# Date 2008-01-16 Time 04:31:53 PST -0800 (1200486713.89 s)
#phil __OFF__

Command line arguments: "../354.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4444
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 354

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 48.1033, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0043 1.97055
Completeness in resolution range: 0.948988
Completeness with d_max=infinity: 0.9461

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0043
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 48.1033, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0043 1.97055
Completeness in resolution range: 0.948988
Completeness with d_max=infinity: 0.9461

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0047 -  4.2170 [2169/2198]  1950   219  10.1%
  bin  2:  4.2170 -  3.3595 [2080/2103]  1872   208  10.0%
  bin  3:  3.3595 -  2.9384 [2051/2076]  1846   205  10.0%
  bin  4:  2.9384 -  2.6714 [2027/2044]  1829   198   9.8%
  bin  5:  2.6714 -  2.4809 [2014/2057]  1808   206  10.2%
  bin  6:  2.4809 -  2.3352 [2015/2043]  1821   194   9.6%
  bin  7:  2.3352 -  2.2186 [1989/2025]  1790   199  10.0%
  bin  8:  2.2186 -  2.1223 [2005/2047]  1805   200  10.0%
  bin  9:  2.1223 -  2.0408 [1961/2018]  1760   201  10.2%
  bin 10:  2.0408 -  1.9706 [1278/2031]  1149   129  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/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:
        1.41 -     2.11: 20
        2.11 -     2.80: 804
        2.80 -     3.50: 4481
        3.50 -     4.20: 9366
        4.20 -     4.90: 13792
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.408 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.510 3.040 -x+1,y+1/2,-z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.668 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.722 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.770 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28458 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_354/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/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 = 69.19625 48.10325 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4621   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.282177                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0047 -  4.7036 0.99   1404  159 0.3812 0.4121      6.5821      6.6347|
|  2:  4.7036 -  3.7526 0.99   1354  148 0.4195 0.4080      6.8369      6.8171|
|  3:  3.7526 -  3.2839 0.99   1331  149 0.4398 0.4307      6.6821      6.7197|
|  4:  3.2839 -  2.9863 0.99   1322  136 0.4519 0.4116      6.5154      6.4319|
|  5:  2.9863 -  2.7736 0.99   1307  151 0.5040 0.4574      6.3772      6.3543|
|  6:  2.7736 -  2.6110 0.99   1305  147 0.5094 0.4805       6.281      6.1705|
|  7:  2.6110 -  2.4809 0.98   1282  146 0.5125 0.4543      6.2581      6.1731|
|  8:  2.4809 -  2.3733 0.98   1311  138 0.5107 0.5389      6.1728      6.2227|
|  9:  2.3733 -  2.2823 0.99   1279  145 0.5305 0.5098      6.1203      6.1362|
| 10:  2.2823 -  2.2038 0.98   1290  143 0.5091 0.5397      6.1153      6.1363|
| 11:  2.2038 -  2.1351 0.97   1274  144 0.5201 0.5183      6.0286      6.0247|
| 12:  2.1351 -  2.0742 0.98   1286  143 0.5051 0.4908        5.95      5.9858|
| 13:  2.0742 -  2.0197 0.93   1205  131 0.5060 0.4859      5.8706      5.8715|
| 14:  2.0197 -  1.9706 0.53    680   79 0.5220 0.5249      5.8519      5.7212|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0047 -  4.7036  1404   159  0.64  39.36   0.82     0.67      88662.35|
|  2:  4.7036 -  3.7526  1354   148  0.68  36.74   0.90     0.78     111608.87|
|  3:  3.7526 -  3.2839  1331   149  0.61  42.93   0.91     0.80     111155.37|
|  4:  3.2839 -  2.9863  1322   136  0.56  47.12   0.92     0.77      89619.49|
|  5:  2.9863 -  2.7736  1307   151  0.49  52.79   0.87     0.70      72893.65|
|  6:  2.7736 -  2.6110  1305   147  0.46  55.39   0.89     0.64      62447.05|
|  7:  2.6110 -  2.4809  1282   146  0.41  59.08   0.90     0.55      61287.21|
|  8:  2.4809 -  2.3733  1311   138  0.34  64.28   0.90     0.49      60451.33|
|  9:  2.3733 -  2.2823  1279   145  0.31  66.54   0.91     0.48      57325.79|
| 10:  2.2823 -  2.2038  1290   143  0.33  64.94   0.95     0.49      51542.03|
| 11:  2.2038 -  2.1351  1274   144  0.35  63.71   0.92     0.54      45759.70|
| 12:  2.1351 -  2.0742  1286   143  0.34  64.44   0.96     0.54      42398.58|
| 13:  2.0742 -  2.0197  1205   131  0.33  65.46   0.95     0.50      36402.65|
| 14:  2.0197 -  1.9706   680    79  0.30  67.80   0.95     0.42      31110.36|
|alpha:            min =        0.42 max =            0.80 mean =         0.61|
|beta:             min =    31110.36 max =       111608.87 mean =     67740.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.79|
|phase err.(test): min =        0.00 max =           89.96 mean =        55.63|
|-----------------------------------------------------------------------------|

============================== 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 = 19.343158             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.286   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.293686              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.285   (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 |  1.408 -  1.757:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.757 -  2.106:       16 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.106 -  2.456:       38 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.456 -  2.805:      766 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.805 -  3.154:     2070 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.154 -  3.503:     2411 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.503 -  3.852:     4599 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.852 -  4.202:     4767 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.202 -  4.551:     6218 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.551 -  4.900:     7574 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.408 |       0.611 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4621   ksol= 0.00   Bsol= 0.00   scale= 0.891    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.282177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4638   r_free= 0.4513   ksol= 0.31   Bsol= 20.00   scale= 0.927   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,4.37,-0.21,0.00,-0.00,-0.00); trace/3= 0.67                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.274144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.131667             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.871   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.328858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.073   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4638      final r-factor (work) = 0.3461          |
| start r-factor (free) = 0.4513      final r-factor (free) = 0.3761          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.9408 = 17.13 * 0.50 * 6.2749 + 1.00 * 0.1912                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.8285 = 17.13 * 0.50 * 6.1470 + 1.00 * 0.1742                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3461      final r-factor (work) = 0.3147          |
| start r-factor (free) = 0.3761      final r-factor (free) = 0.3851          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1747 = 1.33 * 1.00 * 6.1470 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0340 = 1.33 * 1.00 * 6.0283 + 1.00 * 0.0232                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.49   18.96    None  None   None       |
|    all(noH): 2823   0      0.00    93.49   18.96    None  None   None       |
|    Sol.    : 438    0      0.00    93.49   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    90.83   15.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.349:  905   |   5:    46.745 -  56.094:  104        |
|      1:     9.349 -  18.698:  789   |   6:    56.094 -  65.443:   58        |
|      2:    18.698 -  28.047:  493   |   7:    65.443 -  74.793:   30        |
|      3:    28.047 -  37.396:  277   |   8:    74.793 -  84.142:   10        |
|      4:    37.396 -  46.745:  151   |   9:    84.142 -  93.491:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3147 r_free = 0.3851             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3143 r_free = 0.3848             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3143   r_free= 0.3848   ksol= 0.31   Bsol= 20.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,4.37,-0.21,0.00,-0.00,-0.00); trace/3= 0.67                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.033838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3132   r_free= 0.3830   ksol= 0.31   Bsol= 41.26   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,2.92,0.30,0.00,0.00,0.00); trace/3= 0.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.033522                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.571176              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.435   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.873980              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.019  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3132      final r-factor (work) = 0.2580          |
| start r-factor (free) = 0.3830      final r-factor (free) = 0.3198          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9992 = 7.57 * 0.50 * 6.0294 + 1.00 * 0.1742                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6500 = 7.57 * 0.50 * 5.9608 + 1.00 * 0.0848                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2580      final r-factor (work) = 0.2383          |
| start r-factor (free) = 0.3198      final r-factor (free) = 0.3106          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1924 = 1.87 * 1.00 * 5.9608 + 1.00 * 0.0219                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9562 = 1.87 * 1.00 * 5.8349 + 1.00 * 0.0217                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.96  19.26    None  None   None       |
|    all(noH): 2823   0      0.00    113.96  19.26    None  None   None       |
|    Sol.    : 438    0      3.43    105.77  42.38    None  None   None       |
|    Mac.    : 2385   0      0.00    113.96  15.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.396: 1241   |   5:    56.978 -  68.373:   75        |
|      1:    11.396 -  22.791:  796   |   6:    68.373 -  79.769:   48        |
|      2:    22.791 -  34.187:  328   |   7:    79.769 -  91.164:   23        |
|      3:    34.187 -  45.582:  182   |   8:    91.164 - 102.560:   17        |
|      4:    45.582 -  56.978:  109   |   9:   102.560 - 113.955:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2383 r_free = 0.3106             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2381 r_free = 0.3108             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2381   r_free= 0.3108   ksol= 0.31   Bsol= 41.26   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,2.92,0.30,0.00,0.00,0.00); trace/3= 0.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.826930                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2381   r_free= 0.3107   ksol= 0.32   Bsol= 50.15   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,2.16,0.34,0.00,0.00,0.00); trace/3= 0.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.826484                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.767285              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.283  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.226216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.385  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2381      final r-factor (work) = 0.2006          |
| start r-factor (free) = 0.3107      final r-factor (free) = 0.2649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0761 = 3.77 * 0.50 * 5.8352 + 1.00 * 0.0848                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9043 = 3.77 * 0.50 * 5.7563 + 1.00 * 0.0615                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2006      final r-factor (work) = 0.1914          |
| start r-factor (free) = 0.2649      final r-factor (free) = 0.2423          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3240 = 0.23 * 1.00 * 5.7563 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2918 = 0.23 * 1.00 * 5.6492 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.72  17.58    None  None   None       |
|    all(noH): 2823   0      0.00    103.72  17.58    None  None   None       |
|    Sol.    : 438    0      4.10    92.86   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    103.72  13.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.372: 1264   |   5:    51.859 -  62.231:   74        |
|      1:    10.372 -  20.744:  854   |   6:    62.231 -  72.603:   43        |
|      2:    20.744 -  31.116:  273   |   7:    72.603 -  82.975:   20        |
|      3:    31.116 -  41.488:  153   |   8:    82.975 -  93.347:   17        |
|      4:    41.488 -  51.859:  120   |   9:    93.347 - 103.719:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1914 r_free = 0.2423             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1912 r_free = 0.2422             target_work(ml) = 5.604         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2422   ksol= 0.32   Bsol= 50.15   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,2.16,0.34,0.00,0.00,0.00); trace/3= 0.53                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.603635                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1912   r_free= 0.2414   ksol= 0.31   Bsol= 50.15   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,0.74,-0.41,0.00,-0.00,-0.00); trace/3= -0.45                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.604450                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.086548              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.144  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.061   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1459          |
| start r-factor (free) = 0.2414      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4361 = 5.09 * 0.50 * 5.6520 + 1.00 * 0.0615                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0359 = 5.09 * 0.50 * 5.4874 + 1.00 * 0.0801                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1459      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1909 = 0.40 * 1.00 * 5.4874 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1204 = 0.40 * 1.00 * 5.3132 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    97.01   17.02    None  None   None       |
|    all(noH): 2823   0      0.94    97.01   17.02    None  None   None       |
|    Sol.    : 438    0      4.35    93.26   42.13    None  None   None       |
|    Mac.    : 2385   0      0.94    97.01   12.41    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:     0.940 -  10.548: 1343   |   5:    48.977 -  58.584:   92        |
|      1:    10.548 -  20.155:  863   |   6:    58.584 -  68.191:   47        |
|      2:    20.155 -  29.762:  182   |   7:    68.191 -  77.799:   24        |
|      3:    29.762 -  39.370:  125   |   8:    77.799 -  87.406:   19        |
|      4:    39.370 -  48.977:  117   |   9:    87.406 -  97.013:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1327 r_free = 0.1801             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1800             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1800   ksol= 0.31   Bsol= 50.15   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,0.74,-0.41,0.00,-0.00,-0.00); trace/3= -0.45                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.280259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1804   ksol= 0.32   Bsol= 54.25   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.11,-0.65,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.283756                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.264210              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.017  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.078  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1328      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0990 = 2.26 * 0.50 * 5.3165 + 1.00 * 0.0801                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0129 = 2.26 * 0.50 * 5.2584 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1724      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3984 = 0.45 * 1.00 * 5.2584 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3828 = 0.45 * 1.00 * 5.2238 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.69   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    98.69   16.73    None  None   None       |
|    Sol.    : 438    0      4.44    98.64   41.95    None  None   None       |
|    Mac.    : 2385   0      0.00    98.69   12.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.869: 1231   |   5:    49.344 -  59.212:   90        |
|      1:     9.869 -  19.737:  979   |   6:    59.212 -  69.081:   53        |
|      2:    19.737 -  29.606:  196   |   7:    69.081 -  78.950:   19        |
|      3:    29.606 -  39.475:  123   |   8:    78.950 -  88.818:   17        |
|      4:    39.475 -  49.344:  107   |   9:    88.818 -  98.687:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1222 r_free = 0.1709             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1709             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1709   ksol= 0.32   Bsol= 54.25   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.11,-0.65,-0.00,-0.00,-0.00); trace/3= -0.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218453                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0047 -  4.7036 0.99   1404  159 0.1007 0.1388      5.4161      5.5908|
|  2:  4.7036 -  3.7526 0.99   1354  148 0.0889 0.1125       5.477      5.6632|
|  3:  3.7526 -  3.2839 0.99   1331  149 0.1144 0.1647      5.5415       5.878|
|  4:  3.2839 -  2.9863 0.99   1322  136 0.1376 0.1824      5.5439      5.7524|
|  5:  2.9863 -  2.7736 0.99   1307  151 0.1478 0.1891      5.4314      5.6027|
|  6:  2.7736 -  2.6110 0.99   1305  147 0.1446 0.2169      5.3349       5.557|
|  7:  2.6110 -  2.4809 0.98   1282  146 0.1356 0.1759      5.2547      5.4328|
|  8:  2.4809 -  2.3733 0.98   1311  138 0.1326 0.1833      5.1697      5.3817|
|  9:  2.3733 -  2.2823 0.99   1279  145 0.1283 0.1944      5.0907      5.3619|
| 10:  2.2823 -  2.2038 0.98   1290  143 0.1217 0.1878      5.0382      5.2813|
| 11:  2.2038 -  2.1351 0.97   1274  144 0.1231 0.1847      4.9743      5.2479|
| 12:  2.1351 -  2.0742 0.98   1286  143 0.1210 0.1766       4.909      5.1608|
| 13:  2.0742 -  2.0197 0.93   1205  131 0.1194 0.1777      4.8276      5.0977|
| 14:  2.0197 -  1.9706 0.53    680   79 0.1131 0.1898      4.7409      5.0033|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0047 -  4.7036  1404   159  0.93   9.84   0.97     0.94       7886.56|
|  2:  4.7036 -  3.7526  1354   148  0.95   8.69   1.02     1.01       9924.97|
|  3:  3.7526 -  3.2839  1331   149  0.93  12.42   1.03     1.02      11848.40|
|  4:  3.2839 -  2.9863  1322   136  0.90  15.56   1.01     1.00      12317.30|
|  5:  2.9863 -  2.7736  1307   151  0.88  18.21   1.00     0.98      10492.89|
|  6:  2.7736 -  2.6110  1305   147  0.88  18.15   0.98     0.94       8685.93|
|  7:  2.6110 -  2.4809  1282   146  0.89  17.48   0.99     0.95       7497.64|
|  8:  2.4809 -  2.3733  1311   138  0.89  17.14   1.00     0.97       6573.01|
|  9:  2.3733 -  2.2823  1279   145  0.89  17.17   1.00     0.96       5649.82|
| 10:  2.2823 -  2.2038  1290   143  0.89  16.69   0.99     0.96       5152.89|
| 11:  2.2038 -  2.1351  1274   144  0.89  16.87   1.00     0.96       4570.46|
| 12:  2.1351 -  2.0742  1286   143  0.91  15.98   0.99     0.98       4103.21|
| 13:  2.0742 -  2.0197  1205   131  0.90  16.86   0.99     0.99       3575.61|
| 14:  2.0197 -  1.9706   680    79  0.90  16.17   0.97     0.93       2991.40|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2991.40 max =        12317.30 mean =      7439.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.42|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1708   ksol= 0.32   Bsol= 53.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.20,-0.54,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218571                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1708   ksol= 0.32   Bsol= 53.77   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-0.20,-0.54,-0.00,-0.00,-0.00); trace/3= -0.88                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.218571                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0047 -  4.7036 0.99   1404  159 0.1007 0.1388      5.4164      5.5913|
|  2:  4.7036 -  3.7526 0.99   1354  148 0.0889 0.1126      5.4774      5.6637|
|  3:  3.7526 -  3.2839 0.99   1331  149 0.1145 0.1647      5.5418      5.8785|
|  4:  3.2839 -  2.9863 0.99   1322  136 0.1376 0.1823       5.544      5.7523|
|  5:  2.9863 -  2.7736 0.99   1307  151 0.1478 0.1889      5.4312      5.6023|
|  6:  2.7736 -  2.6110 0.99   1305  147 0.1446 0.2164      5.3345      5.5558|
|  7:  2.6110 -  2.4809 0.98   1282  146 0.1357 0.1760      5.2543      5.4326|
|  8:  2.4809 -  2.3733 0.98   1311  138 0.1324 0.1831      5.1698      5.3822|
|  9:  2.3733 -  2.2823 0.99   1279  145 0.1282 0.1947      5.0906      5.3631|
| 10:  2.2823 -  2.2038 0.98   1290  143 0.1216 0.1881      5.0385      5.2827|
| 11:  2.2038 -  2.1351 0.97   1274  144 0.1231 0.1846      4.9745       5.248|
| 12:  2.1351 -  2.0742 0.98   1286  143 0.1209 0.1768      4.9094      5.1615|
| 13:  2.0742 -  2.0197 0.93   1205  131 0.1195 0.1774      4.8282      5.0969|
| 14:  2.0197 -  1.9706 0.53    680   79 0.1131 0.1898      4.7409      5.0028|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0047 -  4.7036  1404   159  0.93   9.84   0.97     0.94       7890.37|
|  2:  4.7036 -  3.7526  1354   148  0.95   8.70   1.02     1.01       9931.48|
|  3:  3.7526 -  3.2839  1331   149  0.93  12.42   1.03     1.02      11858.50|
|  4:  3.2839 -  2.9863  1322   136  0.90  15.56   1.02     1.00      12320.84|
|  5:  2.9863 -  2.7736  1307   151  0.88  18.19   1.01     0.98      10477.61|
|  6:  2.7736 -  2.6110  1305   147  0.88  18.13   0.98     0.94       8674.68|
|  7:  2.6110 -  2.4809  1282   146  0.89  17.47   0.99     0.95       7490.76|
|  8:  2.4809 -  2.3733  1311   138  0.89  17.15   1.00     0.97       6578.25|
|  9:  2.3733 -  2.2823  1279   145  0.89  17.18   1.00     0.96       5659.99|
| 10:  2.2823 -  2.2038  1290   143  0.89  16.70   1.00     0.96       5158.90|
| 11:  2.2038 -  2.1351  1274   144  0.89  16.88   1.00     0.96       4574.13|
| 12:  2.1351 -  2.0742  1286   143  0.91  16.00   1.00     0.98       4110.21|
| 13:  2.0742 -  2.0197  1205   131  0.90  16.86   1.00     0.99       3576.24|
| 14:  2.0197 -  1.9706   680    79  0.90  16.17   0.98     0.93       2986.19|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2986.19 max =        12320.84 mean =      7441.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.42|
|phase err.(test): min =        0.00 max =           89.79 mean =        14.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.746)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.69   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    98.69   16.73    None  None   None       |
|    Sol.    : 438    0      4.44    98.64   41.95    None  None   None       |
|    Mac.    : 2385   0      0.00    98.69   12.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.872: 1231   |   5:    49.347 -  59.215:   90        |
|      1:     9.872 -  19.740:  979   |   6:    59.215 -  69.084:   53        |
|      2:    19.740 -  29.609:  196   |   7:    69.084 -  78.953:   19        |
|      3:    29.609 -  39.478:  123   |   8:    78.953 -  88.821:   17        |
|      4:    39.478 -  49.347:  107   |   9:    88.821 -  98.690:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 4.520
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 330
   mapped sites are within: 0.754 - 4.520

peak=    9.702 closest distance to " CB  SER A 216 " =    1.188
peak=    5.643 closest distance to " O   HOH Z 210 " =    1.369
peak=    5.499 closest distance to " O   HOH Z 120 " =    1.095
peak=    5.466 closest distance to " O   HOH Z 102 " =    1.444
peak=    5.263 closest distance to " NH2 ARG A  56 " =    2.416
peak=    5.243 closest distance to " O   HOH Z 142 " =    1.628
peak=    5.134 closest distance to " CB  SER A  63 " =    1.146
peak=    5.116 closest distance to " O   HOH Z 124 " =    1.559
peak=    5.029 closest distance to " O   HOH Z  80 " =    2.008
peak=    4.935 closest distance to " CG  PRO A  54 " =    1.209
peak=    4.918 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.866 closest distance to " CB  ARG A 275 " =    0.851
peak=    4.859 closest distance to " O   HOH Z  46 " =    1.212
peak=    4.851 closest distance to " O   HOH Z 433 " =    1.846
peak=    4.809 closest distance to " O   HOH Z 402 " =    1.570
peak=    4.809 closest distance to " O   HOH Z 134 " =    2.016
peak=    4.756 closest distance to " CB  GLN A 223 " =    1.335
peak=    4.712 closest distance to " C   PRO A 198 " =    1.523
peak=    4.682 closest distance to " CG  ARG A  66 " =    1.085
peak=    4.626 closest distance to " O   HOH Z 247 " =    1.492
peak=    4.600 closest distance to " O   HOH Z 163 " =    1.668
peak=    4.588 closest distance to " CG  PRO A 213 " =    1.312
peak=    4.536 closest distance to " O   HOH Z   7 " =    1.228
peak=    4.530 closest distance to " O   HOH Z 130 " =    1.140
peak=    4.514 closest distance to " CG  PRO A 198 " =    1.310
peak=    4.514 closest distance to " O   HOH Z 132 " =    1.507
peak=    4.487 closest distance to " O   HOH Z 389 " =    1.964
peak=    4.483 closest distance to " O   HOH Z 209 " =    2.350
peak=    4.461 closest distance to " O   HOH Z  15 " =    2.149
peak=    4.454 closest distance to " CB  PRO A  54 " =    0.865
peak=    4.448 closest distance to " O   HOH Z 272 " =    1.255
peak=    4.420 closest distance to " O   HOH Z 357 " =    1.977
peak=    4.400 closest distance to " O   HOH Z 234 " =    3.753
peak=    4.397 closest distance to " CB  GLN A 183 " =    1.316
peak=    4.359 closest distance to " O   HOH Z  44 " =    2.008
peak=    4.356 closest distance to " O   HOH Z 193 " =    1.645
peak=    4.343 closest distance to " O   HOH Z 203 " =    1.731
peak=    4.296 closest distance to " O   HOH Z 130 " =    2.442
peak=    4.260 closest distance to " O   HOH Z 126 " =    1.625
peak=    4.246 closest distance to " O   HOH Z  49 " =    1.308
peak=    4.246 closest distance to " CB  SER A 141 " =    1.068
peak=    4.220 closest distance to " O   HOH Z 196 " =    1.490
peak=    4.210 closest distance to " O   HOH Z 414 " =    1.781
peak=    4.198 closest distance to " O   HOH Z 408 " =    1.990
peak=    4.171 closest distance to " NZ  LYS A 117 " =    3.102
peak=    4.153 closest distance to " O   SER A  87 " =    2.215
peak=    4.140 closest distance to " CG  PRO A  90 " =    1.229
peak=    4.124 closest distance to " O   HOH Z 214 " =    1.307
peak=    4.118 closest distance to " CB  ARG A 190 " =    1.768
peak=    4.106 closest distance to " O   HOH Z 236 " =    1.413
peak=    4.103 closest distance to " CB AVAL A  41 " =    0.975
peak=    4.087 closest distance to " O   HOH Z  43 " =    1.770
peak=    4.077 closest distance to " O   HOH Z  67 " =    2.153
peak=    4.068 closest distance to " O   HOH Z  97 " =    1.873
peak=    4.058 closest distance to " O   HOH Z 154 " =    1.685
peak=    4.043 closest distance to " O   HOH Z 132 " =    2.445
peak=    4.037 closest distance to " O   HOH Z  61 " =    1.566
peak=    4.026 closest distance to " CB  ASN A 148 " =    1.279
peak=    3.999 closest distance to " CB  SER A  62 " =    0.829
peak=    3.990 closest distance to " O   HOH Z 189 " =    1.811
peak=    3.985 closest distance to " O   HOH Z 431 " =    1.262
peak=    3.971 closest distance to " O   HOH Z  63 " =    2.103
peak=    3.969 closest distance to " CG2 VAL A 197 " =    1.216
peak=    3.965 closest distance to " O   HOH Z 428 " =    1.169
peak=    3.958 closest distance to " CA  ARG A  66 " =    1.151
peak=    3.952 closest distance to " NH2BARG A 145 " =    1.997
peak=    3.950 closest distance to " O   HOH Z 411 " =    3.267
peak=    3.942 closest distance to " CB  SER A   3 " =    1.182
peak=    3.927 closest distance to " CB  GLU A 128 " =    1.165
peak=    3.924 closest distance to " O   HOH Z 272 " =    1.929
peak=    3.919 closest distance to " OE1 GLU A   2 " =    1.875
peak=    3.905 closest distance to " CB  PHE A  16 " =    1.202
peak=    3.899 closest distance to " CD  ARG A 269 " =    1.054
peak=    3.895 closest distance to " O   HOH Z   7 " =    1.131
peak=    3.895 closest distance to " O   HOH Z 406 " =    1.521
peak=    3.892 closest distance to " O   GLY A  23 " =    2.358
peak=    3.890 closest distance to " O   HOH Z  59 " =    2.349
peak=    3.887 closest distance to " CB  LEU A 228 " =    1.191
peak=    3.887 closest distance to " O   HOH Z 365 " =    1.548
peak=    3.886 closest distance to " O   HOH Z 245 " =    1.356
peak=    3.878 closest distance to " ND2 ASN A 187 " =    1.641
peak=    3.864 closest distance to " O   HOH Z 298 " =    2.005
peak=    3.863 closest distance to " O   HOH Z 339 " =    1.374
peak=    3.863 closest distance to " CD2 TRP A 179 " =    1.393
peak=    3.862 closest distance to " CG AARG A 275 " =    1.164
peak=    3.846 closest distance to " O   HOH Z  39 " =    1.876
peak=    3.832 closest distance to " CD  LYS A 166 " =    1.500
peak=    3.831 closest distance to " O   HOH Z 403 " =    2.001
peak=    3.830 closest distance to " O   HOH Z 422 " =    0.786
peak=    3.817 closest distance to " O   HOH Z 345 " =    1.828
peak=    3.806 closest distance to " O   HOH Z 334 " =    1.679
peak=    3.804 closest distance to " C   ILE A 106 " =    1.813
peak=    3.797 closest distance to " CG1 ILE A  33 " =    1.276
peak=    3.792 closest distance to " CB  PRO A  54 " =    1.352
peak=    3.791 closest distance to " CB  TRP A 179 " =    1.086
peak=    3.786 closest distance to " O   HOH Z 437 " =    1.972
peak=    3.784 closest distance to " OE1 GLN A  11 " =    1.915
peak=    3.774 closest distance to " O   HOH Z 371 " =    3.202
peak=    3.769 closest distance to " O   HOH Z  21 " =    1.918
peak=    3.763 closest distance to " O   HOH Z  66 " =    2.070
peak=    3.754 closest distance to " CB  ARG A  79 " =    1.320
peak=    3.752 closest distance to " O   HOH Z  40 " =    1.670
peak=    3.751 closest distance to " NE2 GLN A  11 " =    1.006
peak=    3.742 closest distance to " O   HOH Z 427 " =    3.284
peak=    3.741 closest distance to " O   HOH Z 361 " =    3.159
peak=    3.740 closest distance to " O   HOH Z  20 " =    1.628
peak=    3.733 closest distance to " O   HOH Z  78 " =    1.715
peak=    3.729 closest distance to " O   HOH Z 380 " =    2.186
peak=    3.723 closest distance to " CB  GLU A 152 " =    1.049
peak=    3.717 closest distance to " O   HOH Z 279 " =    1.996
peak=    3.686 closest distance to " O   HOH Z 128 " =    2.382
peak=    3.685 closest distance to " CD  LYS A 119 " =    1.803
peak=    3.679 closest distance to " O   HOH Z 395 " =    1.530
peak=    3.675 closest distance to " CD  ARG A 195 " =    1.120
peak=    3.660 closest distance to " CE  LYS A 119 " =    1.111
peak=    3.659 closest distance to " O   HOH Z 345 " =    2.574
peak=    3.657 closest distance to " O   HOH Z 128 " =    1.983
peak=    3.651 closest distance to " O   HOH Z 423 " =    1.880
peak=    3.645 closest distance to " O   HOH Z 425 " =    1.498
peak=    3.638 closest distance to " O   HOH Z 316 " =    2.814
peak=    3.638 closest distance to " CB  ASN A 285 " =    0.912
peak=    3.631 closest distance to " O   HOH Z 133 " =    1.265
peak=    3.629 closest distance to " CA  ALA A  21 " =    1.231
peak=    3.622 closest distance to " O   THR A 251 " =    1.278
peak=    3.617 closest distance to " O   HOH Z  47 " =    1.377
peak=    3.616 closest distance to " N   ASN A  39 " =    1.265
peak=    3.613 closest distance to " O   HOH Z 369 " =    2.260
peak=    3.613 closest distance to " CB  ALA A  71 " =    1.293
peak=    3.611 closest distance to " CA  VAL A  41 " =    0.889
peak=    3.610 closest distance to " O   HOH Z 289 " =    1.602
peak=    3.608 closest distance to " O   HOH Z 132 " =    1.929
peak=    3.608 closest distance to " O   HOH Z 352 " =    1.240
peak=    3.608 closest distance to " O   HOH Z 303 " =    2.108
peak=    3.601 closest distance to " CA  ASN A 176 " =    1.217
peak=    3.599 closest distance to " CB  GLN A  58 " =    0.944
peak=    3.598 closest distance to " OG BSER A 210 " =    1.194
peak=    3.595 closest distance to " O   HOH Z 375 " =    1.790
peak=    3.593 closest distance to " CA  ALA A  51 " =    0.978
peak=    3.590 closest distance to " O   HOH Z 193 " =    2.247
peak=    3.589 closest distance to " CB  GLU A 277 " =    3.666
peak=    3.585 closest distance to " O   HOH Z 417 " =    3.057
peak=    3.582 closest distance to " CG2 THR A 220 " =    0.843
peak=    3.581 closest distance to " CB  VAL A 202 " =    1.447
peak=    3.574 closest distance to " O   HOH Z 156 " =    2.500
peak=    3.573 closest distance to " CD  ARG A 159 " =    0.814
peak=    3.569 closest distance to " CB  ARG A 269 " =    0.859
peak=    3.564 closest distance to " CG2 ILE A  20 " =    1.327
peak=    3.563 closest distance to " O   HOH Z 435 " =    1.937
peak=    3.562 closest distance to " O   HOH Z 394 " =    1.638
peak=    3.554 closest distance to " O   HOH Z 250 " =    2.423
peak=    3.542 closest distance to " O   HOH Z 130 " =    2.444
peak=    3.539 closest distance to " O   HOH Z 141 " =    1.716
peak=    3.536 closest distance to " O   HOH Z 126 " =    1.881
peak=    3.529 closest distance to " OG1 THR A 294 " =    2.365
peak=    3.527 closest distance to " O   HOH Z 166 " =    1.637
peak=    3.523 closest distance to " O   HOH Z 426 " =    1.466
peak=    3.521 closest distance to " CA  GLU A 152 " =    0.953
peak=    3.519 closest distance to " CB  PRO A 198 " =    1.060
peak=    3.516 closest distance to " CG  GLN A  11 " =    1.404
peak=    3.515 closest distance to " OD1 ASN A  60 " =    1.215
peak=    3.511 closest distance to " CE ALYS A 290 " =    1.127
peak=    3.509 closest distance to " O   HOH Z  59 " =    1.844
peak=    3.503 closest distance to " O   HOH Z 173 " =    2.207
peak=    3.500 closest distance to " O   HOH Z 257 " =    2.200
peak=    3.497 closest distance to " O   HOH Z 128 " =    1.523
peak=    3.497 closest distance to " N   SER A 164 " =    0.984
peak=    3.491 closest distance to " O   ASP A 124 " =    1.749
peak=    3.489 closest distance to " CB  ILE A 199 " =    1.084
peak=    3.484 closest distance to " CB  ALA A 100 " =    1.238
peak=    3.481 closest distance to " O   HOH Z 368 " =    1.983
peak=    3.476 closest distance to " O   HOH Z 261 " =    1.869
peak=    3.474 closest distance to " OH  TYR A  30 " =    1.250
peak=    3.473 closest distance to " O   HOH Z  48 " =    1.699
peak=    3.472 closest distance to " CD  GLN A 194 " =    1.661
peak=    3.470 closest distance to " CA  ARG A 195 " =    1.147
peak=    3.469 closest distance to " O   HOH Z 116 " =    2.392
peak=    3.468 closest distance to " CG  PRO A 243 " =    1.190
peak=    3.467 closest distance to " O   HOH Z 423 " =    3.077
peak=    3.465 closest distance to " OD2 ASP A 286 " =    2.795
peak=    3.463 closest distance to " N   ILE A  33 " =    1.085
peak=    3.462 closest distance to " O   HOH Z 359 " =    1.911
peak=    3.457 closest distance to " O   HOH Z 155 " =    1.393
peak=    3.454 closest distance to " CE1 TYR A 186 " =    1.339
peak=    3.452 closest distance to " CA  ARG A  36 " =    0.994
peak=    3.449 closest distance to " CB  THR A  52 " =    1.078
peak=    3.448 closest distance to " NH2 ARG A 156 " =    1.105
peak=    3.448 closest distance to " O   HOH Z 146 " =    1.372
peak=    3.446 closest distance to " O   HOH Z 365 " =    2.519
peak=    3.446 closest distance to " CB  ALA A 248 " =    1.364
peak=    3.444 closest distance to " CD2 HIS A  81 " =    1.139
peak=    3.444 closest distance to " O   HOH Z 263 " =    2.252
peak=    3.442 closest distance to " NH1AARG A 275 " =    1.065
peak=    3.442 closest distance to " CD2 LEU A 297 " =    0.996
peak=    3.440 closest distance to " CB  SER A  26 " =    1.766
peak=    3.435 closest distance to " CD  PRO A  54 " =    1.108
peak=    3.433 closest distance to " O   HOH Z 195 " =    1.188
peak=    3.429 closest distance to " O   HOH Z 147 " =    1.766
peak=    3.426 closest distance to " O   HOH Z 150 " =    1.681
peak=    3.423 closest distance to " CB  GLN A  89 " =    1.315
peak=    3.422 closest distance to " NH1 ARG A 269 " =    0.764
peak=    3.420 closest distance to " CD  ARG A  36 " =    1.194
peak=    3.410 closest distance to " O   HOH Z  11 " =    1.385
peak=    3.404 closest distance to " O   HOH Z 208 " =    1.612
peak=    3.401 closest distance to " O   HOH Z 271 " =    2.612
peak=    3.401 closest distance to " O   HOH Z 143 " =    1.456
peak=    3.390 closest distance to " O   HOH Z 250 " =    1.745
peak=    3.389 closest distance to " CA  ILE A 263 " =    1.020
peak=    3.378 closest distance to " O   HOH Z 265 " =    2.030
peak=    3.378 closest distance to " CB  PHE A 283 " =    0.754
peak=    3.374 closest distance to " O   HOH Z 427 " =    3.342
peak=    3.372 closest distance to " O   HOH Z 146 " =    1.452
peak=    3.359 closest distance to " CA  GLY A  80 " =    0.872
peak=    3.356 closest distance to " CB  GLN A 194 " =    0.921
peak=    3.355 closest distance to " O   HOH Z 358 " =    2.059
peak=    3.352 closest distance to " O   HOH Z 313 " =    1.927
peak=    3.351 closest distance to " SD AMET A  47 " =    1.380
peak=    3.346 closest distance to " O   GLY A  91 " =    1.285
peak=    3.346 closest distance to " O   HOH Z 344 " =    2.827
peak=    3.343 closest distance to " O   HOH Z 336 " =    1.622
peak=    3.342 closest distance to " O   HOH Z 109 " =    2.180
peak=    3.339 closest distance to " CG  GLN A  77 " =    0.767
peak=    3.339 closest distance to " CH2 TRP A 274 " =    1.986
peak=    3.338 closest distance to " CB  VAL A 265 " =    1.267
peak=    3.334 closest distance to " CD1 LEU A 222 " =    0.870
peak=    3.332 closest distance to " NZ  LYS A 119 " =    1.494
peak=    3.330 closest distance to " CB  MET A 105 " =    1.178
peak=    3.330 closest distance to " O  BHOH Z  74 " =    1.415
peak=    3.329 closest distance to " CG2 THR A 221 " =    1.155
peak=    3.323 closest distance to " CZ3 TRP A  85 " =    0.971
peak=    3.321 closest distance to " CD AARG A 102 " =    2.343
peak=    3.319 closest distance to " O   HOH Z 435 " =    2.814
peak=    3.318 closest distance to " CB  ARG A 139 " =    0.960
peak=    3.316 closest distance to " O   HOH Z 155 " =    3.178
peak=    3.313 closest distance to " O   HOH Z 421 " =    1.958
peak=    3.301 closest distance to " O   HOH Z 374 " =    2.544
peak=    3.300 closest distance to " CA  PRO A  90 " =    0.893
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.430
peak=    3.296 closest distance to " CG2 ILE A 120 " =    1.232
peak=    3.292 closest distance to " CB  TRP A 179 " =    1.914
peak=    3.290 closest distance to " O   HOH Z 412 " =    3.656
peak=    3.283 closest distance to " O   HOH Z 116 " =    1.042
peak=    3.279 closest distance to " CZ  PHE A 218 " =    1.113
peak=    3.279 closest distance to " CA  ALA A 100 " =    1.224
peak=    3.278 closest distance to " CA  SER A  87 " =    1.017
peak=    3.277 closest distance to " CA  LEU A  83 " =    1.424
peak=    3.275 closest distance to " O   HOH Z 402 " =    2.717
peak=    3.271 closest distance to " O   HOH Z 130 " =    2.425
peak=    3.268 closest distance to " OG  SER A  62 " =    3.005
peak=    3.267 closest distance to " CB  GLU A 175 " =    1.373
peak=    3.267 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.261 closest distance to " O   HOH Z 225 " =    1.911
peak=    3.261 closest distance to " CZ  PHE A  38 " =    1.304
peak=    3.258 closest distance to " CA  ASP A 191 " =    0.966
peak=    3.258 closest distance to " O   HOH Z 194 " =    1.883
peak=    3.257 closest distance to " O   HOH Z 126 " =    1.890
peak=    3.257 closest distance to " CB  ASP A 191 " =    1.257
peak=    3.253 closest distance to " O   ALA A 165 " =    1.279
peak=    3.249 closest distance to " ND2 ASN A 301 " =    1.154
peak=    3.248 closest distance to " CA  ALA A 160 " =    0.914
peak=    3.244 closest distance to " O   HOH Z 261 " =    1.736
peak=    3.244 closest distance to " O   HOH Z 404 " =    1.572
peak=    3.241 closest distance to " O   HOH Z  95 " =    1.482
peak=    3.239 closest distance to " O   HOH Z 373 " =    1.647
peak=    3.226 closest distance to " CB  PRO A 213 " =    2.103
peak=    3.224 closest distance to " O   HOH Z 112 " =    1.584
peak=    3.221 closest distance to " ND1 HIS A  81 " =    1.508
peak=    3.221 closest distance to " N   ARG A 156 " =    1.453
peak=    3.219 closest distance to " O   HOH Z 124 " =    3.193
peak=    3.219 closest distance to " CA  VAL A 125 " =    1.218
peak=    3.219 closest distance to " O   HOH Z  88 " =    3.536
peak=    3.208 closest distance to " CA  ASN A 215 " =    1.091
peak=    3.207 closest distance to " CB  GLN A  73 " =    1.145
peak=    3.203 closest distance to " O   HOH Z  38 " =    1.400
peak=    3.202 closest distance to " CB  THR A  31 " =    1.699
peak=    3.202 closest distance to " O   HOH Z 123 " =    2.125
peak=    3.194 closest distance to " N   PHE A 130 " =    1.377
peak=    3.194 closest distance to " O   HOH Z 139 " =    4.520
peak=    3.189 closest distance to " O   TRP A 274 " =    1.703
peak=    3.188 closest distance to " CD  LYS A  76 " =    2.008
peak=    3.187 closest distance to " O   HOH Z  97 " =    2.374
peak=    3.186 closest distance to " O   HOH Z 293 " =    1.925
peak=    3.184 closest distance to " OG BSER A 258 " =    2.810
peak=    3.179 closest distance to " O   HOH Z 419 " =    2.550
peak=    3.175 closest distance to " CG2 THR A  42 " =    0.926
peak=    3.173 closest distance to " O   HOH Z  89 " =    2.371
peak=    3.172 closest distance to " OD1 ASP A 253 " =    1.942
peak=    3.172 closest distance to " O   HOH Z 420 " =    1.794
peak=    3.169 closest distance to " CB  SER A 273 " =    0.843
peak=    3.166 closest distance to " O   HOH Z  30 " =    1.430
peak=    3.163 closest distance to " NZ  LYS A 117 " =    0.789
peak=    3.162 closest distance to " CD  ARG A  36 " =    1.292
peak=    3.159 closest distance to " CB  TRP A 266 " =    1.138
peak=    3.155 closest distance to " O   HOH Z 298 " =    2.322
peak=    3.153 closest distance to " CG  MET A 185 " =    1.209
peak=    3.153 closest distance to " CD  ARG A  66 " =    1.290
peak=    3.151 closest distance to " CB  THR A 157 " =    1.139
peak=    3.148 closest distance to " CA  VAL A 126 " =    0.942
peak=    3.145 closest distance to " O   HOH Z 214 " =    2.650
peak=    3.139 closest distance to " O   HOH Z 280 " =    2.313
peak=    3.138 closest distance to " O   HOH Z 185 " =    1.658
peak=    3.135 closest distance to " O   HOH Z 291 " =    1.410
peak=    3.131 closest distance to " O   HOH Z 145 " =    2.212
peak=    3.129 closest distance to " CB  GLU A 277 " =    0.993
peak=    3.127 closest distance to " O   HOH Z 152 " =    1.841
peak=    3.119 closest distance to " O   HOH Z   1 " =    3.151
peak=    3.106 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.105 closest distance to " NH1AARG A 275 " =    3.502
peak=    3.103 closest distance to " CA  ALA A 295 " =    1.122
peak=    3.103 closest distance to " O   HOH Z 327 " =    1.782
peak=    3.096 closest distance to " O   HOH Z  85 " =    1.914
peak=    3.093 closest distance to " O   HOH Z 118 " =    1.025
peak=    3.090 closest distance to " O   HOH Z 353 " =    2.641
peak=    3.089 closest distance to " CB  ASN A 187 " =    1.397
peak=    3.087 closest distance to " O   HOH Z  35 " =    1.999
peak=    3.086 closest distance to " O   HOH Z 367 " =    3.262
peak=    3.075 closest distance to " CG  MET A  40 " =    2.169
peak=    3.073 closest distance to " CD2 LEU A 255 " =    1.229
peak=    3.066 closest distance to " CG2 VAL A 257 " =    0.815
peak=    3.065 closest distance to " CG  GLN A  58 " =    2.330
peak=    3.064 closest distance to " CB  ALA A  51 " =    0.814
peak=    3.053 closest distance to " O   HOH Z 355 " =    1.819
peak=    3.051 closest distance to " CB  GLU A 152 " =    1.640
peak=    3.049 closest distance to " O   HOH Z  40 " =    2.025
peak=    3.035 closest distance to " O   HOH Z 109 " =    2.871
peak=    3.032 closest distance to " O   HOH Z 280 " =    2.465
peak=    3.011 closest distance to " OD2 ASP A 286 " =    3.006

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.673 - 5.912
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 218
   mapped sites are within: 0.722 - 5.912

peak=   -4.633 closest distance to " O   HOH Z 266 " =    4.610
peak=   -4.474 closest distance to " C   HIS A 108 " =    1.045
peak=   -4.408 closest distance to " OXT GLY A 302 " =    2.699
peak=   -4.396 closest distance to " O   HOH Z 155 " =    1.590
peak=   -4.365 closest distance to " O   VAL A  67 " =    2.840
peak=   -4.232 closest distance to " CG2BVAL A  41 " =    2.749
peak=   -4.144 closest distance to " CB  LEU A 167 " =    2.157
peak=   -4.141 closest distance to " CD  ARG A 156 " =    1.990
peak=   -4.112 closest distance to " O   PRO A 163 " =    2.047
peak=   -4.046 closest distance to " C   THR A 279 " =    1.241
peak=   -4.045 closest distance to " O   HOH Z 210 " =    0.823
peak=   -4.035 closest distance to " CD1 PHE A  59 " =    1.869
peak=   -4.028 closest distance to " O   PRO A 198 " =    1.399
peak=   -3.997 closest distance to " O   HOH Z 422 " =    1.495
peak=   -3.907 closest distance to " CB  PHE A 208 " =    2.400
peak=   -3.904 closest distance to " SG  CYS A 254 " =    3.299
peak=   -3.897 closest distance to " CD1 LEU A 101 " =    2.501
peak=   -3.877 closest distance to " OG  SER A  97 " =    2.189
peak=   -3.872 closest distance to " CG  GLU A  53 " =    1.268
peak=   -3.850 closest distance to " O   HOH Z 120 " =    1.367
peak=   -3.824 closest distance to " O   PHE A 218 " =    1.365
peak=   -3.815 closest distance to " CD2 LEU A 237 " =    2.500
peak=   -3.813 closest distance to " O   ASN A 187 " =    1.501
peak=   -3.811 closest distance to " O   HOH Z 290 " =    0.944
peak=   -3.807 closest distance to " O   HOH Z 422 " =    1.182
peak=   -3.804 closest distance to " O  BHOH Z 338 " =    1.506
peak=   -3.785 closest distance to " O   HOH Z 392 " =    1.274
peak=   -3.783 closest distance to " NE2 GLN A 223 " =    1.185
peak=   -3.768 closest distance to " O   HOH Z 396 " =    1.769
peak=   -3.764 closest distance to " O   HOH Z 196 " =    1.657
peak=   -3.758 closest distance to " CD  GLN A  58 " =    1.039
peak=   -3.752 closest distance to " CD2 TYR A  30 " =    2.709
peak=   -3.748 closest distance to " O   HOH Z 377 " =    1.048
peak=   -3.747 closest distance to " NH2 ARG A  66 " =    1.455
peak=   -3.721 closest distance to " O   HOH Z 424 " =    1.363
peak=   -3.717 closest distance to " O   HOH Z 165 " =    1.889
peak=   -3.712 closest distance to " O   ALA A  34 " =    2.252
peak=   -3.707 closest distance to " O   HOH Z   7 " =    0.932
peak=   -3.707 closest distance to " O   HOH Z 234 " =    4.216
peak=   -3.679 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.677 closest distance to " O   HOH Z  56 " =    1.045
peak=   -3.671 closest distance to " O   HOH Z  15 " =    1.506
peak=   -3.650 closest distance to " CB  ALA A 161 " =    2.482
peak=   -3.647 closest distance to " CD1 TRP A 179 " =    1.128
peak=   -3.634 closest distance to " CG  PRO A 243 " =    1.647
peak=   -3.615 closest distance to " O   HOH Z 109 " =    3.542
peak=   -3.613 closest distance to " C   ASN A 285 " =    2.299
peak=   -3.607 closest distance to " O   ALA A 161 " =    1.636
peak=   -3.600 closest distance to " ND2 ASN A  69 " =    1.555
peak=   -3.600 closest distance to " OD2 ASP A 171 " =    1.715
peak=   -3.599 closest distance to " O   HOH Z 120 " =    0.829
peak=   -3.598 closest distance to " O   HOH Z 377 " =    2.198
peak=   -3.597 closest distance to " O   HOH Z 196 " =    1.953
peak=   -3.581 closest distance to " O   HOH Z 221 " =    1.195
peak=   -3.575 closest distance to " O   TRP A  92 " =    1.980
peak=   -3.567 closest distance to " O   ALA A   1 " =    2.250
peak=   -3.562 closest distance to " O   HOH Z 130 " =    2.446
peak=   -3.556 closest distance to " C   SER A 206 " =    1.578
peak=   -3.549 closest distance to " CG2 THR A 182 " =    2.279
peak=   -3.539 closest distance to " O   HOH Z  38 " =    1.416
peak=   -3.538 closest distance to " O   VAL A 174 " =    1.980
peak=   -3.537 closest distance to " O   HOH Z 137 " =    1.235
peak=   -3.530 closest distance to " O   HOH Z 423 " =    2.297
peak=   -3.528 closest distance to " CA  VAL A 197 " =    0.951
peak=   -3.505 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.503 closest distance to " O   HOH Z 418 " =    1.390
peak=   -3.489 closest distance to " O   HOH Z 120 " =    1.119
peak=   -3.480 closest distance to " CB  ALA A  43 " =    2.477
peak=   -3.473 closest distance to " CG2 THR A  18 " =    2.872
peak=   -3.473 closest distance to " CD1 TYR A 247 " =    2.350
peak=   -3.472 closest distance to " CZ  TYR A 169 " =    1.907
peak=   -3.468 closest distance to " O   HOH Z  52 " =    2.072
peak=   -3.466 closest distance to " OG ASER A 134 " =    1.161
peak=   -3.465 closest distance to " O   HOH Z 426 " =    1.652
peak=   -3.463 closest distance to " CD  GLN A  88 " =    0.806
peak=   -3.450 closest distance to " CD2 LEU A 300 " =    2.696
peak=   -3.445 closest distance to " CB  ASP A 162 " =    2.481
peak=   -3.436 closest distance to " O   HOH Z 311 " =    3.317
peak=   -3.434 closest distance to " CB  ALA A 100 " =    1.705
peak=   -3.432 closest distance to " CD2 LEU A 237 " =    2.263
peak=   -3.425 closest distance to " O   HOH Z 140 " =    0.824
peak=   -3.419 closest distance to " ND2 ASN A  39 " =    1.233
peak=   -3.416 closest distance to " CA  GLY A  98 " =    2.094
peak=   -3.415 closest distance to " NH2 ARG A  36 " =    1.221
peak=   -3.406 closest distance to " CG1 VAL A 197 " =    2.089
peak=   -3.401 closest distance to " CD  ARG A 195 " =    5.050
peak=   -3.392 closest distance to " CG2 ILE A  49 " =    2.596
peak=   -3.391 closest distance to " C   GLY A 133 " =    1.313
peak=   -3.390 closest distance to " O   HOH Z 103 " =    1.851
peak=   -3.378 closest distance to " NH2 ARG A  79 " =    2.083
peak=   -3.376 closest distance to " CA  GLY A 203 " =    2.300
peak=   -3.374 closest distance to " O   ILE A 234 " =    1.276
peak=   -3.371 closest distance to " CG1 VAL A  78 " =    2.822
peak=   -3.368 closest distance to " O   TYR A  15 " =    1.632
peak=   -3.366 closest distance to " O   HOH Z 197 " =    1.882
peak=   -3.362 closest distance to " O   HOH Z 136 " =    1.633
peak=   -3.361 closest distance to " O   HOH Z  35 " =    2.267
peak=   -3.359 closest distance to " O   HOH Z  39 " =    0.722
peak=   -3.355 closest distance to " CD  GLN A 223 " =    1.679
peak=   -3.354 closest distance to " OG  SER A  32 " =    1.121
peak=   -3.354 closest distance to " O   HOH Z 407 " =    1.264
peak=   -3.352 closest distance to " OG  SER A   3 " =    1.696
peak=   -3.344 closest distance to " O   HOH Z 251 " =    1.312
peak=   -3.341 closest distance to " OE2 GLU A   2 " =    1.568
peak=   -3.341 closest distance to " O   HOH Z   6 " =    1.472
peak=   -3.340 closest distance to " O   HOH Z 388 " =    1.958
peak=   -3.339 closest distance to " CD2 PHE A  61 " =    2.115
peak=   -3.338 closest distance to " CG2 VAL A 189 " =    2.227
peak=   -3.336 closest distance to " NE2 GLN A  88 " =    1.839
peak=   -3.335 closest distance to " CG1 VAL A 112 " =    2.433
peak=   -3.330 closest distance to " O   HOH Z 427 " =    1.559
peak=   -3.327 closest distance to " N   ALA A 226 " =    1.908
peak=   -3.325 closest distance to " O   GLN A 194 " =    1.446
peak=   -3.319 closest distance to " CB  ALA A 131 " =    2.315
peak=   -3.318 closest distance to " CA  TYR A  68 " =    2.933
peak=   -3.315 closest distance to " O   HOH Z  71 " =    1.646
peak=   -3.312 closest distance to " O   HOH Z 171 " =    2.191
peak=   -3.307 closest distance to " CD1 PHE A 130 " =    2.276
peak=   -3.307 closest distance to " O   GLY A 196 " =    0.936
peak=   -3.306 closest distance to " CB  ALA A 291 " =    2.164
peak=   -3.304 closest distance to " ND2 ASN A  45 " =    1.529
peak=   -3.303 closest distance to " O   ASP A 107 " =    1.431
peak=   -3.302 closest distance to " CA  GLY A 133 " =    1.926
peak=   -3.298 closest distance to " OG  SER A 141 " =    2.575
peak=   -3.297 closest distance to " O   HOH Z 126 " =    2.015
peak=   -3.297 closest distance to " ND2 ASN A  60 " =    1.338
peak=   -3.294 closest distance to " OE1 GLN A  77 " =    2.005
peak=   -3.293 closest distance to " O   GLY A 196 " =    2.368
peak=   -3.289 closest distance to " N   GLY A  17 " =    1.687
peak=   -3.287 closest distance to " O   GLY A  80 " =    2.702
peak=   -3.283 closest distance to " CG  ARG A 219 " =    2.341
peak=   -3.282 closest distance to " O   LEU A 300 " =    2.526
peak=   -3.280 closest distance to " O   GLN A  11 " =    1.015
peak=   -3.277 closest distance to " O   HOH Z 397 " =    1.251
peak=   -3.277 closest distance to " O   SER A  26 " =    1.404
peak=   -3.274 closest distance to " O   HOH Z 139 " =    3.299
peak=   -3.270 closest distance to " O   HOH Z 393 " =    1.179
peak=   -3.268 closest distance to " NE2 GLN A 103 " =    1.622
peak=   -3.268 closest distance to " CA  SER A 276 " =    1.414
peak=   -3.267 closest distance to " OG BSER A 134 " =    1.260
peak=   -3.260 closest distance to " O   HOH Z  78 " =    1.810
peak=   -3.255 closest distance to " OD2 ASP A 171 " =    2.263
peak=   -3.253 closest distance to " C   ASN A 148 " =    1.680
peak=   -3.247 closest distance to " O   HOH Z 150 " =    2.040
peak=   -3.244 closest distance to " O   ALA A 160 " =    1.536
peak=   -3.243 closest distance to " CG  GLN A  11 " =    1.285
peak=   -3.243 closest distance to " O   HOH Z 368 " =    1.974
peak=   -3.243 closest distance to " CZ  PHE A 218 " =    1.391
peak=   -3.243 closest distance to " CB  ASN A 170 " =    2.090
peak=   -3.242 closest distance to " CB  GLU A 277 " =    1.382
peak=   -3.241 closest distance to " CD  GLU A 236 " =    1.043
peak=   -3.239 closest distance to " CG1 VAL A 112 " =    2.546
peak=   -3.236 closest distance to " ND2 ASN A 187 " =    1.469
peak=   -3.235 closest distance to " CA  GLY A 241 " =    2.225
peak=   -3.231 closest distance to " CD2 PHE A  59 " =    2.323
peak=   -3.227 closest distance to " O   HOH Z 372 " =    2.315
peak=   -3.227 closest distance to " O   SER A   3 " =    1.078
peak=   -3.227 closest distance to " O   MET A  47 " =    2.514
peak=   -3.225 closest distance to " O   HOH Z  37 " =    1.546
peak=   -3.224 closest distance to " CH2 TRP A 150 " =    1.076
peak=   -3.219 closest distance to " O   ALA A  10 " =    1.804
peak=   -3.213 closest distance to " O   HOH Z 126 " =    1.603
peak=   -3.208 closest distance to " O   THR A  52 " =    1.800
peak=   -3.204 closest distance to " N   THR A 220 " =    2.147
peak=   -3.203 closest distance to " O   HOH Z 250 " =    1.434
peak=   -3.201 closest distance to " O   HOH Z  41 " =    2.078
peak=   -3.200 closest distance to " O   HOH Z 222 " =    1.226
peak=   -3.195 closest distance to " OG  SER A  62 " =    1.294
peak=   -3.195 closest distance to " NH1 ARG A  66 " =    2.972
peak=   -3.193 closest distance to " O   HOH Z  46 " =    1.057
peak=   -3.193 closest distance to " OD1 ASN A 173 " =    1.458
peak=   -3.193 closest distance to " O   HOH Z 145 " =    2.148
peak=   -3.192 closest distance to " OD1 ASP A 191 " =    1.658
peak=   -3.192 closest distance to " O   HOH Z 120 " =    2.219
peak=   -3.190 closest distance to " C   VAL A 265 " =    0.876
peak=   -3.188 closest distance to " N   ALA A 248 " =    1.736
peak=   -3.187 closest distance to " O   HOH Z 176 " =    1.638
peak=   -3.182 closest distance to " CE1 TYR A 169 " =    2.098
peak=   -3.181 closest distance to " CG2 THR A   4 " =    1.788
peak=   -3.180 closest distance to " CG  ASN A 110 " =    1.035
peak=   -3.179 closest distance to " O   HOH Z 135 " =    1.581
peak=   -3.174 closest distance to " CB  PRO A 213 " =    1.454
peak=   -3.164 closest distance to " O   HOH Z  30 " =    1.420
peak=   -3.151 closest distance to " C   ALA A   8 " =    1.616
peak=   -3.149 closest distance to " O   HOH Z  17 " =    1.059
peak=   -3.147 closest distance to " O   HOH Z 191 " =    5.912
peak=   -3.145 closest distance to " CE  MET A  93 " =    1.224
peak=   -3.142 closest distance to " OG1 THR A  82 " =    1.307
peak=   -3.141 closest distance to " O   HOH Z 185 " =    2.223
peak=   -3.138 closest distance to " O   HOH Z 426 " =    2.435
peak=   -3.137 closest distance to " O   HOH Z  10 " =    1.525
peak=   -3.131 closest distance to " O   HOH Z 151 " =    1.592
peak=   -3.130 closest distance to " O   ALA A 256 " =    1.480
peak=   -3.129 closest distance to " O   HOH Z 380 " =    4.280
peak=   -3.127 closest distance to " NH2 ARG A  66 " =    5.257
peak=   -3.126 closest distance to " O   HOH Z  94 " =    2.219
peak=   -3.119 closest distance to " CE3 TRP A 150 " =    2.385
peak=   -3.116 closest distance to " O   HOH Z 198 " =    2.113
peak=   -3.113 closest distance to " O   HOH Z 424 " =    3.307
peak=   -3.109 closest distance to " C   GLY A  91 " =    1.374
peak=   -3.101 closest distance to " O   HOH Z 150 " =    1.707
peak=   -3.098 closest distance to " OG BSER A 134 " =    1.786
peak=   -3.091 closest distance to " OG ASER A 216 " =    1.028
peak=   -3.087 closest distance to " O   HOH Z 196 " =    2.028
peak=   -3.074 closest distance to " CG1 VAL A  78 " =    2.566
peak=   -3.062 closest distance to " O   HOH Z 198 " =    1.328
peak=   -3.058 closest distance to " O   HOH Z 313 " =    1.267
peak=   -3.057 closest distance to " O   ASP A 298 " =    1.853
peak=   -3.051 closest distance to " CE2 TRP A  85 " =    0.950
peak=   -3.045 closest distance to " CD2 HIS A 115 " =    0.978
peak=   -3.042 closest distance to " O   GLY A  80 " =    2.476
peak=   -3.040 closest distance to " ND2 ASN A  60 " =    1.552
peak=   -3.022 closest distance to " C   ALA A 158 " =    1.212
peak=   -3.022 closest distance to " O   HOH Z 424 " =    1.116
peak=   -3.008 closest distance to " CG  GLU A   2 " =    1.552
peak=   -3.004 closest distance to " O   ALA A   1 " =    2.354

================= 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    :  0.4721 0.4621   6.282177e+00   6.267639e+00
   1_bss:  0.4638 0.4513   6.274144e+00   6.256102e+00
   1_xyz:  0.3461 0.3761   6.084392e+00   6.142993e+00
   1_adp:  0.3147 0.3851   6.034758e+00   6.154625e+00
   1_occ:  0.3143 0.3848   6.033838e+00   6.153617e+00
   2_bss:  0.3132 0.3830   6.033522e+00   6.153172e+00
   2_xyz:  0.2580 0.3198   5.869100e+00   6.021247e+00
   2_adp:  0.2383 0.3106   5.827057e+00   6.007438e+00
   2_occ:  0.2381 0.3108   5.826930e+00   6.007525e+00
   3_bss:  0.2381 0.3107   5.826484e+00   6.006411e+00
   3_xyz:  0.2006 0.2649   5.661937e+00   5.865573e+00
   3_adp:  0.1914 0.2423   5.604099e+00   5.777275e+00
   3_occ:  0.1912 0.2422   5.603635e+00   5.777308e+00
   4_bss:  0.1912 0.2414   5.604450e+00   5.776088e+00
   4_xyz:  0.1459 0.1908   5.357211e+00   5.560974e+00
   4_adp:  0.1327 0.1801   5.280935e+00   5.500160e+00
   4_occ:  0.1326 0.1800   5.280259e+00   5.499661e+00
   5_bss:  0.1328 0.1804   5.283756e+00   5.502689e+00
   5_xyz:  0.1244 0.1724   5.233250e+00   5.457420e+00
   5_adp:  0.1222 0.1709   5.218666e+00   5.448472e+00
   5_occ:  0.1221 0.1709   5.218453e+00   5.448421e+00
   5_bss:  0.1221 0.1708   5.218571e+00   5.448608e+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:  0.306  20.001  -2.168   4.371  -0.208   0.000  -0.000  -0.000
   1_xyz:  0.306  20.001  -2.168   4.371  -0.208   0.000  -0.000  -0.000
   1_adp:  0.306  20.001  -2.168   4.371  -0.208   0.000  -0.000  -0.000
   1_occ:  0.306  20.001  -2.168   4.371  -0.208   0.000  -0.000  -0.000
   2_bss:  0.305  41.260  -1.276   2.915   0.295   0.000   0.000   0.000
   2_xyz:  0.305  41.260  -1.276   2.915   0.295   0.000   0.000   0.000
   2_adp:  0.305  41.260  -1.276   2.915   0.295   0.000   0.000   0.000
   2_occ:  0.305  41.260  -1.276   2.915   0.295   0.000   0.000   0.000
   3_bss:  0.316  50.147  -0.910   2.161   0.336   0.000   0.000   0.000
   3_xyz:  0.316  50.147  -0.910   2.161   0.336   0.000   0.000   0.000
   3_adp:  0.316  50.147  -0.910   2.161   0.336   0.000   0.000   0.000
   3_occ:  0.316  50.147  -0.910   2.161   0.336   0.000   0.000   0.000
   4_bss:  0.313  50.147  -1.666   0.735  -0.410   0.000  -0.000  -0.000
   4_xyz:  0.313  50.147  -1.666   0.735  -0.410   0.000  -0.000  -0.000
   4_adp:  0.313  50.147  -1.666   0.735  -0.410   0.000  -0.000  -0.000
   4_occ:  0.313  50.147  -1.666   0.735  -0.410   0.000  -0.000  -0.000
   5_bss:  0.323  54.254  -2.002  -0.113  -0.649  -0.000  -0.000  -0.000
   5_xyz:  0.323  54.254  -2.002  -0.113  -0.649  -0.000  -0.000  -0.000
   5_adp:  0.323  54.254  -2.002  -0.113  -0.649  -0.000  -0.000  -0.000
   5_occ:  0.323  54.254  -2.002  -0.113  -0.649  -0.000  -0.000  -0.000
   5_bss:  0.322  53.772  -1.910  -0.204  -0.536  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.776 0.4487  0.6050    67725.167
   1_bss:  54.671 0.4616  0.6364    64363.761
   1_xyz:  42.958 0.6061  0.8089    41516.472
   1_adp:  43.662 0.5971  0.7905    42632.652
   1_occ:  43.605 0.5977  0.7899    42488.687
   2_bss:  43.303 0.6015  0.7987    42118.586
   2_xyz:  34.561 0.7049  0.9158    28137.246
   2_adp:  33.415 0.7185  0.9041    26876.987
   2_occ:  33.408 0.7186  0.9041    26881.347
   3_bss:  33.326 0.7196  0.9023    26744.841
   3_xyz:  27.339 0.7857  0.9660    18504.215
   3_adp:  23.814 0.8242  0.9892    15179.981
   3_occ:  23.795 0.8245  0.9895    15170.470
   4_bss:  23.709 0.8253  0.9568    15088.771
   4_xyz:  18.094 0.8792  0.9896     9169.381
   4_adp:  16.674 0.8922  0.9880     8189.773
   4_occ:  16.664 0.8923  0.9881     8181.811
   5_bss:  16.709 0.8920  0.9717     8265.418
   5_xyz:  15.640 0.9016  0.9764     7553.798
   5_adp:  15.383 0.9039  0.9710     7439.998
   5_occ:  15.379 0.9040  0.9710     7437.395
   5_bss:  15.381 0.9040  0.9727     7438.935
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9116e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9116e-01
   1_xyz:   1.810  0.015  0.107 16.577  0.008  4.110   1.7421e-01
   1_adp:   1.810  0.015  0.107 16.577  0.008  4.110   1.7421e-01
   1_occ:   1.810  0.015  0.107 16.577  0.008  4.110   1.7421e-01
   2_bss:   1.810  0.015  0.107 16.577  0.008  4.110   1.7421e-01
   2_xyz:   1.289  0.009  0.086 14.920  0.005  4.112   8.4775e-02
   2_adp:   1.289  0.009  0.086 14.920  0.005  4.112   8.4775e-02
   2_occ:   1.289  0.009  0.086 14.920  0.005  4.112   8.4775e-02
   3_bss:   1.289  0.009  0.086 14.920  0.005  4.112   8.4775e-02
   3_xyz:   1.021  0.007  0.064 14.300  0.004  4.117   6.1499e-02
   3_adp:   1.021  0.007  0.064 14.300  0.004  4.117   6.1499e-02
   3_occ:   1.021  0.007  0.064 14.300  0.004  4.117   6.1499e-02
   4_bss:   1.021  0.007  0.064 14.300  0.004  4.117   6.1499e-02
   4_xyz:   1.193  0.009  0.080 14.936  0.005  4.115   8.0086e-02
   4_adp:   1.193  0.009  0.080 14.936  0.005  4.115   8.0086e-02
   4_occ:   1.193  0.009  0.080 14.936  0.005  4.115   8.0086e-02
   5_bss:   1.193  0.009  0.080 14.936  0.005  4.115   8.0086e-02
   5_xyz:   1.015  0.007  0.071 14.536  0.004  4.111   5.9770e-02
   5_adp:   1.015  0.007  0.071 14.536  0.004  4.111   5.9770e-02
   5_occ:   1.015  0.007  0.071 14.536  0.004  4.111   5.9770e-02
   5_bss:   1.015  0.007  0.071 14.536  0.004  4.111   5.9770e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.408   2.4147e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.408   2.4147e-01
   1_xyz:  10.148  0.119  0.488 86.156  0.066  1.950   1.3554e-01
   1_adp:  10.148  0.119  0.488 86.156  0.066  1.950   1.3554e-01
   1_occ:  10.148  0.119  0.488 86.156  0.066  1.950   1.3554e-01
   2_bss:  10.148  0.119  0.488 86.156  0.066  1.950   1.3554e-01
   2_xyz:   8.320  0.057  0.305 84.552  0.047  2.065   8.5549e-02
   2_adp:   8.320  0.057  0.305 84.552  0.047  2.065   8.5549e-02
   2_occ:   8.320  0.057  0.305 84.552  0.047  2.065   8.5549e-02
   3_bss:   8.320  0.057  0.305 84.552  0.047  2.065   8.5549e-02
   3_xyz:   7.131  0.042  0.295 86.073  0.043  2.310   5.1605e-02
   3_adp:   7.131  0.042  0.295 86.073  0.043  2.310   5.1605e-02
   3_occ:   7.131  0.042  0.295 86.073  0.043  2.310   5.1605e-02
   4_bss:   7.131  0.042  0.295 86.073  0.043  2.310   5.1605e-02
   4_xyz:   8.443  0.068  0.244 82.704  0.037  2.197   5.8078e-02
   4_adp:   8.443  0.068  0.244 82.704  0.037  2.197   5.8078e-02
   4_occ:   8.443  0.068  0.244 82.704  0.037  2.197   5.8078e-02
   5_bss:   8.443  0.068  0.244 82.704  0.037  2.197   5.8078e-02
   5_xyz:   7.261  0.040  0.254 83.062  0.035  2.346   4.1051e-02
   5_adp:   7.261  0.040  0.254 83.062  0.035  2.346   4.1051e-02
   5_occ:   7.261  0.040  0.254 83.062  0.035  2.346   4.1051e-02
   5_bss:   7.261  0.040  0.254 83.062  0.035  2.346   4.1051e-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:  93.49   0.00  18.96  90.83   0.00  15.52  93.49   0.00  37.74
   1_occ:  93.49   0.00  18.96  90.83   0.00  15.52  93.49   0.00  37.74
   2_bss:  93.49   0.00  18.96  90.83   0.00  15.52  93.49   0.00  37.74
   2_xyz:  93.49   0.00  18.96  90.83   0.00  15.52  93.49   0.00  37.74
   2_adp: 113.96   0.00  19.26 113.96   0.00  15.01 105.77   3.43  42.38
   2_occ: 113.96   0.00  19.26 113.96   0.00  15.01 105.77   3.43  42.38
   3_bss: 113.96   0.00  19.26 113.96   0.00  15.01 105.77   3.43  42.38
   3_xyz: 113.96   0.00  19.26 113.96   0.00  15.01 105.77   3.43  42.38
   3_adp: 103.72   0.00  17.58 103.72   0.00  13.36  92.86   4.10  40.53
   3_occ: 103.72   0.00  17.58 103.72   0.00  13.36  92.86   4.10  40.53
   4_bss: 103.72   0.00  17.58 103.72   0.00  13.36  92.86   4.10  40.53
   4_xyz: 103.72   0.00  17.58 103.72   0.00  13.36  92.86   4.10  40.53
   4_adp:  97.01   0.94  17.02  97.01   0.94  12.41  93.26   4.35  42.13
   4_occ:  97.01   0.94  17.02  97.01   0.94  12.41  93.26   4.35  42.13
   5_bss:  97.01   0.94  17.02  97.01   0.94  12.41  93.26   4.35  42.13
   5_xyz:  97.01   0.94  17.02  97.01   0.94  12.41  93.26   4.35  42.13
   5_adp:  98.69   0.00  16.73  98.69   0.00  12.10  98.64   4.44  41.95
   5_occ:  98.69   0.00  16.73  98.69   0.00  12.10  98.64   4.44  41.95
   5_bss:  98.69   0.00  16.73  98.69   0.00  12.10  98.64   4.44  41.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.884    0.026    0.474
   1_adp:    1.884    0.026    0.474
   1_occ:    1.884    0.026    0.474
   2_bss:    1.884    0.026    0.474
   2_xyz:    1.902    0.054    0.595
   2_adp:    1.902    0.054    0.595
   2_occ:    1.902    0.054    0.595
   3_bss:    1.902    0.054    0.595
   3_xyz:    1.961    0.078    0.719
   3_adp:    1.961    0.078    0.719
   3_occ:    1.961    0.078    0.719
   4_bss:    1.961    0.078    0.719
   4_xyz:    2.026    0.097    0.829
   4_adp:    2.026    0.097    0.829
   4_occ:    2.026    0.097    0.829
   5_bss:    2.026    0.097    0.829
   5_xyz:    2.065    0.052    0.850
   5_adp:    2.065    0.052    0.850
   5_occ:    2.065    0.052    0.850
   5_bss:    2.065    0.052    0.850
------------------------------------------------------------------------

CPU time actual refinement: 335.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/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_354/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_354/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.31 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 135.54 
    weights calculation          = 28.98  
    collect and process          = 6.44   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.76 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 106.67 
    alpha_beta                      = 8.19   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.78 
    fmodel                         = 6.90   
    r_factors                      = 0.23   
    phase_errors                   = 10.50  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 251.12 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.797 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    631 calls, 106.37 s
gradients_fft:          576 calls, 101.80 s

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

# Date 2008-01-16 Time 04:37:41 PST -0800 (1200487061.89 s)
Start R-work = 0.4721, R-free = 0.4621 (no bulk solvent and anisotropic scale)
Final R-work = 0.1407, R-free = 0.1868 (no bulk solvent and anisotropic scale)

Start R-work = 0.4638, R-free = 0.4513
Final R-work = 0.1221, R-free = 0.1708