# Date 2008-01-16 Time 05:35:05 PST -0800 (1200490505.76 s)
#phil __OFF__

Command line arguments: "../792.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22577
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 792

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95137
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927509

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9514

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.95137
Completeness in resolution range: 0.930284
Completeness with d_max=infinity: 0.927509

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1764 [2212/2241]  1992   220   9.9%
  bin  2:  4.1764 -  3.3270 [2116/2139]  1907   209   9.9%
  bin  3:  3.3270 -  2.9099 [2091/2116]  1875   216  10.3%
  bin  4:  2.9099 -  2.6455 [2084/2100]  1883   201   9.6%
  bin  5:  2.6455 -  2.4568 [2052/2091]  1841   211  10.3%
  bin  6:  2.4568 -  2.3125 [2054/2086]  1855   199   9.7%
  bin  7:  2.3125 -  2.1970 [2029/2066]  1823   206  10.2%
  bin  8:  2.1970 -  2.1017 [2036/2078]  1833   203  10.0%
  bin  9:  2.1017 -  2.0210 [2025/2063]  1822   203  10.0%
  bin 10:  2.0210 -  1.9514 [ 890/2077]   799    91  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/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: 0.15 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:
        1.48 -     2.17: 18
        2.17 -     2.85: 1106
        2.85 -     3.53: 4443
        3.53 -     4.22: 9340
        4.22 -     4.90: 13633
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.484 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.526 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.810 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.848 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28535 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_792/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/model_refine_001.geo

CPU time processing inputs: 9.51


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.16465 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3789   r_free= 0.3768   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.167602                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.3093 0.3096      6.4298      6.4269|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.3059 0.2865         6.6       6.543|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.3360 0.3532      6.4909      6.6398|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.3564 0.3496      6.3603      6.3657|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.3850 0.3477      6.2246      6.2167|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.4083 0.3946      6.1561      6.0959|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.3945 0.3599      6.1338      6.0696|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.4174 0.4328       6.062      6.1306|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.4204 0.4198      6.0379      6.0187|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.4400 0.4632      6.0207       6.063|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.4363 0.4983      5.9506      6.0375|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.4373 0.4523      5.8862      5.9381|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.4548 0.4392      5.8251      5.7853|
| 14:  2.0001 -  1.9514 0.26    346   35 0.5679 0.5480      5.8471      5.7962|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.76  28.56   0.86     0.78      49915.88|
|  2:  4.6586 -  3.7164  1380   144  0.79  27.47   0.96     0.88      66328.88|
|  3:  3.7164 -  3.2521  1358   158  0.72  33.24   0.96     0.90      70562.35|
|  4:  3.2521 -  2.9573  1343   149  0.66  38.70   0.98     0.87      62973.17|
|  5:  2.9573 -  2.7467  1328   148  0.61  42.71   0.95     0.82      51144.30|
|  6:  2.7467 -  2.5857  1335   147  0.60  43.56   0.96     0.80      42811.62|
|  7:  2.5857 -  2.4568  1324   149  0.61  42.87   0.99     0.80      39512.07|
|  8:  2.4568 -  2.3502  1312   143  0.57  46.26   0.96     0.80      38059.85|
|  9:  2.3502 -  2.2601  1315   150  0.56  47.75   0.99     0.77      36632.05|
| 10:  2.2601 -  2.1823  1324   144  0.51  51.21   1.02     0.73      37514.41|
| 11:  2.1823 -  2.1143  1298   141  0.48  53.93   1.00     0.69      35740.24|
| 12:  2.1143 -  2.0540  1311   150  0.45  56.22   1.00     0.70      35336.62|
| 13:  2.0540 -  2.0001  1226   139  0.44  57.30   0.99     0.66      30446.97|
| 14:  2.0001 -  1.9514   346    35  0.40  60.25   0.91     0.58      27070.79|
|alpha:            min =        0.58 max =            0.90 mean =         0.78|
|beta:             min =    27070.79 max =        70562.35 mean =     45824.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.88|
|phase err.(test): min =        0.00 max =           90.00 mean =        43.68|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.585164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.274298              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.117   (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 |  1.484 -  1.826:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.826 -  2.167:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.167 -  2.509:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.509 -  2.851:     1071 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.851 -  3.192:     2001 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.192 -  3.534:     2442 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.534 -  3.875:     4653 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.875 -  4.217:     4687 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.217 -  4.558:     6171 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7462 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.484 |       0.436 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3789   r_free= 0.3768   ksol= 0.00   Bsol= 0.00   scale= 0.949    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.167602                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3649   r_free= 0.3624   ksol= 0.30   Bsol= 50.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.89,3.50,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.154788                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.282173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.775   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.058   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3649      final r-factor (work) = 0.2510          |
| start r-factor (free) = 0.3624      final r-factor (free) = 0.2836          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4266 = 5.28 * 0.50 * 6.1519 + 1.00 * 0.1789                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8157 = 5.28 * 0.50 * 5.9519 + 1.00 * 0.0961                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2510      final r-factor (work) = 0.2300          |
| start r-factor (free) = 0.2836      final r-factor (free) = 0.2895          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5900 = 0.60 * 1.00 * 5.9519 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4853 = 0.60 * 1.00 * 5.7691 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.46   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    86.46   17.74    None  None   None       |
|    Sol.    : 438    0      4.51    82.74   40.29    None  None   None       |
|    Mac.    : 2385   0      0.00    86.46   13.60    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.646:  729   |   5:    43.228 -  51.873:   95        |
|      1:     8.646 -  17.291: 1165   |   6:    51.873 -  60.519:   64        |
|      2:    17.291 -  25.937:  383   |   7:    60.519 -  69.165:   35        |
|      3:    25.937 -  34.582:  173   |   8:    69.165 -  77.810:   23        |
|      4:    34.582 -  43.228:  152   |   9:    77.810 -  86.456:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2300 r_free = 0.2895             target_work(ml) = 5.777         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2295 r_free = 0.2895             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2295   r_free= 0.2895   ksol= 0.30   Bsol= 50.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.89,3.50,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.776146                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2266   r_free= 0.2841   ksol= 0.32   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.14,-0.01,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.767458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.401389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.494   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328824              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.080  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2266      final r-factor (work) = 0.1597          |
| start r-factor (free) = 0.2841      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7933 = 4.40 * 0.50 * 5.7696 + 1.00 * 0.0961                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4644 = 4.40 * 0.50 * 5.6352 + 1.00 * 0.0632                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1597      final r-factor (work) = 0.1455          |
| start r-factor (free) = 0.2100      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8645 = 0.33 * 1.00 * 5.6352 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7872 = 0.33 * 1.00 * 5.4088 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.72    81.65   17.51    None  None   None       |
|    all(noH): 2823   0      1.72    81.65   17.51    None  None   None       |
|    Sol.    : 438    0      6.57    78.52   40.93    None  None   None       |
|    Mac.    : 2385   0      1.72    81.65   13.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.720 -   9.713:  937   |   5:    41.686 -  49.679:  118        |
|      1:     9.713 -  17.706: 1092   |   6:    49.679 -  57.673:   80        |
|      2:    17.706 -  25.700:  279   |   7:    57.673 -  65.666:   35        |
|      3:    25.700 -  33.693:  129   |   8:    65.666 -  73.659:   27        |
|      4:    33.693 -  41.686:  116   |   9:    73.659 -  81.652:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1455 r_free = 0.1937             target_work(ml) = 5.371         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1453 r_free = 0.1937             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1453   r_free= 0.1937   ksol= 0.32   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.14,-0.01,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.369790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1449   r_free= 0.1925   ksol= 0.32   Bsol= 42.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.18,-1.42,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364702                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.240767              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279122              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1449      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1221 = 2.24 * 0.50 * 5.4081 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9950 = 2.24 * 0.50 * 5.3020 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1246      final r-factor (work) = 0.1199          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4885 = 0.28 * 1.00 * 5.3020 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4622 = 0.28 * 1.00 * 5.2094 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    85.53   17.25    None  None   None       |
|    all(noH): 2823   0      1.50    85.53   17.25    None  None   None       |
|    Sol.    : 438    0      4.75    78.25   40.22    None  None   None       |
|    Mac.    : 2385   0      1.50    85.53   13.03    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.501 -   9.904:  969   |   5:    43.514 -  51.917:  115        |
|      1:     9.904 -  18.306: 1129   |   6:    51.917 -  60.319:   60        |
|      2:    18.306 -  26.709:  250   |   7:    60.319 -  68.722:   31        |
|      3:    26.709 -  35.111:  120   |   8:    68.722 -  77.124:   20        |
|      4:    35.111 -  43.514:  124   |   9:    77.124 -  85.527:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1199 r_free = 0.1636             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1635             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1635   ksol= 0.32   Bsol= 42.90   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.18,-1.42,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.195537                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1634   ksol= 0.32   Bsol= 43.52   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.25,-1.93,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.196188                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.103265              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.423  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.839312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.622  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5337 = 2.10 * 0.50 * 5.2099 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4938 = 2.10 * 0.50 * 5.1698 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3472 = 0.84 * 1.00 * 5.1698 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3257 = 0.84 * 1.00 * 5.1430 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    95.16   17.31    None  None   None       |
|    all(noH): 2823   0      1.28    95.16   17.31    None  None   None       |
|    Sol.    : 438    0      4.82    84.11   40.73    None  None   None       |
|    Mac.    : 2385   0      1.28    95.16   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.277 -  10.665: 1168   |   5:    48.218 -  57.606:  107        |
|      1:    10.665 -  20.053: 1021   |   6:    57.606 -  66.995:   42        |
|      2:    20.053 -  29.442:  202   |   7:    66.995 -  76.383:   22        |
|      3:    29.442 -  38.830:  128   |   8:    76.383 -  85.771:   11        |
|      4:    38.830 -  48.218:  119   |   9:    85.771 -  95.160:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1584             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1109 r_free = 0.1584             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1584   ksol= 0.32   Bsol= 43.52   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-2.25,-1.93,-0.00,-0.00,-0.00); trace/3= -2.25                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146338                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1583   ksol= 0.32   Bsol= 44.09   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.09,-1.91,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.146295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.189661              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.306  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.638177              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.030  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2596 = 3.19 * 0.50 * 5.1432 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2491 = 3.19 * 0.50 * 5.1279 + 1.00 * 0.0711                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1055          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2816 = 0.64 * 1.00 * 5.1279 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2797 = 0.64 * 1.00 * 5.1250 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.60    99.42   17.03    None  None   None       |
|    all(noH): 2823   0      1.60    99.42   17.03    None  None   None       |
|    Sol.    : 438    0      6.11    85.49   39.96    None  None   None       |
|    Mac.    : 2385   0      1.60    99.42   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.603 -  11.384: 1370   |   5:    50.509 -  60.290:   78        |
|      1:    11.384 -  21.165:  862   |   6:    60.290 -  70.071:   32        |
|      2:    21.165 -  30.947:  193   |   7:    70.071 -  79.853:   19        |
|      3:    30.947 -  40.728:  127   |   8:    79.853 -  89.634:    5        |
|      4:    40.728 -  50.509:  134   |   9:    89.634 -  99.415:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1055 r_free = 0.1581             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1581             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1581   ksol= 0.32   Bsol= 44.09   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.09,-1.91,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.125836                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.0925 0.1286      5.3455      5.5469|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.0788 0.1064      5.3819      5.6053|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.1000 0.1561      5.4266      5.8469|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.1171 0.1525      5.4287      5.5782|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.1227 0.1782      5.2867      5.5098|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.1182 0.1806      5.1932      5.4171|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.1151 0.1720      5.1242      5.3706|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.1106 0.1684      5.0367      5.2712|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.1112 0.1897           5      5.3244|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.1052 0.1689      4.9476      5.2086|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.1093 0.1840      4.9152      5.2823|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.1046 0.1708      4.8484      5.0745|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.1078 0.1741      4.7548      4.9981|
| 14:  2.0001 -  1.9514 0.26    346   35 0.1027 0.1637      4.6233      4.9132|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.94   8.67   0.98     0.95       6852.44|
|  2:  4.6586 -  3.7164  1380   144  0.95   7.80   1.02     1.00       8552.74|
|  3:  3.7164 -  3.2521  1358   158  0.94  11.06   1.03     1.03       9841.92|
|  4:  3.2521 -  2.9573  1343   149  0.92  13.97   1.01     0.99      10371.72|
|  5:  2.9573 -  2.7467  1328   148  0.90  16.09   0.99     0.96       8172.57|
|  6:  2.7467 -  2.5857  1335   147  0.90  16.15   0.98     0.96       7060.78|
|  7:  2.5857 -  2.4568  1324   149  0.91  15.15   0.99     0.95       5990.15|
|  8:  2.4568 -  2.3502  1312   143  0.90  15.71   0.99     0.96       5324.29|
|  9:  2.3502 -  2.2601  1315   150  0.90  15.87   1.00     0.97       4911.04|
| 10:  2.2601 -  2.1823  1324   144  0.91  15.44   0.99     0.96       4522.27|
| 11:  2.1823 -  2.1143  1298   141  0.90  16.63   0.99     0.96       4411.69|
| 12:  2.1143 -  2.0540  1311   150  0.91  15.61   1.00     0.98       3946.66|
| 13:  2.0540 -  2.0001  1226   139  0.90  16.08   0.99     0.98       3240.51|
| 14:  2.0001 -  1.9514   346    35  0.90  15.78   0.99     0.96       2491.96|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2491.96 max =        10371.72 mean =      6368.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.87 mean =        13.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1581   ksol= 0.32   Bsol= 45.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.85,-1.69,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1581   ksol= 0.32   Bsol= 45.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-1.85,-1.69,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125897                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6586 0.99   1430  162 0.0926 0.1287      5.3473       5.549|
|  2:  4.6586 -  3.7164 0.99   1380  144 0.0789 0.1064      5.3829      5.6052|
|  3:  3.7164 -  3.2521 0.99   1358  158 0.1000 0.1562      5.4268      5.8474|
|  4:  3.2521 -  2.9573 0.99   1343  149 0.1171 0.1524      5.4286      5.5778|
|  5:  2.9573 -  2.7467 0.98   1328  148 0.1226 0.1781      5.2863      5.5094|
|  6:  2.7467 -  2.5857 0.99   1335  147 0.1182 0.1807      5.1929       5.417|
|  7:  2.5857 -  2.4568 0.99   1324  149 0.1151 0.1719      5.1242      5.3705|
|  8:  2.4568 -  2.3502 0.99   1312  143 0.1106 0.1683      5.0365      5.2709|
|  9:  2.3502 -  2.2601 0.99   1315  150 0.1112 0.1897           5      5.3244|
| 10:  2.2601 -  2.1823 0.98   1324  144 0.1052 0.1688      4.9474       5.208|
| 11:  2.1823 -  2.1143 0.98   1298  141 0.1092 0.1839       4.915      5.2823|
| 12:  2.1143 -  2.0540 1.00   1311  150 0.1046 0.1707      4.8479       5.074|
| 13:  2.0540 -  2.0001 0.91   1226  139 0.1078 0.1740      4.7545      4.9974|
| 14:  2.0001 -  1.9514 0.26    346   35 0.1027 0.1639      4.6232      4.9136|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9433 -  4.6586  1430   162  0.94   8.68   0.98     0.95       6876.91|
|  2:  4.6586 -  3.7164  1380   144  0.95   7.82   1.02     1.01       8568.62|
|  3:  3.7164 -  3.2521  1358   158  0.94  11.07   1.03     1.03       9846.57|
|  4:  3.2521 -  2.9573  1343   149  0.92  13.97   1.01     1.00      10368.87|
|  5:  2.9573 -  2.7467  1328   148  0.90  16.09   1.00     0.97       8168.38|
|  6:  2.7467 -  2.5857  1335   147  0.90  16.15   0.99     0.96       7055.88|
|  7:  2.5857 -  2.4568  1324   149  0.91  15.15   0.99     0.96       5987.08|
|  8:  2.4568 -  2.3502  1312   143  0.90  15.71   1.00     0.97       5321.39|
|  9:  2.3502 -  2.2601  1315   150  0.90  15.87   1.00     0.97       4908.90|
| 10:  2.2601 -  2.1823  1324   144  0.91  15.44   1.00     0.97       4519.43|
| 11:  2.1823 -  2.1143  1298   141  0.90  16.63   1.00     0.97       4408.51|
| 12:  2.1143 -  2.0540  1311   150  0.91  15.61   1.01     0.99       3941.27|
| 13:  2.0540 -  2.0001  1226   139  0.90  16.08   1.00     0.99       3237.88|
| 14:  2.0001 -  1.9514   346    35  0.90  15.77   1.00     0.97       2491.62|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2491.62 max =        10368.87 mean =      6369.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.13|
|phase err.(test): min =        0.00 max =           89.86 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.725)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.55    99.36   16.97    None  None   None       |
|    all(noH): 2823   0      1.55    99.36   16.97    None  None   None       |
|    Sol.    : 438    0      6.05    85.43   39.90    None  None   None       |
|    Mac.    : 2385   0      1.55    99.36   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.546 -  11.327: 1370   |   5:    50.452 -  60.233:   78        |
|      1:    11.327 -  21.108:  862   |   6:    60.233 -  70.014:   32        |
|      2:    21.108 -  30.889:  193   |   7:    70.014 -  79.795:   19        |
|      3:    30.889 -  40.671:  127   |   8:    79.795 -  89.577:    5        |
|      4:    40.671 -  50.452:  134   |   9:    89.577 -  99.358:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.511 - 5.921
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 309
   mapped sites are within: 0.761 - 5.921

peak=    5.698 closest distance to " NH2 ARG A  56 " =    2.163
peak=    5.358 closest distance to " CB  SER A  63 " =    1.203
peak=    5.305 closest distance to " CB  GLN A 223 " =    1.491
peak=    5.163 closest distance to " CG  PRO A  54 " =    1.143
peak=    5.111 closest distance to " O   HOH Z 126 " =    1.850
peak=    4.971 closest distance to " CB  GLN A 183 " =    1.277
peak=    4.858 closest distance to " O   HOH Z 144 " =    1.646
peak=    4.788 closest distance to " O   HOH Z 232 " =    2.286
peak=    4.778 closest distance to " O   HOH Z 193 " =    1.834
peak=    4.731 closest distance to " NE2 GLN A  11 " =    1.070
peak=    4.631 closest distance to " C   PRO A 198 " =    1.499
peak=    4.576 closest distance to " CB  GLU A 152 " =    1.196
peak=    4.573 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.560 closest distance to " CB  SER A   3 " =    1.370
peak=    4.551 closest distance to " OD2 ASP A 286 " =    2.807
peak=    4.489 closest distance to " OD1 ASN A  69 " =    2.529
peak=    4.472 closest distance to " O   HOH Z 236 " =    1.910
peak=    4.423 closest distance to " CB  ASN A 148 " =    1.563
peak=    4.416 closest distance to " CG  PRO A 213 " =    1.159
peak=    4.398 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.396 closest distance to " CB  TYR A 169 " =    0.761
peak=    4.354 closest distance to " O   HOH Z 180 " =    2.205
peak=    4.316 closest distance to " CB  PRO A  54 " =    0.885
peak=    4.275 closest distance to " O   HOH Z  15 " =    2.143
peak=    4.272 closest distance to " O   HOH Z  78 " =    1.719
peak=    4.265 closest distance to " O   HOH Z 368 " =    2.023
peak=    4.264 closest distance to " O   HOH Z 203 " =    1.849
peak=    4.253 closest distance to " CB  ARG A  79 " =    1.478
peak=    4.246 closest distance to " O   HOH Z 108 " =    1.457
peak=    4.226 closest distance to " CB  GLU A 128 " =    1.180
peak=    4.214 closest distance to " O   HOH Z 427 " =    2.822
peak=    4.202 closest distance to " O   HOH Z 389 " =    1.899
peak=    4.195 closest distance to " O   HOH Z 298 " =    1.861
peak=    4.195 closest distance to " O   HOH Z 234 " =    3.694
peak=    4.156 closest distance to " CA  ALA A  21 " =    1.172
peak=    4.150 closest distance to " CB  VAL A 202 " =    1.668
peak=    4.146 closest distance to " CA  THR A 221 " =    0.967
peak=    4.133 closest distance to " CB  GLU A 277 " =    3.532
peak=    4.126 closest distance to " O   HOH Z  93 " =    2.517
peak=    4.121 closest distance to " O   HOH Z 207 " =    1.829
peak=    4.120 closest distance to " O   HOH Z 344 " =    3.010
peak=    4.112 closest distance to " O   HOH Z 369 " =    1.928
peak=    4.094 closest distance to " O   HOH Z 261 " =    2.041
peak=    4.083 closest distance to " O   HOH Z 134 " =    1.433
peak=    4.082 closest distance to " CB  LEU A 228 " =    1.084
peak=    4.075 closest distance to " ND2 ASN A 187 " =    1.581
peak=    4.059 closest distance to " CB  TRP A 179 " =    1.348
peak=    4.052 closest distance to " NH2BARG A 145 " =    2.131
peak=    4.051 closest distance to " O   HOH Z 316 " =    2.960
peak=    4.048 closest distance to " O   SER A  87 " =    2.227
peak=    4.034 closest distance to " O   HOH Z 371 " =    3.425
peak=    4.024 closest distance to " O   HOH Z 133 " =    2.180
peak=    4.020 closest distance to " O   HOH Z 193 " =    2.093
peak=    4.016 closest distance to " O   HOH Z 426 " =    1.523
peak=    3.998 closest distance to " O   HOH Z 284 " =    2.991
peak=    3.970 closest distance to " O   MET A 105 " =    1.793
peak=    3.969 closest distance to " O   HOH Z 272 " =    1.846
peak=    3.963 closest distance to " O   HOH Z  97 " =    1.868
peak=    3.962 closest distance to " O   HOH Z  54 " =    1.694
peak=    3.935 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.925 closest distance to " O   HOH Z   6 " =    2.167
peak=    3.923 closest distance to " O   HOH Z 209 " =    2.379
peak=    3.922 closest distance to " O   HOH Z 403 " =    1.665
peak=    3.914 closest distance to " O   HOH Z  21 " =    1.632
peak=    3.909 closest distance to " O   HOH Z 197 " =    2.747
peak=    3.897 closest distance to " O   HOH Z  61 " =    1.626
peak=    3.875 closest distance to " CA  ASN A 215 " =    1.249
peak=    3.851 closest distance to " O   HOH Z  59 " =    2.190
peak=    3.837 closest distance to " O   HOH Z 133 " =    1.591
peak=    3.835 closest distance to " O   HOH Z  68 " =    1.669
peak=    3.834 closest distance to " O   HOH Z 279 " =    2.185
peak=    3.826 closest distance to " CA  MET A  40 " =    1.037
peak=    3.822 closest distance to " O   HOH Z 346 " =    1.640
peak=    3.814 closest distance to " O   HOH Z 313 " =    1.701
peak=    3.814 closest distance to " O   HOH Z  10 " =    1.872
peak=    3.813 closest distance to " O   HOH Z 135 " =    1.703
peak=    3.810 closest distance to " O   HOH Z 303 " =    1.959
peak=    3.808 closest distance to " CG  PRO A  90 " =    1.082
peak=    3.799 closest distance to " O   HOH Z 374 " =    2.571
peak=    3.787 closest distance to " OG BSER A 164 " =    2.425
peak=    3.785 closest distance to " O   HOH Z  88 " =    3.373
peak=    3.746 closest distance to " O   HOH Z 214 " =    2.017
peak=    3.744 closest distance to " O   HOH Z 411 " =    1.768
peak=    3.744 closest distance to " CB  ASN A 148 " =    0.998
peak=    3.743 closest distance to " CG2 THR A 221 " =    1.067
peak=    3.737 closest distance to " NH2 ARG A 156 " =    1.184
peak=    3.725 closest distance to " O   HOH Z 423 " =    1.967
peak=    3.723 closest distance to " CA  ASN A 176 " =    1.195
peak=    3.720 closest distance to " O   HOH Z 411 " =    3.828
peak=    3.719 closest distance to " CA  ALA A  51 " =    0.926
peak=    3.717 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.713 closest distance to " O   HOH Z 326 " =    1.516
peak=    3.710 closest distance to " O   HOH Z 278 " =    0.964
peak=    3.696 closest distance to " CG  PRO A 243 " =    1.231
peak=    3.677 closest distance to " CD BLYS A 290 " =    1.149
peak=    3.667 closest distance to " O   HOH Z 158 " =    2.966
peak=    3.667 closest distance to " O   HOH Z 132 " =    2.524
peak=    3.665 closest distance to " CB  VAL A 265 " =    1.268
peak=    3.657 closest distance to " NH1AARG A 145 " =    1.079
peak=    3.650 closest distance to " O   HOH Z 156 " =    3.014
peak=    3.648 closest distance to " NZ  LYS A 117 " =    3.310
peak=    3.647 closest distance to " CD1 LEU A 300 " =    1.219
peak=    3.646 closest distance to " O   ALA A 165 " =    1.385
peak=    3.639 closest distance to " CB  ARG A 190 " =    1.680
peak=    3.637 closest distance to " O   HOH Z 172 " =    3.820
peak=    3.636 closest distance to " O   HOH Z 124 " =    1.379
peak=    3.634 closest distance to " O   HOH Z  20 " =    1.562
peak=    3.629 closest distance to " O   HOH Z  49 " =    2.158
peak=    3.628 closest distance to " CG  MET A 185 " =    1.098
peak=    3.617 closest distance to " O   HOH Z 128 " =    2.336
peak=    3.612 closest distance to " O   HOH Z 108 " =    1.884
peak=    3.609 closest distance to " O   HOH Z 250 " =    1.419
peak=    3.596 closest distance to " CG  ARG A  66 " =    2.428
peak=    3.589 closest distance to " O   HOH Z  43 " =    2.004
peak=    3.588 closest distance to " O   HOH Z 406 " =    1.704
peak=    3.588 closest distance to " O   HOH Z 345 " =    3.290
peak=    3.588 closest distance to " CG2 ILE A 120 " =    1.183
peak=    3.587 closest distance to " O   HOH Z 334 " =    1.470
peak=    3.580 closest distance to " O   HOH Z 427 " =    3.123
peak=    3.579 closest distance to " CB  ARG A 139 " =    0.923
peak=    3.575 closest distance to " OG  SER A  22 " =    2.741
peak=    3.558 closest distance to " O   HOH Z 295 " =    1.451
peak=    3.550 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.548 closest distance to " O   HOH Z 425 " =    1.291
peak=    3.540 closest distance to " CD  LYS A 166 " =    1.297
peak=    3.535 closest distance to " O   HOH Z  44 " =    1.804
peak=    3.535 closest distance to " CG  PRO A 198 " =    1.268
peak=    3.530 closest distance to " O   HOH Z 132 " =    0.908
peak=    3.528 closest distance to " CB  SER A 141 " =    1.049
peak=    3.523 closest distance to " CG1 VAL A 202 " =    1.978
peak=    3.519 closest distance to " O   HOH Z   1 " =    1.956
peak=    3.519 closest distance to " O   HOH Z 173 " =    1.941
peak=    3.519 closest distance to " O   HOH Z 163 " =    1.873
peak=    3.517 closest distance to " O   HOH Z 416 " =    2.734
peak=    3.514 closest distance to " CA  LYS A 117 " =    1.238
peak=    3.505 closest distance to " CB  GLN A  88 " =    1.280
peak=    3.504 closest distance to " O   HOH Z 337 " =    3.646
peak=    3.504 closest distance to " N   ARG A 156 " =    1.358
peak=    3.502 closest distance to " CG1BVAL A  72 " =    1.599
peak=    3.501 closest distance to " CA  ASP A 140 " =    1.121
peak=    3.500 closest distance to " O   HOH Z 425 " =    1.945
peak=    3.499 closest distance to " CA  ALA A 291 " =    0.910
peak=    3.470 closest distance to " O   ALA A 158 " =    1.257
peak=    3.469 closest distance to " O   ALA A   1 " =    1.525
peak=    3.466 closest distance to " O   HOH Z 273 " =    2.701
peak=    3.466 closest distance to " CD2 LEU A 255 " =    1.237
peak=    3.465 closest distance to " CA  THR A 264 " =    0.887
peak=    3.464 closest distance to " O   HOH Z 327 " =    1.693
peak=    3.464 closest distance to " CB  ASP A 140 " =    0.961
peak=    3.461 closest distance to " O   HOH Z  40 " =    1.624
peak=    3.458 closest distance to " CG  GLN A  77 " =    2.119
peak=    3.458 closest distance to " O   HOH Z 261 " =    2.056
peak=    3.453 closest distance to " CZ2 TRP A 179 " =    1.618
peak=    3.448 closest distance to " CB  TRP A 266 " =    0.962
peak=    3.448 closest distance to " ND1 HIS A  81 " =    1.507
peak=    3.445 closest distance to " O   HOH Z 281 " =    4.333
peak=    3.439 closest distance to " O   HOH Z 366 " =    2.893
peak=    3.430 closest distance to " O   HOH Z  19 " =    2.389
peak=    3.429 closest distance to " O   HOH Z 183 " =    1.457
peak=    3.427 closest distance to " CD  LYS A 119 " =    1.238
peak=    3.422 closest distance to " O   HOH Z  63 " =    1.902
peak=    3.420 closest distance to " O   HOH Z 263 " =    2.266
peak=    3.416 closest distance to " CD1 ILE A 106 " =    0.958
peak=    3.414 closest distance to " CD2 LEU A 297 " =    0.878
peak=    3.413 closest distance to " CG1 ILE A 151 " =    0.909
peak=    3.406 closest distance to " CB  MET A  47 " =    1.032
peak=    3.406 closest distance to " O   HOH Z  48 " =    1.324
peak=    3.400 closest distance to " O   HOH Z  35 " =    2.620
peak=    3.398 closest distance to " O   HOH Z 409 " =    3.120
peak=    3.397 closest distance to " CA  ILE A  33 " =    1.592
peak=    3.396 closest distance to " OG  SER A  62 " =    3.059
peak=    3.396 closest distance to " NE2 GLN A  58 " =    4.330
peak=    3.392 closest distance to " O   HOH Z 227 " =    1.660
peak=    3.390 closest distance to " O   HOH Z 368 " =    3.658
peak=    3.388 closest distance to " NH2AARG A 190 " =    1.343
peak=    3.380 closest distance to " O   HOH Z 214 " =    2.420
peak=    3.380 closest distance to " O   HOH Z 403 " =    1.385
peak=    3.373 closest distance to " O   HOH Z 260 " =    1.108
peak=    3.372 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.372 closest distance to " O   HOH Z 106 " =    2.321
peak=    3.371 closest distance to " N   ASN A 127 " =    1.241
peak=    3.371 closest distance to " O   HOH Z 353 " =    2.627
peak=    3.368 closest distance to " CD  ARG A 159 " =    0.793
peak=    3.367 closest distance to " CA  ARG A  36 " =    1.114
peak=    3.367 closest distance to " CB  ARG A 259 " =    1.859
peak=    3.366 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.366 closest distance to " O   HOH Z 126 " =    1.569
peak=    3.365 closest distance to " CA  ASN A  74 " =    1.213
peak=    3.364 closest distance to " O   HOH Z 267 " =    2.141
peak=    3.357 closest distance to " O   HOH Z 227 " =    2.237
peak=    3.357 closest distance to " CB  ALA A 291 " =    1.421
peak=    3.354 closest distance to " O   HOH Z 410 " =    1.931
peak=    3.350 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.350 closest distance to " CB  ALA A 248 " =    0.920
peak=    3.335 closest distance to " ND1 HIS A  86 " =    1.910
peak=    3.332 closest distance to " O   HOH Z 106 " =    2.361
peak=    3.323 closest distance to " CA  ALA A 233 " =    1.145
peak=    3.323 closest distance to " CD  ARG A 269 " =    0.918
peak=    3.319 closest distance to " OG BSER A  99 " =    2.157
peak=    3.317 closest distance to " O   HOH Z 189 " =    1.929
peak=    3.316 closest distance to " CG2BVAL A  41 " =    0.812
peak=    3.316 closest distance to " CG2 ILE A  20 " =    1.390
peak=    3.311 closest distance to " CG  LEU A 167 " =    1.227
peak=    3.310 closest distance to " CA  VAL A 126 " =    1.164
peak=    3.307 closest distance to " O   HOH Z 211 " =    2.397
peak=    3.306 closest distance to " NH2 ARG A 219 " =    1.916
peak=    3.304 closest distance to " O   GLY A  57 " =    2.500
peak=    3.301 closest distance to " O   HOH Z 248 " =    1.577
peak=    3.299 closest distance to " CD2 TRP A 179 " =    1.379
peak=    3.298 closest distance to " O   HOH Z 341 " =    1.753
peak=    3.297 closest distance to " O   HOH Z 118 " =    1.404
peak=    3.296 closest distance to " CA  ARG A 195 " =    1.336
peak=    3.294 closest distance to " CA  ALA A 248 " =    1.172
peak=    3.293 closest distance to " O   HOH Z  71 " =    1.962
peak=    3.288 closest distance to " O   TRP A 274 " =    1.888
peak=    3.283 closest distance to " O   HOH Z  66 " =    2.137
peak=    3.283 closest distance to " O   HOH Z 185 " =    1.713
peak=    3.281 closest distance to " O   HOH Z 116 " =    1.847
peak=    3.276 closest distance to " O   HOH Z 263 " =    1.804
peak=    3.276 closest distance to " O   HOH Z 285 " =    1.873
peak=    3.275 closest distance to " O   HOH Z 189 " =    1.314
peak=    3.270 closest distance to " CG  GLN A  58 " =    2.571
peak=    3.270 closest distance to " O   HOH Z  80 " =    1.605
peak=    3.269 closest distance to " N   ASN A  39 " =    1.267
peak=    3.269 closest distance to " O   HOH Z 287 " =    2.240
peak=    3.267 closest distance to " O   HOH Z 368 " =    2.607
peak=    3.262 closest distance to " O   HOH Z 163 " =    1.651
peak=    3.262 closest distance to " CG  MET A 185 " =    1.169
peak=    3.261 closest distance to " O   HOH Z 245 " =    1.300
peak=    3.252 closest distance to " CB  SER A 212 " =    1.085
peak=    3.252 closest distance to " CB  GLU A  46 " =    1.038
peak=    3.250 closest distance to " O   THR A 220 " =    1.438
peak=    3.250 closest distance to " O   HOH Z 292 " =    1.603
peak=    3.249 closest distance to " CB  SER A  62 " =    1.293
peak=    3.245 closest distance to " O   HOH Z 286 " =    2.112
peak=    3.244 closest distance to " O   HOH Z 329 " =    3.419
peak=    3.243 closest distance to " OE2 GLU A  53 " =    2.142
peak=    3.241 closest distance to " O   HOH Z  20 " =    2.099
peak=    3.238 closest distance to " CB  LEU A 143 " =    1.098
peak=    3.236 closest distance to " CB  SER A  26 " =    1.534
peak=    3.227 closest distance to " CG  GLU A 277 " =    2.126
peak=    3.225 closest distance to " O   HOH Z 388 " =    1.859
peak=    3.223 closest distance to " O   HOH Z 365 " =    2.673
peak=    3.221 closest distance to " O   HOH Z 154 " =    2.214
peak=    3.220 closest distance to " O   HOH Z 276 " =    1.256
peak=    3.215 closest distance to " NZ  LYS A 166 " =    2.970
peak=    3.209 closest distance to " SD AMET A  47 " =    0.983
peak=    3.206 closest distance to " O   HOH Z   3 " =    1.637
peak=    3.201 closest distance to " ND2 ASN A 301 " =    1.418
peak=    3.195 closest distance to " CG  LYS A  76 " =    1.074
peak=    3.195 closest distance to " CG  MET A  93 " =    0.933
peak=    3.193 closest distance to " O   THR A  31 " =    1.592
peak=    3.192 closest distance to " CB  ASN A 285 " =    0.910
peak=    3.189 closest distance to " O   HOH Z  66 " =    2.038
peak=    3.187 closest distance to " NH1BARG A 145 " =    1.178
peak=    3.185 closest distance to " O   HOH Z 358 " =    2.177
peak=    3.184 closest distance to " CA  ALA A 158 " =    1.118
peak=    3.183 closest distance to " O   HOH Z 266 " =    2.803
peak=    3.181 closest distance to " CA  GLY A 267 " =    1.121
peak=    3.175 closest distance to " O   HOH Z 402 " =    1.410
peak=    3.175 closest distance to " O   HOH Z 175 " =    2.160
peak=    3.167 closest distance to " O   HOH Z 409 " =    3.657
peak=    3.165 closest distance to " O   HOH Z 193 " =    1.543
peak=    3.162 closest distance to " CG  GLN A  55 " =    2.147
peak=    3.160 closest distance to " CG2 VAL A 174 " =    1.312
peak=    3.157 closest distance to " CG  MET A 113 " =    1.349
peak=    3.155 closest distance to " O   HOH Z 112 " =    1.605
peak=    3.155 closest distance to " NZ  LYS A  76 " =    1.163
peak=    3.151 closest distance to " CA  ASP A 191 " =    0.856
peak=    3.149 closest distance to " CB  TRP A 150 " =    1.499
peak=    3.148 closest distance to " O   HOH Z 301 " =    1.871
peak=    3.144 closest distance to " O   HOH Z 250 " =    1.640
peak=    3.138 closest distance to " CB  TYR A 116 " =    0.950
peak=    3.138 closest distance to " CB  ASN A  39 " =    0.855
peak=    3.134 closest distance to " O   HOH Z 271 " =    2.240
peak=    3.134 closest distance to " O   HOH Z  73 " =    1.449
peak=    3.133 closest distance to " CA  ALA A 154 " =    0.964
peak=    3.129 closest distance to " O   SER A 164 " =    0.943
peak=    3.128 closest distance to " O   HOH Z  78 " =    1.970
peak=    3.125 closest distance to " O   HOH Z 126 " =    2.058
peak=    3.119 closest distance to " O   ALA A   1 " =    1.634
peak=    3.114 closest distance to " CG2 VAL A 257 " =    0.946
peak=    3.111 closest distance to " CB  ALA A  71 " =    1.291
peak=    3.109 closest distance to " CB  PHE A  16 " =    0.980
peak=    3.106 closest distance to " O   HOH Z 345 " =    1.702
peak=    3.105 closest distance to " O   HOH Z 227 " =    1.625
peak=    3.102 closest distance to " CB  MET A  40 " =    0.897
peak=    3.102 closest distance to " CB  THR A 157 " =    0.987
peak=    3.097 closest distance to " CG2 VAL A  78 " =    0.914
peak=    3.093 closest distance to " O   HOH Z 171 " =    2.279
peak=    3.092 closest distance to " O   HOH Z 166 " =    3.589
peak=    3.086 closest distance to " CD  GLN A  58 " =    5.921
peak=    3.084 closest distance to " CB  ASN A 224 " =    1.079
peak=    3.078 closest distance to " O   HOH Z 423 " =    3.203
peak=    3.076 closest distance to " CG2 THR A 220 " =    1.066
peak=    3.062 closest distance to " OD1 ASP A 286 " =    1.543
peak=    3.052 closest distance to " O   HOH Z  71 " =    1.004
peak=    3.050 closest distance to " OE1 GLN A  11 " =    1.922
peak=    3.047 closest distance to " O   HOH Z 336 " =    1.701
peak=    3.046 closest distance to " O   HOH Z 430 " =    5.601
peak=    3.042 closest distance to " CB  ASN A 215 " =    1.099
peak=    3.020 closest distance to " O   HOH Z  64 " =    2.184
peak=    3.019 closest distance to " CD  LYS A 166 " =    1.466

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.851 - 5.311
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 215
   mapped sites are within: 0.851 - 5.311

peak=   -4.811 closest distance to " O   HOH Z 266 " =    4.171
peak=   -4.492 closest distance to " CB  PRO A 243 " =    2.597
peak=   -4.439 closest distance to " O   HOH Z 377 " =    2.030
peak=   -4.414 closest distance to " CD  ARG A 156 " =    1.957
peak=   -4.412 closest distance to " O   HOH Z 372 " =    2.426
peak=   -4.373 closest distance to " O   ILE A 109 " =    2.623
peak=   -4.207 closest distance to " O   HOH Z 198 " =    2.340
peak=   -4.090 closest distance to " SG  CYS A 254 " =    3.273
peak=   -4.067 closest distance to " N   MET A 188 " =    1.905
peak=   -4.058 closest distance to " C   HIS A 108 " =    1.084
peak=   -4.021 closest distance to " OE1 GLN A 223 " =    2.069
peak=   -4.018 closest distance to " O   HOH Z  13 " =    1.516
peak=   -4.016 closest distance to " CD  ARG A 139 " =    1.627
peak=   -3.976 closest distance to " CD1 LEU A 228 " =    2.274
peak=   -3.946 closest distance to " N   ALA A  43 " =    2.483
peak=   -3.937 closest distance to " O   SER A 210 " =    1.925
peak=   -3.928 closest distance to " O   HOH Z  52 " =    1.382
peak=   -3.922 closest distance to " O   PRO A 163 " =    2.065
peak=   -3.919 closest distance to " O   HOH Z 231 " =    2.207
peak=   -3.877 closest distance to " N   GLN A  58 " =    1.677
peak=   -3.874 closest distance to " OXT GLY A 302 " =    2.822
peak=   -3.866 closest distance to " O   PRO A 198 " =    1.356
peak=   -3.854 closest distance to " O   HOH Z  10 " =    1.467
peak=   -3.843 closest distance to " CD2 LEU A 300 " =    2.860
peak=   -3.838 closest distance to " O   HOH Z 290 " =    1.102
peak=   -3.829 closest distance to " O   HOH Z 292 " =    4.517
peak=   -3.806 closest distance to " O   HOH Z 388 " =    2.010
peak=   -3.793 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.790 closest distance to " O   VAL A  67 " =    2.784
peak=   -3.780 closest distance to " CD1 PHE A  59 " =    1.866
peak=   -3.776 closest distance to " CB  TYR A  15 " =    2.160
peak=   -3.776 closest distance to " OG  SER A  97 " =    2.080
peak=   -3.757 closest distance to " O   HOH Z 353 " =    2.235
peak=   -3.748 closest distance to " CZ  TYR A 169 " =    1.755
peak=   -3.742 closest distance to " CE2 TYR A  30 " =    2.765
peak=   -3.736 closest distance to " O   HOH Z 118 " =    2.918
peak=   -3.732 closest distance to " OG BSER A 134 " =    1.251
peak=   -3.729 closest distance to " O   HOH Z  11 " =    1.877
peak=   -3.718 closest distance to " CB  ALA A 291 " =    2.375
peak=   -3.716 closest distance to " CD2 LEU A 237 " =    2.613
peak=   -3.705 closest distance to " N   ALA A 248 " =    1.626
peak=   -3.682 closest distance to " C   ALA A 158 " =    1.217
peak=   -3.677 closest distance to " NE2 GLN A  88 " =    1.928
peak=   -3.673 closest distance to " O   VAL A  67 " =    2.744
peak=   -3.658 closest distance to " CD  LYS A 289 " =    2.483
peak=   -3.658 closest distance to " O   HOH Z  11 " =    1.906
peak=   -3.652 closest distance to " CZ  PHE A  59 " =    1.665
peak=   -3.649 closest distance to " OG BSER A 134 " =    1.676
peak=   -3.644 closest distance to " OG  SER A  62 " =    1.561
peak=   -3.640 closest distance to " CG  ASP A 231 " =    0.851
peak=   -3.635 closest distance to " O   HOH Z 407 " =    3.142
peak=   -3.627 closest distance to " OE2 GLU A   2 " =    1.969
peak=   -3.625 closest distance to " O   HOH Z  19 " =    2.407
peak=   -3.613 closest distance to " O   HOH Z  97 " =    1.836
peak=   -3.603 closest distance to " O   HOH Z  43 " =    1.636
peak=   -3.602 closest distance to " O   HOH Z 185 " =    2.180
peak=   -3.587 closest distance to " O   SER A 135 " =    1.575
peak=   -3.585 closest distance to " O   HOH Z 234 " =    4.118
peak=   -3.582 closest distance to " CZ3 TRP A 179 " =    1.250
peak=   -3.581 closest distance to " CD1 LEU A 101 " =    2.469
peak=   -3.580 closest distance to " CG  PHE A 283 " =    2.664
peak=   -3.577 closest distance to " O   VAL A 174 " =    2.089
peak=   -3.576 closest distance to " CA  VAL A 232 " =    2.564
peak=   -3.576 closest distance to " O   HOH Z 385 " =    2.060
peak=   -3.575 closest distance to " N   THR A 157 " =    1.658
peak=   -3.572 closest distance to " O   HOH Z 102 " =    1.711
peak=   -3.570 closest distance to " O   HOH Z 166 " =    1.435
peak=   -3.558 closest distance to " O   HOH Z 283 " =    1.788
peak=   -3.553 closest distance to " O   HOH Z 166 " =    1.778
peak=   -3.544 closest distance to " NH2 ARG A  79 " =    1.832
peak=   -3.544 closest distance to " OD1 ASN A 148 " =    1.692
peak=   -3.543 closest distance to " NH2 ARG A  66 " =    4.907
peak=   -3.530 closest distance to " O   HOH Z 395 " =    5.166
peak=   -3.529 closest distance to " ND2 ASN A  45 " =    0.990
peak=   -3.529 closest distance to " OG  SER A  87 " =    1.326
peak=   -3.527 closest distance to " O   VAL A 153 " =    2.376
peak=   -3.526 closest distance to " CB  ASN A  39 " =    2.266
peak=   -3.518 closest distance to " C   ASN A 285 " =    2.450
peak=   -3.512 closest distance to " OE1 GLN A  77 " =    1.706
peak=   -3.501 closest distance to " O   HOH Z  93 " =    1.571
peak=   -3.495 closest distance to " O   HOH Z  98 " =    1.907
peak=   -3.490 closest distance to " NH2 ARG A  66 " =    2.007
peak=   -3.481 closest distance to " OG ASER A 134 " =    1.261
peak=   -3.477 closest distance to " OD1 ASP A 191 " =    1.689
peak=   -3.471 closest distance to " N   SER A 276 " =    1.328
peak=   -3.471 closest distance to " O   HOH Z  76 " =    1.996
peak=   -3.471 closest distance to " O   HOH Z 435 " =    2.663
peak=   -3.468 closest distance to " CA  SER A 146 " =    2.328
peak=   -3.464 closest distance to " ND2 ASN A 187 " =    1.440
peak=   -3.463 closest distance to " CB  SER A 245 " =    2.465
peak=   -3.452 closest distance to " CG  PRO A 163 " =    2.522
peak=   -3.447 closest distance to " C   LEU A 143 " =    1.220
peak=   -3.447 closest distance to " CB  ASP A 132 " =    2.386
peak=   -3.435 closest distance to " SG ACYS A 201 " =    2.102
peak=   -3.428 closest distance to " CE  MET A 105 " =    2.039
peak=   -3.422 closest distance to " O   HOH Z  38 " =    1.501
peak=   -3.417 closest distance to " O   HOH Z 361 " =    3.441
peak=   -3.407 closest distance to " CG  GLU A  53 " =    1.458
peak=   -3.401 closest distance to " CE  MET A  93 " =    1.250
peak=   -3.398 closest distance to " O   HOH Z 148 " =    3.321
peak=   -3.395 closest distance to " O   HOH Z 436 " =    1.480
peak=   -3.391 closest distance to " CG1 VAL A 112 " =    2.776
peak=   -3.386 closest distance to " CA  GLY A 133 " =    1.930
peak=   -3.385 closest distance to " NH2AARG A 275 " =    5.311
peak=   -3.366 closest distance to " CE2 PHE A 218 " =    2.446
peak=   -3.357 closest distance to " O   HOH Z 311 " =    3.578
peak=   -3.355 closest distance to " OD1 ASP A 171 " =    1.530
peak=   -3.352 closest distance to " CZ  PHE A  38 " =    2.392
peak=   -3.349 closest distance to " CE3 TRP A 274 " =    2.421
peak=   -3.346 closest distance to " O   ALA A 256 " =    1.562
peak=   -3.343 closest distance to " OD2 ASP A 171 " =    1.632
peak=   -3.337 closest distance to " CE  MET A 105 " =    1.871
peak=   -3.333 closest distance to " CG  LEU A  83 " =    1.940
peak=   -3.333 closest distance to " O   HOH Z  90 " =    2.943
peak=   -3.327 closest distance to " CG2 VAL A 189 " =    2.085
peak=   -3.326 closest distance to " CB  ALA A  51 " =    1.810
peak=   -3.324 closest distance to " CE2 TYR A 186 " =    2.132
peak=   -3.316 closest distance to " O   HOH Z  88 " =    1.941
peak=   -3.312 closest distance to " O   PHE A 218 " =    1.597
peak=   -3.311 closest distance to " OH  TYR A 214 " =    1.310
peak=   -3.305 closest distance to " O   HOH Z 275 " =    1.497
peak=   -3.302 closest distance to " CD1 ILE A 239 " =    2.581
peak=   -3.302 closest distance to " O   PRO A 198 " =    1.307
peak=   -3.302 closest distance to " O   GLY A 196 " =    1.085
peak=   -3.295 closest distance to " O   HOH Z  15 " =    1.582
peak=   -3.291 closest distance to " CB  PHE A 192 " =    1.876
peak=   -3.291 closest distance to " O   HOH Z  47 " =    1.475
peak=   -3.290 closest distance to " OG1 THR A 178 " =    1.207
peak=   -3.288 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.284 closest distance to " NH2 ARG A 159 " =    2.407
peak=   -3.284 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.282 closest distance to " CG  ASP A  50 " =    2.471
peak=   -3.281 closest distance to " ND2 ASN A  45 " =    1.217
peak=   -3.276 closest distance to " CD1 LEU A 101 " =    2.617
peak=   -3.274 closest distance to " OE1 GLN A  88 " =    1.242
peak=   -3.272 closest distance to " C   MET A 188 " =    1.555
peak=   -3.271 closest distance to " N   GLN A 122 " =    1.521
peak=   -3.269 closest distance to " CG  ARG A  66 " =    2.381
peak=   -3.268 closest distance to " O   HOH Z 266 " =    4.554
peak=   -3.267 closest distance to " O   HOH Z 265 " =    1.941
peak=   -3.266 closest distance to " CG2AVAL A  41 " =    2.805
peak=   -3.264 closest distance to " O   HOH Z  60 " =    2.327
peak=   -3.261 closest distance to " O   VAL A 125 " =    2.214
peak=   -3.259 closest distance to " OD2 ASP A 270 " =    1.491
peak=   -3.257 closest distance to " CD2 LEU A 237 " =    2.527
peak=   -3.257 closest distance to " CB  ALA A 248 " =    1.946
peak=   -3.249 closest distance to " CB  PRO A 163 " =    2.613
peak=   -3.245 closest distance to " CE  LYS A  76 " =    2.976
peak=   -3.245 closest distance to " CG2 ILE A 263 " =    2.239
peak=   -3.244 closest distance to " CB  CYS A 201 " =    2.541
peak=   -3.239 closest distance to " O   HOH Z 281 " =    2.698
peak=   -3.238 closest distance to " N   HIS A 115 " =    1.876
peak=   -3.235 closest distance to " NE2 GLN A  58 " =    1.123
peak=   -3.232 closest distance to " O   HOH Z 396 " =    1.594
peak=   -3.229 closest distance to " O   ASN A 249 " =    1.605
peak=   -3.228 closest distance to " O   HOH Z  60 " =    2.024
peak=   -3.228 closest distance to " O   HOH Z 211 " =    1.800
peak=   -3.226 closest distance to " CB  ALA A 291 " =    2.202
peak=   -3.225 closest distance to " CD2 TYR A 293 " =    2.067
peak=   -3.219 closest distance to " O   HOH Z 427 " =    1.416
peak=   -3.218 closest distance to " CB  SER A 258 " =    2.063
peak=   -3.218 closest distance to " O   HOH Z 417 " =    2.508
peak=   -3.213 closest distance to " O   LYS A 117 " =    1.660
peak=   -3.207 closest distance to " O   HOH Z 111 " =    2.488
peak=   -3.203 closest distance to " OD2 ASP A 171 " =    2.267
peak=   -3.202 closest distance to " O   HOH Z 200 " =    4.866
peak=   -3.202 closest distance to " O   HOH Z 409 " =    4.692
peak=   -3.201 closest distance to " O   HOH Z 108 " =    2.365
peak=   -3.201 closest distance to " OD1 ASN A 187 " =    1.556
peak=   -3.199 closest distance to " O   GLY A 118 " =    2.231
peak=   -3.197 closest distance to " O   HOH Z 278 " =    2.288
peak=   -3.196 closest distance to " O   HOH Z 137 " =    1.478
peak=   -3.196 closest distance to " ND2 ASN A 301 " =    2.022
peak=   -3.194 closest distance to " O   GLY A  80 " =    2.535
peak=   -3.190 closest distance to " N   ALA A 226 " =    2.052
peak=   -3.190 closest distance to " CB  CYS A 254 " =    2.427
peak=   -3.189 closest distance to " O   LEU A 167 " =    1.489
peak=   -3.180 closest distance to " CD1 ILE A 239 " =    2.020
peak=   -3.177 closest distance to " N   ALA A 248 " =    2.218
peak=   -3.174 closest distance to " OE1 GLN A 223 " =    2.031
peak=   -3.172 closest distance to " CG  GLN A 278 " =    2.227
peak=   -3.166 closest distance to " CG2 ILE A  49 " =    2.707
peak=   -3.162 closest distance to " CG2 ILE A  20 " =    2.759
peak=   -3.162 closest distance to " O   HOH Z 165 " =    2.009
peak=   -3.149 closest distance to " O   HOH Z 378 " =    1.292
peak=   -3.149 closest distance to " O   HOH Z 405 " =    2.525
peak=   -3.146 closest distance to " CZ  ARG A 259 " =    0.903
peak=   -3.141 closest distance to " O   HOH Z 139 " =    2.894
peak=   -3.140 closest distance to " O   HOH Z 263 " =    2.986
peak=   -3.135 closest distance to " O   HOH Z 198 " =    1.536
peak=   -3.133 closest distance to " CG2 ILE A  20 " =    2.814
peak=   -3.132 closest distance to " CD1 PHE A  16 " =    2.660
peak=   -3.131 closest distance to " O   HOH Z 389 " =    1.736
peak=   -3.122 closest distance to " ND2 ASN A 249 " =    2.208
peak=   -3.116 closest distance to " CE3 TRP A  70 " =    1.810
peak=   -3.114 closest distance to " OXT GLY A 302 " =    3.123
peak=   -3.114 closest distance to " SD  MET A 188 " =    2.272
peak=   -3.113 closest distance to " O   HOH Z 264 " =    1.825
peak=   -3.113 closest distance to " O   HOH Z 310 " =    3.410
peak=   -3.109 closest distance to " CD  PRO A  90 " =    1.869
peak=   -3.108 closest distance to " O   HOH Z 252 " =    4.334
peak=   -3.106 closest distance to " O   HOH Z 323 " =    1.362
peak=   -3.106 closest distance to " O   HOH Z 241 " =    1.507
peak=   -3.103 closest distance to " O   HOH Z  71 " =    1.426
peak=   -3.100 closest distance to " CB  TRP A  85 " =    2.613
peak=   -3.097 closest distance to " CB  LEU A 167 " =    2.142
peak=   -3.085 closest distance to " CB  ALA A  10 " =    2.121
peak=   -3.075 closest distance to " O   ALA A  51 " =    1.380
peak=   -3.065 closest distance to " CG  ARG A 259 " =    2.912
peak=   -3.060 closest distance to " CG  ARG A 269 " =    2.385
peak=   -3.054 closest distance to " O   PRO A 198 " =    1.752
peak=   -3.050 closest distance to " O   HOH Z 411 " =    3.492
peak=   -3.042 closest distance to " C   SER A 206 " =    1.489
peak=   -3.039 closest distance to " ND2 ASN A  39 " =    1.464

================= 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    :  0.3789 0.3768   6.167602e+00   6.178174e+00
   1_bss:  0.3649 0.3624   6.154788e+00   6.152563e+00
   1_xyz:  0.2510 0.2836   5.827150e+00   5.922916e+00
   1_adp:  0.2300 0.2895   5.776964e+00   5.939589e+00
   1_occ:  0.2295 0.2895   5.776146e+00   5.938972e+00
   2_bss:  0.2266 0.2841   5.767458e+00   5.928617e+00
   2_xyz:  0.1597 0.2100   5.451133e+00   5.653822e+00
   2_adp:  0.1455 0.1937   5.370823e+00   5.581754e+00
   2_occ:  0.1453 0.1937   5.369790e+00   5.580787e+00
   3_bss:  0.1449 0.1925   5.364702e+00   5.574972e+00
   3_xyz:  0.1246 0.1666   5.226164e+00   5.443309e+00
   3_adp:  0.1199 0.1636   5.196193e+00   5.418647e+00
   3_occ:  0.1198 0.1635   5.195537e+00   5.418191e+00
   4_bss:  0.1200 0.1634   5.196188e+00   5.418613e+00
   4_xyz:  0.1126 0.1574   5.149436e+00   5.381450e+00
   4_adp:  0.1110 0.1584   5.146396e+00   5.385259e+00
   4_occ:  0.1109 0.1584   5.146338e+00   5.385425e+00
   5_bss:  0.1109 0.1583   5.146295e+00   5.385343e+00
   5_xyz:  0.1061 0.1582   5.127260e+00   5.383617e+00
   5_adp:  0.1055 0.1581   5.125833e+00   5.384110e+00
   5_occ:  0.1055 0.1581   5.125836e+00   5.384312e+00
   5_bss:  0.1054 0.1581   5.125897e+00   5.384294e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -2.642  -1.892   3.505  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -2.642  -1.892   3.505  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -2.642  -1.892   3.505  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -2.642  -1.892   3.505  -0.000   0.000   0.000
   2_bss:  0.322  50.000  -2.614  -2.136  -0.011  -0.000  -0.000  -0.000
   2_xyz:  0.322  50.000  -2.614  -2.136  -0.011  -0.000  -0.000  -0.000
   2_adp:  0.322  50.000  -2.614  -2.136  -0.011  -0.000  -0.000  -0.000
   2_occ:  0.322  50.000  -2.614  -2.136  -0.011  -0.000  -0.000  -0.000
   3_bss:  0.317  42.901  -2.510  -2.180  -1.417  -0.000  -0.000  -0.000
   3_xyz:  0.317  42.901  -2.510  -2.180  -1.417  -0.000  -0.000  -0.000
   3_adp:  0.317  42.901  -2.510  -2.180  -1.417  -0.000  -0.000  -0.000
   3_occ:  0.317  42.901  -2.510  -2.180  -1.417  -0.000  -0.000  -0.000
   4_bss:  0.317  43.515  -2.567  -2.248  -1.928  -0.000  -0.000  -0.000
   4_xyz:  0.317  43.515  -2.567  -2.248  -1.928  -0.000  -0.000  -0.000
   4_adp:  0.317  43.515  -2.567  -2.248  -1.928  -0.000  -0.000  -0.000
   4_occ:  0.317  43.515  -2.567  -2.248  -1.928  -0.000  -0.000  -0.000
   5_bss:  0.318  44.088  -2.397  -2.088  -1.907  -0.000  -0.000  -0.000
   5_xyz:  0.318  44.088  -2.397  -2.088  -1.907  -0.000  -0.000  -0.000
   5_adp:  0.318  44.088  -2.397  -2.088  -1.907  -0.000  -0.000  -0.000
   5_occ:  0.318  44.088  -2.397  -2.088  -1.907  -0.000  -0.000  -0.000
   5_bss:  0.321  45.170  -2.146  -1.853  -1.695  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.860 0.5974  0.7836    45824.807
   1_bss:  42.098 0.6166  0.8014    41422.105
   1_xyz:  29.012 0.7695  0.9575    21595.798
   1_adp:  30.025 0.7572  0.9459    22548.076
   1_occ:  30.023 0.7571  0.9457    22518.943
   2_bss:  29.392 0.7641  0.9131    21827.701
   2_xyz:  20.433 0.8569  0.9833    11243.544
   2_adp:  18.467 0.8762  0.9924     9747.379
   2_occ:  18.445 0.8764  0.9924     9724.918
   3_bss:  18.267 0.8780  0.9770     9584.946
   3_xyz:  15.377 0.9033  0.9875     7182.448
   3_adp:  14.763 0.9088  0.9863     6865.463
   3_occ:  14.749 0.9089  0.9863     6860.369
   4_bss:  14.753 0.9089  0.9782     6882.112
   4_xyz:  14.072 0.9143  0.9802     6345.206
   4_adp:  14.119 0.9141  0.9757     6372.444
   4_occ:  14.118 0.9141  0.9756     6373.382
   5_bss:  14.117 0.9141  0.9796     6375.016
   5_xyz:  14.101 0.9143  0.9791     6372.098
   5_adp:  14.090 0.9144  0.9735     6365.140
   5_occ:  14.089 0.9144  0.9734     6368.683
   5_bss:  14.090 0.9144  0.9796     6369.720
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7888e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7888e-01
   1_xyz:   1.313  0.010  0.080 15.723  0.005  4.110   9.6052e-02
   1_adp:   1.313  0.010  0.080 15.723  0.005  4.110   9.6052e-02
   1_occ:   1.313  0.010  0.080 15.723  0.005  4.110   9.6052e-02
   2_bss:   1.313  0.010  0.080 15.723  0.005  4.110   9.6052e-02
   2_xyz:   1.064  0.007  0.071 14.224  0.005  4.122   6.3151e-02
   2_adp:   1.064  0.007  0.071 14.224  0.005  4.122   6.3151e-02
   2_occ:   1.064  0.007  0.071 14.224  0.005  4.122   6.3151e-02
   3_bss:   1.064  0.007  0.071 14.224  0.005  4.122   6.3151e-02
   3_xyz:   0.954  0.006  0.067 14.377  0.004  4.118   5.4798e-02
   3_adp:   0.954  0.006  0.067 14.377  0.004  4.118   5.4798e-02
   3_occ:   0.954  0.006  0.067 14.377  0.004  4.118   5.4798e-02
   4_bss:   0.954  0.006  0.067 14.377  0.004  4.118   5.4798e-02
   4_xyz:   0.999  0.006  0.071 14.439  0.004  4.120   5.7144e-02
   4_adp:   0.999  0.006  0.071 14.439  0.004  4.120   5.7144e-02
   4_occ:   0.999  0.006  0.071 14.439  0.004  4.120   5.7144e-02
   5_bss:   0.999  0.006  0.071 14.439  0.004  4.120   5.7144e-02
   5_xyz:   1.124  0.009  0.080 14.839  0.005  4.121   7.1077e-02
   5_adp:   1.124  0.009  0.080 14.839  0.005  4.121   7.1077e-02
   5_occ:   1.124  0.009  0.080 14.839  0.005  4.121   7.1077e-02
   5_bss:   1.124  0.009  0.080 14.839  0.005  4.121   7.1077e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.484   2.4018e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.484   2.4018e-01
   1_xyz:   8.077  0.057  0.262 87.068  0.026  2.070   9.1477e-02
   1_adp:   8.077  0.057  0.262 87.068  0.026  2.070   9.1477e-02
   1_occ:   8.077  0.057  0.262 87.068  0.026  2.070   9.1477e-02
   2_bss:   8.077  0.057  0.262 87.068  0.026  2.070   9.1477e-02
   2_xyz:   6.553  0.046  0.271 79.903  0.037  2.348   5.2193e-02
   2_adp:   6.553  0.046  0.271 79.903  0.037  2.348   5.2193e-02
   2_occ:   6.553  0.046  0.271 79.903  0.037  2.348   5.2193e-02
   3_bss:   6.553  0.046  0.271 79.903  0.037  2.348   5.2193e-02
   3_xyz:   6.704  0.046  0.262 83.944  0.032  2.317   7.7247e-02
   3_adp:   6.704  0.046  0.262 83.944  0.032  2.317   7.7247e-02
   3_occ:   6.704  0.046  0.262 83.944  0.032  2.317   7.7247e-02
   4_bss:   6.704  0.046  0.262 83.944  0.032  2.317   7.7247e-02
   4_xyz:   6.624  0.036  0.218 83.023  0.034  2.343   4.3660e-02
   4_adp:   6.624  0.036  0.218 83.023  0.034  2.343   4.3660e-02
   4_occ:   6.624  0.036  0.218 83.023  0.034  2.343   4.3660e-02
   5_bss:   6.624  0.036  0.218 83.023  0.034  2.343   4.3660e-02
   5_xyz:   7.226  0.046  0.251 82.248  0.036  2.260   5.6683e-02
   5_adp:   7.226  0.046  0.251 82.248  0.036  2.260   5.6683e-02
   5_occ:   7.226  0.046  0.251 82.248  0.036  2.260   5.6683e-02
   5_bss:   7.226  0.046  0.251 82.248  0.036  2.260   5.6683e-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:  86.46   0.00  17.74  86.46   0.00  13.60  82.74   4.51  40.29
   1_occ:  86.46   0.00  17.74  86.46   0.00  13.60  82.74   4.51  40.29
   2_bss:  86.46   0.00  17.74  86.46   0.00  13.60  82.74   4.51  40.29
   2_xyz:  86.46   0.00  17.74  86.46   0.00  13.60  82.74   4.51  40.29
   2_adp:  81.65   1.72  17.51  81.65   1.72  13.20  78.52   6.57  40.93
   2_occ:  81.65   1.72  17.51  81.65   1.72  13.20  78.52   6.57  40.93
   3_bss:  81.65   1.72  17.51  81.65   1.72  13.20  78.52   6.57  40.93
   3_xyz:  81.65   1.72  17.51  81.65   1.72  13.20  78.52   6.57  40.93
   3_adp:  85.53   1.50  17.25  85.53   1.50  13.03  78.25   4.75  40.22
   3_occ:  85.53   1.50  17.25  85.53   1.50  13.03  78.25   4.75  40.22
   4_bss:  85.53   1.50  17.25  85.53   1.50  13.03  78.25   4.75  40.22
   4_xyz:  85.53   1.50  17.25  85.53   1.50  13.03  78.25   4.75  40.22
   4_adp:  95.16   1.28  17.31  95.16   1.28  13.00  84.11   4.82  40.73
   4_occ:  95.16   1.28  17.31  95.16   1.28  13.00  84.11   4.82  40.73
   5_bss:  95.16   1.28  17.31  95.16   1.28  13.00  84.11   4.82  40.73
   5_xyz:  95.16   1.28  17.31  95.16   1.28  13.00  84.11   4.82  40.73
   5_adp:  99.42   1.60  17.03  99.42   1.60  12.82  85.49   6.11  39.96
   5_occ:  99.42   1.60  17.03  99.42   1.60  12.82  85.49   6.11  39.96
   5_bss:  99.36   1.55  16.97  99.36   1.55  12.76  85.43   6.05  39.90
------------------------------------------------------------------------
 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:    1.927    0.016    0.340
   1_adp:    1.927    0.016    0.340
   1_occ:    1.927    0.016    0.340
   2_bss:    1.927    0.016    0.340
   2_xyz:    1.529    0.018    0.455
   2_adp:    1.529    0.018    0.455
   2_occ:    1.529    0.018    0.455
   3_bss:    1.529    0.018    0.455
   3_xyz:    1.606    0.031    0.508
   3_adp:    1.606    0.031    0.508
   3_occ:    1.606    0.031    0.508
   4_bss:    1.606    0.031    0.508
   4_xyz:    1.675    0.041    0.523
   4_adp:    1.675    0.041    0.523
   4_occ:    1.675    0.041    0.523
   5_bss:    1.675    0.041    0.523
   5_xyz:    1.833    0.070    0.540
   5_adp:    1.833    0.070    0.540
   5_occ:    1.833    0.070    0.540
   5_bss:    1.833    0.070    0.540
------------------------------------------------------------------------

CPU time actual refinement: 359.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/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_792/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_792/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.86 
  Macro-tasks:
    bulk solvent and scale       = 38.77  
    individual site refinement   = 154.41 
    weights calculation          = 29.84  
    collect and process          = 6.19   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 229.31 
  Micro-tasks:
    mask                            = 1.96   
    f_calc                          = 119.92 
    alpha_beta                      = 8.15   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 128.96 
    fmodel                         = 6.78   
    r_factors                      = 0.20   
    phase_errors                   = 10.79  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 278.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.005 micro seconds
Total CPU time: 6.21 minutes
from_scatterers_fft:    663 calls, 119.63 s
gradients_fft:          608 calls, 114.71 s

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

# Date 2008-01-16 Time 05:41:17 PST -0800 (1200490877.94 s)
Start R-work = 0.3789, R-free = 0.3768 (no bulk solvent and anisotropic scale)
Final R-work = 0.1298, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.3649, R-free = 0.3624
Final R-work = 0.1054, R-free = 0.1581