# Date 2008-01-16 Time 06:42:36 PST -0800 (1200494556.34 s)
#phil __OFF__

Command line arguments: "../1256.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11185
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1256

-------------------------------------------------------------------------------
  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, 46.6953, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97112
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937093

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9711

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, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97112
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937093

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2192 [2178/2207]  1965   213   9.8%
  bin  2:  4.2192 -  3.3608 [2107/2123]  1893   214  10.2%
  bin  3:  3.3608 -  2.9395 [2069/2088]  1859   210  10.1%
  bin  4:  2.9395 -  2.6723 [2064/2094]  1865   199   9.6%
  bin  5:  2.6723 -  2.4817 [2038/2057]  1834   204  10.0%
  bin  6:  2.4817 -  2.3359 [2049/2074]  1835   214  10.4%
  bin  7:  2.3359 -  2.2193 [2020/2054]  1817   203  10.0%
  bin  8:  2.2193 -  2.1229 [2010/2040]  1814   196   9.8%
  bin  9:  2.1229 -  2.0414 [1996/2051]  1805   191   9.6%
  bin 10:  2.0414 -  1.9711 [1058/2054]   943   115  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.69 -     2.33: 18
        2.33 -     2.97: 1775
        2.97 -     3.62: 4572
        3.62 -     4.26: 9196
        4.26 -     4.90: 12749
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.690 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 "  1.916 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.975 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.048 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28305 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_1256/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 46.69535 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4065   r_free= 0.4059   ksol= 0.00   Bsol= 0.00   scale= 0.929    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.197378                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.3274 0.3319       6.445       6.446|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.3353 0.3172       6.666      6.6838|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.3680 0.3501      6.5246      6.5562|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.3784 0.3915      6.4059      6.3804|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.4201 0.4368      6.2652       6.296|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.4411 0.4316       6.201      6.1985|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.4471 0.4045      6.1811      6.1362|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.4540 0.4346      6.1018       6.109|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.4467 0.4480      6.0687      6.0143|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.4602 0.5420      6.0256      6.1118|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.4796 0.4669      6.0037      6.0169|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.4602 0.4861       5.905        5.96|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.4742 0.4800      5.8535      5.7767|
| 14:  2.0203 -  1.9711 0.40    534   52 0.4669 0.4450      5.7653      5.7709|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.76  28.96   0.84     0.79      51927.41|
|  2:  4.7066 -  3.7543  1371   144  0.78  28.21   0.95     0.87      70209.94|
|  3:  3.7543 -  3.2852  1335   150  0.70  35.63   0.95     0.87      76336.90|
|  4:  3.2852 -  2.9873  1343   155  0.64  40.60   0.95     0.82      71567.81|
|  5:  2.9873 -  2.7746  1323   144  0.54  48.63   0.93     0.72      61176.45|
|  6:  2.7746 -  2.6119  1317   148  0.53  49.66   0.94     0.72      53348.06|
|  7:  2.6119 -  2.4817  1311   138  0.55  47.87   0.95     0.73      45985.26|
|  8:  2.4817 -  2.3741  1297   151  0.56  47.31   0.93     0.78      41129.71|
|  9:  2.3741 -  2.2830  1308   151  0.54  48.90   0.99     0.76      39190.83|
| 10:  2.2830 -  2.2044  1297   141  0.49  52.97   0.97     0.70      39900.71|
| 11:  2.2044 -  2.1357  1307   137  0.44  56.99   0.99     0.65      39734.64|
| 12:  2.1357 -  2.0748  1272   149  0.44  57.34   0.96     0.64      36148.60|
| 13:  2.0748 -  2.0203  1199   138  0.44  57.33   0.97     0.66      30748.34|
| 14:  2.0203 -  1.9711   534    52  0.46  55.46   0.95     0.67      24746.44|
|alpha:            min =        0.64 max =            0.87 mean =         0.75|
|beta:             min =    24746.44 max =        76336.90 mean =     50121.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.98 mean =        46.18|
|phase err.(test): min =        0.00 max =           89.74 mean =        46.35|
|-----------------------------------------------------------------------------|

============================== 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 = 9.070742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.937   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.381383              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.055   (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 |  1.690 -  2.011:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.011 -  2.332:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.332 -  2.653:       71 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.653 -  2.974:     1704 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.974 -  3.295:     1898 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.295 -  3.616:     2674 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.616 -  3.937:     4754 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.937 -  4.258:     4442 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.258 -  4.579:     5803 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.579 -  4.900:     6946 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.690 |       0.238 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4065   r_free= 0.4059   ksol= 0.00   Bsol= 0.00   scale= 0.929    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.197378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3954   r_free= 0.3953   ksol= 0.30   Bsol= 20.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,-2.59,0.62,-0.00,0.00,0.00); trace/3= 0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.186059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.615424              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.218   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.707450              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.848   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3954      final r-factor (work) = 0.2403          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.2744          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7164 = 7.62 * 0.50 * 6.1848 + 1.00 * 0.1665                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8395 = 7.62 * 0.50 * 5.9730 + 1.00 * 0.0961                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2403      final r-factor (work) = 0.2222          |
| start r-factor (free) = 0.2744      final r-factor (free) = 0.2800          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2319 = 0.71 * 1.00 * 5.9730 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0897 = 0.71 * 1.00 * 5.7332 + 1.00 * 0.0338                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.64   17.03    None  None   None       |
|    all(noH): 2823   0      0.00    67.64   17.03    None  None   None       |
|    Sol.    : 438    0      3.70    62.91   38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    67.64   13.09    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 -   6.764:  426   |   5:    33.819 -  40.583:  121        |
|      1:     6.764 -  13.528: 1060   |   6:    40.583 -  47.347:  103        |
|      2:    13.528 -  20.291:  620   |   7:    47.347 -  54.110:   75        |
|      3:    20.291 -  27.055:  246   |   8:    54.110 -  60.874:   44        |
|      4:    27.055 -  33.819:  122   |   9:    60.874 -  67.638:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2222 r_free = 0.2800             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2217 r_free = 0.2799             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2217   r_free= 0.2799   ksol= 0.30   Bsol= 20.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,-2.59,0.62,-0.00,0.00,0.00); trace/3= 0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.740936                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2186   r_free= 0.2775   ksol= 0.34   Bsol= 53.55   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-3.10,-1.39,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.734110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.505254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.041   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.082   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2186      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2775      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2915 = 2.51 * 0.50 * 5.7443 + 1.00 * 0.0961                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1012 = 2.51 * 0.50 * 5.6259 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1669      final r-factor (work) = 0.1551          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9890 = 0.35 * 1.00 * 5.6259 + 1.00 * 0.0310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9080 = 0.35 * 1.00 * 5.4583 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    65.30   17.04    None  None   None       |
|    all(noH): 2823   0      1.71    65.30   17.04    None  None   None       |
|    Sol.    : 438    0      5.36    65.30   39.01    None  None   None       |
|    Mac.    : 2385   0      1.71    59.40   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.711 -   8.070:  573   |   5:    33.505 -  39.864:   95        |
|      1:     8.070 -  14.429: 1144   |   6:    39.864 -  46.223:   89        |
|      2:    14.429 -  20.788:  471   |   7:    46.223 -  52.582:   89        |
|      3:    20.788 -  27.147:  164   |   8:    52.582 -  58.941:   70        |
|      4:    27.147 -  33.505:  109   |   9:    58.941 -  65.300:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1551 r_free = 0.2033             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1549 r_free = 0.2033             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1549   r_free= 0.2033   ksol= 0.34   Bsol= 53.55   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,-3.10,-1.39,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.430950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1549   r_free= 0.2025   ksol= 0.33   Bsol= 53.55   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.73,-1.64,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.428919                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.983323              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.488  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631534              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.923  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1549      final r-factor (work) = 0.1314          |
| start r-factor (free) = 0.2025      final r-factor (free) = 0.1757          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4667 = 1.98 * 0.50 * 5.4581 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3640 = 1.98 * 0.50 * 5.3573 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1314      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1757      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3917 = 0.63 * 1.00 * 5.3573 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3262 = 0.63 * 1.00 * 5.2514 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.32    85.70   17.62    None  None   None       |
|    all(noH): 2823   0      0.32    85.70   17.62    None  None   None       |
|    Sol.    : 438    0      6.10    85.70   41.91    None  None   None       |
|    Mac.    : 2385   0      0.32    83.79   13.16    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:     0.317 -   8.856:  704   |   5:    43.010 -  51.548:   95        |
|      1:     8.856 -  17.394: 1311   |   6:    51.548 -  60.087:   79        |
|      2:    17.394 -  25.933:  323   |   7:    60.087 -  68.625:   53        |
|      3:    25.933 -  34.471:  118   |   8:    68.625 -  77.164:   19        |
|      4:    34.471 -  43.010:  112   |   9:    77.164 -  85.702:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1251 r_free = 0.1689             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1687             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1687   ksol= 0.33   Bsol= 53.55   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.73,-1.64,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233018                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1690   ksol= 0.33   Bsol= 55.02   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-2.83,-1.91,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.233250                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.657811              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.965  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342779              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.742  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0317 = 2.66 * 0.50 * 5.2527 + 1.00 * 0.0514                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9686 = 2.66 * 0.50 * 5.1948 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7903 = 0.34 * 1.00 * 5.1948 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7797 = 0.34 * 1.00 * 5.1661 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    88.59   17.29    None  None   None       |
|    all(noH): 2823   0      0.91    88.59   17.29    None  None   None       |
|    Sol.    : 438    0      6.20    85.05   40.38    None  None   None       |
|    Mac.    : 2385   0      0.91    88.59   13.05    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:     0.906 -   9.675:  925   |   5:    44.748 -  53.516:   99        |
|      1:     9.675 -  18.443: 1185   |   6:    53.516 -  62.284:   55        |
|      2:    18.443 -  27.211:  254   |   7:    62.284 -  71.052:   35        |
|      3:    27.211 -  35.979:  125   |   8:    71.052 -  79.821:    7        |
|      4:    35.979 -  44.748:  129   |   9:    79.821 -  88.589:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1599             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1597             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1597   ksol= 0.33   Bsol= 55.02   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.93,-2.83,-1.91,-0.00,-0.00,-0.00); trace/3= -2.22                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.158892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1597   ksol= 0.33   Bsol= 55.02   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.64,-1.82,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.158904                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.411364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.140157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.314  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7110 = 1.41 * 0.50 * 5.1662 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6977 = 1.41 * 0.50 * 5.1680 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7331 = 0.14 * 1.00 * 5.1680 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7332 = 0.14 * 1.00 * 5.1787 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.96    86.97   16.88    None  None   None       |
|    all(noH): 2823   0      1.96    86.97   16.88    None  None   None       |
|    Sol.    : 438    0      6.31    82.05   38.47    None  None   None       |
|    Mac.    : 2385   0      1.96    86.97   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.955 -  10.457: 1098   |   5:    44.462 -  52.963:   99        |
|      1:    10.457 -  18.958: 1058   |   6:    52.963 -  61.464:   54        |
|      2:    18.958 -  27.459:  231   |   7:    61.464 -  69.966:   20        |
|      3:    27.459 -  35.961:  121   |   8:    69.966 -  78.467:    7        |
|      4:    35.961 -  44.462:  127   |   9:    78.467 -  86.968:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1603             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1601             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1601   ksol= 0.33   Bsol= 55.02   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-2.64,-1.82,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175141                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.1031 0.1366      5.4157      5.5983|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.0897 0.1074      5.4716      5.6276|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.1093 0.1646       5.488      5.8915|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.1287 0.1532      5.4948      5.5845|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.1407 0.1823       5.357      5.5599|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.1259 0.1784      5.2165      5.4535|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.1283 0.1646       5.186       5.337|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.1191 0.1774      5.0615      5.3601|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.1240 0.1971      5.0656      5.3533|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.1159 0.1704      4.9585      5.2123|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.1189 0.1766       4.963      5.2997|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.1151 0.1696      4.8935      5.1309|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.1259 0.1710       4.832       5.041|
| 14:  2.0203 -  1.9711 0.40    534   52 0.1074 0.1650      4.6422      4.9402|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.94   9.43   0.97     0.95       7517.40|
|  2:  4.7066 -  3.7543  1371   144  0.95   8.27   1.01     1.00       9331.90|
|  3:  3.7543 -  3.2852  1335   150  0.93  11.66   1.02     1.01      10581.92|
|  4:  3.2852 -  2.9873  1343   155  0.91  14.51   1.00     0.98      11032.17|
|  5:  2.9873 -  2.7746  1323   144  0.90  16.12   0.99     0.98       8480.23|
|  6:  2.7746 -  2.6119  1317   148  0.90  15.98   0.98     0.96       6972.33|
|  7:  2.6119 -  2.4817  1311   138  0.91  15.34   1.00     0.98       6265.95|
|  8:  2.4817 -  2.3741  1297   151  0.91  15.41   0.98     0.96       5181.15|
|  9:  2.3741 -  2.2830  1308   151  0.90  15.88   1.00     0.96       5107.02|
| 10:  2.2830 -  2.2044  1297   141  0.91  14.98   0.99     0.96       4232.29|
| 11:  2.2044 -  2.1357  1307   137  0.90  16.66   0.99     0.95       4423.12|
| 12:  2.1357 -  2.0748  1272   149  0.91  15.96   1.01     1.01       4131.31|
| 13:  2.0748 -  2.0203  1199   138  0.90  16.33   0.99     0.99       3459.27|
| 14:  2.0203 -  1.9711   534    52  0.91  14.88   0.98     0.94       2425.71|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2425.71 max =        11032.17 mean =      6600.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.29|
|phase err.(test): min =        0.00 max =           88.99 mean =        13.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1601   ksol= 0.33   Bsol= 54.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.59,-1.78,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175118                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1601   ksol= 0.33   Bsol= 54.95   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.59,-1.78,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.175118                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7066 0.99   1416  161 0.1031 0.1365      5.4155      5.5976|
|  2:  4.7066 -  3.7543 0.99   1371  144 0.0897 0.1073      5.4713      5.6273|
|  3:  3.7543 -  3.2852 0.99   1335  150 0.1093 0.1645      5.4878      5.8912|
|  4:  3.2852 -  2.9873 0.99   1343  155 0.1287 0.1532      5.4948      5.5846|
|  5:  2.9873 -  2.7746 0.99   1323  144 0.1408 0.1823      5.3572      5.5601|
|  6:  2.7746 -  2.6119 0.99   1317  148 0.1259 0.1784      5.2165      5.4534|
|  7:  2.6119 -  2.4817 0.99   1311  138 0.1282 0.1646      5.1856      5.3366|
|  8:  2.4817 -  2.3741 0.98   1297  151 0.1191 0.1773      5.0614      5.3598|
|  9:  2.3741 -  2.2830 0.98   1308  151 0.1240 0.1971      5.0654      5.3532|
| 10:  2.2830 -  2.2044 0.99   1297  141 0.1160 0.1703      4.9585      5.2122|
| 11:  2.2044 -  2.1357 0.99   1307  137 0.1189 0.1767      4.9629         5.3|
| 12:  2.1357 -  2.0748 0.97   1272  149 0.1152 0.1697      4.8939      5.1316|
| 13:  2.0748 -  2.0203 0.92   1199  138 0.1259 0.1711      4.8322      5.0411|
| 14:  2.0203 -  1.9711 0.40    534   52 0.1074 0.1651       4.643      4.9408|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1995 -  4.7066  1416   161  0.94   9.42   0.97     0.95       7511.38|
|  2:  4.7066 -  3.7543  1371   144  0.95   8.26   1.01     1.00       9324.17|
|  3:  3.7543 -  3.2852  1335   150  0.93  11.66   1.02     1.01      10574.64|
|  4:  3.2852 -  2.9873  1343   155  0.91  14.51   1.00     0.98      11034.61|
|  5:  2.9873 -  2.7746  1323   144  0.90  16.12   0.99     0.97       8481.05|
|  6:  2.7746 -  2.6119  1317   148  0.90  15.98   0.98     0.96       6970.05|
|  7:  2.6119 -  2.4817  1311   138  0.91  15.33   0.99     0.97       6261.95|
|  8:  2.4817 -  2.3741  1297   151  0.91  15.41   0.98     0.96       5179.71|
|  9:  2.3741 -  2.2830  1308   151  0.90  15.87   1.00     0.96       5105.64|
| 10:  2.2830 -  2.2044  1297   141  0.91  14.98   0.99     0.96       4230.57|
| 11:  2.2044 -  2.1357  1307   137  0.90  16.66   0.99     0.94       4420.65|
| 12:  2.1357 -  2.0748  1272   149  0.91  15.96   1.00     1.01       4134.00|
| 13:  2.0748 -  2.0203  1199   138  0.90  16.34   0.99     0.98       3462.99|
| 14:  2.0203 -  1.9711   534    52  0.91  14.90   0.97     0.94       2429.95|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2429.95 max =        11034.61 mean =      6598.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.29|
|phase err.(test): min =        0.00 max =           88.99 mean =        13.75|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.948)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.89    86.90   16.81    None  None   None       |
|    all(noH): 2823   0      1.89    86.90   16.81    None  None   None       |
|    Sol.    : 438    0      6.24    81.98   38.40    None  None   None       |
|    Mac.    : 2385   0      1.89    86.90   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.885 -  10.386: 1098   |   5:    44.391 -  52.893:   99        |
|      1:    10.386 -  18.888: 1058   |   6:    52.893 -  61.394:   54        |
|      2:    18.888 -  27.389:  231   |   7:    61.394 -  69.895:   20        |
|      3:    27.389 -  35.890:  121   |   8:    69.895 -  78.397:    7        |
|      4:    35.890 -  44.391:  127   |   9:    78.397 -  86.898:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.598 - 4.452
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 314
   mapped sites are within: 0.706 - 4.452

peak=    5.828 closest distance to " CB  GLN A 223 " =    1.441
peak=    5.602 closest distance to " O   HOH Z 111 " =    2.122
peak=    5.441 closest distance to " CG  PRO A  54 " =    1.328
peak=    5.379 closest distance to " CG  PRO A 213 " =    1.281
peak=    5.183 closest distance to " CB  SER A  63 " =    1.342
peak=    5.155 closest distance to " CG  PRO A  90 " =    1.139
peak=    4.992 closest distance to " O   HOH Z 126 " =    1.953
peak=    4.985 closest distance to " CB  PRO A  54 " =    0.939
peak=    4.951 closest distance to " CG  PRO A 198 " =    1.335
peak=    4.892 closest distance to " NE2 GLN A  11 " =    1.168
peak=    4.774 closest distance to " O   HOH Z 232 " =    2.246
peak=    4.754 closest distance to " CB  GLU A 128 " =    1.033
peak=    4.729 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.729 closest distance to " CB  LEU A 228 " =    1.041
peak=    4.642 closest distance to " C   PRO A 198 " =    1.589
peak=    4.547 closest distance to " NH2AARG A 102 " =    0.974
peak=    4.529 closest distance to " CG  PRO A 243 " =    1.110
peak=    4.475 closest distance to " O   HOH Z 236 " =    1.966
peak=    4.425 closest distance to " CB  ASN A 148 " =    1.241
peak=    4.389 closest distance to " O   HOH Z 298 " =    1.900
peak=    4.384 closest distance to " CB  GLU A 152 " =    1.220
peak=    4.379 closest distance to " CB  ASN A 187 " =    1.065
peak=    4.378 closest distance to " CB  SER A   3 " =    1.461
peak=    4.369 closest distance to " CB  GLN A 183 " =    1.190
peak=    4.364 closest distance to " O   HOH Z  15 " =    2.184
peak=    4.333 closest distance to " CG  PRO A 280 " =    0.802
peak=    4.324 closest distance to " O   HOH Z 425 " =    1.456
peak=    4.305 closest distance to " O   HOH Z 132 " =    2.453
peak=    4.301 closest distance to " O   HOH Z 193 " =    1.881
peak=    4.267 closest distance to " ND2 ASN A 187 " =    1.500
peak=    4.253 closest distance to " CA  TYR A  30 " =    1.004
peak=    4.232 closest distance to " O   HOH Z  78 " =    1.969
peak=    4.230 closest distance to " CD BLYS A 290 " =    1.076
peak=    4.215 closest distance to " CB  SER A 216 " =    0.840
peak=    4.202 closest distance to " OD2 ASP A 286 " =    2.992
peak=    4.159 closest distance to " O   HOH Z 183 " =    1.597
peak=    4.134 closest distance to " O   HOH Z 144 " =    1.651
peak=    4.121 closest distance to " O   HOH Z 135 " =    1.785
peak=    4.102 closest distance to " CA  THR A 264 " =    0.863
peak=    4.097 closest distance to " O   HOH Z 368 " =    1.977
peak=    4.089 closest distance to " O   HOH Z 344 " =    3.307
peak=    4.078 closest distance to " NH1AARG A 145 " =    1.161
peak=    4.053 closest distance to " CZ  PHE A 192 " =    0.907
peak=    4.051 closest distance to " O   HOH Z 369 " =    1.953
peak=    4.047 closest distance to " NH2 ARG A 156 " =    1.263
peak=    4.035 closest distance to " O   HOH Z 193 " =    1.876
peak=    4.028 closest distance to " CG1 ILE A  33 " =    1.332
peak=    4.027 closest distance to " O   HOH Z 437 " =    1.683
peak=    4.021 closest distance to " CD  ARG A 159 " =    0.796
peak=    4.015 closest distance to " O   HOH Z 112 " =    1.456
peak=    4.013 closest distance to " CD1 LEU A 300 " =    1.334
peak=    4.002 closest distance to " CB  VAL A 265 " =    1.248
peak=    3.982 closest distance to " O   HOH Z 108 " =    2.152
peak=    3.981 closest distance to " CG2 VAL A 257 " =    0.970
peak=    3.970 closest distance to " O   HOH Z 189 " =    2.473
peak=    3.953 closest distance to " N   ASN A  39 " =    1.287
peak=    3.940 closest distance to " CB  TRP A 266 " =    0.919
peak=    3.939 closest distance to " O   HOH Z 316 " =    3.088
peak=    3.934 closest distance to " CG2 THR A 221 " =    0.996
peak=    3.930 closest distance to " O   HOH Z 234 " =    3.821
peak=    3.924 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.921 closest distance to " O   HOH Z 134 " =    1.443
peak=    3.916 closest distance to " O   HOH Z  21 " =    1.684
peak=    3.910 closest distance to " CB  ASP A 124 " =    0.758
peak=    3.894 closest distance to " CA  PRO A  54 " =    1.344
peak=    3.886 closest distance to " CA  ASP A 124 " =    0.751
peak=    3.879 closest distance to " O   HOH Z 423 " =    1.639
peak=    3.863 closest distance to " O   HOH Z 346 " =    1.700
peak=    3.863 closest distance to " CB  VAL A 202 " =    1.589
peak=    3.845 closest distance to " CB  ARG A  79 " =    1.329
peak=    3.843 closest distance to " NH2BARG A 145 " =    2.073
peak=    3.838 closest distance to " O   HOH Z 247 " =    1.332
peak=    3.829 closest distance to " O   HOH Z 303 " =    2.217
peak=    3.829 closest distance to " O   HOH Z 180 " =    2.049
peak=    3.828 closest distance to " O   HOH Z  88 " =    3.598
peak=    3.819 closest distance to " CZ  PHE A 218 " =    1.001
peak=    3.817 closest distance to " CA  SER A  87 " =    0.895
peak=    3.811 closest distance to " O   HOH Z   9 " =    2.068
peak=    3.811 closest distance to " CB  SER A 212 " =    1.176
peak=    3.787 closest distance to " NH1 ARG A  56 " =    1.033
peak=    3.785 closest distance to " CZ  PHE A 208 " =    1.155
peak=    3.780 closest distance to " OD1 ASN A  69 " =    2.621
peak=    3.776 closest distance to " CB  TYR A 169 " =    0.785
peak=    3.775 closest distance to " ND2 ASN A 110 " =    1.883
peak=    3.764 closest distance to " CA  ASP A 191 " =    0.738
peak=    3.762 closest distance to " CA  ALA A  21 " =    1.163
peak=    3.758 closest distance to " CB  MET A  40 " =    0.744
peak=    3.748 closest distance to " O   HOH Z  58 " =    1.731
peak=    3.742 closest distance to " CB  MET A  47 " =    1.000
peak=    3.741 closest distance to " CB  LEU A 143 " =    1.108
peak=    3.734 closest distance to " CA  ASN A 215 " =    1.247
peak=    3.729 closest distance to " CA  THR A 221 " =    0.917
peak=    3.717 closest distance to " O   HOH Z  10 " =    1.885
peak=    3.715 closest distance to " CD2 LEU A 255 " =    1.537
peak=    3.712 closest distance to " O   HOH Z  48 " =    1.457
peak=    3.708 closest distance to " CB  GLU A 236 " =    1.244
peak=    3.707 closest distance to " O   HOH Z 272 " =    1.879
peak=    3.705 closest distance to " CA  ALA A 154 " =    0.989
peak=    3.698 closest distance to " ND1 HIS A  86 " =    1.790
peak=    3.697 closest distance to " O   HOH Z  64 " =    2.236
peak=    3.696 closest distance to " O   HOH Z 108 " =    1.430
peak=    3.691 closest distance to " CB  ILE A 234 " =    1.049
peak=    3.687 closest distance to " O   HOH Z  40 " =    2.148
peak=    3.676 closest distance to " O   HOH Z   1 " =    1.981
peak=    3.672 closest distance to " O   HOH Z  49 " =    2.107
peak=    3.666 closest distance to " OD1 ASN A 217 " =    1.599
peak=    3.654 closest distance to " CA  MET A  40 " =    1.117
peak=    3.645 closest distance to " NH2AARG A 190 " =    1.395
peak=    3.644 closest distance to " CD  LYS A 166 " =    1.261
peak=    3.643 closest distance to " CB  GLU A 152 " =    1.454
peak=    3.641 closest distance to " O   HOH Z 389 " =    1.935
peak=    3.633 closest distance to " O   HOH Z 409 " =    2.774
peak=    3.624 closest distance to " O   HOH Z  59 " =    2.130
peak=    3.624 closest distance to " N   GLN A 278 " =    0.824
peak=    3.622 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.619 closest distance to " O   HOH Z 217 " =    3.098
peak=    3.612 closest distance to " O   HOH Z 261 " =    1.829
peak=    3.611 closest distance to " CB  ALA A 291 " =    1.382
peak=    3.606 closest distance to " CB  ASN A  39 " =    0.953
peak=    3.605 closest distance to " O   ASN A 209 " =    1.365
peak=    3.603 closest distance to " CG1 ILE A 151 " =    0.961
peak=    3.601 closest distance to " CE  LYS A  76 " =    0.887
peak=    3.588 closest distance to " N   ASN A 127 " =    1.270
peak=    3.582 closest distance to " CA  GLN A 223 " =    0.967
peak=    3.579 closest distance to " N   TYR A  15 " =    0.759
peak=    3.579 closest distance to " CA  LYS A  48 " =    1.315
peak=    3.578 closest distance to " O   HOH Z 327 " =    2.146
peak=    3.576 closest distance to " CB  TRP A 179 " =    1.585
peak=    3.569 closest distance to " O   HOH Z 213 " =    1.966
peak=    3.567 closest distance to " O   HOH Z 427 " =    2.957
peak=    3.558 closest distance to " O   HOH Z 133 " =    2.445
peak=    3.558 closest distance to " CZ3 TRP A 123 " =    1.249
peak=    3.556 closest distance to " O   HOH Z 281 " =    4.452
peak=    3.556 closest distance to " CG BARG A 275 " =    1.526
peak=    3.548 closest distance to " O   HOH Z 193 " =    2.133
peak=    3.546 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.536 closest distance to " O   HOH Z 295 " =    1.506
peak=    3.533 closest distance to " O   HOH Z 411 " =    3.624
peak=    3.529 closest distance to " O   MET A 105 " =    1.813
peak=    3.529 closest distance to " CD  ARG A 219 " =    1.038
peak=    3.525 closest distance to " CB  ARG A 190 " =    1.624
peak=    3.520 closest distance to " CB  PRO A 198 " =    0.858
peak=    3.516 closest distance to " CD2 HIS A  81 " =    1.306
peak=    3.514 closest distance to " O   HOH Z 313 " =    1.836
peak=    3.513 closest distance to " CB  ALA A 104 " =    0.706
peak=    3.511 closest distance to " CG  ARG A 159 " =    0.928
peak=    3.508 closest distance to " CA  ARG A 102 " =    1.246
peak=    3.505 closest distance to " O   HOH Z 371 " =    2.909
peak=    3.502 closest distance to " NE AARG A 275 " =    1.483
peak=    3.501 closest distance to " OE1 GLN A  11 " =    2.171
peak=    3.500 closest distance to " O   HOH Z  20 " =    2.021
peak=    3.496 closest distance to " OH  TYR A 186 " =    1.133
peak=    3.494 closest distance to " CD  ARG A 269 " =    0.918
peak=    3.493 closest distance to " CA  ILE A 234 " =    0.997
peak=    3.491 closest distance to " CD1 ILE A 106 " =    0.768
peak=    3.490 closest distance to " O   HOH Z 227 " =    1.656
peak=    3.489 closest distance to " N   ARG A 156 " =    1.388
peak=    3.488 closest distance to " CB  SER A 210 " =    0.783
peak=    3.484 closest distance to " O   HOH Z  61 " =    1.599
peak=    3.476 closest distance to " CB  ALA A 248 " =    0.952
peak=    3.474 closest distance to " O   HOH Z 265 " =    2.281
peak=    3.472 closest distance to " CA  LEU A 282 " =    1.130
peak=    3.471 closest distance to " CB  ALA A 184 " =    1.002
peak=    3.466 closest distance to " O   HOH Z 171 " =    3.974
peak=    3.463 closest distance to " CB  ILE A 120 " =    1.115
peak=    3.461 closest distance to " O   HOH Z   1 " =    1.794
peak=    3.459 closest distance to " O   THR A 220 " =    1.418
peak=    3.447 closest distance to " CG1 VAL A 153 " =    0.956
peak=    3.441 closest distance to " O   HOH Z 219 " =    2.210
peak=    3.437 closest distance to " O   HOH Z 175 " =    3.609
peak=    3.437 closest distance to " O   HOH Z 133 " =    1.710
peak=    3.426 closest distance to " O   HOH Z 282 " =    1.373
peak=    3.426 closest distance to " O   HOH Z 163 " =    1.903
peak=    3.422 closest distance to " CG  GLN A  88 " =    1.027
peak=    3.421 closest distance to " NZ  LYS A 166 " =    3.000
peak=    3.413 closest distance to " O   HOH Z 214 " =    1.857
peak=    3.412 closest distance to " O   HOH Z   4 " =    2.010
peak=    3.411 closest distance to " O   HOH Z 426 " =    1.614
peak=    3.404 closest distance to " CA  GLU A 152 " =    0.862
peak=    3.404 closest distance to " CG  MET A 113 " =    1.469
peak=    3.399 closest distance to " CD  ARG A  66 " =    2.152
peak=    3.399 closest distance to " O   HOH Z 302 " =    1.923
peak=    3.398 closest distance to " O   HOH Z 291 " =    1.950
peak=    3.396 closest distance to " OG1 THR A 294 " =    1.666
peak=    3.396 closest distance to " ND1 HIS A  81 " =    1.602
peak=    3.395 closest distance to " CG BARG A 102 " =    1.893
peak=    3.395 closest distance to " O   HOH Z 158 " =    2.741
peak=    3.390 closest distance to " CD  ARG A  14 " =    1.329
peak=    3.389 closest distance to " O   HOH Z 368 " =    3.598
peak=    3.386 closest distance to " N   PHE A 130 " =    1.219
peak=    3.382 closest distance to " O   HOH Z 188 " =    2.143
peak=    3.382 closest distance to " O   HOH Z 407 " =    2.147
peak=    3.380 closest distance to " O   HOH Z 184 " =    1.540
peak=    3.376 closest distance to " N   ALA A 154 " =    0.843
peak=    3.374 closest distance to " O   HOH Z 211 " =    2.515
peak=    3.374 closest distance to " O   HOH Z 126 " =    1.528
peak=    3.374 closest distance to " O   HOH Z  68 " =    1.578
peak=    3.372 closest distance to " CA  GLY A 267 " =    1.220
peak=    3.371 closest distance to " CB  ASP A 171 " =    0.737
peak=    3.363 closest distance to " O   THR A 251 " =    1.222
peak=    3.362 closest distance to " O   HOH Z 152 " =    2.453
peak=    3.352 closest distance to " O   HOH Z 334 " =    1.627
peak=    3.351 closest distance to " O   HOH Z 250 " =    1.485
peak=    3.350 closest distance to " CB  ALA A  71 " =    1.407
peak=    3.345 closest distance to " C   TYR A 214 " =    1.572
peak=    3.342 closest distance to " OD1BASN A 224 " =    2.237
peak=    3.341 closest distance to " O   HOH Z  64 " =    2.193
peak=    3.341 closest distance to " CA  ALA A 158 " =    1.108
peak=    3.336 closest distance to " O   HOH Z  44 " =    1.784
peak=    3.332 closest distance to " CG AARG A 275 " =    1.180
peak=    3.328 closest distance to " O   HOH Z 130 " =    3.828
peak=    3.327 closest distance to " CA  TYR A 186 " =    1.470
peak=    3.326 closest distance to " O   HOH Z 273 " =    2.752
peak=    3.325 closest distance to " CA  ALA A  51 " =    0.916
peak=    3.324 closest distance to " CG  GLN A 144 " =    0.895
peak=    3.321 closest distance to " O   HOH Z 287 " =    1.831
peak=    3.319 closest distance to " O   HOH Z  44 " =    3.239
peak=    3.319 closest distance to " CA  ALA A 299 " =    0.916
peak=    3.319 closest distance to " O   HOH Z 383 " =    2.049
peak=    3.318 closest distance to " CB  TRP A 123 " =    1.070
peak=    3.315 closest distance to " CB  ALA A  34 " =    1.073
peak=    3.315 closest distance to " O   HOH Z 163 " =    1.790
peak=    3.310 closest distance to " O   HOH Z 345 " =    3.587
peak=    3.306 closest distance to " CG1BVAL A  72 " =    1.587
peak=    3.304 closest distance to " O   HOH Z 403 " =    1.371
peak=    3.304 closest distance to " O   HOH Z 391 " =    2.955
peak=    3.303 closest distance to " CD  LYS A 119 " =    1.239
peak=    3.301 closest distance to " O   HOH Z 387 " =    3.253
peak=    3.300 closest distance to " CG2 VAL A 112 " =    0.894
peak=    3.293 closest distance to " O   HOH Z 286 " =    2.300
peak=    3.291 closest distance to " O   HOH Z 280 " =    3.139
peak=    3.287 closest distance to " CG  GLU A 277 " =    3.164
peak=    3.284 closest distance to " O   HOH Z 166 " =    3.679
peak=    3.278 closest distance to " O   HOH Z 149 " =    2.035
peak=    3.273 closest distance to " O   ALA A 165 " =    1.390
peak=    3.271 closest distance to " NE AARG A 102 " =    1.295
peak=    3.268 closest distance to " CB  SER A 276 " =    1.338
peak=    3.258 closest distance to " O   HOH Z 128 " =    1.506
peak=    3.255 closest distance to " O   GLY A  57 " =    2.538
peak=    3.252 closest distance to " O   HOH Z  49 " =    2.374
peak=    3.252 closest distance to " O   HOH Z 214 " =    2.499
peak=    3.248 closest distance to " CB  THR A 157 " =    1.125
peak=    3.248 closest distance to " CA  ASP A 140 " =    1.270
peak=    3.247 closest distance to " NZ ALYS A 290 " =    1.152
peak=    3.244 closest distance to " CA  ARG A  36 " =    1.210
peak=    3.235 closest distance to " CA  GLU A  46 " =    0.746
peak=    3.232 closest distance to " OG  SER A 206 " =    1.212
peak=    3.230 closest distance to " CD1AILE A 234 " =    1.102
peak=    3.225 closest distance to " CD  GLN A 240 " =    1.634
peak=    3.225 closest distance to " CB  ARG A 139 " =    0.915
peak=    3.224 closest distance to " O   ALA A   1 " =    1.499
peak=    3.222 closest distance to " O   TRP A 274 " =    1.716
peak=    3.218 closest distance to " O   HOH Z  40 " =    1.926
peak=    3.218 closest distance to " CB  ASN A 142 " =    0.912
peak=    3.215 closest distance to " O   HOH Z  80 " =    1.605
peak=    3.211 closest distance to " O   HOH Z 352 " =    1.803
peak=    3.209 closest distance to " OE1 GLN A  58 " =    1.159
peak=    3.207 closest distance to " CA  ASP A 162 " =    1.146
peak=    3.205 closest distance to " O   HOH Z 216 " =    2.567
peak=    3.204 closest distance to " O   HOH Z  97 " =    1.892
peak=    3.201 closest distance to " O   HOH Z 353 " =    2.729
peak=    3.200 closest distance to " O   HOH Z 144 " =    1.752
peak=    3.197 closest distance to " CB  GLU A 277 " =    3.641
peak=    3.194 closest distance to " O   SER A  87 " =    2.402
peak=    3.192 closest distance to " OD1 ASP A 171 " =    1.308
peak=    3.191 closest distance to " O   HOH Z  66 " =    1.933
peak=    3.187 closest distance to " O   HOH Z 148 " =    3.281
peak=    3.186 closest distance to " CG  GLN A  55 " =    1.768
peak=    3.184 closest distance to " O   HOH Z 379 " =    1.980
peak=    3.183 closest distance to " O  BHOH Z 338 " =    2.441
peak=    3.183 closest distance to " CB  TYR A 116 " =    0.866
peak=    3.182 closest distance to " OD1 ASP A 238 " =    1.078
peak=    3.182 closest distance to " CB  ALA A 137 " =    1.012
peak=    3.182 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.177 closest distance to " CD1 ILE A  33 " =    1.520
peak=    3.176 closest distance to " O   HOH Z  85 " =    2.218
peak=    3.167 closest distance to " CB  LEU A 237 " =    0.784
peak=    3.166 closest distance to " O   HOH Z 410 " =    1.755
peak=    3.163 closest distance to " CB  ASN A 110 " =    1.138
peak=    3.156 closest distance to " O   LEU A 300 " =    1.437
peak=    3.149 closest distance to " O   HOH Z 156 " =    2.857
peak=    3.149 closest distance to " CD1 LEU A 228 " =    1.983
peak=    3.149 closest distance to " O   HOH Z   2 " =    1.549
peak=    3.148 closest distance to " O   HOH Z 153 " =    1.812
peak=    3.148 closest distance to " OG BSER A 164 " =    2.572
peak=    3.147 closest distance to " O   HOH Z 305 " =    3.718
peak=    3.146 closest distance to " CB  ALA A 248 " =    1.216
peak=    3.142 closest distance to " C   GLU A 277 " =    1.467
peak=    3.139 closest distance to " O   SER A  32 " =    1.727
peak=    3.135 closest distance to " CB  LEU A 255 " =    0.847
peak=    3.129 closest distance to " CB  PHE A  16 " =    1.050
peak=    3.128 closest distance to " O   TYR A 116 " =    1.290
peak=    3.124 closest distance to " CB  ALA A 100 " =    1.316
peak=    3.121 closest distance to " CA  GLN A  88 " =    1.566
peak=    3.118 closest distance to " CB  ARG A 138 " =    1.067
peak=    3.116 closest distance to " O   HOH Z 332 " =    1.589
peak=    3.115 closest distance to " CA  ASP A 270 " =    1.051
peak=    3.107 closest distance to " O   HOH Z 163 " =    1.632
peak=    3.104 closest distance to " O   HOH Z 299 " =    2.474
peak=    3.104 closest distance to " CE1 TYR A 214 " =    1.018
peak=    3.103 closest distance to " CB  PRO A 243 " =    1.277
peak=    3.099 closest distance to " O   HOH Z 271 " =    2.288
peak=    3.095 closest distance to " O   HOH Z 281 " =    1.958
peak=    3.092 closest distance to " O   HOH Z 392 " =    2.123
peak=    3.090 closest distance to " O   HOH Z 217 " =    1.472
peak=    3.090 closest distance to " O   HOH Z 213 " =    2.717
peak=    3.088 closest distance to " CB  ALA A 114 " =    1.050
peak=    3.086 closest distance to " O   HOH Z 294 " =    1.561
peak=    3.086 closest distance to " O   HOH Z 215 " =    1.617
peak=    3.084 closest distance to " CE2 TYR A 247 " =    1.312
peak=    3.057 closest distance to " CA  ALA A 233 " =    1.559
peak=    3.009 closest distance to " CB  TYR A 169 " =    1.281

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 183         
Filter by distance & map next to the model:
   mapped sites are within: 0.526 - 5.661
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 181 from: 183
   mapped sites are within: 0.715 - 5.661

peak=   -4.982 closest distance to " O   HOH Z 290 " =    1.077
peak=   -4.685 closest distance to " O   HOH Z 377 " =    1.393
peak=   -4.419 closest distance to " CB  PRO A 243 " =    2.556
peak=   -4.419 closest distance to " O   PRO A 198 " =    1.209
peak=   -4.098 closest distance to " CD  ARG A  14 " =    3.313
peak=   -4.092 closest distance to " O   HOH Z 198 " =    2.250
peak=   -4.068 closest distance to " CG  MET A 105 " =    0.963
peak=   -4.033 closest distance to " C   ALA A 158 " =    1.351
peak=   -4.002 closest distance to " N   ALA A  43 " =    2.383
peak=   -3.989 closest distance to " CZ3 TRP A 179 " =    1.136
peak=   -3.975 closest distance to " ND2 ASN A  45 " =    0.945
peak=   -3.975 closest distance to " CD  GLN A  88 " =    0.813
peak=   -3.963 closest distance to " OE1 GLN A  88 " =    0.980
peak=   -3.950 closest distance to " O   HOH Z 266 " =    4.663
peak=   -3.946 closest distance to " O   HOH Z  52 " =    1.278
peak=   -3.919 closest distance to " CG  GLN A 223 " =    1.777
peak=   -3.903 closest distance to " CD1 LEU A 228 " =    2.464
peak=   -3.886 closest distance to " CE2 TYR A  30 " =    2.848
peak=   -3.884 closest distance to " O   HOH Z 231 " =    1.801
peak=   -3.873 closest distance to " CB  ALA A  43 " =    2.479
peak=   -3.865 closest distance to " C   ASN A 285 " =    2.552
peak=   -3.857 closest distance to " O   HOH Z 407 " =    3.440
peak=   -3.844 closest distance to " O   HOH Z 231 " =    1.145
peak=   -3.820 closest distance to " O   HOH Z 372 " =    2.458
peak=   -3.819 closest distance to " NH2AARG A 275 " =    5.661
peak=   -3.795 closest distance to " O   GLY A 211 " =    1.436
peak=   -3.781 closest distance to " O   HOH Z  43 " =    1.499
peak=   -3.765 closest distance to " O   HOH Z 389 " =    1.956
peak=   -3.764 closest distance to " CB  TRP A  85 " =    2.416
peak=   -3.761 closest distance to " CD  ARG A 156 " =    1.889
peak=   -3.756 closest distance to " CA  ASP A  27 " =    2.493
peak=   -3.754 closest distance to " O   HOH Z 388 " =    1.949
peak=   -3.746 closest distance to " CB  PHE A 283 " =    2.768
peak=   -3.745 closest distance to " O   HOH Z 184 " =    1.801
peak=   -3.744 closest distance to " CG  ASP A 231 " =    0.746
peak=   -3.736 closest distance to " CD1 PHE A  59 " =    1.810
peak=   -3.730 closest distance to " O   HOH Z 377 " =    0.806
peak=   -3.729 closest distance to " O   HOH Z 353 " =    2.253
peak=   -3.719 closest distance to " C   LEU A 222 " =    0.749
peak=   -3.698 closest distance to " CA  GLY A  98 " =    2.025
peak=   -3.692 closest distance to " O   HOH Z 185 " =    2.300
peak=   -3.689 closest distance to " O   VAL A  67 " =    2.694
peak=   -3.679 closest distance to " CE  MET A  93 " =    1.157
peak=   -3.661 closest distance to " CB  ASN A  39 " =    2.094
peak=   -3.661 closest distance to " O   HOH Z 351 " =    1.416
peak=   -3.659 closest distance to " CB  CYS A 254 " =    2.193
peak=   -3.651 closest distance to " SG  CYS A 254 " =    3.196
peak=   -3.622 closest distance to " CB  PRO A  54 " =    2.504
peak=   -3.622 closest distance to " O   HOH Z 275 " =    1.603
peak=   -3.611 closest distance to " O   HOH Z 435 " =    2.748
peak=   -3.608 closest distance to " N   THR A 157 " =    1.574
peak=   -3.604 closest distance to " CD  ARG A 195 " =    5.133
peak=   -3.603 closest distance to " O   HOH Z 222 " =    1.091
peak=   -3.590 closest distance to " C   ASN A 187 " =    1.834
peak=   -3.575 closest distance to " OD1 ASP A 191 " =    1.711
peak=   -3.559 closest distance to " O   PRO A 163 " =    1.923
peak=   -3.555 closest distance to " O   ALA A 161 " =    1.437
peak=   -3.537 closest distance to " OD1 ASN A 148 " =    1.642
peak=   -3.536 closest distance to " OG  SER A  97 " =    2.183
peak=   -3.534 closest distance to " CG  GLU A 152 " =    0.789
peak=   -3.533 closest distance to " O   HOH Z 298 " =    1.233
peak=   -3.533 closest distance to " N   SER A 212 " =    1.808
peak=   -3.533 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.500 closest distance to " CG1 VAL A 250 " =    2.593
peak=   -3.491 closest distance to " CD2 TYR A 293 " =    2.093
peak=   -3.478 closest distance to " O   ILE A 109 " =    2.588
peak=   -3.473 closest distance to " OG BSER A 134 " =    1.212
peak=   -3.468 closest distance to " CA  GLY A 241 " =    2.327
peak=   -3.446 closest distance to " CZ BARG A 275 " =    1.861
peak=   -3.444 closest distance to " CA  GLY A 241 " =    3.034
peak=   -3.440 closest distance to " CD1 ILE A 239 " =    1.990
peak=   -3.438 closest distance to " CG  GLU A  53 " =    1.294
peak=   -3.434 closest distance to " O   GLY A 196 " =    1.192
peak=   -3.433 closest distance to " CE3 TRP A 150 " =    1.844
peak=   -3.433 closest distance to " O   HOH Z  98 " =    2.189
peak=   -3.432 closest distance to " O   SER A  62 " =    2.128
peak=   -3.431 closest distance to " OXT GLY A 302 " =    2.817
peak=   -3.429 closest distance to " O   HOH Z 118 " =    2.822
peak=   -3.427 closest distance to " O   HOH Z  38 " =    1.469
peak=   -3.422 closest distance to " CG1 VAL A 112 " =    2.815
peak=   -3.420 closest distance to " CA  GLY A 203 " =    2.254
peak=   -3.417 closest distance to " O   HOH Z  10 " =    1.538
peak=   -3.411 closest distance to " OG BSER A 134 " =    1.671
peak=   -3.407 closest distance to " C   LEU A 143 " =    1.460
peak=   -3.385 closest distance to " O   HOH Z 426 " =    1.690
peak=   -3.382 closest distance to " CD2 LEU A 143 " =    2.589
peak=   -3.372 closest distance to " O   HOH Z  71 " =    1.100
peak=   -3.365 closest distance to " NE2 GLN A  88 " =    0.950
peak=   -3.362 closest distance to " OG  SER A   3 " =    1.747
peak=   -3.357 closest distance to " O   TYR A 247 " =    2.839
peak=   -3.353 closest distance to " O   HOH Z 111 " =    2.289
peak=   -3.348 closest distance to " CG  PRO A 163 " =    2.329
peak=   -3.345 closest distance to " O   VAL A 189 " =    2.471
peak=   -3.341 closest distance to " C   HIS A 108 " =    1.069
peak=   -3.335 closest distance to " O   HOH Z 266 " =    5.147
peak=   -3.328 closest distance to " O   HOH Z 417 " =    2.610
peak=   -3.326 closest distance to " CE  MET A 105 " =    2.199
peak=   -3.325 closest distance to " O   HOH Z 337 " =    1.483
peak=   -3.321 closest distance to " O   HOH Z 103 " =    1.898
peak=   -3.320 closest distance to " CG  ARG A 269 " =    2.583
peak=   -3.318 closest distance to " O   HOH Z 128 " =    2.567
peak=   -3.310 closest distance to " O   HOH Z 241 " =    1.149
peak=   -3.308 closest distance to " CD1 TRP A 179 " =    0.834
peak=   -3.306 closest distance to " ND2 ASN A 249 " =    2.012
peak=   -3.301 closest distance to " CG1 VAL A 197 " =    2.310
peak=   -3.301 closest distance to " O   HOH Z 211 " =    1.570
peak=   -3.299 closest distance to " CG  LEU A  83 " =    1.924
peak=   -3.298 closest distance to " CB  PHE A 192 " =    1.958
peak=   -3.298 closest distance to " CD  LYS A 289 " =    2.520
peak=   -3.291 closest distance to " O   HOH Z  13 " =    1.235
peak=   -3.286 closest distance to " SG ACYS A 201 " =    2.121
peak=   -3.286 closest distance to " CB  PRO A 163 " =    2.630
peak=   -3.282 closest distance to " CB  ALA A   9 " =    2.592
peak=   -3.277 closest distance to " O   HOH Z 313 " =    2.018
peak=   -3.276 closest distance to " O   HOH Z 198 " =    1.402
peak=   -3.275 closest distance to " N   GLN A  58 " =    1.848
peak=   -3.267 closest distance to " CD1 LEU A   5 " =    2.549
peak=   -3.254 closest distance to " O   ASP A 231 " =    2.587
peak=   -3.252 closest distance to " CD2 PHE A  59 " =    2.573
peak=   -3.248 closest distance to " CG2 VAL A 232 " =    2.119
peak=   -3.245 closest distance to " O   HOH Z 243 " =    2.059
peak=   -3.240 closest distance to " O   VAL A 125 " =    2.238
peak=   -3.231 closest distance to " CG  TRP A 266 " =    1.717
peak=   -3.229 closest distance to " CB  LEU A 167 " =    2.215
peak=   -3.227 closest distance to " N   THR A 264 " =    1.095
peak=   -3.226 closest distance to " O   HOH Z 281 " =    2.708
peak=   -3.226 closest distance to " CD1 ILE A 199 " =    2.683
peak=   -3.222 closest distance to " O   HOH Z  76 " =    1.630
peak=   -3.218 closest distance to " CD  ARG A 139 " =    1.717
peak=   -3.212 closest distance to " O   GLY A  80 " =    2.406
peak=   -3.210 closest distance to " O   ALA A 180 " =    1.308
peak=   -3.204 closest distance to " O   ASP A 231 " =    2.540
peak=   -3.204 closest distance to " O   HOH Z 128 " =    4.027
peak=   -3.203 closest distance to " O   HOH Z 298 " =    2.646
peak=   -3.201 closest distance to " N   ALA A 226 " =    2.129
peak=   -3.197 closest distance to " NH2 ARG A  79 " =    1.824
peak=   -3.195 closest distance to " O   HOH Z 166 " =    1.364
peak=   -3.195 closest distance to " CD2 TRP A 274 " =    2.457
peak=   -3.191 closest distance to " O   HOH Z 394 " =    1.474
peak=   -3.189 closest distance to " O   HOH Z  11 " =    1.942
peak=   -3.179 closest distance to " CE1 TYR A 169 " =    2.452
peak=   -3.178 closest distance to " O   HOH Z 423 " =    1.065
peak=   -3.177 closest distance to " O   HOH Z 168 " =    1.527
peak=   -3.175 closest distance to " CG1 VAL A 125 " =    1.941
peak=   -3.175 closest distance to " O   HOH Z 176 " =    0.715
peak=   -3.173 closest distance to " CA  ARG A 139 " =    0.994
peak=   -3.171 closest distance to " CD1 LEU A 297 " =    2.619
peak=   -3.167 closest distance to " OXT GLY A 302 " =    3.320
peak=   -3.154 closest distance to " CD1 LEU A 101 " =    2.509
peak=   -3.148 closest distance to " O   HOH Z 114 " =    0.968
peak=   -3.148 closest distance to " OE1 GLN A  77 " =    2.223
peak=   -3.147 closest distance to " O   HOH Z 252 " =    4.272
peak=   -3.145 closest distance to " CD  ARG A 159 " =    1.279
peak=   -3.143 closest distance to " CB  ALA A 291 " =    2.277
peak=   -3.139 closest distance to " O   TYR A  30 " =    2.864
peak=   -3.138 closest distance to " CB  ASP A 286 " =    1.991
peak=   -3.135 closest distance to " O   HOH Z  60 " =    2.278
peak=   -3.134 closest distance to " CB  TYR A  15 " =    2.165
peak=   -3.134 closest distance to " ND2 ASN A 215 " =    2.243
peak=   -3.131 closest distance to " O   HOH Z 402 " =    1.483
peak=   -3.130 closest distance to " NH1 ARG A 195 " =    2.620
peak=   -3.127 closest distance to " O   HOH Z 317 " =    2.496
peak=   -3.120 closest distance to " O   HOH Z  90 " =    1.526
peak=   -3.118 closest distance to " O   HOH Z 309 " =    2.321
peak=   -3.114 closest distance to " O   HOH Z 210 " =    0.788
peak=   -3.110 closest distance to " O   HOH Z 390 " =    2.277
peak=   -3.104 closest distance to " O   HOH Z 177 " =    1.616
peak=   -3.097 closest distance to " O   HOH Z  93 " =    1.087
peak=   -3.084 closest distance to " CG2 VAL A 189 " =    2.024
peak=   -3.084 closest distance to " O   PRO A 243 " =    1.994
peak=   -3.074 closest distance to " O   HOH Z 166 " =    1.862
peak=   -3.071 closest distance to " O   HOH Z 417 " =    2.758
peak=   -3.068 closest distance to " CG2 ILE A  20 " =    2.817
peak=   -3.066 closest distance to " CZ  ARG A  66 " =    0.790
peak=   -3.063 closest distance to " OD2 ASP A 171 " =    1.909
peak=   -3.062 closest distance to " O   SER A 271 " =    2.336
peak=   -3.060 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.053 closest distance to " C   GLN A 240 " =    2.196
peak=   -3.046 closest distance to " O   ASN A 249 " =    1.576
peak=   -3.043 closest distance to " O   HOH Z  73 " =    2.173
peak=   -3.037 closest distance to " O   SER A  22 " =    2.370

================= 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    :  0.4065 0.4059   6.197378e+00   6.199843e+00
   1_bss:  0.3954 0.3953   6.186059e+00   6.184904e+00
   1_xyz:  0.2403 0.2744   5.784241e+00   5.892374e+00
   1_adp:  0.2222 0.2800   5.742632e+00   5.914644e+00
   1_occ:  0.2217 0.2799   5.740936e+00   5.913345e+00
   2_bss:  0.2186 0.2775   5.734110e+00   5.905989e+00
   2_xyz:  0.1669 0.2149   5.489562e+00   5.689915e+00
   2_adp:  0.1551 0.2033   5.431468e+00   5.638245e+00
   2_occ:  0.1549 0.2033   5.430950e+00   5.638046e+00
   3_bss:  0.1549 0.2025   5.428919e+00   5.635489e+00
   3_xyz:  0.1314 0.1757   5.273622e+00   5.498246e+00
   3_adp:  0.1251 0.1689   5.233451e+00   5.465520e+00
   3_occ:  0.1250 0.1687   5.233018e+00   5.465250e+00
   4_bss:  0.1252 0.1690   5.233250e+00   5.465578e+00
   4_xyz:  0.1146 0.1619   5.169200e+00   5.419129e+00
   4_adp:  0.1135 0.1599   5.159325e+00   5.407657e+00
   4_occ:  0.1134 0.1597   5.158892e+00   5.407421e+00
   5_bss:  0.1133 0.1597   5.158904e+00   5.407393e+00
   5_xyz:  0.1152 0.1610   5.172804e+00   5.415388e+00
   5_adp:  0.1164 0.1603   5.175583e+00   5.411701e+00
   5_occ:  0.1164 0.1601   5.175141e+00   5.411452e+00
   5_bss:  0.1164 0.1601   5.175118e+00   5.411392e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   2.976  -2.593   0.623  -0.000   0.000   0.000
   1_xyz:  0.300  20.000   2.976  -2.593   0.623  -0.000   0.000   0.000
   1_adp:  0.300  20.000   2.976  -2.593   0.623  -0.000   0.000   0.000
   1_occ:  0.300  20.000   2.976  -2.593   0.623  -0.000   0.000   0.000
   2_bss:  0.337  53.547  -0.567  -3.097  -1.385  -0.000  -0.000  -0.000
   2_xyz:  0.337  53.547  -0.567  -3.097  -1.385  -0.000  -0.000  -0.000
   2_adp:  0.337  53.547  -0.567  -3.097  -1.385  -0.000  -0.000  -0.000
   2_occ:  0.337  53.547  -0.567  -3.097  -1.385  -0.000  -0.000  -0.000
   3_bss:  0.331  53.547  -1.386  -2.726  -1.636  -0.000  -0.000  -0.000
   3_xyz:  0.331  53.547  -1.386  -2.726  -1.636  -0.000  -0.000  -0.000
   3_adp:  0.331  53.547  -1.386  -2.726  -1.636  -0.000  -0.000  -0.000
   3_occ:  0.331  53.547  -1.386  -2.726  -1.636  -0.000  -0.000  -0.000
   4_bss:  0.329  55.017  -1.927  -2.833  -1.910  -0.000  -0.000  -0.000
   4_xyz:  0.329  55.017  -1.927  -2.833  -1.910  -0.000  -0.000  -0.000
   4_adp:  0.329  55.017  -1.927  -2.833  -1.910  -0.000  -0.000  -0.000
   4_occ:  0.329  55.017  -1.927  -2.833  -1.910  -0.000  -0.000  -0.000
   5_bss:  0.329  55.017  -1.920  -2.643  -1.816  -0.000  -0.000  -0.000
   5_xyz:  0.329  55.017  -1.920  -2.643  -1.816  -0.000  -0.000  -0.000
   5_adp:  0.329  55.017  -1.920  -2.643  -1.816  -0.000  -0.000  -0.000
   5_occ:  0.329  55.017  -1.920  -2.643  -1.816  -0.000  -0.000  -0.000
   5_bss:  0.329  54.947  -1.959  -2.593  -1.781  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.193 0.5689  0.7466    50121.407
   1_bss:  44.982 0.5822  0.7753    46852.568
   1_xyz:  27.524 0.7859  0.9849    19991.160
   1_adp:  28.618 0.7731  0.9755    20994.226
   1_occ:  28.593 0.7732  0.9753    20914.177
   2_bss:  28.213 0.7773  0.9144    20497.900
   2_xyz:  21.209 0.8497  0.9673    12122.449
   2_adp:  19.577 0.8664  0.9742    10932.085
   2_occ:  19.570 0.8665  0.9741    10924.847
   3_bss:  19.486 0.8671  0.9656    10801.705
   3_xyz:  16.213 0.8964  0.9824     7926.244
   3_adp:  15.433 0.9033  0.9825     7387.609
   3_occ:  15.417 0.9035  0.9824     7373.139
   4_bss:  15.414 0.9035  0.9719     7373.264
   4_xyz:  14.528 0.9106  0.9750     6689.850
   4_adp:  14.250 0.9131  0.9731     6560.610
   4_occ:  14.239 0.9132  0.9731     6551.160
   5_bss:  14.241 0.9132  0.9764     6549.358
   5_xyz:  14.364 0.9123  0.9751     6640.713
   5_adp:  14.251 0.9134  0.9744     6611.210
   5_occ:  14.241 0.9134  0.9743     6601.204
   5_bss:  14.239 0.9135  0.9725     6599.409
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6649e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6649e-01
   1_xyz:   1.293  0.010  0.086 15.561  0.005  4.114   9.6064e-02
   1_adp:   1.293  0.010  0.086 15.561  0.005  4.114   9.6064e-02
   1_occ:   1.293  0.010  0.086 15.561  0.005  4.114   9.6064e-02
   2_bss:   1.293  0.010  0.086 15.561  0.005  4.114   9.6064e-02
   2_xyz:   0.988  0.006  0.069 13.798  0.004  4.127   5.4033e-02
   2_adp:   0.988  0.006  0.069 13.798  0.004  4.127   5.4033e-02
   2_occ:   0.988  0.006  0.069 13.798  0.004  4.127   5.4033e-02
   3_bss:   0.988  0.006  0.069 13.798  0.004  4.127   5.4033e-02
   3_xyz:   0.929  0.006  0.067 14.153  0.003  4.122   5.1362e-02
   3_adp:   0.929  0.006  0.067 14.153  0.003  4.122   5.1362e-02
   3_occ:   0.929  0.006  0.067 14.153  0.003  4.122   5.1362e-02
   4_bss:   0.929  0.006  0.067 14.153  0.003  4.122   5.1362e-02
   4_xyz:   1.057  0.008  0.075 14.450  0.004  4.128   6.5263e-02
   4_adp:   1.057  0.008  0.075 14.450  0.004  4.128   6.5263e-02
   4_occ:   1.057  0.008  0.075 14.450  0.004  4.128   6.5263e-02
   5_bss:   1.057  0.008  0.075 14.450  0.004  4.128   6.5263e-02
   5_xyz:   0.919  0.006  0.067 14.114  0.003  4.127   5.0746e-02
   5_adp:   0.919  0.006  0.067 14.114  0.003  4.127   5.0746e-02
   5_occ:   0.919  0.006  0.067 14.114  0.003  4.127   5.0746e-02
   5_bss:   0.919  0.006  0.067 14.114  0.003  4.127   5.0746e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.690   2.4101e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.690   2.4101e-01
   1_xyz:  10.336  0.057  0.336 89.172  0.036  2.213   8.4138e-02
   1_adp:  10.336  0.057  0.336 89.172  0.036  2.213   8.4138e-02
   1_occ:  10.336  0.057  0.336 89.172  0.036  2.213   8.4138e-02
   2_bss:  10.336  0.057  0.336 89.172  0.036  2.213   8.4138e-02
   2_xyz:   7.708  0.027  0.209 83.081  0.039  2.355   6.6720e-02
   2_adp:   7.708  0.027  0.209 83.081  0.039  2.355   6.6720e-02
   2_occ:   7.708  0.027  0.209 83.081  0.039  2.355   6.6720e-02
   3_bss:   7.708  0.027  0.209 83.081  0.039  2.355   6.6720e-02
   3_xyz:   8.805  0.051  0.230 81.039  0.027  2.331   3.6385e-02
   3_adp:   8.805  0.051  0.230 81.039  0.027  2.331   3.6385e-02
   3_occ:   8.805  0.051  0.230 81.039  0.027  2.331   3.6385e-02
   4_bss:   8.805  0.051  0.230 81.039  0.027  2.331   3.6385e-02
   4_xyz:   8.163  0.042  0.230 84.338  0.035  2.289   7.4395e-02
   4_adp:   8.163  0.042  0.230 84.338  0.035  2.289   7.4395e-02
   4_occ:   8.163  0.042  0.230 84.338  0.035  2.289   7.4395e-02
   5_bss:   8.163  0.042  0.230 84.338  0.035  2.289   7.4395e-02
   5_xyz:   8.142  0.043  0.205 83.166  0.030  2.386   4.1229e-02
   5_adp:   8.142  0.043  0.205 83.166  0.030  2.386   4.1229e-02
   5_occ:   8.142  0.043  0.205 83.166  0.030  2.386   4.1229e-02
   5_bss:   8.142  0.043  0.205 83.166  0.030  2.386   4.1229e-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:  67.64   0.00  17.03  67.64   0.00  13.09  62.91   3.70  38.49
   1_occ:  67.64   0.00  17.03  67.64   0.00  13.09  62.91   3.70  38.49
   2_bss:  67.64   0.00  17.03  67.64   0.00  13.09  62.91   3.70  38.49
   2_xyz:  67.64   0.00  17.03  67.64   0.00  13.09  62.91   3.70  38.49
   2_adp:  65.30   1.71  17.04  59.40   1.71  13.00  65.30   5.36  39.01
   2_occ:  65.30   1.71  17.04  59.40   1.71  13.00  65.30   5.36  39.01
   3_bss:  65.30   1.71  17.04  59.40   1.71  13.00  65.30   5.36  39.01
   3_xyz:  65.30   1.71  17.04  59.40   1.71  13.00  65.30   5.36  39.01
   3_adp:  85.70   0.32  17.62  83.79   0.32  13.16  85.70   6.10  41.91
   3_occ:  85.70   0.32  17.62  83.79   0.32  13.16  85.70   6.10  41.91
   4_bss:  85.70   0.32  17.62  83.79   0.32  13.16  85.70   6.10  41.91
   4_xyz:  85.70   0.32  17.62  83.79   0.32  13.16  85.70   6.10  41.91
   4_adp:  88.59   0.91  17.29  88.59   0.91  13.05  85.05   6.20  40.38
   4_occ:  88.59   0.91  17.29  88.59   0.91  13.05  85.05   6.20  40.38
   5_bss:  88.59   0.91  17.29  88.59   0.91  13.05  85.05   6.20  40.38
   5_xyz:  88.59   0.91  17.29  88.59   0.91  13.05  85.05   6.20  40.38
   5_adp:  86.97   1.96  16.88  86.97   1.96  12.92  82.05   6.31  38.47
   5_occ:  86.97   1.96  16.88  86.97   1.96  12.92  82.05   6.31  38.47
   5_bss:  86.90   1.89  16.81  86.90   1.89  12.85  81.98   6.24  38.40
------------------------------------------------------------------------
 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:    1.658    0.019    0.398
   1_adp:    1.658    0.019    0.398
   1_occ:    1.658    0.019    0.398
   2_bss:    1.658    0.019    0.398
   2_xyz:    1.142    0.037    0.464
   2_adp:    1.142    0.037    0.464
   2_occ:    1.142    0.037    0.464
   3_bss:    1.142    0.037    0.464
   3_xyz:    1.167    0.054    0.535
   3_adp:    1.167    0.054    0.535
   3_occ:    1.167    0.054    0.535
   4_bss:    1.167    0.054    0.535
   4_xyz:    1.188    0.042    0.559
   4_adp:    1.188    0.042    0.559
   4_occ:    1.188    0.042    0.559
   5_bss:    1.188    0.042    0.559
   5_xyz:    1.173    0.065    0.565
   5_adp:    1.173    0.065    0.565
   5_occ:    1.173    0.065    0.565
   5_bss:    1.173    0.065    0.565
------------------------------------------------------------------------

CPU time actual refinement: 342.01


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/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_1256/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1256/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.85 
  Macro-tasks:
    bulk solvent and scale       = 42.53  
    individual site refinement   = 138.04 
    weights calculation          = 29.79  
    collect and process          = 6.50   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 216.94 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 110.38 
    alpha_beta                      = 8.04   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 118.20 
    fmodel                         = 7.07   
    r_factors                      = 0.24   
    phase_errors                   = 10.98  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 258.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.845 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    645 calls, 109.98 s
gradients_fft:          590 calls, 104.90 s

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

# Date 2008-01-16 Time 06:48:31 PST -0800 (1200494911.17 s)
Start R-work = 0.4065, R-free = 0.4059 (no bulk solvent and anisotropic scale)
Final R-work = 0.1412, R-free = 0.1824 (no bulk solvent and anisotropic scale)

Start R-work = 0.3954, R-free = 0.3953
Final R-work = 0.1164, R-free = 0.1601