# Date 2008-01-16 Time 05:08:29 PST -0800 (1200488909.79 s)
#phil __OFF__

Command line arguments: "../614.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8410
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 614

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 88.1178, 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: (70.25, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.95359
Completeness in resolution range: 0.925231
Completeness with d_max=infinity: 0.922573

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   1.9536

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.95359
Completeness in resolution range: 0.925231
Completeness with d_max=infinity: 0.922573

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0740 -  4.1817 [2221/2247]  1998   223  10.0%
  bin  2:  4.1817 -  3.3309 [2141/2161]  1930   211   9.9%
  bin  3:  3.3309 -  2.9133 [2104/2123]  1895   209   9.9%
  bin  4:  2.9133 -  2.6485 [2102/2132]  1880   222  10.6%
  bin  5:  2.6485 -  2.4596 [2075/2094]  1871   204   9.8%
  bin  6:  2.4596 -  2.3151 [2069/2094]  1862   207  10.0%
  bin  7:  2.3151 -  2.1995 [2053/2081]  1849   204   9.9%
  bin  8:  2.1995 -  2.1041 [2062/2098]  1850   212  10.3%
  bin  9:  2.1041 -  2.0233 [2003/2078]  1816   187   9.3%
  bin 10:  2.0233 -  1.9536 [ 759/2064]   679    80  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 33
        2.27 -     2.93: 1558
        2.93 -     3.58: 4524
        3.58 -     4.24: 9237
        4.24 -     4.90: 13055
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.612 3.040 -x+1,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.745 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.768 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28402 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_614/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/model_refine_001.geo

CPU time processing inputs: 9.75


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4713   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286802                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6648 0.99   1439  159 0.3864 0.3811      6.6098      6.5825|
|  2:  4.6648 -  3.7209 0.99   1392  157 0.4118 0.4125      6.8277      6.7975|
|  3:  3.7209 -  3.2560 0.99   1368  150 0.4392 0.4261      6.6794      6.6682|
|  4:  3.2560 -  2.9608 0.99   1351  152 0.4733 0.5017      6.5386      6.5397|
|  5:  2.9608 -  2.7499 0.99   1351  149 0.5000 0.4767      6.3569      6.3964|
|  6:  2.7499 -  2.5886 0.99   1340  146 0.4960 0.5239      6.2647      6.1966|
|  7:  2.5886 -  2.4596 0.99   1333  156 0.4925 0.5063      6.2291      6.1718|
|  8:  2.4596 -  2.3529 0.98   1328  150 0.5206 0.5208      6.1663      6.1578|
|  9:  2.3529 -  2.2627 0.98   1312  140 0.5037 0.5476      6.1179      6.2159|
| 10:  2.2627 -  2.1848 1.00   1354  147 0.5147 0.5418      6.0693      6.0817|
| 11:  2.1848 -  2.1167 0.98   1315  147 0.5063 0.4740       6.018       6.025|
| 12:  2.1167 -  2.0563 0.98   1310  142 0.5050 0.4865      5.9317       5.932|
| 13:  2.0563 -  2.0023 0.86   1142  131 0.5071 0.4901      5.8855      5.7822|
| 14:  2.0023 -  1.9536 0.22    295   33 0.5212 0.5006      5.8461      5.8745|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.6648  1439   159  0.72  32.75   0.81     0.77      69335.14|
|  2:  4.6648 -  3.7209  1392   157  0.68  36.83   0.89     0.79     117009.64|
|  3:  3.7209 -  3.2560  1368   150  0.54  48.45   0.92     0.73     128871.62|
|  4:  3.2560 -  2.9608  1351   152  0.43  57.29   0.89     0.62     120372.52|
|  5:  2.9608 -  2.7499  1351   149  0.38  61.30   0.87     0.56      87421.89|
|  6:  2.7499 -  2.5886  1340   146  0.36  62.74   0.89     0.52      74033.16|
|  7:  2.5886 -  2.4596  1333   156  0.36  62.64   0.92     0.51      64688.26|
|  8:  2.4596 -  2.3529  1328   150  0.33  65.00   0.90     0.49      60818.33|
|  9:  2.3529 -  2.2627  1312   140  0.32  66.15   0.93     0.47      57160.77|
| 10:  2.2627 -  2.1848  1354   147  0.32  66.29   0.92     0.48      51056.24|
| 11:  2.1848 -  2.1167  1315   147  0.32  66.03   0.96     0.50      48846.47|
| 12:  2.1167 -  2.0563  1310   142  0.34  64.55   0.94     0.54      42136.86|
| 13:  2.0563 -  2.0023  1142   131  0.34  64.84   0.95     0.56      36644.77|
| 14:  2.0023 -  1.9536   295    33  0.39  60.73   1.00     0.56      28793.02|
|alpha:            min =        0.47 max =            0.79 mean =         0.58|
|beta:             min =    28793.02 max =       128871.62 mean =     73725.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.78|
|phase err.(test): min =        0.00 max =           89.94 mean =        58.28|
|-----------------------------------------------------------------------------|

============================== 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 = 12.470776             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.632   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.942996              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.630   (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 |  1.612 -  1.940:       15 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.940 -  2.269:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.269 -  2.598:       52 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.598 -  2.927:     1506 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.927 -  3.256:     1921 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.256 -  3.585:     2603 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.585 -  3.913:     4737 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.913 -  4.242:     4500 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.242 -  4.571:     5956 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.571 -  4.900:     7099 |
|-----------------------------------------------------------------------------|
|-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 |        0.191 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.612 |       0.600 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4713   ksol= 0.00   Bsol= 0.00   scale= 0.887    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.286802                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4572   r_free= 0.4637   ksol= 0.34   Bsol= 42.69   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,1.89,2.62,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.280886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.648772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.511   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.328309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.352   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4572      final r-factor (work) = 0.3939          |
| start r-factor (free) = 0.4637      final r-factor (free) = 0.4333          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4657 = 9.65 * 0.50 * 6.2754 + 1.00 * 0.1907                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.0330 = 9.65 * 0.50 * 6.2024 + 1.00 * 0.1100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3939      final r-factor (work) = 0.3650          |
| start r-factor (free) = 0.4333      final r-factor (free) = 0.4400          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2448 = 1.33 * 1.00 * 6.2024 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1817 = 1.33 * 1.00 * 6.1455 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.02   19.05    None  None   None       |
|    all(noH): 2823   0      0.00    99.02   19.05    None  None   None       |
|    Sol.    : 438    0      0.00    99.02   34.16    None  None   None       |
|    Mac.    : 2385   0      0.00    81.03   16.27    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 -   9.902:  807   |   5:    49.508 -  59.409:   82        |
|      1:     9.902 -  19.803:  953   |   6:    59.409 -  69.311:   26        |
|      2:    19.803 -  29.705:  564   |   7:    69.311 -  79.212:   16        |
|      3:    29.705 -  39.606:  240   |   8:    79.212 -  89.114:    6        |
|      4:    39.606 -  49.508:  127   |   9:    89.114 -  99.015:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3650 r_free = 0.4400             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3645 r_free = 0.4411             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3645   r_free= 0.4411   ksol= 0.34   Bsol= 42.69   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,1.89,2.62,0.00,0.00,0.00); trace/3= 0.37                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.148151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3646   r_free= 0.4386   ksol= 0.36   Bsol= 69.11   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,0.74,1.50,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.151516                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.570796             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.226  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.628923              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.119  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3646      final r-factor (work) = 0.2964          |
| start r-factor (free) = 0.4386      final r-factor (free) = 0.3817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.0507 = 16.57 * 0.50 * 6.1482 + 1.00 * 0.1100                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.5097 = 16.57 * 0.50 * 6.0807 + 1.00 * 0.1283                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2964      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3817      final r-factor (free) = 0.3665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8430 = 0.63 * 1.00 * 6.0807 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7703 = 0.63 * 1.00 * 5.9748 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.28   18.54    None  None   None       |
|    all(noH): 2823   0      0.00    98.28   18.54    None  None   None       |
|    Sol.    : 438    0      0.82    98.28   36.20    None  None   None       |
|    Mac.    : 2385   0      0.00    77.10   15.30    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 -   9.828:  830   |   5:    49.140 -  58.968:   65        |
|      1:     9.828 -  19.656:  992   |   6:    58.968 -  68.796:   34        |
|      2:    19.656 -  29.484:  490   |   7:    68.796 -  78.624:   10        |
|      3:    29.484 -  39.312:  280   |   8:    78.624 -  88.452:    3        |
|      4:    39.312 -  49.140:  117   |   9:    88.452 -  98.280:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2776 r_free = 0.3665             target_work(ml) = 5.954         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2773 r_free = 0.3661             target_work(ml) = 5.953         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2773   r_free= 0.3661   ksol= 0.36   Bsol= 69.11   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,0.74,1.50,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.953373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2772   r_free= 0.3637   ksol= 0.36   Bsol= 77.83   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-0.53,0.71,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.950797                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.067062              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.872  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.666615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.281  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2772      final r-factor (work) = 0.2249          |
| start r-factor (free) = 0.3637      final r-factor (free) = 0.2949          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2397 = 7.07 * 0.50 * 5.9746 + 1.00 * 0.1283                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8539 = 7.07 * 0.50 * 5.8815 + 1.00 * 0.0715                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2249      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.2949      final r-factor (free) = 0.2837          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.9850 = 8.67 * 1.00 * 5.8815 + 1.00 * 0.0125                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 49.5546 = 8.67 * 1.00 * 5.7153 + 1.00 * 0.0222                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.81  20.57    None  None   None       |
|    all(noH): 2823   0      0.00    117.81  20.57    None  None   None       |
|    Sol.    : 438    0      3.57    117.81  50.79    None  None   None       |
|    Mac.    : 2385   0      0.00    106.51  15.02    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:     0.000 -  11.781: 1252   |   5:    58.903 -  70.683:   92        |
|      1:    11.781 -  23.561:  828   |   6:    70.683 -  82.464:   58        |
|      2:    23.561 -  35.342:  268   |   7:    82.464 -  94.244:   33        |
|      3:    35.342 -  47.122:  157   |   8:    94.244 - 106.025:   18        |
|      4:    47.122 -  58.903:  111   |   9:   106.025 - 117.805:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2017 r_free = 0.2837             target_work(ml) = 5.693         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2018 r_free = 0.2836             target_work(ml) = 5.693         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2018   r_free= 0.2836   ksol= 0.36   Bsol= 77.83   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.20,-0.53,0.71,-0.00,0.00,0.00); trace/3= -0.34                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.692967                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2017   r_free= 0.2842   ksol= 0.34   Bsol= 80.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.36,0.36,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.692555                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.729383              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.248  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.253940              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2017      final r-factor (work) = 0.1655          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2313          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5888 = 4.73 * 0.50 * 5.7163 + 1.00 * 0.0715                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3534 = 4.73 * 0.50 * 5.6176 + 1.00 * 0.0696                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1655      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2313      final r-factor (free) = 0.2089          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0663 = 1.25 * 1.00 * 5.6176 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8728 = 1.25 * 1.00 * 5.4680 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.20  19.38    None  None   None       |
|    all(noH): 2823   0      0.00    122.20  19.38    None  None   None       |
|    Sol.    : 438    0      5.64    122.20  51.18    None  None   None       |
|    Mac.    : 2385   0      0.00    106.40  13.54    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 -  12.220: 1446   |   5:    61.099 -  73.319:   79        |
|      1:    12.220 -  24.440:  784   |   6:    73.319 -  85.539:   62        |
|      2:    24.440 -  36.659:  184   |   7:    85.539 -  97.758:   17        |
|      3:    36.659 -  48.879:  118   |   8:    97.758 - 109.978:   18        |
|      4:    48.879 -  61.099:  112   |   9:   109.978 - 122.198:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1504 r_free = 0.2089             target_work(ml) = 5.412         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1503 r_free = 0.2088             target_work(ml) = 5.411         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1503   r_free= 0.2088   ksol= 0.34   Bsol= 80.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.69,-1.36,0.36,-0.00,0.00,0.00); trace/3= -0.90                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.411394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.2087   ksol= 0.33   Bsol= 69.35   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.84,0.19,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.409647                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.066943              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.474  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.591233              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.269  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1506      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.2087      final r-factor (free) = 0.1925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7211 = 2.07 * 0.50 * 5.4685 + 1.00 * 0.0696                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6119 = 2.07 * 0.50 * 5.3821 + 1.00 * 0.0497                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1395      final r-factor (work) = 0.1343          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5802 = 1.59 * 1.00 * 5.3821 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4861 = 1.59 * 1.00 * 5.3239 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.24  18.74    None  None   None       |
|    all(noH): 2823   0      0.00    126.24  18.74    None  None   None       |
|    Sol.    : 438    0      5.70    126.24  50.27    None  None   None       |
|    Mac.    : 2385   0      0.00    110.55  12.95    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 -  12.624: 1598   |   5:    63.122 -  75.746:   70        |
|      1:    12.624 -  25.249:  686   |   6:    75.746 -  88.371:   53        |
|      2:    25.249 -  37.873:  171   |   7:    88.371 - 100.995:   20        |
|      3:    37.873 -  50.498:  111   |   8:   100.995 - 113.619:   13        |
|      4:    50.498 -  63.122:   99   |   9:   113.619 - 126.244:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1343 r_free = 0.1866             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1343 r_free = 0.1865             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1865   ksol= 0.33   Bsol= 69.35   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.78,-1.84,0.19,-0.00,0.00,0.00); trace/3= -1.14                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306120                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6648 0.99   1439  159 0.0988 0.1341      5.4058       5.632|
|  2:  4.6648 -  3.7209 0.99   1392  157 0.0912 0.1219      5.5097      5.7462|
|  3:  3.7209 -  3.2560 0.99   1368  150 0.1243 0.1736      5.6026      5.9247|
|  4:  3.2560 -  2.9608 0.99   1351  152 0.1581 0.2126      5.6477      5.8154|
|  5:  2.9608 -  2.7499 0.99   1351  149 0.1647 0.2135      5.5227      5.7741|
|  6:  2.7499 -  2.5886 0.99   1340  146 0.1552 0.2365      5.3894      5.6155|
|  7:  2.5886 -  2.4596 0.99   1333  156 0.1525 0.1977      5.3397      5.5039|
|  8:  2.4596 -  2.3529 0.98   1328  150 0.1527 0.2102      5.2641      5.5132|
|  9:  2.3529 -  2.2627 0.98   1312  140 0.1454 0.2089      5.2058      5.4624|
| 10:  2.2627 -  2.1848 1.00   1354  147 0.1389 0.1877      5.0922      5.2894|
| 11:  2.1848 -  2.1167 0.98   1315  147 0.1365 0.2198      5.0957      5.4558|
| 12:  2.1167 -  2.0563 0.98   1310  142 0.1421 0.2144      5.0271      5.2764|
| 13:  2.0563 -  2.0023 0.86   1142  131 0.1289 0.1825       4.896      5.0723|
| 14:  2.0023 -  1.9536 0.22    295   33 0.1195 0.1783      4.7804      5.0359|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.6648  1439   159  0.93   9.83   0.97     0.94       7988.90|
|  2:  4.6648 -  3.7209  1392   157  0.95   8.87   1.03     1.01      10581.85|
|  3:  3.7209 -  3.2560  1368   150  0.91  14.04   1.06     1.05      13761.52|
|  4:  3.2560 -  2.9608  1351   152  0.88  18.19   1.03     1.00      15377.50|
|  5:  2.9608 -  2.7499  1351   149  0.86  20.27   1.01     0.98      12848.43|
|  6:  2.7499 -  2.5886  1340   146  0.86  20.37   0.99     0.95      10134.90|
|  7:  2.5886 -  2.4596  1333   156  0.87  19.98   1.01     0.98       9281.06|
|  8:  2.4596 -  2.3529  1328   150  0.87  19.88   1.01     0.97       7884.93|
|  9:  2.3529 -  2.2627  1312   140  0.87  19.71   1.00     0.94       7089.94|
| 10:  2.2627 -  2.1848  1354   147  0.88  18.78   1.01     0.97       5785.40|
| 11:  2.1848 -  2.1167  1315   147  0.87  19.33   1.00     0.94       5924.38|
| 12:  2.1167 -  2.0563  1310   142  0.87  19.55   1.02     1.01       5387.95|
| 13:  2.0563 -  2.0023  1142   131  0.87  19.54   1.00     0.97       4302.08|
| 14:  2.0023 -  1.9536   295    33  0.93  13.83   0.99     0.98       3020.90|
|alpha:            min =        0.94 max =            1.05 mean =         0.98|
|beta:             min =     3020.90 max =        15377.50 mean =      8927.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.96 mean =        17.40|
|phase err.(test): min =        0.00 max =           89.35 mean =        16.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1865   ksol= 0.32   Bsol= 65.88   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.10,0.07,-0.00,0.00,0.00); trace/3= -1.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305816                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1343   r_free= 0.1865   ksol= 0.32   Bsol= 65.88   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-2.10,0.07,-0.00,0.00,0.00); trace/3= -1.31                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305816                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6648 0.99   1439  159 0.0988 0.1339      5.4051      5.6306|
|  2:  4.6648 -  3.7209 0.99   1392  157 0.0910 0.1218      5.5087      5.7442|
|  3:  3.7209 -  3.2560 0.99   1368  150 0.1242 0.1737      5.6021      5.9245|
|  4:  3.2560 -  2.9608 0.99   1351  152 0.1581 0.2127      5.6477      5.8156|
|  5:  2.9608 -  2.7499 0.99   1351  149 0.1647 0.2135      5.5226      5.7745|
|  6:  2.7499 -  2.5886 0.99   1340  146 0.1552 0.2363       5.389      5.6151|
|  7:  2.5886 -  2.4596 0.99   1333  156 0.1525 0.1980      5.3396      5.5041|
|  8:  2.4596 -  2.3529 0.98   1328  150 0.1527 0.2104      5.2642      5.5139|
|  9:  2.3529 -  2.2627 0.98   1312  140 0.1453 0.2086      5.2059      5.4614|
| 10:  2.2627 -  2.1848 1.00   1354  147 0.1388 0.1879       5.092      5.2906|
| 11:  2.1848 -  2.1167 0.98   1315  147 0.1364 0.2200      5.0953      5.4566|
| 12:  2.1167 -  2.0563 0.98   1310  142 0.1420 0.2141      5.0271      5.2759|
| 13:  2.0563 -  2.0023 0.86   1142  131 0.1290 0.1823      4.8955      5.0708|
| 14:  2.0023 -  1.9536 0.22    295   33 0.1196 0.1781      4.7793      5.0334|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.6648  1439   159  0.93   9.82   0.97     0.94       7982.73|
|  2:  4.6648 -  3.7209  1392   157  0.95   8.86   1.03     1.01      10564.58|
|  3:  3.7209 -  3.2560  1368   150  0.91  14.02   1.05     1.05      13739.75|
|  4:  3.2560 -  2.9608  1351   152  0.88  18.18   1.03     1.00      15364.12|
|  5:  2.9608 -  2.7499  1351   149  0.86  20.27   1.00     0.98      12845.12|
|  6:  2.7499 -  2.5886  1340   146  0.86  20.36   0.99     0.94      10130.98|
|  7:  2.5886 -  2.4596  1333   156  0.87  19.97   1.01     0.97       9281.11|
|  8:  2.4596 -  2.3529  1328   150  0.87  19.89   1.00     0.97       7889.29|
|  9:  2.3529 -  2.2627  1312   140  0.87  19.71   1.00     0.94       7096.25|
| 10:  2.2627 -  2.1848  1354   147  0.88  18.77   1.00     0.97       5786.46|
| 11:  2.1848 -  2.1167  1315   147  0.87  19.34   0.99     0.93       5928.88|
| 12:  2.1167 -  2.0563  1310   142  0.87  19.54   1.01     1.00       5385.79|
| 13:  2.0563 -  2.0023  1142   131  0.87  19.51   0.99     0.96       4293.90|
| 14:  2.0023 -  1.9536   295    33  0.93  13.75   0.98     0.97       3006.00|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3006.00 max =        15364.12 mean =      8922.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.39|
|phase err.(test): min =        0.00 max =           89.44 mean =        16.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.730)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.25  18.74    None  None   None       |
|    all(noH): 2823   0      0.00    126.25  18.74    None  None   None       |
|    Sol.    : 438    0      5.71    126.25  50.27    None  None   None       |
|    Mac.    : 2385   0      0.00    110.55  12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  12.627: 1598   |   5:    63.125 -  75.749:   70        |
|      1:    12.627 -  25.252:  686   |   6:    75.749 -  88.374:   53        |
|      2:    25.252 -  37.876:  171   |   7:    88.374 - 100.998:   20        |
|      3:    37.876 -  50.501:  111   |   8:   100.998 - 113.622:   13        |
|      4:    50.501 -  63.125:   99   |   9:   113.622 - 126.247:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 354         
Filter by distance & map next to the model:
   mapped sites are within: 0.614 - 4.472
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 350 from: 354
   mapped sites are within: 0.757 - 4.472

peak=    8.477 closest distance to " O   HOH Z 390 " =    1.395
peak=    7.142 closest distance to " O   HOH Z 385 " =    2.058
peak=    6.871 closest distance to " O   HOH Z 245 " =    1.315
peak=    5.760 closest distance to " O   HOH Z  77 " =    1.183
peak=    5.741 closest distance to " O   HOH Z 103 " =    1.084
peak=    5.598 closest distance to " O   HOH Z 130 " =    0.991
peak=    5.548 closest distance to " O   HOH Z 422 " =    1.212
peak=    5.525 closest distance to " O   HOH Z 222 " =    1.540
peak=    5.516 closest distance to " O   HOH Z 431 " =    1.847
peak=    5.493 closest distance to " O   HOH Z  29 " =    1.745
peak=    5.455 closest distance to " O   HOH Z 287 " =    2.106
peak=    5.371 closest distance to " O   HOH Z 417 " =    2.918
peak=    5.294 closest distance to " O   HOH Z 293 " =    1.532
peak=    5.282 closest distance to " O   HOH Z  66 " =    1.227
peak=    5.232 closest distance to " CG  PRO A  90 " =    1.428
peak=    5.223 closest distance to " O   HOH Z 105 " =    1.371
peak=    5.216 closest distance to " O   HOH Z  63 " =    1.993
peak=    5.166 closest distance to " O   HOH Z 278 " =    1.293
peak=    5.084 closest distance to " O   HOH Z  65 " =    1.581
peak=    5.044 closest distance to " O   HOH Z  46 " =    1.195
peak=    4.963 closest distance to " O   HOH Z   7 " =    2.034
peak=    4.945 closest distance to " O   HOH Z 403 " =    2.043
peak=    4.939 closest distance to " NE2 GLN A  11 " =    1.369
peak=    4.921 closest distance to " O   HOH Z 142 " =    1.920
peak=    4.890 closest distance to " CB  SER A 216 " =    1.055
peak=    4.888 closest distance to " O   HOH Z 418 " =    1.262
peak=    4.874 closest distance to " O   HOH Z  69 " =    1.973
peak=    4.839 closest distance to " CG  PRO A  54 " =    1.445
peak=    4.822 closest distance to " O  BHOH Z  74 " =    1.107
peak=    4.813 closest distance to " O   HOH Z 145 " =    1.936
peak=    4.795 closest distance to " CG2 ILE A 120 " =    1.108
peak=    4.761 closest distance to " O   HOH Z 427 " =    2.046
peak=    4.728 closest distance to " O   HOH Z 359 " =    1.712
peak=    4.674 closest distance to " O   HOH Z 427 " =    1.227
peak=    4.646 closest distance to " O   HOH Z 419 " =    2.532
peak=    4.628 closest distance to " O   HOH Z  63 " =    1.785
peak=    4.530 closest distance to " NH1AARG A 145 " =    1.251
peak=    4.446 closest distance to " O   HOH Z 232 " =    2.179
peak=    4.426 closest distance to " O   HOH Z 415 " =    1.057
peak=    4.390 closest distance to " O   HOH Z 139 " =    1.182
peak=    4.372 closest distance to " O   HOH Z 380 " =    2.266
peak=    4.365 closest distance to " O   HOH Z 316 " =    3.063
peak=    4.364 closest distance to " O   HOH Z  92 " =    1.320
peak=    4.326 closest distance to " O   HOH Z   9 " =    1.887
peak=    4.299 closest distance to " O   PRO A 198 " =    1.309
peak=    4.289 closest distance to " O   HOH Z  39 " =    1.428
peak=    4.286 closest distance to " O   HOH Z 298 " =    1.923
peak=    4.285 closest distance to " CB  ALA A 114 " =    0.926
peak=    4.284 closest distance to " O   HOH Z 295 " =    1.168
peak=    4.260 closest distance to " CB  PRO A  54 " =    1.229
peak=    4.238 closest distance to " O   HOH Z 423 " =    2.239
peak=    4.201 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.200 closest distance to " N   TYR A  15 " =    1.175
peak=    4.199 closest distance to " N   GLN A 278 " =    1.064
peak=    4.192 closest distance to " O   HOH Z  11 " =    1.172
peak=    4.190 closest distance to " O   HOH Z 276 " =    1.389
peak=    4.185 closest distance to " CA  TYR A  30 " =    1.164
peak=    4.184 closest distance to " CB  ASN A 148 " =    1.407
peak=    4.184 closest distance to " NZ  LYS A 117 " =    3.070
peak=    4.174 closest distance to " O   HOH Z 381 " =    1.162
peak=    4.129 closest distance to " CZ3 TRP A 266 " =    1.152
peak=    4.120 closest distance to " CB  SER A  63 " =    1.403
peak=    4.100 closest distance to " CB  GLN A 223 " =    1.547
peak=    4.099 closest distance to " CG  TRP A 179 " =    2.158
peak=    4.095 closest distance to " CB  ARG A 275 " =    1.121
peak=    4.064 closest distance to " CD  ARG A  66 " =    2.343
peak=    4.055 closest distance to " O   HOH Z 272 " =    1.877
peak=    4.055 closest distance to " O   HOH Z 158 " =    1.152
peak=    4.051 closest distance to " O   HOH Z 375 " =    1.068
peak=    4.011 closest distance to " O   HOH Z 424 " =    1.259
peak=    3.990 closest distance to " O   HOH Z 211 " =    1.203
peak=    3.942 closest distance to " O   HOH Z 368 " =    3.462
peak=    3.939 closest distance to " CB  GLU A 128 " =    1.035
peak=    3.935 closest distance to " O   HOH Z 127 " =    0.981
peak=    3.920 closest distance to " O   HOH Z 225 " =    1.836
peak=    3.918 closest distance to " CE  LYS A 119 " =    1.261
peak=    3.914 closest distance to " CB  SER A  99 " =    0.910
peak=    3.909 closest distance to " O   HOH Z 258 " =    2.085
peak=    3.908 closest distance to " CE3 TRP A 274 " =    1.393
peak=    3.900 closest distance to " O   HOH Z 133 " =    0.868
peak=    3.895 closest distance to " O   HOH Z 361 " =    1.436
peak=    3.894 closest distance to " O   HOH Z  49 " =    1.460
peak=    3.893 closest distance to " O   HOH Z 112 " =    1.262
peak=    3.891 closest distance to " NZ  LYS A 119 " =    2.266
peak=    3.891 closest distance to " O   HOH Z 392 " =    1.272
peak=    3.886 closest distance to " CB  ASP A 124 " =    0.918
peak=    3.884 closest distance to " O   HOH Z 358 " =    1.317
peak=    3.862 closest distance to " O   HOH Z 425 " =    1.445
peak=    3.860 closest distance to " CG  PRO A 213 " =    1.265
peak=    3.859 closest distance to " CG  GLN A  58 " =    1.074
peak=    3.851 closest distance to " CB  VAL A 202 " =    1.679
peak=    3.850 closest distance to " O   HOH Z 365 " =    1.486
peak=    3.846 closest distance to " CA  PHE A 283 " =    1.330
peak=    3.843 closest distance to " O   HOH Z  78 " =    1.884
peak=    3.842 closest distance to " CG  LYS A  76 " =    1.741
peak=    3.840 closest distance to " CG2 VAL A 257 " =    0.835
peak=    3.834 closest distance to " CB  TRP A 179 " =    1.471
peak=    3.824 closest distance to " O   HOH Z 362 " =    1.954
peak=    3.823 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.808 closest distance to " O   HOH Z 143 " =    1.277
peak=    3.807 closest distance to " O   HOH Z 282 " =    1.812
peak=    3.801 closest distance to " O   HOH Z 437 " =    2.050
peak=    3.800 closest distance to " O   HOH Z 153 " =    3.577
peak=    3.794 closest distance to " NH2 ARG A  56 " =    2.042
peak=    3.786 closest distance to " N   GLU A   2 " =    1.480
peak=    3.784 closest distance to " O   HOH Z 193 " =    1.901
peak=    3.779 closest distance to " O   TYR A 116 " =    1.289
peak=    3.774 closest distance to " CA  ARG A 102 " =    1.110
peak=    3.771 closest distance to " CB  SER A 276 " =    1.181
peak=    3.764 closest distance to " O   HOH Z  61 " =    1.769
peak=    3.760 closest distance to " O   HOH Z 434 " =    1.581
peak=    3.759 closest distance to " O   HOH Z 244 " =    1.560
peak=    3.758 closest distance to " O   HOH Z  67 " =    1.289
peak=    3.752 closest distance to " O   HOH Z 378 " =    1.121
peak=    3.751 closest distance to " NZ  LYS A 117 " =    1.211
peak=    3.750 closest distance to " O   HOH Z 119 " =    1.523
peak=    3.747 closest distance to " O   HOH Z 146 " =    1.551
peak=    3.743 closest distance to " NZ  LYS A 166 " =    1.069
peak=    3.739 closest distance to " CB  GLU A 277 " =    3.676
peak=    3.739 closest distance to " O   HOH Z 280 " =    1.459
peak=    3.722 closest distance to " O   HOH Z 259 " =    2.306
peak=    3.709 closest distance to " CG  GLN A  89 " =    1.566
peak=    3.694 closest distance to " ND2BASN A 224 " =    0.930
peak=    3.693 closest distance to " NE1 TRP A 274 " =    1.052
peak=    3.691 closest distance to " CA  ALA A  51 " =    1.052
peak=    3.682 closest distance to " CB  TRP A 266 " =    1.062
peak=    3.678 closest distance to " ND2 ASN A  60 " =    2.939
peak=    3.678 closest distance to " CD  GLN A  77 " =    1.219
peak=    3.677 closest distance to " O   HOH Z  97 " =    1.443
peak=    3.673 closest distance to " SD BMET A  47 " =    1.116
peak=    3.666 closest distance to " OG ASER A 212 " =    1.440
peak=    3.666 closest distance to " NH2AARG A 145 " =    1.271
peak=    3.659 closest distance to " C   GLN A  73 " =    1.019
peak=    3.653 closest distance to " O   HOH Z   6 " =    1.615
peak=    3.650 closest distance to " CE3 TRP A 150 " =    1.122
peak=    3.646 closest distance to " O   HOH Z 426 " =    1.104
peak=    3.645 closest distance to " CE  MET A  93 " =    1.415
peak=    3.643 closest distance to " NH2AARG A 190 " =    1.892
peak=    3.642 closest distance to " O   HOH Z  91 " =    2.315
peak=    3.640 closest distance to " O   HOH Z 117 " =    1.092
peak=    3.637 closest distance to " O   HOH Z 424 " =    3.092
peak=    3.625 closest distance to " O   HOH Z  44 " =    1.943
peak=    3.624 closest distance to " CG2 THR A 221 " =    1.285
peak=    3.618 closest distance to " O   HOH Z 156 " =    3.405
peak=    3.613 closest distance to " O   HOH Z 368 " =    1.783
peak=    3.611 closest distance to " O   HOH Z 124 " =    1.439
peak=    3.610 closest distance to " CB  PRO A  90 " =    1.038
peak=    3.607 closest distance to " CB  ARG A 219 " =    0.789
peak=    3.598 closest distance to " O   HOH Z 327 " =    1.745
peak=    3.594 closest distance to " O   HOH Z 371 " =    1.893
peak=    3.594 closest distance to " CG1 VAL A 296 " =    1.146
peak=    3.578 closest distance to " O   HOH Z  88 " =    3.596
peak=    3.577 closest distance to " CB  THR A  31 " =    1.634
peak=    3.560 closest distance to " C   HIS A 115 " =    1.008
peak=    3.557 closest distance to " CA  GLU A 152 " =    0.925
peak=    3.551 closest distance to " CB  SER A 273 " =    0.991
peak=    3.542 closest distance to " O   HOH Z 104 " =    1.693
peak=    3.541 closest distance to " O   HOH Z 365 " =    2.517
peak=    3.540 closest distance to " CB  TYR A 116 " =    1.242
peak=    3.539 closest distance to " CG2 ILE A 239 " =    1.057
peak=    3.537 closest distance to " O   HOH Z  59 " =    1.871
peak=    3.535 closest distance to " CA  VAL A 125 " =    1.087
peak=    3.533 closest distance to " CA  ALA A 160 " =    0.956
peak=    3.531 closest distance to " CB  MET A  40 " =    0.808
peak=    3.528 closest distance to " CG2BVAL A  41 " =    0.993
peak=    3.526 closest distance to " OG  SER A  26 " =    1.444
peak=    3.523 closest distance to " O   HOH Z  58 " =    1.770
peak=    3.522 closest distance to " NZ BLYS A 290 " =    0.944
peak=    3.519 closest distance to " O   HOH Z 425 " =    2.110
peak=    3.515 closest distance to " C   VAL A  72 " =    0.951
peak=    3.509 closest distance to " O   HOH Z 414 " =    1.350
peak=    3.507 closest distance to " OD1 ASP A 238 " =    1.005
peak=    3.506 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.503 closest distance to " O   HOH Z  40 " =    2.247
peak=    3.500 closest distance to " CA  SER A  87 " =    1.053
peak=    3.500 closest distance to " OG BSER A 164 " =    2.313
peak=    3.497 closest distance to " O   HOH Z 405 " =    1.692
peak=    3.496 closest distance to " O   HOH Z 215 " =    1.591
peak=    3.489 closest distance to " O   HOH Z  57 " =    1.240
peak=    3.484 closest distance to " N   ALA A   1 " =    1.552
peak=    3.482 closest distance to " CG2 ILE A  20 " =    1.562
peak=    3.480 closest distance to " O   HOH Z   7 " =    2.816
peak=    3.478 closest distance to " O   HOH Z  76 " =    1.229
peak=    3.476 closest distance to " OG BSER A 258 " =    3.640
peak=    3.474 closest distance to " OE1 GLU A   2 " =    1.383
peak=    3.474 closest distance to " CB  PHE A 225 " =    1.354
peak=    3.467 closest distance to " CB  TRP A 274 " =    1.093
peak=    3.465 closest distance to " CA  ARG A  36 " =    1.124
peak=    3.462 closest distance to " O   ASN A 142 " =    1.111
peak=    3.462 closest distance to " O   HOH Z 106 " =    4.034
peak=    3.461 closest distance to " O   HOH Z 214 " =    2.395
peak=    3.459 closest distance to " O   HOH Z  43 " =    1.166
peak=    3.449 closest distance to " CZ  PHE A 218 " =    1.219
peak=    3.447 closest distance to " O   HOH Z 220 " =    1.378
peak=    3.446 closest distance to " CG  GLU A 277 " =    2.009
peak=    3.442 closest distance to " O   HOH Z 147 " =    1.189
peak=    3.442 closest distance to " CG  ARG A 159 " =    0.884
peak=    3.441 closest distance to " CZ  PHE A  38 " =    1.342
peak=    3.439 closest distance to " CB  LYS A 290 " =    0.944
peak=    3.426 closest distance to " CB  ALA A 242 " =    1.265
peak=    3.426 closest distance to " O   HOH Z 423 " =    1.827
peak=    3.426 closest distance to " O   HOH Z 126 " =    1.412
peak=    3.422 closest distance to " OE2 GLU A  53 " =    2.108
peak=    3.422 closest distance to " O   HOH Z 352 " =    1.669
peak=    3.421 closest distance to " O   HOH Z  90 " =    2.284
peak=    3.419 closest distance to " O   HOH Z 207 " =    0.864
peak=    3.418 closest distance to " N   ALA A 292 " =    1.166
peak=    3.411 closest distance to " O   HOH Z 219 " =    3.707
peak=    3.411 closest distance to " O   HOH Z  51 " =    1.737
peak=    3.405 closest distance to " CG  LEU A 167 " =    1.336
peak=    3.404 closest distance to " O   HOH Z 201 " =    1.747
peak=    3.402 closest distance to " O   HOH Z 363 " =    1.074
peak=    3.400 closest distance to " O   HOH Z  29 " =    1.501
peak=    3.400 closest distance to " O   HOH Z  44 " =    2.989
peak=    3.397 closest distance to " O   GLY A 211 " =    1.082
peak=    3.394 closest distance to " O   ASN A  69 " =    1.407
peak=    3.393 closest distance to " CD  ARG A 159 " =    0.870
peak=    3.388 closest distance to " ND2 ASN A 249 " =    0.757
peak=    3.386 closest distance to " CB  SER A 210 " =    0.991
peak=    3.385 closest distance to " O   HOH Z 157 " =    1.581
peak=    3.382 closest distance to " CB  SER A   3 " =    1.416
peak=    3.380 closest distance to " O   HOH Z 156 " =    3.280
peak=    3.370 closest distance to " O   HOH Z 222 " =    2.326
peak=    3.370 closest distance to " CD2 TRP A 179 " =    1.492
peak=    3.370 closest distance to " O   HOH Z 236 " =    1.351
peak=    3.366 closest distance to " CA  TYR A 116 " =    1.474
peak=    3.366 closest distance to " OE1 GLN A 240 " =    1.583
peak=    3.361 closest distance to " CE2 PHE A  16 " =    0.789
peak=    3.355 closest distance to " CG  GLN A  11 " =    2.235
peak=    3.354 closest distance to " O   HOH Z  30 " =    1.899
peak=    3.350 closest distance to " O   HOH Z 172 " =    2.096
peak=    3.347 closest distance to " CA  ASN A 127 " =    1.252
peak=    3.346 closest distance to " NE2 HIS A 207 " =    1.093
peak=    3.346 closest distance to " CA  LEU A 282 " =    1.132
peak=    3.342 closest distance to " CG2 VAL A 202 " =    1.599
peak=    3.339 closest distance to " NE2 GLN A  73 " =    1.652
peak=    3.339 closest distance to " O   HOH Z 116 " =    1.161
peak=    3.338 closest distance to " O   HOH Z 393 " =    1.257
peak=    3.330 closest distance to " CA  MET A 105 " =    0.939
peak=    3.328 closest distance to " OD1 ASN A  45 " =    1.355
peak=    3.323 closest distance to " N   VAL A 125 " =    1.505
peak=    3.321 closest distance to " CB  PHE A  61 " =    1.189
peak=    3.319 closest distance to " O   HOH Z 258 " =    1.066
peak=    3.317 closest distance to " CA  CYS A 260 " =    1.322
peak=    3.309 closest distance to " O   HOH Z 119 " =    4.309
peak=    3.308 closest distance to " O   ALA A 165 " =    1.466
peak=    3.308 closest distance to " CB  ASP A 272 " =    0.987
peak=    3.305 closest distance to " CB  MET A  47 " =    1.071
peak=    3.305 closest distance to " CB  VAL A 296 " =    1.465
peak=    3.301 closest distance to " CD  LYS A 166 " =    1.537
peak=    3.300 closest distance to " O   HOH Z  27 " =    0.941
peak=    3.300 closest distance to " O   HOH Z 191 " =    3.147
peak=    3.300 closest distance to " CD1 LEU A 300 " =    0.988
peak=    3.299 closest distance to " OG1 THR A 221 " =    1.194
peak=    3.297 closest distance to " O   HOH Z 411 " =    3.556
peak=    3.297 closest distance to " CB  PHE A 130 " =    1.022
peak=    3.294 closest distance to " O   HOH Z  32 " =    2.402
peak=    3.287 closest distance to " N   CYS A 260 " =    0.946
peak=    3.286 closest distance to " CA  ARG A 159 " =    1.210
peak=    3.279 closest distance to " O   HOH Z 357 " =    2.146
peak=    3.274 closest distance to " CB  ASP A 140 " =    1.059
peak=    3.274 closest distance to " CG  GLN A 205 " =    1.238
peak=    3.274 closest distance to " CB  GLU A 152 " =    1.113
peak=    3.271 closest distance to " CA  ARG A 195 " =    1.398
peak=    3.266 closest distance to " O   HOH Z  26 " =    1.495
peak=    3.265 closest distance to " CA  ASN A 176 " =    1.168
peak=    3.265 closest distance to " CB  LEU A 300 " =    0.912
peak=    3.264 closest distance to " O   HOH Z 265 " =    1.947
peak=    3.263 closest distance to " CB  ALA A 233 " =    1.158
peak=    3.262 closest distance to " O   HOH Z  88 " =    2.659
peak=    3.260 closest distance to " CB  ASN A 215 " =    1.176
peak=    3.256 closest distance to " O   HOH Z  17 " =    1.796
peak=    3.256 closest distance to " O   HOH Z 194 " =    2.233
peak=    3.252 closest distance to " CB  ASP A 200 " =    0.975
peak=    3.249 closest distance to " CB  ALA A 114 " =    0.955
peak=    3.247 closest distance to " O   HOH Z 390 " =    2.435
peak=    3.245 closest distance to " O   HOH Z  83 " =    1.120
peak=    3.240 closest distance to " O   HOH Z  47 " =    2.065
peak=    3.237 closest distance to " N   SER A  97 " =    0.860
peak=    3.235 closest distance to " CD  ARG A  79 " =    0.979
peak=    3.233 closest distance to " CG2 VAL A 232 " =    1.147
peak=    3.231 closest distance to " O   HOH Z 323 " =    1.642
peak=    3.231 closest distance to " CA  ALA A 129 " =    1.201
peak=    3.227 closest distance to " O   HOH Z 422 " =    2.015
peak=    3.227 closest distance to " OD1 ASP A 171 " =    1.310
peak=    3.225 closest distance to " CG AARG A 275 " =    1.321
peak=    3.225 closest distance to " O   THR A 294 " =    1.055
peak=    3.221 closest distance to " N   VAL A 296 " =    1.851
peak=    3.219 closest distance to " N   ALA A 165 " =    1.275
peak=    3.219 closest distance to " OG BSER A  99 " =    2.264
peak=    3.218 closest distance to " O   HOH Z 394 " =    3.725
peak=    3.215 closest distance to " ND1 HIS A  81 " =    1.617
peak=    3.213 closest distance to " CB  ASN A 187 " =    0.971
peak=    3.211 closest distance to " CB  VAL A 265 " =    1.327
peak=    3.210 closest distance to " CE  LYS A  48 " =    1.205
peak=    3.209 closest distance to " OD2 ASP A 286 " =    2.354
peak=    3.209 closest distance to " CB  ASN A 110 " =    1.073
peak=    3.207 closest distance to " CB  ARG A 138 " =    0.916
peak=    3.203 closest distance to " O   HOH Z 273 " =    1.199
peak=    3.202 closest distance to " O   HOH Z  78 " =    1.930
peak=    3.200 closest distance to " CB  ALA A  43 " =    0.910
peak=    3.198 closest distance to " O   HOH Z 122 " =    2.117
peak=    3.197 closest distance to " O   HOH Z 290 " =    1.102
peak=    3.192 closest distance to " O   HOH Z 406 " =    1.451
peak=    3.192 closest distance to " O   HOH Z 217 " =    1.082
peak=    3.192 closest distance to " O   HOH Z  68 " =    1.958
peak=    3.191 closest distance to " CA  SER A  95 " =    0.918
peak=    3.191 closest distance to " O   HOH Z 208 " =    1.244
peak=    3.190 closest distance to " CB  LEU A 237 " =    0.779
peak=    3.186 closest distance to " O   HOH Z 387 " =    2.675
peak=    3.175 closest distance to " O   HOH Z 344 " =    3.083
peak=    3.174 closest distance to " O   HOH Z  28 " =    0.974
peak=    3.166 closest distance to " O   HOH Z  21 " =    1.377
peak=    3.165 closest distance to " CD  ARG A 138 " =    0.887
peak=    3.165 closest distance to " O   HOH Z 180 " =    2.254
peak=    3.163 closest distance to " CA  ASN A 215 " =    0.985
peak=    3.162 closest distance to " CB  ASN A 142 " =    0.964
peak=    3.162 closest distance to " NH1 ARG A  14 " =    0.986
peak=    3.160 closest distance to " CB  ARG A 190 " =    1.706
peak=    3.159 closest distance to " O   HOH Z 145 " =    1.941
peak=    3.158 closest distance to " CA  LEU A  83 " =    1.647
peak=    3.157 closest distance to " CB  ILE A 120 " =    1.389
peak=    3.156 closest distance to " O   HOH Z 130 " =    2.031
peak=    3.149 closest distance to " O   HOH Z 296 " =    1.055
peak=    3.149 closest distance to " O   HOH Z 394 " =    1.575
peak=    3.147 closest distance to " N   GLY A 302 " =    0.948
peak=    3.146 closest distance to " CB  ASP A 171 " =    0.758
peak=    3.144 closest distance to " CB  LEU A 228 " =    1.162
peak=    3.140 closest distance to " NZ  LYS A 119 " =    2.063
peak=    3.136 closest distance to " CB  SER A  62 " =    1.006
peak=    3.135 closest distance to " N   ILE A  33 " =    1.050
peak=    3.126 closest distance to " O   HOH Z  67 " =    1.279
peak=    3.122 closest distance to " NE2 GLN A  58 " =    4.472
peak=    3.119 closest distance to " NZ  LYS A  48 " =    1.295
peak=    3.118 closest distance to " C   GLU A 277 " =    1.331
peak=    3.116 closest distance to " CG  LYS A 119 " =    0.984
peak=    3.109 closest distance to " O   HOH Z 298 " =    4.318
peak=    3.105 closest distance to " N   ILE A 109 " =    1.628
peak=    3.100 closest distance to " CE AMET A  47 " =    1.323
peak=    3.089 closest distance to " O   HOH Z 345 " =    2.077
peak=    3.084 closest distance to " CB  TYR A  30 " =    1.640
peak=    3.076 closest distance to " O   HOH Z 248 " =    1.704
peak=    3.074 closest distance to " OD2 ASP A 286 " =    2.483
peak=    3.070 closest distance to " CA  ASN A  74 " =    1.309
peak=    3.070 closest distance to " O   HOH Z 251 " =    1.413
peak=    3.063 closest distance to " N   ARG A  66 " =    0.997
peak=    3.049 closest distance to " CB  VAL A 230 " =    0.821
peak=    3.045 closest distance to " O   HOH Z 389 " =    1.854
peak=    3.010 closest distance to " CB  TRP A 150 " =    0.803
peak=    2.965 closest distance to " O   HOH Z  40 " =    1.426

                           ----------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: 0.752 - 5.689
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 210
   mapped sites are within: 0.752 - 5.689

peak=   -4.613 closest distance to " O   HOH Z  28 " =    1.096
peak=   -4.304 closest distance to " O   PRO A 198 " =    1.095
peak=   -4.265 closest distance to " CZ2 TRP A  92 " =    2.813
peak=   -4.137 closest distance to " CG  MET A 105 " =    1.019
peak=   -4.128 closest distance to " OG  SER A  32 " =    0.917
peak=   -4.114 closest distance to " O   HOH Z  60 " =    1.707
peak=   -4.113 closest distance to " O   HOH Z 415 " =    0.973
peak=   -4.063 closest distance to " O   ALA A  10 " =    1.596
peak=   -4.061 closest distance to " OD1 ASP A 191 " =    1.901
peak=   -4.040 closest distance to " O   HOH Z 385 " =    1.379
peak=   -4.016 closest distance to " OE1 GLU A  44 " =    1.955
peak=   -4.006 closest distance to " CD1 TRP A 179 " =    1.144
peak=   -3.987 closest distance to " O   SER A 135 " =    1.512
peak=   -3.960 closest distance to " O   HOH Z 103 " =    0.752
peak=   -3.937 closest distance to " N   THR A 157 " =    1.640
peak=   -3.936 closest distance to " O   HOH Z 105 " =    2.046
peak=   -3.933 closest distance to " O   HOH Z  39 " =    0.921
peak=   -3.925 closest distance to " O   HOH Z 216 " =    1.441
peak=   -3.879 closest distance to " O   HOH Z  69 " =    1.483
peak=   -3.869 closest distance to " OE1 GLU A 277 " =    2.152
peak=   -3.858 closest distance to " CD  ARG A  14 " =    3.131
peak=   -3.854 closest distance to " NE2 GLN A 122 " =    1.008
peak=   -3.841 closest distance to " OG  SER A  63 " =    1.380
peak=   -3.830 closest distance to " O   HOH Z 231 " =    1.124
peak=   -3.828 closest distance to " O   GLU A 152 " =    1.420
peak=   -3.828 closest distance to " CB  GLN A  55 " =    1.220
peak=   -3.828 closest distance to " O   HOH Z 313 " =    1.103
peak=   -3.810 closest distance to " CA  ASP A  27 " =    2.471
peak=   -3.796 closest distance to " CB  PRO A 243 " =    2.579
peak=   -3.780 closest distance to " O   HOH Z 266 " =    5.037
peak=   -3.772 closest distance to " CZ2 TRP A 274 " =    0.957
peak=   -3.768 closest distance to " CD2 TYR A 293 " =    1.815
peak=   -3.766 closest distance to " O   HOH Z 111 " =    1.780
peak=   -3.762 closest distance to " O   GLN A 240 " =    3.201
peak=   -3.724 closest distance to " CB  ALA A   9 " =    2.400
peak=   -3.718 closest distance to " CG  TRP A 266 " =    1.799
peak=   -3.715 closest distance to " CD  ARG A 156 " =    2.014
peak=   -3.709 closest distance to " CB  ALA A 131 " =    1.912
peak=   -3.706 closest distance to " NE2 GLN A 194 " =    1.908
peak=   -3.705 closest distance to " N   GLN A  58 " =    1.290
peak=   -3.698 closest distance to " O   HOH Z 130 " =    0.912
peak=   -3.673 closest distance to " O   HOH Z 298 " =    2.542
peak=   -3.668 closest distance to " O   HOH Z  24 " =    0.880
peak=   -3.666 closest distance to " CA  GLY A  98 " =    1.782
peak=   -3.661 closest distance to " O   SER A  22 " =    2.604
peak=   -3.653 closest distance to " O   HOH Z 131 " =    3.874
peak=   -3.651 closest distance to " O   HOH Z 389 " =    2.315
peak=   -3.640 closest distance to " NE2 GLN A  55 " =    1.047
peak=   -3.639 closest distance to " OG  SER A  97 " =    2.139
peak=   -3.615 closest distance to " O   ILE A  49 " =    1.708
peak=   -3.610 closest distance to " CA  GLY A 133 " =    2.059
peak=   -3.609 closest distance to " O   HOH Z 198 " =    1.642
peak=   -3.596 closest distance to " CG2 ILE A 120 " =    0.902
peak=   -3.588 closest distance to " CD  LYS A 166 " =    2.639
peak=   -3.588 closest distance to " OE1 GLN A 223 " =    2.389
peak=   -3.587 closest distance to " CB  ALA A 291 " =    2.214
peak=   -3.586 closest distance to " OD2 ASP A 272 " =    1.422
peak=   -3.582 closest distance to " CD2 PHE A  61 " =    1.939
peak=   -3.581 closest distance to " CZ  PHE A  59 " =    1.488
peak=   -3.573 closest distance to " NH2 ARG A 219 " =    2.018
peak=   -3.570 closest distance to " OG  SER A  87 " =    1.846
peak=   -3.562 closest distance to " CG2AVAL A  41 " =    2.754
peak=   -3.552 closest distance to " NZ  LYS A 166 " =    1.621
peak=   -3.551 closest distance to " O   HOH Z 276 " =    1.249
peak=   -3.550 closest distance to " CA  HIS A 207 " =    1.200
peak=   -3.543 closest distance to " ND2 ASN A 285 " =    2.094
peak=   -3.539 closest distance to " O   HOH Z 129 " =    3.550
peak=   -3.537 closest distance to " CB  ASN A  45 " =    2.089
peak=   -3.534 closest distance to " O   HOH Z 368 " =    1.527
peak=   -3.534 closest distance to " O   HOH Z   5 " =    1.320
peak=   -3.533 closest distance to " NE2 GLN A  77 " =    1.504
peak=   -3.528 closest distance to " OG  SER A 245 " =    1.602
peak=   -3.526 closest distance to " O   PHE A 218 " =    1.547
peak=   -3.514 closest distance to " O   PRO A 163 " =    1.512
peak=   -3.513 closest distance to " O   HOH Z 100 " =    1.259
peak=   -3.511 closest distance to " O   HOH Z 181 " =    1.669
peak=   -3.509 closest distance to " CG2 VAL A 202 " =    1.967
peak=   -3.505 closest distance to " O   GLY A  80 " =    2.541
peak=   -3.496 closest distance to " O   HOH Z 163 " =    1.842
peak=   -3.494 closest distance to " OG BSER A 134 " =    1.633
peak=   -3.493 closest distance to " O   HOH Z 143 " =    1.192
peak=   -3.487 closest distance to " O   HOH Z 425 " =    0.916
peak=   -3.486 closest distance to " CE2 TYR A  30 " =    2.553
peak=   -3.480 closest distance to " CE3 TRP A 274 " =    2.340
peak=   -3.478 closest distance to " O   HOH Z  52 " =    0.982
peak=   -3.464 closest distance to " O   HOH Z 412 " =    3.614
peak=   -3.450 closest distance to " CB  ASP A 171 " =    2.274
peak=   -3.444 closest distance to " CG1 VAL A 265 " =    2.362
peak=   -3.440 closest distance to " CZ  PHE A 130 " =    1.003
peak=   -3.432 closest distance to " O   HOH Z 147 " =    2.013
peak=   -3.412 closest distance to " O   ASP A 124 " =    1.472
peak=   -3.411 closest distance to " O   GLY A 203 " =    2.551
peak=   -3.387 closest distance to " O   ARG A 145 " =    1.195
peak=   -3.382 closest distance to " O  BHOH Z  74 " =    0.792
peak=   -3.376 closest distance to " O   HOH Z 324 " =    0.889
peak=   -3.370 closest distance to " N   ALA A   1 " =    1.669
peak=   -3.369 closest distance to " O   HOH Z 389 " =    0.998
peak=   -3.367 closest distance to " CB  ALA A  43 " =    2.519
peak=   -3.366 closest distance to " CB  SER A 210 " =    1.113
peak=   -3.363 closest distance to " CD2 TYR A 116 " =    2.169
peak=   -3.359 closest distance to " N   ALA A  84 " =    1.664
peak=   -3.358 closest distance to " C   PHE A  59 " =    1.054
peak=   -3.357 closest distance to " O   HOH Z 404 " =    1.369
peak=   -3.357 closest distance to " NE2 GLN A 223 " =    1.851
peak=   -3.356 closest distance to " CD2 LEU A 222 " =    2.131
peak=   -3.346 closest distance to " O   HOH Z 128 " =    2.477
peak=   -3.344 closest distance to " N   ASN A 127 " =    1.254
peak=   -3.339 closest distance to " O   HOH Z  49 " =    1.348
peak=   -3.336 closest distance to " CE1 TYR A  15 " =    2.358
peak=   -3.333 closest distance to " CB  TRP A  85 " =    2.126
peak=   -3.333 closest distance to " CG2 ILE A  20 " =    2.753
peak=   -3.328 closest distance to " O   HOH Z  71 " =    1.432
peak=   -3.328 closest distance to " CB  ASP A 132 " =    2.562
peak=   -3.322 closest distance to " O   HOH Z 251 " =    0.964
peak=   -3.322 closest distance to " O   HOH Z 412 " =    5.689
peak=   -3.320 closest distance to " ND2 ASN A 209 " =    1.820
peak=   -3.318 closest distance to " O   HOH Z 390 " =    2.443
peak=   -3.309 closest distance to " CB  ALA A 100 " =    2.040
peak=   -3.306 closest distance to " O   HOH Z 238 " =    0.996
peak=   -3.302 closest distance to " O   HOH Z  88 " =    2.188
peak=   -3.302 closest distance to " CB  TYR A  15 " =    2.160
peak=   -3.301 closest distance to " O   HOH Z 381 " =    1.169
peak=   -3.300 closest distance to " CZ3 TRP A 179 " =    1.402
peak=   -3.300 closest distance to " O   HOH Z 372 " =    2.636
peak=   -3.297 closest distance to " CA  GLY A 241 " =    2.186
peak=   -3.296 closest distance to " O   HOH Z 165 " =    2.349
peak=   -3.292 closest distance to " O   HOH Z 275 " =    1.492
peak=   -3.285 closest distance to " O   HOH Z 102 " =    1.677
peak=   -3.283 closest distance to " CB  PHE A  59 " =    1.957
peak=   -3.282 closest distance to " O   HOH Z 348 " =    1.901
peak=   -3.278 closest distance to " C   ALA A 299 " =    1.332
peak=   -3.276 closest distance to " CA  GLY A 241 " =    2.131
peak=   -3.274 closest distance to " CG2 ILE A 151 " =    2.561
peak=   -3.274 closest distance to " O   HOH Z 351 " =    1.700
peak=   -3.273 closest distance to " C   GLU A   2 " =    1.903
peak=   -3.267 closest distance to " CA  ILE A 120 " =    1.206
peak=   -3.262 closest distance to " O   HOH Z 427 " =    2.091
peak=   -3.257 closest distance to " O   HOH Z 126 " =    1.868
peak=   -3.255 closest distance to " OE2 GLU A 152 " =    1.418
peak=   -3.253 closest distance to " N   ARG A 159 " =    2.096
peak=   -3.250 closest distance to " CD1 LEU A 101 " =    2.174
peak=   -3.250 closest distance to " C   HIS A 108 " =    1.294
peak=   -3.246 closest distance to " O   HOH Z 123 " =    2.432
peak=   -3.244 closest distance to " O   HOH Z 231 " =    2.012
peak=   -3.241 closest distance to " CB  ALA A 233 " =    2.359
peak=   -3.237 closest distance to " O   LYS A  76 " =    1.928
peak=   -3.230 closest distance to " CE BMET A  47 " =    1.379
peak=   -3.224 closest distance to " CZ  TYR A 169 " =    2.019
peak=   -3.220 closest distance to " OE2 GLU A 152 " =    2.198
peak=   -3.217 closest distance to " CB  PRO A  54 " =    2.290
peak=   -3.212 closest distance to " O   HOH Z 275 " =    1.770
peak=   -3.209 closest distance to " N   ALA A  43 " =    2.669
peak=   -3.207 closest distance to " O   HOH Z 429 " =    1.791
peak=   -3.205 closest distance to " OD1 ASP A 238 " =    1.789
peak=   -3.197 closest distance to " CD2 LEU A 237 " =    2.674
peak=   -3.197 closest distance to " O   HOH Z  22 " =    2.701
peak=   -3.195 closest distance to " CZ  PHE A  38 " =    2.339
peak=   -3.193 closest distance to " NE2 GLN A 278 " =    1.626
peak=   -3.193 closest distance to " CG  PRO A 243 " =    1.721
peak=   -3.193 closest distance to " CA  GLY A 203 " =    2.434
peak=   -3.191 closest distance to " OE2 GLU A 175 " =    1.316
peak=   -3.189 closest distance to " OE1 GLN A 183 " =    1.651
peak=   -3.189 closest distance to " ND2 ASN A 249 " =    2.141
peak=   -3.182 closest distance to " O   HOH Z 179 " =    1.622
peak=   -3.181 closest distance to " O   HOH Z 407 " =    3.034
peak=   -3.181 closest distance to " O   LEU A 261 " =    1.282
peak=   -3.180 closest distance to " N   ARG A 138 " =    1.679
peak=   -3.180 closest distance to " OE1 GLU A 236 " =    1.122
peak=   -3.179 closest distance to " O   HOH Z  37 " =    1.494
peak=   -3.176 closest distance to " O   HOH Z 359 " =    1.466
peak=   -3.172 closest distance to " O   HOH Z 328 " =    1.040
peak=   -3.171 closest distance to " N   VAL A 232 " =    2.189
peak=   -3.171 closest distance to " O   HOH Z 377 " =    2.050
peak=   -3.169 closest distance to " O   HOH Z 200 " =    3.604
peak=   -3.169 closest distance to " O   HOH Z  68 " =    1.489
peak=   -3.168 closest distance to " CG  LEU A 281 " =    1.937
peak=   -3.167 closest distance to " CD2 HIS A 207 " =    1.541
peak=   -3.166 closest distance to " O   ASP A 253 " =    1.830
peak=   -3.165 closest distance to " O   HOH Z 390 " =    1.223
peak=   -3.161 closest distance to " O   HOH Z 215 " =    1.614
peak=   -3.158 closest distance to " O   HOH Z 211 " =    0.836
peak=   -3.158 closest distance to " N   GLN A 223 " =    2.046
peak=   -3.153 closest distance to " CG  LEU A  83 " =    2.107
peak=   -3.152 closest distance to " OH  TYR A 247 " =    1.532
peak=   -3.151 closest distance to " O   HOH Z 323 " =    2.176
peak=   -3.144 closest distance to " O   HOH Z 288 " =    1.412
peak=   -3.142 closest distance to " O   HOH Z 337 " =    1.605
peak=   -3.141 closest distance to " CB  ALA A 248 " =    2.156
peak=   -3.139 closest distance to " N   VAL A 125 " =    1.001
peak=   -3.131 closest distance to " CG  ARG A 259 " =    2.318
peak=   -3.127 closest distance to " O   ASP A 298 " =    1.919
peak=   -3.123 closest distance to " O   HOH Z 185 " =    1.974
peak=   -3.122 closest distance to " N   GLU A 277 " =    1.365
peak=   -3.121 closest distance to " O   HOH Z  56 " =    1.961
peak=   -3.116 closest distance to " OD2 ASP A 171 " =    1.593
peak=   -3.116 closest distance to " CD2 LEU A  25 " =    2.182
peak=   -3.109 closest distance to " O   PRO A 163 " =    1.072
peak=   -3.106 closest distance to " CG2BVAL A  41 " =    1.283
peak=   -3.101 closest distance to " CE  LYS A  76 " =    2.933
peak=   -3.099 closest distance to " O   ALA A 137 " =    0.894
peak=   -3.084 closest distance to " NH2AARG A 275 " =    5.327
peak=   -3.083 closest distance to " O   HOH Z 212 " =    0.911
peak=   -3.079 closest distance to " O   HOH Z 268 " =    2.981
peak=   -3.078 closest distance to " C   GLY A 203 " =    1.361
peak=   -3.057 closest distance to " O   HOH Z 218 " =    3.898
peak=   -3.052 closest distance to " O   HOH Z 357 " =    1.861
peak=   -3.046 closest distance to " OG ASER A  12 " =    1.720
peak=   -3.045 closest distance to " O   TRP A  70 " =    1.483
peak=   -3.043 closest distance to " N   LYS A 166 " =    1.881
peak=   -3.031 closest distance to " CG  GLU A 128 " =    1.586

================= 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    :  0.4686 0.4713   6.286802e+00   6.276627e+00
   1_bss:  0.4572 0.4637   6.280886e+00   6.267793e+00
   1_xyz:  0.3939 0.4333   6.183125e+00   6.231683e+00
   1_adp:  0.3650 0.4400   6.148262e+00   6.238387e+00
   1_occ:  0.3645 0.4411   6.148151e+00   6.239128e+00
   2_bss:  0.3646 0.4386   6.151516e+00   6.240932e+00
   2_xyz:  0.2964 0.3817   5.996474e+00   6.145530e+00
   2_adp:  0.2776 0.3665   5.954276e+00   6.115714e+00
   2_occ:  0.2773 0.3661   5.953373e+00   6.115193e+00
   3_bss:  0.2772 0.3637   5.950797e+00   6.112623e+00
   3_xyz:  0.2249 0.2949   5.764569e+00   5.952459e+00
   3_adp:  0.2017 0.2837   5.693321e+00   5.915857e+00
   3_occ:  0.2018 0.2836   5.692967e+00   5.915899e+00
   4_bss:  0.2017 0.2842   5.692555e+00   5.915505e+00
   4_xyz:  0.1655 0.2313   5.501163e+00   5.750201e+00
   4_adp:  0.1504 0.2089   5.412069e+00   5.656062e+00
   4_occ:  0.1503 0.2088   5.411394e+00   5.655348e+00
   5_bss:  0.1506 0.2087   5.409647e+00   5.653098e+00
   5_xyz:  0.1395 0.1925   5.337326e+00   5.577269e+00
   5_adp:  0.1343 0.1866   5.306316e+00   5.543906e+00
   5_occ:  0.1343 0.1865   5.306120e+00   5.543769e+00
   5_bss:  0.1343 0.1865   5.305816e+00   5.543468e+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:  0.340  42.692  -3.413   1.894   2.615   0.000   0.000   0.000
   1_xyz:  0.340  42.692  -3.413   1.894   2.615   0.000   0.000   0.000
   1_adp:  0.340  42.692  -3.413   1.894   2.615   0.000   0.000   0.000
   1_occ:  0.340  42.692  -3.413   1.894   2.615   0.000   0.000   0.000
   2_bss:  0.357  69.114  -1.403   0.738   1.499   0.000   0.000   0.000
   2_xyz:  0.357  69.114  -1.403   0.738   1.499   0.000   0.000   0.000
   2_adp:  0.357  69.114  -1.403   0.738   1.499   0.000   0.000   0.000
   2_occ:  0.357  69.114  -1.403   0.738   1.499   0.000   0.000   0.000
   3_bss:  0.358  77.826  -1.200  -0.525   0.714  -0.000   0.000   0.000
   3_xyz:  0.358  77.826  -1.200  -0.525   0.714  -0.000   0.000   0.000
   3_adp:  0.358  77.826  -1.200  -0.525   0.714  -0.000   0.000   0.000
   3_occ:  0.358  77.826  -1.200  -0.525   0.714  -0.000   0.000   0.000
   4_bss:  0.341  80.000  -1.689  -1.360   0.356  -0.000   0.000   0.000
   4_xyz:  0.341  80.000  -1.689  -1.360   0.356  -0.000   0.000   0.000
   4_adp:  0.341  80.000  -1.689  -1.360   0.356  -0.000   0.000   0.000
   4_occ:  0.341  80.000  -1.689  -1.360   0.356  -0.000   0.000   0.000
   5_bss:  0.326  69.353  -1.783  -1.842   0.190  -0.000   0.000   0.000
   5_xyz:  0.326  69.353  -1.783  -1.842   0.190  -0.000   0.000   0.000
   5_adp:  0.326  69.353  -1.783  -1.842   0.190  -0.000   0.000   0.000
   5_occ:  0.326  69.353  -1.783  -1.842   0.190  -0.000   0.000   0.000
   5_bss:  0.322  65.880  -1.896  -2.097   0.068  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.830 0.4219  0.5822    73728.671
   1_bss:  56.627 0.4364  0.6148    71104.126
   1_xyz:  51.405 0.5019  0.6933    59566.965
   1_adp:  52.135 0.4922  0.6911    61278.332
   1_occ:  52.216 0.4912  0.6893    61495.560
   2_bss:  52.109 0.4925  0.6908    61548.504
   2_xyz:  42.559 0.6103  0.8475    41974.322
   2_adp:  39.824 0.6440  0.8763    38394.534
   2_occ:  39.786 0.6444  0.8767    38305.090
   3_bss:  39.564 0.6467  0.8613    37808.338
   3_xyz:  30.520 0.7507  0.9590    23497.937
   3_adp:  28.769 0.7700  0.9544    21140.667
   3_occ:  28.758 0.7701  0.9543    21116.598
   4_bss:  28.729 0.7704  0.9360    21114.861
   4_xyz:  23.100 0.8292  0.9792    13830.965
   4_adp:  20.331 0.8577  0.9834    11295.151
   4_occ:  20.309 0.8579  0.9832    11267.194
   5_bss:  20.247 0.8583  0.9748    11175.453
   5_xyz:  18.215 0.8780  0.9839     9475.860
   5_adp:  17.334 0.8867  0.9784     8936.231
   5_occ:  17.329 0.8867  0.9782     8928.331
   5_bss:  17.321 0.8868  0.9727     8923.474
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.9069e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.9069e-01
   1_xyz:   1.410  0.010  0.096 15.645  0.006  4.104   1.1004e-01
   1_adp:   1.410  0.010  0.096 15.645  0.006  4.104   1.1004e-01
   1_occ:   1.410  0.010  0.096 15.645  0.006  4.104   1.1004e-01
   2_bss:   1.410  0.010  0.096 15.645  0.006  4.104   1.1004e-01
   2_xyz:   1.481  0.012  0.103 16.326  0.005  4.106   1.2831e-01
   2_adp:   1.481  0.012  0.103 16.326  0.005  4.106   1.2831e-01
   2_occ:   1.481  0.012  0.103 16.326  0.005  4.106   1.2831e-01
   3_bss:   1.481  0.012  0.103 16.326  0.005  4.106   1.2831e-01
   3_xyz:   1.098  0.008  0.081 14.831  0.004  4.107   7.1518e-02
   3_adp:   1.098  0.008  0.081 14.831  0.004  4.107   7.1518e-02
   3_occ:   1.098  0.008  0.081 14.831  0.004  4.107   7.1518e-02
   4_bss:   1.098  0.008  0.081 14.831  0.004  4.107   7.1518e-02
   4_xyz:   1.085  0.008  0.078 14.741  0.004  4.118   6.9567e-02
   4_adp:   1.085  0.008  0.078 14.741  0.004  4.118   6.9567e-02
   4_occ:   1.085  0.008  0.078 14.741  0.004  4.118   6.9567e-02
   5_bss:   1.085  0.008  0.078 14.741  0.004  4.118   6.9567e-02
   5_xyz:   0.888  0.005  0.065 14.380  0.003  4.110   4.9687e-02
   5_adp:   0.888  0.005  0.065 14.380  0.003  4.110   4.9687e-02
   5_occ:   0.888  0.005  0.065 14.380  0.003  4.110   4.9687e-02
   5_bss:   0.888  0.005  0.065 14.380  0.003  4.110   4.9687e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.612   2.4141e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.612   2.4141e-01
   1_xyz:   8.837  0.059  0.348 80.493  0.053  2.061   9.1438e-02
   1_adp:   8.837  0.059  0.348 80.493  0.053  2.061   9.1438e-02
   1_occ:   8.837  0.059  0.348 80.493  0.053  2.061   9.1438e-02
   2_bss:   8.837  0.059  0.348 80.493  0.053  2.061   9.1438e-02
   2_xyz:   9.693  0.067  0.335 86.550  0.030  1.941   1.2044e-01
   2_adp:   9.693  0.067  0.335 86.550  0.030  1.941   1.2044e-01
   2_occ:   9.693  0.067  0.335 86.550  0.030  1.941   1.2044e-01
   3_bss:   9.693  0.067  0.335 86.550  0.030  1.941   1.2044e-01
   3_xyz:   6.898  0.055  0.266 79.219  0.027  2.305   6.5186e-02
   3_adp:   6.898  0.055  0.266 79.219  0.027  2.305   6.5186e-02
   3_occ:   6.898  0.055  0.266 79.219  0.027  2.305   6.5186e-02
   4_bss:   6.898  0.055  0.266 79.219  0.027  2.305   6.5186e-02
   4_xyz:   6.451  0.061  0.228 83.449  0.038  2.334   9.4428e-02
   4_adp:   6.451  0.061  0.228 83.449  0.038  2.334   9.4428e-02
   4_occ:   6.451  0.061  0.228 83.449  0.038  2.334   9.4428e-02
   5_bss:   6.451  0.061  0.228 83.449  0.038  2.334   9.4428e-02
   5_xyz:   7.493  0.041  0.215 80.167  0.029  2.365   3.4773e-02
   5_adp:   7.493  0.041  0.215 80.167  0.029  2.365   3.4773e-02
   5_occ:   7.493  0.041  0.215 80.167  0.029  2.365   3.4773e-02
   5_bss:   7.493  0.041  0.215 80.167  0.029  2.365   3.4773e-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:  99.02   0.00  19.05  81.03   0.00  16.27  99.02   0.00  34.16
   1_occ:  99.02   0.00  19.05  81.03   0.00  16.27  99.02   0.00  34.16
   2_bss:  99.02   0.00  19.05  81.03   0.00  16.27  99.02   0.00  34.16
   2_xyz:  99.02   0.00  19.05  81.03   0.00  16.27  99.02   0.00  34.16
   2_adp:  98.28   0.00  18.54  77.10   0.00  15.30  98.28   0.82  36.20
   2_occ:  98.28   0.00  18.54  77.10   0.00  15.30  98.28   0.82  36.20
   3_bss:  98.28   0.00  18.54  77.10   0.00  15.30  98.28   0.82  36.20
   3_xyz:  98.28   0.00  18.54  77.10   0.00  15.30  98.28   0.82  36.20
   3_adp: 117.81   0.00  20.57 106.51   0.00  15.02 117.81   3.57  50.79
   3_occ: 117.81   0.00  20.57 106.51   0.00  15.02 117.81   3.57  50.79
   4_bss: 117.81   0.00  20.57 106.51   0.00  15.02 117.81   3.57  50.79
   4_xyz: 117.81   0.00  20.57 106.51   0.00  15.02 117.81   3.57  50.79
   4_adp: 122.20   0.00  19.38 106.40   0.00  13.54 122.20   5.64  51.18
   4_occ: 122.20   0.00  19.38 106.40   0.00  13.54 122.20   5.64  51.18
   5_bss: 122.20   0.00  19.38 106.40   0.00  13.54 122.20   5.64  51.18
   5_xyz: 122.20   0.00  19.38 106.40   0.00  13.54 122.20   5.64  51.18
   5_adp: 126.24   0.00  18.74 110.55   0.00  12.95 126.24   5.70  50.27
   5_occ: 126.24   0.00  18.74 110.55   0.00  12.95 126.24   5.70  50.27
   5_bss: 126.25   0.00  18.74 110.55   0.00  12.95 126.25   5.71  50.27
------------------------------------------------------------------------
 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:    1.693    0.017    0.286
   1_adp:    1.693    0.017    0.286
   1_occ:    1.693    0.017    0.286
   2_bss:    1.693    0.017    0.286
   2_xyz:    1.716    0.039    0.597
   2_adp:    1.716    0.039    0.597
   2_occ:    1.716    0.039    0.597
   3_bss:    1.716    0.039    0.597
   3_xyz:    1.635    0.069    0.718
   3_adp:    1.635    0.069    0.718
   3_occ:    1.635    0.069    0.718
   4_bss:    1.635    0.069    0.718
   4_xyz:    1.730    0.070    0.815
   4_adp:    1.730    0.070    0.815
   4_occ:    1.730    0.070    0.815
   5_bss:    1.730    0.070    0.815
   5_xyz:    1.759    0.069    0.843
   5_adp:    1.759    0.069    0.843
   5_occ:    1.759    0.069    0.843
   5_bss:    1.759    0.069    0.843
------------------------------------------------------------------------

CPU time actual refinement: 339.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/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_614/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_614/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.44 
  Macro-tasks:
    bulk solvent and scale       = 48.90  
    individual site refinement   = 133.41 
    weights calculation          = 29.41  
    collect and process          = 6.35   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 218.17 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 106.12 
    alpha_beta                      = 8.03   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 112.93 
    fmodel                         = 7.89   
    r_factors                      = 0.21   
    phase_errors                   = 9.93   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 248.92 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.882 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    626 calls, 105.80 s
gradients_fft:          571 calls, 100.51 s

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

# Date 2008-01-16 Time 05:14:21 PST -0800 (1200489261.76 s)
Start R-work = 0.4686, R-free = 0.4713 (no bulk solvent and anisotropic scale)
Final R-work = 0.1531, R-free = 0.2017 (no bulk solvent and anisotropic scale)

Start R-work = 0.4572, R-free = 0.4637
Final R-work = 0.1343, R-free = 0.1865