# Date 2008-01-16 Time 05:42:32 PST -0800 (1200490952.37 s)
#phil __OFF__

Command line arguments: "../846.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27154
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 846

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 88.5498, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01073
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   2.0107

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 2.01073
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.3020 [2174/2202]  1954   220  10.1%
  bin  2:  4.3020 -  3.4276 [2068/2087]  1864   204   9.9%
  bin  3:  3.4276 -  2.9982 [2065/2085]  1857   208  10.1%
  bin  4:  2.9982 -  2.7258 [2032/2057]  1830   202   9.9%
  bin  5:  2.7258 -  2.5314 [2013/2032]  1808   205  10.2%
  bin  6:  2.5314 -  2.3827 [2007/2053]  1810   197   9.8%
  bin  7:  2.3827 -  2.2638 [1999/2032]  1801   198   9.9%
  bin  8:  2.2638 -  2.1656 [2002/2038]  1796   206  10.3%
  bin  9:  2.1656 -  2.0824 [1989/2018]  1794   195   9.8%
  bin 10:  2.0824 -  2.0107 [1240/2017]  1116   124  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/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:
        1.58 -     2.24: 11
        2.24 -     2.91: 1371
        2.91 -     3.57: 4339
        3.57 -     4.24: 8945
        4.24 -     4.90: 12916
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.576 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.762 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.762 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A  24 " - " OG  SER A  95 "  1.957 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 27577 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_846/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/model_refine_001.geo

CPU time processing inputs: 8.91


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4854   r_free= 0.4785   ksol= 0.00   Bsol= 0.00   scale= 0.854    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.296613                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7980 0.99   1406  157 0.3925 0.3829      6.5944      6.5588|
|  2:  4.7980 -  3.8286 0.99   1353  152 0.4403 0.4730      6.8957      6.9463|
|  3:  3.8286 -  3.3506 0.99   1331  149 0.4733 0.4290      6.7283      6.6475|
|  4:  3.3506 -  3.0469 0.99   1319  137 0.4767 0.4818       6.546      6.5029|
|  5:  3.0469 -  2.8301 0.99   1308  150 0.5112 0.4530      6.3841      6.4117|
|  6:  2.8301 -  2.6642 0.98   1302  145 0.5173 0.5115      6.2772      6.1771|
|  7:  2.6642 -  2.5314 0.99   1294  149 0.5112 0.4782      6.2527      6.1599|
|  8:  2.5314 -  2.4217 0.98   1303  139 0.5143 0.5014      6.1868      6.1814|
|  9:  2.4217 -  2.3288 0.98   1294  146 0.5198 0.5335      6.1109      6.1964|
| 10:  2.3288 -  2.2487 0.98   1274  141 0.5288 0.4817      6.1095      6.0983|
| 11:  2.2487 -  2.1786 0.99   1283  145 0.5251 0.5232      6.0356      6.0538|
| 12:  2.1786 -  2.1165 0.98   1283  138 0.5221 0.5966      5.9652       6.009|
| 13:  2.1165 -  2.0609 0.97   1258  139 0.5358 0.5316      5.8917      5.8287|
| 14:  2.0609 -  2.0107 0.48    622   72 0.4929 0.5055      5.8563      5.7899|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7980  1406   157  0.69  35.36   0.80     0.72      75983.43|
|  2:  4.7980 -  3.8286  1353   152  0.68  36.79   0.87     0.76     114497.31|
|  3:  3.8286 -  3.3506  1331   149  0.58  45.63   0.85     0.73     119853.75|
|  4:  3.3506 -  3.0469  1319   137  0.48  53.33   0.86     0.63     106941.37|
|  5:  3.0469 -  2.8301  1308   150  0.41  59.34   0.85     0.55      81930.53|
|  6:  2.8301 -  2.6642  1302   145  0.36  63.03   0.84     0.49      72184.96|
|  7:  2.6642 -  2.5314  1294   149  0.36  62.89   0.88     0.48      64595.12|
|  8:  2.5314 -  2.4217  1303   139  0.34  64.42   0.87     0.47      60375.79|
|  9:  2.4217 -  2.3288  1294   146  0.32  66.08   0.87     0.47      57548.87|
| 10:  2.3288 -  2.2487  1274   141  0.33  65.31   0.90     0.48      51630.35|
| 11:  2.2487 -  2.1786  1283   145  0.29  68.05   0.88     0.44      50155.76|
| 12:  2.1786 -  2.1165  1283   138  0.26  70.51   0.89     0.39      46723.68|
| 13:  2.1165 -  2.0609  1258   139  0.23  72.87   0.87     0.35      41210.32|
| 14:  2.0609 -  2.0107   622    72  0.30  67.89   0.95     0.37      30168.15|
|alpha:            min =        0.35 max =            0.76 mean =         0.53|
|beta:             min =    30168.15 max =       119853.75 mean =     71519.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.76|
|phase err.(test): min =        0.00 max =           89.81 mean =        59.08|
|-----------------------------------------------------------------------------|

============================== 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 = 11.880224             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.309   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.349242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.748   (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 |  1.576 -  1.909:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.909 -  2.241:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.241 -  2.573:       22 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.573 -  2.906:     1349 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.906 -  3.238:     1865 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.238 -  3.571:     2474 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.571 -  3.903:     4579 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.903 -  4.235:     4366 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.235 -  4.568:     5869 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.568 -  4.900:     7047 |
|-----------------------------------------------------------------------------|
|-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 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.576 |       0.236 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4854   r_free= 0.4785   ksol= 0.00   Bsol= 0.00   scale= 0.854    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.296613                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4764   r_free= 0.4693   ksol= 0.29   Bsol= 50.00   scale= 0.899   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.71,3.46,3.43,0.00,0.00,0.00); trace/3= 1.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.290877                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.782607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.812   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.476285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4764      final r-factor (work) = 0.4049          |
| start r-factor (free) = 0.4693      final r-factor (free) = 0.4348          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9266 = 9.78 * 0.50 * 6.2881 + 1.00 * 0.1698                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4988 = 9.78 * 0.50 * 6.2059 + 1.00 * 0.1438                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4049      final r-factor (work) = 0.3725          |
| start r-factor (free) = 0.4348      final r-factor (free) = 0.4393          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1676 = 1.48 * 1.00 * 6.2059 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0971 = 1.48 * 1.00 * 6.1466 + 1.00 * 0.0229                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.40  19.69    None  None   None       |
|    all(noH): 2823   0      0.00    107.40  19.69    None  None   None       |
|    Sol.    : 438    0      0.00    107.40  36.59    None  None   None       |
|    Mac.    : 2385   0      0.00    89.54   16.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.740:  921   |   5:    53.700 -  64.440:   53        |
|      1:    10.740 -  21.480:  891   |   6:    64.440 -  75.180:   48        |
|      2:    21.480 -  32.220:  530   |   7:    75.180 -  85.920:   12        |
|      3:    32.220 -  42.960:  246   |   8:    85.920 -  96.660:    5        |
|      4:    42.960 -  53.700:  116   |   9:    96.660 - 107.400:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3725 r_free = 0.4393             target_work(ml) = 6.150         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3719 r_free = 0.4388             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3719   r_free= 0.4388   ksol= 0.29   Bsol= 50.00   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.71,3.46,3.43,0.00,0.00,0.00); trace/3= 1.06                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.149387                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3709   r_free= 0.4372   ksol= 0.30   Bsol= 64.09   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.52,2.50,0.00,0.00,0.00); trace/3= 1.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.151880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.995762             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.300   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.943106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.446  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3709      final r-factor (work) = 0.3157          |
| start r-factor (free) = 0.4372      final r-factor (free) = 0.3854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.0299 = 12.00 * 0.50 * 6.1499 + 1.00 * 0.1438                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6419 = 12.00 * 0.50 * 6.0916 + 1.00 * 0.1054                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3157      final r-factor (work) = 0.3025          |
| start r-factor (free) = 0.3854      final r-factor (free) = 0.3761          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7680 = 0.94 * 1.00 * 6.0916 + 1.00 * 0.0230                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7138 = 0.94 * 1.00 * 6.0127 + 1.00 * 0.0432                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.27  19.31    None  None   None       |
|    all(noH): 2823   0      0.00    126.27  19.31    None  None   None       |
|    Sol.    : 438    0      0.00    107.81  37.39    None  None   None       |
|    Mac.    : 2385   0      0.00    126.27  15.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.627: 1158   |   5:    63.133 -  75.760:   49        |
|      1:    12.627 -  25.253:  908   |   6:    75.760 -  88.386:   15        |
|      2:    25.253 -  37.880:  444   |   7:    88.386 - 101.013:    3        |
|      3:    37.880 -  50.507:  177   |   8:   101.013 - 113.640:    1        |
|      4:    50.507 -  63.133:   67   |   9:   113.640 - 126.266:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3025 r_free = 0.3761             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3023 r_free = 0.3763             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3023   r_free= 0.3763   ksol= 0.30   Bsol= 64.09   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,2.52,2.50,0.00,0.00,0.00); trace/3= 1.33                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.006019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3026   r_free= 0.3763   ksol= 0.33   Bsol= 72.44   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,2.17,1.83,0.00,0.00,0.00); trace/3= 1.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.007824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.652295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.218  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.920490              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.484   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3026      final r-factor (work) = 0.2525          |
| start r-factor (free) = 0.3763      final r-factor (free) = 0.3149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1139 = 7.65 * 0.50 * 6.0135 + 1.00 * 0.1054                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8092 = 7.65 * 0.50 * 5.9394 + 1.00 * 0.0840                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2525      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.3149      final r-factor (free) = 0.2930          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4300 = 1.92 * 1.00 * 5.9394 + 1.00 * 0.0234                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1656 = 1.92 * 1.00 * 5.8027 + 1.00 * 0.0216                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.34  19.35    None  None   None       |
|    all(noH): 2823   0      0.00    115.34  19.35    None  None   None       |
|    Sol.    : 438    0      0.00    115.34  46.04    None  None   None       |
|    Mac.    : 2385   0      0.00    106.75  14.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.534: 1261   |   5:    57.670 -  69.204:   72        |
|      1:    11.534 -  23.068:  821   |   6:    69.204 -  80.738:   59        |
|      2:    23.068 -  34.602:  283   |   7:    80.738 -  92.272:   33        |
|      3:    34.602 -  46.136:  171   |   8:    92.272 - 103.806:    6        |
|      4:    46.136 -  57.670:  112   |   9:   103.806 - 115.340:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2285 r_free = 0.2930             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2284 r_free = 0.2927             target_work(ml) = 5.769         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2284   r_free= 0.2927   ksol= 0.33   Bsol= 72.44   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,2.17,1.83,0.00,0.00,0.00); trace/3= 1.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.769413                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2284   r_free= 0.2922   ksol= 0.34   Bsol= 91.69   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,1.01,1.13,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.769552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.642483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.267  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358539              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.702  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2284      final r-factor (work) = 0.1828          |
| start r-factor (free) = 0.2922      final r-factor (free) = 0.2346          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3601 = 6.64 * 0.50 * 5.8039 + 1.00 * 0.0840                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9611 = 6.64 * 0.50 * 5.6823 + 1.00 * 0.0889                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1828      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2346      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0591 = 0.36 * 1.00 * 5.6823 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0034 = 0.36 * 1.00 * 5.5279 + 1.00 * 0.0215                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.06  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    110.06  17.56    None  None   None       |
|    Sol.    : 438    0      3.77    110.06  44.83    None  None   None       |
|    Mac.    : 2385   0      0.00    98.08   12.56    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.006: 1379   |   5:    55.029 -  66.034:   86        |
|      1:    11.006 -  22.011:  825   |   6:    66.034 -  77.040:   47        |
|      2:    22.011 -  33.017:  205   |   7:    77.040 -  88.046:   19        |
|      3:    33.017 -  44.023:  130   |   8:    88.046 -  99.051:    8        |
|      4:    44.023 -  55.029:  121   |   9:    99.051 - 110.057:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1677 r_free = 0.2172             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1675 r_free = 0.2171             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2171   ksol= 0.34   Bsol= 91.69   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,1.01,1.13,0.00,0.00,0.00); trace/3= 0.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.489322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1676   r_free= 0.2165   ksol= 0.34   Bsol= 84.36   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.22,0.77,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.488658                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.615503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.421  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.462320              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.550   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1676      final r-factor (work) = 0.1488          |
| start r-factor (free) = 0.2165      final r-factor (free) = 0.1945          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3187 = 2.62 * 0.50 * 5.5284 + 1.00 * 0.0889                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1777 = 2.62 * 0.50 * 5.4387 + 1.00 * 0.0652                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1488      final r-factor (work) = 0.1440          |
| start r-factor (free) = 0.1945      final r-factor (free) = 0.1932          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5300 = 0.46 * 1.00 * 5.4387 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5115 = 0.46 * 1.00 * 5.3709 + 1.00 * 0.0284                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.97  17.26    None  None   None       |
|    all(noH): 2823   0      0.00    125.97  17.26    None  None   None       |
|    Sol.    : 438    0      3.70    110.37  44.71    None  None   None       |
|    Mac.    : 2385   0      0.00    125.97  12.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.597: 1657   |   5:    62.984 -  75.581:   72        |
|      1:    12.597 -  25.194:  643   |   6:    75.581 -  88.178:   22        |
|      2:    25.194 -  37.791:  172   |   7:    88.178 - 100.775:    8        |
|      3:    37.791 -  50.387:  142   |   8:   100.775 - 113.372:    3        |
|      4:    50.387 -  62.984:  103   |   9:   113.372 - 125.969:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1440 r_free = 0.1932             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1439 r_free = 0.1932             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1439   r_free= 0.1932   ksol= 0.34   Bsol= 84.36   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.22,0.77,0.00,0.00,0.00); trace/3= -0.05                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.365146                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7980 0.99   1406  157 0.1061 0.1470      5.4719      5.6804|
|  2:  4.7980 -  3.8286 0.99   1353  152 0.0989 0.1172      5.5694      5.7358|
|  3:  3.8286 -  3.3506 0.99   1331  149 0.1308 0.1809      5.6701      6.0263|
|  4:  3.3506 -  3.0469 0.99   1319  137 0.1557 0.2045      5.6603       5.806|
|  5:  3.0469 -  2.8301 0.99   1308  150 0.1765 0.1893      5.5714      5.6771|
|  6:  2.8301 -  2.6642 0.98   1302  145 0.1663 0.2630       5.441      5.7007|
|  7:  2.6642 -  2.5314 0.99   1294  149 0.1676 0.2054      5.4216      5.5706|
|  8:  2.5314 -  2.4217 0.98   1303  139 0.1655 0.2310      5.3619      5.6101|
|  9:  2.4217 -  2.3288 0.98   1294  146 0.1660 0.2428      5.3014      5.5773|
| 10:  2.3288 -  2.2487 0.98   1274  141 0.1536 0.1900      5.2136      5.3155|
| 11:  2.2487 -  2.1786 0.99   1283  145 0.1512 0.2291      5.1513      5.5029|
| 12:  2.1786 -  2.1165 0.98   1283  138 0.1439 0.2163      5.0693      5.3511|
| 13:  2.1165 -  2.0609 0.97   1258  139 0.1503 0.1896      4.9986       5.125|
| 14:  2.0609 -  2.0107 0.48    622   72 0.1452 0.2106      4.9336        5.19|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7980  1406   157  0.93  10.68   0.95     0.92       8978.22|
|  2:  4.7980 -  3.8286  1353   152  0.94  10.08   1.00     0.98      11771.82|
|  3:  3.8286 -  3.3506  1331   149  0.91  14.31   1.02     1.02      14938.98|
|  4:  3.3506 -  3.0469  1319   137  0.89  17.56   1.01     0.98      15545.37|
|  5:  3.0469 -  2.8301  1308   150  0.86  20.70   1.00     0.97      13237.39|
|  6:  2.8301 -  2.6642  1302   145  0.86  20.70   0.97     0.94      10726.39|
|  7:  2.6642 -  2.5314  1294   149  0.86  20.68   1.00     0.95      10313.06|
|  8:  2.5314 -  2.4217  1303   139  0.85  21.33   0.99     0.94       9577.64|
|  9:  2.4217 -  2.3288  1294   146  0.85  21.73   0.99     0.92       8410.85|
| 10:  2.3288 -  2.2487  1274   141  0.86  20.94   0.99     0.94       7212.91|
| 11:  2.2487 -  2.1786  1283   145  0.87  20.20   0.98     0.92       6399.06|
| 12:  2.1786 -  2.1165  1283   138  0.88  19.26   1.00     0.99       5774.93|
| 13:  2.1165 -  2.0609  1258   139  0.86  20.41   0.97     0.94       4925.18|
| 14:  2.0609 -  2.0107   622    72  0.87  19.09   0.94     0.89       4144.33|
|alpha:            min =        0.89 max =            1.02 mean =         0.95|
|beta:             min =     4144.33 max =        15545.37 mean =      9671.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.29|
|phase err.(test): min =        0.00 max =           89.92 mean =        17.49|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1935   ksol= 0.33   Bsol= 82.98   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.12,0.71,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.366521                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1444   r_free= 0.1935   ksol= 0.33   Bsol= 82.98   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.27,-0.12,0.71,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.366521                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.7980 0.99   1406  157 0.1082 0.1477      5.4817      5.6848|
|  2:  4.7980 -  3.8286 0.99   1353  152 0.1004 0.1174      5.5772      5.7359|
|  3:  3.8286 -  3.3506 0.99   1331  149 0.1309 0.1805      5.6705      6.0259|
|  4:  3.3506 -  3.0469 0.99   1319  137 0.1557 0.2048      5.6613       5.808|
|  5:  3.0469 -  2.8301 0.99   1308  150 0.1766 0.1896      5.5726      5.6786|
|  6:  2.8301 -  2.6642 0.98   1302  145 0.1661 0.2626      5.4405      5.6987|
|  7:  2.6642 -  2.5314 0.99   1294  149 0.1677 0.2057      5.4211      5.5706|
|  8:  2.5314 -  2.4217 0.98   1303  139 0.1654 0.2312      5.3615      5.6106|
|  9:  2.4217 -  2.3288 0.98   1294  146 0.1659 0.2429       5.301      5.5772|
| 10:  2.3288 -  2.2487 0.98   1274  141 0.1536 0.1905      5.2138      5.3163|
| 11:  2.2487 -  2.1786 0.99   1283  145 0.1510 0.2289      5.1507       5.502|
| 12:  2.1786 -  2.1165 0.98   1283  138 0.1439 0.2167      5.0692      5.3526|
| 13:  2.1165 -  2.0609 0.97   1258  139 0.1504 0.1892      4.9985       5.124|
| 14:  2.0609 -  2.0107 0.48    622   72 0.1452 0.2100       4.933       5.189|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1489 -  4.7980  1406   157  0.93  10.83   0.95     0.91       9115.95|
|  2:  4.7980 -  3.8286  1353   152  0.94  10.09   1.00     0.98      11813.62|
|  3:  3.8286 -  3.3506  1331   149  0.91  14.28   1.02     1.02      14911.47|
|  4:  3.3506 -  3.0469  1319   137  0.89  17.60   1.00     0.98      15590.69|
|  5:  3.0469 -  2.8301  1308   150  0.86  20.72   1.00     0.97      13258.54|
|  6:  2.8301 -  2.6642  1302   145  0.86  20.68   0.97     0.93      10717.11|
|  7:  2.6642 -  2.5314  1294   149  0.86  20.65   0.99     0.95      10297.90|
|  8:  2.5314 -  2.4217  1303   139  0.85  21.31   0.98     0.93       9568.67|
|  9:  2.4217 -  2.3288  1294   146  0.85  21.73   0.98     0.91       8412.68|
| 10:  2.3288 -  2.2487  1274   141  0.86  20.94   0.98     0.93       7217.93|
| 11:  2.2487 -  2.1786  1283   145  0.87  20.19   0.98     0.91       6402.27|
| 12:  2.1786 -  2.1165  1283   138  0.88  19.26   0.99     0.98       5776.02|
| 13:  2.1165 -  2.0609  1258   139  0.86  20.39   0.96     0.94       4919.53|
| 14:  2.0609 -  2.0107   622    72  0.87  19.07   0.94     0.88       4131.73|
|alpha:            min =        0.88 max =            1.02 mean =         0.95|
|beta:             min =     4131.73 max =        15590.69 mean =      9686.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.30|
|phase err.(test): min =        0.00 max =           89.31 mean =        17.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.475)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.97  17.26    None  None   None       |
|    all(noH): 2823   0      0.00    125.97  17.26    None  None   None       |
|    Sol.    : 438    0      3.70    110.38  44.72    None  None   None       |
|    Mac.    : 2385   0      0.00    125.97  12.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  12.600: 1657   |   5:    62.987 -  75.584:   72        |
|      1:    12.600 -  25.197:  643   |   6:    75.584 -  88.181:   22        |
|      2:    25.197 -  37.794:  172   |   7:    88.181 - 100.778:    8        |
|      3:    37.794 -  50.390:  142   |   8:   100.778 - 113.375:    3        |
|      4:    50.390 -  62.987:  103   |   9:   113.375 - 125.972:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.590 - 5.357
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 331
   mapped sites are within: 0.726 - 5.357

peak=    9.327 closest distance to " O  BHOH Z  74 " =    1.352
peak=    7.180 closest distance to " O   HOH Z  69 " =    1.127
peak=    6.974 closest distance to " O   GLN A  11 " =    1.037
peak=    6.861 closest distance to " O   HOH Z  41 " =    1.313
peak=    5.903 closest distance to " O   HOH Z 138 " =    0.967
peak=    5.644 closest distance to " O   HOH Z  54 " =    1.635
peak=    5.516 closest distance to " O   HOH Z 117 " =    1.541
peak=    5.192 closest distance to " OD1 ASN A  69 " =    0.943
peak=    5.175 closest distance to " O   HOH Z 248 " =    1.536
peak=    5.128 closest distance to " O   HOH Z  69 " =    1.886
peak=    4.985 closest distance to " OD1 ASN A 301 " =    1.032
peak=    4.927 closest distance to " O   HOH Z 210 " =    1.554
peak=    4.864 closest distance to " CG AARG A 275 " =    1.130
peak=    4.782 closest distance to " N   SER A 164 " =    0.941
peak=    4.699 closest distance to " O   HOH Z  65 " =    1.142
peak=    4.693 closest distance to " NH2AARG A 145 " =    1.221
peak=    4.643 closest distance to " O   HOH Z 412 " =    3.345
peak=    4.618 closest distance to " O   HOH Z  49 " =    1.603
peak=    4.609 closest distance to " CG2 VAL A 197 " =    1.302
peak=    4.587 closest distance to " CG  GLN A  77 " =    0.836
peak=    4.581 closest distance to " CB  ASN A  39 " =    0.841
peak=    4.563 closest distance to " CB  SER A  63 " =    1.248
peak=    4.487 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.472 closest distance to " CG  PRO A  54 " =    1.416
peak=    4.450 closest distance to " CB  TRP A 179 " =    1.399
peak=    4.429 closest distance to " CD2 TRP A 179 " =    1.209
peak=    4.407 closest distance to " CG1 ILE A 120 " =    1.136
peak=    4.392 closest distance to " CB  GLN A 223 " =    1.454
peak=    4.379 closest distance to " OH  TYR A  68 " =    0.952
peak=    4.342 closest distance to " CZ3 TRP A 266 " =    1.135
peak=    4.342 closest distance to " CA  ALA A 100 " =    1.114
peak=    4.321 closest distance to " O   HOH Z 422 " =    1.083
peak=    4.319 closest distance to " O   HOH Z 425 " =    1.685
peak=    4.309 closest distance to " O   HOH Z 147 " =    1.494
peak=    4.308 closest distance to " CA  GLN A  11 " =    1.312
peak=    4.227 closest distance to " O   PRO A 198 " =    1.644
peak=    4.211 closest distance to " CZ  PHE A 218 " =    1.163
peak=    4.197 closest distance to " CG  GLN A  11 " =    1.117
peak=    4.148 closest distance to " O   HOH Z 431 " =    1.220
peak=    4.136 closest distance to " CD2 TYR A  68 " =    0.821
peak=    4.132 closest distance to " O   HOH Z  35 " =    2.156
peak=    4.120 closest distance to " CZ  PHE A  38 " =    1.167
peak=    4.080 closest distance to " CG  PRO A  90 " =    1.261
peak=    4.076 closest distance to " O   HOH Z 426 " =    1.215
peak=    4.069 closest distance to " O   HOH Z 261 " =    2.208
peak=    4.063 closest distance to " O   HOH Z 222 " =    0.971
peak=    4.034 closest distance to " CG2BVAL A  41 " =    0.909
peak=    4.018 closest distance to " CB  MET A  40 " =    0.945
peak=    4.015 closest distance to " NH2 ARG A  56 " =    1.187
peak=    4.004 closest distance to " O   ASP A 200 " =    1.648
peak=    3.994 closest distance to " O   HOH Z 139 " =    1.368
peak=    3.971 closest distance to " NE2 GLN A  77 " =    3.114
peak=    3.961 closest distance to " OE1 GLN A  88 " =    1.029
peak=    3.955 closest distance to " CB  ALA A 291 " =    1.095
peak=    3.951 closest distance to " O   HOH Z 113 " =    1.892
peak=    3.949 closest distance to " NH1AARG A 145 " =    1.459
peak=    3.939 closest distance to " CB  GLU A  37 " =    1.020
peak=    3.938 closest distance to " CB  GLN A 183 " =    1.160
peak=    3.936 closest distance to " O   HOH Z 346 " =    1.714
peak=    3.936 closest distance to " CB  VAL A 202 " =    1.417
peak=    3.917 closest distance to " O   HOH Z 358 " =    1.471
peak=    3.916 closest distance to " NE2 GLN A  11 " =    1.247
peak=    3.901 closest distance to " O   HOH Z 394 " =    1.642
peak=    3.899 closest distance to " O   THR A 251 " =    1.179
peak=    3.897 closest distance to " CB  PRO A  54 " =    0.881
peak=    3.875 closest distance to " CE1 HIS A 115 " =    1.034
peak=    3.869 closest distance to " CB  GLU A 128 " =    0.957
peak=    3.858 closest distance to " O   HOH Z 362 " =    3.163
peak=    3.858 closest distance to " O   HOH Z 214 " =    1.982
peak=    3.848 closest distance to " O   HOH Z 234 " =    3.942
peak=    3.838 closest distance to " CB  SER A  62 " =    0.957
peak=    3.829 closest distance to " O   HOH Z  63 " =    1.410
peak=    3.829 closest distance to " O   HOH Z 134 " =    1.930
peak=    3.824 closest distance to " O   HOH Z  27 " =    1.156
peak=    3.821 closest distance to " CB  THR A  52 " =    0.842
peak=    3.813 closest distance to " O   HOH Z 200 " =    1.787
peak=    3.808 closest distance to " CB  ARG A 190 " =    1.824
peak=    3.806 closest distance to " CD  ARG A  66 " =    2.709
peak=    3.799 closest distance to " O   SER A  87 " =    2.350
peak=    3.795 closest distance to " CA  ARG A 195 " =    1.183
peak=    3.782 closest distance to " O   HOH Z 149 " =    1.987
peak=    3.776 closest distance to " O   HOH Z  67 " =    1.045
peak=    3.771 closest distance to " N   TYR A  15 " =    0.864
peak=    3.760 closest distance to " O   VAL A 112 " =    1.855
peak=    3.758 closest distance to " O   HOH Z 343 " =    2.536
peak=    3.758 closest distance to " O   HOH Z  88 " =    3.385
peak=    3.751 closest distance to " O   HOH Z  76 " =    1.252
peak=    3.746 closest distance to " CG  LYS A  76 " =    1.163
peak=    3.736 closest distance to " CB  GLU A  46 " =    1.105
peak=    3.735 closest distance to " CG  PRO A 198 " =    1.217
peak=    3.720 closest distance to " CB  ARG A 275 " =    0.840
peak=    3.719 closest distance to " O   HOH Z 137 " =    2.178
peak=    3.718 closest distance to " O   HOH Z 406 " =    1.786
peak=    3.718 closest distance to " CD1 LEU A  96 " =    0.729
peak=    3.716 closest distance to " O   HOH Z  18 " =    2.261
peak=    3.712 closest distance to " O   HOH Z 107 " =    0.921
peak=    3.712 closest distance to " O   HOH Z  40 " =    1.741
peak=    3.707 closest distance to " O  BHOH Z 338 " =    1.055
peak=    3.691 closest distance to " O   HOH Z 417 " =    3.064
peak=    3.685 closest distance to " CG1AVAL A 121 " =    0.751
peak=    3.684 closest distance to " O   HOH Z 395 " =    1.708
peak=    3.678 closest distance to " O   HOH Z 369 " =    2.037
peak=    3.678 closest distance to " O   HOH Z 350 " =    0.874
peak=    3.677 closest distance to " O   HOH Z  48 " =    2.283
peak=    3.673 closest distance to " NH1 ARG A 269 " =    0.775
peak=    3.670 closest distance to " ND2 ASN A  69 " =    1.412
peak=    3.665 closest distance to " O   HOH Z 126 " =    1.574
peak=    3.659 closest distance to " CD  ARG A 159 " =    0.871
peak=    3.658 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.648 closest distance to " O   HOH Z 176 " =    1.714
peak=    3.645 closest distance to " CD  ARG A 269 " =    0.837
peak=    3.644 closest distance to " O   HOH Z 437 " =    1.802
peak=    3.644 closest distance to " ND2 ASN A 249 " =    0.943
peak=    3.644 closest distance to " CB  GLU A 152 " =    1.183
peak=    3.643 closest distance to " O   HOH Z 132 " =    3.219
peak=    3.642 closest distance to " CB  LEU A  83 " =    0.829
peak=    3.642 closest distance to " O   HOH Z 365 " =    2.188
peak=    3.641 closest distance to " CB  ASN A  45 " =    1.068
peak=    3.639 closest distance to " CB  MET A  47 " =    0.946
peak=    3.635 closest distance to " CD  LYS A 166 " =    1.743
peak=    3.631 closest distance to " CA  ARG A  36 " =    1.051
peak=    3.627 closest distance to " NH2 ARG A 156 " =    1.106
peak=    3.624 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.623 closest distance to " O   HOH Z 415 " =    1.120
peak=    3.622 closest distance to " CB  ASN A 142 " =    1.040
peak=    3.622 closest distance to " O   HOH Z 128 " =    1.390
peak=    3.612 closest distance to " O   HOH Z 189 " =    2.963
peak=    3.610 closest distance to " O   HOH Z 250 " =    1.282
peak=    3.607 closest distance to " CB  ASN A 148 " =    1.606
peak=    3.603 closest distance to " NH1 ARG A  36 " =    1.341
peak=    3.600 closest distance to " CD  LYS A  76 " =    1.810
peak=    3.589 closest distance to " O   HOH Z 159 " =    1.153
peak=    3.586 closest distance to " O   HOH Z 295 " =    1.052
peak=    3.578 closest distance to " O   HOH Z 146 " =    1.754
peak=    3.560 closest distance to " O   ALA A 165 " =    1.452
peak=    3.557 closest distance to " CB  SER A 210 " =    1.004
peak=    3.550 closest distance to " O   HOH Z 197 " =    5.357
peak=    3.540 closest distance to " CA  ALA A  51 " =    1.014
peak=    3.536 closest distance to " O   HOH Z 418 " =    1.896
peak=    3.535 closest distance to " O   HOH Z 213 " =    1.705
peak=    3.532 closest distance to " O   HOH Z  26 " =    1.194
peak=    3.532 closest distance to " CE3 TRP A  85 " =    1.164
peak=    3.530 closest distance to " O   HOH Z 421 " =    1.548
peak=    3.525 closest distance to " NH1BARG A 102 " =    0.947
peak=    3.525 closest distance to " CB  GLN A  88 " =    1.302
peak=    3.524 closest distance to " N   THR A  52 " =    1.264
peak=    3.519 closest distance to " CA  ARG A 139 " =    1.368
peak=    3.517 closest distance to " CA  GLY A   6 " =    0.854
peak=    3.512 closest distance to " CB  ASP A 140 " =    0.726
peak=    3.505 closest distance to " CB  ASN A 187 " =    1.142
peak=    3.505 closest distance to " O   HOH Z  85 " =    1.971
peak=    3.505 closest distance to " O   HOH Z 377 " =    1.438
peak=    3.501 closest distance to " CA  ALA A 295 " =    1.077
peak=    3.500 closest distance to " CE1 TYR A 186 " =    1.408
peak=    3.500 closest distance to " O   HOH Z 196 " =    1.398
peak=    3.499 closest distance to " CG2 THR A 221 " =    1.069
peak=    3.489 closest distance to " O   HOH Z 287 " =    1.685
peak=    3.479 closest distance to " CA  GLY A 196 " =    0.894
peak=    3.471 closest distance to " CB  ASP A 191 " =    1.215
peak=    3.464 closest distance to " O   HOH Z 298 " =    2.133
peak=    3.464 closest distance to " OH  TYR A 116 " =    1.268
peak=    3.463 closest distance to " CG1 VAL A 153 " =    1.130
peak=    3.461 closest distance to " CG2AVAL A 121 " =    1.786
peak=    3.460 closest distance to " O   HOH Z 427 " =    3.312
peak=    3.459 closest distance to " CB  ALA A 114 " =    0.765
peak=    3.449 closest distance to " CA  ALA A 160 " =    0.969
peak=    3.445 closest distance to " O   HOH Z 279 " =    1.001
peak=    3.444 closest distance to " CG  GLU A  37 " =    0.996
peak=    3.440 closest distance to " CA  ALA A 154 " =    1.058
peak=    3.436 closest distance to " N   SER A 271 " =    1.106
peak=    3.431 closest distance to " O   HOH Z 359 " =    1.619
peak=    3.431 closest distance to " CG2 VAL A 268 " =    1.134
peak=    3.426 closest distance to " OG1 THR A 221 " =    1.742
peak=    3.426 closest distance to " OG BSER A  99 " =    2.884
peak=    3.426 closest distance to " CB  GLU A 277 " =    3.888
peak=    3.423 closest distance to " CA  CYS A 260 " =    1.355
peak=    3.421 closest distance to " O   HOH Z 199 " =    1.491
peak=    3.421 closest distance to " O   HOH Z  73 " =    2.490
peak=    3.420 closest distance to " N   ALA A   1 " =    2.246
peak=    3.416 closest distance to " CD  ARG A 195 " =    1.024
peak=    3.415 closest distance to " CA  ARG A 156 " =    1.060
peak=    3.414 closest distance to " CB  GLN A  89 " =    1.266
peak=    3.411 closest distance to " CB  LEU A 101 " =    1.250
peak=    3.408 closest distance to " CB  ASN A 285 " =    0.757
peak=    3.400 closest distance to " CB  MET A 105 " =    1.004
peak=    3.398 closest distance to " ND2 ASN A 301 " =    0.949
peak=    3.397 closest distance to " O   HOH Z 232 " =    2.517
peak=    3.396 closest distance to " CG  MET A 188 " =    0.942
peak=    3.395 closest distance to " O   HOH Z  80 " =    2.137
peak=    3.386 closest distance to " O   HOH Z 193 " =    2.109
peak=    3.385 closest distance to " O   HOH Z 403 " =    1.606
peak=    3.385 closest distance to " O   HOH Z 272 " =    1.301
peak=    3.385 closest distance to " CB  SER A 288 " =    0.839
peak=    3.381 closest distance to " CB  PHE A  16 " =    1.474
peak=    3.377 closest distance to " CD  ARG A  36 " =    0.929
peak=    3.373 closest distance to " O   HOH Z 301 " =    1.560
peak=    3.370 closest distance to " CG  GLN A 205 " =    1.173
peak=    3.369 closest distance to " ND2 ASN A 249 " =    2.075
peak=    3.367 closest distance to " N   TYR A 247 " =    1.252
peak=    3.363 closest distance to " CB  ALA A 299 " =    0.783
peak=    3.363 closest distance to " O   HOH Z 287 " =    2.111
peak=    3.360 closest distance to " CB  TRP A 266 " =    0.920
peak=    3.356 closest distance to " NE  ARG A  36 " =    1.014
peak=    3.355 closest distance to " CA  GLY A  23 " =    1.021
peak=    3.354 closest distance to " OE1 GLN A  58 " =    0.991
peak=    3.348 closest distance to " OG  SER A 276 " =    1.631
peak=    3.338 closest distance to " O   HOH Z 402 " =    1.721
peak=    3.329 closest distance to " O   HOH Z 214 " =    2.467
peak=    3.328 closest distance to " CB  ARG A 156 " =    1.064
peak=    3.327 closest distance to " CB  SER A  62 " =    1.021
peak=    3.325 closest distance to " CA  THR A 246 " =    1.068
peak=    3.325 closest distance to " O   HOH Z 299 " =    4.277
peak=    3.324 closest distance to " O  BHOH Z 338 " =    2.338
peak=    3.322 closest distance to " O   HOH Z 401 " =    1.221
peak=    3.319 closest distance to " CA  PRO A 198 " =    1.177
peak=    3.317 closest distance to " ND2 ASN A 187 " =    1.553
peak=    3.317 closest distance to " CB  PRO A  90 " =    1.070
peak=    3.311 closest distance to " O   HOH Z 343 " =    1.536
peak=    3.308 closest distance to " CA  GLN A 223 " =    0.847
peak=    3.307 closest distance to " O   HOH Z 284 " =    3.016
peak=    3.306 closest distance to " O   HOH Z  54 " =    1.788
peak=    3.305 closest distance to " CB  ALA A 256 " =    1.417
peak=    3.302 closest distance to " OG1 THR A  82 " =    0.995
peak=    3.301 closest distance to " O   HOH Z  50 " =    3.401
peak=    3.299 closest distance to " CB  TYR A 172 " =    0.948
peak=    3.290 closest distance to " CB  VAL A 265 " =    1.256
peak=    3.287 closest distance to " CE1 TYR A  30 " =    0.983
peak=    3.285 closest distance to " CA  ASN A 217 " =    1.413
peak=    3.283 closest distance to " O   THR A 220 " =    1.107
peak=    3.282 closest distance to " O   SER A   3 " =    0.781
peak=    3.280 closest distance to " CB  ASP A 124 " =    0.888
peak=    3.275 closest distance to " O   HOH Z   1 " =    2.758
peak=    3.273 closest distance to " O   HOH Z 144 " =    1.495
peak=    3.273 closest distance to " O   HOH Z 394 " =    4.292
peak=    3.270 closest distance to " O   HOH Z 124 " =    1.182
peak=    3.270 closest distance to " CG1 ILE A  33 " =    1.235
peak=    3.268 closest distance to " CA  GLN A  94 " =    0.864
peak=    3.267 closest distance to " NH1 ARG A  14 " =    1.352
peak=    3.267 closest distance to " CG2 THR A  42 " =    0.818
peak=    3.267 closest distance to " CB  ARG A  79 " =    0.865
peak=    3.264 closest distance to " O   HOH Z 258 " =    2.162
peak=    3.261 closest distance to " N   GLU A   2 " =    0.903
peak=    3.258 closest distance to " O   HOH Z   9 " =    1.197
peak=    3.257 closest distance to " CB  PHE A 283 " =    0.801
peak=    3.254 closest distance to " CG  MET A 185 " =    1.112
peak=    3.253 closest distance to " O   HOH Z 156 " =    2.725
peak=    3.251 closest distance to " CA  ASP A 162 " =    0.957
peak=    3.250 closest distance to " O   HOH Z 195 " =    1.658
peak=    3.241 closest distance to " O   VAL A  72 " =    1.162
peak=    3.240 closest distance to " O   HOH Z  21 " =    1.733
peak=    3.231 closest distance to " CA  VAL A 112 " =    1.039
peak=    3.230 closest distance to " NH1 ARG A 138 " =    1.036
peak=    3.230 closest distance to " O   HOH Z 221 " =    1.271
peak=    3.228 closest distance to " O   ALA A  84 " =    1.349
peak=    3.227 closest distance to " O   HOH Z 428 " =    1.046
peak=    3.225 closest distance to " CA  ASN A 249 " =    1.259
peak=    3.224 closest distance to " CB  VAL A 296 " =    1.527
peak=    3.224 closest distance to " CG  LEU A 167 " =    1.040
peak=    3.223 closest distance to " CB  VAL A 126 " =    0.810
peak=    3.223 closest distance to " CA  GLU A 152 " =    0.972
peak=    3.221 closest distance to " N   ILE A  33 " =    0.968
peak=    3.221 closest distance to " CA  ILE A 106 " =    0.833
peak=    3.220 closest distance to " NH2AARG A 190 " =    2.008
peak=    3.218 closest distance to " N   VAL A 126 " =    1.691
peak=    3.216 closest distance to " O   HOH Z 126 " =    2.379
peak=    3.212 closest distance to " CB  GLU A   2 " =    1.016
peak=    3.210 closest distance to " O   HOH Z 419 " =    1.762
peak=    3.210 closest distance to " CD  ARG A  24 " =    1.249
peak=    3.205 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.205 closest distance to " OD2 ASP A  27 " =    1.169
peak=    3.204 closest distance to " CA  HIS A 115 " =    1.025
peak=    3.204 closest distance to " OG  SER A  62 " =    2.887
peak=    3.203 closest distance to " OG  SER A 135 " =    1.300
peak=    3.203 closest distance to " O   HOH Z  44 " =    1.799
peak=    3.201 closest distance to " O   HOH Z 435 " =    2.679
peak=    3.199 closest distance to " N   HIS A 108 " =    1.750
peak=    3.196 closest distance to " O   HOH Z 316 " =    3.066
peak=    3.194 closest distance to " N   VAL A 265 " =    1.111
peak=    3.192 closest distance to " CZ3 TRP A  85 " =    1.198
peak=    3.189 closest distance to " CB  ALA A   1 " =    1.071
peak=    3.188 closest distance to " OG  SER A  62 " =    2.886
peak=    3.187 closest distance to " O   HOH Z  43 " =    2.106
peak=    3.183 closest distance to " O   HOH Z 299 " =    1.187
peak=    3.182 closest distance to " O   HOH Z 223 " =    1.236
peak=    3.180 closest distance to " O   HOH Z 139 " =    4.209
peak=    3.175 closest distance to " CG2 ILE A 234 " =    1.192
peak=    3.174 closest distance to " O   PRO A 213 " =    1.497
peak=    3.173 closest distance to " N   ALA A 180 " =    0.731
peak=    3.173 closest distance to " CG2 VAL A 126 " =    1.016
peak=    3.170 closest distance to " OE2 GLU A   2 " =    2.037
peak=    3.167 closest distance to " CG2 THR A 220 " =    0.792
peak=    3.163 closest distance to " O   HOH Z 433 " =    1.674
peak=    3.160 closest distance to " ND2 ASN A 127 " =    1.008
peak=    3.160 closest distance to " ND2 ASN A 176 " =    0.827
peak=    3.160 closest distance to " NE2 GLN A  58 " =    5.155
peak=    3.152 closest distance to " OE1 GLN A  58 " =    3.625
peak=    3.152 closest distance to " CB  PRO A 243 " =    1.626
peak=    3.152 closest distance to " CB  SER A  97 " =    1.731
peak=    3.149 closest distance to " O   TYR A 116 " =    1.286
peak=    3.143 closest distance to " O   HOH Z 303 " =    2.515
peak=    3.143 closest distance to " ND2BASN A 224 " =    0.857
peak=    3.137 closest distance to " CA  SER A  87 " =    0.927
peak=    3.137 closest distance to " O   HOH Z  38 " =    1.514
peak=    3.136 closest distance to " O   HOH Z 293 " =    2.200
peak=    3.134 closest distance to " O   HOH Z 344 " =    3.265
peak=    3.132 closest distance to " O   THR A 182 " =    1.462
peak=    3.130 closest distance to " O   HOH Z 265 " =    2.090
peak=    3.129 closest distance to " CG1 VAL A 257 " =    1.267
peak=    3.124 closest distance to " NZ  LYS A 117 " =    2.853
peak=    3.123 closest distance to " O   HOH Z 133 " =    3.030
peak=    3.122 closest distance to " CG  PRO A 213 " =    1.275
peak=    3.122 closest distance to " OE1 GLU A   2 " =    1.243
peak=    3.119 closest distance to " CB  GLN A 194 " =    1.004
peak=    3.118 closest distance to " O   HOH Z 369 " =    1.343
peak=    3.115 closest distance to " C   ALA A 299 " =    1.156
peak=    3.111 closest distance to " N   LYS A 166 " =    0.949
peak=    3.097 closest distance to " O   HOH Z 298 " =    1.946
peak=    3.095 closest distance to " CZ3 TRP A 274 " =    4.564
peak=    3.088 closest distance to " O   HOH Z 344 " =    1.908
peak=    3.086 closest distance to " CB  ALA A 100 " =    1.386
peak=    3.085 closest distance to " O   PRO A  90 " =    1.592
peak=    3.069 closest distance to " NZ  LYS A 117 " =    0.958
peak=    3.029 closest distance to " N   ALA A 292 " =    0.989
peak=    3.020 closest distance to " O   HOH Z  73 " =    1.997

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 5.867
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 227
   mapped sites are within: 0.709 - 5.867

peak=   -4.571 closest distance to " CD  GLN A 223 " =    1.359
peak=   -4.508 closest distance to " O   HOH Z 418 " =    1.179
peak=   -4.315 closest distance to " O   HOH Z 166 " =    1.325
peak=   -4.242 closest distance to " O   HOH Z 114 " =    0.836
peak=   -4.176 closest distance to " CG  ARG A 269 " =    2.451
peak=   -4.147 closest distance to " O   HOH Z 411 " =    5.484
peak=   -4.120 closest distance to " N   ALA A  43 " =    2.758
peak=   -4.103 closest distance to " CG  PRO A 243 " =    1.690
peak=   -4.089 closest distance to " O   PRO A 198 " =    1.279
peak=   -4.062 closest distance to " CB  PRO A 243 " =    2.927
peak=   -4.049 closest distance to " O   HOH Z 150 " =    1.977
peak=   -4.011 closest distance to " O   HOH Z 211 " =    0.905
peak=   -3.985 closest distance to " O   HOH Z 203 " =    1.258
peak=   -3.984 closest distance to " CG  GLN A  58 " =    1.153
peak=   -3.961 closest distance to " CE2 PHE A  61 " =    2.777
peak=   -3.956 closest distance to " CD1 PHE A  59 " =    2.027
peak=   -3.891 closest distance to " O   HOH Z 128 " =    2.812
peak=   -3.859 closest distance to " CG  GLN A  11 " =    1.085
peak=   -3.853 closest distance to " CG2 ILE A  20 " =    2.625
peak=   -3.821 closest distance to " O   VAL A 174 " =    2.127
peak=   -3.805 closest distance to " N   ARG A 275 " =    1.176
peak=   -3.796 closest distance to " O   HOH Z 407 " =    0.973
peak=   -3.796 closest distance to " CD2 LEU A 237 " =    2.560
peak=   -3.783 closest distance to " SD  MET A 105 " =    2.398
peak=   -3.782 closest distance to " OD2 ASP A 171 " =    1.880
peak=   -3.777 closest distance to " OD1 ASN A 148 " =    1.305
peak=   -3.736 closest distance to " CD  ARG A  14 " =    3.244
peak=   -3.726 closest distance to " CD1 PHE A 130 " =    2.342
peak=   -3.719 closest distance to " O   HOH Z   7 " =    0.924
peak=   -3.717 closest distance to " O   HOH Z 259 " =    0.892
peak=   -3.717 closest distance to " O   HOH Z 166 " =    2.380
peak=   -3.697 closest distance to " CG  ARG A 259 " =    1.561
peak=   -3.695 closest distance to " C   ASN A 285 " =    2.269
peak=   -3.693 closest distance to " CD  GLN A 223 " =    0.845
peak=   -3.692 closest distance to " O   HOH Z 155 " =    2.124
peak=   -3.678 closest distance to " O   HOH Z 377 " =    0.709
peak=   -3.661 closest distance to " O   HOH Z  10 " =    1.740
peak=   -3.656 closest distance to " O   HOH Z  40 " =    2.918
peak=   -3.655 closest distance to " O   VAL A  67 " =    2.879
peak=   -3.655 closest distance to " CG2 VAL A 189 " =    2.236
peak=   -3.653 closest distance to " O   HOH Z 250 " =    1.922
peak=   -3.651 closest distance to " O   HOH Z 222 " =    1.027
peak=   -3.647 closest distance to " CZ  TYR A 169 " =    1.884
peak=   -3.644 closest distance to " CG  GLU A  53 " =    1.436
peak=   -3.641 closest distance to " O   HOH Z  37 " =    1.408
peak=   -3.633 closest distance to " CG1 VAL A 112 " =    2.656
peak=   -3.631 closest distance to " O   HOH Z  19 " =    2.324
peak=   -3.626 closest distance to " CG2BVAL A 121 " =    1.379
peak=   -3.626 closest distance to " OE1 GLN A  88 " =    1.118
peak=   -3.609 closest distance to " O   HOH Z 134 " =    2.487
peak=   -3.606 closest distance to " CA  VAL A 197 " =    0.987
peak=   -3.599 closest distance to " O   ARG A 275 " =    2.056
peak=   -3.592 closest distance to " O   SER A 210 " =    1.787
peak=   -3.572 closest distance to " CB  SER A 146 " =    2.211
peak=   -3.563 closest distance to " CA  SER A 164 " =    2.105
peak=   -3.559 closest distance to " CG  LEU A  83 " =    2.092
peak=   -3.558 closest distance to " O   HOH Z 196 " =    1.619
peak=   -3.544 closest distance to " CD  GLN A  88 " =    0.927
peak=   -3.543 closest distance to " CB  ALA A 131 " =    2.445
peak=   -3.541 closest distance to " O   HOH Z  67 " =    1.571
peak=   -3.529 closest distance to " CG  ASN A  45 " =    0.829
peak=   -3.523 closest distance to " O   HOH Z 156 " =    3.658
peak=   -3.522 closest distance to " CB  ALA A  43 " =    2.817
peak=   -3.520 closest distance to " O   HOH Z   7 " =    1.362
peak=   -3.510 closest distance to " O   HOH Z 198 " =    1.576
peak=   -3.504 closest distance to " O   HOH Z 151 " =    1.607
peak=   -3.503 closest distance to " CG2 THR A 221 " =    2.393
peak=   -3.501 closest distance to " CG1 VAL A 189 " =    2.528
peak=   -3.499 closest distance to " CG  LEU A 281 " =    2.008
peak=   -3.499 closest distance to " O   GLY A  17 " =    1.079
peak=   -3.498 closest distance to " O   HOH Z 407 " =    3.717
peak=   -3.497 closest distance to " CG  GLN A 103 " =    2.354
peak=   -3.488 closest distance to " O   HOH Z 340 " =    1.450
peak=   -3.480 closest distance to " O   HOH Z 216 " =    0.751
peak=   -3.476 closest distance to " O   HOH Z 133 " =    1.661
peak=   -3.474 closest distance to " O   HOH Z 251 " =    4.563
peak=   -3.471 closest distance to " O   HOH Z 155 " =    1.691
peak=   -3.470 closest distance to " O   GLN A 240 " =    3.455
peak=   -3.465 closest distance to " CA  GLU A 277 " =    1.225
peak=   -3.464 closest distance to " CB  PRO A 280 " =    2.168
peak=   -3.462 closest distance to " O   HOH Z 186 " =    3.903
peak=   -3.459 closest distance to " OD1 ASP A 171 " =    1.563
peak=   -3.458 closest distance to " SD  MET A  40 " =    2.029
peak=   -3.456 closest distance to " CB  ALA A 291 " =    2.582
peak=   -3.456 closest distance to " CG2 ILE A  49 " =    2.733
peak=   -3.441 closest distance to " CD  GLU A 236 " =    1.106
peak=   -3.437 closest distance to " O   HOH Z 185 " =    2.760
peak=   -3.435 closest distance to " O   HOH Z  41 " =    2.417
peak=   -3.434 closest distance to " O   ASP A 171 " =    1.003
peak=   -3.431 closest distance to " O   HOH Z 184 " =    1.621
peak=   -3.429 closest distance to " CD2 TYR A 293 " =    1.834
peak=   -3.428 closest distance to " NE2 GLN A 194 " =    2.320
peak=   -3.427 closest distance to " C   VAL A 265 " =    0.828
peak=   -3.419 closest distance to " ND2 ASN A  60 " =    2.125
peak=   -3.414 closest distance to " O   HOH Z 290 " =    1.126
peak=   -3.407 closest distance to " N   ALA A 242 " =    1.764
peak=   -3.400 closest distance to " N   SER A 134 " =    1.174
peak=   -3.397 closest distance to " ND2BASN A 224 " =    1.447
peak=   -3.396 closest distance to " CD  GLN A  77 " =    1.127
peak=   -3.391 closest distance to " O   HOH Z 424 " =    2.867
peak=   -3.390 closest distance to " N   GLN A  58 " =    1.718
peak=   -3.386 closest distance to " O   HOH Z 287 " =    1.548
peak=   -3.385 closest distance to " CE3 TRP A 274 " =    2.097
peak=   -3.385 closest distance to " O   HOH Z 371 " =    0.828
peak=   -3.383 closest distance to " O   MET A  47 " =    2.392
peak=   -3.378 closest distance to " OXT GLY A 302 " =    3.105
peak=   -3.376 closest distance to " O   HOH Z 273 " =    0.787
peak=   -3.373 closest distance to " ND2 ASN A  60 " =    1.418
peak=   -3.370 closest distance to " CG1BVAL A  72 " =    1.994
peak=   -3.368 closest distance to " O   HOH Z 221 " =    0.940
peak=   -3.368 closest distance to " O   ARG A  79 " =    1.199
peak=   -3.367 closest distance to " CZ  PHE A  38 " =    1.129
peak=   -3.367 closest distance to " CG  MET A 105 " =    0.912
peak=   -3.365 closest distance to " CA  ASP A  65 " =    1.248
peak=   -3.359 closest distance to " O   HOH Z  52 " =    1.924
peak=   -3.354 closest distance to " CD2 PHE A  61 " =    2.031
peak=   -3.348 closest distance to " N   ILE A 120 " =    1.123
peak=   -3.347 closest distance to " CZ  TYR A  68 " =    1.139
peak=   -3.346 closest distance to " CG1 VAL A 112 " =    2.685
peak=   -3.345 closest distance to " CE3 TRP A 150 " =    1.732
peak=   -3.345 closest distance to " O   HOH Z 368 " =    1.963
peak=   -3.341 closest distance to " CB  PRO A  54 " =    2.675
peak=   -3.334 closest distance to " O   GLN A  11 " =    1.052
peak=   -3.333 closest distance to " O   HOH Z  55 " =    1.544
peak=   -3.332 closest distance to " O   HOH Z  54 " =    1.467
peak=   -3.331 closest distance to " SG  CYS A 254 " =    3.305
peak=   -3.331 closest distance to " O   HOH Z 394 " =    1.720
peak=   -3.328 closest distance to " O   ASN A  69 " =    1.195
peak=   -3.322 closest distance to " O   HOH Z 139 " =    5.555
peak=   -3.322 closest distance to " O   HOH Z  83 " =    1.178
peak=   -3.317 closest distance to " O   SER A   3 " =    1.086
peak=   -3.311 closest distance to " OD1 ASN A  39 " =    0.940
peak=   -3.310 closest distance to " O   HOH Z 246 " =    1.504
peak=   -3.302 closest distance to " NH2 ARG A  36 " =    1.192
peak=   -3.302 closest distance to " O   HOH Z 197 " =    1.610
peak=   -3.301 closest distance to " CD1 ILE A 263 " =    2.003
peak=   -3.300 closest distance to " O   HOH Z  35 " =    1.477
peak=   -3.295 closest distance to " CB  ALA A 100 " =    2.191
peak=   -3.293 closest distance to " O   HOH Z  64 " =    1.896
peak=   -3.288 closest distance to " SD  MET A  93 " =    1.607
peak=   -3.286 closest distance to " O   HOH Z 287 " =    1.641
peak=   -3.285 closest distance to " O   HOH Z 278 " =    1.058
peak=   -3.285 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.271 closest distance to " O   HOH Z 207 " =    1.436
peak=   -3.269 closest distance to " N   GLN A  11 " =    1.235
peak=   -3.268 closest distance to " CD2 HIS A 115 " =    1.094
peak=   -3.266 closest distance to " CB  ALA A  10 " =    2.211
peak=   -3.264 closest distance to " O   HOH Z 189 " =    1.806
peak=   -3.263 closest distance to " O   ALA A   7 " =    1.430
peak=   -3.263 closest distance to " O   THR A 251 " =    1.828
peak=   -3.262 closest distance to " CD1 ILE A 109 " =    2.708
peak=   -3.258 closest distance to " O   HOH Z 403 " =    0.828
peak=   -3.249 closest distance to " O   HOH Z 191 " =    5.867
peak=   -3.247 closest distance to " O   HOH Z  60 " =    1.398
peak=   -3.243 closest distance to " OD1 ASN A 301 " =    0.909
peak=   -3.243 closest distance to " O   HOH Z 392 " =    1.218
peak=   -3.239 closest distance to " CA  TRP A 274 " =    0.995
peak=   -3.237 closest distance to " O   HOH Z 137 " =    1.342
peak=   -3.236 closest distance to " CB  PHE A 130 " =    1.089
peak=   -3.234 closest distance to " CD  ARG A  79 " =    1.235
peak=   -3.234 closest distance to " O   HOH Z  88 " =    2.898
peak=   -3.232 closest distance to " CZ  ARG A 259 " =    0.817
peak=   -3.230 closest distance to " O   VAL A 121 " =    0.866
peak=   -3.230 closest distance to " CE1 HIS A  81 " =    1.568
peak=   -3.229 closest distance to " CB  ASN A  45 " =    2.201
peak=   -3.228 closest distance to " O   HOH Z  23 " =    1.566
peak=   -3.228 closest distance to " O   HOH Z 174 " =    1.831
peak=   -3.225 closest distance to " CA  GLY A 241 " =    2.265
peak=   -3.225 closest distance to " O   HOH Z 165 " =    1.823
peak=   -3.223 closest distance to " O   HOH Z 135 " =    2.942
peak=   -3.222 closest distance to " CD1 LEU A 101 " =    2.490
peak=   -3.220 closest distance to " CZ2 TRP A 179 " =    1.249
peak=   -3.220 closest distance to " OG BSER A 210 " =    2.421
peak=   -3.219 closest distance to " O  BHOH Z 338 " =    1.241
peak=   -3.218 closest distance to " NH2 ARG A  66 " =    2.060
peak=   -3.218 closest distance to " O   HOH Z 154 " =    1.135
peak=   -3.217 closest distance to " CB  ASP A 162 " =    2.526
peak=   -3.214 closest distance to " CD1 LEU A 167 " =    1.990
peak=   -3.200 closest distance to " O   HOH Z 203 " =    0.956
peak=   -3.198 closest distance to " OG  SER A 276 " =    0.965
peak=   -3.197 closest distance to " O   HOH Z   6 " =    1.175
peak=   -3.196 closest distance to " CG2BVAL A  41 " =    1.522
peak=   -3.195 closest distance to " O   HOH Z 434 " =    1.154
peak=   -3.194 closest distance to " O   HOH Z 428 " =    1.459
peak=   -3.193 closest distance to " O   HOH Z 148 " =    3.778
peak=   -3.192 closest distance to " O   HOH Z 400 " =    1.559
peak=   -3.191 closest distance to " O   SER A 271 " =    2.169
peak=   -3.187 closest distance to " O   HOH Z 290 " =    0.844
peak=   -3.187 closest distance to " CG  ASP A  50 " =    2.328
peak=   -3.180 closest distance to " O   HOH Z 198 " =    1.639
peak=   -3.179 closest distance to " N   ALA A 184 " =    0.971
peak=   -3.172 closest distance to " O   SER A 276 " =    1.780
peak=   -3.172 closest distance to " CG2 VAL A 202 " =    2.678
peak=   -3.170 closest distance to " C   LEU A 101 " =    1.125
peak=   -3.164 closest distance to " O   GLN A 240 " =    3.231
peak=   -3.162 closest distance to " O   HOH Z 122 " =    1.095
peak=   -3.149 closest distance to " CD1 ILE A 151 " =    2.557
peak=   -3.140 closest distance to " NH2 ARG A  79 " =    1.632
peak=   -3.139 closest distance to " CG  ARG A 259 " =    2.492
peak=   -3.139 closest distance to " ND2 ASN A  45 " =    1.702
peak=   -3.134 closest distance to " O   HOH Z 345 " =    3.221
peak=   -3.134 closest distance to " CD  LYS A 289 " =    2.233
peak=   -3.129 closest distance to " OG  SER A  62 " =    4.422
peak=   -3.128 closest distance to " O   HOH Z 216 " =    3.762
peak=   -3.126 closest distance to " O   HOH Z  60 " =    1.781
peak=   -3.125 closest distance to " O   HOH Z 336 " =    5.129
peak=   -3.121 closest distance to " CG2 THR A 264 " =    2.307
peak=   -3.114 closest distance to " O   HOH Z 398 " =    2.220
peak=   -3.106 closest distance to " O   HOH Z 193 " =    1.364
peak=   -3.104 closest distance to " CG  PRO A 163 " =    2.495
peak=   -3.092 closest distance to " O   ASN A 110 " =    2.530
peak=   -3.084 closest distance to " O   MET A 113 " =    1.359
peak=   -3.081 closest distance to " OE2 GLU A 277 " =    2.819
peak=   -3.072 closest distance to " CG2BVAL A  41 " =    2.125
peak=   -3.067 closest distance to " CG  ASP A 124 " =    1.052
peak=   -3.051 closest distance to " O   HOH Z  86 " =    2.656
peak=   -3.045 closest distance to " O   HOH Z 124 " =    1.918
peak=   -3.044 closest distance to " O   HOH Z 380 " =    4.515
peak=   -3.035 closest distance to " O   HOH Z 211 " =    1.550
peak=   -3.034 closest distance to " CG  ARG A 219 " =    2.501
peak=   -3.029 closest distance to " O   HOH Z 340 " =    1.926

================= 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    :  0.4854 0.4785   6.296613e+00   6.278746e+00
   1_bss:  0.4764 0.4693   6.290877e+00   6.271182e+00
   1_xyz:  0.4049 0.4348   6.188810e+00   6.222898e+00
   1_adp:  0.3725 0.4393   6.149824e+00   6.230460e+00
   1_occ:  0.3719 0.4388   6.149387e+00   6.230934e+00
   2_bss:  0.3709 0.4372   6.151880e+00   6.232823e+00
   2_xyz:  0.3157 0.3854   6.027089e+00   6.153702e+00
   2_adp:  0.3025 0.3761   6.006467e+00   6.142719e+00
   2_occ:  0.3023 0.3763   6.006019e+00   6.142603e+00
   3_bss:  0.3026 0.3763   6.007824e+00   6.142773e+00
   3_xyz:  0.2525 0.3149   5.846022e+00   6.009877e+00
   3_adp:  0.2285 0.2930   5.770006e+00   5.952313e+00
   3_occ:  0.2284 0.2927   5.769413e+00   5.951849e+00
   4_bss:  0.2284 0.2922   5.769552e+00   5.951971e+00
   4_xyz:  0.1828 0.2346   5.561378e+00   5.765184e+00
   4_adp:  0.1677 0.2172   5.490247e+00   5.692321e+00
   4_occ:  0.1675 0.2171   5.489322e+00   5.691592e+00
   5_bss:  0.1676 0.2165   5.488658e+00   5.690518e+00
   5_xyz:  0.1488 0.1945   5.387075e+00   5.592667e+00
   5_adp:  0.1440 0.1932   5.365454e+00   5.579793e+00
   5_occ:  0.1439 0.1932   5.365146e+00   5.580000e+00
   5_bss:  0.1444 0.1935   5.366521e+00   5.580443e+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:  0.289  50.000  -3.709   3.465   3.430   0.000   0.000   0.000
   1_xyz:  0.289  50.000  -3.709   3.465   3.430   0.000   0.000   0.000
   1_adp:  0.289  50.000  -3.709   3.465   3.430   0.000   0.000   0.000
   1_occ:  0.289  50.000  -3.709   3.465   3.430   0.000   0.000   0.000
   2_bss:  0.303  64.095  -1.017   2.520   2.502   0.000   0.000   0.000
   2_xyz:  0.303  64.095  -1.017   2.520   2.502   0.000   0.000   0.000
   2_adp:  0.303  64.095  -1.017   2.520   2.502   0.000   0.000   0.000
   2_occ:  0.303  64.095  -1.017   2.520   2.502   0.000   0.000   0.000
   3_bss:  0.326  72.440  -0.538   2.172   1.831   0.000   0.000   0.000
   3_xyz:  0.326  72.440  -0.538   2.172   1.831   0.000   0.000   0.000
   3_adp:  0.326  72.440  -0.538   2.172   1.831   0.000   0.000   0.000
   3_occ:  0.326  72.440  -0.538   2.172   1.831   0.000   0.000   0.000
   4_bss:  0.340  91.686  -0.839   1.009   1.128   0.000   0.000   0.000
   4_xyz:  0.340  91.686  -0.839   1.009   1.128   0.000   0.000   0.000
   4_adp:  0.340  91.686  -0.839   1.009   1.128   0.000   0.000   0.000
   4_occ:  0.340  91.686  -0.839   1.009   1.128   0.000   0.000   0.000
   5_bss:  0.339  84.358  -1.157   0.221   0.773   0.000   0.000   0.000
   5_xyz:  0.339  84.358  -1.157   0.221   0.773   0.000   0.000   0.000
   5_adp:  0.339  84.358  -1.157   0.221   0.773   0.000   0.000   0.000
   5_occ:  0.339  84.358  -1.157   0.221   0.773   0.000   0.000   0.000
   5_bss:  0.332  82.978  -1.267  -0.118   0.711  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.793 0.4092  0.5316    71509.590
   1_bss:  57.190 0.4291  0.5832    68862.342
   1_xyz:  51.688 0.4978  0.6631    56677.253
   1_adp:  52.338 0.4894  0.6560    58198.211
   1_occ:  52.358 0.4892  0.6551    58279.269
   2_bss:  52.094 0.4928  0.6690    58289.606
   2_xyz:  43.404 0.6008  0.8078    42878.197
   2_adp:  42.065 0.6174  0.8133    41088.310
   2_occ:  42.077 0.6173  0.8126    41047.381
   3_bss:  42.051 0.6176  0.8091    41124.670
   3_xyz:  33.746 0.7153  0.9215    27612.994
   3_adp:  30.479 0.7526  0.9263    23335.042
   3_occ:  30.454 0.7528  0.9261    23295.391
   4_bss:  30.380 0.7537  0.9051    23236.907
   4_xyz:  23.728 0.8238  0.9579    14309.674
   4_adp:  21.284 0.8493  0.9594    12273.359
   4_occ:  21.263 0.8495  0.9598    12262.481
   5_bss:  21.191 0.8500  0.9439    12169.487
   5_xyz:  18.591 0.8753  0.9581     9839.135
   5_adp:  18.206 0.8791  0.9522     9667.055
   5_occ:  18.207 0.8791  0.9523     9670.007
   5_bss:  18.212 0.8791  0.9467     9684.570
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6985e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6985e-01
   1_xyz:   1.544  0.012  0.093 15.766  0.006  4.113   1.4375e-01
   1_adp:   1.544  0.012  0.093 15.766  0.006  4.113   1.4375e-01
   1_occ:   1.544  0.012  0.093 15.766  0.006  4.113   1.4375e-01
   2_bss:   1.544  0.012  0.093 15.766  0.006  4.113   1.4375e-01
   2_xyz:   1.398  0.010  0.093 15.236  0.005  4.106   1.0543e-01
   2_adp:   1.398  0.010  0.093 15.236  0.005  4.106   1.0543e-01
   2_occ:   1.398  0.010  0.093 15.236  0.005  4.106   1.0543e-01
   3_bss:   1.398  0.010  0.093 15.236  0.005  4.106   1.0543e-01
   3_xyz:   1.185  0.010  0.080 15.048  0.005  4.110   8.3968e-02
   3_adp:   1.185  0.010  0.080 15.048  0.005  4.110   8.3968e-02
   3_occ:   1.185  0.010  0.080 15.048  0.005  4.110   8.3968e-02
   4_bss:   1.185  0.010  0.080 15.048  0.005  4.110   8.3968e-02
   4_xyz:   1.241  0.011  0.086 14.843  0.004  4.132   8.8912e-02
   4_adp:   1.241  0.011  0.086 14.843  0.004  4.132   8.8912e-02
   4_occ:   1.241  0.011  0.086 14.843  0.004  4.132   8.8912e-02
   5_bss:   1.241  0.011  0.086 14.843  0.004  4.132   8.8912e-02
   5_xyz:   1.053  0.008  0.075 14.520  0.004  4.118   6.5246e-02
   5_adp:   1.053  0.008  0.075 14.520  0.004  4.118   6.5246e-02
   5_occ:   1.053  0.008  0.075 14.520  0.004  4.118   6.5246e-02
   5_bss:   1.053  0.008  0.075 14.520  0.004  4.118   6.5246e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.576   2.4608e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.576   2.4608e-01
   1_xyz:  11.114  0.097  0.302 82.992  0.045  2.042   2.8937e-01
   1_adp:  11.114  0.097  0.302 82.992  0.045  2.042   2.8937e-01
   1_occ:  11.114  0.097  0.302 82.992  0.045  2.042   2.8937e-01
   2_bss:  11.114  0.097  0.302 82.992  0.045  2.042   2.8937e-01
   2_xyz:  10.126  0.051  0.329 84.779  0.031  2.196   1.0298e-01
   2_adp:  10.126  0.051  0.329 84.779  0.031  2.196   1.0298e-01
   2_occ:  10.126  0.051  0.329 84.779  0.031  2.196   1.0298e-01
   3_bss:  10.126  0.051  0.329 84.779  0.031  2.196   1.0298e-01
   3_xyz:   8.542  0.116  0.272 84.189  0.043  2.216   8.4002e-02
   3_adp:   8.542  0.116  0.272 84.189  0.043  2.216   8.4002e-02
   3_occ:   8.542  0.116  0.272 84.189  0.043  2.216   8.4002e-02
   4_bss:   8.542  0.116  0.272 84.189  0.043  2.216   8.4002e-02
   4_xyz:   8.205  0.064  0.246 86.906  0.043  2.177   6.4490e-02
   4_adp:   8.205  0.064  0.246 86.906  0.043  2.177   6.4490e-02
   4_occ:   8.205  0.064  0.246 86.906  0.043  2.177   6.4490e-02
   5_bss:   8.205  0.064  0.246 86.906  0.043  2.177   6.4490e-02
   5_xyz:   8.000  0.044  0.232 82.997  0.040  2.265   4.7826e-02
   5_adp:   8.000  0.044  0.232 82.997  0.040  2.265   4.7826e-02
   5_occ:   8.000  0.044  0.232 82.997  0.040  2.265   4.7826e-02
   5_bss:   8.000  0.044  0.232 82.997  0.040  2.265   4.7826e-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: 107.40   0.00  19.69  89.54   0.00  16.58 107.40   0.00  36.59
   1_occ: 107.40   0.00  19.69  89.54   0.00  16.58 107.40   0.00  36.59
   2_bss: 107.40   0.00  19.69  89.54   0.00  16.58 107.40   0.00  36.59
   2_xyz: 107.40   0.00  19.69  89.54   0.00  16.58 107.40   0.00  36.59
   2_adp: 126.27   0.00  19.31 126.27   0.00  15.99 107.81   0.00  37.39
   2_occ: 126.27   0.00  19.31 126.27   0.00  15.99 107.81   0.00  37.39
   3_bss: 126.27   0.00  19.31 126.27   0.00  15.99 107.81   0.00  37.39
   3_xyz: 126.27   0.00  19.31 126.27   0.00  15.99 107.81   0.00  37.39
   3_adp: 115.34   0.00  19.35 106.75   0.00  14.45 115.34   0.00  46.04
   3_occ: 115.34   0.00  19.35 106.75   0.00  14.45 115.34   0.00  46.04
   4_bss: 115.34   0.00  19.35 106.75   0.00  14.45 115.34   0.00  46.04
   4_xyz: 115.34   0.00  19.35 106.75   0.00  14.45 115.34   0.00  46.04
   4_adp: 110.06   0.00  17.56  98.08   0.00  12.56 110.06   3.77  44.83
   4_occ: 110.06   0.00  17.56  98.08   0.00  12.56 110.06   3.77  44.83
   5_bss: 110.06   0.00  17.56  98.08   0.00  12.56 110.06   3.77  44.83
   5_xyz: 110.06   0.00  17.56  98.08   0.00  12.56 110.06   3.77  44.83
   5_adp: 125.97   0.00  17.26 125.97   0.00  12.22 110.37   3.70  44.71
   5_occ: 125.97   0.00  17.26 125.97   0.00  12.22 110.37   3.70  44.71
   5_bss: 125.97   0.00  17.26 125.97   0.00  12.22 110.38   3.70  44.72
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.714    0.021    0.329
   1_adp:    1.714    0.021    0.329
   1_occ:    1.714    0.021    0.329
   2_bss:    1.714    0.021    0.329
   2_xyz:    1.375    0.044    0.523
   2_adp:    1.375    0.044    0.523
   2_occ:    1.375    0.044    0.523
   3_bss:    1.375    0.044    0.523
   3_xyz:    1.557    0.050    0.720
   3_adp:    1.557    0.050    0.720
   3_occ:    1.557    0.050    0.720
   4_bss:    1.557    0.050    0.720
   4_xyz:    1.642    0.103    0.840
   4_adp:    1.642    0.103    0.840
   4_occ:    1.642    0.103    0.840
   5_bss:    1.642    0.103    0.840
   5_xyz:    1.782    0.131    0.894
   5_adp:    1.782    0.131    0.894
   5_occ:    1.782    0.131    0.894
   5_bss:    1.782    0.131    0.894
------------------------------------------------------------------------

CPU time actual refinement: 345.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/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_846/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_846/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.25 
  Macro-tasks:
    bulk solvent and scale       = 52.15  
    individual site refinement   = 135.15 
    weights calculation          = 29.21  
    collect and process          = 6.48   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 223.09 
  Micro-tasks:
    mask                            = 2.75   
    f_calc                          = 108.25 
    alpha_beta                      = 8.54   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 111.80 
    fmodel                         = 8.06   
    r_factors                      = 0.29   
    phase_errors                   = 10.92  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 252.01 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.929 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    636 calls, 107.86 s
gradients_fft:          581 calls, 100.77 s

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

# Date 2008-01-16 Time 05:48:30 PST -0800 (1200491310.77 s)
Start R-work = 0.4854, R-free = 0.4785 (no bulk solvent and anisotropic scale)
Final R-work = 0.1600, R-free = 0.2069 (no bulk solvent and anisotropic scale)

Start R-work = 0.4764, R-free = 0.4693
Final R-work = 0.1444, R-free = 0.1935