# Date 2008-01-16 Time 06:47:23 PST -0800 (1200494843.69 s)
#phil __OFF__

Command line arguments: "../1281.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14367
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1281

-------------------------------------------------------------------------------
  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: (72.0062, 47.1647, 86.39, 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: 2.85, per 1000 atoms: 1.01


================================== 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: (72.0062, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00105
Completeness in resolution range: 0.95907
Completeness with d_max=infinity: 0.956167

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   2.0010

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: (72.0062, 47.1647, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00105
Completeness in resolution range: 0.95907
Completeness with d_max=infinity: 0.956167

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2824 [2142/2168]  1931   211   9.9%
  bin  2:  4.2824 -  3.4115 [2063/2082]  1855   208  10.1%
  bin  3:  3.4115 -  2.9839 [2030/2049]  1825   205  10.1%
  bin  4:  2.9839 -  2.7128 [2014/2044]  1813   201  10.0%
  bin  5:  2.7128 -  2.5193 [2016/2035]  1819   197   9.8%
  bin  6:  2.5193 -  2.3713 [1983/2008]  1777   206  10.4%
  bin  7:  2.3713 -  2.2529 [1988/2016]  1791   197   9.9%
  bin  8:  2.2529 -  2.1552 [1971/2007]  1778   193   9.8%
  bin  9:  2.1552 -  2.0724 [1976/2018]  1775   201  10.2%
  bin 10:  2.0724 -  2.0010 [1406/1998]  1266   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/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: 0.12 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:
        1.54 -     2.21: 4
        2.21 -     2.88: 1258
        2.88 -     3.56: 4365
        3.56 -     4.23: 9129
        4.23 -     4.90: 13170
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.538 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.034 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.083 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27921 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_1281/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/model_refine_001.geo

CPU time processing inputs: 7.80


============================ 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 = 72.00625 47.16465 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3484   r_free= 0.3408   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.109619                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7766 0.99   1389  155 0.2991 0.2839      6.3834      6.3184|
|  2:  4.7766 -  3.8108 0.99   1345  146 0.2757 0.2737      6.5461      6.5048|
|  3:  3.8108 -  3.3348 0.99   1312  147 0.3045 0.2861       6.423      6.4402|
|  4:  3.3348 -  3.0325 0.99   1317  153 0.3252 0.2870      6.3087       6.222|
|  5:  3.0325 -  2.8166 0.99   1295  139 0.3510 0.3935      6.1677      6.3002|
|  6:  2.8166 -  2.6514 0.99   1285  143 0.3714 0.3544      6.1112      6.0863|
|  7:  2.6514 -  2.5193 0.99   1300  139 0.3774 0.3627      6.0976      6.1376|
|  8:  2.5193 -  2.4100 0.98   1263  149 0.3861 0.3582      6.0253      5.9867|
|  9:  2.4100 -  2.3176 0.98   1275  146 0.3831 0.3948      5.9868      6.0705|
| 10:  2.3176 -  2.2379 0.99   1279  139 0.3879 0.4085      5.9643      6.0056|
| 11:  2.2379 -  2.1681 0.98   1284  138 0.4148 0.4157      5.9418      5.9573|
| 12:  2.1681 -  2.1063 0.97   1247  139 0.4117 0.4041      5.8695      5.9278|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.4102 0.4117      5.7892      5.7206|
| 14:  2.0510 -  2.0010 0.59    781   86 0.3766 0.3613        5.68      5.6446|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7766  1389   155  0.79  26.33   0.85     0.81      42912.04|
|  2:  4.7766 -  3.8108  1345   146  0.83  23.23   0.96     0.89      49969.35|
|  3:  3.8108 -  3.3348  1312   147  0.78  28.26   0.96     0.90      51365.00|
|  4:  3.3348 -  3.0325  1317   153  0.75  31.39   0.96     0.88      46854.35|
|  5:  3.0325 -  2.8166  1295   139  0.65  39.35   0.96     0.82      42808.99|
|  6:  2.8166 -  2.6514  1285   143  0.64  40.54   0.97     0.82      38569.92|
|  7:  2.6514 -  2.5193  1300   139  0.64  40.77   0.97     0.81      35934.68|
|  8:  2.5193 -  2.4100  1263   149  0.63  41.44   0.95     0.83      32678.94|
|  9:  2.4100 -  2.3176  1275   146  0.61  43.27   1.00     0.80      31645.81|
| 10:  2.3176 -  2.2379  1279   139  0.60  44.51   1.00     0.79      30221.03|
| 11:  2.2379 -  2.1681  1284   138  0.58  46.19   1.00     0.79      29086.28|
| 12:  2.1681 -  2.1063  1247   139  0.61  43.67   0.99     0.84      25517.18|
| 13:  2.1063 -  2.0510  1258   140  0.62  42.66   0.96     0.86      20472.27|
| 14:  2.0510 -  2.0010   781    86  0.67  38.54   1.02     0.85      14263.83|
|alpha:            min =        0.79 max =            0.90 mean =         0.83|
|beta:             min =    14263.83 max =        51365.00 mean =     35959.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.67|
|phase err.(work): min =        0.00 max =           89.96 mean =        37.68|
|phase err.(test): min =        0.00 max =           89.98 mean =        37.00|
|-----------------------------------------------------------------------------|

============================== 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 = 3.707934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.787   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.903136              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.575   (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 |  1.538 -  1.875:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.875 -  2.211:        2 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.211 -  2.547:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.547 -  2.883:     1239 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.883 -  3.219:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.219 -  3.555:     2492 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.555 -  3.892:     4623 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.892 -  4.228:     4506 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.228 -  4.564:     6015 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.564 -  4.900:     7155 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.538 |       0.177 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3484   r_free= 0.3408   ksol= 0.00   Bsol= 0.00   scale= 0.944    |
|                                                                             |
| 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:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.109619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3346   r_free= 0.3264   ksol= 0.31   Bsol= 59.47   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,-2.11,-1.92,-0.00,-0.00,-0.00); trace/3= -0.22                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.088846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.322700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.085   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.492047              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.202   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3346      final r-factor (work) = 0.2341          |
| start r-factor (free) = 0.3264      final r-factor (free) = 0.2566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2854 = 3.32 * 0.50 * 6.0922 + 1.00 * 0.1641                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8372 = 3.32 * 0.50 * 5.8747 + 1.00 * 0.0773                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2341      final r-factor (work) = 0.2175          |
| start r-factor (free) = 0.2566      final r-factor (free) = 0.2608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8977 = 0.49 * 1.00 * 5.8747 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9576 = 0.49 * 1.00 * 5.7111 + 1.00 * 0.1475                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.26  16.78    None  None   None       |
|    all(noH): 2823   0      0.00    103.26  16.78    None  None   None       |
|    Sol.    : 438    0      6.25    64.51   37.68    None  None   None       |
|    Mac.    : 2385   0      0.00    103.26  12.94    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.326:  978   |   5:    51.629 -  61.955:   72        |
|      1:    10.326 -  20.652: 1186   |   6:    61.955 -  72.281:    3        |
|      2:    20.652 -  30.978:  286   |   7:    72.281 -  82.607:    0        |
|      3:    30.978 -  41.303:  169   |   8:    82.607 -  92.933:    0        |
|      4:    41.303 -  51.629:  128   |   9:    92.933 - 103.258:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2175 r_free = 0.2608             target_work(ml) = 5.715         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2171 r_free = 0.2601             target_work(ml) = 5.713         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2171   r_free= 0.2601   ksol= 0.31   Bsol= 59.47   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,-2.11,-1.92,-0.00,-0.00,-0.00); trace/3= -0.22                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.712997                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2152   r_free= 0.2570   ksol= 0.33   Bsol= 64.35   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,-2.51,-1.84,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.708307                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.415812              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.352   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.161328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 87.464   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2152      final r-factor (work) = 0.1548          |
| start r-factor (free) = 0.2570      final r-factor (free) = 0.1992          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8355 = 3.42 * 0.50 * 5.7135 + 1.00 * 0.0773                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5661 = 3.42 * 0.50 * 5.5655 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1548      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.1992      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5260 = 1.16 * 1.00 * 5.5655 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2514 = 1.16 * 1.00 * 5.3728 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.26   17.92    None  None   None       |
|    all(noH): 2823   0      0.00    92.26   17.92    None  None   None       |
|    Sol.    : 438    0      5.03    92.26   43.01    None  None   None       |
|    Mac.    : 2385   0      0.00    86.46   13.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.226:  831   |   5:    46.131 -  55.357:   91        |
|      1:     9.226 -  18.452: 1233   |   6:    55.357 -  64.583:   83        |
|      2:    18.452 -  27.678:  282   |   7:    64.583 -  73.809:   45        |
|      3:    27.678 -  36.905:  136   |   8:    73.809 -  83.035:   19        |
|      4:    36.905 -  46.131:   97   |   9:    83.035 -  92.261:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1421 r_free = 0.1899             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1420 r_free = 0.1897             target_work(ml) = 5.350         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1897   ksol= 0.33   Bsol= 64.35   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.31,-2.51,-1.84,-0.00,-0.00,-0.00); trace/3= -1.55                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.350199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1418   r_free= 0.1891   ksol= 0.34   Bsol= 71.43   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.37,-1.54,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.349109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.177930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.571  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340664              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.193  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1418      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1714          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5982 = 3.18 * 0.50 * 5.3730 + 1.00 * 0.0607                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4695 = 3.18 * 0.50 * 5.2875 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1224      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1714      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8129 = 0.34 * 1.00 * 5.2875 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7877 = 0.34 * 1.00 * 5.2189 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.39   17.48    None  None   None       |
|    all(noH): 2823   0      0.00    90.39   17.48    None  None   None       |
|    Sol.    : 438    0      0.00    90.39   41.48    None  None   None       |
|    Mac.    : 2385   0      0.60    87.83   13.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.039:  796   |   5:    45.193 -  54.232:   91        |
|      1:     9.039 -  18.077: 1285   |   6:    54.232 -  63.270:   74        |
|      2:    18.077 -  27.116:  269   |   7:    63.270 -  72.309:   36        |
|      3:    27.116 -  36.154:  134   |   8:    72.309 -  81.347:   14        |
|      4:    36.154 -  45.193:  116   |   9:    81.347 -  90.386:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1660             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1657             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1657   ksol= 0.34   Bsol= 71.43   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.34,-2.37,-1.54,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200323                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1655   ksol= 0.33   Bsol= 63.97   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-2.31,-1.40,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199779                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.771159              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.237  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.410813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.888  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9080 = 3.77 * 0.50 * 5.2182 + 1.00 * 0.0686                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8418 = 3.77 * 0.50 * 5.1746 + 1.00 * 0.0846                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1117      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1356 = 0.41 * 1.00 * 5.1746 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1276 = 0.41 * 1.00 * 5.1560 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.13   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    90.13   17.18    None  None   None       |
|    Sol.    : 438    0      0.00    90.13   40.44    None  None   None       |
|    Mac.    : 2385   0      0.57    88.17   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.013:  820   |   5:    45.067 -  54.080:   93        |
|      1:     9.013 -  18.027: 1264   |   6:    54.080 -  63.093:   76        |
|      2:    18.027 -  27.040:  273   |   7:    63.093 -  72.106:   26        |
|      3:    27.040 -  36.053:  138   |   8:    72.106 -  81.120:    9        |
|      4:    36.053 -  45.067:  116   |   9:    81.120 -  90.133:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1624             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1623             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1623   ksol= 0.33   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-2.31,-1.40,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.154006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1619   ksol= 0.32   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.21,-1.30,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154282                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.580992              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.374  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.772852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.872  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7387 = 2.58 * 0.50 * 5.1563 + 1.00 * 0.0846                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7282 = 2.58 * 0.50 * 5.1594 + 1.00 * 0.0700                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9969 = 0.77 * 1.00 * 5.1594 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9997 = 0.77 * 1.00 * 5.1624 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.28   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    90.28   17.04    None  None   None       |
|    Sol.    : 438    0      2.13    90.28   40.45    None  None   None       |
|    Mac.    : 2385   0      0.00    88.51   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.028:  866   |   5:    45.139 -  54.167:   92        |
|      1:     9.028 -  18.056: 1223   |   6:    54.167 -  63.194:   75        |
|      2:    18.056 -  27.083:  270   |   7:    63.194 -  72.222:   28        |
|      3:    27.083 -  36.111:  135   |   8:    72.222 -  81.250:    7        |
|      4:    36.111 -  45.139:  118   |   9:    81.250 -  90.278:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1632             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1633             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1633   ksol= 0.32   Bsol= 63.97   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.21,-1.30,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7766 0.99   1389  155 0.0993 0.1320      5.3963      5.5514|
|  2:  4.7766 -  3.8108 0.99   1345  146 0.0855 0.1059      5.4362       5.615|
|  3:  3.8108 -  3.3348 0.99   1312  147 0.1030 0.1550      5.4632      5.8728|
|  4:  3.3348 -  3.0325 0.99   1317  153 0.1188 0.1582      5.4685      5.6109|
|  5:  3.0325 -  2.8166 0.99   1295  139 0.1367 0.1897      5.3592      5.6108|
|  6:  2.8166 -  2.6514 0.99   1285  143 0.1249 0.1874      5.2461      5.4906|
|  7:  2.6514 -  2.5193 0.99   1300  139 0.1248 0.1700      5.1944      5.3818|
|  8:  2.5193 -  2.4100 0.98   1263  149 0.1185 0.1823      5.0816      5.3936|
|  9:  2.4100 -  2.3176 0.98   1275  146 0.1173 0.1808      5.0567      5.3469|
| 10:  2.3176 -  2.2379 0.99   1279  139 0.1108 0.1847       4.969      5.2517|
| 11:  2.2379 -  2.1681 0.98   1284  138 0.1147 0.1850      4.9705      5.3168|
| 12:  2.1681 -  2.1063 0.97   1247  139 0.1126 0.1659       4.915      5.1247|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.1196 0.1885      4.8308      5.1399|
| 14:  2.0510 -  2.0010 0.59    781   86 0.1020 0.1773      4.6679      4.9623|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7766  1389   155  0.94   9.48   0.97     0.94       7510.20|
|  2:  4.7766 -  3.8108  1345   146  0.95   8.14   1.00     0.98       9121.68|
|  3:  3.8108 -  3.3348  1312   147  0.93  11.28   1.01     1.01      10391.41|
|  4:  3.3348 -  3.0325  1317   153  0.92  14.09   1.00     0.98      11026.10|
|  5:  3.0325 -  2.8166  1295   139  0.89  16.90   0.99     0.96       9097.84|
|  6:  2.8166 -  2.6514  1285   143  0.89  16.78   0.98     0.95       7827.75|
|  7:  2.6514 -  2.5193  1300   139  0.90  16.07   0.99     0.97       6798.91|
|  8:  2.5193 -  2.4100  1263   149  0.90  16.03   0.98     0.95       5567.20|
|  9:  2.4100 -  2.3176  1275   146  0.91  15.70   0.99     0.95       5300.93|
| 10:  2.3176 -  2.2379  1279   139  0.90  15.88   0.98     0.94       4522.63|
| 11:  2.2379 -  2.1681  1284   138  0.89  16.86   0.97     0.93       4685.86|
| 12:  2.1681 -  2.1063  1247   139  0.91  15.71   0.99     0.98       4365.88|
| 13:  2.1063 -  2.0510  1258   140  0.89  17.48   0.98     0.96       3755.48|
| 14:  2.0510 -  2.0010   781    86  0.91  14.96   0.95     0.91       2662.39|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2662.39 max =        11026.10 mean =      6771.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.59|
|phase err.(test): min =        0.00 max =           88.92 mean =        14.16|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1632   ksol= 0.32   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-2.03,-1.11,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1632   ksol= 0.32   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.68,-2.03,-1.11,-0.00,-0.00,-0.00); trace/3= -1.61                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165484                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7766 0.99   1389  155 0.0993 0.1321      5.3969      5.5522|
|  2:  4.7766 -  3.8108 0.99   1345  146 0.0856 0.1058      5.4363      5.6145|
|  3:  3.8108 -  3.3348 0.99   1312  147 0.1030 0.1550      5.4629      5.8725|
|  4:  3.3348 -  3.0325 0.99   1317  153 0.1188 0.1582      5.4684      5.6109|
|  5:  3.0325 -  2.8166 0.99   1295  139 0.1367 0.1897      5.3593      5.6109|
|  6:  2.8166 -  2.6514 0.99   1285  143 0.1249 0.1873      5.2461      5.4903|
|  7:  2.6514 -  2.5193 0.99   1300  139 0.1248 0.1700      5.1942      5.3816|
|  8:  2.5193 -  2.4100 0.98   1263  149 0.1185 0.1823      5.0816      5.3937|
|  9:  2.4100 -  2.3176 0.98   1275  146 0.1174 0.1807      5.0569      5.3466|
| 10:  2.3176 -  2.2379 0.99   1279  139 0.1107 0.1847      4.9691      5.2519|
| 11:  2.2379 -  2.1681 0.98   1284  138 0.1147 0.1852      4.9708      5.3173|
| 12:  2.1681 -  2.1063 0.97   1247  139 0.1127 0.1661      4.9153      5.1252|
| 13:  2.1063 -  2.0510 1.00   1258  140 0.1196 0.1886      4.8308      5.1399|
| 14:  2.0510 -  2.0010 0.59    781   86 0.1020 0.1774      4.6683      4.9624|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7766  1389   155  0.94   9.48   0.97     0.94       7519.60|
|  2:  4.7766 -  3.8108  1345   146  0.95   8.14   1.00     0.99       9123.19|
|  3:  3.8108 -  3.3348  1312   147  0.93  11.27   1.02     1.01      10383.07|
|  4:  3.3348 -  3.0325  1317   153  0.92  14.09   1.00     0.98      11025.75|
|  5:  3.0325 -  2.8166  1295   139  0.89  16.90   0.99     0.97       9096.73|
|  6:  2.8166 -  2.6514  1285   143  0.89  16.78   0.98     0.96       7827.25|
|  7:  2.6514 -  2.5193  1300   139  0.90  16.07   0.99     0.97       6797.03|
|  8:  2.5193 -  2.4100  1263   149  0.90  16.03   0.98     0.96       5566.95|
|  9:  2.4100 -  2.3176  1275   146  0.91  15.70   0.99     0.96       5299.26|
| 10:  2.3176 -  2.2379  1279   139  0.90  15.88   0.99     0.94       4523.46|
| 11:  2.2379 -  2.1681  1284   138  0.89  16.86   0.98     0.94       4687.04|
| 12:  2.1681 -  2.1063  1247   139  0.91  15.72   1.00     0.98       4369.87|
| 13:  2.1063 -  2.0510  1258   140  0.89  17.49   0.99     0.97       3756.77|
| 14:  2.0510 -  2.0010   781    86  0.91  14.97   0.96     0.92       2664.21|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2664.21 max =        11025.75 mean =      6771.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.60|
|phase err.(test): min =        0.00 max =           88.92 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.28   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    90.28   17.05    None  None   None       |
|    Sol.    : 438    0      2.13    90.28   40.45    None  None   None       |
|    Mac.    : 2385   0      0.00    88.51   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.031:  866   |   5:    45.142 -  54.170:   92        |
|      1:     9.031 -  18.059: 1223   |   6:    54.170 -  63.197:   75        |
|      2:    18.059 -  27.086:  270   |   7:    63.197 -  72.225:   28        |
|      3:    27.086 -  36.114:  135   |   8:    72.225 -  81.253:    7        |
|      4:    36.114 -  45.142:  118   |   9:    81.253 -  90.281:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 4.681
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 308
   mapped sites are within: 0.704 - 4.681

peak=    5.876 closest distance to " CB  GLN A 223 " =    1.444
peak=    5.305 closest distance to " CG  PRO A  54 " =    1.300
peak=    5.243 closest distance to " O   HOH Z 111 " =    1.939
peak=    5.043 closest distance to " CB  SER A  63 " =    1.286
peak=    4.924 closest distance to " O   HOH Z 232 " =    2.231
peak=    4.814 closest distance to " CG  PRO A 213 " =    1.262
peak=    4.774 closest distance to " O   HOH Z 126 " =    1.936
peak=    4.663 closest distance to " CB  PRO A  54 " =    0.907
peak=    4.644 closest distance to " O   HOH Z 369 " =    1.995
peak=    4.615 closest distance to " CB  GLN A 183 " =    1.251
peak=    4.582 closest distance to " O   HOH Z  78 " =    1.734
peak=    4.577 closest distance to " C   PRO A 198 " =    1.543
peak=    4.574 closest distance to " CB  LEU A 228 " =    1.058
peak=    4.520 closest distance to " O   HOH Z 298 " =    1.997
peak=    4.458 closest distance to " CB  GLU A 128 " =    1.082
peak=    4.414 closest distance to " CA  TYR A  30 " =    0.978
peak=    4.413 closest distance to " NE2 GLN A  11 " =    1.128
peak=    4.409 closest distance to " O   HOH Z  15 " =    2.155
peak=    4.404 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.376 closest distance to " CB  ARG A 190 " =    1.635
peak=    4.359 closest distance to " CZ  PHE A 218 " =    1.085
peak=    4.332 closest distance to " CG  PRO A 198 " =    1.279
peak=    4.306 closest distance to " CZ  PHE A 192 " =    0.953
peak=    4.303 closest distance to " CB  ASN A 148 " =    1.421
peak=    4.300 closest distance to " CB  ARG A  79 " =    1.404
peak=    4.269 closest distance to " CB  GLU A 152 " =    1.192
peak=    4.192 closest distance to " CG  PRO A  90 " =    1.078
peak=    4.191 closest distance to " CD  ARG A 159 " =    0.830
peak=    4.185 closest distance to " CB  TRP A 266 " =    0.977
peak=    4.162 closest distance to " O   HOH Z 368 " =    2.160
peak=    4.151 closest distance to " NH1AARG A 145 " =    1.204
peak=    4.131 closest distance to " CA  MET A  40 " =    1.169
peak=    4.103 closest distance to " CG  PRO A 243 " =    1.114
peak=    4.092 closest distance to " O   HOH Z 180 " =    2.160
peak=    4.086 closest distance to " CD ALYS A 290 " =    1.017
peak=    4.064 closest distance to " O   HOH Z 234 " =    3.883
peak=    4.056 closest distance to " O   HOH Z 236 " =    2.196
peak=    4.052 closest distance to " O   HOH Z 183 " =    1.409
peak=    4.051 closest distance to " CG1 ILE A  33 " =    1.278
peak=    4.044 closest distance to " CD1 LEU A 300 " =    1.234
peak=    4.024 closest distance to " O   MET A 105 " =    1.877
peak=    4.023 closest distance to " O   HOH Z 261 " =    2.062
peak=    4.012 closest distance to " O   HOH Z 425 " =    1.323
peak=    4.008 closest distance to " CB  GLU A 277 " =    3.707
peak=    4.000 closest distance to " CB  ASP A 124 " =    0.717
peak=    3.998 closest distance to " CB  VAL A 265 " =    1.275
peak=    3.996 closest distance to " NH2 ARG A 156 " =    1.178
peak=    3.986 closest distance to " CG2 THR A 221 " =    1.019
peak=    3.957 closest distance to " O   HOH Z  54 " =    2.287
peak=    3.947 closest distance to " O   HOH Z 193 " =    1.787
peak=    3.925 closest distance to " CB  ASP A 140 " =    0.919
peak=    3.901 closest distance to " O   HOH Z 193 " =    1.959
peak=    3.901 closest distance to " CD  ARG A 269 " =    0.930
peak=    3.898 closest distance to " ND2 ASN A 187 " =    1.446
peak=    3.893 closest distance to " O   HOH Z  21 " =    1.800
peak=    3.885 closest distance to " O   HOH Z 427 " =    3.122
peak=    3.877 closest distance to " O   HOH Z  88 " =    3.792
peak=    3.863 closest distance to " CB  TYR A 169 " =    0.708
peak=    3.860 closest distance to " CB  SER A   3 " =    1.404
peak=    3.856 closest distance to " O   HOH Z  20 " =    1.972
peak=    3.810 closest distance to " O   HOH Z 316 " =    3.157
peak=    3.808 closest distance to " O   HOH Z 217 " =    3.285
peak=    3.807 closest distance to " O   HOH Z 133 " =    2.416
peak=    3.802 closest distance to " O   HOH Z 272 " =    1.955
peak=    3.787 closest distance to " O   HOH Z 411 " =    3.815
peak=    3.785 closest distance to " O   HOH Z 132 " =    2.664
peak=    3.782 closest distance to " O   HOH Z 135 " =    1.803
peak=    3.778 closest distance to " CA  ASP A 124 " =    0.723
peak=    3.777 closest distance to " O   HOH Z 303 " =    2.102
peak=    3.775 closest distance to " CA  ASN A 215 " =    1.230
peak=    3.774 closest distance to " O   HOH Z 213 " =    1.952
peak=    3.767 closest distance to " CG BARG A 275 " =    1.542
peak=    3.765 closest distance to " CB  SER A 212 " =    1.123
peak=    3.764 closest distance to " ND2 ASN A 110 " =    1.689
peak=    3.760 closest distance to " CG  LEU A 167 " =    1.240
peak=    3.758 closest distance to " O   HOH Z 189 " =    2.689
peak=    3.756 closest distance to " CA  THR A 264 " =    0.866
peak=    3.746 closest distance to " OD1 ASN A  69 " =    2.663
peak=    3.728 closest distance to " O   HOH Z 250 " =    1.494
peak=    3.726 closest distance to " O   HOH Z 108 " =    2.594
peak=    3.718 closest distance to " CD  ARG A  66 " =    2.216
peak=    3.717 closest distance to " O   HOH Z 346 " =    1.631
peak=    3.717 closest distance to " OD1 ASN A 217 " =    1.732
peak=    3.699 closest distance to " CB  SER A 216 " =    0.842
peak=    3.699 closest distance to " CB  ASN A 187 " =    1.288
peak=    3.694 closest distance to " CB  VAL A 202 " =    1.634
peak=    3.687 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.684 closest distance to " CA  ASP A 191 " =    0.828
peak=    3.680 closest distance to " O   HOH Z  66 " =    2.094
peak=    3.670 closest distance to " CG2 VAL A 257 " =    0.931
peak=    3.668 closest distance to " O   HOH Z 158 " =    3.064
peak=    3.668 closest distance to " O   HOH Z 403 " =    1.710
peak=    3.663 closest distance to " O   HOH Z  44 " =    2.286
peak=    3.661 closest distance to " CE  LYS A  76 " =    0.848
peak=    3.660 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.655 closest distance to " O   HOH Z 142 " =    1.594
peak=    3.654 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.645 closest distance to " CD  ARG A  66 " =    2.208
peak=    3.631 closest distance to " O   HOH Z  61 " =    1.568
peak=    3.627 closest distance to " O   HOH Z 368 " =    3.742
peak=    3.626 closest distance to " O   HOH Z 214 " =    2.017
peak=    3.625 closest distance to " O   HOH Z 344 " =    3.258
peak=    3.623 closest distance to " O   HOH Z 285 " =    2.911
peak=    3.617 closest distance to " CB  LEU A 143 " =    1.146
peak=    3.608 closest distance to " O   HOH Z  97 " =    2.055
peak=    3.605 closest distance to " CA  PRO A  54 " =    1.371
peak=    3.588 closest distance to " OD2 ASP A 286 " =    2.953
peak=    3.584 closest distance to " CB  GLU A  46 " =    0.978
peak=    3.576 closest distance to " N   ASN A 127 " =    1.289
peak=    3.576 closest distance to " CD1 ILE A 106 " =    0.842
peak=    3.575 closest distance to " CB  ASN A  39 " =    0.949
peak=    3.572 closest distance to " CB  TRP A 179 " =    1.511
peak=    3.571 closest distance to " O   ALA A 165 " =    1.422
peak=    3.568 closest distance to " CG1 VAL A 153 " =    0.961
peak=    3.560 closest distance to " CD2 LEU A 255 " =    1.543
peak=    3.557 closest distance to " CZ  PHE A 208 " =    1.164
peak=    3.555 closest distance to " N   VAL A 126 " =    1.353
peak=    3.549 closest distance to " O   HOH Z 128 " =    2.186
peak=    3.545 closest distance to " O   HOH Z  58 " =    1.439
peak=    3.531 closest distance to " O   HOH Z 171 " =    3.843
peak=    3.528 closest distance to " CG1 ILE A 151 " =    1.003
peak=    3.525 closest distance to " N   ASN A  39 " =    1.316
peak=    3.524 closest distance to " CB  TYR A 169 " =    0.823
peak=    3.524 closest distance to " N   ARG A 156 " =    1.383
peak=    3.516 closest distance to " CB  ILE A 120 " =    1.267
peak=    3.511 closest distance to " O   HOH Z  53 " =    2.574
peak=    3.507 closest distance to " CA  ALA A 160 " =    0.901
peak=    3.502 closest distance to " O   HOH Z 133 " =    1.740
peak=    3.497 closest distance to " O   HOH Z 371 " =    3.306
peak=    3.492 closest distance to " CB  MET A  47 " =    1.039
peak=    3.490 closest distance to " O   SER A  87 " =    2.338
peak=    3.485 closest distance to " NE2 HIS A 207 " =    1.340
peak=    3.483 closest distance to " CD  ARG A 219 " =    1.055
peak=    3.483 closest distance to " CD2 LEU A 297 " =    0.849
peak=    3.478 closest distance to " CA  ALA A 158 " =    1.172
peak=    3.475 closest distance to " ND1 HIS A  86 " =    1.782
peak=    3.469 closest distance to " CB  ALA A   1 " =    4.681
peak=    3.469 closest distance to " O   HOH Z 126 " =    1.801
peak=    3.469 closest distance to " ND2 ASN A 249 " =    1.970
peak=    3.466 closest distance to " CA  ALA A  51 " =    0.907
peak=    3.461 closest distance to " CB  ALA A   9 " =    1.606
peak=    3.461 closest distance to " O   HOH Z 112 " =    1.502
peak=    3.456 closest distance to " O   HOH Z 134 " =    1.354
peak=    3.454 closest distance to " CA  ALA A  21 " =    1.269
peak=    3.450 closest distance to " O   HOH Z 147 " =    1.789
peak=    3.446 closest distance to " CB  LYS A 193 " =    0.999
peak=    3.445 closest distance to " CD1AILE A 234 " =    0.968
peak=    3.444 closest distance to " O   HOH Z  80 " =    1.556
peak=    3.442 closest distance to " CB  MET A  40 " =    0.766
peak=    3.441 closest distance to " CB  THR A  82 " =    1.431
peak=    3.436 closest distance to " O   HOH Z 163 " =    1.621
peak=    3.435 closest distance to " O   HOH Z 406 " =    1.643
peak=    3.435 closest distance to " CB  ALA A  34 " =    0.918
peak=    3.427 closest distance to " O   HOH Z 426 " =    1.555
peak=    3.427 closest distance to " O   HOH Z 352 " =    1.920
peak=    3.426 closest distance to " O   THR A 251 " =    1.310
peak=    3.425 closest distance to " NH2AARG A 275 " =    3.627
peak=    3.424 closest distance to " CA  ARG A  36 " =    1.191
peak=    3.423 closest distance to " O   HOH Z 193 " =    2.224
peak=    3.416 closest distance to " O   HOH Z 227 " =    1.725
peak=    3.415 closest distance to " N   TYR A  15 " =    0.787
peak=    3.412 closest distance to " NE  ARG A  79 " =    1.167
peak=    3.412 closest distance to " O   HOH Z 197 " =    2.937
peak=    3.408 closest distance to " OH  TYR A 186 " =    1.049
peak=    3.406 closest distance to " CA  ALA A 295 " =    1.112
peak=    3.403 closest distance to " O   HOH Z 128 " =    2.373
peak=    3.403 closest distance to " CA  ALA A 154 " =    0.986
peak=    3.397 closest distance to " O   HOH Z  10 " =    1.847
peak=    3.394 closest distance to " CG  ARG A 159 " =    0.939
peak=    3.389 closest distance to " CB  LEU A 237 " =    0.720
peak=    3.388 closest distance to " CB  ASN A 142 " =    0.939
peak=    3.386 closest distance to " O   HOH Z 172 " =    3.674
peak=    3.386 closest distance to " O   TYR A 116 " =    1.296
peak=    3.384 closest distance to " CB  ALA A 248 " =    0.960
peak=    3.383 closest distance to " O   HOH Z 423 " =    1.800
peak=    3.382 closest distance to " CG1BVAL A  72 " =    1.669
peak=    3.379 closest distance to " O  BHOH Z 338 " =    2.372
peak=    3.371 closest distance to " CB  SER A 141 " =    0.979
peak=    3.371 closest distance to " NE2 HIS A 115 " =    0.985
peak=    3.364 closest distance to " CD  ARG A  14 " =    1.294
peak=    3.364 closest distance to " O   HOH Z  68 " =    1.655
peak=    3.362 closest distance to " O   ALA A 158 " =    1.330
peak=    3.362 closest distance to " O   THR A 220 " =    1.317
peak=    3.360 closest distance to " CA  SER A  87 " =    1.034
peak=    3.356 closest distance to " CG2BVAL A  41 " =    0.881
peak=    3.356 closest distance to " CB  ALA A 291 " =    1.412
peak=    3.353 closest distance to " O   HOH Z 247 " =    1.298
peak=    3.353 closest distance to " O   HOH Z   1 " =    2.090
peak=    3.349 closest distance to " O   HOH Z 327 " =    2.857
peak=    3.346 closest distance to " CG2 VAL A 197 " =    1.179
peak=    3.346 closest distance to " O   HOH Z 116 " =    1.885
peak=    3.344 closest distance to " ND1 HIS A  81 " =    1.676
peak=    3.338 closest distance to " O   HOH Z 425 " =    2.069
peak=    3.336 closest distance to " CB  ALA A 100 " =    1.285
peak=    3.333 closest distance to " O   HOH Z  61 " =    1.493
peak=    3.332 closest distance to " CA  MET A 105 " =    1.049
peak=    3.329 closest distance to " O   HOH Z 313 " =    1.789
peak=    3.325 closest distance to " CB  PRO A 163 " =    4.191
peak=    3.321 closest distance to " CA  LYS A 117 " =    1.194
peak=    3.319 closest distance to " CB  ALA A 242 " =    0.880
peak=    3.319 closest distance to " CA  THR A 221 " =    0.913
peak=    3.313 closest distance to " CB  ASN A 110 " =    1.247
peak=    3.310 closest distance to " O   HOH Z 280 " =    2.964
peak=    3.305 closest distance to " O   HOH Z 329 " =    3.809
peak=    3.303 closest distance to " O   HOH Z 126 " =    1.549
peak=    3.302 closest distance to " CB  TYR A 116 " =    0.869
peak=    3.298 closest distance to " CE2 TYR A 186 " =    0.887
peak=    3.295 closest distance to " CA  TYR A 116 " =    1.408
peak=    3.295 closest distance to " O   HOH Z 419 " =    3.195
peak=    3.294 closest distance to " O   HOH Z 383 " =    2.093
peak=    3.291 closest distance to " O   ASP A 124 " =    1.074
peak=    3.284 closest distance to " C   TYR A 214 " =    1.528
peak=    3.283 closest distance to " O   HOH Z 286 " =    2.298
peak=    3.283 closest distance to " O   HOH Z  62 " =    2.260
peak=    3.280 closest distance to " O   HOH Z 391 " =    2.954
peak=    3.278 closest distance to " CB  ALA A  43 " =    0.880
peak=    3.277 closest distance to " CD  LYS A 119 " =    1.310
peak=    3.276 closest distance to " O   HOH Z  49 " =    2.223
peak=    3.273 closest distance to " O   HOH Z 305 " =    3.668
peak=    3.270 closest distance to " CD1 LEU A 228 " =    1.972
peak=    3.270 closest distance to " OG BSER A 164 " =    2.346
peak=    3.269 closest distance to " OE1 GLN A 278 " =    0.965
peak=    3.267 closest distance to " O   HOH Z 295 " =    1.501
peak=    3.266 closest distance to " CG  MET A 185 " =    1.045
peak=    3.266 closest distance to " O   HOH Z 403 " =    1.353
peak=    3.260 closest distance to " CB  TRP A 150 " =    1.273
peak=    3.259 closest distance to " O   HOH Z 327 " =    2.022
peak=    3.258 closest distance to " O   HOH Z 359 " =    1.495
peak=    3.258 closest distance to " O   HOH Z 148 " =    3.315
peak=    3.258 closest distance to " O   HOH Z  66 " =    2.032
peak=    3.254 closest distance to " O   HOH Z 245 " =    1.254
peak=    3.251 closest distance to " CB  ARG A 139 " =    0.904
peak=    3.247 closest distance to " CB  GLN A 103 " =    0.924
peak=    3.247 closest distance to " O   HOH Z 409 " =    3.029
peak=    3.246 closest distance to " CA  GLU A  46 " =    0.742
peak=    3.245 closest distance to " O   HOH Z 188 " =    2.162
peak=    3.240 closest distance to " OE1 GLN A  11 " =    2.170
peak=    3.239 closest distance to " CB  GLN A  89 " =    1.216
peak=    3.237 closest distance to " CB  PHE A 283 " =    0.808
peak=    3.233 closest distance to " O   HOH Z 219 " =    1.853
peak=    3.229 closest distance to " CA  LYS A 290 " =    1.309
peak=    3.228 closest distance to " NH2 ARG A  79 " =    1.465
peak=    3.219 closest distance to " OE1 GLN A 240 " =    1.668
peak=    3.214 closest distance to " O   TRP A 274 " =    1.823
peak=    3.213 closest distance to " O   HOH Z 345 " =    1.725
peak=    3.208 closest distance to " O   HOH Z  44 " =    3.182
peak=    3.207 closest distance to " CA  ASP A 140 " =    1.196
peak=    3.204 closest distance to " O   HOH Z 298 " =    2.625
peak=    3.203 closest distance to " O   HOH Z  49 " =    2.764
peak=    3.199 closest distance to " CB  ARG A 138 " =    1.079
peak=    3.199 closest distance to " CB  ALA A 104 " =    0.774
peak=    3.199 closest distance to " CB  PHE A  16 " =    0.971
peak=    3.199 closest distance to " O   HOH Z 166 " =    3.570
peak=    3.197 closest distance to " O   HOH Z  64 " =    1.976
peak=    3.194 closest distance to " CZ  PHE A  38 " =    1.283
peak=    3.193 closest distance to " O   HOH Z 294 " =    1.594
peak=    3.193 closest distance to " OE1 GLU A 152 " =    0.873
peak=    3.186 closest distance to " CG  GLU A  37 " =    0.876
peak=    3.178 closest distance to " O   HOH Z  97 " =    2.913
peak=    3.178 closest distance to " O   THR A  31 " =    1.516
peak=    3.175 closest distance to " CG2 THR A 220 " =    0.997
peak=    3.175 closest distance to " O   HOH Z 325 " =    2.447
peak=    3.172 closest distance to " O   HOH Z 273 " =    2.808
peak=    3.169 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.166 closest distance to " CA  ALA A  84 " =    1.475
peak=    3.160 closest distance to " CA  ALA A 299 " =    0.906
peak=    3.157 closest distance to " O   HOH Z 185 " =    1.963
peak=    3.156 closest distance to " O   HOH Z 213 " =    2.547
peak=    3.153 closest distance to " O   HOH Z  85 " =    2.272
peak=    3.152 closest distance to " O  BHOH Z  74 " =    1.365
peak=    3.151 closest distance to " CA  GLU A 152 " =    0.824
peak=    3.150 closest distance to " CA  ALA A 233 " =    1.571
peak=    3.134 closest distance to " CG  MET A 185 " =    1.255
peak=    3.131 closest distance to " CD2 TRP A 179 " =    1.333
peak=    3.128 closest distance to " N   SER A 135 " =    1.335
peak=    3.118 closest distance to " O   HOH Z 184 " =    1.335
peak=    3.116 closest distance to " CG  MET A 113 " =    1.795
peak=    3.111 closest distance to " O   HOH Z  88 " =    3.047
peak=    3.110 closest distance to " NH1 ARG A 138 " =    1.044
peak=    3.099 closest distance to " CA  ILE A  33 " =    1.743
peak=    3.096 closest distance to " O   HOH Z  59 " =    2.151
peak=    3.096 closest distance to " O   HOH Z 350 " =    1.647
peak=    3.096 closest distance to " CB  HIS A 108 " =    0.820
peak=    3.092 closest distance to " CB  SER A  62 " =    1.202
peak=    3.092 closest distance to " CG1 ILE A  49 " =    1.498
peak=    3.092 closest distance to " O   HOH Z 422 " =    2.678
peak=    3.088 closest distance to " CB  GLU A 152 " =    1.493
peak=    3.086 closest distance to " O   HOH Z 156 " =    2.910
peak=    3.085 closest distance to " NH1BARG A 145 " =    1.040
peak=    3.084 closest distance to " O   HOH Z 302 " =    2.006
peak=    3.083 closest distance to " CB  ALA A 248 " =    1.222
peak=    3.081 closest distance to " O   HOH Z 172 " =    3.864
peak=    3.080 closest distance to " O   HOH Z 345 " =    3.537
peak=    3.078 closest distance to " CB  ILE A 199 " =    1.042
peak=    3.077 closest distance to " CG BARG A 102 " =    1.894
peak=    3.067 closest distance to " O   HOH Z 310 " =    2.204
peak=    3.064 closest distance to " NH1 ARG A  56 " =    1.044
peak=    3.042 closest distance to " OD2 ASP A 200 " =    1.277
peak=    3.036 closest distance to " CA  LEU A  83 " =    1.591
peak=    3.029 closest distance to " O   HOH Z 149 " =    2.051
peak=    3.020 closest distance to " CB  ASP A 140 " =    0.704
peak=    3.018 closest distance to " O   HOH Z 387 " =    3.079

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.816 - 5.783
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.816 - 5.783

peak=   -4.335 closest distance to " O   HOH Z 377 " =    1.798
peak=   -4.307 closest distance to " O   HOH Z 266 " =    5.122
peak=   -4.279 closest distance to " CE2 TYR A  30 " =    2.754
peak=   -4.273 closest distance to " CB  PRO A 243 " =    2.627
peak=   -4.233 closest distance to " CG1 VAL A 250 " =    2.672
peak=   -4.227 closest distance to " O   HOH Z 372 " =    2.469
peak=   -4.139 closest distance to " CD  ARG A 156 " =    2.043
peak=   -4.125 closest distance to " CZ3 TRP A 179 " =    1.102
peak=   -4.102 closest distance to " N   ALA A  43 " =    2.483
peak=   -4.100 closest distance to " O   HOH Z  52 " =    1.430
peak=   -4.096 closest distance to " O   VAL A  67 " =    2.684
peak=   -4.074 closest distance to " OE1 GLN A 223 " =    1.941
peak=   -4.074 closest distance to " CD  ARG A  14 " =    3.446
peak=   -4.035 closest distance to " OG  SER A  97 " =    2.224
peak=   -4.000 closest distance to " O   HOH Z  10 " =    1.555
peak=   -3.992 closest distance to " O   PRO A 198 " =    1.304
peak=   -3.968 closest distance to " O   ILE A 109 " =    2.604
peak=   -3.921 closest distance to " O   HOH Z 290 " =    1.223
peak=   -3.909 closest distance to " CA  GLY A 241 " =    3.097
peak=   -3.907 closest distance to " O   HOH Z  38 " =    1.117
peak=   -3.855 closest distance to " CD2 TYR A 293 " =    2.039
peak=   -3.840 closest distance to " C   ASN A 187 " =    1.821
peak=   -3.836 closest distance to " OD1 ASN A 148 " =    1.612
peak=   -3.809 closest distance to " O   HOH Z 231 " =    2.216
peak=   -3.806 closest distance to " O   HOH Z 118 " =    3.352
peak=   -3.801 closest distance to " O   HOH Z 426 " =    1.711
peak=   -3.796 closest distance to " O   HOH Z 389 " =    1.976
peak=   -3.777 closest distance to " O   HOH Z  73 " =    2.102
peak=   -3.763 closest distance to " CD  GLN A  88 " =    0.876
peak=   -3.760 closest distance to " C   ASN A 285 " =    2.505
peak=   -3.734 closest distance to " NH2AARG A 275 " =    5.637
peak=   -3.730 closest distance to " O   VAL A 189 " =    2.568
peak=   -3.729 closest distance to " CD1 PHE A  59 " =    1.892
peak=   -3.720 closest distance to " C   HIS A 108 " =    1.075
peak=   -3.710 closest distance to " CG  MET A 105 " =    0.966
peak=   -3.708 closest distance to " CD  GLN A  58 " =    1.031
peak=   -3.699 closest distance to " O   GLY A 211 " =    1.497
peak=   -3.699 closest distance to " O   HOH Z 353 " =    2.171
peak=   -3.697 closest distance to " O   HOH Z 198 " =    2.202
peak=   -3.697 closest distance to " CA  GLY A 203 " =    2.326
peak=   -3.684 closest distance to " C   ALA A 158 " =    1.361
peak=   -3.659 closest distance to " CB  ALA A 291 " =    2.284
peak=   -3.651 closest distance to " ND2 ASN A  45 " =    1.059
peak=   -3.650 closest distance to " O   HOH Z 407 " =    3.508
peak=   -3.649 closest distance to " O   HOH Z  43 " =    1.533
peak=   -3.647 closest distance to " CA  GLY A 241 " =    2.282
peak=   -3.639 closest distance to " CD1 LEU A 228 " =    2.444
peak=   -3.636 closest distance to " CD1 LEU A 101 " =    2.456
peak=   -3.630 closest distance to " CG1 VAL A 112 " =    2.930
peak=   -3.603 closest distance to " C   LEU A 143 " =    1.283
peak=   -3.600 closest distance to " NE2 GLN A  88 " =    1.957
peak=   -3.592 closest distance to " O   HOH Z 185 " =    2.391
peak=   -3.590 closest distance to " O   HOH Z 111 " =    1.990
peak=   -3.576 closest distance to " CB  ALA A 291 " =    2.302
peak=   -3.562 closest distance to " O   HOH Z  60 " =    2.559
peak=   -3.561 closest distance to " OXT GLY A 302 " =    2.992
peak=   -3.550 closest distance to " CD1 ILE A 151 " =    2.384
peak=   -3.548 closest distance to " N   SER A 212 " =    2.054
peak=   -3.545 closest distance to " OG BSER A 134 " =    1.383
peak=   -3.531 closest distance to " CB  PRO A 163 " =    2.564
peak=   -3.528 closest distance to " CG  GLU A  53 " =    1.362
peak=   -3.523 closest distance to " O   HOH Z  19 " =    2.495
peak=   -3.520 closest distance to " ND2 ASN A  45 " =    1.810
peak=   -3.520 closest distance to " NH2 ARG A  66 " =    2.044
peak=   -3.496 closest distance to " CB  ARG A  79 " =    2.620
peak=   -3.495 closest distance to " O   HOH Z 394 " =    1.547
peak=   -3.494 closest distance to " O   HOH Z 243 " =    2.063
peak=   -3.493 closest distance to " OG BSER A 134 " =    1.876
peak=   -3.482 closest distance to " O   HOH Z 393 " =    1.403
peak=   -3.481 closest distance to " O   ALA A  10 " =    1.727
peak=   -3.469 closest distance to " CG2 ILE A  49 " =    2.814
peak=   -3.467 closest distance to " CA  GLY A 241 " =    2.821
peak=   -3.466 closest distance to " O   HOH Z 377 " =    1.344
peak=   -3.464 closest distance to " O   HOH Z 196 " =    2.080
peak=   -3.457 closest distance to " CG  PHE A 283 " =    2.838
peak=   -3.457 closest distance to " O   PRO A 163 " =    2.140
peak=   -3.457 closest distance to " OD1 ASP A 191 " =    1.756
peak=   -3.452 closest distance to " O   HOH Z 350 " =    1.623
peak=   -3.448 closest distance to " O   HOH Z  51 " =    1.716
peak=   -3.446 closest distance to " CG1 VAL A 125 " =    2.001
peak=   -3.437 closest distance to " CD2 PHE A  61 " =    2.574
peak=   -3.417 closest distance to " N   ALA A 226 " =    2.208
peak=   -3.413 closest distance to " O   HOH Z  11 " =    1.841
peak=   -3.413 closest distance to " O   HOH Z 396 " =    1.864
peak=   -3.411 closest distance to " CB  PRO A  54 " =    2.514
peak=   -3.410 closest distance to " CB  ALA A  43 " =    2.646
peak=   -3.410 closest distance to " CB  TRP A  85 " =    2.410
peak=   -3.405 closest distance to " O   HOH Z 435 " =    2.747
peak=   -3.404 closest distance to " CG2 THR A 221 " =    2.238
peak=   -3.403 closest distance to " CG2 ILE A 263 " =    2.391
peak=   -3.391 closest distance to " OD2 ASP A 171 " =    1.932
peak=   -3.391 closest distance to " O   HOH Z 275 " =    1.608
peak=   -3.388 closest distance to " CD  ARG A 195 " =    5.089
peak=   -3.380 closest distance to " CE  MET A 105 " =    2.220
peak=   -3.379 closest distance to " OD1 ASN A 187 " =    1.605
peak=   -3.378 closest distance to " CB  ASN A  39 " =    2.233
peak=   -3.373 closest distance to " ND2BASN A 224 " =    1.748
peak=   -3.371 closest distance to " CG  ASP A 231 " =    0.838
peak=   -3.366 closest distance to " OG  SER A  87 " =    1.423
peak=   -3.364 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.351 closest distance to " O   HOH Z 103 " =    1.826
peak=   -3.351 closest distance to " CD  ARG A 139 " =    1.581
peak=   -3.348 closest distance to " CG  ARG A 269 " =    2.530
peak=   -3.344 closest distance to " NE2 GLN A 194 " =    1.854
peak=   -3.340 closest distance to " CG  ARG A  66 " =    2.224
peak=   -3.339 closest distance to " O   HOH Z 166 " =    1.882
peak=   -3.329 closest distance to " ND2 ASN A 249 " =    2.483
peak=   -3.328 closest distance to " O   HOH Z 177 " =    1.620
peak=   -3.328 closest distance to " CE2 PHE A 218 " =    2.400
peak=   -3.328 closest distance to " O   VAL A  67 " =    2.809
peak=   -3.327 closest distance to " CB  ASP A 286 " =    2.160
peak=   -3.323 closest distance to " CD2 PHE A  59 " =    2.559
peak=   -3.322 closest distance to " O   GLY A  80 " =    2.325
peak=   -3.320 closest distance to " O   HOH Z 106 " =    1.953
peak=   -3.317 closest distance to " CG1 VAL A 197 " =    2.426
peak=   -3.312 closest distance to " ND2 ASN A  60 " =    1.965
peak=   -3.309 closest distance to " CE3 TRP A  70 " =    1.847
peak=   -3.308 closest distance to " O   HOH Z 351 " =    1.522
peak=   -3.305 closest distance to " O   HOH Z  13 " =    1.484
peak=   -3.304 closest distance to " N   THR A 157 " =    1.603
peak=   -3.303 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.303 closest distance to " O   HOH Z 198 " =    1.423
peak=   -3.300 closest distance to " SG ACYS A 201 " =    2.034
peak=   -3.297 closest distance to " C   LEU A 222 " =    0.816
peak=   -3.288 closest distance to " CA  SER A 135 " =    1.330
peak=   -3.287 closest distance to " OG ASER A 134 " =    1.292
peak=   -3.287 closest distance to " CG  PRO A 243 " =    1.746
peak=   -3.284 closest distance to " CB  ALA A   7 " =    2.275
peak=   -3.284 closest distance to " ND2 ASN A  60 " =    1.433
peak=   -3.281 closest distance to " N   LYS A 166 " =    2.031
peak=   -3.280 closest distance to " O   ASN A 301 " =    1.472
peak=   -3.279 closest distance to " C   SER A 206 " =    1.483
peak=   -3.275 closest distance to " O   HOH Z 298 " =    2.561
peak=   -3.275 closest distance to " CD  PRO A 213 " =    2.252
peak=   -3.272 closest distance to " O   HOH Z 211 " =    1.553
peak=   -3.272 closest distance to " OG  SER A  62 " =    1.687
peak=   -3.271 closest distance to " NH1 ARG A 195 " =    2.673
peak=   -3.271 closest distance to " CB  CYS A 254 " =    2.377
peak=   -3.267 closest distance to " CE BMET A  47 " =    2.110
peak=   -3.266 closest distance to " CD1 ILE A 239 " =    2.055
peak=   -3.265 closest distance to " SD BMET A  47 " =    0.963
peak=   -3.263 closest distance to " CD  GLN A  88 " =    0.817
peak=   -3.256 closest distance to " O   HOH Z 241 " =    1.276
peak=   -3.255 closest distance to " CZ  TYR A 169 " =    1.793
peak=   -3.252 closest distance to " OE2 GLU A   2 " =    1.745
peak=   -3.248 closest distance to " CG2 VAL A 189 " =    2.121
peak=   -3.235 closest distance to " O   HOH Z 189 " =    2.037
peak=   -3.232 closest distance to " NE2 GLN A 103 " =    1.753
peak=   -3.230 closest distance to " CD2 LEU A 167 " =    1.851
peak=   -3.228 closest distance to " O   HOH Z 114 " =    1.607
peak=   -3.228 closest distance to " O   HOH Z 253 " =    4.338
peak=   -3.227 closest distance to " O   HOH Z 417 " =    2.629
peak=   -3.221 closest distance to " O   HOH Z 388 " =    1.995
peak=   -3.217 closest distance to " OD1 ASP A 171 " =    1.550
peak=   -3.216 closest distance to " O   HOH Z 222 " =    1.306
peak=   -3.215 closest distance to " OD1 ASP A 191 " =    1.630
peak=   -3.214 closest distance to " O   TYR A 247 " =    2.915
peak=   -3.213 closest distance to " OE1 GLN A  88 " =    1.224
peak=   -3.207 closest distance to " CE3 TRP A 274 " =    2.552
peak=   -3.205 closest distance to " CG  TRP A 266 " =    1.782
peak=   -3.201 closest distance to " N   ASP A 171 " =    2.402
peak=   -3.199 closest distance to " CB  TYR A  15 " =    2.199
peak=   -3.198 closest distance to " N   SER A   3 " =    2.131
peak=   -3.197 closest distance to " CB  ALA A 248 " =    2.550
peak=   -3.197 closest distance to " NH2 ARG A  79 " =    1.516
peak=   -3.196 closest distance to " CD2 PHE A 225 " =    1.202
peak=   -3.194 closest distance to " O   HOH Z 191 " =    5.783
peak=   -3.194 closest distance to " CB  ASP A 132 " =    2.333
peak=   -3.189 closest distance to " CA  GLY A  98 " =    2.156
peak=   -3.188 closest distance to " O   ASP A  27 " =    2.042
peak=   -3.188 closest distance to " CE  MET A  93 " =    1.392
peak=   -3.184 closest distance to " CG  PRO A 163 " =    2.323
peak=   -3.182 closest distance to " O   HOH Z  51 " =    1.461
peak=   -3.170 closest distance to " O   PHE A 218 " =    1.528
peak=   -3.166 closest distance to " O   HOH Z   6 " =    1.541
peak=   -3.154 closest distance to " CB  ALA A 291 " =    2.225
peak=   -3.153 closest distance to " CD1 LEU A  83 " =    2.765
peak=   -3.148 closest distance to " CB  PHE A 208 " =    2.283
peak=   -3.147 closest distance to " CD  ARG A  79 " =    1.116
peak=   -3.138 closest distance to " O   VAL A 125 " =    2.319
peak=   -3.137 closest distance to " O   HOH Z  90 " =    1.577
peak=   -3.133 closest distance to " OH  TYR A 247 " =    1.847
peak=   -3.133 closest distance to " O   HOH Z 166 " =    1.674
peak=   -3.127 closest distance to " C   GLY A  17 " =    1.259
peak=   -3.119 closest distance to " O   HOH Z 252 " =    4.208
peak=   -3.115 closest distance to " O   GLY A 196 " =    1.232
peak=   -3.109 closest distance to " O   HOH Z 390 " =    2.266
peak=   -3.106 closest distance to " O   HOH Z 184 " =    1.733
peak=   -3.093 closest distance to " CD2 TRP A 274 " =    2.442
peak=   -3.086 closest distance to " CZ  PHE A  59 " =    1.766
peak=   -3.086 closest distance to " CZ  ARG A  66 " =    0.909
peak=   -3.086 closest distance to " CD2 TYR A 247 " =    2.428
peak=   -3.064 closest distance to " CE3 TRP A 150 " =    1.954
peak=   -3.046 closest distance to " O   HOH Z 234 " =    4.388
peak=   -3.041 closest distance to " O   PRO A 198 " =    1.396
peak=   -3.040 closest distance to " O   HOH Z 380 " =    5.110
peak=   -3.016 closest distance to " O   HOH Z 176 " =    0.872

================= 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    :  0.3484 0.3408   6.109619e+00   6.111482e+00
   1_bss:  0.3346 0.3264   6.088846e+00   6.088530e+00
   1_xyz:  0.2341 0.2566   5.765167e+00   5.844634e+00
   1_adp:  0.2175 0.2608   5.714931e+00   5.859007e+00
   1_occ:  0.2171 0.2601   5.712997e+00   5.857298e+00
   2_bss:  0.2152 0.2570   5.708307e+00   5.852132e+00
   2_xyz:  0.1548 0.1992   5.415697e+00   5.614322e+00
   2_adp:  0.1421 0.1899   5.350535e+00   5.569398e+00
   2_occ:  0.1420 0.1897   5.350199e+00   5.569348e+00
   3_bss:  0.1418 0.1891   5.349109e+00   5.566969e+00
   3_xyz:  0.1224 0.1714   5.228957e+00   5.471063e+00
   3_adp:  0.1190 0.1660   5.200813e+00   5.442943e+00
   3_occ:  0.1189 0.1657   5.200323e+00   5.442632e+00
   4_bss:  0.1188 0.1655   5.199779e+00   5.442044e+00
   4_xyz:  0.1117 0.1629   5.159203e+00   5.416259e+00
   4_adp:  0.1108 0.1624   5.154010e+00   5.412144e+00
   4_occ:  0.1108 0.1623   5.154006e+00   5.412377e+00
   5_bss:  0.1112 0.1619   5.154282e+00   5.411397e+00
   5_xyz:  0.1122 0.1626   5.164405e+00   5.418429e+00
   5_adp:  0.1120 0.1632   5.165230e+00   5.421752e+00
   5_occ:  0.1120 0.1633   5.165378e+00   5.422076e+00
   5_bss:  0.1119 0.1632   5.165484e+00   5.422113e+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:  0.313  59.467   3.376  -2.111  -1.925  -0.000  -0.000  -0.000
   1_xyz:  0.313  59.467   3.376  -2.111  -1.925  -0.000  -0.000  -0.000
   1_adp:  0.313  59.467   3.376  -2.111  -1.925  -0.000  -0.000  -0.000
   1_occ:  0.313  59.467   3.376  -2.111  -1.925  -0.000  -0.000  -0.000
   2_bss:  0.333  64.351  -0.308  -2.509  -1.839  -0.000  -0.000  -0.000
   2_xyz:  0.333  64.351  -0.308  -2.509  -1.839  -0.000  -0.000  -0.000
   2_adp:  0.333  64.351  -0.308  -2.509  -1.839  -0.000  -0.000  -0.000
   2_occ:  0.333  64.351  -0.308  -2.509  -1.839  -0.000  -0.000  -0.000
   3_bss:  0.336  71.434  -1.345  -2.369  -1.539  -0.000  -0.000  -0.000
   3_xyz:  0.336  71.434  -1.345  -2.369  -1.539  -0.000  -0.000  -0.000
   3_adp:  0.336  71.434  -1.345  -2.369  -1.539  -0.000  -0.000  -0.000
   3_occ:  0.336  71.434  -1.345  -2.369  -1.539  -0.000  -0.000  -0.000
   4_bss:  0.326  63.966  -1.750  -2.306  -1.400  -0.000  -0.000  -0.000
   4_xyz:  0.326  63.966  -1.750  -2.306  -1.400  -0.000  -0.000  -0.000
   4_adp:  0.326  63.966  -1.750  -2.306  -1.400  -0.000  -0.000  -0.000
   4_occ:  0.326  63.966  -1.750  -2.306  -1.400  -0.000  -0.000  -0.000
   5_bss:  0.324  63.966  -1.804  -2.214  -1.303  -0.000  -0.000  -0.000
   5_xyz:  0.324  63.966  -1.804  -2.214  -1.303  -0.000  -0.000  -0.000
   5_adp:  0.324  63.966  -1.804  -2.214  -1.303  -0.000  -0.000  -0.000
   5_occ:  0.324  63.966  -1.804  -2.214  -1.303  -0.000  -0.000  -0.000
   5_bss:  0.324  63.969  -1.683  -2.030  -1.115  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  37.610 0.6734  0.8340    35960.647
   1_bss:  36.473 0.6854  0.8470    33242.660
   1_xyz:  25.846 0.8036  0.9629    17667.550
   1_adp:  26.537 0.7954  0.9561    18185.143
   1_occ:  26.518 0.7954  0.9558    18093.145
   2_bss:  26.238 0.7985  0.9166    17854.556
   2_xyz:  19.170 0.8693  0.9679    10200.054
   2_adp:  17.964 0.8808  0.9697     9247.340
   2_occ:  17.958 0.8808  0.9695     9245.776
   3_bss:  17.902 0.8813  0.9624     9182.834
   3_xyz:  15.733 0.9005  0.9726     7492.795
   3_adp:  14.990 0.9070  0.9710     7090.911
   3_occ:  14.981 0.9071  0.9709     7080.977
   4_bss:  14.978 0.9071  0.9684     7065.046
   4_xyz:  14.437 0.9116  0.9711     6688.527
   4_adp:  14.331 0.9125  0.9662     6656.287
   4_occ:  14.336 0.9125  0.9661     6654.916
   5_bss:  14.352 0.9123  0.9673     6637.713
   5_xyz:  14.480 0.9114  0.9655     6721.736
   5_adp:  14.543 0.9109  0.9588     6767.738
   5_occ:  14.550 0.9108  0.9588     6771.812
   5_bss:  14.553 0.9108  0.9644     6772.224
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6408e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6408e-01
   1_xyz:   1.170  0.009  0.077 15.330  0.004  4.116   7.7311e-02
   1_adp:   1.170  0.009  0.077 15.330  0.004  4.116   7.7311e-02
   1_occ:   1.170  0.009  0.077 15.330  0.004  4.116   7.7311e-02
   2_bss:   1.170  0.009  0.077 15.330  0.004  4.116   7.7311e-02
   2_xyz:   1.029  0.007  0.073 14.471  0.004  4.132   6.0710e-02
   2_adp:   1.029  0.007  0.073 14.471  0.004  4.132   6.0710e-02
   2_occ:   1.029  0.007  0.073 14.471  0.004  4.132   6.0710e-02
   3_bss:   1.029  0.007  0.073 14.471  0.004  4.132   6.0710e-02
   3_xyz:   1.072  0.010  0.077 14.640  0.004  4.142   6.7871e-02
   3_adp:   1.072  0.010  0.077 14.640  0.004  4.142   6.7871e-02
   3_occ:   1.072  0.010  0.077 14.640  0.004  4.142   6.7871e-02
   4_bss:   1.072  0.010  0.077 14.640  0.004  4.142   6.7871e-02
   4_xyz:   1.177  0.012  0.087 14.857  0.005  4.131   8.4583e-02
   4_adp:   1.177  0.012  0.087 14.857  0.005  4.131   8.4583e-02
   4_occ:   1.177  0.012  0.087 14.857  0.005  4.131   8.4583e-02
   5_bss:   1.177  0.012  0.087 14.857  0.005  4.131   8.4583e-02
   5_xyz:   1.081  0.010  0.080 14.603  0.004  4.131   7.0036e-02
   5_adp:   1.081  0.010  0.080 14.603  0.004  4.131   7.0036e-02
   5_occ:   1.081  0.010  0.080 14.603  0.004  4.131   7.0036e-02
   5_bss:   1.081  0.010  0.080 14.603  0.004  4.131   7.0036e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.538   2.4359e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.538   2.4359e-01
   1_xyz:   9.012  0.051  0.293 88.498  0.029  2.073   7.0989e-02
   1_adp:   9.012  0.051  0.293 88.498  0.029  2.073   7.0989e-02
   1_occ:   9.012  0.051  0.293 88.498  0.029  2.073   7.0989e-02
   2_bss:   9.012  0.051  0.293 88.498  0.029  2.073   7.0989e-02
   2_xyz:   7.811  0.044  0.255 85.906  0.039  2.356   4.7238e-02
   2_adp:   7.811  0.044  0.255 85.906  0.039  2.356   4.7238e-02
   2_occ:   7.811  0.044  0.255 85.906  0.039  2.356   4.7238e-02
   3_bss:   7.811  0.044  0.255 85.906  0.039  2.356   4.7238e-02
   3_xyz:   8.626  0.046  0.234 82.177  0.040  2.323   4.8574e-02
   3_adp:   8.626  0.046  0.234 82.177  0.040  2.323   4.8574e-02
   3_occ:   8.626  0.046  0.234 82.177  0.040  2.323   4.8574e-02
   4_bss:   8.626  0.046  0.234 82.177  0.040  2.323   4.8574e-02
   4_xyz:   8.002  0.054  0.278 83.215  0.044  2.298   6.4621e-02
   4_adp:   8.002  0.054  0.278 83.215  0.044  2.298   6.4621e-02
   4_occ:   8.002  0.054  0.278 83.215  0.044  2.298   6.4621e-02
   5_bss:   8.002  0.054  0.278 83.215  0.044  2.298   6.4621e-02
   5_xyz:   8.094  0.049  0.240 82.125  0.041  2.369   4.9544e-02
   5_adp:   8.094  0.049  0.240 82.125  0.041  2.369   4.9544e-02
   5_occ:   8.094  0.049  0.240 82.125  0.041  2.369   4.9544e-02
   5_bss:   8.094  0.049  0.240 82.125  0.041  2.369   4.9544e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 103.26   0.00  16.78 103.26   0.00  12.94  64.51   6.25  37.68
   1_occ: 103.26   0.00  16.78 103.26   0.00  12.94  64.51   6.25  37.68
   2_bss: 103.26   0.00  16.78 103.26   0.00  12.94  64.51   6.25  37.68
   2_xyz: 103.26   0.00  16.78 103.26   0.00  12.94  64.51   6.25  37.68
   2_adp:  92.26   0.00  17.92  86.46   0.00  13.31  92.26   5.03  43.01
   2_occ:  92.26   0.00  17.92  86.46   0.00  13.31  92.26   5.03  43.01
   3_bss:  92.26   0.00  17.92  86.46   0.00  13.31  92.26   5.03  43.01
   3_xyz:  92.26   0.00  17.92  86.46   0.00  13.31  92.26   5.03  43.01
   3_adp:  90.39   0.00  17.48  87.83   0.60  13.07  90.39   0.00  41.48
   3_occ:  90.39   0.00  17.48  87.83   0.60  13.07  90.39   0.00  41.48
   4_bss:  90.39   0.00  17.48  87.83   0.60  13.07  90.39   0.00  41.48
   4_xyz:  90.39   0.00  17.48  87.83   0.60  13.07  90.39   0.00  41.48
   4_adp:  90.13   0.00  17.18  88.17   0.57  12.91  90.13   0.00  40.44
   4_occ:  90.13   0.00  17.18  88.17   0.57  12.91  90.13   0.00  40.44
   5_bss:  90.13   0.00  17.18  88.17   0.57  12.91  90.13   0.00  40.44
   5_xyz:  90.13   0.00  17.18  88.17   0.57  12.91  90.13   0.00  40.44
   5_adp:  90.28   0.00  17.04  88.51   0.00  12.75  90.28   2.13  40.45
   5_occ:  90.28   0.00  17.04  88.51   0.00  12.75  90.28   2.13  40.45
   5_bss:  90.28   0.00  17.05  88.51   0.00  12.75  90.28   2.13  40.45
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.613    0.009    0.280
   1_adp:    1.613    0.009    0.280
   1_occ:    1.613    0.009    0.280
   2_bss:    1.613    0.009    0.280
   2_xyz:    0.992    0.017    0.391
   2_adp:    0.992    0.017    0.391
   2_occ:    0.992    0.017    0.391
   3_bss:    0.992    0.017    0.391
   3_xyz:    1.022    0.021    0.448
   3_adp:    1.022    0.021    0.448
   3_occ:    1.022    0.021    0.448
   4_bss:    1.022    0.021    0.448
   4_xyz:    1.004    0.024    0.467
   4_adp:    1.004    0.024    0.467
   4_occ:    1.004    0.024    0.467
   5_bss:    1.004    0.024    0.467
   5_xyz:    1.084    0.029    0.476
   5_adp:    1.084    0.029    0.476
   5_occ:    1.084    0.029    0.476
   5_bss:    1.084    0.029    0.476
------------------------------------------------------------------------

CPU time actual refinement: 267.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/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_1281/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1281/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 267.51 
  Macro-tasks:
    bulk solvent and scale       = 32.19  
    individual site refinement   = 106.06 
    weights calculation          = 24.83  
    collect and process          = 5.51   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 168.67 
  Micro-tasks:
    mask                            = 1.48   
    f_calc                          = 84.50  
    alpha_beta                      = 7.01   
    target                          = 0.96   
    gradients_wrt_atomic_parameters = 91.06  
    fmodel                         = 5.59   
    r_factors                      = 0.17   
    phase_errors                   = 9.30   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 200.28 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.872 micro seconds
Total CPU time: 4.65 minutes
from_scatterers_fft:    624 calls, 84.26 s
gradients_fft:          569 calls, 80.24 s

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

# Date 2008-01-16 Time 06:52:01 PST -0800 (1200495121.94 s)
Start R-work = 0.3484, R-free = 0.3408 (no bulk solvent and anisotropic scale)
Final R-work = 0.1335, R-free = 0.1811 (no bulk solvent and anisotropic scale)

Start R-work = 0.3346, R-free = 0.3264
Final R-work = 0.1119, R-free = 0.1632