# Date 2008-01-16 Time 06:03:39 PST -0800 (1200492219.42 s)
#phil __OFF__

Command line arguments: "../987.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32351
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 987

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 45.9914, 87.6859, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 1.96398
Completeness in resolution range: 0.924358
Completeness with d_max=infinity: 0.921749

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2189
                             d_min =   1.9640

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2189 1.96398
Completeness in resolution range: 0.924358
Completeness with d_max=infinity: 0.921749

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2193 -  4.2043 [2219/2246]  1998   221  10.0%
  bin  2:  4.2043 -  3.3488 [2148/2168]  1933   215  10.0%
  bin  3:  3.3488 -  2.9289 [2104/2123]  1894   210  10.0%
  bin  4:  2.9289 -  2.6627 [2081/2111]  1865   216  10.4%
  bin  5:  2.6627 -  2.4727 [2089/2108]  1889   200   9.6%
  bin  6:  2.4727 -  2.3274 [2073/2098]  1865   208  10.0%
  bin  7:  2.3274 -  2.2112 [2046/2074]  1835   211  10.3%
  bin  8:  2.2112 -  2.1152 [2054/2090]  1846   208  10.1%
  bin  9:  2.1152 -  2.0340 [2031/2073]  1838   193   9.5%
  bin 10:  2.0340 -  1.9640 [ 744/2101]   667    77  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/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: 0.13 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:
        1.81 -     2.42: 33
        2.42 -     3.04: 2199
        3.04 -     3.66: 4685
        3.66 -     4.28: 8988
        4.28 -     4.90: 12282
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.922 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28182 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_987/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/model_refine_001.geo

CPU time processing inputs: 8.97


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 45.9914 87.68585 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: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4582   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.269507                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.6902 0.99   1440  160 0.3681 0.3465      6.5567      6.5035|
|  2:  4.6902 -  3.7409 0.99   1389  154 0.3877 0.3789      6.7947      6.7357|
|  3:  3.7409 -  3.2734 0.99   1365  153 0.4157 0.3906       6.626      6.6331|
|  4:  3.2734 -  2.9766 0.99   1353  153 0.4520 0.4934      6.5096       6.524|
|  5:  2.9766 -  2.7646 0.99   1349  148 0.4869 0.4716      6.3472      6.3671|
|  6:  2.7646 -  2.6024 0.99   1341  146 0.4812 0.5051      6.2447      6.2051|
|  7:  2.6024 -  2.4727 0.99   1342  148 0.4970 0.4876      6.2214      6.1659|
|  8:  2.4727 -  2.3655 0.98   1316  151 0.5170 0.5375      6.1705      6.1664|
|  9:  2.3655 -  2.2747 0.98   1335  145 0.5006 0.5233      6.1112      6.1695|
| 10:  2.2747 -  2.1964 1.00   1318  157 0.5268 0.5158      6.0648      6.0536|
| 11:  2.1964 -  2.1280 0.98   1316  141 0.5060 0.5472      6.0235      6.0564|
| 12:  2.1280 -  2.0673 0.98   1299  141 0.5172 0.4948      5.9294       5.927|
| 13:  2.0673 -  2.0130 0.88   1188  129 0.5108 0.4944      5.8731      5.8041|
| 14:  2.0130 -  1.9640 0.21    279   33 0.5149 0.6048       5.863       5.913|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.6902  1440   160  0.75  30.23   0.82     0.79      59029.38|
|  2:  4.6902 -  3.7409  1389   154  0.74  32.04   0.91     0.84      94142.41|
|  3:  3.7409 -  3.2734  1365   153  0.61  43.42   0.93     0.79     107268.35|
|  4:  3.2734 -  2.9766  1353   153  0.50  51.68   0.89     0.69     102958.54|
|  5:  2.9766 -  2.7646  1349   148  0.42  57.86   0.89     0.61      81899.32|
|  6:  2.7646 -  2.6024  1341   146  0.40  60.02   0.90     0.57      70356.91|
|  7:  2.6024 -  2.4727  1342   148  0.38  61.55   0.91     0.53      63459.19|
|  8:  2.4727 -  2.3655  1316   151  0.35  63.38   0.89     0.51      58045.11|
|  9:  2.3655 -  2.2747  1335   145  0.36  62.95   0.93     0.52      53378.63|
| 10:  2.2747 -  2.1964  1318   157  0.35  63.67   0.91     0.53      48093.32|
| 11:  2.1964 -  2.1280  1316   141  0.32  65.85   0.95     0.50      48353.51|
| 12:  2.1280 -  2.0673  1299   141  0.29  68.39   0.91     0.46      44597.46|
| 13:  2.0673 -  2.0130  1188   129  0.28  69.27   0.94     0.47      39220.82|
| 14:  2.0130 -  1.9640   279    33  0.39  60.93   0.97     0.54      29216.19|
|alpha:            min =        0.46 max =            0.84 mean =         0.60|
|beta:             min =    29216.19 max =       107268.35 mean =     66864.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.84|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.16|
|-----------------------------------------------------------------------------|

============================== 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 = 13.669881             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.670931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.660   (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 |  1.806 -  2.115:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      200 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1999 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1863 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2822 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4638 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4350 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5601 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6681 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.303 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    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: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4573   r_free= 0.4582   ksol= 0.00   Bsol= 0.00   scale= 0.894    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.269507                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4495   r_free= 0.4542   ksol= 0.30   Bsol= 50.00   scale= 0.932   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,1.65,1.10,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.264199                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.333673             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.870   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.252798              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.279   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4495      final r-factor (work) = 0.3168          |
| start r-factor (free) = 0.4542      final r-factor (free) = 0.3585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6380 = 11.33 * 0.50 * 6.2586 + 1.00 * 0.1715                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.8567 = 11.33 * 0.50 * 6.1258 + 1.00 * 0.1426                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3168      final r-factor (work) = 0.2858          |
| start r-factor (free) = 0.3585      final r-factor (free) = 0.3711          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6806 = 1.25 * 1.00 * 6.1258 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4869 = 1.25 * 1.00 * 5.9595 + 1.00 * 0.0209                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.98  18.94    None  None   None       |
|    all(noH): 2823   0      0.00    103.98  18.94    None  None   None       |
|    Sol.    : 438    0      0.00    103.98  42.45    None  None   None       |
|    Mac.    : 2385   0      0.00    72.17   14.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.398:  997   |   5:    51.989 -  62.386:   87        |
|      1:    10.398 -  20.795:  926   |   6:    62.386 -  72.784:   46        |
|      2:    20.795 -  31.193:  413   |   7:    72.784 -  83.182:   18        |
|      3:    31.193 -  41.591:  207   |   8:    83.182 -  93.579:    7        |
|      4:    41.591 -  51.989:  120   |   9:    93.579 - 103.977:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2858 r_free = 0.3711             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2852 r_free = 0.3714             target_work(ml) = 5.975         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2852   r_free= 0.3714   ksol= 0.30   Bsol= 50.00   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,1.65,1.10,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.974566                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2843   r_free= 0.3696   ksol= 0.34   Bsol= 76.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.48,0.28,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.974487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.577864              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.096   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.417748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.342  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2843      final r-factor (work) = 0.2199          |
| start r-factor (free) = 0.3696      final r-factor (free) = 0.2879          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7462 = 6.58 * 0.50 * 5.9605 + 1.00 * 0.1425                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4339 = 6.58 * 0.50 * 5.8869 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2199      final r-factor (work) = 0.2038          |
| start r-factor (free) = 0.2879      final r-factor (free) = 0.2666          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4792 = 0.42 * 1.00 * 5.8869 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3986 = 0.42 * 1.00 * 5.7142 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.92   18.19    None  None   None       |
|    all(noH): 2823   0      0.00    99.92   18.19    None  None   None       |
|    Sol.    : 438    0      3.52    99.92   42.66    None  None   None       |
|    Mac.    : 2385   0      0.00    86.93   13.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.993:  976   |   5:    49.962 -  59.955:   82        |
|      1:     9.993 -  19.985: 1071   |   6:    59.955 -  69.947:   54        |
|      2:    19.985 -  29.977:  306   |   7:    69.947 -  79.940:   27        |
|      3:    29.977 -  39.970:  160   |   8:    79.940 -  89.932:    3        |
|      4:    39.970 -  49.962:  143   |   9:    89.932 -  99.925:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2038 r_free = 0.2666             target_work(ml) = 5.681         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2037 r_free = 0.2663             target_work(ml) = 5.680         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2037   r_free= 0.2663   ksol= 0.34   Bsol= 76.39   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.48,0.28,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.680340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2037   r_free= 0.2660   ksol= 0.34   Bsol= 72.96   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-1.47,-0.11,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.678985                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.271262              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.461  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.871  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2037      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2660      final r-factor (free) = 0.2058          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1330 = 5.27 * 0.50 * 5.7143 + 1.00 * 0.0722                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7360 = 5.27 * 0.50 * 5.5642 + 1.00 * 0.0708                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.2058      final r-factor (free) = 0.1928          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4873 = 0.27 * 1.00 * 5.5642 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4373 = 0.27 * 1.00 * 5.3837 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.00    94.62   17.65    None  None   None       |
|    all(noH): 2823   0      1.00    94.62   17.65    None  None   None       |
|    Sol.    : 438    0      6.12    94.62   42.88    None  None   None       |
|    Mac.    : 2385   0      1.00    87.16   13.02    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:     1.002 -  10.363: 1097   |   5:    47.810 -  57.172:  106        |
|      1:    10.363 -  19.725: 1035   |   6:    57.172 -  66.533:   69        |
|      2:    19.725 -  29.087:  236   |   7:    66.533 -  75.895:   28        |
|      3:    29.087 -  38.448:  134   |   8:    75.895 -  85.257:    7        |
|      4:    38.448 -  47.810:  109   |   9:    85.257 -  94.618:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1410 r_free = 0.1928             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1409 r_free = 0.1924             target_work(ml) = 5.346         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1409   r_free= 0.1924   ksol= 0.34   Bsol= 72.96   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.64,-1.47,-0.11,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.345654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1918   ksol= 0.32   Bsol= 64.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.48,-0.71,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.343924                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.239645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.727  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.376015              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.170  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1281          |
| start r-factor (free) = 0.1918      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1043 = 2.24 * 0.50 * 5.3878 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9965 = 2.24 * 0.50 * 5.3049 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1281      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1746      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0039 = 0.38 * 1.00 * 5.3049 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9803 = 0.38 * 1.00 * 5.2408 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.35    92.89   17.56    None  None   None       |
|    all(noH): 2823   0      0.35    92.89   17.56    None  None   None       |
|    Sol.    : 438    0      2.04    92.89   42.93    None  None   None       |
|    Mac.    : 2385   0      0.35    92.31   12.90    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:     0.349 -   9.603:  954   |   5:    46.620 -  55.874:   95        |
|      1:     9.603 -  18.858: 1164   |   6:    55.874 -  65.128:   71        |
|      2:    18.858 -  28.112:  246   |   7:    65.128 -  74.382:   41        |
|      3:    28.112 -  37.366:  131   |   8:    74.382 -  83.636:   16        |
|      4:    37.366 -  46.620:  101   |   9:    83.636 -  92.890:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1721             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1245 r_free = 0.1721             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1721   ksol= 0.32   Bsol= 64.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.48,-0.71,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1721   ksol= 0.32   Bsol= 64.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.48,-0.71,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.233662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.600887              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.923  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.119  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8711 = 2.60 * 0.50 * 5.2407 + 1.00 * 0.0559                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8365 = 2.60 * 0.50 * 5.2064 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1685 = 0.22 * 1.00 * 5.2064 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1630 = 0.22 * 1.00 * 5.1854 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.69    92.73   17.27    None  None   None       |
|    all(noH): 2823   0      0.69    92.73   17.27    None  None   None       |
|    Sol.    : 438    0      3.66    91.12   41.65    None  None   None       |
|    Mac.    : 2385   0      0.69    92.73   12.79    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:     0.692 -   9.895: 1032   |   5:    46.711 -  55.914:  103        |
|      1:     9.895 -  19.099: 1119   |   6:    55.914 -  65.118:   59        |
|      2:    19.099 -  28.303:  233   |   7:    65.118 -  74.322:   36        |
|      3:    28.303 -  37.507:  133   |   8:    74.322 -  83.526:   13        |
|      4:    37.507 -  46.711:   91   |   9:    83.526 -  92.730:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1163 r_free = 0.1631             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1162 r_free = 0.1630             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1162   r_free= 0.1630   ksol= 0.32   Bsol= 64.93   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.48,-0.71,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.179976                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.6902 0.99   1440  160 0.0949 0.1323      5.3669      5.6167|
|  2:  4.6902 -  3.7409 0.99   1389  154 0.0850 0.1150      5.4468      5.6507|
|  3:  3.7409 -  3.2734 0.99   1365  153 0.1120 0.1607      5.5061      5.8159|
|  4:  3.2734 -  2.9766 0.99   1353  153 0.1312 0.1732      5.4907      5.6255|
|  5:  2.9766 -  2.7646 0.99   1349  148 0.1396 0.1833      5.3544      5.6078|
|  6:  2.7646 -  2.6024 0.99   1341  146 0.1326 0.1941      5.2299      5.4736|
|  7:  2.6024 -  2.4727 0.99   1342  148 0.1328 0.1605      5.1975      5.3158|
|  8:  2.4727 -  2.3655 0.98   1316  151 0.1240 0.1789      5.0949      5.3739|
|  9:  2.3655 -  2.2747 0.98   1335  145 0.1238 0.1935      5.0659      5.3524|
| 10:  2.2747 -  2.1964 1.00   1318  157 0.1140 0.1656      4.9456      5.1833|
| 11:  2.1964 -  2.1280 0.98   1316  141 0.1159 0.1813      4.9487      5.3563|
| 12:  2.1280 -  2.0673 0.98   1299  141 0.1198 0.1885      4.8986      5.1459|
| 13:  2.0673 -  2.0130 0.88   1188  129 0.1170 0.1644       4.803      4.9987|
| 14:  2.0130 -  1.9640 0.21    279   33 0.0988 0.1612      4.6773      4.9875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.6902  1440   160  0.94   8.98   0.97     0.94       7037.58|
|  2:  4.6902 -  3.7409  1389   154  0.95   8.14   1.01     1.00       9416.79|
|  3:  3.7409 -  3.2734  1365   153  0.93  12.11   1.03     1.02      11089.47|
|  4:  3.2734 -  2.9766  1353   153  0.91  15.17   1.01     0.98      11073.09|
|  5:  2.9766 -  2.7646  1349   148  0.90  15.89   1.00     0.98       8450.76|
|  6:  2.7646 -  2.6024  1341   146  0.89  16.64   0.98     0.97       7107.57|
|  7:  2.6024 -  2.4727  1342   148  0.91  15.66   1.00     0.97       6416.14|
|  8:  2.4727 -  2.3655  1316   151  0.90  16.32   0.99     0.95       5543.64|
|  9:  2.3655 -  2.2747  1335   145  0.90  16.35   1.00     0.96       5317.92|
| 10:  2.2747 -  2.1964  1318   157  0.90  15.71   1.01     0.98       4340.00|
| 11:  2.1964 -  2.1280  1316   141  0.90  16.25   0.99     0.93       4296.72|
| 12:  2.1280 -  2.0673  1299   141  0.90  16.33   1.00     1.02       4078.71|
| 13:  2.0673 -  2.0130  1188   129  0.89  17.33   0.99     0.97       3522.06|
| 14:  2.0130 -  1.9640   279    33  0.93  13.33   0.99     0.96       2694.46|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2694.46 max =        11089.47 mean =      6742.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.58|
|phase err.(test): min =        0.00 max =           88.57 mean =        14.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1621   ksol= 0.32   Bsol= 59.10   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.66,-0.75,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1621   ksol= 0.32   Bsol= 59.10   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.20,-2.66,-0.75,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176843                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2193 -  4.6902 0.99   1440  160 0.0945 0.1288      5.3412      5.5796|
|  2:  4.6902 -  3.7409 0.99   1389  154 0.0849 0.1111       5.434      5.6314|
|  3:  3.7409 -  3.2734 0.99   1365  153 0.1126 0.1591      5.5028      5.8095|
|  4:  3.2734 -  2.9766 0.99   1353  153 0.1312 0.1740      5.4906      5.6284|
|  5:  2.9766 -  2.7646 0.99   1349  148 0.1397 0.1836      5.3556      5.6088|
|  6:  2.7646 -  2.6024 0.99   1341  146 0.1324 0.1946      5.2307      5.4744|
|  7:  2.6024 -  2.4727 0.99   1342  148 0.1329 0.1607      5.1984      5.3168|
|  8:  2.4727 -  2.3655 0.98   1316  151 0.1240 0.1791      5.0951      5.3736|
|  9:  2.3655 -  2.2747 0.98   1335  145 0.1238 0.1928      5.0654      5.3509|
| 10:  2.2747 -  2.1964 1.00   1318  157 0.1140 0.1661      4.9461      5.1881|
| 11:  2.1964 -  2.1280 0.98   1316  141 0.1157 0.1814      4.9492      5.3565|
| 12:  2.1280 -  2.0673 0.98   1299  141 0.1197 0.1883      4.8993      5.1452|
| 13:  2.0673 -  2.0130 0.88   1188  129 0.1168 0.1639      4.8022      4.9977|
| 14:  2.0130 -  1.9640 0.21    279   33 0.0990 0.1611      4.6758      4.9858|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2193 -  4.6902  1440   160  0.94   8.46   0.97     0.94       6397.02|
|  2:  4.6902 -  3.7409  1389   154  0.95   7.79   1.01     1.00       8851.03|
|  3:  3.7409 -  3.2734  1365   153  0.93  11.92   1.02     1.02      10836.69|
|  4:  3.2734 -  2.9766  1353   153  0.91  15.14   1.01     0.98      11049.52|
|  5:  2.9766 -  2.7646  1349   148  0.90  15.95   1.00     0.98       8481.56|
|  6:  2.7646 -  2.6024  1341   146  0.89  16.66   0.98     0.97       7132.15|
|  7:  2.6024 -  2.4727  1342   148  0.91  15.67   0.99     0.97       6430.03|
|  8:  2.4727 -  2.3655  1316   151  0.90  16.31   0.98     0.95       5540.45|
|  9:  2.3655 -  2.2747  1335   145  0.90  16.33   0.99     0.95       5310.24|
| 10:  2.2747 -  2.1964  1318   157  0.90  15.72   1.00     0.98       4352.76|
| 11:  2.1964 -  2.1280  1316   141  0.90  16.30   0.98     0.93       4316.16|
| 12:  2.1280 -  2.0673  1299   141  0.90  16.36   1.00     1.01       4090.00|
| 13:  2.0673 -  2.0130  1188   129  0.89  17.32   0.98     0.97       3517.81|
| 14:  2.0130 -  1.9640   279    33  0.93  13.26   0.98     0.95       2682.54|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2682.54 max =        11049.52 mean =      6631.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.50|
|phase err.(test): min =        0.00 max =           88.41 mean =        13.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.962)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.67    92.71   17.25    None  None   None       |
|    all(noH): 2823   0      0.67    92.71   17.25    None  None   None       |
|    Sol.    : 438    0      3.63    91.10   41.63    None  None   None       |
|    Mac.    : 2385   0      0.67    92.71   12.77    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:     0.669 -   9.872: 1032   |   5:    46.688 -  55.891:  103        |
|      1:     9.872 -  19.076: 1119   |   6:    55.891 -  65.095:   59        |
|      2:    19.076 -  28.280:  233   |   7:    65.095 -  74.299:   36        |
|      3:    28.280 -  37.484:  133   |   8:    74.299 -  83.503:   13        |
|      4:    37.484 -  46.688:   91   |   9:    83.503 -  92.707:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 341         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 4.735
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 337 from: 341
   mapped sites are within: 0.705 - 4.735

peak=    6.309 closest distance to " NE2 GLN A  11 " =    1.304
peak=    5.554 closest distance to " O   HOH Z   7 " =    1.768
peak=    5.392 closest distance to " CG  PRO A  54 " =    1.423
peak=    5.303 closest distance to " O   HOH Z 222 " =    1.202
peak=    5.294 closest distance to " O   HOH Z 111 " =    2.015
peak=    5.248 closest distance to " O   HOH Z 144 " =    1.921
peak=    5.235 closest distance to " CB  GLN A 223 " =    1.551
peak=    5.139 closest distance to " O   HOH Z 369 " =    2.161
peak=    5.078 closest distance to " O   HOH Z 126 " =    2.030
peak=    5.065 closest distance to " O   HOH Z 417 " =    2.170
peak=    5.061 closest distance to " O   HOH Z  63 " =    1.626
peak=    5.023 closest distance to " O   HOH Z 423 " =    2.130
peak=    4.975 closest distance to " O   HOH Z 232 " =    2.206
peak=    4.854 closest distance to " O   HOH Z 287 " =    2.133
peak=    4.736 closest distance to " O   HOH Z   9 " =    1.838
peak=    4.682 closest distance to " CB  SER A  63 " =    1.303
peak=    4.605 closest distance to " CB  ASN A 148 " =    1.462
peak=    4.404 closest distance to " O   HOH Z 133 " =    2.426
peak=    4.403 closest distance to " O   HOH Z 298 " =    2.168
peak=    4.396 closest distance to " CB  ARG A 190 " =    1.568
peak=    4.374 closest distance to " CG  PRO A 213 " =    1.310
peak=    4.363 closest distance to " O   HOH Z  78 " =    1.594
peak=    4.359 closest distance to " O   HOH Z 183 " =    1.512
peak=    4.355 closest distance to " CB  PRO A  54 " =    1.009
peak=    4.339 closest distance to " O   HOH Z 425 " =    1.491
peak=    4.329 closest distance to " O   HOH Z 427 " =    2.496
peak=    4.327 closest distance to " O   HOH Z 419 " =    2.069
peak=    4.303 closest distance to " ND2 ASN A 187 " =    1.534
peak=    4.301 closest distance to " O   HOH Z 126 " =    1.520
peak=    4.262 closest distance to " O   HOH Z 380 " =    1.839
peak=    4.258 closest distance to " CD  ARG A 159 " =    0.826
peak=    4.232 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.219 closest distance to " CG  TRP A 179 " =    2.126
peak=    4.205 closest distance to " CB  GLN A 183 " =    1.212
peak=    4.169 closest distance to " CG  PRO A 198 " =    1.314
peak=    4.164 closest distance to " O   HOH Z 375 " =    0.932
peak=    4.155 closest distance to " O   HOH Z 316 " =    3.112
peak=    4.143 closest distance to " O   HOH Z  61 " =    1.655
peak=    4.125 closest distance to " O   HOH Z 437 " =    1.771
peak=    4.108 closest distance to " CG  PRO A  90 " =    1.423
peak=    4.081 closest distance to " CB  ASN A 142 " =    0.938
peak=    4.039 closest distance to " O   HOH Z   1 " =    1.850
peak=    4.029 closest distance to " O   HOH Z   2 " =    1.807
peak=    4.025 closest distance to " CA  TYR A  30 " =    1.065
peak=    4.014 closest distance to " CD  ARG A  66 " =    2.084
peak=    3.993 closest distance to " O   HOH Z 225 " =    1.548
peak=    3.987 closest distance to " ND1 HIS A  86 " =    1.701
peak=    3.986 closest distance to " CB  LEU A 228 " =    1.082
peak=    3.961 closest distance to " CG2 THR A 221 " =    0.994
peak=    3.945 closest distance to " O   PRO A 198 " =    1.592
peak=    3.938 closest distance to " CG  PRO A 280 " =    0.855
peak=    3.935 closest distance to " O   HOH Z 193 " =    1.585
peak=    3.922 closest distance to " CB  SER A 216 " =    0.932
peak=    3.922 closest distance to " CZ3 TRP A 266 " =    1.174
peak=    3.916 closest distance to " O   HOH Z  61 " =    1.661
peak=    3.915 closest distance to " CB  SER A   3 " =    1.530
peak=    3.910 closest distance to " O   HOH Z  49 " =    1.077
peak=    3.893 closest distance to " O   HOH Z 128 " =    2.209
peak=    3.881 closest distance to " NZ  LYS A 117 " =    2.859
peak=    3.880 closest distance to " O   HOH Z  88 " =    3.896
peak=    3.863 closest distance to " O   HOH Z 195 " =    1.454
peak=    3.858 closest distance to " CB  SER A 212 " =    1.259
peak=    3.854 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.842 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.838 closest distance to " O   HOH Z 362 " =    1.825
peak=    3.837 closest distance to " O   HOH Z  69 " =    2.215
peak=    3.829 closest distance to " O   HOH Z 394 " =    1.695
peak=    3.823 closest distance to " O   HOH Z 403 " =    1.409
peak=    3.814 closest distance to " CD2 TRP A 179 " =    1.201
peak=    3.802 closest distance to " CB  ASN A 187 " =    1.046
peak=    3.789 closest distance to " CZ  PHE A 218 " =    1.103
peak=    3.780 closest distance to " O   HOH Z  10 " =    1.736
peak=    3.778 closest distance to " CB  GLU A 128 " =    1.000
peak=    3.767 closest distance to " O   HOH Z 414 " =    1.284
peak=    3.767 closest distance to " CB  GLU A  46 " =    0.976
peak=    3.764 closest distance to " CG  LEU A 167 " =    1.281
peak=    3.764 closest distance to " CB  ARG A  79 " =    1.277
peak=    3.760 closest distance to " CB  VAL A 265 " =    1.357
peak=    3.754 closest distance to " N   CYS A 260 " =    0.817
peak=    3.753 closest distance to " O   TYR A 116 " =    1.337
peak=    3.753 closest distance to " O   HOH Z 214 " =    2.196
peak=    3.739 closest distance to " CE  LYS A  76 " =    0.890
peak=    3.731 closest distance to " O   HOH Z 201 " =    1.644
peak=    3.730 closest distance to " O   SER A  87 " =    2.404
peak=    3.719 closest distance to " O   HOH Z 405 " =    1.486
peak=    3.717 closest distance to " O   HOH Z   7 " =    3.517
peak=    3.716 closest distance to " CA  ARG A 195 " =    1.291
peak=    3.713 closest distance to " O   HOH Z 272 " =    1.756
peak=    3.711 closest distance to " O   HOH Z 352 " =    1.694
peak=    3.705 closest distance to " O   HOH Z 145 " =    1.679
peak=    3.701 closest distance to " CA  TYR A 116 " =    1.398
peak=    3.698 closest distance to " O   HOH Z 422 " =    2.746
peak=    3.697 closest distance to " CG2 VAL A 257 " =    0.882
peak=    3.696 closest distance to " O   HOH Z  68 " =    2.020
peak=    3.695 closest distance to " CB  ASP A 124 " =    0.783
peak=    3.686 closest distance to " O   HOH Z  58 " =    1.871
peak=    3.682 closest distance to " CB  TYR A 169 " =    0.736
peak=    3.678 closest distance to " O   HOH Z  44 " =    2.666
peak=    3.675 closest distance to " O   HOH Z   1 " =    1.648
peak=    3.659 closest distance to " O   HOH Z 258 " =    2.150
peak=    3.659 closest distance to " O   HOH Z 128 " =    1.803
peak=    3.656 closest distance to " CA  SER A  87 " =    0.989
peak=    3.650 closest distance to " O   HOH Z  40 " =    2.132
peak=    3.649 closest distance to " O   HOH Z 286 " =    1.991
peak=    3.634 closest distance to " N   SER A  97 " =    0.866
peak=    3.630 closest distance to " CA  ASN A 127 " =    1.088
peak=    3.626 closest distance to " O   HOH Z 145 " =    2.032
peak=    3.622 closest distance to " CA  VAL A 125 " =    1.164
peak=    3.618 closest distance to " O   HOH Z  78 " =    2.037
peak=    3.617 closest distance to " CB  GLU A 277 " =    3.668
peak=    3.616 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.611 closest distance to " O   HOH Z 158 " =    2.708
peak=    3.608 closest distance to " O   HOH Z 116 " =    3.193
peak=    3.607 closest distance to " O   HOH Z 132 " =    2.559
peak=    3.605 closest distance to " CA  THR A 264 " =    0.870
peak=    3.597 closest distance to " O   HOH Z 434 " =    1.412
peak=    3.597 closest distance to " O   HOH Z 250 " =    1.421
peak=    3.596 closest distance to " N   ALA A   1 " =    2.193
peak=    3.582 closest distance to " CB  TRP A 266 " =    1.032
peak=    3.580 closest distance to " CB  VAL A 202 " =    1.589
peak=    3.579 closest distance to " CB  TRP A 150 " =    1.190
peak=    3.578 closest distance to " CB  TYR A 169 " =    0.855
peak=    3.576 closest distance to " CB  THR A 157 " =    1.197
peak=    3.567 closest distance to " O   HOH Z  21 " =    1.731
peak=    3.560 closest distance to " O   HOH Z 368 " =    1.840
peak=    3.556 closest distance to " CA  ALA A 160 " =    1.014
peak=    3.555 closest distance to " NH1AARG A 145 " =    1.210
peak=    3.550 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.547 closest distance to " CB  GLU A 152 " =    1.138
peak=    3.547 closest distance to " CD  LYS A  76 " =    1.879
peak=    3.545 closest distance to " CD1 LEU A 300 " =    1.200
peak=    3.545 closest distance to " CB  GLN A  88 " =    1.270
peak=    3.542 closest distance to " CG  PRO A 243 " =    1.037
peak=    3.541 closest distance to " CA  ALA A 158 " =    1.123
peak=    3.539 closest distance to " CE3 TRP A 274 " =    1.297
peak=    3.527 closest distance to " O   ASN A 209 " =    1.432
peak=    3.512 closest distance to " O   HOH Z 115 " =    1.714
peak=    3.509 closest distance to " O   HOH Z 367 " =    2.354
peak=    3.505 closest distance to " CB  ALA A   1 " =    4.735
peak=    3.505 closest distance to " NE2 HIS A 207 " =    1.168
peak=    3.501 closest distance to " CA  ILE A 234 " =    1.037
peak=    3.495 closest distance to " O   HOH Z 368 " =    3.663
peak=    3.495 closest distance to " CA  ALA A 233 " =    0.937
peak=    3.494 closest distance to " CG1BVAL A  72 " =    1.508
peak=    3.493 closest distance to " O   HOH Z 188 " =    2.309
peak=    3.491 closest distance to " O   HOH Z 147 " =    1.776
peak=    3.488 closest distance to " OD1 ASN A  69 " =    2.587
peak=    3.486 closest distance to " CB  SER A 276 " =    1.159
peak=    3.482 closest distance to " CB  PRO A 243 " =    1.264
peak=    3.476 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.475 closest distance to " O   HOH Z 171 " =    2.813
peak=    3.474 closest distance to " O   HOH Z 406 " =    1.611
peak=    3.457 closest distance to " O   HOH Z 346 " =    1.715
peak=    3.455 closest distance to " CB  THR A  82 " =    1.214
peak=    3.452 closest distance to " O   HOH Z 181 " =    2.140
peak=    3.451 closest distance to " O   HOH Z 132 " =    3.874
peak=    3.451 closest distance to " CB  ILE A 120 " =    1.383
peak=    3.445 closest distance to " OG BSER A 134 " =    2.915
peak=    3.438 closest distance to " NH2AARG A 190 " =    1.774
peak=    3.436 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.433 closest distance to " O   HOH Z  44 " =    1.793
peak=    3.428 closest distance to " CA  THR A 221 " =    0.964
peak=    3.428 closest distance to " O   HOH Z 327 " =    1.822
peak=    3.425 closest distance to " CA  PRO A  54 " =    1.359
peak=    3.423 closest distance to " CA  MET A 105 " =    0.881
peak=    3.422 closest distance to " O   HOH Z  30 " =    1.697
peak=    3.420 closest distance to " CB  ALA A 114 " =    1.470
peak=    3.413 closest distance to " CB  SER A 210 " =    0.832
peak=    3.410 closest distance to " N   GLN A 278 " =    1.245
peak=    3.407 closest distance to " CB  MET A  47 " =    1.171
peak=    3.404 closest distance to " O   HOH Z 171 " =    2.499
peak=    3.404 closest distance to " CG1 ILE A 151 " =    1.100
peak=    3.403 closest distance to " O   HOH Z 373 " =    1.517
peak=    3.403 closest distance to " O   HOH Z 234 " =    3.803
peak=    3.402 closest distance to " CA  GLU A  46 " =    1.042
peak=    3.400 closest distance to " O   HOH Z 172 " =    2.439
peak=    3.399 closest distance to " O   HOH Z 392 " =    1.239
peak=    3.399 closest distance to " O   HOH Z 128 " =    2.001
peak=    3.399 closest distance to " O   HOH Z 365 " =    2.689
peak=    3.399 closest distance to " O   HOH Z 217 " =    1.460
peak=    3.397 closest distance to " N   TYR A  15 " =    0.852
peak=    3.395 closest distance to " CD2 PHE A  59 " =    1.788
peak=    3.395 closest distance to " O   HOH Z 119 " =    1.638
peak=    3.394 closest distance to " O   HOH Z 325 " =    2.284
peak=    3.388 closest distance to " O   HOH Z 154 " =    2.011
peak=    3.386 closest distance to " OG  SER A  62 " =    3.012
peak=    3.382 closest distance to " NE AARG A 275 " =    1.468
peak=    3.379 closest distance to " O   HOH Z 130 " =    3.662
peak=    3.374 closest distance to " O   HOH Z 388 " =    2.078
peak=    3.371 closest distance to " O   HOH Z 368 " =    4.256
peak=    3.371 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.370 closest distance to " O   HOH Z 409 " =    3.251
peak=    3.370 closest distance to " O   HOH Z 122 " =    1.963
peak=    3.370 closest distance to " CD  ARG A 269 " =    0.945
peak=    3.368 closest distance to " CD  LYS A 166 " =    1.286
peak=    3.366 closest distance to " O   HOH Z 184 " =    1.621
peak=    3.363 closest distance to " N   VAL A 296 " =    1.689
peak=    3.360 closest distance to " CA  ALA A 180 " =    1.369
peak=    3.358 closest distance to " O   HOH Z  97 " =    2.000
peak=    3.358 closest distance to " O   ASN A  74 " =    1.469
peak=    3.357 closest distance to " CA  SER A  95 " =    0.984
peak=    3.353 closest distance to " O   HOH Z 302 " =    1.682
peak=    3.352 closest distance to " ND1 HIS A  81 " =    1.752
peak=    3.352 closest distance to " ND2BASN A 224 " =    0.891
peak=    3.351 closest distance to " CE3 TRP A  85 " =    0.942
peak=    3.351 closest distance to " O   HOH Z 193 " =    2.160
peak=    3.348 closest distance to " CD BLYS A 290 " =    0.952
peak=    3.348 closest distance to " O   HOH Z 211 " =    1.084
peak=    3.345 closest distance to " CB  ALA A 248 " =    1.014
peak=    3.344 closest distance to " O   HOH Z  59 " =    1.663
peak=    3.343 closest distance to " CB  LEU A 143 " =    1.120
peak=    3.342 closest distance to " O   HOH Z 411 " =    3.868
peak=    3.340 closest distance to " O   HOH Z 148 " =    3.412
peak=    3.338 closest distance to " O   HOH Z 218 " =    1.760
peak=    3.338 closest distance to " O   HOH Z  20 " =    1.766
peak=    3.335 closest distance to " O   HOH Z 343 " =    3.355
peak=    3.332 closest distance to " CB  LEU A  83 " =    0.760
peak=    3.330 closest distance to " CA  VAL A 121 " =    1.041
peak=    3.329 closest distance to " O   HOH Z 385 " =    3.911
peak=    3.328 closest distance to " O   HOH Z 116 " =    1.753
peak=    3.324 closest distance to " O   HOH Z 345 " =    1.815
peak=    3.320 closest distance to " O   MET A 105 " =    1.657
peak=    3.320 closest distance to " CG  ARG A 159 " =    0.760
peak=    3.319 closest distance to " CB  TYR A  30 " =    1.359
peak=    3.315 closest distance to " O   HOH Z 394 " =    3.948
peak=    3.314 closest distance to " CB  LEU A 255 " =    1.342
peak=    3.311 closest distance to " CA  ALA A 160 " =    1.421
peak=    3.310 closest distance to " CD  PRO A 243 " =    1.828
peak=    3.309 closest distance to " CA  ARG A 159 " =    1.313
peak=    3.309 closest distance to " O   HOH Z 248 " =    1.614
peak=    3.307 closest distance to " O   HOH Z 130 " =    2.095
peak=    3.306 closest distance to " CA  GLU A 152 " =    1.199
peak=    3.304 closest distance to " OG BSER A  99 " =    2.291
peak=    3.302 closest distance to " OH  TYR A 186 " =    1.145
peak=    3.298 closest distance to " O   HOH Z   9 " =    1.707
peak=    3.295 closest distance to " O   HOH Z 432 " =    1.766
peak=    3.293 closest distance to " CG2 ILE A  20 " =    1.526
peak=    3.292 closest distance to " O   ILE A  20 " =    2.115
peak=    3.289 closest distance to " CB  GLU A 236 " =    1.189
peak=    3.286 closest distance to " O   PRO A 198 " =    1.322
peak=    3.283 closest distance to " O   HOH Z 285 " =    2.644
peak=    3.282 closest distance to " CZ  PHE A  38 " =    1.284
peak=    3.280 closest distance to " CB  TRP A 179 " =    1.597
peak=    3.279 closest distance to " O   HOH Z 438 " =    2.070
peak=    3.278 closest distance to " O   HOH Z 233 " =    1.962
peak=    3.277 closest distance to " CA  GLY A 241 " =    0.785
peak=    3.276 closest distance to " CG AARG A 275 " =    1.256
peak=    3.275 closest distance to " O   HOH Z 371 " =    2.848
peak=    3.275 closest distance to " CB  ARG A 138 " =    0.969
peak=    3.275 closest distance to " O   HOH Z 189 " =    2.624
peak=    3.269 closest distance to " O   HOH Z 109 " =    2.512
peak=    3.269 closest distance to " NH1 ARG A  14 " =    1.052
peak=    3.265 closest distance to " O   HOH Z 310 " =    2.380
peak=    3.263 closest distance to " O   HOH Z  51 " =    1.834
peak=    3.260 closest distance to " CG  MET A 113 " =    1.318
peak=    3.256 closest distance to " CA  TYR A  30 " =    1.069
peak=    3.251 closest distance to " O   HOH Z   3 " =    2.005
peak=    3.250 closest distance to " CB  LEU A 237 " =    0.791
peak=    3.246 closest distance to " CG  LYS A 119 " =    1.101
peak=    3.243 closest distance to " N   SER A 146 " =    1.745
peak=    3.243 closest distance to " O   HOH Z 378 " =    1.017
peak=    3.238 closest distance to " O   HOH Z 153 " =    1.728
peak=    3.235 closest distance to " O   HOH Z  88 " =    2.978
peak=    3.233 closest distance to " CA  ARG A  36 " =    1.169
peak=    3.233 closest distance to " O   HOH Z 409 " =    2.150
peak=    3.232 closest distance to " O   HOH Z 389 " =    1.913
peak=    3.229 closest distance to " O   HOH Z 244 " =    1.686
peak=    3.228 closest distance to " CA  GLY A 267 " =    1.174
peak=    3.228 closest distance to " O   HOH Z 291 " =    1.561
peak=    3.228 closest distance to " O   HOH Z 430 " =    1.709
peak=    3.226 closest distance to " N   ARG A 156 " =    1.281
peak=    3.224 closest distance to " O   HOH Z 240 " =    2.106
peak=    3.223 closest distance to " CB  THR A  31 " =    1.633
peak=    3.221 closest distance to " CA  ASP A 124 " =    0.759
peak=    3.221 closest distance to " O   HOH Z 294 " =    1.502
peak=    3.220 closest distance to " O   HOH Z 219 " =    4.351
peak=    3.214 closest distance to " CE3 TRP A 150 " =    1.081
peak=    3.214 closest distance to " O   HOH Z  66 " =    2.182
peak=    3.214 closest distance to " CD2 LEU A 255 " =    1.728
peak=    3.212 closest distance to " CB  ALA A 114 " =    0.962
peak=    3.208 closest distance to " O   HOH Z 357 " =    1.981
peak=    3.207 closest distance to " CB  SER A  22 " =    0.947
peak=    3.205 closest distance to " O   HOH Z 222 " =    2.345
peak=    3.205 closest distance to " CA  ALA A 154 " =    0.987
peak=    3.204 closest distance to " CB  MET A  40 " =    0.761
peak=    3.204 closest distance to " O   THR A 220 " =    1.589
peak=    3.202 closest distance to " CG1 VAL A 153 " =    0.951
peak=    3.202 closest distance to " O   HOH Z 274 " =    2.171
peak=    3.187 closest distance to " O   HOH Z 153 " =    3.620
peak=    3.180 closest distance to " O   HOH Z 359 " =    1.361
peak=    3.178 closest distance to " CB  ALA A  43 " =    0.813
peak=    3.177 closest distance to " CB  ASP A 171 " =    0.705
peak=    3.174 closest distance to " O   HOH Z 359 " =    4.073
peak=    3.172 closest distance to " OD1 ASN A 217 " =    1.467
peak=    3.171 closest distance to " CA  ARG A 156 " =    1.074
peak=    3.170 closest distance to " O   HOH Z 285 " =    2.193
peak=    3.168 closest distance to " CA  ALA A  21 " =    1.187
peak=    3.167 closest distance to " CB  LEU A 300 " =    0.900
peak=    3.163 closest distance to " CG  GLU A 277 " =    1.903
peak=    3.162 closest distance to " O   HOH Z 172 " =    4.660
peak=    3.159 closest distance to " O   HOH Z 280 " =    3.001
peak=    3.158 closest distance to " CG  GLN A 278 " =    1.281
peak=    3.156 closest distance to " CG BARG A 275 " =    1.435
peak=    3.151 closest distance to " NH2 ARG A 219 " =    1.836
peak=    3.149 closest distance to " O   THR A 294 " =    1.015
peak=    3.148 closest distance to " CD2 TYR A 186 " =    1.089
peak=    3.146 closest distance to " CA  GLY A 136 " =    0.931
peak=    3.143 closest distance to " O   HOH Z  85 " =    2.078
peak=    3.136 closest distance to " O   HOH Z 218 " =    1.855
peak=    3.135 closest distance to " CD1 ILE A  33 " =    1.665
peak=    3.132 closest distance to " CB  PHE A 204 " =    0.761
peak=    3.131 closest distance to " CB  ASN A 215 " =    1.099
peak=    3.131 closest distance to " O   HOH Z  57 " =    1.073
peak=    3.128 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.124 closest distance to " CA  ALA A 129 " =    1.283
peak=    3.124 closest distance to " CD2 LEU A 297 " =    0.970
peak=    3.115 closest distance to " O   CYS A 168 " =    1.491
peak=    3.109 closest distance to " OE1 GLU A  37 " =    1.396
peak=    3.105 closest distance to " O   HOH Z 313 " =    1.570
peak=    3.105 closest distance to " CB  GLU A 236 " =    1.218
peak=    3.101 closest distance to " O   HOH Z 273 " =    2.925
peak=    3.098 closest distance to " CG2 VAL A 189 " =    1.357
peak=    3.097 closest distance to " O   HOH Z 272 " =    2.217
peak=    3.096 closest distance to " O   HOH Z 234 " =    3.992
peak=    3.092 closest distance to " N   ASN A 127 " =    1.388
peak=    3.090 closest distance to " CA  LEU A 101 " =    1.512
peak=    3.089 closest distance to " OE1 GLN A 240 " =    1.612
peak=    3.089 closest distance to " NH1BARG A 145 " =    1.335
peak=    3.085 closest distance to " O   HOH Z 110 " =    1.645
peak=    3.074 closest distance to " CA  TYR A 186 " =    1.531
peak=    3.069 closest distance to " O   HOH Z 135 " =    1.863
peak=    3.065 closest distance to " O   LEU A 300 " =    1.293
peak=    3.062 closest distance to " O   HOH Z 425 " =    2.011
peak=    3.060 closest distance to " O   HOH Z 134 " =    2.487
peak=    3.052 closest distance to " CB  ASN A 285 " =    0.880
peak=    3.050 closest distance to " CB  TYR A  30 " =    1.193
peak=    3.041 closest distance to " CG BARG A 102 " =    1.876

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.476 - 5.550
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 210
   mapped sites are within: 0.788 - 5.550

peak=   -4.541 closest distance to " CB  PRO A 243 " =    2.594
peak=   -4.504 closest distance to " CD  ARG A  14 " =    3.394
peak=   -4.467 closest distance to " O   HOH Z 377 " =    1.854
peak=   -4.330 closest distance to " O   PRO A 198 " =    1.190
peak=   -4.266 closest distance to " O   HOH Z 231 " =    0.805
peak=   -4.264 closest distance to " CA  GLY A  98 " =    1.842
peak=   -4.240 closest distance to " CD  ARG A 156 " =    2.111
peak=   -4.238 closest distance to " O   HOH Z 290 " =    1.131
peak=   -4.107 closest distance to " CB  ALA A  43 " =    2.487
peak=   -4.083 closest distance to " O   HOH Z 351 " =    1.559
peak=   -4.046 closest distance to " O   HOH Z  60 " =    1.723
peak=   -4.018 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.985 closest distance to " CZ3 TRP A 179 " =    1.212
peak=   -3.908 closest distance to " O   HOH Z 185 " =    2.100
peak=   -3.900 closest distance to " O   HOH Z 211 " =    1.135
peak=   -3.898 closest distance to " O   ALA A  10 " =    1.670
peak=   -3.897 closest distance to " OD1 ASP A 191 " =    1.893
peak=   -3.894 closest distance to " O   HOH Z 131 " =    4.095
peak=   -3.890 closest distance to " OG BSER A 134 " =    1.458
peak=   -3.887 closest distance to " NH2 ARG A  79 " =    2.058
peak=   -3.875 closest distance to " CE BMET A  47 " =    1.362
peak=   -3.871 closest distance to " CA  GLY A 241 " =    2.277
peak=   -3.869 closest distance to " O   PRO A 243 " =    2.362
peak=   -3.851 closest distance to " O   SER A 135 " =    1.414
peak=   -3.830 closest distance to " O   HOH Z 407 " =    3.267
peak=   -3.807 closest distance to " ND2 ASN A 249 " =    2.146
peak=   -3.803 closest distance to " O   HOH Z  52 " =    1.156
peak=   -3.802 closest distance to " O   SER A  22 " =    2.702
peak=   -3.774 closest distance to " O   HOH Z 282 " =    4.556
peak=   -3.767 closest distance to " N   ASP A 171 " =    2.434
peak=   -3.740 closest distance to " O   HOH Z 231 " =    1.935
peak=   -3.736 closest distance to " O   VAL A  67 " =    2.733
peak=   -3.720 closest distance to " CD1 LEU A 255 " =    2.983
peak=   -3.710 closest distance to " O   HOH Z 266 " =    5.185
peak=   -3.690 closest distance to " O   HOH Z 313 " =    1.641
peak=   -3.686 closest distance to " CG2 THR A  18 " =    2.779
peak=   -3.683 closest distance to " O   HOH Z  65 " =    1.266
peak=   -3.682 closest distance to " O   HOH Z  73 " =    2.048
peak=   -3.670 closest distance to " CG1 VAL A 112 " =    2.579
peak=   -3.668 closest distance to " O   HOH Z 389 " =    2.166
peak=   -3.661 closest distance to " O   HOH Z  39 " =    1.093
peak=   -3.657 closest distance to " CE2 TYR A  30 " =    2.609
peak=   -3.654 closest distance to " CB  ASP A  27 " =    2.463
peak=   -3.654 closest distance to " CG  MET A 105 " =    0.953
peak=   -3.636 closest distance to " CB  ALA A   9 " =    2.439
peak=   -3.616 closest distance to " O   HOH Z   1 " =    1.336
peak=   -3.612 closest distance to " CD  LYS A 289 " =    2.309
peak=   -3.609 closest distance to " CA  GLY A 133 " =    2.021
peak=   -3.601 closest distance to " N   THR A 157 " =    1.534
peak=   -3.599 closest distance to " O   HOH Z 118 " =    1.323
peak=   -3.593 closest distance to " O   HOH Z  38 " =    1.407
peak=   -3.591 closest distance to " O   PRO A 163 " =    1.943
peak=   -3.583 closest distance to " O   HOH Z 111 " =    1.753
peak=   -3.580 closest distance to " CB  ALA A 158 " =    1.680
peak=   -3.578 closest distance to " CB  ALA A 248 " =    2.055
peak=   -3.575 closest distance to " O   HOH Z 372 " =    2.530
peak=   -3.570 closest distance to " N   ALA A  43 " =    2.625
peak=   -3.561 closest distance to " CB  ALA A 114 " =    2.504
peak=   -3.546 closest distance to " CG  ASN A  39 " =    1.655
peak=   -3.540 closest distance to " O   HOH Z  22 " =    2.343
peak=   -3.539 closest distance to " CA  GLY A 203 " =    2.337
peak=   -3.524 closest distance to " O   TYR A 247 " =    2.880
peak=   -3.523 closest distance to " ND2 ASN A  60 " =    4.032
peak=   -3.521 closest distance to " CG  GLN A 223 " =    2.181
peak=   -3.517 closest distance to " O   ILE A  49 " =    1.600
peak=   -3.514 closest distance to " CB  TRP A  85 " =    2.425
peak=   -3.504 closest distance to " CG  GLN A  88 " =    0.849
peak=   -3.498 closest distance to " O   HOH Z  24 " =    1.215
peak=   -3.496 closest distance to " O   HOH Z  11 " =    1.793
peak=   -3.491 closest distance to " CB  PHE A 130 " =    1.259
peak=   -3.488 closest distance to " CB  PRO A  54 " =    2.430
peak=   -3.484 closest distance to " O   HOH Z 286 " =    1.729
peak=   -3.474 closest distance to " CD1 LEU A 101 " =    2.290
peak=   -3.465 closest distance to " C   HIS A 108 " =    1.193
peak=   -3.447 closest distance to " O   HOH Z 348 " =    2.315
peak=   -3.447 closest distance to " OG BSER A 134 " =    1.780
peak=   -3.446 closest distance to " CG2 ILE A 151 " =    2.513
peak=   -3.442 closest distance to " O   HOH Z 412 " =    4.414
peak=   -3.441 closest distance to " O   HOH Z  90 " =    2.823
peak=   -3.439 closest distance to " CB  ASN A  39 " =    2.273
peak=   -3.435 closest distance to " CD2 LEU A 143 " =    2.599
peak=   -3.435 closest distance to " O   HOH Z 216 " =    1.571
peak=   -3.434 closest distance to " O   HOH Z  32 " =    2.096
peak=   -3.433 closest distance to " O   HOH Z 298 " =    2.440
peak=   -3.423 closest distance to " OG  SER A  97 " =    2.152
peak=   -3.423 closest distance to " O   HOH Z 166 " =    1.262
peak=   -3.421 closest distance to " CD  LYS A 166 " =    2.442
peak=   -3.421 closest distance to " NH2AARG A 275 " =    5.550
peak=   -3.418 closest distance to " CD2 TYR A 293 " =    1.938
peak=   -3.416 closest distance to " OG  SER A  87 " =    1.348
peak=   -3.412 closest distance to " CB  ASP A 132 " =    2.354
peak=   -3.411 closest distance to " O   HOH Z  49 " =    1.362
peak=   -3.410 closest distance to " NZ  LYS A 166 " =    1.188
peak=   -3.407 closest distance to " CD1 ILE A 239 " =    2.285
peak=   -3.402 closest distance to " O   HOH Z 140 " =    1.258
peak=   -3.398 closest distance to " CG  PHE A 283 " =    2.733
peak=   -3.397 closest distance to " O   HOH Z 114 " =    0.827
peak=   -3.395 closest distance to " CG2 THR A 178 " =    2.187
peak=   -3.389 closest distance to " OXT GLY A 302 " =    3.402
peak=   -3.384 closest distance to " O   HOH Z 147 " =    1.281
peak=   -3.378 closest distance to " O   SER A 141 " =    1.829
peak=   -3.376 closest distance to " O   HOH Z 275 " =    1.742
peak=   -3.372 closest distance to " O   HOH Z 281 " =    2.695
peak=   -3.369 closest distance to " CE  MET A 105 " =    2.527
peak=   -3.369 closest distance to " OD1 ASP A 171 " =    1.667
peak=   -3.362 closest distance to " OG  SER A 245 " =    1.319
peak=   -3.359 closest distance to " O   HOH Z  51 " =    0.988
peak=   -3.357 closest distance to " O   HOH Z 318 " =    1.661
peak=   -3.357 closest distance to " ND2 ASN A  45 " =    2.285
peak=   -3.356 closest distance to " CB  PRO A 163 " =    2.481
peak=   -3.356 closest distance to " CG1 VAL A 112 " =    2.646
peak=   -3.355 closest distance to " O   HOH Z 357 " =    2.144
peak=   -3.354 closest distance to " O   ASP A 162 " =    2.217
peak=   -3.354 closest distance to " CE2 PHE A 218 " =    2.461
peak=   -3.351 closest distance to " CG1 VAL A 197 " =    2.317
peak=   -3.350 closest distance to " CE3 TRP A 274 " =    2.480
peak=   -3.334 closest distance to " CD  GLU A 277 " =    1.150
peak=   -3.332 closest distance to " CG  GLN A 240 " =    2.345
peak=   -3.329 closest distance to " CG1 VAL A 112 " =    3.180
peak=   -3.329 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.327 closest distance to " CD1 PHE A  59 " =    2.076
peak=   -3.326 closest distance to " CG2 ILE A  49 " =    2.778
peak=   -3.326 closest distance to " O   PRO A 198 " =    1.338
peak=   -3.322 closest distance to " O   HOH Z 384 " =    2.922
peak=   -3.316 closest distance to " O   ALA A 180 " =    1.204
peak=   -3.309 closest distance to " C   ALA A 114 " =    2.508
peak=   -3.309 closest distance to " O   GLU A 152 " =    1.398
peak=   -3.308 closest distance to " O   HOH Z 317 " =    1.341
peak=   -3.306 closest distance to " ND2 ASN A 285 " =    2.140
peak=   -3.292 closest distance to " CG1 VAL A 250 " =    2.753
peak=   -3.289 closest distance to " CD  PRO A 213 " =    2.001
peak=   -3.288 closest distance to " O   HOH Z 426 " =    1.613
peak=   -3.286 closest distance to " ND2BASN A 224 " =    1.618
peak=   -3.284 closest distance to " CB  CYS A 254 " =    2.187
peak=   -3.283 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.279 closest distance to " NE2 GLN A  58 " =    3.040
peak=   -3.278 closest distance to " CB  PHE A 192 " =    1.747
peak=   -3.276 closest distance to " O   HOH Z 152 " =    4.698
peak=   -3.273 closest distance to " ND2 ASN A 187 " =    1.410
peak=   -3.272 closest distance to " OD1 ASN A 148 " =    1.506
peak=   -3.271 closest distance to " CG  LEU A  83 " =    2.001
peak=   -3.271 closest distance to " CE  LYS A  76 " =    2.879
peak=   -3.264 closest distance to " O   ALA A   7 " =    1.496
peak=   -3.258 closest distance to " CB  GLN A  55 " =    1.425
peak=   -3.256 closest distance to " O   HOH Z 275 " =    1.498
peak=   -3.255 closest distance to " O   HOH Z  28 " =    1.692
peak=   -3.253 closest distance to " OE1 GLN A  88 " =    1.188
peak=   -3.249 closest distance to " O   VAL A 189 " =    2.486
peak=   -3.249 closest distance to " CD  GLN A  58 " =    0.788
peak=   -3.248 closest distance to " N   GLN A  58 " =    1.721
peak=   -3.245 closest distance to " CD2 PHE A 130 " =    2.983
peak=   -3.243 closest distance to " O   HOH Z  69 " =    2.013
peak=   -3.240 closest distance to " CG  ARG A 269 " =    2.528
peak=   -3.239 closest distance to " C   LYS A  76 " =    1.415
peak=   -3.237 closest distance to " CG1 VAL A  78 " =    2.543
peak=   -3.232 closest distance to " NE2 GLN A  55 " =    1.362
peak=   -3.232 closest distance to " O   HOH Z 337 " =    1.326
peak=   -3.230 closest distance to " OG1 THR A  82 " =    2.049
peak=   -3.229 closest distance to " CA  GLY A 241 " =    3.152
peak=   -3.224 closest distance to " O   HOH Z 152 " =    0.863
peak=   -3.216 closest distance to " O   GLN A 240 " =    2.079
peak=   -3.213 closest distance to " O   GLY A 211 " =    1.150
peak=   -3.212 closest distance to " CD1 TRP A 179 " =    1.055
peak=   -3.211 closest distance to " O   HOH Z  53 " =    1.738
peak=   -3.210 closest distance to " O   ARG A  56 " =    4.348
peak=   -3.206 closest distance to " O   HOH Z 218 " =    3.875
peak=   -3.203 closest distance to " O   HOH Z 198 " =    1.997
peak=   -3.202 closest distance to " CB  ALA A 227 " =    2.418
peak=   -3.198 closest distance to " OE1 GLN A  58 " =    3.191
peak=   -3.196 closest distance to " CZ  PHE A  16 " =    2.274
peak=   -3.196 closest distance to " O   HOH Z 174 " =    2.743
peak=   -3.192 closest distance to " CG  LEU A 167 " =    0.951
peak=   -3.186 closest distance to " O   ASP A  27 " =    1.710
peak=   -3.177 closest distance to " C   LEU A 143 " =    1.325
peak=   -3.176 closest distance to " O   HOH Z 191 " =    5.410
peak=   -3.173 closest distance to " O   HOH Z  68 " =    1.443
peak=   -3.169 closest distance to " OD2 ASP A 171 " =    2.296
peak=   -3.168 closest distance to " N   ASP A 270 " =    1.426
peak=   -3.164 closest distance to " O   ALA A   1 " =    1.711
peak=   -3.161 closest distance to " NE2 GLN A 278 " =    1.808
peak=   -3.160 closest distance to " O   VAL A 125 " =    2.324
peak=   -3.145 closest distance to " O   ARG A 145 " =    1.311
peak=   -3.139 closest distance to " O   HOH Z 134 " =    3.315
peak=   -3.139 closest distance to " O   HOH Z 200 " =    3.495
peak=   -3.133 closest distance to " O   HOH Z 359 " =    3.219
peak=   -3.130 closest distance to " O   HOH Z 368 " =    1.555
peak=   -3.130 closest distance to " O   HOH Z 406 " =    2.320
peak=   -3.125 closest distance to " CD  ARG A  79 " =    1.091
peak=   -3.123 closest distance to " CG2 VAL A 189 " =    1.888
peak=   -3.113 closest distance to " CB  ALA A 131 " =    1.951
peak=   -3.101 closest distance to " CG2 ILE A  20 " =    3.007
peak=   -3.101 closest distance to " O   HOH Z 134 " =    3.564
peak=   -3.096 closest distance to " O   GLY A  17 " =    1.142
peak=   -3.093 closest distance to " O   HOH Z 128 " =    2.558
peak=   -3.090 closest distance to " C   LEU A 222 " =    0.853
peak=   -3.085 closest distance to " O   HOH Z 145 " =    1.763
peak=   -3.080 closest distance to " O   HOH Z 166 " =    1.687
peak=   -3.077 closest distance to " OD1 ASN A 187 " =    1.367
peak=   -3.071 closest distance to " O   HOH Z 193 " =    1.531
peak=   -3.064 closest distance to " O   SER A 210 " =    1.873
peak=   -3.044 closest distance to " CD2 PHE A  16 " =    2.391
peak=   -3.042 closest distance to " CD2 TYR A 293 " =    2.142
peak=   -3.032 closest distance to " O   HOH Z 163 " =    1.689
peak=   -3.031 closest distance to " O   HOH Z 389 " =    1.568
peak=   -3.027 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.002 closest distance to " O   HOH Z 282 " =    4.448

================= 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    :  0.4573 0.4582   6.269507e+00   6.258985e+00
   1_bss:  0.4495 0.4542   6.264199e+00   6.252207e+00
   1_xyz:  0.3168 0.3585   6.021019e+00   6.091603e+00
   1_adp:  0.2858 0.3711   5.974715e+00   6.118133e+00
   1_occ:  0.2852 0.3714   5.974566e+00   6.118819e+00
   2_bss:  0.2843 0.3696   5.974487e+00   6.117377e+00
   2_xyz:  0.2199 0.2879   5.742100e+00   5.930172e+00
   2_adp:  0.2038 0.2666   5.680846e+00   5.870075e+00
   2_occ:  0.2037 0.2663   5.680340e+00   5.869687e+00
   3_bss:  0.2037 0.2660   5.678985e+00   5.868668e+00
   3_xyz:  0.1528 0.2058   5.417131e+00   5.641316e+00
   3_adp:  0.1410 0.1928   5.346210e+00   5.572220e+00
   3_occ:  0.1409 0.1924   5.345654e+00   5.571616e+00
   4_bss:  0.1411 0.1918   5.343924e+00   5.568788e+00
   4_xyz:  0.1281 0.1746   5.253557e+00   5.482660e+00
   4_adp:  0.1246 0.1721   5.233813e+00   5.466829e+00
   4_occ:  0.1245 0.1721   5.233662e+00   5.466807e+00
   5_bss:  0.1245 0.1721   5.233662e+00   5.466807e+00
   5_xyz:  0.1168 0.1650   5.186069e+00   5.433296e+00
   5_adp:  0.1163 0.1631   5.180185e+00   5.424789e+00
   5_occ:  0.1162 0.1630   5.179976e+00   5.424626e+00
   5_bss:  0.1164 0.1621   5.176843e+00   5.420121e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -1.103   1.648   1.102   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -1.103   1.648   1.102   0.000   0.000   0.000
   1_adp:  0.300  50.000  -1.103   1.648   1.102   0.000   0.000   0.000
   1_occ:  0.300  50.000  -1.103   1.648   1.102   0.000   0.000   0.000
   2_bss:  0.343  76.387  -1.227  -0.477   0.276  -0.000   0.000   0.000
   2_xyz:  0.343  76.387  -1.227  -0.477   0.276  -0.000   0.000   0.000
   2_adp:  0.343  76.387  -1.227  -0.477   0.276  -0.000   0.000   0.000
   2_occ:  0.343  76.387  -1.227  -0.477   0.276  -0.000   0.000   0.000
   3_bss:  0.337  72.957  -1.639  -1.470  -0.105  -0.000  -0.000  -0.000
   3_xyz:  0.337  72.957  -1.639  -1.470  -0.105  -0.000  -0.000  -0.000
   3_adp:  0.337  72.957  -1.639  -1.470  -0.105  -0.000  -0.000  -0.000
   3_occ:  0.337  72.957  -1.639  -1.470  -0.105  -0.000  -0.000  -0.000
   4_bss:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   4_xyz:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   4_adp:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   4_occ:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   5_bss:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   5_xyz:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   5_adp:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   5_occ:  0.325  64.929  -2.154  -2.475  -0.712  -0.000  -0.000  -0.000
   5_bss:  0.317  59.101  -2.201  -2.660  -0.745  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.875 0.4459  0.6032    66869.506
   1_bss:  55.443 0.4502  0.6267    65403.364
   1_xyz:  38.026 0.6666  0.8796    35362.696
   1_adp:  40.189 0.6396  0.8487    38443.629
   1_occ:  40.288 0.6383  0.8457    38502.945
   2_bss:  40.080 0.6408  0.8208    38251.883
   2_xyz:  29.657 0.7599  0.9427    21772.534
   2_adp:  26.882 0.7911  0.9599    18685.475
   2_occ:  26.872 0.7912  0.9598    18663.622
   3_bss:  26.782 0.7920  0.9403    18555.827
   3_xyz:  19.967 0.8610  0.9879    10767.973
   3_adp:  18.134 0.8791  0.9926     9423.691
   3_occ:  18.123 0.8792  0.9924     9402.402
   4_bss:  18.039 0.8799  0.9684     9309.195
   4_xyz:  15.880 0.8991  0.9760     7589.193
   4_adp:  15.518 0.9026  0.9729     7387.017
   4_occ:  15.518 0.9025  0.9727     7383.773
   5_bss:  15.518 0.9025  0.9727     7383.773
   5_xyz:  14.766 0.9088  0.9769     6856.966
   5_adp:  14.519 0.9111  0.9752     6749.619
   5_occ:  14.521 0.9110  0.9752     6743.445
   5_bss:  14.443 0.9115  0.9716     6632.378
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7151e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7151e-01
   1_xyz:   1.568  0.012  0.105 16.291  0.007  4.114   1.4259e-01
   1_adp:   1.568  0.012  0.105 16.291  0.007  4.114   1.4259e-01
   1_occ:   1.568  0.012  0.105 16.291  0.007  4.114   1.4259e-01
   2_bss:   1.568  0.012  0.105 16.291  0.007  4.114   1.4259e-01
   2_xyz:   1.138  0.008  0.085 14.657  0.004  4.108   7.2235e-02
   2_adp:   1.138  0.008  0.085 14.657  0.004  4.108   7.2235e-02
   2_occ:   1.138  0.008  0.085 14.657  0.004  4.108   7.2235e-02
   3_bss:   1.138  0.008  0.085 14.657  0.004  4.108   7.2235e-02
   3_xyz:   1.101  0.009  0.076 14.718  0.004  4.118   7.0834e-02
   3_adp:   1.101  0.009  0.076 14.718  0.004  4.118   7.0834e-02
   3_occ:   1.101  0.009  0.076 14.718  0.004  4.118   7.0834e-02
   4_bss:   1.101  0.009  0.076 14.718  0.004  4.118   7.0834e-02
   4_xyz:   0.968  0.007  0.072 14.333  0.004  4.113   5.5928e-02
   4_adp:   0.968  0.007  0.072 14.333  0.004  4.113   5.5928e-02
   4_occ:   0.968  0.007  0.072 14.333  0.004  4.113   5.5928e-02
   5_bss:   0.968  0.007  0.072 14.333  0.004  4.113   5.5928e-02
   5_xyz:   1.053  0.009  0.078 14.531  0.004  4.117   6.5939e-02
   5_adp:   1.053  0.009  0.078 14.531  0.004  4.117   6.5939e-02
   5_occ:   1.053  0.009  0.078 14.531  0.004  4.117   6.5939e-02
   5_bss:   1.053  0.009  0.078 14.531  0.004  4.117   6.5939e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4188e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4188e-01
   1_xyz:   8.417  0.093  0.313 83.761  0.060  2.081   1.6129e-01
   1_adp:   8.417  0.093  0.313 83.761  0.060  2.081   1.6129e-01
   1_occ:   8.417  0.093  0.313 83.761  0.060  2.081   1.6129e-01
   2_bss:   8.417  0.093  0.313 83.761  0.060  2.081   1.6129e-01
   2_xyz:   6.955  0.057  0.279 80.266  0.044  2.252   7.4346e-02
   2_adp:   6.955  0.057  0.279 80.266  0.044  2.252   7.4346e-02
   2_occ:   6.955  0.057  0.279 80.266  0.044  2.252   7.4346e-02
   3_bss:   6.955  0.057  0.279 80.266  0.044  2.252   7.4346e-02
   3_xyz:   8.515  0.045  0.246 82.245  0.019  2.257   6.6983e-02
   3_adp:   8.515  0.045  0.246 82.245  0.019  2.257   6.6983e-02
   3_occ:   8.515  0.045  0.246 82.245  0.019  2.257   6.6983e-02
   4_bss:   8.515  0.045  0.246 82.245  0.019  2.257   6.6983e-02
   4_xyz:   7.886  0.040  0.209 81.901  0.032  2.385   3.8957e-02
   4_adp:   7.886  0.040  0.209 81.901  0.032  2.385   3.8957e-02
   4_occ:   7.886  0.040  0.209 81.901  0.032  2.385   3.8957e-02
   5_bss:   7.886  0.040  0.209 81.901  0.032  2.385   3.8957e-02
   5_xyz:   8.091  0.047  0.254 84.512  0.030  2.280   4.9864e-02
   5_adp:   8.091  0.047  0.254 84.512  0.030  2.280   4.9864e-02
   5_occ:   8.091  0.047  0.254 84.512  0.030  2.280   4.9864e-02
   5_bss:   8.091  0.047  0.254 84.512  0.030  2.280   4.9864e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 103.98   0.00  18.94  72.17   0.00  14.62 103.98   0.00  42.45
   1_occ: 103.98   0.00  18.94  72.17   0.00  14.62 103.98   0.00  42.45
   2_bss: 103.98   0.00  18.94  72.17   0.00  14.62 103.98   0.00  42.45
   2_xyz: 103.98   0.00  18.94  72.17   0.00  14.62 103.98   0.00  42.45
   2_adp:  99.92   0.00  18.19  86.93   0.00  13.70  99.92   3.52  42.66
   2_occ:  99.92   0.00  18.19  86.93   0.00  13.70  99.92   3.52  42.66
   3_bss:  99.92   0.00  18.19  86.93   0.00  13.70  99.92   3.52  42.66
   3_xyz:  99.92   0.00  18.19  86.93   0.00  13.70  99.92   3.52  42.66
   3_adp:  94.62   1.00  17.65  87.16   1.00  13.02  94.62   6.12  42.88
   3_occ:  94.62   1.00  17.65  87.16   1.00  13.02  94.62   6.12  42.88
   4_bss:  94.62   1.00  17.65  87.16   1.00  13.02  94.62   6.12  42.88
   4_xyz:  94.62   1.00  17.65  87.16   1.00  13.02  94.62   6.12  42.88
   4_adp:  92.89   0.35  17.56  92.31   0.35  12.90  92.89   2.04  42.93
   4_occ:  92.89   0.35  17.56  92.31   0.35  12.90  92.89   2.04  42.93
   5_bss:  92.89   0.35  17.56  92.31   0.35  12.90  92.89   2.04  42.93
   5_xyz:  92.89   0.35  17.56  92.31   0.35  12.90  92.89   2.04  42.93
   5_adp:  92.73   0.69  17.27  92.73   0.69  12.79  91.12   3.66  41.65
   5_occ:  92.73   0.69  17.27  92.73   0.69  12.79  91.12   3.66  41.65
   5_bss:  92.71   0.67  17.25  92.71   0.67  12.77  91.10   3.63  41.63
------------------------------------------------------------------------
 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:    1.720    0.016    0.469
   1_adp:    1.720    0.016    0.469
   1_occ:    1.720    0.016    0.469
   2_bss:    1.720    0.016    0.469
   2_xyz:    1.494    0.040    0.564
   2_adp:    1.494    0.040    0.564
   2_occ:    1.494    0.040    0.564
   3_bss:    1.494    0.040    0.564
   3_xyz:    1.453    0.007    0.695
   3_adp:    1.453    0.007    0.695
   3_occ:    1.453    0.007    0.695
   4_bss:    1.453    0.007    0.695
   4_xyz:    1.472    0.042    0.722
   4_adp:    1.472    0.042    0.722
   4_occ:    1.472    0.042    0.722
   5_bss:    1.472    0.042    0.722
   5_xyz:    1.611    0.077    0.744
   5_adp:    1.611    0.077    0.744
   5_occ:    1.611    0.077    0.744
   5_bss:    1.611    0.077    0.744
------------------------------------------------------------------------

CPU time actual refinement: 354.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/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_987/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_987/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.69 
  Macro-tasks:
    bulk solvent and scale       = 44.94  
    individual site refinement   = 143.64 
    weights calculation          = 30.55  
    collect and process          = 6.64   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 225.88 
  Micro-tasks:
    mask                            = 2.27   
    f_calc                          = 115.94 
    alpha_beta                      = 8.32   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 118.61 
    fmodel                         = 7.41   
    r_factors                      = 0.19   
    phase_errors                   = 11.50  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 265.70 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.030 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    642 calls, 115.51 s
gradients_fft:          587 calls, 107.30 s

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

# Date 2008-01-16 Time 06:09:47 PST -0800 (1200492587.66 s)
Start R-work = 0.4573, R-free = 0.4582 (no bulk solvent and anisotropic scale)
Final R-work = 0.1391, R-free = 0.1822 (no bulk solvent and anisotropic scale)

Start R-work = 0.4495, R-free = 0.4542
Final R-work = 0.1164, R-free = 0.1621