81 " =    1.640
peak=    3.309 closest distance to " CB  ASN A 110 " =    1.092
peak=    3.308 closest distance to " O   HOH Z 213 " =    2.006
peak=    3.306 closest distance to " O   HOH Z 371 " =    1.790
peak=    3.303 closest distance to " CD  ARG A 219 " =    1.127
peak=    3.301 closest distance to " O   HOH Z 185 " =    1.759
peak=    3.292 closest distance to " O   HOH Z 435 " =    1.893
peak=    3.291 closest distance to " CG  LEU A 167 " =    1.258
peak=    3.291 closest distance to " O   HOH Z 411 " =    1.770
peak=    3.291 closest distance to " CB  GLN A  89 " =    1.292
peak=    3.287 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.285 closest distance to " CE BLYS A 290 " =    1.112
peak=    3.278 closest distance to " O   HOH Z 327 " =    1.685
peak=    3.277 closest distance to " CB  ALA A   9 " =    1.526
peak=    3.275 closest distance to " O   ALA A   1 " =    1.679
peak=    3.274 closest distance to " CG  MET A 185 " =    1.111
peak=    3.274 closest distance to " OD1BASN A 224 " =    2.356
peak=    3.273 closest distance to " O   HOH Z  44 " =    3.101
peak=    3.272 closest distance to " O   HOH Z 123 " =    2.294
peak=    3.271 closest distance to " O   HOH Z  85 " =    2.242
peak=    3.264 closest distance to " CA  LYS A 117 " =    1.198
peak=    3.260 closest distance to " N   ASN A  39 " =    1.237
peak=    3.251 closest distance to " CB  SER A  26 " =    1.577
peak=    3.249 closest distance to " OG1 THR A 294 " =    2.409
peak=    3.249 closest distance to " O   HOH Z   1 " =    1.741
peak=    3.248 closest distance to " CA  ILE A  33 " =    1.485
peak=    3.238 closest distance to " CB  ALA A 248 " =    0.890
peak=    3.237 closest distance to " N   GLN A 278 " =    1.101
peak=    3.237 closest distance to " O   HOH Z 423 " =    2.879
peak=    3.236 closest distance to " O   HOH Z 171 " =    1.999
peak=    3.234 closest distance to " CB  HIS A 108 " =    0.788
peak=    3.233 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.228 closest distance to " O   HOH Z  89 " =    2.107
peak=    3.227 closest distance to " O   HOH Z 116 " =    1.745
peak=    3.226 closest distance to " O   HOH Z  96 " =    2.055
peak=    3.225 closest distance to " CA  ALA A 291 " =    0.896
peak=    3.225 closest distance to " O   HOH Z 144 " =    1.881
peak=    3.224 closest distance to " O   HOH Z 302 " =    1.939
peak=    3.219 closest distance to " O   HOH Z  97 " =    1.932
peak=    3.219 closest distance to " CA  ASN A 217 " =    1.243
peak=    3.213 closest distance to " O   HOH Z 433 " =    1.764
peak=    3.205 closest distance to " O   HOH Z 383 " =    1.678
peak=    3.202 closest distance to " CB  LEU A 255 " =    0.801
peak=    3.199 closest distance to " O   HOH Z 421 " =    1.694
peak=    3.185 closest distance to " CD1 ILE A 263 " =    1.292
peak=    3.180 closest distance to " O   HOH Z  49 " =    2.172
peak=    3.180 closest distance to " O   HOH Z 437 " =    1.424
peak=    3.177 closest distance to " N   ASN A 127 " =    1.241
peak=    3.175 closest distance to " O   HOH Z  49 " =    2.721
peak=    3.173 closest distance to " O   HOH Z 411 " =    3.881
peak=    3.173 closest distance to " O   HOH Z 406 " =    1.589
peak=    3.166 closest distance to " O   HOH Z 345 " =    1.715
peak=    3.164 closest distance to " CB  THR A 235 " =    1.076
peak=    3.164 closest distance to " CA  ARG A  36 " =    1.010
peak=    3.161 closest distance to " O   HOH Z 292 " =    1.734
peak=    3.152 closest distance to " CB  TYR A 116 " =    0.801
peak=    3.144 closest distance to " CD2 HIS A  81 " =    1.158
peak=    3.141 closest distance to " O   TRP A 274 " =    1.858
peak=    3.137 closest distance to " O   HOH Z  59 " =    1.935
peak=    3.136 closest distance to " O   HOH Z 258 " =    1.867
peak=    3.135 closest distance to " CA  MET A 105 " =    0.908
peak=    3.135 closest distance to " CG2 ILE A  20 " =    1.346
peak=    3.132 closest distance to " O   HOH Z 299 " =    4.453
peak=    3.129 closest distance to " O   HOH Z  88 " =    1.974
peak=    3.125 closest distance to " CA  ALA A 154 " =    0.939
peak=    3.122 closest distance to " CA  ALA A 158 " =    1.201
peak=    3.121 closest distance to " O   HOH Z 336 " =    1.846
peak=    3.119 closest distance to " CG  GLN A  89 " =    1.524
peak=    3.116 closest distance to " CB  VAL A 126 " =    1.025
peak=    3.115 closest distance to " CB  SER A  62 " =    1.234
peak=    3.108 closest distance to " NH2BARG A 190 " =    1.921
peak=    3.105 closest distance to " CB  MET A  47 " =    1.212
peak=    3.105 closest distance to " CB  ALA A  71 " =    1.324
peak=    3.101 closest distance to " CB  ASN A 215 " =    1.123
peak=    3.096 closest distance to " NH1BARG A 145 " =    1.228
peak=    3.096 closest distance to " O   HOH Z 353 " =    2.687
peak=    3.093 closest distance to " O   HOH Z 359 " =    3.993
peak=    3.088 closest distance to " O   HOH Z 409 " =    2.831
peak=    3.080 closest distance to " CZ3 TRP A 123 " =    1.276
peak=    3.079 closest distance to " CB  ARG A 138 " =    0.983
peak=    3.076 closest distance to " O   HOH Z 365 " =    3.152
peak=    3.073 closest distance to " N   SER A 135 " =    1.267
peak=    3.059 closest distance to " O   HOH Z 298 " =    2.510
peak=    3.043 closest distance to " CB  TRP A 150 " =    1.381
peak=    3.031 closest distance to " O   HOH Z 152 " =    1.768
peak=    3.028 closest distance to " O   ALA A 158 " =    1.308
peak=    3.026 closest distance to " O   HOH Z 391 " =    2.895
peak=    3.006 closest distance to " CD  LYS A 119 " =    1.349

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.551 - 5.321
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 211
   mapped sites are within: 0.743 - 5.321

peak=   -4.726 closest distance to " O   HOH Z 266 " =    4.927
peak=   -4.608 closest distance to " CD  ARG A 156 " =    2.030
peak=   -4.539 closest distance to " CB  PRO A 243 " =    2.635
peak=   -4.420 closest distance to " O   VAL A  67 " =    2.710
peak=   -4.318 closest distance to " O   HOH Z 290 " =    1.207
peak=   -4.304 closest distance to " CG  GLN A 223 " =    1.752
peak=   -4.255 closest distance to " O   HOH Z 389 " =    1.913
peak=   -4.186 closest distance to " SG  CYS A 254 " =    3.514
peak=   -4.158 closest distance to " O   HOH Z 435 " =    2.812
peak=   -4.128 closest distance to " CZ3 TRP A 179 " =    1.141
peak=   -4.111 closest distance to " C   HIS A 108 " =    1.153
peak=   -4.089 closest distance to " CD  GLN A  58 " =    0.966
peak=   -4.040 closest distance to " OG BSER A 134 " =    1.238
peak=   -4.023 closest distance to " O   HOH Z 198 " =    2.101
peak=   -3.967 closest distance to " CD  ARG A 139 " =    1.601
peak=   -3.965 closest distance to " CA  VAL A  67 " =    2.746
peak=   -3.964 closest distance to " CB  ALA A 161 " =    2.549
peak=   -3.948 closest distance to " CD1 PHE A  59 " =    1.858
peak=   -3.934 closest distance to " O   HOH Z 372 " =    2.465
peak=   -3.930 closest distance to " O   HOH Z 377 " =    2.146
peak=   -3.900 closest distance to " O   HOH Z 211 " =    1.690
peak=   -3.884 closest distance to " CG1 VAL A 112 " =    2.824
peak=   -3.837 closest distance to " N   ALA A  43 " =    2.649
peak=   -3.831 closest distance to " O   HOH Z 231 " =    2.236
peak=   -3.831 closest distance to " O   HOH Z  10 " =    1.506
peak=   -3.830 closest distance to " O   HOH Z 198 " =    1.285
peak=   -3.821 closest distance to " O   HOH Z 114 " =    3.147
peak=   -3.816 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.813 closest distance to " CE  MET A 105 " =    2.352
peak=   -3.813 closest distance to " ND2 ASN A  45 " =    1.778
peak=   -3.800 closest distance to " O   HOH Z 313 " =    1.934
peak=   -3.798 closest distance to " O   HOH Z 196 " =    2.038
peak=   -3.792 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.791 closest distance to " CG  PHE A 283 " =    2.760
peak=   -3.780 closest distance to " OD1 ASP A 171 " =    1.647
peak=   -3.774 closest distance to " O   HOH Z  43 " =    1.598
peak=   -3.756 closest distance to " O   HOH Z 185 " =    2.235
peak=   -3.754 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.749 closest distance to " CG1 VAL A 112 " =    2.598
peak=   -3.748 closest distance to " O   HOH Z 311 " =    3.643
peak=   -3.741 closest distance to " CD2 PHE A 192 " =    2.024
peak=   -3.739 closest distance to " CB  ALA A 291 " =    2.383
peak=   -3.733 closest distance to " O   HOH Z 353 " =    2.170
peak=   -3.727 closest distance to " CB  ASN A  39 " =    2.289
peak=   -3.721 closest distance to " O   HOH Z 407 " =    3.119
peak=   -3.712 closest distance to " O   HOH Z 126 " =    1.887
peak=   -3.707 closest distance to " CE2 PHE A 218 " =    2.436
peak=   -3.688 closest distance to " O   HOH Z  60 " =    2.404
peak=   -3.683 closest distance to " O   HOH Z 351 " =    1.489
peak=   -3.661 closest distance to " O   PRO A 198 " =    1.296
peak=   -3.658 closest distance to " CZ  TYR A 169 " =    1.635
peak=   -3.658 closest distance to " OXT GLY A 302 " =    2.787
peak=   -3.658 closest distance to " CZ  PHE A  59 " =    1.523
peak=   -3.647 closest distance to " CB  PRO A 163 " =    2.502
peak=   -3.638 closest distance to " NH2AARG A 275 " =    5.321
peak=   -3.628 closest distance to " CG  ARG A 269 " =    2.344
peak=   -3.619 closest distance to " CD1 LEU A 228 " =    2.255
peak=   -3.618 closest distance to " CE2 TYR A  30 " =    2.771
peak=   -3.616 closest distance to " C   ALA A 158 " =    1.321
peak=   -3.608 closest distance to " N   ASP A 286 " =    2.447
peak=   -3.590 closest distance to " SG ACYS A 201 " =    1.978
peak=   -3.582 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.576 closest distance to " O   ALA A 161 " =    1.704
peak=   -3.570 closest distance to " NH2 ARG A  79 " =    1.624
peak=   -3.555 closest distance to " O   PRO A 163 " =    2.011
peak=   -3.549 closest distance to " C   GLN A  58 " =    1.976
peak=   -3.538 closest distance to " OG  SER A  97 " =    2.202
peak=   -3.529 closest distance to " CD1 LEU A 101 " =    2.341
peak=   -3.524 closest distance to " O   VAL A 189 " =    2.601
peak=   -3.511 closest distance to " NE2 GLN A 278 " =    1.708
peak=   -3.510 closest distance to " CD1 LEU A 297 " =    2.394
peak=   -3.506 closest distance to " CA  GLY A 241 " =    3.066
peak=   -3.487 closest distance to " O   HOH Z  52 " =    1.267
peak=   -3.483 closest distance to " O   ARG A 145 " =    1.577
peak=   -3.482 closest distance to " NH2BARG A 275 " =    1.790
peak=   -3.476 closest distance to " O   HOH Z 295 " =    1.562
peak=   -3.465 closest distance to " OG BSER A 134 " =    1.703
peak=   -3.465 closest distance to " CA  GLY A 203 " =    2.319
peak=   -3.461 closest distance to " N   SER A 212 " =    1.971
peak=   -3.457 closest distance to " NH2 ARG A  79 " =    1.948
peak=   -3.445 closest distance to " O   GLY A 211 " =    1.417
peak=   -3.436 closest distance to " N   ALA A 248 " =    1.649
peak=   -3.434 closest distance to " CG  GLU A 152 " =    0.797
peak=   -3.423 closest distance to " NH1 ARG A 195 " =    2.510
peak=   -3.422 closest distance to " CE  MET A 105 " =    2.261
peak=   -3.418 closest distance to " CB  ASP A 132 " =    2.273
peak=   -3.418 closest distance to " CB  TYR A  15 " =    2.149
peak=   -3.411 closest distance to " C   LEU A 143 " =    1.097
peak=   -3.398 closest distance to " CG1 VAL A 230 " =    2.167
peak=   -3.393 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.390 closest distance to " O   SER A  95 " =    1.506
peak=   -3.389 closest distance to " O   HOH Z 298 " =    1.238
peak=   -3.385 closest distance to " O   HOH Z 359 " =    3.212
peak=   -3.382 closest distance to " CZ3 TRP A 274 " =    1.104
peak=   -3.377 closest distance to " O   HOH Z  11 " =    1.742
peak=   -3.367 closest distance to " CA  GLY A 133 " =    1.994
peak=   -3.365 closest distance to " CB  ALA A 248 " =    2.430
peak=   -3.364 closest distance to " OD1 ASN A 148 " =    1.593
peak=   -3.363 closest distance to " CA  GLY A  98 " =    1.907
peak=   -3.352 closest distance to " CG  TRP A 266 " =    1.870
peak=   -3.350 closest distance to " CD2 PHE A  61 " =    2.504
peak=   -3.349 closest distance to " N   THR A 235 " =    1.345
peak=   -3.343 closest distance to " O   HOH Z 377 " =    0.743
peak=   -3.337 closest distance to " ND2 ASN A 249 " =    2.076
peak=   -3.336 closest distance to " O   HOH Z 244 " =    2.022
peak=   -3.327 closest distance to " O   HOH Z  38 " =    1.516
peak=   -3.317 closest distance to " CB  ASP A 286 " =    2.105
peak=   -3.313 closest distance to " CB  CYS A 254 " =    2.430
peak=   -3.312 closest distance to " O   PRO A 198 " =    1.256
peak=   -3.312 closest distance to " CD  ARG A 195 " =    5.207
peak=   -3.309 closest distance to " CG1 VAL A 197 " =    2.181
peak=   -3.309 closest distance to " CB  ASP A 132 " =    2.368
peak=   -3.309 closest distance to " O   GLN A 240 " =    2.087
peak=   -3.307 closest distance to " OG  SER A  62 " =    1.547
peak=   -3.299 closest distance to " O   LYS A 117 " =    1.736
peak=   -3.299 closest distance to " O   HOH Z 253 " =    3.849
peak=   -3.296 closest distance to " NE2 GLN A 194 " =    1.705
peak=   -3.294 closest distance to " CE  LYS A  76 " =    2.865
peak=   -3.294 closest distance to " O   HOH Z 394 " =    1.414
peak=   -3.292 closest distance to " O   SER A 135 " =    1.477
peak=   -3.291 closest distance to " OD2 ASP A 171 " =    2.273
peak=   -3.290 closest distance to " CG  GLU A 277 " =    1.221
peak=   -3.281 closest distance to " C   MET A 188 " =    1.367
peak=   -3.280 closest distance to " O   HOH Z  13 " =    1.511
peak=   -3.279 closest distance to " CG  PHE A 283 " =    2.659
peak=   -3.274 closest distance to " N   THR A 157 " =    1.585
peak=   -3.270 closest distance to " O   HOH Z 282 " =    1.143
peak=   -3.268 closest distance to " C   VAL A 174 " =    1.792
peak=   -3.265 closest distance to " O   HOH Z  73 " =    2.174
peak=   -3.263 closest distance to " O   HOH Z 174 " =    2.458
peak=   -3.259 closest distance to " CG  ARG A  66 " =    2.345
peak=   -3.259 closest distance to " CG1 VAL A 250 " =    2.692
peak=   -3.255 closest distance to " O   HOH Z 388 " =    1.858
peak=   -3.242 closest distance to " CG2 THR A 221 " =    2.109
peak=   -3.240 closest distance to " O   HOH Z 148 " =    1.844
peak=   -3.238 closest distance to " O   PHE A 218 " =    1.568
peak=   -3.231 closest distance to " OG  SER A  26 " =    1.115
peak=   -3.230 closest distance to " CA  GLY A 241 " =    2.792
peak=   -3.228 closest distance to " O   LYS A 289 " =    2.968
peak=   -3.225 closest distance to " OD1 ASN A 187 " =    1.561
peak=   -3.225 closest distance to " CD2 LEU A 237 " =    2.716
peak=   -3.225 closest distance to " O   LEU A 101 " =    2.828
peak=   -3.218 closest distance to " CB  PHE A 208 " =    2.235
peak=   -3.216 closest distance to " O   HOH Z 322 " =    1.578
peak=   -3.206 closest distance to " CD1 ILE A 239 " =    2.225
peak=   -3.205 closest distance to " O   HOH Z  76 " =    1.903
peak=   -3.202 closest distance to " NZ  LYS A 119 " =    3.466
peak=   -3.201 closest distance to " O   HOH Z 371 " =    1.582
peak=   -3.201 closest distance to " CE BMET A  47 " =    2.024
peak=   -3.200 closest distance to " CA  ASP A 298 " =    1.084
peak=   -3.197 closest distance to " O   ILE A 120 " =    1.456
peak=   -3.196 closest distance to " CB  TRP A  85 " =    2.487
peak=   -3.191 closest distance to " O   HOH Z  88 " =    1.908
peak=   -3.190 closest distance to " O   HOH Z 317 " =    1.564
peak=   -3.189 closest distance to " O   MET A  40 " =    2.745
peak=   -3.189 closest distance to " CG  ARG A 269 " =    2.048
peak=   -3.187 closest distance to " O   HOH Z  89 " =    2.935
peak=   -3.184 closest distance to " CG2 THR A 178 " =    2.252
peak=   -3.181 closest distance to " OE1 GLN A  88 " =    1.187
peak=   -3.181 closest distance to " O   HOH Z   6 " =    1.454
peak=   -3.177 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.177 closest distance to " O   HOH Z  37 " =    1.898
peak=   -3.174 closest distance to " O   HOH Z 114 " =    1.654
peak=   -3.170 closest distance to " OD1AASN A 224 " =    1.757
peak=   -3.170 closest distance to " O   HOH Z 166 " =    1.529
peak=   -3.169 closest distance to " O   ALA A 292 " =    2.034
peak=   -3.168 closest distance to " O   HOH Z 137 " =    1.545
peak=   -3.167 closest distance to " CD2 LEU A 300 " =    2.868
peak=   -3.165 closest distance to " C   ASP A 231 " =    2.690
peak=   -3.165 closest distance to " OH  TYR A 214 " =    1.239
peak=   -3.162 closest distance to " OD2 ASP A 191 " =    1.491
peak=   -3.161 closest distance to " O   HOH Z 290 " =    0.919
peak=   -3.159 closest distance to " O   HOH Z  51 " =    1.553
peak=   -3.156 closest distance to " CG  GLU A   2 " =    1.877
peak=   -3.148 closest distance to " O   HOH Z 241 " =    1.344
peak=   -3.148 closest distance to " OXT GLY A 302 " =    3.378
peak=   -3.146 closest distance to " O   SER A  22 " =    2.408
peak=   -3.144 closest distance to " CB  LEU A  83 " =    2.392
peak=   -3.144 closest distance to " O   HOH Z 385 " =    1.887
peak=   -3.142 closest distance to " O   VAL A 153 " =    2.337
peak=   -3.141 closest distance to " O   HOH Z 377 " =    1.208
peak=   -3.140 closest distance to " OH  TYR A 247 " =    2.030
peak=   -3.137 closest distance to " O   TRP A  70 " =    1.564
peak=   -3.134 closest distance to " O   ALA A  51 " =    1.417
peak=   -3.130 closest distance to " O   HOH Z 111 " =    2.223
peak=   -3.124 closest distance to " OD2 ASP A 171 " =    1.828
peak=   -3.124 closest distance to " ND2 ASN A  60 " =    1.407
peak=   -3.115 closest distance to " O   HOH Z 166 " =    1.996
peak=   -3.111 closest distance to " O   VAL A 174 " =    2.042
peak=   -3.110 closest distance to " CD  GLN A  88 " =    0.783
peak=   -3.104 closest distance to " O   HOH Z  91 " =    1.634
peak=   -3.097 closest distance to " O   HOH Z 323 " =    1.356
peak=   -3.096 closest distance to " O   HOH Z 426 " =    1.570
peak=   -3.091 closest distance to " O   ALA A  10 " =    1.637
peak=   -3.091 closest distance to " O   HOH Z 175 " =    4.319
peak=   -3.089 closest distance to " OD2 ASP A  50 " =    1.661
peak=   -3.087 closest distance to " O   HOH Z 184 " =    1.777
peak=   -3.083 closest distance to " CD1 ILE A 199 " =    2.496
peak=   -3.082 closest distance to " CE  LYS A  76 " =    2.842
peak=   -3.070 closest distance to " O   GLN A 240 " =    2.398
peak=   -3.061 closest distance to " CG  PRO A 163 " =    2.556
peak=   -3.048 closest distance to " O   HOH Z 210 " =    1.097
peak=   -3.042 closest distance to " OD2 ASP A 171 " =    2.376
peak=   -3.039 closest distance to " O   HOH Z 234 " =    4.120
peak=   -3.029 closest distance to " CD1 LEU A 228 " =    2.049
peak=   -3.026 closest distance to " O   HOH Z  41 " =    2.564

================= 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    :  0.2307 0.2308   5.721157e+00   5.717614e+00
   1_bss:  0.2125 0.2124   5.683636e+00   5.669217e+00
   1_xyz:  0.1326 0.1525   5.234677e+00   5.356946e+00
   1_adp:  0.1248 0.1523   5.188112e+00   5.363614e+00
   1_occ:  0.1243 0.1523   5.185002e+00   5.362239e+00
   2_bss:  0.1248 0.1520   5.187295e+00   5.361878e+00
   2_xyz:  0.1125 0.1477   5.110017e+00   5.323988e+00
   2_adp:  0.1075 0.1483   5.090181e+00   5.329468e+00
   2_occ:  0.1074 0.1484   5.090282e+00   5.329968e+00
   3_bss:  0.1073 0.1483   5.090359e+00   5.330030e+00
   3_xyz:  0.1065 0.1497   5.091921e+00   5.339355e+00
   3_adp:  0.1061 0.1503   5.093033e+00   5.344059e+00
   3_occ:  0.1060 0.1504   5.093321e+00   5.344629e+00
   4_bss:  0.1059 0.1505   5.093508e+00   5.344821e+00
   4_xyz:  0.1072 0.1521   5.104865e+00   5.357285e+00
   4_adp:  0.1071 0.1521   5.104907e+00   5.358351e+00
   4_occ:  0.1071 0.1522   5.105158e+00   5.358811e+00
   5_bss:  0.1070 0.1522   5.105233e+00   5.358862e+00
   5_xyz:  0.1047 0.1524   5.093896e+00   5.357234e+00
   5_adp:  0.1053 0.1524   5.095531e+00   5.356584e+00
   5_occ:  0.1052 0.1525   5.095650e+00   5.356761e+00
   5_bss:  0.1052 0.1526   5.095774e+00   5.356866e+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:  0.328  45.961  -2.551  -2.063  -1.447  -0.000  -0.000  -0.000
   1_xyz:  0.328  45.961  -2.551  -2.063  -1.447  -0.000  -0.000  -0.000
   1_adp:  0.328  45.961  -2.551  -2.063  -1.447  -0.000  -0.000  -0.000
   1_occ:  0.328  45.961  -2.551  -2.063  -1.447  -0.000  -0.000  -0.000
   2_bss:  0.318  47.626  -2.850  -2.692  -1.726  -0.000  -0.000  -0.000
   2_xyz:  0.318  47.626  -2.850  -2.692  -1.726  -0.000  -0.000  -0.000
   2_adp:  0.318  47.626  -2.850  -2.692  -1.726  -0.000  -0.000  -0.000
   2_occ:  0.318  47.626  -2.850  -2.692  -1.726  -0.000  -0.000  -0.000
   3_bss:  0.318  47.626  -2.567  -2.482  -1.471  -0.000  -0.000  -0.000
   3_xyz:  0.318  47.626  -2.567  -2.482  -1.471  -0.000  -0.000  -0.000
   3_adp:  0.318  47.626  -2.567  -2.482  -1.471  -0.000  -0.000  -0.000
   3_occ:  0.318  47.626  -2.567  -2.482  -1.471  -0.000  -0.000  -0.000
   4_bss:  0.323  47.626  -2.371  -2.325  -1.283  -0.000  -0.000  -0.000
   4_xyz:  0.323  47.626  -2.371  -2.325  -1.283  -0.000  -0.000  -0.000
   4_adp:  0.323  47.626  -2.371  -2.325  -1.283  -0.000  -0.000  -0.000
   4_occ:  0.323  47.626  -2.371  -2.325  -1.283  -0.000  -0.000  -0.000
   5_bss:  0.323  47.626  -2.230  -2.201  -1.139  -0.000  -0.000  -0.000
   5_xyz:  0.323  47.626  -2.230  -2.201  -1.139  -0.000  -0.000  -0.000
   5_adp:  0.323  47.626  -2.230  -2.201  -1.139  -0.000  -0.000  -0.000
   5_occ:  0.323  47.626  -2.230  -2.201  -1.139  -0.000  -0.000  -0.000
   5_bss:  0.324  47.572  -2.032  -2.017  -0.936  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  20.968 0.8566  1.0164    14306.094
   1_bss:  19.473 0.8694  0.9598    11292.784
   1_xyz:  13.183 0.9220  0.9882     6050.986
   1_adp:  13.359 0.9204  0.9858     6097.550
   1_occ:  13.311 0.9207  0.9856     6045.989
   2_bss:  13.288 0.9209  0.9715     6027.113
   2_xyz:  12.507 0.9269  0.9740     5584.895
   2_adp:  12.690 0.9253  0.9705     5575.891
   2_occ:  12.700 0.9252  0.9703     5580.746
   3_bss:  12.702 0.9252  0.9792     5582.751
   3_xyz:  12.845 0.9243  0.9781     5716.379
   3_adp:  12.936 0.9236  0.9728     5754.363
   3_occ:  12.948 0.9235  0.9726     5760.166
   4_bss:  12.954 0.9234  0.9791     5764.731
   4_xyz:  13.156 0.9220  0.9785     5915.828
   4_adp:  13.178 0.9218  0.9730     5926.223
   4_occ:  13.187 0.9217  0.9729     5930.819
   5_bss:  13.188 0.9217  0.9778     5932.074
   5_xyz:  13.159 0.9219  0.9782     5923.318
   5_adp:  13.140 0.9220  0.9735     5927.820
   5_occ:  13.145 0.9219  0.9735     5928.681
   5_bss:  13.148 0.9219  0.9785     5931.176
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5961e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5961e-01
   1_xyz:   0.963  0.007  0.071 15.230  0.004  4.110   5.7051e-02
   1_adp:   0.963  0.007  0.071 15.230  0.004  4.110   5.7051e-02
   1_occ:   0.963  0.007  0.071 15.230  0.004  4.110   5.7051e-02
   2_bss:   0.963  0.007  0.071 15.230  0.004  4.110   5.7051e-02
   2_xyz:   1.055  0.009  0.081 15.373  0.004  4.111   6.9772e-02
   2_adp:   1.055  0.009  0.081 15.373  0.004  4.111   6.9772e-02
   2_occ:   1.055  0.009  0.081 15.373  0.004  4.111   6.9772e-02
   3_bss:   1.055  0.009  0.081 15.373  0.004  4.111   6.9772e-02
   3_xyz:   1.013  0.008  0.079 15.280  0.004  4.112   6.4910e-02
   3_adp:   1.013  0.008  0.079 15.280  0.004  4.112   6.4910e-02
   3_occ:   1.013  0.008  0.079 15.280  0.004  4.112   6.4910e-02
   4_bss:   1.013  0.008  0.079 15.280  0.004  4.112   6.4910e-02
   4_xyz:   0.950  0.007  0.074 15.093  0.004  4.112   5.7891e-02
   4_adp:   0.950  0.007  0.074 15.093  0.004  4.112   5.7891e-02
   4_occ:   0.950  0.007  0.074 15.093  0.004  4.112   5.7891e-02
   5_bss:   0.950  0.007  0.074 15.093  0.004  4.112   5.7891e-02
   5_xyz:   1.044  0.009  0.081 15.275  0.004  4.117   6.8122e-02
   5_adp:   1.044  0.009  0.081 15.275  0.004  4.117   6.8122e-02
   5_occ:   1.044  0.009  0.081 15.275  0.004  4.117   6.8122e-02
   5_bss:   1.044  0.009  0.081 15.275  0.004  4.117   6.8122e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4064e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4064e-01
   1_xyz:   7.560  0.035  0.270 86.389  0.033  2.366   4.4479e-02
   1_adp:   7.560  0.035  0.270 86.389  0.033  2.366   4.4479e-02
   1_occ:   7.560  0.035  0.270 86.389  0.033  2.366   4.4479e-02
   2_bss:   7.560  0.035  0.270 86.389  0.033  2.366   4.4479e-02
   2_xyz:   6.885  0.043  0.274 84.285  0.035  2.243   5.6276e-02
   2_adp:   6.885  0.043  0.274 84.285  0.035  2.243   5.6276e-02
   2_occ:   6.885  0.043  0.274 84.285  0.035  2.243   5.6276e-02
   3_bss:   6.885  0.043  0.274 84.285  0.035  2.243   5.6276e-02
   3_xyz:   6.788  0.043  0.257 83.837  0.037  2.312   4.9647e-02
   3_adp:   6.788  0.043  0.257 83.837  0.037  2.312   4.9647e-02
   3_occ:   6.788  0.043  0.257 83.837  0.037  2.312   4.9647e-02
   4_bss:   6.788  0.043  0.257 83.837  0.037  2.312   4.9647e-02
   4_xyz:   6.791  0.041  0.231 83.643  0.034  2.322   3.9509e-02
   4_adp:   6.791  0.041  0.231 83.643  0.034  2.322   3.9509e-02
   4_occ:   6.791  0.041  0.231 83.643  0.034  2.322   3.9509e-02
   5_bss:   6.791  0.041  0.231 83.643  0.034  2.322   3.9509e-02
   5_xyz:   6.678  0.045  0.264 83.514  0.037  2.267   5.3764e-02
   5_adp:   6.678  0.045  0.264 83.514  0.037  2.267   5.3764e-02
   5_occ:   6.678  0.045  0.264 83.514  0.037  2.267   5.3764e-02
   5_bss:   6.678  0.045  0.264 83.514  0.037  2.267   5.3764e-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:  73.07   0.00  16.23  73.07   0.00  12.43  62.44   6.65  36.90
   1_occ:  73.07   0.00  16.23  73.07   0.00  12.43  62.44   6.65  36.90
   2_bss:  73.07   0.00  16.23  73.07   0.00  12.43  62.44   6.65  36.90
   2_xyz:  73.07   0.00  16.23  73.07   0.00  12.43  62.44   6.65  36.90
   2_adp:  71.76   1.68  16.71  71.76   1.68  12.82  69.93   4.81  37.93
   2_occ:  71.76   1.68  16.71  71.76   1.68  12.82  69.93   4.81  37.93
   3_bss:  71.76   1.68  16.71  71.76   1.68  12.82  69.93   4.81  37.93
   3_xyz:  71.76   1.68  16.71  71.76   1.68  12.82  69.93   4.81  37.93
   3_adp:  74.23   1.50  16.59  74.23   1.50  12.73  70.54   5.98  37.62
   3_occ:  74.23   1.50  16.59  74.23   1.50  12.73  70.54   5.98  37.62
   4_bss:  74.23   1.50  16.59  74.23   1.50  12.73  70.54   5.98  37.62
   4_xyz:  74.23   1.50  16.59  74.23   1.50  12.73  70.54   5.98  37.62
   4_adp:  74.96   1.30  16.45  74.96   1.30  12.60  70.59   6.41  37.44
   4_occ:  74.96   1.30  16.45  74.96   1.30  12.60  70.59   6.41  37.44
   5_bss:  74.96   1.30  16.45  74.96   1.30  12.60  70.59   6.41  37.44
   5_xyz:  74.96   1.30  16.45  74.96   1.30  12.60  70.59   6.41  37.44
   5_adp:  75.63   1.51  16.14  75.63   1.51  12.42  69.70   6.30  36.41
   5_occ:  75.63   1.51  16.14  75.63   1.51  12.42  69.70   6.30  36.41
   5_bss:  75.57   1.46  16.09  75.57   1.46  12.37  69.65   6.24  36.36
------------------------------------------------------------------------
 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:    0.601    0.011    0.189
   1_adp:    0.601    0.011    0.189
   1_occ:    0.601    0.011    0.189
   2_bss:    0.601    0.011    0.189
   2_xyz:    0.565    0.012    0.220
   2_adp:    0.565    0.012    0.220
   2_occ:    0.565    0.012    0.220
   3_bss:    0.565    0.012    0.220
   3_xyz:    0.763    0.017    0.226
   3_adp:    0.763    0.017    0.226
   3_occ:    0.763    0.017    0.226
   4_bss:    0.763    0.017    0.226
   4_xyz:    0.943    0.016    0.233
   4_adp:    0.943    0.016    0.233
   4_occ:    0.943    0.016    0.233
   5_bss:    0.943    0.016    0.233
   5_xyz:    1.016    0.013    0.235
   5_adp:    1.016    0.013    0.235
   5_occ:    1.016    0.013    0.235
   5_bss:    1.016    0.013    0.235
------------------------------------------------------------------------

CPU time actual refinement: 316.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/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_774/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_774/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 316.59 
  Macro-tasks:
    bulk solvent and scale       = 36.66  
    individual site refinement   = 127.79 
    weights calculation          = 30.14  
    collect and process          = 6.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 201.36 
  Micro-tasks:
    mask                            = 0.61   
    f_calc                          = 99.72  
    alpha_beta                      = 7.99   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 108.19 
    fmodel                         = 6.77   
    r_factors                      = 0.14   
    phase_errors                   = 11.29  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 236.03 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.536 micro seconds
Total CPU time: 5.50 minutes
from_scatterers_fft:    635 calls, 99.41 s
gradients_fft:          580 calls, 94.99 s

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

# Date 2008-01-16 Time 05:37:16 PST -0800 (1200490636.77 s)
Start R-work = 0.2307, R-free = 0.2308 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1721 (no bulk solvent and anisotropic scale)

Start R-work = 0.2125, R-free = 0.2124
Final R-work = 0.1052, R-free = 0.1526