# Date 2008-01-16 Time 06:17:45 PST -0800 (1200493065.98 s)
#phil __OFF__

Command line arguments: "../1090.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11811
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1090

-------------------------------------------------------------------------------
  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: (71.655, 45.7567, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.95157
Completeness in resolution range: 0.939656
Completeness with d_max=infinity: 0.936959

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9516

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: (71.655, 45.7567, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.95157
Completeness in resolution range: 0.939656
Completeness with d_max=infinity: 0.936959

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1778 [2186/2213]  1971   215   9.8%
  bin  2:  4.1778 -  3.3276 [2096/2116]  1883   213  10.2%
  bin  3:  3.3276 -  2.9104 [2084/2103]  1873   211  10.1%
  bin  4:  2.9104 -  2.6458 [2045/2075]  1841   204  10.0%
  bin  5:  2.6458 -  2.4571 [2058/2077]  1857   201   9.8%
  bin  6:  2.4571 -  2.3127 [2016/2041]  1804   212  10.5%
  bin  7:  2.3127 -  2.1973 [2049/2077]  1846   203   9.9%
  bin  8:  2.1973 -  2.1019 [2011/2047]  1818   193   9.6%
  bin  9:  2.1019 -  2.0212 [1965/2048]  1774   191   9.7%
  bin 10:  2.0212 -  1.9516 [1079/2050]   963   116  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/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:
        1.22 -     1.96: 13
        1.96 -     2.69: 187
        2.69 -     3.43: 4601
        3.43 -     4.16: 9520
        4.16 -     4.90: 14431
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.225 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.611 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.687 3.040 -x+1/2,-y+1,z+1/2
  " OG BSER A 216 " - " O   HOH Z 113 "  1.734 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28747 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_1090/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/model_refine_001.geo

CPU time processing inputs: 9.62


============================ 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 = 71.655 45.75675 84.6622 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: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5024   r_free= 0.5029   ksol= 0.00   Bsol= 0.00   scale= 0.872    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.303613                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6606 0.99   1420  162 0.4146 0.4329      6.6179      6.6769|
|  2:  4.6606 -  3.7173 0.99   1367  148 0.4525 0.4504      6.8714      6.8675|
|  3:  3.7173 -  3.2527 0.99   1336  142 0.4881 0.4578      6.7234      6.7477|
|  4:  3.2527 -  2.9578 0.99   1346  162 0.4978 0.5033       6.567      6.5218|
|  5:  2.9578 -  2.7471 0.99   1315  141 0.5275 0.5421      6.3882      6.3833|
|  6:  2.7471 -  2.5860 0.99   1316  148 0.5415 0.5304       6.304       6.285|
|  7:  2.5860 -  2.4571 0.99   1325  141 0.5350 0.5032      6.2548      6.1819|
|  8:  2.4571 -  2.3505 0.98   1287  152 0.5422 0.5357      6.1702      6.2002|
|  9:  2.3505 -  2.2603 0.98   1310  145 0.5357 0.5644      6.1515      6.1396|
| 10:  2.2603 -  2.1826 1.00   1279  148 0.5366 0.5509      6.0925      6.1019|
| 11:  2.1826 -  2.1145 0.98   1319  132 0.5364 0.5640      6.0441      6.0721|
| 12:  2.1145 -  2.0542 0.98   1278  152 0.5263 0.5666      5.9583      5.9929|
| 13:  2.0542 -  2.0003 0.89   1168  129 0.5432 0.5036      5.8785      5.8197|
| 14:  2.0003 -  1.9516 0.42    564   57 0.5421 0.4630      5.8364       5.801|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6606  1420   162  0.65  38.67   0.80     0.73      89198.08|
|  2:  4.6606 -  3.7173  1367   148  0.63  41.56   0.88     0.75     139038.21|
|  3:  3.7173 -  3.2527  1336   142  0.48  53.34   0.89     0.67     150438.33|
|  4:  3.2527 -  2.9578  1346   162  0.34  64.04   0.90     0.51     139303.81|
|  5:  2.9578 -  2.7471  1315   141  0.23  73.08   0.85     0.34     107057.40|
|  6:  2.7471 -  2.5860  1316   148  0.19  75.57   0.86     0.29      92023.83|
|  7:  2.5860 -  2.4571  1325   141  0.22  73.84   0.88     0.31      75899.30|
|  8:  2.4571 -  2.3505  1287   152  0.25  71.57   0.89     0.37      67371.41|
|  9:  2.3505 -  2.2603  1310   145  0.24  72.08   0.92     0.35      61101.53|
| 10:  2.2603 -  2.1826  1279   148  0.19  76.05   0.91     0.29      58677.41|
| 11:  2.1826 -  2.1145  1319   132  0.13  80.36   0.95     0.20      56710.97|
| 12:  2.1145 -  2.0542  1278   152  0.15  78.56   0.94     0.25      50310.21|
| 13:  2.0542 -  2.0003  1168   129  0.23  72.60   0.93     0.39      40522.87|
| 14:  2.0003 -  1.9516   564    57  0.38  61.86   0.95     0.59      29407.66|
|alpha:            min =        0.20 max =            0.75 mean =         0.43|
|beta:             min =    29407.66 max =       150438.33 mean =     85790.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.50|
|phase err.(test): min =        0.00 max =           89.99 mean =        66.69|
|-----------------------------------------------------------------------------|

============================== 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 = 24.982319             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.358   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.701476              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.786   (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 |  1.225 -  1.592:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.592 -  1.960:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.960 -  2.327:       28 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.327 -  2.695:      159 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.695 -  3.062:     2261 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.062 -  3.430:     2340 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.430 -  3.797:     4135 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.797 -  4.165:     5385 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.165 -  4.532:     6466 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.532 -  4.900:     7965 |
|-----------------------------------------------------------------------------|
|-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 |        0.197 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.225 |       0.727 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    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: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5024   r_free= 0.5029   ksol= 0.00   Bsol= 0.00   scale= 0.872    |
|                                                                             |
| 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:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.303613                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4958   r_free= 0.4959   ksol= 0.30   Bsol= 20.00   scale= 0.901   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,0.75,0.18,0.00,0.00,0.00); trace/3= 0.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.302619                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.139681             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.443   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.045622              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.360   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4958      final r-factor (work) = 0.4159          |
| start r-factor (free) = 0.4959      final r-factor (free) = 0.4544          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.4697 = 19.14 * 0.50 * 6.2982 + 1.00 * 0.1974                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.8316 = 19.14 * 0.50 * 6.2346 + 1.00 * 0.1679                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4159      final r-factor (work) = 0.3818          |
| start r-factor (free) = 0.4544      final r-factor (free) = 0.4661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7596 = 2.05 * 1.00 * 6.2346 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.6431 = 2.05 * 1.00 * 6.1683 + 1.00 * 0.0252                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.83  19.75    None  None   None       |
|    all(noH): 2823   0      0.00    103.83  19.75    None  None   None       |
|    Sol.    : 438    0      0.00    103.83  32.87    None  None   None       |
|    Mac.    : 2385   0      0.00    89.55   17.35    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 -  10.383:  853   |   5:    51.913 -  62.296:   59        |
|      1:    10.383 -  20.765:  860   |   6:    62.296 -  72.678:   28        |
|      2:    20.765 -  31.148:  586   |   7:    72.678 -  83.061:   16        |
|      3:    31.148 -  41.530:  272   |   8:    83.061 -  93.443:    5        |
|      4:    41.530 -  51.913:  140   |   9:    93.443 - 103.826:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3818 r_free = 0.4661             target_work(ml) = 6.176         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3813 r_free = 0.4655             target_work(ml) = 6.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3813   r_free= 0.4655   ksol= 0.30   Bsol= 20.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,0.75,0.18,0.00,0.00,0.00); trace/3= 0.16                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.174794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3817   r_free= 0.4643   ksol= 0.35   Bsol= 57.17   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,0.64,0.76,0.00,0.00,0.00); trace/3= 0.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.176951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.701248             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.280   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.841433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.580  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3817      final r-factor (work) = 0.3250          |
| start r-factor (free) = 0.4643      final r-factor (free) = 0.4098          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 67.1284 = 21.70 * 0.50 * 6.1711 + 1.00 * 0.1679                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.6572 = 21.70 * 0.50 * 6.1319 + 1.00 * 0.1217                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3250      final r-factor (work) = 0.3060          |
| start r-factor (free) = 0.4098      final r-factor (free) = 0.3972          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1848 = 0.84 * 1.00 * 6.1319 + 1.00 * 0.0251                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1009 = 0.84 * 1.00 * 6.0446 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.24  18.64    None  None   None       |
|    all(noH): 2823   0      0.00    101.24  18.64    None  None   None       |
|    Sol.    : 438    0      0.00    101.24  33.87    None  None   None       |
|    Mac.    : 2385   0      0.00    91.32   15.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.124:  887   |   5:    50.621 -  60.745:   72        |
|      1:    10.124 -  20.248:  928   |   6:    60.745 -  70.869:   22        |
|      2:    20.248 -  30.372:  536   |   7:    70.869 -  80.993:    6        |
|      3:    30.372 -  40.497:  249   |   8:    80.993 -  91.117:    5        |
|      4:    40.497 -  50.621:  114   |   9:    91.117 - 101.241:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3060 r_free = 0.3972             target_work(ml) = 6.029         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3059 r_free = 0.3966             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3059   r_free= 0.3966   ksol= 0.35   Bsol= 57.17   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,0.64,0.76,0.00,0.00,0.00); trace/3= 0.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.028185                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3065   r_free= 0.3960   ksol= 0.37   Bsol= 70.76   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.36,-0.03,0.66,-0.00,0.00,0.00); trace/3= 0.33                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.025957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.368454              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.432  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.121481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.492  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3065      final r-factor (work) = 0.2670          |
| start r-factor (free) = 0.3960      final r-factor (free) = 0.3516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3695 = 6.37 * 0.50 * 6.0447 + 1.00 * 0.1217                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1131 = 6.37 * 0.50 * 5.9817 + 1.00 * 0.0660                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2670      final r-factor (work) = 0.2602          |
| start r-factor (free) = 0.3516      final r-factor (free) = 0.3492          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7232 = 1.12 * 1.00 * 5.9817 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6548 = 1.12 * 1.00 * 5.9046 + 1.00 * 0.0330                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.63  18.65    None  None   None       |
|    all(noH): 2823   0      0.00    101.63  18.65    None  None   None       |
|    Sol.    : 438    0      0.00    101.63  35.22    None  None   None       |
|    Mac.    : 2385   0      0.00    91.64   15.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.163:  882   |   5:    50.813 -  60.976:   72        |
|      1:    10.163 -  20.325:  948   |   6:    60.976 -  71.138:   23        |
|      2:    20.325 -  30.488:  510   |   7:    71.138 -  81.301:    6        |
|      3:    30.488 -  40.650:  255   |   8:    81.301 -  91.463:    5        |
|      4:    40.650 -  50.813:  118   |   9:    91.463 - 101.626:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2602 r_free = 0.3492             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2601 r_free = 0.3489             target_work(ml) = 5.898         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2601   r_free= 0.3489   ksol= 0.37   Bsol= 70.76   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.36,-0.03,0.66,-0.00,0.00,0.00); trace/3= 0.33                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.897856                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2600   r_free= 0.3478   ksol= 0.34   Bsol= 55.85   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.63,0.13,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.896033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.370370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.140  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.213981              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.082   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2600      final r-factor (work) = 0.2188          |
| start r-factor (free) = 0.3478      final r-factor (free) = 0.2934          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9184 = 5.37 * 0.50 * 5.9037 + 1.00 * 0.0660                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7313 = 5.37 * 0.50 * 5.8309 + 1.00 * 0.0743                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2188      final r-factor (work) = 0.1897          |
| start r-factor (free) = 0.2934      final r-factor (free) = 0.2591          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9273 = 2.21 * 1.00 * 5.8309 + 1.00 * 0.0178                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5952 = 2.21 * 1.00 * 5.6812 + 1.00 * 0.0171                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.01  18.89    None  None   None       |
|    all(noH): 2823   0      0.00    106.01  18.89    None  None   None       |
|    Sol.    : 438    0      4.45    105.18  46.62    None  None   None       |
|    Mac.    : 2385   0      0.00    106.01  13.80    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 -  10.601: 1176   |   5:    53.003 -  63.604:  105        |
|      1:    10.601 -  21.201:  911   |   6:    63.604 -  74.205:   71        |
|      2:    21.201 -  31.802:  243   |   7:    74.205 -  84.805:   26        |
|      3:    31.802 -  42.403:  147   |   8:    84.805 -  95.406:   10        |
|      4:    42.403 -  53.003:  131   |   9:    95.406 - 106.007:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1897 r_free = 0.2591             target_work(ml) = 5.622         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1894 r_free = 0.2591             target_work(ml) = 5.621         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1894   r_free= 0.2591   ksol= 0.34   Bsol= 55.85   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.23,-0.63,0.13,-0.00,0.00,0.00); trace/3= -0.25                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.621126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1897   r_free= 0.2590   ksol= 0.33   Bsol= 56.73   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-1.41,-0.27,-0.00,-0.00,-0.00); trace/3= -0.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.620559                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.822164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.009  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.788262              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 111.022  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2590      final r-factor (free) = 0.2225          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9324 = 3.82 * 0.50 * 5.6817 + 1.00 * 0.0743                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6681 = 3.82 * 0.50 * 5.5521 + 1.00 * 0.0577                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1592      final r-factor (work) = 0.1475          |
| start r-factor (free) = 0.2225      final r-factor (free) = 0.2061          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3933 = 0.79 * 1.00 * 5.5521 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2961 = 0.79 * 1.00 * 5.4335 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.29  18.11    None  None   None       |
|    all(noH): 2823   0      0.00    108.29  18.11    None  None   None       |
|    Sol.    : 438    0      5.03    105.31  47.45    None  None   None       |
|    Mac.    : 2385   0      0.00    108.29  12.72    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 -  10.829: 1362   |   5:    54.143 -  64.971:  103        |
|      1:    10.829 -  21.657:  829   |   6:    64.971 -  75.800:   61        |
|      2:    21.657 -  32.486:  202   |   7:    75.800 -  86.629:   25        |
|      3:    32.486 -  43.314:  113   |   8:    86.629 -  97.457:    8        |
|      4:    43.314 -  54.143:  115   |   9:    97.457 - 108.286:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1475 r_free = 0.2061             target_work(ml) = 5.393         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1473 r_free = 0.2057             target_work(ml) = 5.391         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.2057   ksol= 0.33   Bsol= 56.73   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-1.41,-0.27,-0.00,-0.00,-0.00); trace/3= -0.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.391175                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6606 0.99   1420  162 0.1090 0.1486      5.4836      5.7044|
|  2:  4.6606 -  3.7173 0.99   1367  148 0.1000 0.1360      5.5999      5.8575|
|  3:  3.7173 -  3.2527 0.99   1336  142 0.1386 0.1884      5.6935      6.0195|
|  4:  3.2527 -  2.9578 0.99   1346  162 0.1625 0.2313      5.7188      5.9072|
|  5:  2.9578 -  2.7471 0.99   1315  141 0.1768 0.2305      5.5941      5.8127|
|  6:  2.7471 -  2.5860 0.99   1316  148 0.1688 0.2394       5.486      5.6645|
|  7:  2.5860 -  2.4571 0.99   1325  141 0.1652 0.2360      5.4019      5.6261|
|  8:  2.4571 -  2.3505 0.98   1287  152 0.1664 0.2274      5.3403      5.5778|
|  9:  2.3505 -  2.2603 0.98   1310  145 0.1627 0.2490      5.3155      5.5544|
| 10:  2.2603 -  2.1826 1.00   1279  148 0.1535 0.2432      5.2231      5.4914|
| 11:  2.1826 -  2.1145 0.98   1319  132 0.1489 0.2223      5.1712      5.4883|
| 12:  2.1145 -  2.0542 0.98   1278  152 0.1466 0.2096      5.0916      5.3236|
| 13:  2.0542 -  2.0003 0.89   1168  129 0.1657 0.2426      5.0605       5.306|
| 14:  2.0003 -  1.9516 0.42    564   57 0.1664 0.1763       4.986      5.1421|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6606  1420   162  0.92  11.85   0.97     0.95       9996.41|
|  2:  4.6606 -  3.7173  1367   148  0.94  10.44   1.04     1.02      12914.18|
|  3:  3.7173 -  3.2527  1336   142  0.90  15.74   1.07     1.07      16256.31|
|  4:  3.2527 -  2.9578  1346   162  0.86  20.64   1.05     1.01      19273.24|
|  5:  2.9578 -  2.7471  1315   141  0.84  22.52   1.02     0.98      15308.93|
|  6:  2.7471 -  2.5860  1316   148  0.84  22.34   1.02     0.98      12843.16|
|  7:  2.5860 -  2.4571  1325   141  0.84  22.11   1.02     0.97      10847.47|
|  8:  2.4571 -  2.3505  1287   152  0.85  22.05   1.01     0.96       9493.61|
|  9:  2.3505 -  2.2603  1310   145  0.84  22.69   1.03     0.97       9230.91|
| 10:  2.2603 -  2.1826  1279   148  0.85  21.57   1.02     0.98       7896.27|
| 11:  2.1826 -  2.1145  1319   132  0.85  21.78   1.03     0.97       7256.97|
| 12:  2.1145 -  2.0542  1278   152  0.85  21.44   1.02     0.98       6432.15|
| 13:  2.0542 -  2.0003  1168   129  0.85  22.31   1.03     1.01       5692.08|
| 14:  2.0003 -  1.9516   564    57  0.86  20.96   1.01     0.98       4503.76|
|alpha:            min =        0.95 max =            1.07 mean =         0.99|
|beta:             min =     4503.76 max =        19273.24 mean =     10907.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           90.00 mean =        19.74|
|phase err.(test): min =        0.00 max =           89.97 mean =        19.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.2056   ksol= 0.32   Bsol= 53.59   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,-1.86,-0.72,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.390371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.2056   ksol= 0.32   Bsol= 53.59   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,-1.86,-0.72,-0.00,-0.00,-0.00); trace/3= -1.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.390371                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6606 0.99   1420  162 0.1078 0.1462      5.4695      5.6873|
|  2:  4.6606 -  3.7173 0.99   1367  148 0.1009 0.1362      5.6007      5.8615|
|  3:  3.7173 -  3.2527 0.99   1336  142 0.1388 0.1881       5.695      6.0163|
|  4:  3.2527 -  2.9578 0.99   1346  162 0.1627 0.2323      5.7202      5.9113|
|  5:  2.9578 -  2.7471 0.99   1315  141 0.1769 0.2306      5.5947      5.8134|
|  6:  2.7471 -  2.5860 0.99   1316  148 0.1691 0.2397      5.4873      5.6663|
|  7:  2.5860 -  2.4571 0.99   1325  141 0.1651 0.2364       5.402      5.6268|
|  8:  2.4571 -  2.3505 0.98   1287  152 0.1663 0.2276      5.3405      5.5792|
|  9:  2.3505 -  2.2603 0.98   1310  145 0.1624 0.2492      5.3151       5.555|
| 10:  2.2603 -  2.1826 1.00   1279  148 0.1536 0.2431      5.2232      5.4914|
| 11:  2.1826 -  2.1145 0.98   1319  132 0.1488 0.2218      5.1707      5.4879|
| 12:  2.1145 -  2.0542 0.98   1278  152 0.1466 0.2096      5.0912       5.323|
| 13:  2.0542 -  2.0003 0.89   1168  129 0.1657 0.2424      5.0604      5.3067|
| 14:  2.0003 -  1.9516 0.42    564   57 0.1664 0.1764      4.9855      5.1411|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6606  1420   162  0.92  11.56   0.97     0.94       9545.57|
|  2:  4.6606 -  3.7173  1367   148  0.94  10.31   1.03     1.02      12725.34|
|  3:  3.7173 -  3.2527  1336   142  0.90  15.77   1.06     1.06      16320.61|
|  4:  3.2527 -  2.9578  1346   162  0.86  20.66   1.03     1.00      19337.57|
|  5:  2.9578 -  2.7471  1315   141  0.84  22.55   1.01     0.97      15349.93|
|  6:  2.7471 -  2.5860  1316   148  0.84  22.37   1.00     0.96      12878.71|
|  7:  2.5860 -  2.4571  1325   141  0.84  22.10   1.00     0.96      10859.64|
|  8:  2.4571 -  2.3505  1287   152  0.85  22.07   0.99     0.95       9509.70|
|  9:  2.3505 -  2.2603  1310   145  0.84  22.69   1.01     0.95       9239.03|
| 10:  2.2603 -  2.1826  1279   148  0.85  21.56   1.00     0.96       7899.90|
| 11:  2.1826 -  2.1145  1319   132  0.85  21.77   1.01     0.95       7255.29|
| 12:  2.1145 -  2.0542  1278   152  0.85  21.43   0.99     0.96       6424.54|
| 13:  2.0542 -  2.0003  1168   129  0.85  22.29   1.00     0.98       5687.18|
| 14:  2.0003 -  1.9516   564    57  0.86  20.93   0.98     0.95       4495.44|
|alpha:            min =        0.94 max =            1.06 mean =         0.97|
|beta:             min =     4495.44 max =        19337.57 mean =     10874.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.85 mean =        19.71|
|phase err.(test): min =        0.00 max =           89.86 mean =        18.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.568)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.29  18.11    None  None   None       |
|    all(noH): 2823   0      0.00    108.29  18.11    None  None   None       |
|    Sol.    : 438    0      5.04    105.31  47.45    None  None   None       |
|    Mac.    : 2385   0      0.00    108.29  12.72    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 -  10.832: 1362   |   5:    54.146 -  64.974:  103        |
|      1:    10.832 -  21.660:  829   |   6:    64.974 -  75.803:   61        |
|      2:    21.660 -  32.489:  202   |   7:    75.803 -  86.632:   25        |
|      3:    32.489 -  43.317:  113   |   8:    86.632 -  97.460:    8        |
|      4:    43.317 -  54.146:  115   |   9:    97.460 - 108.289:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 352         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.856
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 349 from: 352
   mapped sites are within: 0.728 - 5.856

peak=    8.410 closest distance to " O   HOH Z 138 " =    1.252
peak=    8.106 closest distance to " O   HOH Z 390 " =    1.516
peak=    6.482 closest distance to " O   HOH Z 289 " =    1.772
peak=    6.317 closest distance to " O   HOH Z 159 " =    1.168
peak=    6.139 closest distance to " O   HOH Z 350 " =    1.593
peak=    6.114 closest distance to " O   HOH Z 120 " =    1.566
peak=    6.079 closest distance to " O   HOH Z  61 " =    1.897
peak=    5.944 closest distance to " O   HOH Z 103 " =    1.104
peak=    5.941 closest distance to " O   HOH Z 205 " =    1.209
peak=    5.805 closest distance to " O   HOH Z 385 " =    1.500
peak=    5.630 closest distance to " O   SER A  62 " =    1.016
peak=    5.426 closest distance to " O   HOH Z 381 " =    1.290
peak=    5.359 closest distance to " O   HOH Z 431 " =    1.596
peak=    5.336 closest distance to " O   HOH Z  65 " =    1.666
peak=    5.303 closest distance to " O   HOH Z 117 " =    1.574
peak=    5.284 closest distance to " CG  PRO A  90 " =    1.123
peak=    5.253 closest distance to " O   HOH Z  93 " =    1.735
peak=    5.233 closest distance to " O   HOH Z 214 " =    2.046
peak=    5.206 closest distance to " CA  SER A  62 " =    1.059
peak=    5.177 closest distance to " O   HOH Z 222 " =    1.812
peak=    5.157 closest distance to " O   HOH Z 403 " =    1.669
peak=    5.149 closest distance to " O   HOH Z  41 " =    1.034
peak=    5.136 closest distance to " N   SER A  63 " =    0.858
peak=    5.136 closest distance to " O   HOH Z 182 " =    1.643
peak=    5.117 closest distance to " NE2 GLN A  11 " =    1.498
peak=    5.059 closest distance to " O   HOH Z 133 " =    1.726
peak=    5.052 closest distance to " O   HOH Z  78 " =    1.883
peak=    5.026 closest distance to " CB  SER A 216 " =    1.044
peak=    4.983 closest distance to " O   HOH Z 415 " =    1.268
peak=    4.866 closest distance to " O   HOH Z 130 " =    0.990
peak=    4.841 closest distance to " O   HOH Z   7 " =    2.090
peak=    4.753 closest distance to " O   HOH Z 417 " =    2.042
peak=    4.730 closest distance to " O   HOH Z 131 " =    1.139
peak=    4.727 closest distance to " O   HOH Z 416 " =    1.488
peak=    4.620 closest distance to " CB  PRO A  54 " =    1.186
peak=    4.617 closest distance to " OE1 GLN A  88 " =    1.072
peak=    4.615 closest distance to " O   HOH Z 124 " =    1.193
peak=    4.592 closest distance to " O   HOH Z 245 " =    1.271
peak=    4.576 closest distance to " O   HOH Z  37 " =    1.293
peak=    4.572 closest distance to " O   HOH Z  59 " =    1.494
peak=    4.566 closest distance to " N   GLU A   2 " =    1.398
peak=    4.543 closest distance to " O   HOH Z 278 " =    1.339
peak=    4.522 closest distance to " O   HOH Z 414 " =    1.898
peak=    4.478 closest distance to " O   HOH Z 244 " =    1.493
peak=    4.478 closest distance to " O   HOH Z 258 " =    1.379
peak=    4.475 closest distance to " NH2BARG A 102 " =    1.080
peak=    4.442 closest distance to " N   GLN A 278 " =    1.114
peak=    4.437 closest distance to " O   HOH Z 363 " =    1.309
peak=    4.420 closest distance to " O   HOH Z 358 " =    1.370
peak=    4.419 closest distance to " CG  PRO A 198 " =    1.432
peak=    4.405 closest distance to " O   HOH Z 232 " =    2.093
peak=    4.400 closest distance to " CE  MET A  93 " =    1.554
peak=    4.391 closest distance to " O   HOH Z 399 " =    0.856
peak=    4.379 closest distance to " O   HOH Z 374 " =    1.217
peak=    4.358 closest distance to " O   HOH Z 144 " =    1.795
peak=    4.352 closest distance to " O   HOH Z 383 " =    1.236
peak=    4.347 closest distance to " O   HOH Z  49 " =    1.618
peak=    4.334 closest distance to " ND2 ASN A 249 " =    1.888
peak=    4.331 closest distance to " O   HOH Z 427 " =    1.895
peak=    4.324 closest distance to " O   HOH Z 316 " =    2.948
peak=    4.319 closest distance to " O   ALA A 165 " =    1.201
peak=    4.312 closest distance to " O   HOH Z  29 " =    1.128
peak=    4.301 closest distance to " O   HOH Z 427 " =    1.797
peak=    4.278 closest distance to " O   HOH Z 179 " =    1.091
peak=    4.272 closest distance to " CB  ASP A 124 " =    1.022
peak=    4.228 closest distance to " CG  LEU A 167 " =    1.280
peak=    4.210 closest distance to " O   SER A  87 " =    2.247
peak=    4.198 closest distance to " OD1 ASP A  50 " =    1.111
peak=    4.181 closest distance to " O   HOH Z 402 " =    1.404
peak=    4.177 closest distance to " O   HOH Z 147 " =    1.749
peak=    4.170 closest distance to " O   HOH Z  63 " =    1.736
peak=    4.144 closest distance to " O   HOH Z 424 " =    1.284
peak=    4.142 closest distance to " O   HOH Z 112 " =    1.124
peak=    4.136 closest distance to " CA  TYR A  30 " =    1.141
peak=    4.133 closest distance to " NZ BLYS A 290 " =    1.294
peak=    4.120 closest distance to " O   HOH Z 178 " =    1.194
peak=    4.115 closest distance to " O   HOH Z  28 " =    1.790
peak=    4.095 closest distance to " O   HOH Z 134 " =    1.805
peak=    4.091 closest distance to " O   ASN A 285 " =    0.910
peak=    4.087 closest distance to " CB  MET A  47 " =    1.286
peak=    4.073 closest distance to " O   HOH Z 284 " =    1.678
peak=    4.070 closest distance to " CA  GLY A  98 " =    1.137
peak=    4.063 closest distance to " O   HOH Z 400 " =    0.806
peak=    4.056 closest distance to " O   HOH Z 344 " =    1.235
peak=    4.042 closest distance to " CG2 THR A 279 " =    1.349
peak=    4.039 closest distance to " O   HOH Z 126 " =    1.672
peak=    4.037 closest distance to " O   PRO A 198 " =    1.303
peak=    4.034 closest distance to " CB  ARG A 275 " =    1.165
peak=    4.026 closest distance to " O   HOH Z 119 " =    1.279
peak=    3.991 closest distance to " N   ARG A 156 " =    1.285
peak=    3.990 closest distance to " O   HOH Z 183 " =    1.588
peak=    3.977 closest distance to " N   GLY A 287 " =    0.958
peak=    3.971 closest distance to " OE1 GLN A  58 " =    5.314
peak=    3.943 closest distance to " O   HOH Z 126 " =    1.982
peak=    3.930 closest distance to " CD ALYS A 290 " =    1.161
peak=    3.929 closest distance to " N   TYR A  15 " =    1.192
peak=    3.914 closest distance to " O   HOH Z 411 " =    3.132
peak=    3.911 closest distance to " O   HOH Z   5 " =    1.446
peak=    3.890 closest distance to " O   HOH Z 287 " =    2.107
peak=    3.889 closest distance to " CG  GLN A  88 " =    0.989
peak=    3.885 closest distance to " O   HOH Z 139 " =    1.647
peak=    3.877 closest distance to " CB  SER A  63 " =    1.615
peak=    3.870 closest distance to " O   HOH Z 111 " =    1.645
peak=    3.860 closest distance to " O   HOH Z 255 " =    0.915
peak=    3.858 closest distance to " NZ  LYS A 117 " =    1.183
peak=    3.855 closest distance to " O   HOH Z 186 " =    1.566
peak=    3.845 closest distance to " CB  ASN A  60 " =    0.843
peak=    3.844 closest distance to " CB  TRP A 266 " =    0.948
peak=    3.843 closest distance to " O   HOH Z  53 " =    2.410
peak=    3.842 closest distance to " O   HOH Z   2 " =    1.959
peak=    3.834 closest distance to " O   HOH Z 233 " =    1.441
peak=    3.827 closest distance to " O   HOH Z   9 " =    1.120
peak=    3.827 closest distance to " ND2 ASN A 285 " =    0.971
peak=    3.810 closest distance to " O   HOH Z 132 " =    1.326
peak=    3.804 closest distance to " CB  PRO A  54 " =    1.241
peak=    3.799 closest distance to " O   HOH Z 145 " =    2.417
peak=    3.797 closest distance to " N   GLN A  73 " =    1.483
peak=    3.791 closest distance to " CG  PRO A 213 " =    1.274
peak=    3.788 closest distance to " OG ASER A 134 " =    1.335
peak=    3.771 closest distance to " CB  GLU A 128 " =    1.049
peak=    3.763 closest distance to " CB  ALA A 233 " =    1.282
peak=    3.760 closest distance to " O   HOH Z 215 " =    1.566
peak=    3.752 closest distance to " O   HOH Z  11 " =    1.392
peak=    3.752 closest distance to " OD1 ASP A 238 " =    0.942
peak=    3.741 closest distance to " CB  ASN A 148 " =    1.339
peak=    3.739 closest distance to " O   HOH Z  46 " =    1.188
peak=    3.728 closest distance to " CE3 TRP A 274 " =    1.411
peak=    3.724 closest distance to " O   HOH Z 276 " =    1.304
peak=    3.722 closest distance to " O   HOH Z 371 " =    2.135
peak=    3.717 closest distance to " O   HOH Z 368 " =    1.659
peak=    3.710 closest distance to " O   HOH Z  48 " =    1.920
peak=    3.702 closest distance to " CG2 THR A 221 " =    1.176
peak=    3.694 closest distance to " O   HOH Z  54 " =    1.363
peak=    3.689 closest distance to " O   HOH Z 325 " =    1.923
peak=    3.681 closest distance to " O   HOH Z  39 " =    1.180
peak=    3.679 closest distance to " O   HOH Z 199 " =    1.273
peak=    3.678 closest distance to " O   HOH Z 116 " =    1.242
peak=    3.666 closest distance to " CB  GLN A 183 " =    1.111
peak=    3.662 closest distance to " CA  LEU A 282 " =    1.068
peak=    3.659 closest distance to " O   HOH Z   6 " =    1.926
peak=    3.643 closest distance to " O   ASN A 217 " =    1.236
peak=    3.643 closest distance to " N   PHE A 130 " =    1.198
peak=    3.641 closest distance to " ND2 ASN A  60 " =    3.092
peak=    3.639 closest distance to " O   HOH Z 246 " =    1.334
peak=    3.638 closest distance to " O   HOH Z 272 " =    1.833
peak=    3.635 closest distance to " CD1 PHE A 283 " =    1.205
peak=    3.635 closest distance to " O   HOH Z 269 " =    1.282
peak=    3.623 closest distance to " OG BSER A  12 " =    1.043
peak=    3.612 closest distance to " O   HOH Z 410 " =    1.238
peak=    3.609 closest distance to " O   HOH Z  84 " =    0.827
peak=    3.599 closest distance to " CG  LYS A 166 " =    1.398
peak=    3.588 closest distance to " CD  GLN A 240 " =    2.075
peak=    3.587 closest distance to " O   HOH Z 189 " =    1.978
peak=    3.586 closest distance to " CB  ALA A   1 " =    1.111
peak=    3.584 closest distance to " CD2 TRP A 179 " =    2.072
peak=    3.578 closest distance to " CG  PHE A  59 " =    1.111
peak=    3.570 closest distance to " CA  ALA A 295 " =    1.054
peak=    3.568 closest distance to " CB  ALA A 104 " =    1.279
peak=    3.566 closest distance to " CG1BVAL A 121 " =    1.891
peak=    3.557 closest distance to " O   ARG A  14 " =    1.048
peak=    3.556 closest distance to " O   ASP A 286 " =    2.369
peak=    3.549 closest distance to " O   HOH Z 221 " =    1.944
peak=    3.541 closest distance to " CA  SER A  12 " =    1.423
peak=    3.540 closest distance to " O   HOH Z 225 " =    1.736
peak=    3.538 closest distance to " O   HOH Z  88 " =    3.780
peak=    3.536 closest distance to " O   HOH Z 364 " =    1.372
peak=    3.530 closest distance to " O   HOH Z 298 " =    2.174
peak=    3.529 closest distance to " N   CYS A 260 " =    0.976
peak=    3.528 closest distance to " O   HOH Z 311 " =    1.592
peak=    3.527 closest distance to " NH2BARG A 190 " =    1.575
peak=    3.527 closest distance to " C   ASP A  50 " =    1.123
peak=    3.523 closest distance to " O   HOH Z 114 " =    1.845
peak=    3.521 closest distance to " O   HOH Z 434 " =    1.577
peak=    3.521 closest distance to " CZ  PHE A  38 " =    1.415
peak=    3.521 closest distance to " O   HOH Z 380 " =    2.015
peak=    3.516 closest distance to " CA  ARG A 195 " =    1.382
peak=    3.516 closest distance to " CA  GLU A  46 " =    0.764
peak=    3.514 closest distance to " NH1 ARG A  56 " =    1.266
peak=    3.512 closest distance to " CB  ASN A 148 " =    2.042
peak=    3.511 closest distance to " CE AMET A  47 " =    1.537
peak=    3.506 closest distance to " O   HOH Z 128 " =    1.566
peak=    3.504 closest distance to " O   HOH Z 151 " =    1.601
peak=    3.503 closest distance to " CG  PRO A 243 " =    1.192
peak=    3.498 closest distance to " CD  ARG A 138 " =    0.905
peak=    3.497 closest distance to " O   HOH Z  57 " =    1.304
peak=    3.497 closest distance to " CB  ALA A  10 " =    1.216
peak=    3.489 closest distance to " O   HOH Z 369 " =    1.555
peak=    3.488 closest distance to " O   HOH Z  69 " =    2.141
peak=    3.486 closest distance to " NE1 TRP A 274 " =    1.120
peak=    3.483 closest distance to " O   HOH Z 158 " =    1.400
peak=    3.482 closest distance to " O   HOH Z 146 " =    1.582
peak=    3.471 closest distance to " O   HOH Z 284 " =    1.343
peak=    3.468 closest distance to " CD2 LEU A  25 " =    1.047
peak=    3.467 closest distance to " O  BHOH Z 338 " =    2.188
peak=    3.464 closest distance to " O   HOH Z 293 " =    1.184
peak=    3.461 closest distance to " O   HOH Z 217 " =    2.755
peak=    3.452 closest distance to " CA  ALA A  21 " =    1.269
peak=    3.450 closest distance to " O   HOH Z 105 " =    1.319
peak=    3.446 closest distance to " N   ASN A 285 " =    0.851
peak=    3.445 closest distance to " O   HOH Z 130 " =    2.282
peak=    3.444 closest distance to " O   HOH Z 127 " =    0.965
peak=    3.442 closest distance to " O   HOH Z 302 " =    1.522
peak=    3.435 closest distance to " CB  LEU A 143 " =    1.005
peak=    3.434 closest distance to " O   HOH Z  32 " =    2.279
peak=    3.431 closest distance to " CB  PHE A 225 " =    1.529
peak=    3.430 closest distance to " N   ALA A 100 " =    0.869
peak=    3.428 closest distance to " O   HOH Z 211 " =    1.623
peak=    3.427 closest distance to " O   HOH Z  47 " =    1.636
peak=    3.426 closest distance to " OG  SER A  26 " =    1.279
peak=    3.426 closest distance to " O   HOH Z  22 " =    1.842
peak=    3.418 closest distance to " O   HOH Z 319 " =    1.374
peak=    3.415 closest distance to " CB  ASP A 132 " =    3.775
peak=    3.414 closest distance to " OG BSER A 258 " =    1.090
peak=    3.413 closest distance to " OD2 ASP A 270 " =    1.011
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.410 closest distance to " O   HOH Z 393 " =    1.385
peak=    3.407 closest distance to " O   HOH Z 166 " =    1.350
peak=    3.405 closest distance to " OD1 ASP A 286 " =    1.065
peak=    3.405 closest distance to " O   HOH Z 426 " =    1.176
peak=    3.401 closest distance to " O   HOH Z  67 " =    1.854
peak=    3.401 closest distance to " O   HOH Z  11 " =    2.066
peak=    3.399 closest distance to " CB  LYS A 290 " =    0.962
peak=    3.399 closest distance to " CB  GLN A 223 " =    1.520
peak=    3.397 closest distance to " O   HOH Z  44 " =    2.904
peak=    3.396 closest distance to " NH1AARG A 145 " =    1.208
peak=    3.391 closest distance to " CD1 LEU A 281 " =    1.521
peak=    3.382 closest distance to " O   HOH Z 133 " =    2.036
peak=    3.375 closest distance to " CZ  PHE A  16 " =    1.001
peak=    3.374 closest distance to " N   ALA A  64 " =    1.010
peak=    3.373 closest distance to " O   HOH Z 155 " =    2.278
peak=    3.371 closest distance to " CB  GLU A 152 " =    1.214
peak=    3.367 closest distance to " CA  ALA A 160 " =    0.799
peak=    3.367 closest distance to " O   HOH Z 207 " =    2.202
peak=    3.365 closest distance to " N   ASN A 127 " =    1.562
peak=    3.363 closest distance to " O   HOH Z 392 " =    1.296
peak=    3.361 closest distance to " O   GLY A 302 " =    1.680
peak=    3.360 closest distance to " O   HOH Z 239 " =    1.279
peak=    3.359 closest distance to " CD  LYS A 119 " =    1.142
peak=    3.356 closest distance to " NE AARG A 275 " =    1.492
peak=    3.353 closest distance to " O   HOH Z 148 " =    2.111
peak=    3.352 closest distance to " O   HOH Z 108 " =    2.145
peak=    3.352 closest distance to " CB  ARG A  56 " =    1.204
peak=    3.347 closest distance to " CB  TRP A 179 " =    1.575
peak=    3.344 closest distance to " O   HOH Z 409 " =    1.995
peak=    3.344 closest distance to " CA  GLU A 152 " =    1.045
peak=    3.341 closest distance to " O   HOH Z  69 " =    1.175
peak=    3.341 closest distance to " CD2 LEU A 300 " =    1.150
peak=    3.340 closest distance to " O   GLN A 278 " =    1.383
peak=    3.339 closest distance to " O   HOH Z 200 " =    5.856
peak=    3.337 closest distance to " O   HOH Z 352 " =    1.587
peak=    3.337 closest distance to " CD1 LEU A 228 " =    1.830
peak=    3.336 closest distance to " CA  ARG A  36 " =    1.354
peak=    3.336 closest distance to " O   HOH Z 128 " =    2.141
peak=    3.333 closest distance to " O   HOH Z 389 " =    2.515
peak=    3.329 closest distance to " CB  ALA A 161 " =    1.037
peak=    3.327 closest distance to " O   HOH Z  37 " =    2.686
peak=    3.327 closest distance to " O   ALA A 233 " =    1.729
peak=    3.321 closest distance to " CB  GLU A 236 " =    1.511
peak=    3.320 closest distance to " CA  THR A 264 " =    0.839
peak=    3.316 closest distance to " O   HOH Z 365 " =    5.597
peak=    3.314 closest distance to " O   HOH Z  92 " =    1.072
peak=    3.313 closest distance to " O   HOH Z 110 " =    1.435
peak=    3.310 closest distance to " O   HOH Z 135 " =    1.929
peak=    3.304 closest distance to " CB  PHE A  16 " =    1.112
peak=    3.304 closest distance to " CB  SER A   3 " =    1.525
peak=    3.302 closest distance to " O   HOH Z  43 " =    1.282
peak=    3.302 closest distance to " OD1 ASN A 217 " =    1.724
peak=    3.297 closest distance to " N   ALA A   1 " =    1.675
peak=    3.288 closest distance to " CB  VAL A 296 " =    1.413
peak=    3.286 closest distance to " CD2 LEU A 281 " =    1.151
peak=    3.283 closest distance to " CD1BILE A 234 " =    0.921
peak=    3.282 closest distance to " OD2 ASP A 286 " =    2.675
peak=    3.281 closest distance to " N   SER A 210 " =    1.067
peak=    3.277 closest distance to " CB  ASN A 285 " =    1.029
peak=    3.275 closest distance to " CG2 THR A 251 " =    1.615
peak=    3.275 closest distance to " O   ASN A  60 " =    1.325
peak=    3.273 closest distance to " CB  SER A 276 " =    1.291
peak=    3.263 closest distance to " O   HOH Z  49 " =    2.731
peak=    3.263 closest distance to " CE2 TRP A  70 " =    1.628
peak=    3.263 closest distance to " O   HOH Z  33 " =    1.897
peak=    3.263 closest distance to " O   VAL A  72 " =    1.074
peak=    3.262 closest distance to " O   HOH Z 412 " =    1.677
peak=    3.262 closest distance to " O   HOH Z 215 " =    2.056
peak=    3.254 closest distance to " CB  ARG A  79 " =    0.950
peak=    3.251 closest distance to " O   HOH Z   4 " =    1.059
peak=    3.251 closest distance to " O   HOH Z  30 " =    1.898
peak=    3.251 closest distance to " CZ3 TRP A 123 " =    1.269
peak=    3.246 closest distance to " O   HOH Z 220 " =    1.361
peak=    3.241 closest distance to " O   HOH Z 193 " =    2.010
peak=    3.239 closest distance to " O   HOH Z 181 " =    2.410
peak=    3.237 closest distance to " CA  SER A 271 " =    0.873
peak=    3.235 closest distance to " O   HOH Z 139 " =    2.634
peak=    3.224 closest distance to " O   HOH Z 171 " =    2.382
peak=    3.221 closest distance to " CG  GLN A  89 " =    1.543
peak=    3.220 closest distance to " O   HOH Z 437 " =    2.527
peak=    3.220 closest distance to " O   HOH Z 326 " =    2.262
peak=    3.217 closest distance to " OG1 THR A 246 " =    3.193
peak=    3.215 closest distance to " CB  THR A 235 " =    1.283
peak=    3.214 closest distance to " O   HOH Z  76 " =    1.035
peak=    3.213 closest distance to " CB  ASP A 200 " =    0.882
peak=    3.211 closest distance to " CA  ASP A 124 " =    0.728
peak=    3.207 closest distance to " CG  GLU A   2 " =    1.055
peak=    3.206 closest distance to " O   HOH Z 422 " =    2.869
peak=    3.206 closest distance to " O   HOH Z  44 " =    2.406
peak=    3.206 closest distance to " O   HOH Z 202 " =    1.709
peak=    3.202 closest distance to " O   HOH Z 258 " =    1.878
peak=    3.200 closest distance to " O   HOH Z 361 " =    1.387
peak=    3.193 closest distance to " ND2 ASN A  60 " =    1.230
peak=    3.191 closest distance to " O   HOH Z 334 " =    1.547
peak=    3.190 closest distance to " O   ASN A 301 " =    2.128
peak=    3.189 closest distance to " OG  SER A 276 " =    0.890
peak=    3.187 closest distance to " CA  ASN A 284 " =    1.098
peak=    3.187 closest distance to " O   HOH Z 303 " =    1.646
peak=    3.187 closest distance to " O   HOH Z 271 " =    2.445
peak=    3.181 closest distance to " O   HOH Z 277 " =    2.248
peak=    3.180 closest distance to " CB  ARG A 102 " =    0.945
peak=    3.178 closest distance to " C   ASN A 215 " =    1.180
peak=    3.177 closest distance to " CB  ASP A 298 " =    1.082
peak=    3.173 closest distance to " O   HOH Z 286 " =    2.400
peak=    3.173 closest distance to " O   HOH Z 269 " =    3.273
peak=    3.172 closest distance to " O   HOH Z 124 " =    2.500
peak=    3.172 closest distance to " CB  ASP A 140 " =    0.754
peak=    3.164 closest distance to " O   HOH Z 274 " =    1.905
peak=    3.162 closest distance to " CZ  PHE A 218 " =    1.097
peak=    3.159 closest distance to " C   TRP A 177 " =    1.549
peak=    3.155 closest distance to " CA  ILE A 234 " =    1.213
peak=    3.155 closest distance to " O   HOH Z 152 " =    2.451
peak=    3.153 closest distance to " NE  ARG A 138 " =    1.078
peak=    3.152 closest distance to " O   HOH Z 362 " =    2.112
peak=    3.151 closest distance to " CB  ARG A 156 " =    1.109
peak=    3.147 closest distance to " CD  ARG A  66 " =    2.109
peak=    3.143 closest distance to " CG1 VAL A 202 " =    2.188
peak=    3.143 closest distance to " ND2 ASN A  74 " =    2.070
peak=    3.140 closest distance to " O   HOH Z 384 " =    1.486
peak=    3.139 closest distance to " OD1 ASN A  45 " =    1.332
peak=    3.137 closest distance to " C   THR A  18 " =    1.185
peak=    3.131 closest distance to " CD BARG A 102 " =    1.209
peak=    3.128 closest distance to " O   HOH Z 281 " =    2.061
peak=    3.125 closest distance to " SD  MET A 188 " =    1.481
peak=    3.120 closest distance to " C   ASP A 132 " =    1.103
peak=    3.117 closest distance to " CZ3 TRP A 274 " =    2.264
peak=    3.115 closest distance to " O   HOH Z 436 " =    2.331
peak=    3.094 closest distance to " O   HOH Z  32 " =    1.642
peak=    3.071 closest distance to " O   HOH Z 358 " =    2.935
peak=    3.070 closest distance to " O   HOH Z 361 " =    2.859
peak=    3.066 closest distance to " O   HOH Z 407 " =    1.842
peak=    3.061 closest distance to " O   HOH Z 104 " =    1.632
peak=    3.060 closest distance to " O   HOH Z 365 " =    2.745
peak=    3.017 closest distance to " N   GLN A  58 " =    0.985

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.617 - 5.839
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.701 - 5.839

peak=   -5.645 closest distance to " O   SER A  62 " =    1.097
peak=   -4.461 closest distance to " C   SER A  63 " =    0.949
peak=   -4.429 closest distance to " OG  SER A  97 " =    2.212
peak=   -4.404 closest distance to " CG  GLN A  88 " =    0.864
peak=   -4.383 closest distance to " CA  GLY A 133 " =    1.989
peak=   -4.344 closest distance to " O   PRO A 198 " =    1.192
peak=   -4.266 closest distance to " OG ASER A 134 " =    1.092
peak=   -4.251 closest distance to " CD  ARG A  14 " =    2.998
peak=   -4.215 closest distance to " ND2 ASN A 209 " =    1.732
peak=   -4.200 closest distance to " O   HOH Z 377 " =    1.790
peak=   -4.195 closest distance to " CB  ASN A 285 " =    2.095
peak=   -4.158 closest distance to " CG  MET A 105 " =    0.872
peak=   -4.141 closest distance to " O   HOH Z  60 " =    2.075
peak=   -4.109 closest distance to " CD1 TRP A 179 " =    1.134
peak=   -4.059 closest distance to " O   HOH Z  39 " =    1.239
peak=   -4.009 closest distance to " O   HOH Z 404 " =    0.930
peak=   -4.000 closest distance to " OG  SER A  63 " =    1.142
peak=   -3.978 closest distance to " O   ASP A 191 " =    1.946
peak=   -3.922 closest distance to " O   HOH Z  77 " =    1.706
peak=   -3.912 closest distance to " O   ALA A  51 " =    1.476
peak=   -3.906 closest distance to " CA  ASN A 127 " =    1.362
peak=   -3.902 closest distance to " NH2AARG A 275 " =    5.839
peak=   -3.902 closest distance to " CB  ALA A 248 " =    1.811
peak=   -3.897 closest distance to " CD2 LEU A 143 " =    2.437
peak=   -3.894 closest distance to " N   GLN A  58 " =    1.288
peak=   -3.893 closest distance to " O   HOH Z 290 " =    1.156
peak=   -3.871 closest distance to " O   HOH Z  84 " =    1.295
peak=   -3.788 closest distance to " CD2 LEU A 237 " =    2.424
peak=   -3.775 closest distance to " O   HOH Z 114 " =    4.490
peak=   -3.762 closest distance to " O   HOH Z 438 " =    0.901
peak=   -3.742 closest distance to " O   SER A 146 " =    1.560
peak=   -3.737 closest distance to " O   HOH Z  56 " =    0.859
peak=   -3.731 closest distance to " O   HOH Z  24 " =    1.067
peak=   -3.728 closest distance to " O   HOH Z 234 " =    4.724
peak=   -3.727 closest distance to " O   HOH Z 417 " =    1.574
peak=   -3.719 closest distance to " O   SER A 135 " =    1.683
peak=   -3.717 closest distance to " N   ASP A 171 " =    2.474
peak=   -3.711 closest distance to " CA  GLN A  55 " =    1.064
peak=   -3.692 closest distance to " CB  ALA A 227 " =    2.167
peak=   -3.690 closest distance to " N   ALA A  43 " =    2.365
peak=   -3.685 closest distance to " O   HOH Z 409 " =    3.373
peak=   -3.675 closest distance to " CA  SER A  63 " =    1.174
peak=   -3.671 closest distance to " CG1BVAL A  72 " =    1.896
peak=   -3.649 closest distance to " CD2 TYR A 116 " =    2.200
peak=   -3.642 closest distance to " O   HOH Z 388 " =    2.106
peak=   -3.639 closest distance to " O   TRP A  70 " =    1.414
peak=   -3.615 closest distance to " O   HOH Z 266 " =    4.255
peak=   -3.611 closest distance to " OD2 ASP A 270 " =    1.079
peak=   -3.604 closest distance to " C   ASP A  50 " =    1.121
peak=   -3.589 closest distance to " NE2 GLN A  55 " =    0.796
peak=   -3.581 closest distance to " CZ  PHE A  59 " =    1.528
peak=   -3.580 closest distance to " CG  PRO A 163 " =    2.447
peak=   -3.563 closest distance to " N   LEU A 282 " =    2.197
peak=   -3.560 closest distance to " O   HOH Z  97 " =    0.966
peak=   -3.554 closest distance to " O   HOH Z 401 " =    1.024
peak=   -3.552 closest distance to " O   HOH Z 163 " =    1.442
peak=   -3.551 closest distance to " CA  LEU A 143 " =    0.985
peak=   -3.548 closest distance to " O   HOH Z 140 " =    4.279
peak=   -3.545 closest distance to " O   HOH Z  90 " =    2.055
peak=   -3.532 closest distance to " CG  ASP A  50 " =    0.825
peak=   -3.530 closest distance to " O   HOH Z 231 " =    0.991
peak=   -3.529 closest distance to " O   HOH Z 381 " =    1.139
peak=   -3.525 closest distance to " OD2 ASP A 140 " =    1.310
peak=   -3.519 closest distance to " CG2 VAL A 125 " =    1.498
peak=   -3.518 closest distance to " O   HOH Z 117 " =    0.709
peak=   -3.516 closest distance to " O   HOH Z 102 " =    2.150
peak=   -3.510 closest distance to " OG1 THR A 157 " =    1.730
peak=   -3.506 closest distance to " O   HOH Z 221 " =    1.515
peak=   -3.505 closest distance to " O   ALA A 165 " =    1.213
peak=   -3.504 closest distance to " O   HOH Z  14 " =    1.396
peak=   -3.501 closest distance to " NH1 ARG A  56 " =    2.418
peak=   -3.480 closest distance to " OG BSER A 134 " =    1.785
peak=   -3.473 closest distance to " O   HOH Z 139 " =    2.358
peak=   -3.467 closest distance to " O   HOH Z 388 " =    1.647
peak=   -3.464 closest distance to " O   HOH Z 415 " =    1.226
peak=   -3.460 closest distance to " O   HOH Z 179 " =    1.089
peak=   -3.460 closest distance to " OE1 GLN A  58 " =    2.510
peak=   -3.456 closest distance to " CA  GLY A  17 " =    1.515
peak=   -3.454 closest distance to " C   VAL A  72 " =    1.051
peak=   -3.447 closest distance to " O   HOH Z 426 " =    1.643
peak=   -3.440 closest distance to " O   ASN A 301 " =    1.594
peak=   -3.440 closest distance to " CA  SER A  63 " =    0.847
peak=   -3.435 closest distance to " O   THR A 235 " =    1.237
peak=   -3.427 closest distance to " O   HOH Z  51 " =    0.760
peak=   -3.425 closest distance to " O   HOH Z  86 " =    1.032
peak=   -3.424 closest distance to " CA  ARG A  56 " =    1.019
peak=   -3.419 closest distance to " O   PHE A 208 " =    1.511
peak=   -3.414 closest distance to " O   HOH Z 255 " =    0.889
peak=   -3.408 closest distance to " CZ3 TRP A 179 " =    1.441
peak=   -3.405 closest distance to " CG  ASN A 127 " =    1.815
peak=   -3.400 closest distance to " O   LYS A  76 " =    1.047
peak=   -3.398 closest distance to " N   HIS A 115 " =    1.927
peak=   -3.395 closest distance to " O   HOH Z 308 " =    2.002
peak=   -3.390 closest distance to " CG1BVAL A  72 " =    4.753
peak=   -3.388 closest distance to " O   HOH Z 359 " =    1.735
peak=   -3.385 closest distance to " OD1 ASN A  39 " =    2.136
peak=   -3.373 closest distance to " O   GLY A  98 " =    2.221
peak=   -3.368 closest distance to " CG BLYS A 290 " =    0.892
peak=   -3.366 closest distance to " O   HOH Z 168 " =    3.057
peak=   -3.364 closest distance to " O   ILE A  49 " =    1.610
peak=   -3.362 closest distance to " N   SER A  62 " =    1.026
peak=   -3.361 closest distance to " O   HOH Z 431 " =    1.223
peak=   -3.358 closest distance to " OE1 GLN A  55 " =    2.191
peak=   -3.357 closest distance to " O   HOH Z 231 " =    1.961
peak=   -3.354 closest distance to " O   HOH Z 166 " =    0.801
peak=   -3.354 closest distance to " O   PRO A 243 " =    2.464
peak=   -3.353 closest distance to " OD1 ASN A 176 " =    1.080
peak=   -3.350 closest distance to " CG2BVAL A  41 " =    1.307
peak=   -3.347 closest distance to " CE  MET A 113 " =    2.317
peak=   -3.345 closest distance to " O   LEU A 297 " =    0.804
peak=   -3.343 closest distance to " O   HOH Z 119 " =    1.129
peak=   -3.340 closest distance to " O   HOH Z 208 " =    0.900
peak=   -3.340 closest distance to " CB  ALA A 291 " =    1.972
peak=   -3.337 closest distance to " O   HOH Z 358 " =    1.444
peak=   -3.335 closest distance to " N   ARG A 156 " =    1.058
peak=   -3.334 closest distance to " CA  GLY A 241 " =    2.147
peak=   -3.334 closest distance to " CD  LYS A 166 " =    2.550
peak=   -3.331 closest distance to " CB  TYR A  68 " =    1.119
peak=   -3.329 closest distance to " O   HOH Z 138 " =    1.121
peak=   -3.328 closest distance to " O   TYR A  30 " =    1.927
peak=   -3.328 closest distance to " C   HIS A 108 " =    1.206
peak=   -3.326 closest distance to " CG  GLU A   2 " =    2.141
peak=   -3.325 closest distance to " O   GLN A 194 " =    1.120
peak=   -3.324 closest distance to " O   ILE A 106 " =    2.141
peak=   -3.319 closest distance to " ND2 ASN A 285 " =    2.072
peak=   -3.317 closest distance to " N   ASN A  60 " =    1.068
peak=   -3.316 closest distance to " O   HOH Z 135 " =    0.722
peak=   -3.314 closest distance to " O   HOH Z 109 " =    1.206
peak=   -3.308 closest distance to " CD  LYS A 119 " =    0.943
peak=   -3.307 closest distance to " CD  LYS A 289 " =    2.500
peak=   -3.301 closest distance to " CE2 TYR A  30 " =    2.453
peak=   -3.300 closest distance to " O   HOH Z  96 " =    1.323
peak=   -3.296 closest distance to " O   ALA A   1 " =    1.190
peak=   -3.289 closest distance to " CE1 PHE A 225 " =    1.533
peak=   -3.283 closest distance to " CZ  TYR A 172 " =    1.760
peak=   -3.282 closest distance to " O   HOH Z 292 " =    5.628
peak=   -3.282 closest distance to " O   HOH Z 323 " =    1.886
peak=   -3.273 closest distance to " O   HOH Z  52 " =    1.004
peak=   -3.263 closest distance to " OH  TYR A 214 " =    1.099
peak=   -3.260 closest distance to " O   HOH Z 368 " =    1.617
peak=   -3.259 closest distance to " O   HOH Z 406 " =    2.169
peak=   -3.256 closest distance to " O   HOH Z 410 " =    2.482
peak=   -3.243 closest distance to " O   HOH Z 235 " =    1.194
peak=   -3.237 closest distance to " O   HOH Z 185 " =    2.559
peak=   -3.230 closest distance to " O   HOH Z 156 " =    1.466
peak=   -3.228 closest distance to " N   SER A 206 " =    2.034
peak=   -3.226 closest distance to " O   HOH Z 347 " =    0.956
peak=   -3.225 closest distance to " O   TRP A  92 " =    1.638
peak=   -3.223 closest distance to " OG  SER A  32 " =    0.701
peak=   -3.223 closest distance to " CB  ALA A 244 " =    2.155
peak=   -3.222 closest distance to " NH2 ARG A 159 " =    2.513
peak=   -3.217 closest distance to " CA  VAL A 121 " =    2.717
peak=   -3.215 closest distance to " CA  ASP A  27 " =    2.520
peak=   -3.213 closest distance to " CB  SER A  63 " =    3.579
peak=   -3.210 closest distance to " CD1 ILE A  33 " =    1.730
peak=   -3.210 closest distance to " CA  GLY A  98 " =    1.901
peak=   -3.207 closest distance to " CD  GLN A  58 " =    1.131
peak=   -3.206 closest distance to " CB  ALA A   9 " =    2.526
peak=   -3.205 closest distance to " O   HOH Z 264 " =    1.370
peak=   -3.201 closest distance to " N   ASN A 127 " =    1.509
peak=   -3.201 closest distance to " O   HOH Z  93 " =    2.015
peak=   -3.200 closest distance to " O   VAL A 189 " =    2.363
peak=   -3.199 closest distance to " O   HOH Z   4 " =    1.150
peak=   -3.199 closest distance to " CG  ARG A 219 " =    2.283
peak=   -3.193 closest distance to " N   ASN A 284 " =    1.057
peak=   -3.193 closest distance to " CG  GLU A 152 " =    2.629
peak=   -3.193 closest distance to " O   HOH Z 236 " =    2.182
peak=   -3.192 closest distance to " OE1 GLN A  88 " =    0.887
peak=   -3.189 closest distance to " O   HOH Z  68 " =    1.650
peak=   -3.185 closest distance to " CZ2 TRP A  92 " =    2.516
peak=   -3.184 closest distance to " CG AARG A 275 " =    2.435
peak=   -3.180 closest distance to " CA  HIS A  86 " =    1.949
peak=   -3.178 closest distance to " CE3 TRP A 274 " =    2.528
peak=   -3.141 closest distance to " CD2 TYR A 293 " =    1.999
peak=   -3.140 closest distance to " O   HOH Z 158 " =    1.730
peak=   -3.139 closest distance to " O   HOH Z  60 " =    1.228
peak=   -3.138 closest distance to " O   SER A  62 " =    1.486
peak=   -3.138 closest distance to " O   HOH Z  13 " =    1.371
peak=   -3.137 closest distance to " CG  GLN A  73 " =    1.329
peak=   -3.135 closest distance to " OE1 GLN A  89 " =    1.509
peak=   -3.135 closest distance to " O   ASP A 253 " =    1.663
peak=   -3.132 closest distance to " OD1 ASP A 171 " =    1.394
peak=   -3.132 closest distance to " O   HOH Z  43 " =    1.198
peak=   -3.122 closest distance to " OD1 ASP A  27 " =    1.812
peak=   -3.122 closest distance to " O   HOH Z 244 " =    1.359
peak=   -3.113 closest distance to " CD1 TYR A 214 " =    1.566
peak=   -3.110 closest distance to " O   SER A  22 " =    2.782
peak=   -3.106 closest distance to " O   HOH Z 428 " =    1.857
peak=   -3.099 closest distance to " CA  ASN A 217 " =    1.644
peak=   -3.099 closest distance to " OG1 THR A 279 " =    1.428
peak=   -3.089 closest distance to " O   SER A   3 " =    1.536
peak=   -3.088 closest distance to " O   MET A  47 " =    2.723
peak=   -3.084 closest distance to " N   SER A 276 " =    0.986
peak=   -3.082 closest distance to " CB  ASP A 286 " =    1.751
peak=   -3.078 closest distance to " O   HOH Z  37 " =    1.441
peak=   -3.078 closest distance to " CB  ALA A 291 " =    1.983
peak=   -3.061 closest distance to " OH  TYR A 247 " =    1.482
peak=   -3.060 closest distance to " OD1 ASN A 301 " =    2.009
peak=   -3.054 closest distance to " O   HOH Z  86 " =    0.834
peak=   -3.053 closest distance to " O   HOH Z  88 " =    1.819
peak=   -3.048 closest distance to " O   HOH Z  95 " =    1.576
peak=   -3.039 closest distance to " O   HOH Z  28 " =    0.930
peak=   -3.019 closest distance to " CG1 VAL A 265 " =    2.496

================= 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    :  0.5024 0.5029   6.303613e+00   6.301271e+00
   1_bss:  0.4958 0.4959   6.302619e+00   6.295734e+00
   1_xyz:  0.4159 0.4544   6.204648e+00   6.253068e+00
   1_adp:  0.3818 0.4661   6.175982e+00   6.262747e+00
   1_occ:  0.3813 0.4655   6.174794e+00   6.262187e+00
   2_bss:  0.3817 0.4643   6.176951e+00   6.261102e+00
   2_xyz:  0.3250 0.4098   6.059274e+00   6.199238e+00
   2_adp:  0.3060 0.3972   6.028810e+00   6.174543e+00
   2_occ:  0.3059 0.3966   6.028185e+00   6.173895e+00
   3_bss:  0.3065 0.3960   6.025957e+00   6.172592e+00
   3_xyz:  0.2670 0.3516   5.915642e+00   6.084201e+00
   3_adp:  0.2602 0.3492   5.898414e+00   6.075343e+00
   3_occ:  0.2601 0.3489   5.897856e+00   6.074957e+00
   4_bss:  0.2600 0.3478   5.896033e+00   6.072663e+00
   4_xyz:  0.2188 0.2934   5.740882e+00   5.937249e+00
   4_adp:  0.1897 0.2591   5.621931e+00   5.846040e+00
   4_occ:  0.1894 0.2591   5.621126e+00   5.845312e+00
   5_bss:  0.1897 0.2590   5.620559e+00   5.844257e+00
   5_xyz:  0.1592 0.2225   5.460586e+00   5.703904e+00
   5_adp:  0.1475 0.2061   5.392575e+00   5.632586e+00
   5_occ:  0.1473 0.2057   5.391175e+00   5.631012e+00
   5_bss:  0.1475 0.2056   5.390371e+00   5.630336e+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:  0.300  20.000  -0.466   0.753   0.183   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -0.466   0.753   0.183   0.000   0.000   0.000
   1_adp:  0.300  20.000  -0.466   0.753   0.183   0.000   0.000   0.000
   1_occ:  0.300  20.000  -0.466   0.753   0.183   0.000   0.000   0.000
   2_bss:  0.355  57.172   0.378   0.642   0.760   0.000   0.000   0.000
   2_xyz:  0.355  57.172   0.378   0.642   0.760   0.000   0.000   0.000
   2_adp:  0.355  57.172   0.378   0.642   0.760   0.000   0.000   0.000
   2_occ:  0.355  57.172   0.378   0.642   0.760   0.000   0.000   0.000
   3_bss:  0.367  70.762   0.357  -0.033   0.658  -0.000   0.000   0.000
   3_xyz:  0.367  70.762   0.357  -0.033   0.658  -0.000   0.000   0.000
   3_adp:  0.367  70.762   0.357  -0.033   0.658  -0.000   0.000   0.000
   3_occ:  0.367  70.762   0.357  -0.033   0.658  -0.000   0.000   0.000
   4_bss:  0.343  55.847  -0.229  -0.633   0.125  -0.000   0.000   0.000
   4_xyz:  0.343  55.847  -0.229  -0.633   0.125  -0.000   0.000   0.000
   4_adp:  0.343  55.847  -0.229  -0.633   0.125  -0.000   0.000   0.000
   4_occ:  0.343  55.847  -0.229  -0.633   0.125  -0.000   0.000   0.000
   5_bss:  0.331  56.725  -0.500  -1.415  -0.270  -0.000  -0.000  -0.000
   5_xyz:  0.331  56.725  -0.500  -1.415  -0.270  -0.000  -0.000  -0.000
   5_adp:  0.331  56.725  -0.500  -1.415  -0.270  -0.000  -0.000  -0.000
   5_occ:  0.331  56.725  -0.500  -1.415  -0.270  -0.000  -0.000  -0.000
   5_bss:  0.321  53.594  -0.905  -1.863  -0.719  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.520 0.3084  0.4283    85796.797
   1_bss:  65.982 0.3142  0.4442    83396.379
   1_xyz:  55.892 0.4446  0.6183    65736.274
   1_adp:  57.447 0.4244  0.5951    68314.309
   1_occ:  57.330 0.4258  0.5959    68032.418
   2_bss:  57.337 0.4257  0.6066    67997.339
   2_xyz:  47.409 0.5509  0.7825    49997.615
   2_adp:  44.412 0.5887  0.8152    46233.587
   2_occ:  44.395 0.5889  0.8147    46112.003
   3_bss:  44.233 0.5906  0.8085    45612.597
   3_xyz:  37.253 0.6746  0.9043    33989.394
   3_adp:  36.507 0.6836  0.9115    33011.708
   3_occ:  36.506 0.6836  0.9113    32972.716
   4_bss:  36.406 0.6845  0.8939    32696.738
   4_xyz:  29.965 0.7570  0.9605    22402.365
   4_adp:  26.095 0.7993  0.9751    17772.819
   4_occ:  26.064 0.7996  0.9750    17721.528
   5_bss:  26.041 0.7998  0.9584    17686.035
   5_xyz:  21.739 0.8435  0.9873    12608.607
   5_adp:  19.715 0.8642  0.9884    10963.838
   5_occ:  19.665 0.8646  0.9884    10910.833
   5_bss:  19.633 0.8648  0.9731    10877.020
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9743e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9743e-01
   1_xyz:   1.747  0.013  0.118 16.525  0.006  4.101   1.6786e-01
   1_adp:   1.747  0.013  0.118 16.525  0.006  4.101   1.6786e-01
   1_occ:   1.747  0.013  0.118 16.525  0.006  4.101   1.6786e-01
   2_bss:   1.747  0.013  0.118 16.525  0.006  4.101   1.6786e-01
   2_xyz:   1.451  0.011  0.097 15.951  0.006  4.104   1.2172e-01
   2_adp:   1.451  0.011  0.097 15.951  0.006  4.104   1.2172e-01
   2_occ:   1.451  0.011  0.097 15.951  0.006  4.104   1.2172e-01
   3_bss:   1.451  0.011  0.097 15.951  0.006  4.104   1.2172e-01
   3_xyz:   1.011  0.007  0.068 14.761  0.004  4.114   6.5970e-02
   3_adp:   1.011  0.007  0.068 14.761  0.004  4.114   6.5970e-02
   3_occ:   1.011  0.007  0.068 14.761  0.004  4.114   6.5970e-02
   4_bss:   1.011  0.007  0.068 14.761  0.004  4.114   6.5970e-02
   4_xyz:   1.145  0.008  0.079 14.422  0.004  4.115   7.4291e-02
   4_adp:   1.145  0.008  0.079 14.422  0.004  4.115   7.4291e-02
   4_occ:   1.145  0.008  0.079 14.422  0.004  4.115   7.4291e-02
   5_bss:   1.145  0.008  0.079 14.422  0.004  4.115   7.4291e-02
   5_xyz:   0.981  0.006  0.067 14.128  0.003  4.108   5.7672e-02
   5_adp:   0.981  0.006  0.067 14.128  0.003  4.108   5.7672e-02
   5_occ:   0.981  0.006  0.067 14.128  0.003  4.108   5.7672e-02
   5_bss:   0.981  0.006  0.067 14.128  0.003  4.108   5.7672e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.225   2.3967e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.225   2.3967e-01
   1_xyz:  11.498  0.070  0.492 87.416  0.053  1.919   1.3686e-01
   1_adp:  11.498  0.070  0.492 87.416  0.053  1.919   1.3686e-01
   1_occ:  11.498  0.070  0.492 87.416  0.053  1.919   1.3686e-01
   2_bss:  11.498  0.070  0.492 87.416  0.053  1.919   1.3686e-01
   2_xyz:   9.970  0.060  0.390 87.042  0.075  2.077   1.2594e-01
   2_adp:   9.970  0.060  0.390 87.042  0.075  2.077   1.2594e-01
   2_occ:   9.970  0.060  0.390 87.042  0.075  2.077   1.2594e-01
   3_bss:   9.970  0.060  0.390 87.042  0.075  2.077   1.2594e-01
   3_xyz:   7.786  0.054  0.311 83.529  0.020  2.277   6.2468e-02
   3_adp:   7.786  0.054  0.311 83.529  0.020  2.277   6.2468e-02
   3_occ:   7.786  0.054  0.311 83.529  0.020  2.277   6.2468e-02
   4_bss:   7.786  0.054  0.311 83.529  0.020  2.277   6.2468e-02
   4_xyz:   6.763  0.050  0.232 83.575  0.045  2.210   6.2874e-02
   4_adp:   6.763  0.050  0.232 83.575  0.045  2.210   6.2874e-02
   4_occ:   6.763  0.050  0.232 83.575  0.045  2.210   6.2874e-02
   5_bss:   6.763  0.050  0.232 83.575  0.045  2.210   6.2874e-02
   5_xyz:   8.353  0.043  0.224 77.604  0.024  2.287   5.0219e-02
   5_adp:   8.353  0.043  0.224 77.604  0.024  2.287   5.0219e-02
   5_occ:   8.353  0.043  0.224 77.604  0.024  2.287   5.0219e-02
   5_bss:   8.353  0.043  0.224 77.604  0.024  2.287   5.0219e-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: 103.83   0.00  19.75  89.55   0.00  17.35 103.83   0.00  32.87
   1_occ: 103.83   0.00  19.75  89.55   0.00  17.35 103.83   0.00  32.87
   2_bss: 103.83   0.00  19.75  89.55   0.00  17.35 103.83   0.00  32.87
   2_xyz: 103.83   0.00  19.75  89.55   0.00  17.35 103.83   0.00  32.87
   2_adp: 101.24   0.00  18.64  91.32   0.00  15.84 101.24   0.00  33.87
   2_occ: 101.24   0.00  18.64  91.32   0.00  15.84 101.24   0.00  33.87
   3_bss: 101.24   0.00  18.64  91.32   0.00  15.84 101.24   0.00  33.87
   3_xyz: 101.24   0.00  18.64  91.32   0.00  15.84 101.24   0.00  33.87
   3_adp: 101.63   0.00  18.65  91.64   0.00  15.60 101.63   0.00  35.22
   3_occ: 101.63   0.00  18.65  91.64   0.00  15.60 101.63   0.00  35.22
   4_bss: 101.63   0.00  18.65  91.64   0.00  15.60 101.63   0.00  35.22
   4_xyz: 101.63   0.00  18.65  91.64   0.00  15.60 101.63   0.00  35.22
   4_adp: 106.01   0.00  18.89 106.01   0.00  13.80 105.18   4.45  46.62
   4_occ: 106.01   0.00  18.89 106.01   0.00  13.80 105.18   4.45  46.62
   5_bss: 106.01   0.00  18.89 106.01   0.00  13.80 105.18   4.45  46.62
   5_xyz: 106.01   0.00  18.89 106.01   0.00  13.80 105.18   4.45  46.62
   5_adp: 108.29   0.00  18.11 108.29   0.00  12.72 105.31   5.03  47.45
   5_occ: 108.29   0.00  18.11 108.29   0.00  12.72 105.31   5.03  47.45
   5_bss: 108.29   0.00  18.11 108.29   0.00  12.72 105.31   5.04  47.45
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.422    0.015    0.388
   1_adp:    2.422    0.015    0.388
   1_occ:    2.422    0.015    0.388
   2_bss:    2.422    0.015    0.388
   2_xyz:    1.800    0.045    0.597
   2_adp:    1.800    0.045    0.597
   2_occ:    1.800    0.045    0.597
   3_bss:    1.800    0.045    0.597
   3_xyz:    1.617    0.071    0.697
   3_adp:    1.617    0.071    0.697
   3_occ:    1.617    0.071    0.697
   4_bss:    1.617    0.071    0.697
   4_xyz:    1.738    0.071    0.840
   4_adp:    1.738    0.071    0.840
   4_occ:    1.738    0.071    0.840
   5_bss:    1.738    0.071    0.840
   5_xyz:    1.739    0.089    0.908
   5_adp:    1.739    0.089    0.908
   5_occ:    1.739    0.089    0.908
   5_bss:    1.739    0.089    0.908
------------------------------------------------------------------------

CPU time actual refinement: 350.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/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_1090/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1090/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 350.58 
  Macro-tasks:
    bulk solvent and scale       = 45.89  
    individual site refinement   = 146.44 
    weights calculation          = 30.85  
    collect and process          = 6.30   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 229.59 
  Micro-tasks:
    mask                            = 3.24   
    f_calc                          = 112.64 
    alpha_beta                      = 8.28   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 119.47 
    fmodel                         = 7.04   
    r_factors                      = 0.29   
    phase_errors                   = 9.37   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 261.72 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.058 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    596 calls, 112.31 s
gradients_fft:          541 calls, 107.45 s

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

# Date 2008-01-16 Time 06:23:50 PST -0800 (1200493430.85 s)
Start R-work = 0.5024, R-free = 0.5029 (no bulk solvent and anisotropic scale)
Final R-work = 0.1638, R-free = 0.2212 (no bulk solvent and anisotropic scale)

Start R-work = 0.4958, R-free = 0.4959
Final R-work = 0.1475, R-free = 0.2056