# Date 2008-01-16 Time 04:15:16 PST -0800 (1200485716.70 s)
#phil __OFF__

Command line arguments: "../244.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12921
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 244

-------------------------------------------------------------------------------
  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: (69.1963, 45.7567, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


================================== 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: (69.1963, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.9522
Completeness in resolution range: 0.969273
Completeness with d_max=infinity: 0.966261

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7691
                             d_min =   1.9522

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: (69.1963, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.9522
Completeness in resolution range: 0.969273
Completeness with d_max=infinity: 0.966261

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7695 -  4.1771 [2119/2143]  1906   213  10.1%
  bin  2:  4.1771 -  3.3280 [2038/2058]  1835   203  10.0%
  bin  3:  3.3280 -  2.9110 [2014/2033]  1814   200   9.9%
  bin  4:  2.9110 -  2.6465 [1999/2029]  1799   200  10.0%
  bin  5:  2.6465 -  2.4577 [1988/2007]  1788   200  10.1%
  bin  6:  2.4577 -  2.3134 [1960/1985]  1761   199  10.2%
  bin  7:  2.3134 -  2.1979 [1954/1982]  1760   194   9.9%
  bin  8:  2.1979 -  2.1025 [1967/2003]  1772   195   9.9%
  bin  9:  2.1025 -  2.0218 [1947/1989]  1754   193   9.9%
  bin 10:  2.0218 -  1.9522 [1603/1981]  1441   162  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.21 -     1.95: 18
        1.95 -     2.69: 203
        2.69 -     3.42: 4630
        3.42 -     4.16: 9635
        4.16 -     4.90: 14679
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.212 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.460 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.527 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.596 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.639 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29160 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_244/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/model_refine_001.geo

CPU time processing inputs: 9.62


============================ 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 = 69.19625 45.75675 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4792   ksol= 0.00   Bsol= 0.00   scale= 0.901    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.286115                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.6589 0.99   1382  153 0.3980 0.4030      6.5988      6.6137|
|  2:  4.6589 -  3.7173 0.99   1324  149 0.4275 0.3935      6.8277      6.7907|
|  3:  3.7173 -  3.2532 0.99   1297  142 0.4646 0.4386      6.7288      6.7849|
|  4:  3.2532 -  2.9583 0.99   1291  145 0.4679 0.4528       6.553      6.5057|
|  5:  2.9583 -  2.7477 0.99   1280  143 0.5065 0.4883      6.3826      6.4024|
|  6:  2.7477 -  2.5866 0.99   1298  140 0.5074 0.5416      6.2977      6.2235|
|  7:  2.5866 -  2.4577 0.99   1270  144 0.5058 0.5168      6.2444      6.2276|
|  8:  2.4577 -  2.3512 0.98   1259  138 0.5224 0.5011      6.1978      6.1731|
|  9:  2.3512 -  2.2610 0.98   1265  143 0.5220 0.5243      6.1223      6.1599|
| 10:  2.2610 -  2.1832 1.00   1262  143 0.5081 0.5588      6.1108      6.1513|
| 11:  2.1832 -  2.1152 0.97   1262  135 0.5166 0.5355       6.034      6.0686|
| 12:  2.1152 -  2.0549 0.98   1238  141 0.4972 0.4811      5.9744      5.9662|
| 13:  2.0549 -  2.0009 0.99   1287  141 0.5055 0.5066      5.8886      5.8573|
| 14:  2.0009 -  1.9522 0.73    915  102 0.5309 0.4922      5.8511      5.7732|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.6589  1382   153  0.65  38.36   0.82     0.72      86481.37|
|  2:  4.6589 -  3.7173  1324   149  0.66  38.63   0.90     0.79     123544.09|
|  3:  3.7173 -  3.2532  1297   142  0.56  47.08   0.92     0.76     129361.07|
|  4:  3.2532 -  2.9583  1291   145  0.46  54.63   0.94     0.66     115536.91|
|  5:  2.9583 -  2.7477  1280   143  0.37  61.78   0.89     0.54      88944.94|
|  6:  2.7477 -  2.5866  1298   140  0.33  64.92   0.89     0.46      78157.79|
|  7:  2.5866 -  2.4577  1270   144  0.29  68.25   0.92     0.41      72180.46|
|  8:  2.4577 -  2.3512  1259   138  0.27  69.72   0.95     0.41      67418.98|
|  9:  2.3512 -  2.2610  1265   143  0.28  69.05   0.90     0.42      60987.11|
| 10:  2.2610 -  2.1832  1262   143  0.32  65.91   0.96     0.47      51709.49|
| 11:  2.1832 -  2.1152  1262   135  0.34  64.74   0.97     0.53      47093.59|
| 12:  2.1152 -  2.0549  1238   141  0.37  62.15   1.01     0.58      40742.80|
| 13:  2.0549 -  2.0009  1287   141  0.38  61.47   0.97     0.60      34524.82|
| 14:  2.0009 -  1.9522   915   102  0.42  58.61   0.99     0.60      26133.27|
|alpha:            min =        0.41 max =            0.79 mean =         0.57|
|beta:             min =    26133.27 max =       129361.07 mean =     74446.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.73|
|phase err.(test): min =        0.00 max =           89.89 mean =        58.64|
|-----------------------------------------------------------------------------|

============================== 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 = 17.908543             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.698   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.842968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.375   (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 |  1.212 -  1.581:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.581 -  1.949:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.949 -  2.318:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.318 -  2.687:      169 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.687 -  3.056:     2242 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.056 -  3.425:     2388 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.425 -  3.794:     4163 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.794 -  4.162:     5472 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.162 -  4.531:     6572 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.531 -  4.900:     8107 |
|-----------------------------------------------------------------------------|
|-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 |        0.210 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.212 |       0.951 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4797   r_free= 0.4792   ksol= 0.00   Bsol= 0.00   scale= 0.901    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.286115                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4710   r_free= 0.4668   ksol= 0.35   Bsol= 12.97   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,1.80,-0.07,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.281464                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.913073             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.562   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.596611              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.245   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4710      final r-factor (work) = 0.3762          |
| start r-factor (free) = 0.4668      final r-factor (free) = 0.4078          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.8909 = 13.91 * 0.50 * 6.2791 + 1.00 * 0.2101                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.1847 = 13.91 * 0.50 * 6.1862 + 1.00 * 0.1499                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3762      final r-factor (work) = 0.3421          |
| start r-factor (free) = 0.4078      final r-factor (free) = 0.4237          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8832 = 1.60 * 1.00 * 6.1862 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7538 = 1.60 * 1.00 * 6.0944 + 1.00 * 0.0235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.52   19.01    None  None   None       |
|    all(noH): 2823   0      0.00    95.52   19.01    None  None   None       |
|    Sol.    : 438    0      0.00    92.65   35.28    None  None   None       |
|    Mac.    : 2385   0      0.00    95.52   16.02    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 -   9.552:  821   |   5:    47.760 -  57.312:   77        |
|      1:     9.552 -  19.104:  883   |   6:    57.312 -  66.864:   34        |
|      2:    19.104 -  28.656:  510   |   7:    66.864 -  76.416:   15        |
|      3:    28.656 -  38.208:  306   |   8:    76.416 -  85.968:    8        |
|      4:    38.208 -  47.760:  165   |   9:    85.968 -  95.520:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3421 r_free = 0.4237             target_work(ml) = 6.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3419 r_free = 0.4246             target_work(ml) = 6.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3419   r_free= 0.4246   ksol= 0.35   Bsol= 12.97   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.37,1.80,-0.07,0.00,-0.00,-0.00); trace/3= -0.21                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.103337                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3412   r_free= 0.4228   ksol= 0.35   Bsol= 48.74   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,0.97,-0.09,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.103068                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.588006              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.475  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.580113              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.597  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3412      final r-factor (work) = 0.2923          |
| start r-factor (free) = 0.4228      final r-factor (free) = 0.3694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.3262 = 8.59 * 0.50 * 6.0960 + 1.00 * 0.1497                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0602 = 8.59 * 0.50 * 6.0506 + 1.00 * 0.0790                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2923      final r-factor (work) = 0.2821          |
| start r-factor (free) = 0.3694      final r-factor (free) = 0.3554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5328 = 0.58 * 1.00 * 6.0506 + 1.00 * 0.0228                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4799 = 0.58 * 1.00 * 5.9776 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.26   17.78    None  None   None       |
|    all(noH): 2823   0      0.00    92.26   17.78    None  None   None       |
|    Sol.    : 438    0      1.76    88.50   34.15    None  None   None       |
|    Mac.    : 2385   0      0.00    92.26   14.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.226:  811   |   5:    46.128 -  55.354:   82        |
|      1:     9.226 -  18.451:  998   |   6:    55.354 -  64.579:   27        |
|      2:    18.451 -  27.677:  474   |   7:    64.579 -  73.805:   10        |
|      3:    27.677 -  36.902:  267   |   8:    73.805 -  83.030:    5        |
|      4:    36.902 -  46.128:  145   |   9:    83.030 -  92.256:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2821 r_free = 0.3554             target_work(ml) = 5.962         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2817 r_free = 0.3553             target_work(ml) = 5.962         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2817   r_free= 0.3553   ksol= 0.35   Bsol= 48.74   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,0.97,-0.09,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.962098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2824   r_free= 0.3547   ksol= 0.35   Bsol= 48.74   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,0.97,-0.09,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.961152                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.451590              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.493  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 161.137  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2824      final r-factor (work) = 0.2170          |
| start r-factor (free) = 0.3547      final r-factor (free) = 0.2854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3290 = 9.45 * 0.50 * 5.9778 + 1.00 * 0.0790                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7875 = 9.45 * 0.50 * 5.8603 + 1.00 * 0.0928                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2170      final r-factor (work) = 0.1936          |
| start r-factor (free) = 0.2854      final r-factor (free) = 0.2588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6585 = 0.45 * 1.00 * 5.8603 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5745 = 0.45 * 1.00 * 5.6790 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.82   17.25    None  None   None       |
|    all(noH): 2823   0      0.00    91.82   17.25    None  None   None       |
|    Sol.    : 438    0      4.96    88.06   39.50    None  None   None       |
|    Mac.    : 2385   0      0.00    91.82   13.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.182:  946   |   5:    45.912 -  55.094:  109        |
|      1:     9.182 -  18.365: 1033   |   6:    55.094 -  64.276:   60        |
|      2:    18.365 -  27.547:  335   |   7:    64.276 -  73.459:   17        |
|      3:    27.547 -  36.729:  176   |   8:    73.459 -  82.641:    6        |
|      4:    36.729 -  45.912:  138   |   9:    82.641 -  91.823:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1936 r_free = 0.2588             target_work(ml) = 5.630         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1933 r_free = 0.2581             target_work(ml) = 5.628         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1933   r_free= 0.2581   ksol= 0.35   Bsol= 48.74   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,0.97,-0.09,0.00,-0.00,-0.00); trace/3= -0.12                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.627734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1926   r_free= 0.2549   ksol= 0.35   Bsol= 48.74   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-0.97,-0.60,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.621917                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.892235              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.468   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.265205              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.885  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1926      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2549      final r-factor (free) = 0.2042          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1493 = 3.89 * 0.50 * 5.6813 + 1.00 * 0.0928                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8190 = 3.89 * 0.50 * 5.5277 + 1.00 * 0.0616                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1415          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4758 = 0.27 * 1.00 * 5.5277 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4348 = 0.27 * 1.00 * 5.3781 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    90.13   16.89    None  None   None       |
|    all(noH): 2823   0      1.08    90.13   16.89    None  None   None       |
|    Sol.    : 438    0      4.19    85.96   40.77    None  None   None       |
|    Mac.    : 2385   0      1.08    90.13   12.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.079 -   9.984: 1156   |   5:    45.603 -  54.507:  120        |
|      1:     9.984 -  18.889:  986   |   6:    54.507 -  63.412:   71        |
|      2:    18.889 -  27.793:  218   |   7:    63.412 -  72.317:   23        |
|      3:    27.793 -  36.698:  132   |   8:    72.317 -  81.222:    8        |
|      4:    36.698 -  45.603:  105   |   9:    81.222 -  90.126:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1415 r_free = 0.1938             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1412 r_free = 0.1931             target_work(ml) = 5.344         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1412   r_free= 0.1931   ksol= 0.35   Bsol= 48.74   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-0.97,-0.60,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.343789                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1413   r_free= 0.1927   ksol= 0.32   Bsol= 37.06   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.76,-0.81,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.341976                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.132500              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.620  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.548  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1413      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1927      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7966 = 2.13 * 0.50 * 5.3786 + 1.00 * 0.0616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7015 = 2.13 * 0.50 * 5.2966 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1750      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4670 = 0.28 * 1.00 * 5.2966 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4479 = 0.28 * 1.00 * 5.2271 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.92    90.05   16.66    None  None   None       |
|    all(noH): 2823   0      0.92    90.05   16.66    None  None   None       |
|    Sol.    : 438    0      4.94    86.17   40.69    None  None   None       |
|    Mac.    : 2385   0      0.92    90.05   12.25    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:     0.918 -   9.831: 1148   |   5:    45.482 -  54.395:  104        |
|      1:     9.831 -  18.744: 1023   |   6:    54.395 -  63.308:   78        |
|      2:    18.744 -  27.656:  209   |   7:    63.308 -  72.220:   24        |
|      3:    27.656 -  36.569:  116   |   8:    72.220 -  81.133:    9        |
|      4:    36.569 -  45.482:  108   |   9:    81.133 -  90.046:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1705             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1701             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1701   ksol= 0.32   Bsol= 37.06   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-1.76,-0.81,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211310                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.6589 0.99   1382  153 0.1064 0.1335      5.4365      5.5789|
|  2:  4.6589 -  3.7173 0.99   1324  149 0.0921 0.1239      5.5145      5.7391|
|  3:  3.7173 -  3.2532 0.99   1297  142 0.1190 0.1612      5.5852      5.9322|
|  4:  3.2532 -  2.9583 0.99   1291  145 0.1353 0.1902      5.5581      5.7478|
|  5:  2.9583 -  2.7477 0.99   1280  143 0.1478 0.1922      5.4195       5.604|
|  6:  2.7477 -  2.5866 0.99   1298  140 0.1283 0.1765      5.2589      5.4139|
|  7:  2.5866 -  2.4577 0.99   1270  144 0.1402 0.1759      5.2237      5.4505|
|  8:  2.4577 -  2.3512 0.98   1259  138 0.1323 0.1868      5.1655      5.4154|
|  9:  2.3512 -  2.2610 0.98   1265  143 0.1306 0.1871      5.1002      5.3069|
| 10:  2.2610 -  2.1832 1.00   1262  143 0.1222 0.1860      5.0276      5.2537|
| 11:  2.1832 -  2.1152 0.97   1262  135 0.1236 0.1891      4.9906       5.336|
| 12:  2.1152 -  2.0549 0.98   1238  141 0.1226 0.1768      4.9433      5.2103|
| 13:  2.0549 -  2.0009 0.99   1287  141 0.1218 0.2026      4.8413      5.1629|
| 14:  2.0009 -  1.9522 0.73    915  102 0.1119 0.1601      4.6948      4.9037|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.6589  1382   153  0.93  10.00   0.99     0.96       7872.25|
|  2:  4.6589 -  3.7173  1324   149  0.95   8.88   1.04     1.02      10528.72|
|  3:  3.7173 -  3.2532  1297   142  0.92  13.07   1.05     1.03      12925.84|
|  4:  3.2532 -  2.9583  1291   145  0.90  15.64   1.03     1.00      12922.92|
|  5:  2.9583 -  2.7477  1280   143  0.89  16.72   1.01     0.98       9352.97|
|  6:  2.7477 -  2.5866  1298   140  0.90  16.39   0.99     0.96       7558.35|
|  7:  2.5866 -  2.4577  1270   144  0.89  17.02   1.00     0.98       6805.26|
|  8:  2.4577 -  2.3512  1259   138  0.90  16.54   1.01     1.01       6220.46|
|  9:  2.3512 -  2.2610  1265   143  0.90  16.31   1.02     0.99       5554.67|
| 10:  2.2610 -  2.1832  1262   143  0.90  16.47   1.02     0.99       4952.99|
| 11:  2.1832 -  2.1152  1262   135  0.89  17.30   1.02     0.98       4743.83|
| 12:  2.1152 -  2.0549  1238   141  0.90  16.65   1.03     1.01       4470.18|
| 13:  2.0549 -  2.0009  1287   141  0.89  16.82   1.03     1.02       3590.31|
| 14:  2.0009 -  1.9522   915   102  0.92  14.21   1.01     0.98       2598.82|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2598.82 max =        12925.84 mean =      7278.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        15.11|
|phase err.(test): min =        0.00 max =           89.91 mean =        14.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1701   ksol= 0.31   Bsol= 37.03   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.73,-0.78,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210976                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1701   ksol= 0.31   Bsol= 37.03   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-1.73,-0.78,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210976                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.6589 0.99   1382  153 0.1061 0.1330      5.4315      5.5752|
|  2:  4.6589 -  3.7173 0.99   1324  149 0.0925 0.1243      5.5157      5.7421|
|  3:  3.7173 -  3.2532 0.99   1297  142 0.1191 0.1615      5.5867      5.9339|
|  4:  3.2532 -  2.9583 0.99   1291  145 0.1353 0.1902      5.5585      5.7474|
|  5:  2.9583 -  2.7477 0.99   1280  143 0.1478 0.1921      5.4195      5.6037|
|  6:  2.7477 -  2.5866 0.99   1298  140 0.1283 0.1765      5.2587      5.4137|
|  7:  2.5866 -  2.4577 0.99   1270  144 0.1402 0.1759      5.2233      5.4502|
|  8:  2.4577 -  2.3512 0.98   1259  138 0.1323 0.1866      5.1651      5.4147|
|  9:  2.3512 -  2.2610 0.98   1265  143 0.1306 0.1871      5.0999      5.3068|
| 10:  2.2610 -  2.1832 1.00   1262  143 0.1221 0.1860      5.0274      5.2534|
| 11:  2.1832 -  2.1152 0.97   1262  135 0.1236 0.1890      4.9904      5.3357|
| 12:  2.1152 -  2.0549 0.98   1238  141 0.1226 0.1767      4.9431      5.2101|
| 13:  2.0549 -  2.0009 0.99   1287  141 0.1218 0.2025      4.8411      5.1628|
| 14:  2.0009 -  1.9522 0.73    915  102 0.1119 0.1600      4.6945      4.9034|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.6589  1382   153  0.93   9.92   0.99     0.96       7763.51|
|  2:  4.6589 -  3.7173  1324   149  0.95   8.86   1.04     1.02      10504.64|
|  3:  3.7173 -  3.2532  1297   142  0.92  13.11   1.05     1.03      12984.77|
|  4:  3.2532 -  2.9583  1291   145  0.90  15.64   1.03     1.00      12937.34|
|  5:  2.9583 -  2.7477  1280   143  0.89  16.72   1.01     0.98       9350.28|
|  6:  2.7477 -  2.5866  1298   140  0.90  16.38   0.99     0.96       7552.68|
|  7:  2.5866 -  2.4577  1270   144  0.89  17.00   1.00     0.98       6797.45|
|  8:  2.4577 -  2.3512  1259   138  0.90  16.53   1.01     1.01       6213.53|
|  9:  2.3512 -  2.2610  1265   143  0.90  16.30   1.02     0.99       5550.45|
| 10:  2.2610 -  2.1832  1262   143  0.90  16.46   1.02     0.99       4950.36|
| 11:  2.1832 -  2.1152  1262   135  0.89  17.30   1.02     0.98       4741.76|
| 12:  2.1152 -  2.0549  1238   141  0.90  16.64   1.03     1.01       4467.87|
| 13:  2.0549 -  2.0009  1287   141  0.89  16.82   1.03     1.02       3588.54|
| 14:  2.0009 -  1.9522   915   102  0.92  14.21   1.01     0.98       2597.46|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2597.46 max =        12984.77 mean =      7270.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        15.10|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.66|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.235)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.89    90.01   16.63    None  None   None       |
|    all(noH): 2823   0      0.89    90.01   16.63    None  None   None       |
|    Sol.    : 438    0      4.91    86.14   40.66    None  None   None       |
|    Mac.    : 2385   0      0.89    90.01   12.21    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:     0.886 -   9.799: 1148   |   5:    45.450 -  54.363:  104        |
|      1:     9.799 -  18.712: 1023   |   6:    54.363 -  63.276:   78        |
|      2:    18.712 -  27.625:  209   |   7:    63.276 -  72.189:   24        |
|      3:    27.625 -  36.538:  116   |   8:    72.189 -  81.102:    9        |
|      4:    36.538 -  45.450:  108   |   9:    81.102 -  90.014:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.659 - 5.725
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 307
   mapped sites are within: 0.761 - 5.725

peak=    7.293 closest distance to " O   HOH Z 387 " =    2.018
peak=    7.267 closest distance to " O   HOH Z 130 " =    1.283
peak=    6.932 closest distance to " O   HOH Z 431 " =    2.265
peak=    6.474 closest distance to " O   HOH Z  65 " =    1.719
peak=    5.907 closest distance to " NE2 GLN A  11 " =    1.391
peak=    5.882 closest distance to " O   HOH Z   7 " =    2.020
peak=    5.853 closest distance to " O   HOH Z 289 " =    1.309
peak=    5.790 closest distance to " O   HOH Z 142 " =    1.804
peak=    5.735 closest distance to " O   HOH Z 427 " =    1.433
peak=    5.580 closest distance to " O   HOH Z 126 " =    2.063
peak=    5.569 closest distance to " O   HOH Z 245 " =    1.256
peak=    5.533 closest distance to " O   HOH Z 222 " =    1.444
peak=    5.515 closest distance to " O   HOH Z 112 " =    1.909
peak=    5.482 closest distance to " O   HOH Z  49 " =    1.571
peak=    5.386 closest distance to " O   HOH Z 415 " =    1.202
peak=    5.356 closest distance to " O   HOH Z 236 " =    1.648
peak=    5.331 closest distance to " O   HOH Z  61 " =    1.644
peak=    5.269 closest distance to " O   HOH Z 403 " =    1.717
peak=    5.265 closest distance to " O   HOH Z 390 " =    1.111
peak=    5.249 closest distance to " O   HOH Z 417 " =    2.065
peak=    5.221 closest distance to " CB  ARG A 275 " =    1.044
peak=    5.206 closest distance to " O   HOH Z  28 " =    1.446
peak=    5.183 closest distance to " CG  PRO A  54 " =    1.281
peak=    5.173 closest distance to " O   HOH Z  29 " =    1.342
peak=    5.144 closest distance to " O   HOH Z 287 " =    1.970
peak=    5.127 closest distance to " O   HOH Z 414 " =    1.684
peak=    5.024 closest distance to " O   HOH Z  78 " =    1.678
peak=    4.992 closest distance to " O   HOH Z 124 " =    1.544
peak=    4.891 closest distance to " NH2 ARG A  56 " =    1.988
peak=    4.853 closest distance to " O   HOH Z 145 " =    1.548
peak=    4.838 closest distance to " CG  PRO A 213 " =    1.264
peak=    4.738 closest distance to " O   ASP A 286 " =    2.506
peak=    4.681 closest distance to " O   HOH Z 416 " =    1.314
peak=    4.679 closest distance to " O   HOH Z 232 " =    2.143
peak=    4.630 closest distance to " O   HOH Z 358 " =    1.265
peak=    4.580 closest distance to " O   HOH Z 278 " =    1.202
peak=    4.566 closest distance to " O   HOH Z 402 " =    1.540
peak=    4.545 closest distance to " O   HOH Z 369 " =    1.898
peak=    4.542 closest distance to " O   HOH Z  92 " =    1.351
peak=    4.542 closest distance to " O   HOH Z 363 " =    1.086
peak=    4.538 closest distance to " O   HOH Z 424 " =    1.172
peak=    4.522 closest distance to " CB  PRO A  54 " =    1.080
peak=    4.480 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.381 closest distance to " O   HOH Z 214 " =    1.337
peak=    4.379 closest distance to " O   HOH Z 130 " =    2.500
peak=    4.367 closest distance to " CA  TYR A  30 " =    1.015
peak=    4.354 closest distance to " CB  SER A   3 " =    1.265
peak=    4.336 closest distance to " O   HOH Z 158 " =    1.504
peak=    4.329 closest distance to " O   PRO A 198 " =    1.276
peak=    4.324 closest distance to " NZ  LYS A 117 " =    1.239
peak=    4.320 closest distance to " O   HOH Z 120 " =    0.874
peak=    4.302 closest distance to " O   HOH Z 423 " =    1.592
peak=    4.256 closest distance to " CB  ALA A   1 " =    1.038
peak=    4.253 closest distance to " O   HOH Z 193 " =    1.798
peak=    4.249 closest distance to " O   HOH Z 316 " =    2.871
peak=    4.211 closest distance to " O   HOH Z 427 " =    1.752
peak=    4.208 closest distance to " O   HOH Z  63 " =    1.830
peak=    4.175 closest distance to " CB  ASN A 148 " =    1.891
peak=    4.170 closest distance to " O   HOH Z  61 " =    1.459
peak=    4.161 closest distance to " O   HOH Z 352 " =    1.422
peak=    4.156 closest distance to " O   HOH Z 368 " =    3.575
peak=    4.149 closest distance to " O   HOH Z  24 " =    1.688
peak=    4.146 closest distance to " O   HOH Z 380 " =    1.850
peak=    4.137 closest distance to " NZ  LYS A 117 " =    2.999
peak=    4.134 closest distance to " CB  SER A 276 " =    1.195
peak=    4.120 closest distance to " O   HOH Z 234 " =    3.622
peak=    4.116 closest distance to " O   HOH Z 244 " =    1.451
peak=    4.109 closest distance to " O   HOH Z  11 " =    1.914
peak=    4.073 closest distance to " O   HOH Z  47 " =    1.597
peak=    4.069 closest distance to " O   HOH Z 211 " =    1.155
peak=    4.062 closest distance to " O   HOH Z 117 " =    1.226
peak=    4.054 closest distance to " O   HOH Z 132 " =    1.075
peak=    4.033 closest distance to " O   HOH Z 385 " =    1.629
peak=    4.032 closest distance to " O   HOH Z 366 " =    2.482
peak=    4.011 closest distance to " O   HOH Z 371 " =    2.105
peak=    4.005 closest distance to " CB  GLU A 128 " =    0.952
peak=    3.996 closest distance to " CB  GLN A 223 " =    1.461
peak=    3.986 closest distance to " O   HOH Z 261 " =    1.916
peak=    3.980 closest distance to " O   HOH Z 298 " =    1.852
peak=    3.964 closest distance to " O   HOH Z 213 " =    1.705
peak=    3.940 closest distance to " O   HOH Z 392 " =    1.380
peak=    3.914 closest distance to " O   HOH Z 215 " =    1.255
peak=    3.909 closest distance to " O   HOH Z 412 " =    2.135
peak=    3.881 closest distance to " O   HOH Z 156 " =    3.099
peak=    3.872 closest distance to " O   HOH Z 139 " =    1.419
peak=    3.862 closest distance to " CA  ALA A 299 " =    1.005
peak=    3.861 closest distance to " CG2 VAL A 257 " =    0.899
peak=    3.845 closest distance to " CB  GLU A 277 " =    1.055
peak=    3.837 closest distance to " O   SER A  87 " =    2.238
peak=    3.826 closest distance to " CG  PRO A  90 " =    1.161
peak=    3.825 closest distance to " CG  PRO A 198 " =    1.318
peak=    3.824 closest distance to " O   HOH Z 106 " =    2.453
peak=    3.818 closest distance to " CB  GLU A 152 " =    1.237
peak=    3.815 closest distance to " CG1BVAL A 121 " =    2.086
peak=    3.810 closest distance to " O   HOH Z  65 " =    1.484
peak=    3.799 closest distance to " CB  SER A 216 " =    1.000
peak=    3.798 closest distance to " CG2 THR A 221 " =    1.361
peak=    3.795 closest distance to " O   HOH Z 419 " =    1.919
peak=    3.780 closest distance to " O   HOH Z 425 " =    1.432
peak=    3.776 closest distance to " O   HOH Z   9 " =    1.068
peak=    3.756 closest distance to " O   HOH Z 413 " =    1.762
peak=    3.746 closest distance to " O   HOH Z 434 " =    1.457
peak=    3.743 closest distance to " O   HOH Z 108 " =    1.781
peak=    3.735 closest distance to " CG  TRP A 179 " =    2.072
peak=    3.721 closest distance to " CD1 ILE A 263 " =    1.249
peak=    3.719 closest distance to " O   HOH Z  59 " =    1.536
peak=    3.719 closest distance to " O   HOH Z 302 " =    1.397
peak=    3.713 closest distance to " CB  GLN A 183 " =    1.090
peak=    3.703 closest distance to " OG BSER A 212 " =    2.695
peak=    3.701 closest distance to " CA  LEU A 282 " =    1.101
peak=    3.695 closest distance to " CB  VAL A 265 " =    1.323
peak=    3.689 closest distance to " O   HOH Z 223 " =    0.982
peak=    3.688 closest distance to " O   HOH Z  17 " =    2.172
peak=    3.688 closest distance to " O   HOH Z   6 " =    2.170
peak=    3.682 closest distance to " O   HOH Z 196 " =    1.909
peak=    3.682 closest distance to " OD2 ASP A 286 " =    2.414
peak=    3.678 closest distance to " CA  PHE A 283 " =    1.262
peak=    3.674 closest distance to " CB  ARG A 102 " =    0.869
peak=    3.672 closest distance to " O   HOH Z 212 " =    1.672
peak=    3.666 closest distance to " O   HOH Z 128 " =    2.028
peak=    3.666 closest distance to " O   HOH Z 368 " =    1.988
peak=    3.665 closest distance to " CG2AVAL A 121 " =    2.552
peak=    3.660 closest distance to " O   HOH Z 128 " =    2.112
peak=    3.656 closest distance to " NH1AARG A 145 " =    1.032
peak=    3.648 closest distance to " O   HOH Z 258 " =    2.107
peak=    3.647 closest distance to " OD1 ASP A 286 " =    1.143
peak=    3.642 closest distance to " O   HOH Z  44 " =    1.786
peak=    3.637 closest distance to " O   HOH Z 152 " =    2.389
peak=    3.633 closest distance to " CG  GLN A 223 " =    1.839
peak=    3.632 closest distance to " O   HOH Z 311 " =    1.504
peak=    3.629 closest distance to " CB  LEU A 300 " =    0.978
peak=    3.626 closest distance to " O   HOH Z 327 " =    1.978
peak=    3.622 closest distance to " N   ALA A   1 " =    2.587
peak=    3.612 closest distance to " O   HOH Z 425 " =    2.114
peak=    3.598 closest distance to " O   HOH Z 422 " =    2.566
peak=    3.587 closest distance to " N   GLU A   2 " =    1.211
peak=    3.581 closest distance to " OG BSER A  99 " =    2.275
peak=    3.578 closest distance to " O   HOH Z 227 " =    1.884
peak=    3.575 closest distance to " NE2 GLN A  58 " =    3.718
peak=    3.574 closest distance to " N   ALA A   1 " =    1.331
peak=    3.570 closest distance to " CE  MET A  93 " =    1.416
peak=    3.564 closest distance to " CG  LEU A 281 " =    0.838
peak=    3.559 closest distance to " O   HOH Z 250 " =    1.494
peak=    3.556 closest distance to " O   HOH Z 329 " =    3.141
peak=    3.554 closest distance to " CG1 ILE A 120 " =    1.444
peak=    3.549 closest distance to " O   HOH Z  89 " =    2.158
peak=    3.538 closest distance to " O   HOH Z 108 " =    1.633
peak=    3.536 closest distance to " O   HOH Z 119 " =    4.198
peak=    3.535 closest distance to " O   HOH Z 276 " =    1.280
peak=    3.528 closest distance to " CB  SER A  63 " =    1.284
peak=    3.521 closest distance to " O   HOH Z 119 " =    1.566
peak=    3.516 closest distance to " CB AVAL A  41 " =    1.016
peak=    3.514 closest distance to " OG  SER A  62 " =    2.992
peak=    3.513 closest distance to " O  BHOH Z  74 " =    1.198
peak=    3.512 closest distance to " NH1BARG A 145 " =    1.549
peak=    3.511 closest distance to " N   GLN A 278 " =    1.026
peak=    3.510 closest distance to " OG BSER A 164 " =    2.087
peak=    3.509 closest distance to " O   HOH Z   7 " =    3.159
peak=    3.502 closest distance to " CB  THR A  31 " =    1.553
peak=    3.500 closest distance to " CG  GLN A 240 " =    3.521
peak=    3.499 closest distance to " O   HOH Z 426 " =    1.078
peak=    3.497 closest distance to " O   HOH Z 393 " =    1.429
peak=    3.497 closest distance to " OG  SER A  22 " =    2.659
peak=    3.491 closest distance to " NE1 TRP A 274 " =    1.035
peak=    3.487 closest distance to " O   HOH Z 389 " =    1.588
peak=    3.485 closest distance to " O   HOH Z 291 " =    1.580
peak=    3.484 closest distance to " CB  VAL A 202 " =    1.549
peak=    3.482 closest distance to " OG1 THR A 246 " =    1.264
peak=    3.480 closest distance to " O   HOH Z  69 " =    2.197
peak=    3.476 closest distance to " O   HOH Z  32 " =    2.015
peak=    3.471 closest distance to " O   HOH Z 385 " =    3.250
peak=    3.471 closest distance to " OD1 ASN A  45 " =    1.231
peak=    3.470 closest distance to " O   HOH Z 153 " =    3.440
peak=    3.463 closest distance to " CB  ASP A 200 " =    0.978
peak=    3.457 closest distance to " CG  GLN A  11 " =    2.076
peak=    3.456 closest distance to " CB  ALA A  21 " =    1.754
peak=    3.448 closest distance to " NH2AARG A 190 " =    1.415
peak=    3.446 closest distance to " O   HOH Z 158 " =    3.130
peak=    3.442 closest distance to " CG  LYS A 166 " =    1.338
peak=    3.441 closest distance to " CG  PRO A 243 " =    1.163
peak=    3.440 closest distance to " NE AARG A 275 " =    1.683
peak=    3.440 closest distance to " CD  LYS A 166 " =    1.627
peak=    3.436 closest distance to " CB  ALA A  84 " =    1.669
peak=    3.434 closest distance to " CA  ASN A 127 " =    1.051
peak=    3.433 closest distance to " O   HOH Z 155 " =    1.970
peak=    3.431 closest distance to " CB  SER A  26 " =    1.644
peak=    3.427 closest distance to " O   HOH Z  44 " =    2.919
peak=    3.426 closest distance to " O   HOH Z 435 " =    1.858
peak=    3.424 closest distance to " NH2 ARG A 219 " =    1.649
peak=    3.418 closest distance to " O   HOH Z 378 " =    1.029
peak=    3.415 closest distance to " O   HOH Z 383 " =    2.133
peak=    3.410 closest distance to " O   HOH Z 291 " =    1.787
peak=    3.409 closest distance to " O   HOH Z 222 " =    2.056
peak=    3.403 closest distance to " C   PHE A 208 " =    1.106
peak=    3.399 closest distance to " O   HOH Z 418 " =    0.910
peak=    3.394 closest distance to " O   HOH Z  88 " =    2.717
peak=    3.388 closest distance to " CB  PHE A 130 " =    0.927
peak=    3.388 closest distance to " O   HOH Z  80 " =    1.955
peak=    3.386 closest distance to " O   HOH Z 375 " =    0.977
peak=    3.386 closest distance to " O   HOH Z 405 " =    1.529
peak=    3.384 closest distance to " O   HOH Z 151 " =    1.730
peak=    3.382 closest distance to " CB  ASN A  39 " =    0.811
peak=    3.379 closest distance to " O   HOH Z  93 " =    1.840
peak=    3.377 closest distance to " O   HOH Z 400 " =    0.796
peak=    3.375 closest distance to " CB  MET A 105 " =    0.988
peak=    3.365 closest distance to " O   HOH Z   9 " =    2.148
peak=    3.363 closest distance to " ND2 ASN A 187 " =    1.531
peak=    3.361 closest distance to " CZ3 TRP A 274 " =    2.079
peak=    3.358 closest distance to " O   HOH Z  55 " =    1.805
peak=    3.349 closest distance to " O   HOH Z 311 " =    2.383
peak=    3.349 closest distance to " O   HOH Z 142 " =    1.780
peak=    3.342 closest distance to " O   HOH Z  97 " =    1.931
peak=    3.341 closest distance to " O   HOH Z  57 " =    1.968
peak=    3.335 closest distance to " CB  ARG A 138 " =    0.867
peak=    3.335 closest distance to " O   HOH Z 388 " =    2.014
peak=    3.329 closest distance to " N   HIS A  86 " =    1.904
peak=    3.325 closest distance to " O   HOH Z 326 " =    1.818
peak=    3.324 closest distance to " CD2 TRP A 179 " =    1.493
peak=    3.321 closest distance to " O   HOH Z 334 " =    1.739
peak=    3.319 closest distance to " CG  LEU A 167 " =    1.224
peak=    3.316 closest distance to " O   HOH Z 411 " =    3.576
peak=    3.310 closest distance to " N   TYR A  15 " =    1.168
peak=    3.307 closest distance to " O   HOH Z 207 " =    2.182
peak=    3.307 closest distance to " O   HOH Z 384 " =    1.312
peak=    3.306 closest distance to " O   HOH Z  50 " =    1.838
peak=    3.299 closest distance to " O   HOH Z 365 " =    1.644
peak=    3.298 closest distance to " OE1 GLU A  37 " =    1.189
peak=    3.294 closest distance to " O   HOH Z 214 " =    1.916
peak=    3.291 closest distance to " O   HOH Z 173 " =    2.029
peak=    3.281 closest distance to " O   GLY A 302 " =    2.413
peak=    3.278 closest distance to " CB  SER A  26 " =    1.464
peak=    3.277 closest distance to " CB  TRP A 266 " =    1.116
peak=    3.274 closest distance to " CZ  PHE A  38 " =    1.230
peak=    3.274 closest distance to " CZ2 TRP A 150 " =    1.109
peak=    3.274 closest distance to " CB  TRP A 179 " =    1.249
peak=    3.273 closest distance to " CB  LYS A 290 " =    1.353
peak=    3.270 closest distance to " O   HOH Z 111 " =    2.557
peak=    3.265 closest distance to " O   HOH Z 175 " =    1.834
peak=    3.261 closest distance to " CB  MET A 105 " =    0.902
peak=    3.257 closest distance to " O   HOH Z 424 " =    2.878
peak=    3.256 closest distance to " CB  TYR A 116 " =    1.147
peak=    3.249 closest distance to " O   HOH Z 116 " =    2.334
peak=    3.247 closest distance to " O   HOH Z  97 " =    1.183
peak=    3.246 closest distance to " OE2 GLU A  53 " =    1.950
peak=    3.244 closest distance to " CG2 ILE A 239 " =    1.024
peak=    3.242 closest distance to " O   GLY A 147 " =    1.471
peak=    3.240 closest distance to " O   HOH Z 123 " =    1.325
peak=    3.240 closest distance to " O   HOH Z 344 " =    2.902
peak=    3.239 closest distance to " CA  GLU A 152 " =    1.227
peak=    3.234 closest distance to " CB  THR A 157 " =    1.030
peak=    3.232 closest distance to " CG2 VAL A 232 " =    1.148
peak=    3.228 closest distance to " CG  LYS A  76 " =    1.318
peak=    3.227 closest distance to " O   HOH Z 282 " =    1.551
peak=    3.227 closest distance to " O   HOH Z 126 " =    1.459
peak=    3.226 closest distance to " NE2 GLN A 278 " =    3.587
peak=    3.224 closest distance to " CA  ALA A  21 " =    1.088
peak=    3.224 closest distance to " NZ BLYS A 290 " =    0.888
peak=    3.221 closest distance to " OG1 THR A 221 " =    1.306
peak=    3.220 closest distance to " O   HOH Z 272 " =    2.022
peak=    3.218 closest distance to " CA  MET A  40 " =    1.159
peak=    3.216 closest distance to " CA  ASN A 284 " =    1.077
peak=    3.215 closest distance to " O   HOH Z 185 " =    1.664
peak=    3.207 closest distance to " CB  ALA A 248 " =    1.076
peak=    3.206 closest distance to " O   HOH Z 285 " =    1.778
peak=    3.202 closest distance to " O   HOH Z 128 " =    1.873
peak=    3.196 closest distance to " O   HOH Z  18 " =    1.787
peak=    3.195 closest distance to " O   HOH Z 112 " =    1.879
peak=    3.191 closest distance to " O   HOH Z 158 " =    2.307
peak=    3.190 closest distance to " O   HOH Z 334 " =    1.428
peak=    3.185 closest distance to " CB  ASN A 215 " =    1.008
peak=    3.182 closest distance to " CB  GLU A 277 " =    3.356
peak=    3.169 closest distance to " NH2BARG A 145 " =    2.071
peak=    3.168 closest distance to " O   HOH Z 409 " =    2.244
peak=    3.167 closest distance to " CD  GLN A  58 " =    5.725
peak=    3.167 closest distance to " O   HOH Z 147 " =    1.282
peak=    3.167 closest distance to " CA  ILE A 234 " =    0.970
peak=    3.161 closest distance to " O   HOH Z 247 " =    1.197
peak=    3.158 closest distance to " CB  ARG A  79 " =    1.142
peak=    3.153 closest distance to " ND1 HIS A  81 " =    1.291
peak=    3.149 closest distance to " O   HOH Z 375 " =    2.310
peak=    3.142 closest distance to " O   ALA A 165 " =    1.301
peak=    3.140 closest distance to " OD1 ASN A  69 " =    2.456
peak=    3.138 closest distance to " O   ALA A 242 " =    1.280
peak=    3.137 closest distance to " O   ALA A   1 " =    1.597
peak=    3.137 closest distance to " CB  GLU A 236 " =    1.617
peak=    3.134 closest distance to " O   HOH Z   1 " =    1.703
peak=    3.130 closest distance to " CB  SER A  99 " =    1.223
peak=    3.130 closest distance to " CA  ALA A 158 " =    1.181
peak=    3.128 closest distance to " O   HOH Z  68 " =    1.691
peak=    3.125 closest distance to " O   HOH Z 233 " =    2.171
peak=    3.119 closest distance to " O   HOH Z 303 " =    1.706
peak=    3.116 closest distance to " OD1 ASN A 217 " =    1.673
peak=    3.114 closest distance to " CD  ARG A 138 " =    0.761
peak=    3.113 closest distance to " O   HOH Z 171 " =    2.300
peak=    3.096 closest distance to " C   VAL A 265 " =    1.249
peak=    3.087 closest distance to " CD  LYS A 119 " =    1.862
peak=    3.080 closest distance to " O   HOH Z 189 " =    1.930
peak=    3.076 closest distance to " O   HOH Z 248 " =    2.107
peak=    3.073 closest distance to " O   HOH Z 214 " =    3.121
peak=    3.055 closest distance to " CE AMET A  47 " =    1.202
peak=    3.055 closest distance to " CG  LYS A 119 " =    0.988
peak=    3.049 closest distance to " O   HOH Z 419 " =    1.364
peak=    3.031 closest distance to " O   HOH Z   5 " =    1.162
peak=    3.021 closest distance to " CB  ARG A 156 " =    0.982
peak=    3.018 closest distance to " O   HOH Z 156 " =    2.523

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.600 - 4.563
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 192
   mapped sites are within: 0.713 - 4.563

peak=   -4.686 closest distance to " O   HOH Z 385 " =    1.060
peak=   -4.446 closest distance to " O   HOH Z  60 " =    1.899
peak=   -4.403 closest distance to " O   HOH Z 290 " =    1.045
peak=   -4.352 closest distance to " O   PRO A 198 " =    1.143
peak=   -4.166 closest distance to " CA  GLY A  98 " =    1.810
peak=   -4.051 closest distance to " CD  ARG A  14 " =    3.025
peak=   -4.007 closest distance to " O   HOH Z 409 " =    3.086
peak=   -3.992 closest distance to " O   MET A  40 " =    2.770
peak=   -3.968 closest distance to " NH2 ARG A  79 " =    1.969
peak=   -3.963 closest distance to " CZ  PHE A  59 " =    1.392
peak=   -3.923 closest distance to " O   ILE A  49 " =    1.591
peak=   -3.909 closest distance to " O   HOH Z 372 " =    2.629
peak=   -3.900 closest distance to " O   HOH Z  88 " =    1.811
peak=   -3.879 closest distance to " N   GLN A  58 " =    1.678
peak=   -3.870 closest distance to " CB  ALA A 291 " =    2.184
peak=   -3.868 closest distance to " O   HOH Z 438 " =    0.857
peak=   -3.867 closest distance to " OG  SER A  97 " =    1.941
peak=   -3.852 closest distance to " O   SER A  22 " =    2.551
peak=   -3.834 closest distance to " OE1 GLU A 277 " =    2.016
peak=   -3.830 closest distance to " O   HOH Z 313 " =    1.210
peak=   -3.824 closest distance to " O   SER A 135 " =    1.613
peak=   -3.782 closest distance to " CB  PRO A 243 " =    2.527
peak=   -3.770 closest distance to " CD2 LEU A 237 " =    2.368
peak=   -3.767 closest distance to " CD  ARG A 156 " =    1.981
peak=   -3.766 closest distance to " O   HOH Z  43 " =    1.859
peak=   -3.756 closest distance to " O   PHE A 218 " =    1.526
peak=   -3.753 closest distance to " C   HIS A 108 " =    1.259
peak=   -3.746 closest distance to " CB  ALA A 248 " =    2.098
peak=   -3.743 closest distance to " CG  MET A 105 " =    0.933
peak=   -3.735 closest distance to " CD1 LEU A 101 " =    2.254
peak=   -3.725 closest distance to " O   HOH Z 416 " =    0.765
peak=   -3.717 closest distance to " NH2 ARG A 219 " =    1.634
peak=   -3.716 closest distance to " N   ALA A   1 " =    1.107
peak=   -3.709 closest distance to " CA  GLY A 133 " =    1.863
peak=   -3.703 closest distance to " O   HOH Z 298 " =    1.042
peak=   -3.701 closest distance to " O   HOH Z 244 " =    1.334
peak=   -3.694 closest distance to " N   VAL A  72 " =    1.666
peak=   -3.690 closest distance to " O   HOH Z  37 " =    1.373
peak=   -3.683 closest distance to " O   ALA A  51 " =    1.361
peak=   -3.681 closest distance to " O   HOH Z 236 " =    2.284
peak=   -3.672 closest distance to " N   ALA A 248 " =    1.510
peak=   -3.655 closest distance to " O   ARG A 145 " =    1.478
peak=   -3.640 closest distance to " O   ALA A 161 " =    1.788
peak=   -3.630 closest distance to " O   HOH Z 393 " =    2.890
peak=   -3.630 closest distance to " N   THR A 157 " =    1.545
peak=   -3.627 closest distance to " O   HOH Z  24 " =    1.151
peak=   -3.614 closest distance to " O   HOH Z 195 " =    1.844
peak=   -3.608 closest distance to " O   HOH Z  61 " =    0.942
peak=   -3.606 closest distance to " O   HOH Z  56 " =    1.415
peak=   -3.601 closest distance to " O   HOH Z 412 " =    4.550
peak=   -3.591 closest distance to " OD2 ASP A 171 " =    1.962
peak=   -3.587 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.586 closest distance to " O   HOH Z 388 " =    2.058
peak=   -3.586 closest distance to " OG BSER A 134 " =    1.350
peak=   -3.574 closest distance to " CB  TYR A  15 " =    2.110
peak=   -3.569 closest distance to " OG  SER A 245 " =    1.218
peak=   -3.568 closest distance to " OD2 ASP A 191 " =    1.475
peak=   -3.567 closest distance to " O   PRO A  54 " =    1.443
peak=   -3.564 closest distance to " OXT GLY A 302 " =    2.888
peak=   -3.544 closest distance to " O   SER A  95 " =    1.189
peak=   -3.543 closest distance to " O   HOH Z 425 " =    0.882
peak=   -3.542 closest distance to " CB  ASN A 285 " =    1.926
peak=   -3.536 closest distance to " O   VAL A  67 " =    2.897
peak=   -3.535 closest distance to " O   HOH Z 131 " =    4.164
peak=   -3.533 closest distance to " O   HOH Z  13 " =    1.525
peak=   -3.528 closest distance to " CG  ASP A 231 " =    0.792
peak=   -3.524 closest distance to " O   HOH Z  22 " =    2.506
peak=   -3.521 closest distance to " O   HOH Z 137 " =    1.384
peak=   -3.515 closest distance to " O   HOH Z 415 " =    1.062
peak=   -3.511 closest distance to " O   PRO A 243 " =    2.421
peak=   -3.506 closest distance to " CG  GLN A  58 " =    1.289
peak=   -3.482 closest distance to " O   HOH Z 250 " =    1.363
peak=   -3.481 closest distance to " O   HOH Z 288 " =    1.412
peak=   -3.475 closest distance to " CD2 TYR A 293 " =    1.763
peak=   -3.472 closest distance to " CA  GLY A 241 " =    2.121
peak=   -3.457 closest distance to " CG  LEU A  83 " =    1.979
peak=   -3.455 closest distance to " ND2 ASN A 252 " =    1.565
peak=   -3.450 closest distance to " O   HOH Z  64 " =    0.908
peak=   -3.447 closest distance to " O   VAL A 189 " =    2.338
peak=   -3.444 closest distance to " O   HOH Z 211 " =    1.357
peak=   -3.430 closest distance to " N   PRO A 163 " =    1.554
peak=   -3.427 closest distance to " CD  LYS A 289 " =    2.374
peak=   -3.427 closest distance to " CG  ASN A 301 " =    2.115
peak=   -3.425 closest distance to " CE2 TYR A  30 " =    2.729
peak=   -3.419 closest distance to " CB  ASN A  39 " =    2.189
peak=   -3.418 closest distance to " C   ALA A 114 " =    1.952
peak=   -3.412 closest distance to " OG  SER A   3 " =    1.540
peak=   -3.411 closest distance to " OG BSER A  99 " =    1.505
peak=   -3.411 closest distance to " CB  CYS A 201 " =    2.338
peak=   -3.410 closest distance to " O   HOH Z 426 " =    2.213
peak=   -3.410 closest distance to " O   HOH Z 197 " =    3.195
peak=   -3.407 closest distance to " O   HOH Z 198 " =    1.797
peak=   -3.398 closest distance to " O   HOH Z 278 " =    0.942
peak=   -3.396 closest distance to " O   HOH Z 122 " =    2.417
peak=   -3.396 closest distance to " CB  ALA A   7 " =    1.835
peak=   -3.393 closest distance to " O   HOH Z  28 " =    2.019
peak=   -3.381 closest distance to " O   HOH Z  93 " =    1.551
peak=   -3.376 closest distance to " O   VAL A 174 " =    2.215
peak=   -3.369 closest distance to " O   ALA A   1 " =    1.254
peak=   -3.367 closest distance to " O   HOH Z 218 " =    3.616
peak=   -3.356 closest distance to " O   HOH Z 266 " =    4.374
peak=   -3.354 closest distance to " CD  GLN A 223 " =    1.350
peak=   -3.354 closest distance to " O   HOH Z  51 " =    1.588
peak=   -3.351 closest distance to " OD2 ASP A  27 " =    1.613
peak=   -3.341 closest distance to " O   HOH Z 185 " =    1.979
peak=   -3.337 closest distance to " O   TRP A  70 " =    1.356
peak=   -3.330 closest distance to " O   VAL A 197 " =    1.100
peak=   -3.328 closest distance to " O   HOH Z 318 " =    1.612
peak=   -3.322 closest distance to " O   HOH Z 406 " =    1.873
peak=   -3.322 closest distance to " OG  SER A  63 " =    1.197
peak=   -3.321 closest distance to " CB  ALA A 227 " =    2.279
peak=   -3.321 closest distance to " CB  ALA A  43 " =    2.123
peak=   -3.320 closest distance to " ND2 ASN A 209 " =    1.832
peak=   -3.313 closest distance to " CB  TRP A 274 " =    2.650
peak=   -3.308 closest distance to " CA  GLY A 302 " =    3.145
peak=   -3.308 closest distance to " O   HOH Z   1 " =    3.599
peak=   -3.304 closest distance to " O   THR A 235 " =    1.331
peak=   -3.302 closest distance to " CG  GLN A  88 " =    0.888
peak=   -3.294 closest distance to " N   GLN A  58 " =    1.153
peak=   -3.292 closest distance to " O   VAL A  67 " =    2.918
peak=   -3.289 closest distance to " ND2 ASN A  60 " =    1.332
peak=   -3.288 closest distance to " NE2 GLN A 278 " =    1.746
peak=   -3.285 closest distance to " N   GLN A 122 " =    1.344
peak=   -3.280 closest distance to " OG ASER A 134 " =    1.187
peak=   -3.273 closest distance to " ND2 ASN A  39 " =    1.229
peak=   -3.272 closest distance to " CZ2 TRP A 274 " =    1.014
peak=   -3.265 closest distance to " CB  PHE A 208 " =    2.064
peak=   -3.265 closest distance to " O   HOH Z  39 " =    1.484
peak=   -3.263 closest distance to " O   HOH Z 166 " =    1.508
peak=   -3.263 closest distance to " O   HOH Z 147 " =    1.304
peak=   -3.261 closest distance to " NE2 GLN A  55 " =    0.859
peak=   -3.261 closest distance to " O   ILE A 120 " =    2.208
peak=   -3.261 closest distance to " OG ASER A 216 " =    1.225
peak=   -3.256 closest distance to " CE  MET A 105 " =    2.311
peak=   -3.247 closest distance to " O   HOH Z 165 " =    2.351
peak=   -3.246 closest distance to " N   LYS A 166 " =    1.900
peak=   -3.246 closest distance to " CD  GLN A  58 " =    0.938
peak=   -3.238 closest distance to " O   HOH Z 208 " =    0.819
peak=   -3.238 closest distance to " O   HOH Z 359 " =    3.631
peak=   -3.234 closest distance to " CG  GLN A 223 " =    1.091
peak=   -3.234 closest distance to " NE1 TRP A 179 " =    1.184
peak=   -3.231 closest distance to " CG  PHE A 283 " =    2.534
peak=   -3.228 closest distance to " O   GLN A 194 " =    1.408
peak=   -3.225 closest distance to " OE1 GLN A 183 " =    1.416
peak=   -3.220 closest distance to " NE  ARG A  36 " =    1.850
peak=   -3.215 closest distance to " ND2 ASN A 187 " =    1.378
peak=   -3.212 closest distance to " CG  ARG A 259 " =    2.682
peak=   -3.209 closest distance to " O   HOH Z  76 " =    1.248
peak=   -3.206 closest distance to " C   GLN A 205 " =    1.997
peak=   -3.205 closest distance to " CE3 TRP A 274 " =    2.469
peak=   -3.203 closest distance to " CD2 TRP A 150 " =    0.817
peak=   -3.202 closest distance to " O   HOH Z  49 " =    1.519
peak=   -3.200 closest distance to " CG2BVAL A  72 " =    1.627
peak=   -3.199 closest distance to " O   HOH Z 126 " =    1.875
peak=   -3.194 closest distance to " O   HOH Z 142 " =    0.713
peak=   -3.185 closest distance to " O   HOH Z 125 " =    3.274
peak=   -3.185 closest distance to " CE3 TRP A  70 " =    2.075
peak=   -3.182 closest distance to " O   HOH Z 413 " =    4.563
peak=   -3.176 closest distance to " O   SER A  22 " =    0.964
peak=   -3.172 closest distance to " C   ALA A 158 " =    1.438
peak=   -3.169 closest distance to " OG  SER A  87 " =    1.165
peak=   -3.160 closest distance to " CE3 TRP A 123 " =    1.446
peak=   -3.150 closest distance to " O   HOH Z 377 " =    0.758
peak=   -3.150 closest distance to " O   HOH Z  29 " =    0.759
peak=   -3.147 closest distance to " O   HOH Z  63 " =    2.636
peak=   -3.143 closest distance to " O   ALA A   1 " =    1.449
peak=   -3.141 closest distance to " N   ALA A 226 " =    1.989
peak=   -3.140 closest distance to " O   VAL A 153 " =    2.339
peak=   -3.137 closest distance to " CD  LYS A 166 " =    2.343
peak=   -3.137 closest distance to " OE2 GLU A 152 " =    0.994
peak=   -3.136 closest distance to " O   HOH Z 368 " =    2.548
peak=   -3.135 closest distance to " OG BSER A 134 " =    1.780
peak=   -3.135 closest distance to " O   GLU A 152 " =    1.574
peak=   -3.130 closest distance to " O   HOH Z  77 " =    1.864
peak=   -3.130 closest distance to " CG  GLN A  11 " =    1.900
peak=   -3.129 closest distance to " CB  GLN A  55 " =    1.277
peak=   -3.127 closest distance to " O   THR A 220 " =    1.636
peak=   -3.127 closest distance to " O   ARG A  56 " =    1.336
peak=   -3.123 closest distance to " N   GLY A 302 " =    1.530
peak=   -3.105 closest distance to " O   HOH Z  69 " =    1.821
peak=   -3.104 closest distance to " O   LYS A  48 " =    1.703
peak=   -3.091 closest distance to " O   HOH Z  51 " =    1.176
peak=   -3.091 closest distance to " CG  GLU A 152 " =    1.323
peak=   -3.090 closest distance to " CB  ALA A 100 " =    1.852
peak=   -3.081 closest distance to " O   HOH Z 414 " =    1.198
peak=   -3.079 closest distance to " O   HOH Z 297 " =    3.293
peak=   -3.079 closest distance to " CD  PRO A 198 " =    1.380
peak=   -3.067 closest distance to " OG  SER A 206 " =    1.890
peak=   -3.036 closest distance to " ND2 ASN A 142 " =    2.115
peak=   -3.013 closest distance to " OD2 ASP A 171 " =    1.387

================= 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    :  0.4797 0.4792   6.286115e+00   6.279593e+00
   1_bss:  0.4710 0.4668   6.281464e+00   6.265053e+00
   1_xyz:  0.3762 0.4078   6.144729e+00   6.200687e+00
   1_adp:  0.3421 0.4237   6.103167e+00   6.213864e+00
   1_occ:  0.3419 0.4246   6.103337e+00   6.214611e+00
   2_bss:  0.3412 0.4228   6.103068e+00   6.214148e+00
   2_xyz:  0.2923 0.3694   5.987612e+00   6.130918e+00
   2_adp:  0.2821 0.3554   5.962371e+00   6.109146e+00
   2_occ:  0.2817 0.3553   5.962098e+00   6.109421e+00
   3_bss:  0.2824 0.3547   5.961152e+00   6.108526e+00
   3_xyz:  0.2170 0.2854   5.728859e+00   5.920560e+00
   3_adp:  0.1936 0.2588   5.629794e+00   5.837442e+00
   3_occ:  0.1933 0.2581   5.627734e+00   5.834725e+00
   4_bss:  0.1926 0.2549   5.621917e+00   5.826979e+00
   4_xyz:  0.1528 0.2042   5.409301e+00   5.635376e+00
   4_adp:  0.1415 0.1938   5.345403e+00   5.578221e+00
   4_occ:  0.1412 0.1931   5.343789e+00   5.576224e+00
   5_bss:  0.1413 0.1927   5.341976e+00   5.573980e+00
   5_xyz:  0.1264 0.1750   5.239798e+00   5.474214e+00
   5_adp:  0.1229 0.1705   5.212165e+00   5.447517e+00
   5_occ:  0.1228 0.1701   5.211310e+00   5.446325e+00
   5_bss:  0.1228 0.1701   5.210976e+00   5.446167e+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:  0.351  12.972  -2.368   1.799  -0.072   0.000  -0.000  -0.000
   1_xyz:  0.351  12.972  -2.368   1.799  -0.072   0.000  -0.000  -0.000
   1_adp:  0.351  12.972  -2.368   1.799  -0.072   0.000  -0.000  -0.000
   1_occ:  0.351  12.972  -2.368   1.799  -0.072   0.000  -0.000  -0.000
   2_bss:  0.352  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   2_xyz:  0.352  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   2_adp:  0.352  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   2_occ:  0.352  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   3_bss:  0.347  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   3_xyz:  0.347  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   3_adp:  0.347  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   3_occ:  0.347  48.739  -1.255   0.974  -0.092   0.000  -0.000  -0.000
   4_bss:  0.347  48.739  -1.707  -0.969  -0.604  -0.000  -0.000  -0.000
   4_xyz:  0.347  48.739  -1.707  -0.969  -0.604  -0.000  -0.000  -0.000
   4_adp:  0.347  48.739  -1.707  -0.969  -0.604  -0.000  -0.000  -0.000
   4_occ:  0.347  48.739  -1.707  -0.969  -0.604  -0.000  -0.000  -0.000
   5_bss:  0.317  37.058  -2.019  -1.758  -0.814  -0.000  -0.000  -0.000
   5_xyz:  0.317  37.058  -2.019  -1.758  -0.814  -0.000  -0.000  -0.000
   5_adp:  0.317  37.058  -2.019  -1.758  -0.814  -0.000  -0.000  -0.000
   5_occ:  0.317  37.058  -2.019  -1.758  -0.814  -0.000  -0.000  -0.000
   5_bss:  0.305  37.026  -1.987  -1.727  -0.783  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.722 0.4109  0.5699    74448.553
   1_bss:  57.416 0.4263  0.5858    70077.510
   1_xyz:  46.583 0.5630  0.7551    51253.297
   1_adp:  48.011 0.5447  0.7326    54078.095
   1_occ:  48.114 0.5435  0.7305    54377.414
   2_bss:  47.883 0.5462  0.7426    54052.732
   2_xyz:  40.685 0.6338  0.8571    39889.467
   2_adp:  38.433 0.6613  0.8773    36937.432
   2_occ:  38.446 0.6611  0.8767    36924.882
   3_bss:  38.366 0.6618  0.8771    36696.629
   3_xyz:  29.000 0.7685  0.9832    21398.328
   3_adp:  25.447 0.8074  0.9984    17383.050
   3_occ:  25.361 0.8083  0.9990    17241.701
   4_bss:  25.074 0.8109  0.9673    16799.795
   4_xyz:  19.693 0.8642  1.0009    10724.457
   4_adp:  18.097 0.8799  1.0024     9586.177
   4_occ:  18.052 0.8803  1.0022     9515.535
   5_bss:  17.998 0.8806  0.9859     9433.132
   5_xyz:  15.760 0.9003  0.9953     7648.746
   5_adp:  15.085 0.9063  0.9936     7306.525
   5_occ:  15.064 0.9064  0.9935     7278.704
   5_bss:  15.054 0.9065  0.9934     7271.086
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   2.1015e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   2.1015e-01
   1_xyz:   1.643  0.013  0.114 15.915  0.006  4.097   1.4990e-01
   1_adp:   1.643  0.013  0.114 15.915  0.006  4.097   1.4990e-01
   1_occ:   1.643  0.013  0.114 15.915  0.006  4.097   1.4990e-01
   2_bss:   1.643  0.013  0.114 15.915  0.006  4.097   1.4990e-01
   2_xyz:   1.171  0.008  0.082 14.718  0.005  4.111   7.9047e-02
   2_adp:   1.171  0.008  0.082 14.718  0.005  4.111   7.9047e-02
   2_occ:   1.171  0.008  0.082 14.718  0.005  4.111   7.9047e-02
   3_bss:   1.171  0.008  0.082 14.718  0.005  4.111   7.9047e-02
   3_xyz:   1.266  0.010  0.082 14.908  0.005  4.103   9.2766e-02
   3_adp:   1.266  0.010  0.082 14.908  0.005  4.103   9.2766e-02
   3_occ:   1.266  0.010  0.082 14.908  0.005  4.103   9.2766e-02
   4_bss:   1.266  0.010  0.082 14.908  0.005  4.103   9.2766e-02
   4_xyz:   1.029  0.006  0.069 14.395  0.004  4.105   6.1579e-02
   4_adp:   1.029  0.006  0.069 14.395  0.004  4.105   6.1579e-02
   4_occ:   1.029  0.006  0.069 14.395  0.004  4.105   6.1579e-02
   5_bss:   1.029  0.006  0.069 14.395  0.004  4.105   6.1579e-02
   5_xyz:   0.937  0.005  0.065 14.247  0.004  4.109   5.3969e-02
   5_adp:   0.937  0.005  0.065 14.247  0.004  4.109   5.3969e-02
   5_occ:   0.937  0.005  0.065 14.247  0.004  4.109   5.3969e-02
   5_bss:   0.937  0.005  0.065 14.247  0.004  4.109   5.3969e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.212   2.3760e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.212   2.3760e-01
   1_xyz:  10.302  0.077  0.495 80.167  0.042  1.803   1.1679e-01
   1_adp:  10.302  0.077  0.495 80.167  0.042  1.803   1.1679e-01
   1_occ:  10.302  0.077  0.495 80.167  0.042  1.803   1.1679e-01
   2_bss:  10.302  0.077  0.495 80.167  0.042  1.803   1.1679e-01
   2_xyz:   9.495  0.071  0.291 80.254  0.031  2.144   7.5759e-02
   2_adp:   9.495  0.071  0.291 80.254  0.031  2.144   7.5759e-02
   2_occ:   9.495  0.071  0.291 80.254  0.031  2.144   7.5759e-02
   3_bss:   9.495  0.071  0.291 80.254  0.031  2.144   7.5759e-02
   3_xyz:   8.196  0.052  0.326 84.609  0.024  2.204   1.5049e-01
   3_adp:   8.196  0.052  0.326 84.609  0.024  2.204   1.5049e-01
   3_occ:   8.196  0.052  0.326 84.609  0.024  2.204   1.5049e-01
   4_bss:   8.196  0.052  0.326 84.609  0.024  2.204   1.5049e-01
   4_xyz:   8.778  0.043  0.239 80.211  0.034  2.229   5.2930e-02
   4_adp:   8.778  0.043  0.239 80.211  0.034  2.229   5.2930e-02
   4_occ:   8.778  0.043  0.239 80.211  0.034  2.229   5.2930e-02
   5_bss:   8.778  0.043  0.239 80.211  0.034  2.229   5.2930e-02
   5_xyz:   7.472  0.042  0.211 81.756  0.035  2.315   5.8322e-02
   5_adp:   7.472  0.042  0.211 81.756  0.035  2.315   5.8322e-02
   5_occ:   7.472  0.042  0.211 81.756  0.035  2.315   5.8322e-02
   5_bss:   7.472  0.042  0.211 81.756  0.035  2.315   5.8322e-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:  95.52   0.00  19.01  95.52   0.00  16.02  92.65   0.00  35.28
   1_occ:  95.52   0.00  19.01  95.52   0.00  16.02  92.65   0.00  35.28
   2_bss:  95.52   0.00  19.01  95.52   0.00  16.02  92.65   0.00  35.28
   2_xyz:  95.52   0.00  19.01  95.52   0.00  16.02  92.65   0.00  35.28
   2_adp:  92.26   0.00  17.78  92.26   0.00  14.77  88.50   1.76  34.15
   2_occ:  92.26   0.00  17.78  92.26   0.00  14.77  88.50   1.76  34.15
   3_bss:  92.26   0.00  17.78  92.26   0.00  14.77  88.50   1.76  34.15
   3_xyz:  92.26   0.00  17.78  92.26   0.00  14.77  88.50   1.76  34.15
   3_adp:  91.82   0.00  17.25  91.82   0.00  13.16  88.06   4.96  39.50
   3_occ:  91.82   0.00  17.25  91.82   0.00  13.16  88.06   4.96  39.50
   4_bss:  91.82   0.00  17.25  91.82   0.00  13.16  88.06   4.96  39.50
   4_xyz:  91.82   0.00  17.25  91.82   0.00  13.16  88.06   4.96  39.50
   4_adp:  90.13   1.08  16.89  90.13   1.08  12.50  85.96   4.19  40.77
   4_occ:  90.13   1.08  16.89  90.13   1.08  12.50  85.96   4.19  40.77
   5_bss:  90.13   1.08  16.89  90.13   1.08  12.50  85.96   4.19  40.77
   5_xyz:  90.13   1.08  16.89  90.13   1.08  12.50  85.96   4.19  40.77
   5_adp:  90.05   0.92  16.66  90.05   0.92  12.25  86.17   4.94  40.69
   5_occ:  90.05   0.92  16.66  90.05   0.92  12.25  86.17   4.94  40.69
   5_bss:  90.01   0.89  16.63  90.01   0.89  12.21  86.14   4.91  40.66
------------------------------------------------------------------------
 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:    2.067    0.028    0.390
   1_adp:    2.067    0.028    0.390
   1_occ:    2.067    0.028    0.390
   2_bss:    2.067    0.028    0.390
   2_xyz:    1.633    0.028    0.524
   2_adp:    1.633    0.028    0.524
   2_occ:    1.633    0.028    0.524
   3_bss:    1.633    0.028    0.524
   3_xyz:    1.628    0.063    0.737
   3_adp:    1.628    0.063    0.737
   3_occ:    1.628    0.063    0.737
   4_bss:    1.628    0.063    0.737
   4_xyz:    1.675    0.107    0.827
   4_adp:    1.675    0.107    0.827
   4_occ:    1.675    0.107    0.827
   5_bss:    1.675    0.107    0.827
   5_xyz:    1.729    0.111    0.857
   5_adp:    1.729    0.111    0.857
   5_occ:    1.729    0.111    0.857
   5_bss:    1.729    0.111    0.857
------------------------------------------------------------------------

CPU time actual refinement: 343.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/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_244/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_244/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.89 
  Macro-tasks:
    bulk solvent and scale       = 45.10  
    individual site refinement   = 136.68 
    weights calculation          = 30.51  
    collect and process          = 6.53   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 218.96 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 107.95 
    alpha_beta                      = 8.47   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.95 
    fmodel                         = 7.29   
    r_factors                      = 0.25   
    phase_errors                   = 10.24  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.02 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.910 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    641 calls, 107.71 s
gradients_fft:          586 calls, 102.89 s

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

# Date 2008-01-16 Time 04:21:13 PST -0800 (1200486073.49 s)
Start R-work = 0.4797, R-free = 0.4792 (no bulk solvent and anisotropic scale)
Final R-work = 0.1442, R-free = 0.1867 (no bulk solvent and anisotropic scale)

Start R-work = 0.4710, R-free = 0.4668
Final R-work = 0.1228, R-free = 0.1701