# Date 2008-01-16 Time 05:59:30 PST -0800 (1200491970.30 s)
#phil __OFF__

Command line arguments: "../964.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20284
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 964

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 48.1033, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02048
Completeness in resolution range: 0.971821
Completeness with d_max=infinity: 0.968745

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1439
                             d_min =   2.0205

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1439 2.02048
Completeness in resolution range: 0.971821
Completeness with d_max=infinity: 0.968745

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1443 -  4.3224 [2114/2141]  1903   211  10.0%
  bin  2:  4.3224 -  3.4441 [2030/2046]  1826   204  10.0%
  bin  3:  3.4441 -  3.0126 [2012/2031]  1809   203  10.1%
  bin  4:  3.0126 -  2.7390 [1983/2013]  1791   192   9.7%
  bin  5:  2.7390 -  2.5436 [1968/1987]  1767   201  10.2%
  bin  6:  2.5436 -  2.3943 [1962/1998]  1768   194   9.9%
  bin  7:  2.3943 -  2.2748 [1960/1993]  1765   195   9.9%
  bin  8:  2.2748 -  2.1761 [1941/1975]  1744   197  10.1%
  bin  9:  2.1761 -  2.0925 [1939/1967]  1744   195  10.1%
  bin 10:  2.0925 -  2.0205 [1680/2006]  1513   167   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/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:
        1.58 -     2.24: 6
        2.24 -     2.91: 1384
        2.91 -     3.57: 4369
        3.57 -     4.24: 8986
        4.24 -     4.90: 12954
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.581 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.739 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.940 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.124 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27694 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_964/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 48.10325 87.2539 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: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4447   r_free= 0.4254   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.259240                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.3571 0.3709      6.5267      6.5101|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.3909 0.4003      6.8287      6.8288|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.4212 0.3639      6.6805      6.5719|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.4388 0.4272      6.5188      6.4547|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.4685 0.4038      6.3638      6.3276|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.4714 0.4626      6.2631      6.2082|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.4755 0.4087      6.2262      6.1073|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.4758 0.4349      6.1652      6.1527|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.4801 0.5030      6.0883      6.1442|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.4878 0.4292       6.104      6.0074|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.4880 0.4569      6.0337      6.0523|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.4961 0.4961      5.9639      6.0189|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.4807 0.4733       5.879      5.8656|
| 14:  2.0709 -  2.0205 0.79    998  118 0.4751 0.5135      5.8175      5.7524|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.70  33.97   0.82     0.74      70138.31|
|  2:  4.8205 -  3.8469  1321   146  0.74  31.93   0.90     0.81      90259.24|
|  3:  3.8469 -  3.3667  1299   146  0.66  38.45   0.89     0.81      93673.12|
|  4:  3.3667 -  3.0616  1285   138  0.60  44.30   0.89     0.74      83106.52|
|  5:  3.0616 -  2.8437  1274   143  0.52  50.06   0.88     0.68      66554.69|
|  6:  2.8437 -  2.6770  1277   146  0.51  51.12   0.88     0.66      55287.69|
|  7:  2.6770 -  2.5436  1266   139  0.51  50.97   0.91     0.66      48224.12|
|  8:  2.5436 -  2.4334  1270   142  0.51  51.30   0.92     0.67      45688.77|
|  9:  2.4334 -  2.3400  1259   139  0.49  52.59   0.91     0.68      42578.77|
| 10:  2.3400 -  2.2596  1246   136  0.50  52.05   0.93     0.68      39648.02|
| 11:  2.2596 -  2.1891  1264   147  0.47  54.35   0.93     0.67      38287.13|
| 12:  2.1891 -  2.1267  1257   128  0.43  57.87   0.92     0.62      37678.21|
| 13:  2.1267 -  2.0709  1240   138  0.39  60.65   0.91     0.56      34567.46|
| 14:  2.0709 -  2.0205   998   118  0.37  61.97   0.94     0.50      28358.56|
|alpha:            min =        0.50 max =            0.81 mean =         0.68|
|beta:             min =    28358.56 max =        93673.12 mean =     56067.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.01|
|phase err.(test): min =        0.00 max =           89.99 mean =        49.10|
|-----------------------------------------------------------------------------|

============================== 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 = 7.003621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.945   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.763219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.242   (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 |  1.581 -  1.913:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.913 -  2.245:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.245 -  2.577:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.577 -  2.909:     1363 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.909 -  3.240:     1882 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.240 -  3.572:     2487 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.572 -  3.904:     4612 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.904 -  4.236:     4374 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.236 -  4.568:     5880 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7074 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.581 |       0.200 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    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: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4447   r_free= 0.4254   ksol= 0.00   Bsol= 0.00   scale= 0.886    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.259240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4353   r_free= 0.4174   ksol= 0.28   Bsol= 37.15   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,5.07,-0.38,0.00,-0.00,-0.00); trace/3= 0.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.249257                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.348392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.605   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.860959              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.119   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4353      final r-factor (work) = 0.3555          |
| start r-factor (free) = 0.4174      final r-factor (free) = 0.3808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0006 = 6.35 * 0.50 * 6.2485 + 1.00 * 0.1667                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5765 = 6.35 * 0.50 * 6.1333 + 1.00 * 0.1082                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3555      final r-factor (work) = 0.3272          |
| start r-factor (free) = 0.3808      final r-factor (free) = 0.3914          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2865 = 0.86 * 1.00 * 6.1333 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2426 = 0.86 * 1.00 * 6.0638 + 1.00 * 0.0219                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.26  18.10    None  None   None       |
|    all(noH): 2823   0      0.00    103.26  18.10    None  None   None       |
|    Sol.    : 438    0      0.00    103.26  36.06    None  None   None       |
|    Mac.    : 2385   0      0.00    86.18   14.80    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 -  10.326:  975   |   5:    51.629 -  61.955:   58        |
|      1:    10.326 -  20.652:  949   |   6:    61.955 -  72.281:   47        |
|      2:    20.652 -  30.978:  474   |   7:    72.281 -  82.607:    8        |
|      3:    30.978 -  41.303:  204   |   8:    82.607 -  92.932:    5        |
|      4:    41.303 -  51.629:  102   |   9:    92.932 - 103.258:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3272 r_free = 0.3914             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3269 r_free = 0.3911             target_work(ml) = 6.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3269   r_free= 0.3911   ksol= 0.28   Bsol= 37.15   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.78,5.07,-0.38,0.00,-0.00,-0.00); trace/3= 0.64                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.067729                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3264   r_free= 0.3903   ksol= 0.27   Bsol= 50.74   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,3.17,0.15,0.00,0.00,0.00); trace/3= 0.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.069995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.949200             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.724671              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.845   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3264      final r-factor (work) = 0.2530          |
| start r-factor (free) = 0.3903      final r-factor (free) = 0.3005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3817 = 12.95 * 0.50 * 6.0658 + 1.00 * 0.1082                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.7384 = 12.95 * 0.50 * 5.9642 + 1.00 * 0.1227                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2530      final r-factor (work) = 0.2268          |
| start r-factor (free) = 0.3005      final r-factor (free) = 0.2839          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3422 = 0.72 * 1.00 * 5.9642 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2158 = 0.72 * 1.00 * 5.7821 + 1.00 * 0.0256                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 38     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.31   18.02    None  None   None       |
|    all(noH): 2823   0      0.00    98.31   18.02    None  None   None       |
|    Sol.    : 438    0      0.00    98.31   40.67    None  None   None       |
|    Mac.    : 2385   0      0.00    91.20   13.86    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.831: 1061   |   5:    49.154 -  58.985:   86        |
|      1:     9.831 -  19.662:  919   |   6:    58.985 -  68.816:   56        |
|      2:    19.662 -  29.492:  341   |   7:    68.816 -  78.646:   27        |
|      3:    29.492 -  39.323:  193   |   8:    78.646 -  88.477:   14        |
|      4:    39.323 -  49.154:  123   |   9:    88.477 -  98.308:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2268 r_free = 0.2839             target_work(ml) = 5.761         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2264 r_free = 0.2837             target_work(ml) = 5.760         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2264   r_free= 0.2837   ksol= 0.27   Bsol= 50.74   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,3.17,0.15,0.00,0.00,0.00); trace/3= 0.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.759916                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2253   r_free= 0.2824   ksol= 0.32   Bsol= 69.46   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,1.41,0.22,0.00,0.00,0.00); trace/3= 0.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.757412                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.133351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.048  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311076              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.259  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2253      final r-factor (work) = 0.1784          |
| start r-factor (free) = 0.2824      final r-factor (free) = 0.2232          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9609 = 5.13 * 0.50 * 5.7811 + 1.00 * 0.1227                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6050 = 5.13 * 0.50 * 5.6613 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1784      final r-factor (work) = 0.1681          |
| start r-factor (free) = 0.2232      final r-factor (free) = 0.2121          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7893 = 0.31 * 1.00 * 5.6613 + 1.00 * 0.0282                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7767 = 0.31 * 1.00 * 5.5098 + 1.00 * 0.0627                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.58   17.52    None  None   None       |
|    all(noH): 2823   0      0.00    97.58   17.52    None  None   None       |
|    Sol.    : 438    0      3.62    97.58   41.07    None  None   None       |
|    Mac.    : 2385   0      0.00    88.94   13.19    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:     0.000 -   9.758: 1157   |   5:    48.791 -  58.549:   83        |
|      1:     9.758 -  19.516:  897   |   6:    58.549 -  68.307:   58        |
|      2:    19.516 -  29.274:  283   |   7:    68.307 -  78.065:   29        |
|      3:    29.274 -  39.033:  164   |   8:    78.065 -  87.823:   14        |
|      4:    39.033 -  48.791:  136   |   9:    87.823 -  97.581:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1681 r_free = 0.2121             target_work(ml) = 5.488         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1679 r_free = 0.2118             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1679   r_free= 0.2118   ksol= 0.32   Bsol= 69.46   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,1.41,0.22,0.00,0.00,0.00); trace/3= 0.21                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.487044                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2114   ksol= 0.33   Bsol= 75.22   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,0.29,-0.00,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.486977                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.179474              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.739  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.618868              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.690   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2114      final r-factor (free) = 0.1898          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8357 = 3.18 * 0.50 * 5.5112 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6822 = 3.18 * 0.50 * 5.4143 + 1.00 * 0.0748                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1433      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1898      final r-factor (free) = 0.1831          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7813 = 1.62 * 1.00 * 5.4143 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6216 = 1.62 * 1.00 * 5.3167 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.00  17.36    None  None   None       |
|    all(noH): 2823   0      0.00    106.00  17.36    None  None   None       |
|    Sol.    : 438    0      3.28    104.96  44.38    None  None   None       |
|    Mac.    : 2385   0      0.00    106.00  12.40    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 -  10.600: 1345   |   5:    52.998 -  63.598:   87        |
|      1:    10.600 -  21.199:  872   |   6:    63.598 -  74.198:   63        |
|      2:    21.199 -  31.799:  186   |   7:    74.198 -  84.797:   29        |
|      3:    31.799 -  42.399:  130   |   8:    84.797 -  95.397:   10        |
|      4:    42.399 -  52.998:   97   |   9:    95.397 - 105.997:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1831             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1831             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1831   ksol= 0.33   Bsol= 75.22   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.29,0.29,-0.00,0.00,-0.00,-0.00); trace/3= -0.33                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.294996                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1831   ksol= 0.33   Bsol= 80.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.01,0.28,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.295033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.743913              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.928  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.697622              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.036   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1333      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1831      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3694 = 2.74 * 0.50 * 5.3169 + 1.00 * 0.0748                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3012 = 2.74 * 0.50 * 5.2681 + 1.00 * 0.0736                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1247      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6896 = 0.70 * 1.00 * 5.2681 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6720 = 0.70 * 1.00 * 5.2398 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.30  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    106.30  17.03    None  None   None       |
|    Sol.    : 438    0      3.96    105.44  44.07    None  None   None       |
|    Mac.    : 2385   0      0.00    106.30  12.06    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 -  10.630: 1415   |   5:    53.150 -  63.780:   89        |
|      1:    10.630 -  21.260:  821   |   6:    63.780 -  74.410:   61        |
|      2:    21.260 -  31.890:  176   |   7:    74.410 -  85.040:   27        |
|      3:    31.890 -  42.520:  123   |   8:    85.040 -  95.670:   10        |
|      4:    42.520 -  53.150:   97   |   9:    95.670 - 106.300:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1738             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1233 r_free = 0.1739             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1739   ksol= 0.33   Bsol= 80.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.01,0.28,0.00,0.00,0.00); trace/3= -0.28                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.234583                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.1017 0.1366      5.4298      5.5802|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.0869 0.1098      5.4665      5.6476|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.1094 0.1637       5.525      5.9354|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.1331 0.1743      5.5435      5.6791|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.1482 0.1976      5.4507      5.6494|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.1441 0.2128      5.3474      5.6011|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.1409 0.1822      5.2746      5.4477|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.1334 0.1946      5.1955      5.4598|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.1338 0.2003      5.1331      5.3776|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.1282 0.1906      5.0824      5.3283|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.1312 0.1966       5.036      5.3514|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.1248 0.1839      4.9764      5.2569|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.1294 0.1937      4.9033      5.1367|
| 14:  2.0709 -  2.0205 0.79    998  118 0.1178 0.1977      4.7681       5.069|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.93  10.18   0.96     0.92       8330.79|
|  2:  4.8205 -  3.8469  1321   146  0.95   8.78   1.00     0.98       9970.00|
|  3:  3.8469 -  3.3667  1299   146  0.93  11.99   1.02     1.01      11619.25|
|  4:  3.3667 -  3.0616  1285   138  0.91  15.12   1.01     0.98      12231.41|
|  5:  3.0616 -  2.8437  1274   143  0.88  18.14   1.00     0.98      10873.12|
|  6:  2.8437 -  2.6770  1277   146  0.88  18.12   0.98     0.94       8869.96|
|  7:  2.6770 -  2.5436  1266   139  0.88  17.91   0.99     0.96       7884.43|
|  8:  2.5436 -  2.4334  1270   142  0.89  17.39   0.98     0.94       6797.88|
|  9:  2.4334 -  2.3400  1259   139  0.89  18.00   0.99     0.94       6143.98|
| 10:  2.3400 -  2.2596  1246   136  0.89  17.40   0.99     0.95       5550.77|
| 11:  2.2596 -  2.1891  1264   147  0.88  17.99   0.98     0.93       5120.23|
| 12:  2.1891 -  2.1267  1257   128  0.90  17.02   0.98     0.97       4822.00|
| 13:  2.1267 -  2.0709  1240   138  0.89  17.46   0.97     0.95       4071.86|
| 14:  2.0709 -  2.0205   998   118  0.89  17.08   0.95     0.91       3192.69|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3192.69 max =        12231.41 mean =      7637.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.84 mean =        15.81|
|phase err.(test): min =        0.00 max =           89.29 mean =        15.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1739   ksol= 0.33   Bsol= 74.50   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,-0.06,0.38,-0.00,0.00,0.00); trace/3= -0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.234442                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1233   r_free= 0.1739   ksol= 0.33   Bsol= 74.50   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.03,-0.06,0.38,-0.00,0.00,0.00); trace/3= -0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.234442                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1443 -  4.8205 0.99   1374  153 0.1015 0.1366      5.4281      5.5793|
|  2:  4.8205 -  3.8469 0.99   1321  146 0.0867 0.1095      5.4645       5.644|
|  3:  3.8469 -  3.3667 0.99   1299  146 0.1094 0.1637      5.5245      5.9363|
|  4:  3.3667 -  3.0616 0.99   1285  138 0.1333 0.1743      5.5443      5.6794|
|  5:  3.0616 -  2.8437 0.99   1274  143 0.1484 0.1978      5.4516      5.6501|
|  6:  2.8437 -  2.6770 0.99   1277  146 0.1442 0.2126      5.3477      5.6005|
|  7:  2.6770 -  2.5436 0.99   1266  139 0.1409 0.1824      5.2748      5.4482|
|  8:  2.5436 -  2.4334 0.98   1270  142 0.1335 0.1947      5.1959      5.4599|
|  9:  2.4334 -  2.3400 0.98   1259  139 0.1337 0.2002      5.1332      5.3782|
| 10:  2.3400 -  2.2596 0.98   1246  136 0.1282 0.1910      5.0828      5.3292|
| 11:  2.2596 -  2.1891 1.00   1264  147 0.1311 0.1964       5.036      5.3511|
| 12:  2.1891 -  2.1267 0.97   1257  128 0.1247 0.1840      4.9763      5.2576|
| 13:  2.1267 -  2.0709 0.98   1240  138 0.1295 0.1936      4.9032      5.1368|
| 14:  2.0709 -  2.0205 0.79    998  118 0.1179 0.1975      4.7675      5.0679|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1443 -  4.8205  1374   153  0.93  10.16   0.96     0.92       8306.73|
|  2:  4.8205 -  3.8469  1321   146  0.95   8.77   1.00     0.98       9931.91|
|  3:  3.8469 -  3.3667  1299   146  0.93  11.97   1.02     1.01      11585.33|
|  4:  3.3667 -  3.0616  1285   138  0.91  15.12   1.01     0.98      12245.09|
|  5:  3.0616 -  2.8437  1274   143  0.88  18.14   1.00     0.98      10879.12|
|  6:  2.8437 -  2.6770  1277   146  0.88  18.13   0.98     0.94       8876.67|
|  7:  2.6770 -  2.5436  1266   139  0.88  17.91   0.99     0.96       7885.83|
|  8:  2.5436 -  2.4334  1270   142  0.89  17.40   0.99     0.95       6804.33|
|  9:  2.4334 -  2.3400  1259   139  0.89  18.01   0.99     0.94       6149.73|
| 10:  2.3400 -  2.2596  1246   136  0.89  17.41   0.99     0.95       5556.23|
| 11:  2.2596 -  2.1891  1264   147  0.88  17.99   0.98     0.93       5124.87|
| 12:  2.1891 -  2.1267  1257   128  0.90  17.01   0.98     0.97       4825.02|
| 13:  2.1267 -  2.0709  1240   138  0.89  17.45   0.97     0.95       4069.11|
| 14:  2.0709 -  2.0205   998   118  0.89  17.06   0.95     0.91       3184.75|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3184.75 max =        12245.09 mean =      7633.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.84 mean =        15.81|
|phase err.(test): min =        0.00 max =           89.30 mean =        15.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.410)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.30  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    106.30  17.03    None  None   None       |
|    Sol.    : 438    0      3.97    105.45  44.07    None  None   None       |
|    Mac.    : 2385   0      0.00    106.30  12.07    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 -  10.633: 1415   |   5:    53.153 -  63.783:   89        |
|      1:    10.633 -  21.263:  821   |   6:    63.783 -  74.413:   61        |
|      2:    21.263 -  31.893:  176   |   7:    74.413 -  85.043:   27        |
|      3:    31.893 -  42.523:  123   |   8:    85.043 -  95.673:   10        |
|      4:    42.523 -  53.153:   97   |   9:    95.673 - 106.303:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.229 - 4.957
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 327
   mapped sites are within: 0.715 - 4.957

peak=    6.251 closest distance to " O   HOH Z 210 " =    1.380
peak=    5.559 closest distance to " O   HOH Z 111 " =    2.275
peak=    5.055 closest distance to " O   HOH Z 433 " =    1.916
peak=    5.036 closest distance to " CB  SER A  63 " =    1.290
peak=    5.034 closest distance to " CG  PRO A  54 " =    1.358
peak=    4.834 closest distance to " O   HOH Z 134 " =    1.925
peak=    4.781 closest distance to " CB  GLN A 223 " =    1.340
peak=    4.743 closest distance to " CG  PRO A 213 " =    1.207
peak=    4.718 closest distance to " CA  ALA A  51 " =    1.041
peak=    4.672 closest distance to " O   HOH Z  49 " =    1.127
peak=    4.668 closest distance to " OE1 GLN A  88 " =    0.895
peak=    4.631 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.505 closest distance to " O   HOH Z 425 " =    1.560
peak=    4.475 closest distance to " O   HOH Z 369 " =    2.046
peak=    4.446 closest distance to " CG  PRO A 198 " =    1.217
peak=    4.392 closest distance to " O   HOH Z  44 " =    2.265
peak=    4.378 closest distance to " O   PRO A 198 " =    1.562
peak=    4.321 closest distance to " O   HOH Z 234 " =    3.757
peak=    4.283 closest distance to " O   HOH Z 412 " =    3.388
peak=    4.276 closest distance to " CB  GLU A 128 " =    1.122
peak=    4.264 closest distance to " CD  ARG A 269 " =    0.973
peak=    4.249 closest distance to " O   HOH Z 431 " =    1.066
peak=    4.238 closest distance to " CG  PRO A 280 " =    0.850
peak=    4.235 closest distance to " CB  ARG A 275 " =    0.846
peak=    4.230 closest distance to " O   HOH Z 418 " =    2.191
peak=    4.227 closest distance to " O   HOH Z  43 " =    1.969
peak=    4.220 closest distance to " CA  ARG A 195 " =    1.147
peak=    4.209 closest distance to " CB  TRP A 266 " =    1.059
peak=    4.203 closest distance to " CA  ALA A 160 " =    1.014
peak=    4.199 closest distance to " O   HOH Z 196 " =    1.855
peak=    4.196 closest distance to " O   HOH Z 214 " =    1.395
peak=    4.193 closest distance to " O   HOH Z 232 " =    2.397
peak=    4.189 closest distance to " CB  ARG A 190 " =    1.819
peak=    4.183 closest distance to " CB  VAL A 202 " =    1.529
peak=    4.164 closest distance to " CB  TRP A 179 " =    1.414
peak=    4.142 closest distance to " O   HOH Z  95 " =    1.995
peak=    4.141 closest distance to " O   ALA A 165 " =    1.420
peak=    4.139 closest distance to " CB  PRO A  54 " =    0.903
peak=    4.138 closest distance to " CA  TYR A  30 " =    0.986
peak=    4.093 closest distance to " O   HOH Z 133 " =    2.448
peak=    4.055 closest distance to " NE2 HIS A 115 " =    1.096
peak=    4.033 closest distance to " NH2 ARG A 156 " =    1.169
peak=    4.033 closest distance to " O   HOH Z 422 " =    0.914
peak=    4.026 closest distance to " O   HOH Z 357 " =    2.224
peak=    4.018 closest distance to " CD  LYS A 166 " =    1.503
peak=    3.997 closest distance to " CG1 ILE A  33 " =    1.172
peak=    3.989 closest distance to " CD  ARG A  66 " =    2.708
peak=    3.958 closest distance to " CZ  PHE A 218 " =    1.142
peak=    3.946 closest distance to " O   HOH Z 377 " =    1.243
peak=    3.910 closest distance to " O   HOH Z  15 " =    2.135
peak=    3.903 closest distance to " O   HOH Z 403 " =    1.808
peak=    3.882 closest distance to " O   THR A 251 " =    1.241
peak=    3.868 closest distance to " CB  ASN A 148 " =    1.376
peak=    3.853 closest distance to " O   HOH Z  80 " =    2.138
peak=    3.849 closest distance to " CB  LEU A 228 " =    1.123
peak=    3.847 closest distance to " CB  ARG A  79 " =    1.315
peak=    3.846 closest distance to " O   HOH Z 117 " =    2.105
peak=    3.842 closest distance to " O   HOH Z   7 " =    1.192
peak=    3.838 closest distance to " O   HOH Z 437 " =    1.679
peak=    3.838 closest distance to " CA  GLY A 196 " =    1.075
peak=    3.833 closest distance to " O   HOH Z 139 " =    1.188
peak=    3.815 closest distance to " O   TYR A 116 " =    1.377
peak=    3.806 closest distance to " O   SER A  87 " =    2.297
peak=    3.804 closest distance to " O   HOH Z 128 " =    2.238
peak=    3.773 closest distance to " CB  ASN A 285 " =    0.819
peak=    3.773 closest distance to " OG BSER A 164 " =    2.202
peak=    3.771 closest distance to " O   HOH Z  30 " =    1.601
peak=    3.770 closest distance to " CA  ALA A  21 " =    1.331
peak=    3.768 closest distance to " CZ3 TRP A 266 " =    1.108
peak=    3.767 closest distance to " O   HOH Z 189 " =    2.673
peak=    3.766 closest distance to " CB  GLU A 277 " =    3.832
peak=    3.766 closest distance to " O   HOH Z 423 " =    1.826
peak=    3.765 closest distance to " O   HOH Z  63 " =    1.474
peak=    3.760 closest distance to " O   HOH Z 415 " =    1.306
peak=    3.758 closest distance to " CB  TYR A 169 " =    0.725
peak=    3.758 closest distance to " CD1 LEU A 300 " =    1.139
peak=    3.757 closest distance to " O   HOH Z 154 " =    1.522
peak=    3.750 closest distance to " CA  ALA A 295 " =    1.137
peak=    3.745 closest distance to " CG2BVAL A  41 " =    0.872
peak=    3.744 closest distance to " CB  ASP A 140 " =    0.911
peak=    3.742 closest distance to " O   HOH Z 154 " =    2.330
peak=    3.740 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.739 closest distance to " O   HOH Z  54 " =    1.130
peak=    3.728 closest distance to " O   HOH Z 132 " =    2.879
peak=    3.726 closest distance to " CZ  PHE A  38 " =    1.286
peak=    3.726 closest distance to " O   HOH Z 301 " =    1.516
peak=    3.723 closest distance to " O   HOH Z 394 " =    1.746
peak=    3.722 closest distance to " CG1 VAL A 153 " =    1.081
peak=    3.722 closest distance to " N   SER A 164 " =    0.976
peak=    3.711 closest distance to " CB  SER A  62 " =    0.830
peak=    3.707 closest distance to " OD1 ASN A 217 " =    1.738
peak=    3.706 closest distance to " NE2 GLN A  11 " =    1.078
peak=    3.695 closest distance to " O   HOH Z  20 " =    1.884
peak=    3.686 closest distance to " CA  ALA A 100 " =    1.184
peak=    3.682 closest distance to " CA  PRO A  54 " =    1.376
peak=    3.677 closest distance to " O   HOH Z  40 " =    1.884
peak=    3.666 closest distance to " CD  ARG A 159 " =    0.875
peak=    3.665 closest distance to " CA  ASP A 191 " =    0.966
peak=    3.664 closest distance to " CB  ASP A 124 " =    0.779
peak=    3.663 closest distance to " O   HOH Z 316 " =    3.176
peak=    3.662 closest distance to " CB  SER A 141 " =    1.139
peak=    3.659 closest distance to " CZ3 TRP A  85 " =    0.877
peak=    3.657 closest distance to " O   HOH Z 389 " =    2.041
peak=    3.654 closest distance to " O   HOH Z 284 " =    2.947
peak=    3.648 closest distance to " O   HOH Z  47 " =    1.343
peak=    3.636 closest distance to " O   HOH Z  68 " =    1.962
peak=    3.635 closest distance to " O   HOH Z 406 " =    1.643
peak=    3.635 closest distance to " O   HOH Z 203 " =    1.768
peak=    3.629 closest distance to " CB  MET A 105 " =    1.198
peak=    3.629 closest distance to " N   CYS A 260 " =    0.805
peak=    3.624 closest distance to " O   HOH Z 417 " =    3.039
peak=    3.618 closest distance to " O   HOH Z 200 " =    1.503
peak=    3.614 closest distance to " CA  ILE A 106 " =    0.832
peak=    3.611 closest distance to " O   HOH Z 174 " =    2.113
peak=    3.608 closest distance to " CB  ASN A 142 " =    1.168
peak=    3.596 closest distance to " O   HOH Z 386 " =    2.359
peak=    3.592 closest distance to " CB  MET A  40 " =    0.873
peak=    3.592 closest distance to " O   HOH Z 281 " =    4.957
peak=    3.590 closest distance to " CB  GLU A 152 " =    1.109
peak=    3.588 closest distance to " O   ASN A  74 " =    1.561
peak=    3.580 closest distance to " O   HOH Z 258 " =    2.146
peak=    3.578 closest distance to " N   ILE A  33 " =    0.935
peak=    3.573 closest distance to " CB  ALA A 248 " =    1.270
peak=    3.572 closest distance to " O   HOH Z 128 " =    2.128
peak=    3.568 closest distance to " CB  PHE A 283 " =    0.790
peak=    3.566 closest distance to " CG  PRO A 243 " =    1.143
peak=    3.566 closest distance to " OE1 GLN A  11 " =    2.151
peak=    3.563 closest distance to " CD2 TRP A 179 " =    1.312
peak=    3.561 closest distance to " O   HOH Z 126 " =    1.618
peak=    3.561 closest distance to " O   HOH Z 271 " =    2.498
peak=    3.560 closest distance to " O   HOH Z 298 " =    1.920
peak=    3.559 closest distance to " O   HOH Z 265 " =    1.986
peak=    3.558 closest distance to " O   HOH Z 362 " =    3.121
peak=    3.553 closest distance to " O   HOH Z 346 " =    1.622
peak=    3.544 closest distance to " CA  GLU A  46 " =    0.932
peak=    3.540 closest distance to " O   HOH Z 374 " =    3.182
peak=    3.539 closest distance to " CB  PRO A 280 " =    1.178
peak=    3.535 closest distance to " CD2 LEU A 297 " =    1.024
peak=    3.533 closest distance to " CA  THR A 221 " =    1.644
peak=    3.522 closest distance to " CA  LEU A  83 " =    1.394
peak=    3.516 closest distance to " CB  GLN A  88 " =    1.217
peak=    3.515 closest distance to " CB  GLU A  46 " =    1.130
peak=    3.515 closest distance to " NH1AARG A 145 " =    1.136
peak=    3.513 closest distance to " O   HOH Z 146 " =    1.621
peak=    3.511 closest distance to " OH  TYR A 169 " =    0.879
peak=    3.504 closest distance to " O   HOH Z  48 " =    1.945
peak=    3.503 closest distance to " O   HOH Z  44 " =    1.808
peak=    3.502 closest distance to " O   HOH Z 261 " =    2.094
peak=    3.501 closest distance to " CA  GLN A  88 " =    1.338
peak=    3.499 closest distance to " C   VAL A 265 " =    1.113
peak=    3.499 closest distance to " CG2 THR A 221 " =    1.094
peak=    3.497 closest distance to " O   HOH Z 214 " =    2.852
peak=    3.496 closest distance to " CA  SER A  12 " =    1.594
peak=    3.487 closest distance to " O   HOH Z 185 " =    1.785
peak=    3.486 closest distance to " O   GLY A  57 " =    2.585
peak=    3.481 closest distance to " O   HOH Z 336 " =    1.832
peak=    3.479 closest distance to " CG2 VAL A  78 " =    0.945
peak=    3.476 closest distance to " CB  GLU A  37 " =    0.875
peak=    3.475 closest distance to " OE1 GLN A  58 " =    3.396
peak=    3.474 closest distance to " CB  PRO A 243 " =    1.280
peak=    3.473 closest distance to " O   HOH Z  88 " =    1.773
peak=    3.467 closest distance to " N   ASN A 127 " =    1.215
peak=    3.462 closest distance to " NE2 GLN A  77 " =    3.213
peak=    3.461 closest distance to " O   HOH Z 368 " =    2.085
peak=    3.460 closest distance to " O  BHOH Z 338 " =    2.551
peak=    3.451 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.449 closest distance to " CA  ASP A 124 " =    0.807
peak=    3.443 closest distance to " CD2 LEU A 255 " =    1.494
peak=    3.442 closest distance to " CA  ASN A 217 " =    1.301
peak=    3.434 closest distance to " CD  ARG A 195 " =    0.986
peak=    3.429 closest distance to " CG2 THR A  42 " =    0.940
peak=    3.416 closest distance to " O   HOH Z 303 " =    2.358
peak=    3.414 closest distance to " O   ASP A 200 " =    1.649
peak=    3.413 closest distance to " OD2 ASP A 298 " =    3.657
peak=    3.410 closest distance to " NE1 TRP A  92 " =    1.664
peak=    3.409 closest distance to " CG AARG A 275 " =    1.125
peak=    3.409 closest distance to " ND2 ASN A 187 " =    1.433
peak=    3.408 closest distance to " C   ILE A 106 " =    1.816
peak=    3.406 closest distance to " CA  TRP A  92 " =    0.941
peak=    3.401 closest distance to " O   HOH Z 374 " =    2.647
peak=    3.399 closest distance to " O   HOH Z 371 " =    2.925
peak=    3.397 closest distance to " ND2 ASN A 301 " =    0.961
peak=    3.397 closest distance to " C   ASN A 209 " =    1.126
peak=    3.395 closest distance to " O   HOH Z  49 " =    2.130
peak=    3.395 closest distance to " N   TYR A 116 " =    1.560
peak=    3.387 closest distance to " O   HOH Z 146 " =    1.306
peak=    3.383 closest distance to " CB  PHE A  16 " =    1.386
peak=    3.381 closest distance to " O   HOH Z  78 " =    2.178
peak=    3.376 closest distance to " O   HOH Z  61 " =    1.672
peak=    3.372 closest distance to " CB  VAL A 265 " =    1.343
peak=    3.368 closest distance to " O   HOH Z 415 " =    1.460
peak=    3.367 closest distance to " CA  ARG A 139 " =    1.506
peak=    3.365 closest distance to " O   HOH Z 294 " =    1.616
peak=    3.365 closest distance to " O   HOH Z 193 " =    1.801
peak=    3.364 closest distance to " O   HOH Z 435 " =    2.932
peak=    3.361 closest distance to " O   HOH Z 380 " =    1.909
peak=    3.360 closest distance to " CA  VAL A 125 " =    1.329
peak=    3.354 closest distance to " CG  ARG A 138 " =    1.190
peak=    3.354 closest distance to " CB  ALA A  43 " =    0.938
peak=    3.352 closest distance to " O   HOH Z 245 " =    1.297
peak=    3.351 closest distance to " O   HOH Z 150 " =    1.819
peak=    3.349 closest distance to " CA  TYR A 116 " =    1.347
peak=    3.345 closest distance to " O   HOH Z 383 " =    2.228
peak=    3.340 closest distance to " CG2 VAL A 197 " =    1.192
peak=    3.335 closest distance to " CA  ASP A 162 " =    1.202
peak=    3.332 closest distance to " O   PRO A 213 " =    1.522
peak=    3.332 closest distance to " O   HOH Z 345 " =    1.599
peak=    3.322 closest distance to " CG2 THR A 220 " =    0.760
peak=    3.320 closest distance to " O   HOH Z 201 " =    2.944
peak=    3.319 closest distance to " N   GLY A  98 " =    1.119
peak=    3.317 closest distance to " O   HOH Z 163 " =    1.698
peak=    3.316 closest distance to " N   THR A  52 " =    1.171
peak=    3.315 closest distance to " CA  VAL A  41 " =    0.874
peak=    3.314 closest distance to " O   HOH Z 128 " =    1.872
peak=    3.308 closest distance to " O   HOH Z  50 " =    3.668
peak=    3.303 closest distance to " CG  GLN A  11 " =    1.365
peak=    3.303 closest distance to " O   HOH Z 404 " =    1.491
peak=    3.300 closest distance to " CB  ARG A 190 " =    1.173
peak=    3.299 closest distance to " CB  GLU A 175 " =    1.357
peak=    3.297 closest distance to " CB  MET A  47 " =    0.957
peak=    3.292 closest distance to " O   ALA A 158 " =    1.247
peak=    3.291 closest distance to " CB  LEU A  83 " =    0.846
peak=    3.290 closest distance to " O   HOH Z 367 " =    1.539
peak=    3.289 closest distance to " O   HOH Z 199 " =    1.653
peak=    3.289 closest distance to " N   ASN A  39 " =    1.396
peak=    3.287 closest distance to " CG  GLN A  77 " =    0.770
peak=    3.282 closest distance to " CA  ARG A 102 " =    1.196
peak=    3.278 closest distance to " O   HOH Z 134 " =    2.349
peak=    3.277 closest distance to " O   HOH Z 139 " =    4.894
peak=    3.277 closest distance to " CB  THR A  52 " =    0.818
peak=    3.275 closest distance to " O   HOH Z   7 " =    0.754
peak=    3.275 closest distance to " CE1 HIS A 108 " =    1.112
peak=    3.275 closest distance to " O   HOH Z 343 " =    2.201
peak=    3.274 closest distance to " OD1 ASN A  69 " =    2.404
peak=    3.272 closest distance to " CG  GLU A  37 " =    0.947
peak=    3.271 closest distance to " CG2 ILE A  20 " =    1.356
peak=    3.270 closest distance to " O   HOH Z 423 " =    3.291
peak=    3.267 closest distance to " O   HOH Z 327 " =    1.651
peak=    3.265 closest distance to " O   HOH Z 408 " =    3.042
peak=    3.261 closest distance to " O   ASP A 124 " =    1.408
peak=    3.261 closest distance to " O   HOH Z 428 " =    0.975
peak=    3.261 closest distance to " O   HOH Z 427 " =    3.250
peak=    3.260 closest distance to " CB  GLN A  89 " =    1.194
peak=    3.260 closest distance to " CE3 TRP A 274 " =    3.709
peak=    3.256 closest distance to " CB  SER A   3 " =    1.405
peak=    3.255 closest distance to " NZ  LYS A 117 " =    2.902
peak=    3.254 closest distance to " CD1 LEU A  96 " =    0.796
peak=    3.251 closest distance to " CA  ARG A  36 " =    1.113
peak=    3.250 closest distance to " ND1 HIS A  81 " =    1.473
peak=    3.249 closest distance to " O   HOH Z  54 " =    1.504
peak=    3.248 closest distance to " O   HOH Z 394 " =    4.145
peak=    3.244 closest distance to " O   HOH Z 118 " =    0.924
peak=    3.238 closest distance to " NH1 ARG A  14 " =    1.235
peak=    3.235 closest distance to " CA  LYS A 166 " =    1.394
peak=    3.235 closest distance to " O   HOH Z 298 " =    4.494
peak=    3.233 closest distance to " O   HOH Z 244 " =    1.674
peak=    3.229 closest distance to " CG2 VAL A 126 " =    0.836
peak=    3.225 closest distance to " CD  PRO A  54 " =    1.019
peak=    3.224 closest distance to " O   HOH Z 126 " =    2.458
peak=    3.223 closest distance to " CA  GLU A 152 " =    0.927
peak=    3.222 closest distance to " CB  PRO A 198 " =    0.967
peak=    3.221 closest distance to " CA  ARG A  66 " =    0.927
peak=    3.215 closest distance to " CD1 LEU A 222 " =    0.760
peak=    3.215 closest distance to " OG  SER A 245 " =    1.619
peak=    3.211 closest distance to " O   HOH Z 191 " =    4.129
peak=    3.209 closest distance to " CB  PRO A  90 " =    1.287
peak=    3.203 closest distance to " N   ASN A 252 " =    1.200
peak=    3.202 closest distance to " OG  SER A  62 " =    3.047
peak=    3.201 closest distance to " CA  THR A 246 " =    0.987
peak=    3.200 closest distance to " ND2 ASN A 249 " =    0.840
peak=    3.200 closest distance to " O   GLN A  11 " =    0.906
peak=    3.200 closest distance to " CB  ARG A  79 " =    0.883
peak=    3.199 closest distance to " CB  ARG A 156 " =    0.988
peak=    3.199 closest distance to " CA  MET A 105 " =    1.188
peak=    3.198 closest distance to " O   THR A 220 " =    1.136
peak=    3.193 closest distance to " CA  SER A  87 " =    1.082
peak=    3.181 closest distance to " O   HOH Z 109 " =    2.069
peak=    3.176 closest distance to " O   GLY A  91 " =    1.129
peak=    3.174 closest distance to " N   GLU A  44 " =    1.289
peak=    3.174 closest distance to " CB  GLN A 103 " =    0.892
peak=    3.173 closest distance to " O   HOH Z 173 " =    2.224
peak=    3.171 closest distance to " CA  ARG A 156 " =    1.108
peak=    3.168 closest distance to " CD BLYS A 290 " =    1.008
peak=    3.167 closest distance to " CB  LEU A   5 " =    1.130
peak=    3.166 closest distance to " O   HOH Z  99 " =    2.364
peak=    3.161 closest distance to " CA  ALA A 154 " =    1.045
peak=    3.160 closest distance to " O   HOH Z 248 " =    1.813
peak=    3.156 closest distance to " NH2BARG A 145 " =    1.958
peak=    3.154 closest distance to " NE  ARG A 219 " =    1.657
peak=    3.150 closest distance to " CG2 ILE A 234 " =    0.809
peak=    3.148 closest distance to " NH2BARG A 145 " =    0.993
peak=    3.147 closest distance to " CA  LYS A 117 " =    1.305
peak=    3.145 closest distance to " O   HOH Z 145 " =    3.364
peak=    3.142 closest distance to " O   HOH Z 393 " =    3.929
peak=    3.142 closest distance to " O   HOH Z 421 " =    1.908
peak=    3.141 closest distance to " O   HOH Z 164 " =    3.521
peak=    3.137 closest distance to " O   HOH Z 327 " =    1.977
peak=    3.134 closest distance to " NZ  LYS A 181 " =    0.715
peak=    3.132 closest distance to " CD  ARG A  66 " =    2.474
peak=    3.130 closest distance to " O   HOH Z  22 " =    2.725
peak=    3.129 closest distance to " O   HOH Z 432 " =    1.664
peak=    3.128 closest distance to " O   HOH Z 403 " =    0.902
peak=    3.125 closest distance to " CG2 VAL A 257 " =    0.891
peak=    3.121 closest distance to " O   HOH Z 247 " =    1.458
peak=    3.119 closest distance to " O   HOH Z 147 " =    1.554
peak=    3.118 closest distance to " CB  ALA A 100 " =    1.485
peak=    3.112 closest distance to " CG2 ILE A 120 " =    0.811
peak=    3.109 closest distance to " N   ALA A 292 " =    1.098
peak=    3.109 closest distance to " O   HOH Z 358 " =    1.292
peak=    3.103 closest distance to " CA  ALA A  19 " =    0.801
peak=    3.088 closest distance to " O   HOH Z 344 " =    3.234
peak=    3.087 closest distance to " CG1 ILE A 120 " =    1.025
peak=    3.061 closest distance to " NH2AARG A 275 " =    3.622
peak=    3.060 closest distance to " CZ  PHE A 192 " =    0.972
peak=    3.052 closest distance to " CA  ALA A  84 " =    1.226
peak=    3.050 closest distance to " O   HOH Z 271 " =    1.939
peak=    3.045 closest distance to " O   THR A 182 " =    1.484
peak=    3.043 closest distance to " CB  ALA A  10 " =    1.336
peak=    3.043 closest distance to " CG  ARG A 259 " =    3.659
peak=    3.041 closest distance to " O   HOH Z 261 " =    2.197
peak=    3.039 closest distance to " O   HOH Z 281 " =    2.577
peak=    3.037 closest distance to " CB  TRP A 179 " =    1.873

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.855 - 5.462
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 225
   mapped sites are within: 0.855 - 5.462

peak=   -4.729 closest distance to " CD  GLN A 223 " =    1.461
peak=   -4.633 closest distance to " O   HOH Z 266 " =    5.462
peak=   -4.598 closest distance to " CD1 PHE A  59 " =    1.975
peak=   -4.369 closest distance to " CD  GLN A  58 " =    0.962
peak=   -4.146 closest distance to " O   HOH Z 150 " =    0.899
peak=   -4.121 closest distance to " CA  ASP A 298 " =    1.058
peak=   -4.046 closest distance to " OXT GLY A 302 " =    3.129
peak=   -4.028 closest distance to " CB  ALA A  10 " =    2.104
peak=   -4.023 closest distance to " CG1 VAL A 250 " =    2.712
peak=   -4.015 closest distance to " O   HOH Z 407 " =    0.855
peak=   -4.009 closest distance to " CG1 VAL A 112 " =    2.567
peak=   -3.971 closest distance to " O   SER A 206 " =    1.351
peak=   -3.968 closest distance to " O   HOH Z 166 " =    1.691
peak=   -3.951 closest distance to " O   HOH Z 348 " =    2.374
peak=   -3.945 closest distance to " O   HOH Z 155 " =    1.760
peak=   -3.943 closest distance to " CD  ARG A 156 " =    2.148
peak=   -3.935 closest distance to " NE2 GLN A 223 " =    1.151
peak=   -3.932 closest distance to " CG  ARG A 269 " =    2.366
peak=   -3.919 closest distance to " CE2 PHE A  61 " =    2.641
peak=   -3.918 closest distance to " OG  SER A  97 " =    2.289
peak=   -3.910 closest distance to " OD1 ASP A 191 " =    1.445
peak=   -3.908 closest distance to " O   HOH Z  10 " =    1.676
peak=   -3.882 closest distance to " O   HOH Z   6 " =    1.468
peak=   -3.870 closest distance to " CD  GLN A  88 " =    0.970
peak=   -3.852 closest distance to " CA  GLY A  98 " =    2.239
peak=   -3.848 closest distance to " CD  ARG A  14 " =    3.417
peak=   -3.838 closest distance to " CD1 PHE A 130 " =    2.365
peak=   -3.837 closest distance to " O   HOH Z  19 " =    2.213
peak=   -3.830 closest distance to " CB  ALA A 161 " =    2.643
peak=   -3.820 closest distance to " O   PRO A 198 " =    1.363
peak=   -3.814 closest distance to " C   ASN A 285 " =    2.355
peak=   -3.812 closest distance to " OE1 GLN A  88 " =    1.102
peak=   -3.803 closest distance to " CB  ALA A 291 " =    2.436
peak=   -3.801 closest distance to " CB  PRO A 243 " =    2.778
peak=   -3.801 closest distance to " O   HOH Z 234 " =    4.292
peak=   -3.796 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.791 closest distance to " NH2 ARG A  66 " =    1.738
peak=   -3.786 closest distance to " O   HOH Z 275 " =    1.631
peak=   -3.769 closest distance to " ND2 ASN A  45 " =    1.978
peak=   -3.768 closest distance to " O   HOH Z 166 " =    2.371
peak=   -3.758 closest distance to " CG2 ILE A  49 " =    2.743
peak=   -3.757 closest distance to " OE1 GLN A 223 " =    2.381
peak=   -3.743 closest distance to " O   HOH Z  52 " =    1.681
peak=   -3.719 closest distance to " CD2 PHE A  61 " =    2.109
peak=   -3.713 closest distance to " CA  GLY A 203 " =    2.420
peak=   -3.677 closest distance to " O   HOH Z  37 " =    1.766
peak=   -3.669 closest distance to " CG2 ILE A  20 " =    2.941
peak=   -3.667 closest distance to " O   HOH Z 388 " =    1.872
peak=   -3.662 closest distance to " O   HOH Z 252 " =    3.963
peak=   -3.654 closest distance to " O   HOH Z 308 " =    1.525
peak=   -3.643 closest distance to " CG  PRO A 243 " =    1.713
peak=   -3.640 closest distance to " O   HOH Z  58 " =    0.979
peak=   -3.639 closest distance to " O   VAL A  67 " =    2.728
peak=   -3.631 closest distance to " CG2 VAL A 189 " =    2.191
peak=   -3.631 closest distance to " CD1 LEU A 101 " =    2.529
peak=   -3.629 closest distance to " CE3 TRP A 150 " =    2.077
peak=   -3.627 closest distance to " C   HIS A 108 " =    1.051
peak=   -3.623 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.614 closest distance to " O   HOH Z 109 " =    3.346
peak=   -3.605 closest distance to " NE2 GLN A 194 " =    1.990
peak=   -3.591 closest distance to " O   HOH Z 283 " =    2.227
peak=   -3.587 closest distance to " O   HOH Z 412 " =    2.356
peak=   -3.586 closest distance to " O   HOH Z 418 " =    1.327
peak=   -3.583 closest distance to " O   HOH Z 377 " =    2.127
peak=   -3.579 closest distance to " OG BSER A 210 " =    1.355
peak=   -3.571 closest distance to " O   HOH Z 113 " =    2.205
peak=   -3.566 closest distance to " NE2 GLN A  94 " =    1.865
peak=   -3.554 closest distance to " O   HOH Z 149 " =    1.722
peak=   -3.553 closest distance to " CD2 TYR A 293 " =    1.765
peak=   -3.551 closest distance to " CG  MET A 105 " =    0.934
peak=   -3.550 closest distance to " N   ARG A 275 " =    1.309
peak=   -3.547 closest distance to " O   HOH Z 117 " =    4.625
peak=   -3.545 closest distance to " N   ALA A  43 " =    2.806
peak=   -3.544 closest distance to " O   HOH Z 136 " =    2.320
peak=   -3.537 closest distance to " O   HOH Z 351 " =    1.553
peak=   -3.524 closest distance to " CZ  TYR A 169 " =    1.888
peak=   -3.511 closest distance to " CG  GLN A  11 " =    1.426
peak=   -3.510 closest distance to " O   HOH Z 113 " =    2.325
peak=   -3.508 closest distance to " O   HOH Z 128 " =    2.506
peak=   -3.504 closest distance to " O   HOH Z 377 " =    1.048
peak=   -3.503 closest distance to " ND2 ASN A  45 " =    1.179
peak=   -3.501 closest distance to " O   HOH Z 185 " =    2.590
peak=   -3.491 closest distance to " O   HOH Z  70 " =    2.305
peak=   -3.481 closest distance to " OD2 ASP A 171 " =    1.831
peak=   -3.481 closest distance to " O   HOH Z  90 " =    3.629
peak=   -3.479 closest distance to " CB  ALA A 131 " =    2.418
peak=   -3.476 closest distance to " CG2AVAL A  41 " =    2.847
peak=   -3.470 closest distance to " CA  GLY A 241 " =    3.124
peak=   -3.470 closest distance to " O   HOH Z 109 " =    3.579
peak=   -3.465 closest distance to " CG1 VAL A 189 " =    2.501
peak=   -3.465 closest distance to " O   PRO A 163 " =    2.192
peak=   -3.460 closest distance to " O   HOH Z  91 " =    2.257
peak=   -3.455 closest distance to " O   SER A 210 " =    1.781
peak=   -3.445 closest distance to " CG  PRO A 163 " =    1.755
peak=   -3.442 closest distance to " CB  GLU A 277 " =    1.341
peak=   -3.440 closest distance to " N   ALA A 226 " =    2.136
peak=   -3.425 closest distance to " O   HOH Z 137 " =    2.153
peak=   -3.424 closest distance to " CD2 PHE A 225 " =    1.392
peak=   -3.423 closest distance to " OG1 THR A  82 " =    1.467
peak=   -3.418 closest distance to " O   SER A 276 " =    1.789
peak=   -3.414 closest distance to " O   HOH Z 171 " =    2.350
peak=   -3.413 closest distance to " CZ3 TRP A 179 " =    1.241
peak=   -3.410 closest distance to " O   HOH Z 394 " =    1.657
peak=   -3.399 closest distance to " SD  MET A 105 " =    2.570
peak=   -3.393 closest distance to " CB  ALA A  43 " =    2.676
peak=   -3.391 closest distance to " O   HOH Z 139 " =    3.301
peak=   -3.391 closest distance to " O   TRP A  92 " =    2.009
peak=   -3.385 closest distance to " ND2 ASN A  69 " =    1.557
peak=   -3.384 closest distance to " O   SER A 271 " =    2.119
peak=   -3.376 closest distance to " O   HOH Z 392 " =    1.354
peak=   -3.372 closest distance to " N   GLN A  58 " =    1.452
peak=   -3.370 closest distance to " O   HOH Z 207 " =    1.576
peak=   -3.369 closest distance to " N   ASP A 272 " =    1.300
peak=   -3.369 closest distance to " CD1 LEU A 167 " =    2.014
peak=   -3.363 closest distance to " O   HOH Z 384 " =    2.125
peak=   -3.358 closest distance to " O   HOH Z  49 " =    0.989
peak=   -3.357 closest distance to " O   HOH Z 290 " =    1.111
peak=   -3.357 closest distance to " O   HOH Z 292 " =    4.693
peak=   -3.356 closest distance to " CB  ASP A 132 " =    2.433
peak=   -3.352 closest distance to " OG BSER A 210 " =    2.285
peak=   -3.339 closest distance to " O   ALA A  10 " =    1.912
peak=   -3.339 closest distance to " CB  PHE A 192 " =    1.974
peak=   -3.338 closest distance to " O   HOH Z   7 " =    1.223
peak=   -3.335 closest distance to " O   HOH Z 134 " =    2.153
peak=   -3.335 closest distance to " NH2 ARG A 159 " =    2.398
peak=   -3.334 closest distance to " O   HOH Z 259 " =    2.039
peak=   -3.332 closest distance to " OH  TYR A 169 " =    0.991
peak=   -3.331 closest distance to " CB  ALA A   9 " =    2.616
peak=   -3.325 closest distance to " NE2 GLN A 103 " =    1.828
peak=   -3.322 closest distance to " O   HOH Z  38 " =    1.258
peak=   -3.322 closest distance to " CA  SER A 276 " =    1.471
peak=   -3.320 closest distance to " CG  ASN A  45 " =    0.869
peak=   -3.316 closest distance to " CB  PHE A  16 " =    2.502
peak=   -3.314 closest distance to " O   ASP A 171 " =    1.064
peak=   -3.312 closest distance to " CG2 THR A 221 " =    2.239
peak=   -3.311 closest distance to " NH2BARG A 145 " =    2.400
peak=   -3.310 closest distance to " O   HOH Z 298 " =    2.864
peak=   -3.306 closest distance to " O   HOH Z 128 " =    4.280
peak=   -3.305 closest distance to " C   LEU A 143 " =    1.310
peak=   -3.301 closest distance to " CZ  PHE A  38 " =    2.549
peak=   -3.298 closest distance to " O   HOH Z 301 " =    2.418
peak=   -3.288 closest distance to " O   HOH Z 114 " =    3.950
peak=   -3.286 closest distance to " O   HOH Z 111 " =    1.503
peak=   -3.282 closest distance to " O   HOH Z 251 " =    5.109
peak=   -3.279 closest distance to " OD2 ASP A 171 " =    2.373
peak=   -3.278 closest distance to " O   HOH Z 318 " =    1.410
peak=   -3.276 closest distance to " O   ALA A   1 " =    2.078
peak=   -3.276 closest distance to " CG2 THR A   4 " =    1.862
peak=   -3.273 closest distance to " O   GLY A 262 " =    2.397
peak=   -3.270 closest distance to " O   HOH Z 275 " =    1.878
peak=   -3.266 closest distance to " O   HOH Z 200 " =    1.192
peak=   -3.263 closest distance to " O   SER A 135 " =    1.758
peak=   -3.255 closest distance to " NE  ARG A  66 " =    4.451
peak=   -3.254 closest distance to " O   HOH Z 396 " =    1.870
peak=   -3.254 closest distance to " O   HOH Z 426 " =    1.708
peak=   -3.249 closest distance to " ND2BASN A 224 " =    1.887
peak=   -3.248 closest distance to " O   HOH Z  78 " =    1.945
peak=   -3.247 closest distance to " CE BMET A  47 " =    1.998
peak=   -3.247 closest distance to " OD1 ASP A 171 " =    1.484
peak=   -3.245 closest distance to " CA  VAL A 197 " =    0.987
peak=   -3.245 closest distance to " O   GLY A 196 " =    1.171
peak=   -3.244 closest distance to " C   GLY A  17 " =    1.202
peak=   -3.242 closest distance to " CG  GLU A  53 " =    1.501
peak=   -3.242 closest distance to " O   HOH Z 196 " =    2.024
peak=   -3.240 closest distance to " CB  TRP A  85 " =    2.479
peak=   -3.240 closest distance to " CD1 ILE A 263 " =    2.058
peak=   -3.234 closest distance to " O   HOH Z 368 " =    2.028
peak=   -3.234 closest distance to " OD2 ASP A 298 " =    2.083
peak=   -3.234 closest distance to " CD  ARG A 195 " =    5.085
peak=   -3.230 closest distance to " CG  ARG A 259 " =    2.440
peak=   -3.229 closest distance to " O   LEU A 101 " =    2.142
peak=   -3.228 closest distance to " O   HOH Z 150 " =    1.852
peak=   -3.222 closest distance to " CA  GLY A 133 " =    2.390
peak=   -3.219 closest distance to " OH  TYR A 247 " =    2.300
peak=   -3.219 closest distance to " O   HOH Z  71 " =    1.909
peak=   -3.217 closest distance to " O   ALA A  34 " =    2.587
peak=   -3.208 closest distance to " CE  MET A 105 " =    2.833
peak=   -3.207 closest distance to " O   HOH Z 165 " =    1.836
peak=   -3.204 closest distance to " O   HOH Z  90 " =    2.019
peak=   -3.197 closest distance to " CG  ARG A  66 " =    2.543
peak=   -3.194 closest distance to " O   HOH Z 422 " =    1.550
peak=   -3.194 closest distance to " O   ASP A 253 " =    1.906
peak=   -3.191 closest distance to " C   THR A 264 " =    1.450
peak=   -3.181 closest distance to " O   HOH Z 198 " =    2.383
peak=   -3.176 closest distance to " O   PHE A 218 " =    1.401
peak=   -3.174 closest distance to " O   GLY A 118 " =    2.237
peak=   -3.174 closest distance to " CG  ASP A 231 " =    0.862
peak=   -3.173 closest distance to " O   HOH Z 198 " =    1.435
peak=   -3.171 closest distance to " O   HOH Z 384 " =    2.134
peak=   -3.169 closest distance to " O   HOH Z 174 " =    1.871
peak=   -3.169 closest distance to " O   HOH Z  60 " =    1.665
peak=   -3.156 closest distance to " O   ALA A  34 " =    2.052
peak=   -3.151 closest distance to " C   ALA A 158 " =    1.359
peak=   -3.150 closest distance to " O   HOH Z 413 " =    1.278
peak=   -3.150 closest distance to " C   VAL A 265 " =    0.912
peak=   -3.149 closest distance to " OG  SER A  87 " =    1.705
peak=   -3.145 closest distance to " O   HOH Z  48 " =    1.110
peak=   -3.141 closest distance to " C   ARG A  79 " =    2.734
peak=   -3.138 closest distance to " O   HOH Z 156 " =    3.729
peak=   -3.137 closest distance to " OD1 ASN A 173 " =    1.405
peak=   -3.136 closest distance to " NE  ARG A  79 " =    1.333
peak=   -3.135 closest distance to " O   HOH Z 184 " =    1.669
peak=   -3.129 closest distance to " CA  SER A  62 " =    2.525
peak=   -3.128 closest distance to " CB  ASP A 162 " =    2.538
peak=   -3.128 closest distance to " ND2 ASN A 301 " =    1.986
peak=   -3.127 closest distance to " SD  MET A  40 " =    1.996
peak=   -3.127 closest distance to " O   HOH Z 424 " =    2.939
peak=   -3.127 closest distance to " O   VAL A 174 " =    2.058
peak=   -3.124 closest distance to " N   TYR A  68 " =    2.941
peak=   -3.118 closest distance to " CG2 ILE A 263 " =    2.249
peak=   -3.116 closest distance to " O   HOH Z 109 " =    1.260
peak=   -3.116 closest distance to " O   HOH Z 325 " =    2.009
peak=   -3.114 closest distance to " O   HOH Z 137 " =    1.444
peak=   -3.113 closest distance to " CD2 PHE A  59 " =    2.500
peak=   -3.109 closest distance to " CH2 TRP A 177 " =    1.965
peak=   -3.099 closest distance to " O   HOH Z 106 " =    2.169
peak=   -3.095 closest distance to " CG2 VAL A 189 " =    1.967
peak=   -3.091 closest distance to " CG2BVAL A  41 " =    2.062
peak=   -3.087 closest distance to " CH2 TRP A 150 " =    1.170
peak=   -3.078 closest distance to " O   HOH Z 108 " =    2.158
peak=   -3.069 closest distance to " CD  LYS A 289 " =    2.327
peak=   -3.057 closest distance to " O   HOH Z 219 " =    4.405
peak=   -3.003 closest distance to " CA  GLY A 241 " =    2.878

================= 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    :  0.4447 0.4254   6.259240e+00   6.225892e+00
   1_bss:  0.4353 0.4174   6.249257e+00   6.213836e+00
   1_xyz:  0.3555 0.3808   6.115302e+00   6.151026e+00
   1_adp:  0.3272 0.3914   6.068582e+00   6.163071e+00
   1_occ:  0.3269 0.3911   6.067729e+00   6.162864e+00
   2_bss:  0.3264 0.3903   6.069995e+00   6.164044e+00
   2_xyz:  0.2530 0.3005   5.833423e+00   5.972904e+00
   2_adp:  0.2268 0.2839   5.761119e+00   5.928682e+00
   2_occ:  0.2264 0.2837   5.759916e+00   5.927801e+00
   3_bss:  0.2253 0.2824   5.757412e+00   5.924663e+00
   3_xyz:  0.1784 0.2232   5.538847e+00   5.725651e+00
   3_adp:  0.1681 0.2121   5.487960e+00   5.677147e+00
   3_occ:  0.1679 0.2118   5.487044e+00   5.676460e+00
   4_bss:  0.1681 0.2114   5.486977e+00   5.674458e+00
   4_xyz:  0.1433 0.1898   5.353168e+00   5.566811e+00
   4_adp:  0.1331 0.1831   5.295324e+00   5.524461e+00
   4_occ:  0.1330 0.1831   5.294996e+00   5.524281e+00
   5_bss:  0.1333 0.1831   5.295033e+00   5.523832e+00
   5_xyz:  0.1247 0.1753   5.245643e+00   5.485887e+00
   5_adp:  0.1233 0.1738   5.234384e+00   5.474431e+00
   5_occ:  0.1233 0.1739   5.234583e+00   5.474953e+00
   5_bss:  0.1233 0.1739   5.234442e+00   5.474820e+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:  0.280  37.147  -2.783   5.067  -0.378   0.000  -0.000  -0.000
   1_xyz:  0.280  37.147  -2.783   5.067  -0.378   0.000  -0.000  -0.000
   1_adp:  0.280  37.147  -2.783   5.067  -0.378   0.000  -0.000  -0.000
   1_occ:  0.280  37.147  -2.783   5.067  -0.378   0.000  -0.000  -0.000
   2_bss:  0.272  50.738  -1.411   3.168   0.153   0.000   0.000   0.000
   2_xyz:  0.272  50.738  -1.411   3.168   0.153   0.000   0.000   0.000
   2_adp:  0.272  50.738  -1.411   3.168   0.153   0.000   0.000   0.000
   2_occ:  0.272  50.738  -1.411   3.168   0.153   0.000   0.000   0.000
   3_bss:  0.317  69.462  -0.999   1.413   0.216   0.000   0.000   0.000
   3_xyz:  0.317  69.462  -0.999   1.413   0.216   0.000   0.000   0.000
   3_adp:  0.317  69.462  -0.999   1.413   0.216   0.000   0.000   0.000
   3_occ:  0.317  69.462  -0.999   1.413   0.216   0.000   0.000   0.000
   4_bss:  0.328  75.216  -1.289   0.292  -0.002   0.000  -0.000  -0.000
   4_xyz:  0.328  75.216  -1.289   0.292  -0.002   0.000  -0.000  -0.000
   4_adp:  0.328  75.216  -1.289   0.292  -0.002   0.000  -0.000  -0.000
   4_occ:  0.328  75.216  -1.289   0.292  -0.002   0.000  -0.000  -0.000
   5_bss:  0.332  80.001  -1.122   0.011   0.283   0.000   0.000   0.000
   5_xyz:  0.332  80.001  -1.122   0.011   0.283   0.000   0.000   0.000
   5_adp:  0.332  80.001  -1.122   0.011   0.283   0.000   0.000   0.000
   5_occ:  0.332  80.001  -1.122   0.011   0.283   0.000   0.000   0.000
   5_bss:  0.325  74.499  -1.026  -0.058   0.384  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.017 0.5347  0.6805    56061.452
   1_bss:  48.375 0.5415  0.7050    53579.575
   1_xyz:  43.244 0.6036  0.7740    42795.265
   1_adp:  43.967 0.5946  0.7554    44170.432
   1_occ:  43.985 0.5943  0.7544    44169.391
   2_bss:  43.855 0.5960  0.7595    44154.852
   2_xyz:  32.152 0.7328  0.9140    24619.641
   2_adp:  29.794 0.7596  0.9165    21697.105
   2_occ:  29.753 0.7600  0.9162    21633.922
   3_bss:  29.516 0.7627  0.9076    21362.682
   3_xyz:  22.396 0.8378  0.9657    13041.904
   3_adp:  20.786 0.8545  0.9688    11867.883
   3_occ:  20.760 0.8548  0.9689    11852.804
   4_bss:  20.681 0.8555  0.9517    11763.834
   4_xyz:  17.877 0.8820  0.9650     9157.288
   4_adp:  16.930 0.8903  0.9558     8427.253
   4_occ:  16.921 0.8904  0.9557     8421.535
   5_bss:  16.902 0.8906  0.9578     8399.416
   5_xyz:  16.021 0.8983  0.9634     7767.174
   5_adp:  15.737 0.9009  0.9554     7629.182
   5_occ:  15.745 0.9008  0.9553     7636.186
   5_bss:  15.742 0.9009  0.9570     7632.133
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6672e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6672e-01
   1_xyz:   1.438  0.011  0.089 15.501  0.006  4.114   1.0818e-01
   1_adp:   1.438  0.011  0.089 15.501  0.006  4.114   1.0818e-01
   1_occ:   1.438  0.011  0.089 15.501  0.006  4.114   1.0818e-01
   2_bss:   1.438  0.011  0.089 15.501  0.006  4.114   1.0818e-01
   2_xyz:   1.510  0.012  0.101 16.036  0.005  4.115   1.2267e-01
   2_adp:   1.510  0.012  0.101 16.036  0.005  4.115   1.2267e-01
   2_occ:   1.510  0.012  0.101 16.036  0.005  4.115   1.2267e-01
   3_bss:   1.510  0.012  0.101 16.036  0.005  4.115   1.2267e-01
   3_xyz:   1.119  0.009  0.073 14.991  0.004  4.131   7.4239e-02
   3_adp:   1.119  0.009  0.073 14.991  0.004  4.131   7.4239e-02
   3_occ:   1.119  0.009  0.073 14.991  0.004  4.131   7.4239e-02
   4_bss:   1.119  0.009  0.073 14.991  0.004  4.131   7.4239e-02
   4_xyz:   1.135  0.010  0.080 14.874  0.004  4.132   7.4824e-02
   4_adp:   1.135  0.010  0.080 14.874  0.004  4.132   7.4824e-02
   4_occ:   1.135  0.010  0.080 14.874  0.004  4.132   7.4824e-02
   5_bss:   1.135  0.010  0.080 14.874  0.004  4.132   7.4824e-02
   5_xyz:   1.102  0.010  0.081 14.831  0.004  4.116   7.3584e-02
   5_adp:   1.102  0.010  0.081 14.831  0.004  4.116   7.3584e-02
   5_occ:   1.102  0.010  0.081 14.831  0.004  4.116   7.3584e-02
   5_bss:   1.102  0.010  0.081 14.831  0.004  4.116   7.3584e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.581   2.4520e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.581   2.4520e-01
   1_xyz:   8.592  0.077  0.375 85.180  0.047  2.096   7.4351e-02
   1_adp:   8.592  0.077  0.375 85.180  0.047  2.096   7.4351e-02
   1_occ:   8.592  0.077  0.375 85.180  0.047  2.096   7.4351e-02
   2_bss:   8.592  0.077  0.375 85.180  0.047  2.096   7.4351e-02
   2_xyz:   8.886  0.047  0.277 86.486  0.028  2.116   1.1844e-01
   2_adp:   8.886  0.047  0.277 86.486  0.028  2.116   1.1844e-01
   2_occ:   8.886  0.047  0.277 86.486  0.028  2.116   1.1844e-01
   3_bss:   8.886  0.047  0.277 86.486  0.028  2.116   1.1844e-01
   3_xyz:   8.259  0.058  0.235 83.918  0.043  2.200   7.7963e-02
   3_adp:   8.259  0.058  0.235 83.918  0.043  2.200   7.7963e-02
   3_occ:   8.259  0.058  0.235 83.918  0.043  2.200   7.7963e-02
   4_bss:   8.259  0.058  0.235 83.918  0.043  2.200   7.7963e-02
   4_xyz:   8.082  0.048  0.254 82.794  0.036  2.231   6.9891e-02
   4_adp:   8.082  0.048  0.254 82.794  0.036  2.231   6.9891e-02
   4_occ:   8.082  0.048  0.254 82.794  0.036  2.231   6.9891e-02
   5_bss:   8.082  0.048  0.254 82.794  0.036  2.231   6.9891e-02
   5_xyz:   8.070  0.055  0.257 82.345  0.037  2.169   5.7133e-02
   5_adp:   8.070  0.055  0.257 82.345  0.037  2.169   5.7133e-02
   5_occ:   8.070  0.055  0.257 82.345  0.037  2.169   5.7133e-02
   5_bss:   8.070  0.055  0.257 82.345  0.037  2.169   5.7133e-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: 103.26   0.00  18.10  86.18   0.00  14.80 103.26   0.00  36.06
   1_occ: 103.26   0.00  18.10  86.18   0.00  14.80 103.26   0.00  36.06
   2_bss: 103.26   0.00  18.10  86.18   0.00  14.80 103.26   0.00  36.06
   2_xyz: 103.26   0.00  18.10  86.18   0.00  14.80 103.26   0.00  36.06
   2_adp:  98.31   0.00  18.02  91.20   0.00  13.86  98.31   0.00  40.67
   2_occ:  98.31   0.00  18.02  91.20   0.00  13.86  98.31   0.00  40.67
   3_bss:  98.31   0.00  18.02  91.20   0.00  13.86  98.31   0.00  40.67
   3_xyz:  98.31   0.00  18.02  91.20   0.00  13.86  98.31   0.00  40.67
   3_adp:  97.58   0.00  17.52  88.94   0.00  13.19  97.58   3.62  41.07
   3_occ:  97.58   0.00  17.52  88.94   0.00  13.19  97.58   3.62  41.07
   4_bss:  97.58   0.00  17.52  88.94   0.00  13.19  97.58   3.62  41.07
   4_xyz:  97.58   0.00  17.52  88.94   0.00  13.19  97.58   3.62  41.07
   4_adp: 106.00   0.00  17.36 106.00   0.00  12.40 104.96   3.28  44.38
   4_occ: 106.00   0.00  17.36 106.00   0.00  12.40 104.96   3.28  44.38
   5_bss: 106.00   0.00  17.36 106.00   0.00  12.40 104.96   3.28  44.38
   5_xyz: 106.00   0.00  17.36 106.00   0.00  12.40 104.96   3.28  44.38
   5_adp: 106.30   0.00  17.03 106.30   0.00  12.06 105.44   3.96  44.07
   5_occ: 106.30   0.00  17.03 106.30   0.00  12.06 105.44   3.96  44.07
   5_bss: 106.30   0.00  17.03 106.30   0.00  12.07 105.45   3.97  44.07
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.645    0.028    0.316
   1_adp:    1.645    0.028    0.316
   1_occ:    1.645    0.028    0.316
   2_bss:    1.645    0.028    0.316
   2_xyz:    1.508    0.015    0.602
   2_adp:    1.508    0.015    0.602
   2_occ:    1.508    0.015    0.602
   3_bss:    1.508    0.015    0.602
   3_xyz:    1.524    0.072    0.707
   3_adp:    1.524    0.072    0.707
   3_occ:    1.524    0.072    0.707
   4_bss:    1.524    0.072    0.707
   4_xyz:    1.604    0.081    0.773
   4_adp:    1.604    0.081    0.773
   4_occ:    1.604    0.081    0.773
   5_bss:    1.604    0.081    0.773
   5_xyz:    1.560    0.110    0.794
   5_adp:    1.560    0.110    0.794
   5_occ:    1.560    0.110    0.794
   5_bss:    1.560    0.110    0.794
------------------------------------------------------------------------

CPU time actual refinement: 343.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/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_964/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_964/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.14 
  Macro-tasks:
    bulk solvent and scale       = 49.98  
    individual site refinement   = 139.34 
    weights calculation          = 29.72  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 225.78 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.45 
    alpha_beta                      = 8.68   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 114.80 
    fmodel                         = 8.14   
    r_factors                      = 0.30   
    phase_errors                   = 10.75  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 252.01 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.869 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    633 calls, 105.10 s
gradients_fft:          578 calls, 101.62 s

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

# Date 2008-01-16 Time 06:05:27 PST -0800 (1200492327.64 s)
Start R-work = 0.4447, R-free = 0.4254 (no bulk solvent and anisotropic scale)
Final R-work = 0.1391, R-free = 0.1871 (no bulk solvent and anisotropic scale)

Start R-work = 0.4353, R-free = 0.4174
Final R-work = 0.1233, R-free = 0.1739