# Date 2008-01-16 Time 06:26:21 PST -0800 (1200493581.02 s)
#phil __OFF__

Command line arguments: "../1145.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7653
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1145

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.93, 84.6622, 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: 2.73, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96126
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928169

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9613

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96126
Completeness in resolution range: 0.930903
Completeness with d_max=infinity: 0.928169

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1981 [2203/2233]  1986   217   9.9%
  bin  2:  4.1981 -  3.3440 [2123/2142]  1908   215  10.1%
  bin  3:  3.3440 -  2.9248 [2094/2114]  1884   210  10.0%
  bin  4:  2.9248 -  2.6589 [2083/2108]  1880   203   9.7%
  bin  5:  2.6589 -  2.4692 [2055/2074]  1845   210  10.2%
  bin  6:  2.4692 -  2.3242 [2053/2100]  1851   202   9.8%
  bin  7:  2.3242 -  2.2082 [2045/2077]  1834   211  10.3%
  bin  8:  2.2082 -  2.1123 [2013/2049]  1816   197   9.8%
  bin  9:  2.1123 -  2.0312 [2038/2081]  1835   203  10.0%
  bin 10:  2.0312 -  1.9613 [ 882/2065]   791    91  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/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: 0.11 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:
        1.77 -     2.40: 30
        2.40 -     3.02: 2065
        3.02 -     3.65: 4650
        3.65 -     4.27: 9100
        4.27 -     4.90: 12522
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.770 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.821 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.832 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.959 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28362 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_1145/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/model_refine_001.geo

CPU time processing inputs: 7.76


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.93 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3959   r_free= 0.4027   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.186076                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6831 0.99   1429  161 0.3178 0.3236       6.435      6.4405|
|  2:  4.6831 -  3.7355 0.99   1385  149 0.3196 0.2953      6.6242      6.6297|
|  3:  3.7355 -  3.2688 0.99   1349  154 0.3571 0.3492      6.5053       6.563|
|  4:  3.2688 -  2.9724 0.99   1355  150 0.3735 0.3793      6.3791      6.3695|
|  5:  2.9724 -  2.7607 0.99   1328  145 0.4062 0.4173      6.2491      6.2871|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.4431 0.4292      6.1932      6.1559|
|  7:  2.5988 -  2.4692 0.99   1330  145 0.4266 0.3924      6.1588      6.0969|
|  8:  2.4692 -  2.3622 0.98   1303  148 0.4363 0.4339      6.0838      6.1109|
|  9:  2.3622 -  2.2715 0.98   1322  147 0.4417 0.4643      6.0609      6.0064|
| 10:  2.2715 -  2.1934 0.98   1308  148 0.4545 0.5148      6.0227       6.106|
| 11:  2.1934 -  2.1250 0.99   1335  143 0.4546 0.5318      5.9832      6.0369|
| 12:  2.1250 -  2.0644 0.98   1295  142 0.4507 0.4998      5.9052      5.9586|
| 13:  2.0644 -  2.0102 0.89   1165  141 0.4717 0.4841      5.8407      5.8021|
| 14:  2.0102 -  1.9613 0.29    399   35 0.5029 0.4537      5.7794      5.7204|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6831  1429   161  0.77  28.03   0.85     0.79      48857.42|
|  2:  4.6831 -  3.7355  1385   149  0.79  27.43   0.95     0.88      66670.00|
|  3:  3.7355 -  3.2688  1349   154  0.71  34.54   0.95     0.88      72500.48|
|  4:  3.2688 -  2.9724  1355   150  0.64  40.28   0.97     0.84      68318.23|
|  5:  2.9724 -  2.7607  1328   145  0.56  47.06   0.93     0.75      57849.44|
|  6:  2.7607 -  2.5988  1327   151  0.55  48.37   0.93     0.75      50606.35|
|  7:  2.5988 -  2.4692  1330   145  0.58  46.07   0.96     0.75      43456.51|
|  8:  2.4692 -  2.3622  1303   148  0.57  46.77   0.95     0.80      40137.79|
|  9:  2.3622 -  2.2715  1322   147  0.54  49.05   0.99     0.76      38032.24|
| 10:  2.2715 -  2.1934  1308   148  0.47  54.59   0.97     0.68      41399.66|
| 11:  2.1934 -  2.1250  1335   143  0.41  59.04   1.00     0.61      41534.80|
| 12:  2.1250 -  2.0644  1295   142  0.38  61.44   0.97     0.59      39713.76|
| 13:  2.0644 -  2.0102  1165   141  0.40  60.01   0.97     0.61      32619.80|
| 14:  2.0102 -  1.9613   399    35  0.41  59.04   0.94     0.61      26170.88|
|alpha:            min =        0.59 max =            0.88 mean =         0.74|
|beta:             min =    26170.88 max =        72500.48 mean =     49141.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.97 mean =        46.30|
|phase err.(test): min =        0.00 max =           89.97 mean =        46.42|
|-----------------------------------------------------------------------------|

============================== 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 = 7.933065              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.027   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.412237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.101   (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 |  1.770 -  2.083:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.083 -  2.396:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.396 -  2.709:      128 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.709 -  3.022:     1937 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.022 -  3.335:     1882 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.335 -  3.648:     2768 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.648 -  3.961:     4699 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.961 -  4.274:     4401 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.274 -  4.587:     5711 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.587 -  4.900:     6811 |
|-----------------------------------------------------------------------------|
|-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 |   4.111    4.900  1.770 |       0.293 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3959   r_free= 0.4027   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.186076                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3836   r_free= 0.3918   ksol= 0.31   Bsol= 31.04   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,-3.08,1.97,-0.00,0.00,0.00); trace/3= 0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.174887                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.390448              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.327   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.699675              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.855   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3836      final r-factor (work) = 0.2408          |
| start r-factor (free) = 0.3918      final r-factor (free) = 0.2717          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8929 = 6.39 * 0.50 * 6.1726 + 1.00 * 0.1700                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1641 = 6.39 * 0.50 * 5.9669 + 1.00 * 0.0986                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2408      final r-factor (work) = 0.2223          |
| start r-factor (free) = 0.2717      final r-factor (free) = 0.2804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1812 = 0.70 * 1.00 * 5.9669 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0470 = 0.70 * 1.00 * 5.7299 + 1.00 * 0.0379                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.96   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    69.96   17.07    None  None   None       |
|    Sol.    : 438    0      5.94    63.12   38.72    None  None   None       |
|    Mac.    : 2385   0      0.00    69.96   13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.996:  461   |   5:    34.980 -  41.977:  123        |
|      1:     6.996 -  13.992: 1070   |   6:    41.977 -  48.973:   99        |
|      2:    13.992 -  20.988:  608   |   7:    48.973 -  55.969:   80        |
|      3:    20.988 -  27.984:  219   |   8:    55.969 -  62.965:   31        |
|      4:    27.984 -  34.980:  130   |   9:    62.965 -  69.961:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2223 r_free = 0.2804             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2219 r_free = 0.2804             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2219   r_free= 0.2804   ksol= 0.31   Bsol= 31.04   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,-3.08,1.97,-0.00,0.00,0.00); trace/3= 0.04                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.740715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2190   r_free= 0.2778   ksol= 0.34   Bsol= 54.64   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-3.02,-0.83,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.733343                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.049582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.821   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.407742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.399   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2190      final r-factor (work) = 0.1563          |
| start r-factor (free) = 0.2778      final r-factor (free) = 0.2038          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7144 = 4.05 * 0.50 * 5.7368 + 1.00 * 0.0986                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4220 = 4.05 * 0.50 * 5.6106 + 1.00 * 0.0617                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1563      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.2038      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3187 = 0.41 * 1.00 * 5.6106 + 1.00 * 0.0310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2050 = 0.41 * 1.00 * 5.3857 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    72.92   17.38    None  None   None       |
|    all(noH): 2823   0      1.73    72.92   17.38    None  None   None       |
|    Sol.    : 438    0      5.90    72.11   40.75    None  None   None       |
|    Mac.    : 2385   0      1.73    72.92   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.734 -   8.852:  719   |   5:    37.325 -  44.443:   83        |
|      1:     8.852 -  15.970: 1186   |   6:    44.443 -  51.561:  108        |
|      2:    15.970 -  23.088:  364   |   7:    51.561 -  58.679:   76        |
|      3:    23.088 -  30.207:  126   |   8:    58.679 -  65.797:   39        |
|      4:    30.207 -  37.325:  102   |   9:    65.797 -  72.916:   20        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1401 r_free = 0.1871             target_work(ml) = 5.338         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1400 r_free = 0.1869             target_work(ml) = 5.337         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1400   r_free= 0.1869   ksol= 0.34   Bsol= 54.64   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-3.02,-0.83,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.337031                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1397   r_free= 0.1852   ksol= 0.33   Bsol= 52.30   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.55,-1.56,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.334047                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.668353              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.104  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248135              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.293  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1397      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1852      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2466 = 2.67 * 0.50 * 5.3853 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0996 = 2.67 * 0.50 * 5.2770 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3183 = 0.25 * 1.00 * 5.2770 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2985 = 0.25 * 1.00 * 5.2007 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.66    78.83   17.13    None  None   None       |
|    all(noH): 2823   0      1.66    78.83   17.13    None  None   None       |
|    Sol.    : 438    0      4.24    75.24   39.66    None  None   None       |
|    Mac.    : 2385   0      1.66    78.83   12.99    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:     1.662 -   9.379:  833   |   5:    40.246 -  47.963:   87        |
|      1:     9.379 -  17.096: 1178   |   6:    47.963 -  55.679:   95        |
|      2:    17.096 -  24.812:  315   |   7:    55.679 -  63.396:   42        |
|      3:    24.812 -  32.529:  120   |   8:    63.396 -  71.113:   25        |
|      4:    32.529 -  40.246:  119   |   9:    71.113 -  78.830:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1607             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1605             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1605   ksol= 0.33   Bsol= 52.30   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,-2.55,-1.56,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1603   ksol= 0.33   Bsol= 52.30   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.62,-1.95,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183382                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.179521              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.653  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.761  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7270 = 2.18 * 0.50 * 5.2011 + 1.00 * 0.0591                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6901 = 2.18 * 0.50 * 5.1656 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3737 = 0.46 * 1.00 * 5.1656 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3663 = 0.46 * 1.00 * 5.1481 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    87.28   17.12    None  None   None       |
|    all(noH): 2823   0      1.23    87.28   17.12    None  None   None       |
|    Sol.    : 438    0      4.78    80.65   39.82    None  None   None       |
|    Mac.    : 2385   0      1.23    87.28   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.228 -   9.833:  974   |   5:    44.254 -  52.860:  109        |
|      1:     9.833 -  18.438: 1136   |   6:    52.860 -  61.465:   57        |
|      2:    18.438 -  27.044:  250   |   7:    61.465 -  70.070:   35        |
|      3:    27.044 -  35.649:  126   |   8:    70.070 -  78.675:   10        |
|      4:    35.649 -  44.254:  120   |   9:    78.675 -  87.281:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1575             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1574             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1574   ksol= 0.33   Bsol= 52.30   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.62,-1.95,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148979                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1573   ksol= 0.32   Bsol= 52.26   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.46,-1.93,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149682                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.319043              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.540  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182103              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.324  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1136          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4558 = 1.32 * 0.50 * 5.1476 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4515 = 1.32 * 0.50 * 5.1585 + 1.00 * 0.0493                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9479 = 0.18 * 1.00 * 5.1585 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9487 = 0.18 * 1.00 * 5.1696 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    86.70   16.71    None  None   None       |
|    all(noH): 2823   0      1.65    86.70   16.71    None  None   None       |
|    Sol.    : 438    0      6.27    76.80   37.97    None  None   None       |
|    Mac.    : 2385   0      1.65    86.70   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.646 -  10.151: 1071   |   5:    44.173 -  52.679:  102        |
|      1:    10.151 -  18.657: 1065   |   6:    52.679 -  61.184:   45        |
|      2:    18.657 -  27.162:  241   |   7:    61.184 -  69.690:   21        |
|      3:    27.162 -  35.668:  134   |   8:    69.690 -  78.196:    6        |
|      4:    35.668 -  44.173:  132   |   9:    78.196 -  86.701:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1584             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1584             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1584   ksol= 0.32   Bsol= 52.26   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.46,-1.93,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168611                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6831 0.99   1429  161 0.1011 0.1309      5.4048      5.5774|
|  2:  4.6831 -  3.7355 0.99   1385  149 0.0890 0.1044      5.4585      5.6313|
|  3:  3.7355 -  3.2688 0.99   1349  154 0.1075 0.1654      5.4734      5.8825|
|  4:  3.2688 -  2.9724 0.99   1355  150 0.1259 0.1525      5.4735      5.5733|
|  5:  2.9724 -  2.7607 0.99   1328  145 0.1341 0.1754      5.3325      5.5306|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.1270 0.1864      5.2201      5.4544|
|  7:  2.5988 -  2.4692 0.99   1330  145 0.1262 0.1733      5.1833      5.4033|
|  8:  2.4692 -  2.3622 0.98   1303  148 0.1151 0.1752      5.0467      5.2742|
|  9:  2.3622 -  2.2715 0.98   1322  147 0.1206 0.1862      5.0328      5.3206|
| 10:  2.2715 -  2.1934 0.98   1308  148 0.1152 0.1610      4.9596      5.1984|
| 11:  2.1934 -  2.1250 0.99   1335  143 0.1171 0.1847      4.9627      5.3041|
| 12:  2.1250 -  2.0644 0.98   1295  142 0.1179 0.1675      4.8974      5.1054|
| 13:  2.0644 -  2.0102 0.89   1165  141 0.1202 0.1712      4.8105      5.0444|
| 14:  2.0102 -  1.9613 0.29    399   35 0.1077 0.1713      4.6335      4.9097|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6831  1429   161  0.94   9.12   0.97     0.95       7245.65|
|  2:  4.6831 -  3.7355  1385   149  0.95   8.10   1.01     1.00       9073.20|
|  3:  3.7355 -  3.2688  1349   154  0.93  11.57   1.02     1.02      10419.62|
|  4:  3.2688 -  2.9724  1355   150  0.91  14.29   1.00     0.97      10587.51|
|  5:  2.9724 -  2.7607  1328   145  0.90  15.88   0.99     0.97       8320.48|
|  6:  2.7607 -  2.5988  1327   151  0.90  16.42   0.98     0.96       7146.43|
|  7:  2.5988 -  2.4692  1330   145  0.91  15.31   0.99     0.97       6326.63|
|  8:  2.4692 -  2.3622  1303   148  0.91  15.52   0.98     0.96       5161.38|
|  9:  2.3622 -  2.2715  1322   147  0.90  15.80   1.00     0.97       4896.86|
| 10:  2.2715 -  2.1934  1308   148  0.91  15.10   0.98     0.95       4292.06|
| 11:  2.1934 -  2.1250  1335   143  0.90  16.72   0.99     0.96       4596.99|
| 12:  2.1250 -  2.0644  1295   142  0.90  16.57   1.00     0.99       4204.54|
| 13:  2.0644 -  2.0102  1165   141  0.90  16.14   0.99     0.98       3417.35|
| 14:  2.0102 -  1.9613   399    35  0.90  15.78   0.98     0.94       2421.54|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2421.54 max =        10587.51 mean =      6557.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.47 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1584   ksol= 0.32   Bsol= 48.42   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.32,-1.80,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168816                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1584   ksol= 0.32   Bsol= 48.42   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,-2.32,-1.80,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.168816                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6831 0.99   1429  161 0.1009 0.1307      5.4037      5.5744|
|  2:  4.6831 -  3.7355 0.99   1385  149 0.0886 0.1041      5.4557      5.6292|
|  3:  3.7355 -  3.2688 0.99   1349  154 0.1074 0.1651      5.4719      5.8812|
|  4:  3.2688 -  2.9724 0.99   1355  150 0.1259 0.1526      5.4738      5.5737|
|  5:  2.9724 -  2.7607 0.99   1328  145 0.1343 0.1756      5.3337      5.5315|
|  6:  2.7607 -  2.5988 0.98   1327  151 0.1272 0.1866      5.2213      5.4556|
|  7:  2.5988 -  2.4692 0.99   1330  145 0.1262 0.1734      5.1842      5.4042|
|  8:  2.4692 -  2.3622 0.98   1303  148 0.1152 0.1755      5.0478      5.2758|
|  9:  2.3622 -  2.2715 0.98   1322  147 0.1206 0.1860      5.0335      5.3205|
| 10:  2.2715 -  2.1934 0.98   1308  148 0.1153 0.1610      4.9605      5.1994|
| 11:  2.1934 -  2.1250 0.99   1335  143 0.1172 0.1848      4.9633       5.305|
| 12:  2.1250 -  2.0644 0.98   1295  142 0.1181 0.1677      4.8981      5.1061|
| 13:  2.0644 -  2.0102 0.89   1165  141 0.1202 0.1713       4.811      5.0448|
| 14:  2.0102 -  1.9613 0.29    399   35 0.1078 0.1714      4.6344      4.9105|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6831  1429   161  0.94   9.08   0.97     0.95       7211.73|
|  2:  4.6831 -  3.7355  1385   149  0.95   8.09   1.01     1.00       9032.96|
|  3:  3.7355 -  3.2688  1349   154  0.93  11.54   1.02     1.02      10380.22|
|  4:  3.2688 -  2.9724  1355   150  0.91  14.28   1.00     0.97      10586.43|
|  5:  2.9724 -  2.7607  1328   145  0.90  15.90   0.99     0.97       8330.62|
|  6:  2.7607 -  2.5988  1327   151  0.90  16.45   0.98     0.96       7163.65|
|  7:  2.5988 -  2.4692  1330   145  0.91  15.33   0.99     0.97       6345.07|
|  8:  2.4692 -  2.3622  1303   148  0.91  15.54   0.99     0.96       5173.12|
|  9:  2.3622 -  2.2715  1322   147  0.90  15.81   1.00     0.97       4903.90|
| 10:  2.2715 -  2.1934  1308   148  0.91  15.11   0.99     0.95       4298.95|
| 11:  2.1934 -  2.1250  1335   143  0.90  16.75   0.99     0.96       4604.11|
| 12:  2.1250 -  2.0644  1295   142  0.90  16.59   1.00     1.00       4214.16|
| 13:  2.0644 -  2.0102  1165   141  0.90  16.15   0.99     0.98       3422.82|
| 14:  2.0102 -  1.9613   399    35  0.90  15.80   0.98     0.95       2426.30|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2426.30 max =        10586.43 mean =      6555.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.907)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.59    86.64   16.65    None  None   None       |
|    all(noH): 2823   0      1.59    86.64   16.65    None  None   None       |
|    Sol.    : 438    0      6.22    76.75   37.91    None  None   None       |
|    Mac.    : 2385   0      1.59    86.64   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.587 -  10.092: 1071   |   5:    44.115 -  52.620:  102        |
|      1:    10.092 -  18.598: 1065   |   6:    52.620 -  61.126:   45        |
|      2:    18.598 -  27.104:  241   |   7:    61.126 -  69.631:   21        |
|      3:    27.104 -  35.609:  134   |   8:    69.631 -  78.137:    6        |
|      4:    35.609 -  44.115:  132   |   9:    78.137 -  86.642:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 4.359
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 322
   mapped sites are within: 0.719 - 4.359

peak=    6.012 closest distance to " CB  GLN A 223 " =    1.444
peak=    5.816 closest distance to " O   HOH Z 111 " =    2.196
peak=    5.738 closest distance to " CG  PRO A  54 " =    1.301
peak=    5.468 closest distance to " CG  PRO A 213 " =    1.260
peak=    5.201 closest distance to " CB  SER A  63 " =    1.327
peak=    5.131 closest distance to " O   HOH Z 126 " =    1.944
peak=    5.127 closest distance to " CG  PRO A  90 " =    1.133
peak=    5.005 closest distance to " CG  PRO A 198 " =    1.324
peak=    4.944 closest distance to " CB  PRO A  54 " =    0.925
peak=    4.897 closest distance to " CB  GLU A 128 " =    1.084
peak=    4.764 closest distance to " CB  ARG A 275 " =    0.897
peak=    4.763 closest distance to " O   HOH Z 232 " =    2.221
peak=    4.639 closest distance to " CB  LEU A 228 " =    1.080
peak=    4.624 closest distance to " C   PRO A 198 " =    1.579
peak=    4.566 closest distance to " O   HOH Z 236 " =    2.024
peak=    4.558 closest distance to " NE2 GLN A  11 " =    1.127
peak=    4.504 closest distance to " CB  GLN A 183 " =    1.214
peak=    4.458 closest distance to " CB  ASN A 148 " =    1.339
peak=    4.433 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.414 closest distance to " O   HOH Z  15 " =    2.139
peak=    4.397 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.362 closest distance to " CA  TYR A  30 " =    1.011
peak=    4.361 closest distance to " CB  GLU A 152 " =    1.172
peak=    4.347 closest distance to " O   HOH Z 193 " =    1.963
peak=    4.337 closest distance to " CG  PRO A 280 " =    0.820
peak=    4.316 closest distance to " OD2 ASP A 286 " =    2.929
peak=    4.271 closest distance to " CB  SER A   3 " =    1.389
peak=    4.264 closest distance to " O   HOH Z 135 " =    1.733
peak=    4.243 closest distance to " CB  TYR A 169 " =    0.780
peak=    4.230 closest distance to " OD1 ASN A  69 " =    2.547
peak=    4.198 closest distance to " O   HOH Z 368 " =    1.902
peak=    4.190 closest distance to " O   HOH Z 108 " =    1.590
peak=    4.185 closest distance to " NH2 ARG A 156 " =    1.264
peak=    4.183 closest distance to " CB  ASN A 187 " =    1.281
peak=    4.161 closest distance to " O   HOH Z  21 " =    1.697
peak=    4.128 closest distance to " O   HOH Z 369 " =    1.945
peak=    4.126 closest distance to " O   HOH Z 193 " =    1.750
peak=    4.120 closest distance to " CB  VAL A 202 " =    1.628
peak=    4.113 closest distance to " CB  SER A 216 " =    0.793
peak=    4.109 closest distance to " CA  ALA A  21 " =    1.167
peak=    4.063 closest distance to " O   HOH Z 344 " =    3.138
peak=    4.057 closest distance to " CA  THR A 264 " =    0.872
peak=    4.045 closest distance to " NH2BARG A 102 " =    0.988
peak=    4.040 closest distance to " O   HOH Z 272 " =    1.897
peak=    4.038 closest distance to " O   HOH Z 132 " =    2.518
peak=    4.032 closest distance to " CB  TRP A 266 " =    0.914
peak=    4.024 closest distance to " CA  THR A 221 " =    0.952
peak=    4.008 closest distance to " O   HOH Z  78 " =    1.898
peak=    3.991 closest distance to " O   HOH Z 247 " =    1.382
peak=    3.987 closest distance to " O   HOH Z 234 " =    3.812
peak=    3.985 closest distance to " CD1 LEU A 300 " =    1.283
peak=    3.983 closest distance to " O   HOH Z  78 " =    1.610
peak=    3.982 closest distance to " ND2 ASN A 187 " =    1.568
peak=    3.940 closest distance to " CA  ASP A 124 " =    0.724
peak=    3.923 closest distance to " O   HOH Z  88 " =    3.565
peak=    3.919 closest distance to " O   HOH Z 144 " =    1.610
peak=    3.916 closest distance to " CD  ARG A 159 " =    0.803
peak=    3.913 closest distance to " O   HOH Z 134 " =    1.442
peak=    3.913 closest distance to " O   HOH Z 189 " =    2.360
peak=    3.910 closest distance to " CD BLYS A 290 " =    1.069
peak=    3.906 closest distance to " CD  ARG A 269 " =    0.933
peak=    3.905 closest distance to " O   HOH Z 427 " =    2.966
peak=    3.892 closest distance to " CB  GLU A 152 " =    1.484
peak=    3.888 closest distance to " O   HOH Z 316 " =    3.081
peak=    3.887 closest distance to " CB  VAL A 265 " =    1.238
peak=    3.886 closest distance to " CB  TRP A 179 " =    1.427
peak=    3.885 closest distance to " O   HOH Z  68 " =    1.654
peak=    3.881 closest distance to " O   HOH Z 207 " =    1.853
peak=    3.866 closest distance to " CG2 VAL A 257 " =    0.967
peak=    3.862 closest distance to " O   HOH Z 183 " =    1.524
peak=    3.857 closest distance to " CZ  PHE A 192 " =    0.916
peak=    3.857 closest distance to " O   HOH Z  48 " =    1.427
peak=    3.848 closest distance to " O   HOH Z 389 " =    1.952
peak=    3.843 closest distance to " CB  LEU A 143 " =    1.108
peak=    3.842 closest distance to " O   HOH Z 303 " =    2.087
peak=    3.821 closest distance to " O   HOH Z 346 " =    1.659
peak=    3.818 closest distance to " CG1 ILE A  33 " =    1.337
peak=    3.814 closest distance to " CG2 THR A 221 " =    0.978
peak=    3.812 closest distance to " CB  PRO A 198 " =    0.912
peak=    3.803 closest distance to " NH1AARG A 145 " =    1.080
peak=    3.799 closest distance to " CB  MET A  47 " =    1.020
peak=    3.778 closest distance to " O   HOH Z 352 " =    1.858
peak=    3.765 closest distance to " O   HOH Z  61 " =    1.574
peak=    3.751 closest distance to " CA  ASN A 215 " =    1.228
peak=    3.748 closest distance to " ND1 HIS A  86 " =    1.692
peak=    3.743 closest distance to " O   HOH Z 425 " =    1.393
peak=    3.742 closest distance to " N   ASN A  39 " =    1.325
peak=    3.730 closest distance to " O   HOH Z 108 " =    1.804
peak=    3.726 closest distance to " CG  LEU A 167 " =    1.163
peak=    3.726 closest distance to " CD  ARG A  66 " =    2.327
peak=    3.720 closest distance to " CZ  PHE A 218 " =    1.011
peak=    3.714 closest distance to " CB  ARG A  79 " =    1.401
peak=    3.707 closest distance to " O   HOH Z 295 " =    1.514
peak=    3.706 closest distance to " O   HOH Z  20 " =    1.913
peak=    3.695 closest distance to " CA  MET A  40 " =    1.095
peak=    3.665 closest distance to " O   HOH Z 371 " =    3.122
peak=    3.663 closest distance to " CA  GLY A 241 " =    3.797
peak=    3.660 closest distance to " CZ  PHE A 208 " =    1.176
peak=    3.659 closest distance to " CB  MET A  40 " =    0.801
peak=    3.646 closest distance to " O   HOH Z 133 " =    2.379
peak=    3.643 closest distance to " O   HOH Z 426 " =    1.537
peak=    3.637 closest distance to " N   ARG A 156 " =    1.382
peak=    3.637 closest distance to " CA  ALA A 154 " =    1.027
peak=    3.637 closest distance to " NH2BARG A 145 " =    2.023
peak=    3.627 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.620 closest distance to " O   HOH Z 437 " =    1.612
peak=    3.615 closest distance to " CD  LYS A 119 " =    1.296
peak=    3.613 closest distance to " O   HOH Z  40 " =    2.193
peak=    3.598 closest distance to " O   HOH Z 261 " =    1.897
peak=    3.588 closest distance to " OD1 ASN A 217 " =    1.641
peak=    3.580 closest distance to " O   HOH Z  54 " =    1.698
peak=    3.579 closest distance to " O   HOH Z 281 " =    4.359
peak=    3.577 closest distance to " CA  ASP A 191 " =    0.741
peak=    3.577 closest distance to " O   HOH Z   9 " =    2.096
peak=    3.576 closest distance to " O   HOH Z  97 " =    1.902
peak=    3.576 closest distance to " O   HOH Z 180 " =    2.123
peak=    3.569 closest distance to " CD2 LEU A 255 " =    1.444
peak=    3.568 closest distance to " O   HOH Z  66 " =    2.104
peak=    3.563 closest distance to " CB  ALA A 291 " =    1.371
peak=    3.558 closest distance to " CA  ALA A  51 " =    0.917
peak=    3.555 closest distance to " CB  PHE A  16 " =    1.039
peak=    3.551 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.550 closest distance to " CB  ARG A 190 " =    1.702
peak=    3.548 closest distance to " NH2AARG A 190 " =    1.399
peak=    3.539 closest distance to " O   HOH Z 128 " =    2.228
peak=    3.539 closest distance to " O   HOH Z 227 " =    1.642
peak=    3.537 closest distance to " CB  ALA A 248 " =    0.949
peak=    3.535 closest distance to " O   MET A 105 " =    1.798
peak=    3.527 closest distance to " CG1 ILE A 151 " =    0.946
peak=    3.526 closest distance to " O   HOH Z  10 " =    1.857
peak=    3.520 closest distance to " CG  MET A 113 " =    1.293
peak=    3.519 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.512 closest distance to " CB  ASN A  39 " =    0.914
peak=    3.511 closest distance to " CG1 VAL A 153 " =    1.004
peak=    3.510 closest distance to " CA  GLN A 223 " =    0.977
peak=    3.506 closest distance to " CA  SER A  87 " =    0.909
peak=    3.502 closest distance to " O   HOH Z  93 " =    2.584
peak=    3.501 closest distance to " O   HOH Z   6 " =    2.146
peak=    3.499 closest distance to " CB  SER A 212 " =    1.120
peak=    3.488 closest distance to " O   HOH Z 273 " =    2.645
peak=    3.485 closest distance to " CB  GLU A 277 " =    3.647
peak=    3.475 closest distance to " NZ  LYS A 117 " =    3.355
peak=    3.473 closest distance to " CD  ARG A 219 " =    1.043
peak=    3.469 closest distance to " CA  GLU A 152 " =    0.893
peak=    3.468 closest distance to " CA  TYR A 186 " =    1.405
peak=    3.462 closest distance to " O   HOH Z 193 " =    2.046
peak=    3.461 closest distance to " CG1BVAL A  72 " =    1.625
peak=    3.458 closest distance to " CB  ILE A 234 " =    1.000
peak=    3.456 closest distance to " O   HOH Z   1 " =    1.924
peak=    3.450 closest distance to " NH1BARG A 145 " =    1.200
peak=    3.447 closest distance to " O   HOH Z 209 " =    2.263
peak=    3.446 closest distance to " O   HOH Z  49 " =    2.255
peak=    3.444 closest distance to " O   HOH Z 284 " =    3.144
peak=    3.443 closest distance to " O   HOH Z 368 " =    3.652
peak=    3.442 closest distance to " CB  ARG A 139 " =    0.877
peak=    3.442 closest distance to " O   SER A  87 " =    2.143
peak=    3.440 closest distance to " O   HOH Z 327 " =    2.205
peak=    3.437 closest distance to " O   HOH Z 214 " =    1.966
peak=    3.433 closest distance to " CA  LEU A 282 " =    1.056
peak=    3.430 closest distance to " N   ASN A 127 " =    1.232
peak=    3.429 closest distance to " CD1 ILE A 106 " =    0.833
peak=    3.426 closest distance to " O   HOH Z  66 " =    2.036
peak=    3.422 closest distance to " CB  THR A 157 " =    1.086
peak=    3.419 closest distance to " O   HOH Z 112 " =    1.437
peak=    3.410 closest distance to " O   HOH Z 133 " =    1.720
peak=    3.408 closest distance to " N   TYR A  15 " =    0.756
peak=    3.391 closest distance to " O   HOH Z 171 " =    3.861
peak=    3.391 closest distance to " O   THR A 251 " =    1.189
peak=    3.387 closest distance to " O   HOH Z 313 " =    1.792
peak=    3.386 closest distance to " O   HOH Z 403 " =    1.341
peak=    3.385 closest distance to " CG  GLN A  88 " =    1.020
peak=    3.377 closest distance to " CB  ASP A 171 " =    0.755
peak=    3.376 closest distance to " O   HOH Z 409 " =    3.005
peak=    3.375 closest distance to " ND1 HIS A  81 " =    1.594
peak=    3.375 closest distance to " CB  SER A 141 " =    0.999
peak=    3.373 closest distance to " O   TRP A 274 " =    1.735
peak=    3.369 closest distance to " O   HOH Z 263 " =    2.277
peak=    3.368 closest distance to " CA  ARG A 102 " =    1.217
peak=    3.362 closest distance to " O   THR A 220 " =    1.465
peak=    3.359 closest distance to " CA  ARG A  36 " =    1.205
peak=    3.359 closest distance to " NZ ALYS A 290 " =    1.192
peak=    3.356 closest distance to " OG  SER A 206 " =    1.262
peak=    3.353 closest distance to " O   ALA A 165 " =    1.405
peak=    3.353 closest distance to " CG BARG A 275 " =    1.518
peak=    3.349 closest distance to " C   TYR A 214 " =    1.576
peak=    3.348 closest distance to " CA  ASP A 140 " =    1.217
peak=    3.345 closest distance to " CG2 VAL A  78 " =    1.009
peak=    3.344 closest distance to " O   HOH Z 287 " =    2.156
peak=    3.343 closest distance to " O   HOH Z 158 " =    2.893
peak=    3.341 closest distance to " O   HOH Z 353 " =    2.679
peak=    3.340 closest distance to " N   GLN A 278 " =    0.858
peak=    3.340 closest distance to " O   HOH Z 374 " =    2.722
peak=    3.339 closest distance to " OD1 ASP A 231 " =    1.837
peak=    3.335 closest distance to " O   HOH Z 403 " =    1.679
peak=    3.333 closest distance to " NE AARG A 275 " =    1.468
peak=    3.332 closest distance to " CB  ALA A 161 " =    0.897
peak=    3.328 closest distance to " CG1 ILE A 120 " =    1.107
peak=    3.322 closest distance to " OG1 THR A 294 " =    1.613
peak=    3.321 closest distance to " O   HOH Z 329 " =    3.586
peak=    3.321 closest distance to " CB  ILE A 120 " =    1.172
peak=    3.317 closest distance to " O   HOH Z 147 " =    1.665
peak=    3.315 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.315 closest distance to " CA  ILE A 234 " =    0.915
peak=    3.314 closest distance to " CB  GLU A  46 " =    1.015
peak=    3.313 closest distance to " O   HOH Z  44 " =    3.407
peak=    3.313 closest distance to " O   HOH Z 334 " =    1.531
peak=    3.313 closest distance to " O   HOH Z 271 " =    2.315
peak=    3.308 closest distance to " O   HOH Z   4 " =    1.917
peak=    3.308 closest distance to " OD1 ASP A 238 " =    0.960
peak=    3.299 closest distance to " O   HOH Z 126 " =    1.578
peak=    3.296 closest distance to " O   HOH Z 234 " =    1.786
peak=    3.295 closest distance to " CG2 VAL A 174 " =    1.342
peak=    3.295 closest distance to " O   HOH Z 211 " =    2.351
peak=    3.291 closest distance to " O   HOH Z 261 " =    2.008
peak=    3.291 closest distance to " O   HOH Z 287 " =    1.761
peak=    3.291 closest distance to " O   HOH Z 345 " =    1.801
peak=    3.289 closest distance to " O   HOH Z 411 " =    1.827
peak=    3.289 closest distance to " O   GLY A  57 " =    2.591
peak=    3.286 closest distance to " CG BARG A 102 " =    1.900
peak=    3.279 closest distance to " CA  LYS A 290 " =    1.350
peak=    3.272 closest distance to " CB  ILE A 199 " =    0.889
peak=    3.267 closest distance to " NZ  LYS A 166 " =    3.047
peak=    3.266 closest distance to " O   HOH Z  44 " =    1.817
peak=    3.266 closest distance to " SD AMET A  47 " =    1.073
peak=    3.265 closest distance to " O   HOH Z 213 " =    1.754
peak=    3.263 closest distance to " CG2 ILE A 120 " =    1.200
peak=    3.260 closest distance to " O   HOH Z 407 " =    2.407
peak=    3.259 closest distance to " O   HOH Z  59 " =    2.080
peak=    3.257 closest distance to " O   HOH Z 163 " =    1.554
peak=    3.257 closest distance to " CD2 HIS A  81 " =    1.236
peak=    3.256 closest distance to " O   HOH Z 172 " =    3.689
peak=    3.256 closest distance to " CG2 VAL A 112 " =    0.808
peak=    3.252 closest distance to " OG  SER A  97 " =    3.571
peak=    3.249 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.249 closest distance to " CB  GLU A 236 " =    1.006
peak=    3.246 closest distance to " O   HOH Z 387 " =    3.017
peak=    3.244 closest distance to " OD1BASN A 224 " =    2.240
peak=    3.241 closest distance to " N   ASN A 252 " =    1.403
peak=    3.241 closest distance to " O   HOH Z 245 " =    1.317
peak=    3.237 closest distance to " O   HOH Z 282 " =    1.427
peak=    3.236 closest distance to " O   HOH Z 173 " =    1.864
peak=    3.235 closest distance to " O   HOH Z  54 " =    2.378
peak=    3.233 closest distance to " O   HOH Z 151 " =    2.249
peak=    3.233 closest distance to " CG  ARG A 159 " =    0.983
peak=    3.230 closest distance to " O   HOH Z 116 " =    1.792
peak=    3.230 closest distance to " CG2 THR A 220 " =    1.097
peak=    3.230 closest distance to " CA  VAL A 126 " =    1.021
peak=    3.229 closest distance to " O   HOH Z 345 " =    3.467
peak=    3.226 closest distance to " CG AARG A 275 " =    1.087
peak=    3.224 closest distance to " CA  GLY A 267 " =    1.163
peak=    3.224 closest distance to " CB  ALA A 104 " =    0.719
peak=    3.218 closest distance to " O   HOH Z  80 " =    1.623
peak=    3.218 closest distance to " O   HOH Z 383 " =    1.802
peak=    3.216 closest distance to " O   ALA A   1 " =    1.512
peak=    3.215 closest distance to " O   HOH Z 216 " =    2.595
peak=    3.211 closest distance to " CA  ALA A 158 " =    1.074
peak=    3.209 closest distance to " CB  LEU A 255 " =    0.728
peak=    3.208 closest distance to " O   HOH Z 163 " =    1.975
peak=    3.206 closest distance to " CA  LYS A  48 " =    1.292
peak=    3.206 closest distance to " CZ3 TRP A 123 " =    1.176
peak=    3.204 closest distance to " O   HOH Z 337 " =    3.759
peak=    3.202 closest distance to " CA  ILE A  33 " =    1.657
peak=    3.201 closest distance to " CB  TRP A 123 " =    1.008
peak=    3.200 closest distance to " O   ALA A  10 " =    1.649
peak=    3.199 closest distance to " O   HOH Z 219 " =    2.040
peak=    3.197 closest distance to " CB  TYR A 116 " =    0.936
peak=    3.197 closest distance to " CB  PHE A 283 " =    0.791
peak=    3.193 closest distance to " O   HOH Z 388 " =    2.020
peak=    3.191 closest distance to " OE1 GLN A  11 " =    2.072
peak=    3.191 closest distance to " CA  ALA A 160 " =    0.874
peak=    3.190 closest distance to " O   HOH Z 263 " =    1.659
peak=    3.190 closest distance to " O   HOH Z 425 " =    2.020
peak=    3.189 closest distance to " OG BSER A 258 " =    3.602
peak=    3.188 closest distance to " CD1AILE A 234 " =    1.047
peak=    3.185 closest distance to " CD1 TRP A 266 " =    1.171
peak=    3.185 closest distance to " O   HOH Z 286 " =    2.170
peak=    3.183 closest distance to " N   ALA A 154 " =    0.894
peak=    3.181 closest distance to " CB  TRP A 150 " =    1.592
peak=    3.181 closest distance to " CB  HIS A 108 " =    0.850
peak=    3.177 closest distance to " CG2BVAL A  41 " =    0.877
peak=    3.176 closest distance to " CB  PRO A 243 " =    1.264
peak=    3.176 closest distance to " CG  MET A 185 " =    1.081
peak=    3.173 closest distance to " CD  ARG A  14 " =    1.283
peak=    3.170 closest distance to " O   HOH Z 227 " =    2.012
peak=    3.170 closest distance to " O   HOH Z 406 " =    1.613
peak=    3.163 closest distance to " N   VAL A 126 " =    1.289
peak=    3.162 closest distance to " O   HOH Z 427 " =    3.126
peak=    3.162 closest distance to " CB  ALA A 184 " =    0.968
peak=    3.161 closest distance to " O   HOH Z 305 " =    3.690
peak=    3.158 closest distance to " CB  TRP A 179 " =    1.722
peak=    3.157 closest distance to " OG BSER A 164 " =    2.477
peak=    3.154 closest distance to " CA  ARG A 195 " =    1.200
peak=    3.153 closest distance to " NZ  LYS A  76 " =    1.156
peak=    3.152 closest distance to " NH1 ARG A  56 " =    0.982
peak=    3.152 closest distance to " O   HOH Z  64 " =    2.156
peak=    3.151 closest distance to " O   HOH Z 302 " =    1.947
peak=    3.144 closest distance to " OE1 GLN A  58 " =    1.216
peak=    3.134 closest distance to " O   HOH Z 163 " =    1.742
peak=    3.130 closest distance to " O   GLY A 229 " =    1.733
peak=    3.128 closest distance to " CB  ALA A  34 " =    1.015
peak=    3.122 closest distance to " NH2 ARG A 219 " =    1.827
peak=    3.120 closest distance to " CD BARG A 102 " =    1.303
peak=    3.116 closest distance to " CA  ASP A 162 " =    1.153
peak=    3.114 closest distance to " CG  GLN A 144 " =    0.954
peak=    3.112 closest distance to " CE2 TYR A 247 " =    1.304
peak=    3.111 closest distance to " O   HOH Z  58 " =    1.564
peak=    3.107 closest distance to " OG  SER A  22 " =    2.810
peak=    3.103 closest distance to " O   SER A 164 " =    1.406
peak=    3.095 closest distance to " O   ALA A 158 " =    1.275
peak=    3.093 closest distance to " O   HOH Z 217 " =    1.444
peak=    3.087 closest distance to " CA  VAL A  41 " =    0.869
peak=    3.080 closest distance to " O   HOH Z 273 " =    3.562
peak=    3.077 closest distance to " O   TYR A 116 " =    1.300
peak=    3.068 closest distance to " CB  ALA A 114 " =    1.101
peak=    3.062 closest distance to " O   HOH Z 368 " =    2.532
peak=    3.045 closest distance to " NH1BARG A 145 " =    1.252
peak=    3.044 closest distance to " O   HOH Z 129 " =    3.588
peak=    3.035 closest distance to " CB  TYR A 169 " =    1.272
peak=    3.023 closest distance to " O   HOH Z  68 " =    2.628

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.497 - 5.540
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 195
   mapped sites are within: 0.724 - 5.540

peak=   -4.894 closest distance to " O   HOH Z 290 " =    1.054
peak=   -4.419 closest distance to " CB  PRO A 243 " =    2.597
peak=   -4.343 closest distance to " O   HOH Z 266 " =    4.480
peak=   -4.333 closest distance to " O   HOH Z 198 " =    2.375
peak=   -4.271 closest distance to " O   HOH Z 377 " =    1.614
peak=   -4.251 closest distance to " N   ALA A  43 " =    2.408
peak=   -4.094 closest distance to " CE2 TYR A  30 " =    2.847
peak=   -4.085 closest distance to " ND2 ASN A  45 " =    0.976
peak=   -4.083 closest distance to " CG  GLN A 223 " =    1.722
peak=   -4.065 closest distance to " C   ALA A 158 " =    1.291
peak=   -4.027 closest distance to " O   PRO A 198 " =    1.248
peak=   -4.009 closest distance to " CZ3 TRP A 179 " =    1.189
peak=   -4.004 closest distance to " CA  ASP A  27 " =    2.464
peak=   -3.987 closest distance to " O   ILE A 109 " =    2.624
peak=   -3.980 closest distance to " O   HOH Z 231 " =    1.953
peak=   -3.960 closest distance to " CG  LYS A 193 " =    2.439
peak=   -3.924 closest distance to " CD1 LEU A 228 " =    2.395
peak=   -3.899 closest distance to " O   HOH Z 407 " =    3.360
peak=   -3.893 closest distance to " O   VAL A  67 " =    2.698
peak=   -3.869 closest distance to " C   ASN A 187 " =    1.868
peak=   -3.865 closest distance to " SG  CYS A 254 " =    3.098
peak=   -3.861 closest distance to " O   HOH Z  98 " =    2.053
peak=   -3.857 closest distance to " C   ASN A 285 " =    2.586
peak=   -3.854 closest distance to " O   HOH Z  43 " =    1.545
peak=   -3.837 closest distance to " CD2 LEU A 300 " =    2.994
peak=   -3.821 closest distance to " CD  ARG A  14 " =    3.322
peak=   -3.801 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.778 closest distance to " O   HOH Z  10 " =    1.543
peak=   -3.774 closest distance to " CD  GLN A  88 " =    0.790
peak=   -3.763 closest distance to " CA  SER A 146 " =    2.213
peak=   -3.761 closest distance to " CB  ASN A  39 " =    2.107
peak=   -3.757 closest distance to " CB  CYS A 254 " =    2.245
peak=   -3.757 closest distance to " CZ  TYR A 169 " =    1.711
peak=   -3.749 closest distance to " O   GLY A 211 " =    1.419
peak=   -3.744 closest distance to " NH2AARG A 275 " =    5.540
peak=   -3.710 closest distance to " CD  ARG A 156 " =    1.951
peak=   -3.710 closest distance to " OE1 GLN A  88 " =    1.017
peak=   -3.698 closest distance to " CG  ASP A 231 " =    0.796
peak=   -3.677 closest distance to " O   HOH Z 353 " =    2.195
peak=   -3.663 closest distance to " O   HOH Z 185 " =    2.276
peak=   -3.661 closest distance to " O   HOH Z  38 " =    1.488
peak=   -3.657 closest distance to " OD1 ASP A 191 " =    1.628
peak=   -3.647 closest distance to " O   HOH Z 118 " =    2.780
peak=   -3.644 closest distance to " O   HOH Z  52 " =    1.252
peak=   -3.633 closest distance to " CE  MET A  93 " =    1.179
peak=   -3.629 closest distance to " O   GLY A 196 " =    1.129
peak=   -3.624 closest distance to " CG1 VAL A 250 " =    2.642
peak=   -3.621 closest distance to " O   PRO A 163 " =    1.987
peak=   -3.607 closest distance to " N   GLN A  58 " =    1.834
peak=   -3.606 closest distance to " O   HOH Z  13 " =    1.296
peak=   -3.599 closest distance to " O   HOH Z 351 " =    1.428
peak=   -3.597 closest distance to " CD  ARG A 195 " =    5.148
peak=   -3.577 closest distance to " O   HOH Z 388 " =    1.937
peak=   -3.568 closest distance to " O   HOH Z 275 " =    1.596
peak=   -3.562 closest distance to " OXT GLY A 302 " =    2.863
peak=   -3.558 closest distance to " CB  PHE A 283 " =    2.804
peak=   -3.548 closest distance to " N   ALA A 226 " =    2.137
peak=   -3.543 closest distance to " CD1 LEU A 101 " =    2.498
peak=   -3.540 closest distance to " C   HIS A 108 " =    1.053
peak=   -3.539 closest distance to " CB  TYR A  15 " =    2.197
peak=   -3.526 closest distance to " OD1 ASN A 148 " =    1.669
peak=   -3.522 closest distance to " O   HOH Z 222 " =    1.152
peak=   -3.521 closest distance to " CG  ARG A 269 " =    2.510
peak=   -3.517 closest distance to " CG  LEU A  83 " =    1.907
peak=   -3.515 closest distance to " CD1 PHE A  59 " =    1.835
peak=   -3.507 closest distance to " OG BSER A 134 " =    1.752
peak=   -3.502 closest distance to " O   HOH Z 166 " =    1.827
peak=   -3.502 closest distance to " O   HOH Z  11 " =    1.967
peak=   -3.496 closest distance to " O   HOH Z  92 " =    1.726
peak=   -3.495 closest distance to " O   HOH Z 231 " =    1.219
peak=   -3.490 closest distance to " CE  MET A 105 " =    2.149
peak=   -3.483 closest distance to " O   HOH Z 435 " =    2.754
peak=   -3.481 closest distance to " O   VAL A 153 " =    2.344
peak=   -3.470 closest distance to " O   HOH Z 389 " =    1.889
peak=   -3.462 closest distance to " CE  LYS A  76 " =    2.675
peak=   -3.456 closest distance to " CB  ALA A  43 " =    2.452
peak=   -3.453 closest distance to " O   HOH Z  71 " =    1.129
peak=   -3.450 closest distance to " CB  ALA A 291 " =    2.231
peak=   -3.444 closest distance to " C   LEU A 143 " =    1.380
peak=   -3.441 closest distance to " SD BMET A  47 " =    0.889
peak=   -3.441 closest distance to " N   SER A 212 " =    1.805
peak=   -3.439 closest distance to " O   HOH Z  76 " =    1.777
peak=   -3.431 closest distance to " O   SER A  62 " =    2.132
peak=   -3.429 closest distance to " OG  SER A  97 " =    2.163
peak=   -3.426 closest distance to " NH1 ARG A 195 " =    2.598
peak=   -3.422 closest distance to " CD  GLN A  88 " =    0.923
peak=   -3.416 closest distance to " CD  LYS A 289 " =    2.533
peak=   -3.416 closest distance to " CD1 ILE A 239 " =    2.035
peak=   -3.409 closest distance to " OG BSER A 134 " =    1.197
peak=   -3.407 closest distance to " O   HOH Z 111 " =    2.270
peak=   -3.402 closest distance to " ND2 ASN A 249 " =    1.985
peak=   -3.398 closest distance to " O   HOH Z 252 " =    4.245
peak=   -3.393 closest distance to " CD  ARG A 139 " =    1.618
peak=   -3.376 closest distance to " O   HOH Z 417 " =    2.551
peak=   -3.366 closest distance to " CD2 TYR A 293 " =    2.036
peak=   -3.363 closest distance to " O   HOH Z 426 " =    1.753
peak=   -3.361 closest distance to " CA  GLY A 241 " =    3.020
peak=   -3.355 closest distance to " O   HOH Z 298 " =    1.177
peak=   -3.348 closest distance to " O   HOH Z  11 " =    1.960
peak=   -3.342 closest distance to " O   HOH Z 184 " =    1.770
peak=   -3.341 closest distance to " CA  GLY A 203 " =    2.215
peak=   -3.337 closest distance to " O   HOH Z 266 " =    4.860
peak=   -3.336 closest distance to " CD  GLN A  88 " =    2.093
peak=   -3.335 closest distance to " OG  SER A  62 " =    1.597
peak=   -3.333 closest distance to " CG  GLU A 152 " =    0.832
peak=   -3.333 closest distance to " O   HOH Z  93 " =    2.096
peak=   -3.330 closest distance to " C   LEU A 222 " =    0.724
peak=   -3.329 closest distance to " CZ  PHE A  59 " =    1.642
peak=   -3.326 closest distance to " CB  ALA A 248 " =    1.994
peak=   -3.322 closest distance to " O   HOH Z 148 " =    3.439
peak=   -3.321 closest distance to " CA  GLY A 241 " =    2.279
peak=   -3.321 closest distance to " CG1 VAL A 112 " =    2.869
peak=   -3.317 closest distance to " OD2 ASP A 171 " =    1.837
peak=   -3.310 closest distance to " OG ASER A 134 " =    1.344
peak=   -3.308 closest distance to " CE3 TRP A 150 " =    1.819
peak=   -3.307 closest distance to " SG ACYS A 201 " =    2.160
peak=   -3.303 closest distance to " CB  CYS A 201 " =    2.626
peak=   -3.296 closest distance to " CA  ARG A 139 " =    1.042
peak=   -3.294 closest distance to " CG  PRO A 163 " =    2.395
peak=   -3.292 closest distance to " O   ALA A 161 " =    1.475
peak=   -3.291 closest distance to " O   HOH Z 283 " =    2.182
peak=   -3.291 closest distance to " O   HOH Z 311 " =    3.629
peak=   -3.290 closest distance to " CG1 VAL A 112 " =    2.574
peak=   -3.282 closest distance to " CB  PRO A 163 " =    2.643
peak=   -3.278 closest distance to " NH2 ARG A  79 " =    1.811
peak=   -3.276 closest distance to " O   HOH Z 436 " =    1.359
peak=   -3.274 closest distance to " CG  GLU A  53 " =    1.480
peak=   -3.261 closest distance to " O   VAL A  67 " =    2.566
peak=   -3.255 closest distance to " CA  VAL A 232 " =    2.550
peak=   -3.246 closest distance to " O   ASN A 249 " =    1.601
peak=   -3.241 closest distance to " CD1 ILE A 263 " =    2.509
peak=   -3.238 closest distance to " CB  PHE A 192 " =    1.972
peak=   -3.238 closest distance to " O   GLY A 203 " =    2.501
peak=   -3.237 closest distance to " O   ALA A   7 " =    1.671
peak=   -3.236 closest distance to " O   HOH Z 313 " =    2.101
peak=   -3.235 closest distance to " CZ  ARG A 259 " =    0.894
peak=   -3.218 closest distance to " OD2 ASP A 171 " =    2.241
peak=   -3.216 closest distance to " OD2 ASP A 200 " =    1.353
peak=   -3.215 closest distance to " O   HOH Z 243 " =    2.021
peak=   -3.212 closest distance to " CB  ASP A 132 " =    2.247
peak=   -3.210 closest distance to " OG  SER A   3 " =    1.750
peak=   -3.208 closest distance to " CG1 VAL A 197 " =    2.294
peak=   -3.208 closest distance to " CE2 PHE A 218 " =    2.498
peak=   -3.204 closest distance to " O   HOH Z 211 " =    1.691
peak=   -3.203 closest distance to " O   HOH Z 241 " =    1.205
peak=   -3.201 closest distance to " CG  TRP A 266 " =    1.706
peak=   -3.201 closest distance to " CD  ARG A 159 " =    1.272
peak=   -3.199 closest distance to " O   HOH Z 309 " =    2.428
peak=   -3.196 closest distance to " O   HOH Z  63 " =    1.275
peak=   -3.196 closest distance to " OG1 THR A 246 " =    1.496
peak=   -3.196 closest distance to " O   HOH Z  61 " =    1.597
peak=   -3.193 closest distance to " N   GLY A  23 " =    2.136
peak=   -3.190 closest distance to " OD1 ASN A 249 " =    1.165
peak=   -3.189 closest distance to " O   HOH Z 128 " =    2.490
peak=   -3.181 closest distance to " NE2 GLN A  58 " =    1.201
peak=   -3.174 closest distance to " O   HOH Z 317 " =    2.580
peak=   -3.165 closest distance to " O   SER A  12 " =    1.518
peak=   -3.160 closest distance to " OD2 ASP A  50 " =    2.412
peak=   -3.153 closest distance to " CZ BARG A 275 " =    2.073
peak=   -3.153 closest distance to " O   HOH Z 390 " =    2.327
peak=   -3.150 closest distance to " O   HOH Z 166 " =    1.492
peak=   -3.142 closest distance to " O   HOH Z  60 " =    1.866
peak=   -3.140 closest distance to " O   HOH Z 177 " =    1.637
peak=   -3.137 closest distance to " O   HOH Z 298 " =    2.693
peak=   -3.135 closest distance to " ND2 ASN A  60 " =    1.436
peak=   -3.134 closest distance to " O   HOH Z 393 " =    1.515
peak=   -3.133 closest distance to " CD1 TRP A 179 " =    0.902
peak=   -3.131 closest distance to " OE2 GLU A   2 " =    1.625
peak=   -3.130 closest distance to " O   HOH Z 210 " =    0.932
peak=   -3.130 closest distance to " O   HOH Z 394 " =    1.499
peak=   -3.130 closest distance to " CD1 ILE A 199 " =    2.573
peak=   -3.129 closest distance to " O   HOH Z 234 " =    4.243
peak=   -3.128 closest distance to " CB  ALA A 291 " =    2.340
peak=   -3.125 closest distance to " CG2 VAL A 189 " =    2.055
peak=   -3.122 closest distance to " OG1 THR A 178 " =    1.343
peak=   -3.120 closest distance to " CD2 LEU A 237 " =    2.708
peak=   -3.117 closest distance to " CD1 LEU A 297 " =    2.554
peak=   -3.116 closest distance to " CB  ASP A 132 " =    2.251
peak=   -3.116 closest distance to " CG  GLN A 278 " =    2.303
peak=   -3.115 closest distance to " O   HOH Z 176 " =    0.800
peak=   -3.112 closest distance to " OD1 ASN A 301 " =    1.939
peak=   -3.106 closest distance to " C   GLN A 240 " =    2.243
peak=   -3.105 closest distance to " CE3 TRP A 274 " =    2.564
peak=   -3.104 closest distance to " O   PHE A 218 " =    1.456
peak=   -3.103 closest distance to " O   HOH Z 322 " =    1.390
peak=   -3.099 closest distance to " C   SER A 206 " =    1.434
peak=   -3.096 closest distance to " OG  SER A 245 " =    0.934
peak=   -3.088 closest distance to " CE1 TYR A 169 " =    2.459
peak=   -3.085 closest distance to " CZ  ARG A  66 " =    0.742
peak=   -3.083 closest distance to " CD1 LEU A 101 " =    2.701
peak=   -3.071 closest distance to " O   GLY A  80 " =    2.416
peak=   -3.055 closest distance to " ND2 ASN A 215 " =    2.176

================= 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    :  0.3959 0.4027   6.186076e+00   6.194415e+00
   1_bss:  0.3836 0.3918   6.174887e+00   6.177956e+00
   1_xyz:  0.2408 0.2717   5.782331e+00   5.890182e+00
   1_adp:  0.2223 0.2804   5.742530e+00   5.917814e+00
   1_occ:  0.2219 0.2804   5.740715e+00   5.916381e+00
   2_bss:  0.2190 0.2778   5.733343e+00   5.907425e+00
   2_xyz:  0.1563 0.2038   5.431095e+00   5.641519e+00
   2_adp:  0.1401 0.1871   5.337947e+00   5.556526e+00
   2_occ:  0.1400 0.1869   5.337031e+00   5.555710e+00
   3_bss:  0.1397 0.1852   5.334047e+00   5.551224e+00
   3_xyz:  0.1216 0.1651   5.211716e+00   5.441412e+00
   3_adp:  0.1181 0.1607   5.184395e+00   5.412843e+00
   3_occ:  0.1180 0.1605   5.183872e+00   5.412565e+00
   4_bss:  0.1179 0.1603   5.183382e+00   5.412032e+00
   4_xyz:  0.1129 0.1574   5.153606e+00   5.390318e+00
   4_adp:  0.1114 0.1575   5.149173e+00   5.391119e+00
   4_occ:  0.1114 0.1574   5.148979e+00   5.391164e+00
   5_bss:  0.1114 0.1573   5.149682e+00   5.392873e+00
   5_xyz:  0.1136 0.1588   5.165836e+00   5.405002e+00
   5_adp:  0.1145 0.1584   5.168612e+00   5.403831e+00
   5_occ:  0.1144 0.1584   5.168611e+00   5.404070e+00
   5_bss:  0.1144 0.1584   5.168816e+00   5.404191e+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:  0.307  31.039   1.243  -3.084   1.975  -0.000   0.000   0.000
   1_xyz:  0.307  31.039   1.243  -3.084   1.975  -0.000   0.000   0.000
   1_adp:  0.307  31.039   1.243  -3.084   1.975  -0.000   0.000   0.000
   1_occ:  0.307  31.039   1.243  -3.084   1.975  -0.000   0.000   0.000
   2_bss:  0.337  54.638  -1.159  -3.022  -0.829  -0.000  -0.000  -0.000
   2_xyz:  0.337  54.638  -1.159  -3.022  -0.829  -0.000  -0.000  -0.000
   2_adp:  0.337  54.638  -1.159  -3.022  -0.829  -0.000  -0.000  -0.000
   2_occ:  0.337  54.638  -1.159  -3.022  -0.829  -0.000  -0.000  -0.000
   3_bss:  0.330  52.299  -1.721  -2.552  -1.562  -0.000  -0.000  -0.000
   3_xyz:  0.330  52.299  -1.721  -2.552  -1.562  -0.000  -0.000  -0.000
   3_adp:  0.330  52.299  -1.721  -2.552  -1.562  -0.000  -0.000  -0.000
   3_occ:  0.330  52.299  -1.721  -2.552  -1.562  -0.000  -0.000  -0.000
   4_bss:  0.330  52.299  -2.119  -2.618  -1.951  -0.000  -0.000  -0.000
   4_xyz:  0.330  52.299  -2.119  -2.618  -1.951  -0.000  -0.000  -0.000
   4_adp:  0.330  52.299  -2.119  -2.618  -1.951  -0.000  -0.000  -0.000
   4_occ:  0.330  52.299  -2.119  -2.618  -1.951  -0.000  -0.000  -0.000
   5_bss:  0.324  52.262  -2.059  -2.465  -1.926  -0.000  -0.000  -0.000
   5_xyz:  0.324  52.262  -2.059  -2.465  -1.926  -0.000  -0.000  -0.000
   5_adp:  0.324  52.262  -2.059  -2.465  -1.926  -0.000  -0.000  -0.000
   5_occ:  0.324  52.262  -2.059  -2.465  -1.926  -0.000  -0.000  -0.000
   5_bss:  0.320  48.416  -1.987  -2.322  -1.799  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.310 0.5666  0.7431    49142.526
   1_bss:  45.004 0.5807  0.7668    45673.485
   1_xyz:  27.499 0.7861  0.9794    19825.335
   1_adp:  28.902 0.7697  0.9672    21227.609
   1_occ:  28.883 0.7698  0.9670    21139.587
   2_bss:  28.484 0.7742  0.9157    20745.581
   2_xyz:  20.155 0.8594  0.9776    10892.893
   2_adp:  17.770 0.8826  0.9866     9120.759
   2_occ:  17.742 0.8829  0.9866     9094.843
   3_bss:  17.629 0.8839  0.9762     8978.416
   3_xyz:  15.191 0.9048  0.9857     7037.944
   3_adp:  14.499 0.9110  0.9858     6689.206
   3_occ:  14.488 0.9111  0.9857     6680.316
   4_bss:  14.477 0.9112  0.9757     6673.550
   4_xyz:  14.018 0.9150  0.9762     6336.659
   4_adp:  13.999 0.9153  0.9721     6348.381
   4_occ:  13.995 0.9154  0.9720     6348.467
   5_bss:  14.050 0.9149  0.9746     6386.197
   5_xyz:  14.283 0.9130  0.9732     6538.131
   5_adp:  14.251 0.9133  0.9707     6554.076
   5_occ:  14.253 0.9133  0.9707     6558.079
   5_bss:  14.259 0.9133  0.9724     6556.141
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6999e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6999e-01
   1_xyz:   1.315  0.010  0.085 15.489  0.005  4.116   9.8626e-02
   1_adp:   1.315  0.010  0.085 15.489  0.005  4.116   9.8626e-02
   1_occ:   1.315  0.010  0.085 15.489  0.005  4.116   9.8626e-02
   2_bss:   1.315  0.010  0.085 15.489  0.005  4.116   9.8626e-02
   2_xyz:   1.046  0.007  0.073 14.321  0.004  4.112   6.1712e-02
   2_adp:   1.046  0.007  0.073 14.321  0.004  4.112   6.1712e-02
   2_occ:   1.046  0.007  0.073 14.321  0.004  4.112   6.1712e-02
   3_bss:   1.046  0.007  0.073 14.321  0.004  4.112   6.1712e-02
   3_xyz:   1.012  0.007  0.073 14.377  0.004  4.115   5.9058e-02
   3_adp:   1.012  0.007  0.073 14.377  0.004  4.115   5.9058e-02
   3_occ:   1.012  0.007  0.073 14.377  0.004  4.115   5.9058e-02
   4_bss:   1.012  0.007  0.073 14.377  0.004  4.115   5.9058e-02
   4_xyz:   1.026  0.008  0.074 14.419  0.004  4.118   6.0861e-02
   4_adp:   1.026  0.008  0.074 14.419  0.004  4.118   6.0861e-02
   4_occ:   1.026  0.008  0.074 14.419  0.004  4.118   6.0861e-02
   5_bss:   1.026  0.008  0.074 14.419  0.004  4.118   6.0861e-02
   5_xyz:   0.912  0.006  0.067 14.125  0.003  4.118   4.9337e-02
   5_adp:   0.912  0.006  0.067 14.125  0.003  4.118   4.9337e-02
   5_occ:   0.912  0.006  0.067 14.125  0.003  4.118   4.9337e-02
   5_bss:   0.912  0.006  0.067 14.125  0.003  4.118   4.9337e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.770   2.4078e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.770   2.4078e-01
   1_xyz:  10.292  0.056  0.323 83.668  0.038  2.175   1.2328e-01
   1_adp:  10.292  0.056  0.323 83.668  0.038  2.175   1.2328e-01
   1_occ:  10.292  0.056  0.323 83.668  0.038  2.175   1.2328e-01
   2_bss:  10.292  0.056  0.323 83.668  0.038  2.175   1.2328e-01
   2_xyz:   8.065  0.031  0.236 85.881  0.044  2.381   8.5268e-02
   2_adp:   8.065  0.031  0.236 85.881  0.044  2.381   8.5268e-02
   2_occ:   8.065  0.031  0.236 85.881  0.044  2.381   8.5268e-02
   3_bss:   8.065  0.031  0.236 85.881  0.044  2.381   8.5268e-02
   3_xyz:   8.254  0.051  0.226 82.848  0.033  2.294   4.0396e-02
   3_adp:   8.254  0.051  0.226 82.848  0.033  2.294   4.0396e-02
   3_occ:   8.254  0.051  0.226 82.848  0.033  2.294   4.0396e-02
   4_bss:   8.254  0.051  0.226 82.848  0.033  2.294   4.0396e-02
   4_xyz:   7.595  0.039  0.233 84.439  0.034  2.340   4.3938e-02
   4_adp:   7.595  0.039  0.233 84.439  0.034  2.340   4.3938e-02
   4_occ:   7.595  0.039  0.233 84.439  0.034  2.340   4.3938e-02
   5_bss:   7.595  0.039  0.233 84.439  0.034  2.340   4.3938e-02
   5_xyz:   7.716  0.044  0.209 83.443  0.030  2.388   2.9374e-02
   5_adp:   7.716  0.044  0.209 83.443  0.030  2.388   2.9374e-02
   5_occ:   7.716  0.044  0.209 83.443  0.030  2.388   2.9374e-02
   5_bss:   7.716  0.044  0.209 83.443  0.030  2.388   2.9374e-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:  69.96   0.00  17.07  69.96   0.00  13.10  63.12   5.94  38.72
   1_occ:  69.96   0.00  17.07  69.96   0.00  13.10  63.12   5.94  38.72
   2_bss:  69.96   0.00  17.07  69.96   0.00  13.10  63.12   5.94  38.72
   2_xyz:  69.96   0.00  17.07  69.96   0.00  13.10  63.12   5.94  38.72
   2_adp:  72.92   1.73  17.38  72.92   1.73  13.08  72.11   5.90  40.75
   2_occ:  72.92   1.73  17.38  72.92   1.73  13.08  72.11   5.90  40.75
   3_bss:  72.92   1.73  17.38  72.92   1.73  13.08  72.11   5.90  40.75
   3_xyz:  72.92   1.73  17.38  72.92   1.73  13.08  72.11   5.90  40.75
   3_adp:  78.83   1.66  17.13  78.83   1.66  12.99  75.24   4.24  39.66
   3_occ:  78.83   1.66  17.13  78.83   1.66  12.99  75.24   4.24  39.66
   4_bss:  78.83   1.66  17.13  78.83   1.66  12.99  75.24   4.24  39.66
   4_xyz:  78.83   1.66  17.13  78.83   1.66  12.99  75.24   4.24  39.66
   4_adp:  87.28   1.23  17.12  87.28   1.23  12.95  80.65   4.78  39.82
   4_occ:  87.28   1.23  17.12  87.28   1.23  12.95  80.65   4.78  39.82
   5_bss:  87.28   1.23  17.12  87.28   1.23  12.95  80.65   4.78  39.82
   5_xyz:  87.28   1.23  17.12  87.28   1.23  12.95  80.65   4.78  39.82
   5_adp:  86.70   1.65  16.71  86.70   1.65  12.81  76.80   6.27  37.97
   5_occ:  86.70   1.65  16.71  86.70   1.65  12.81  76.80   6.27  37.97
   5_bss:  86.64   1.59  16.65  86.64   1.59  12.75  76.75   6.22  37.91
------------------------------------------------------------------------
 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:    1.863    0.020    0.391
   1_adp:    1.863    0.020    0.391
   1_occ:    1.863    0.020    0.391
   2_bss:    1.863    0.020    0.391
   2_xyz:    1.170    0.020    0.476
   2_adp:    1.170    0.020    0.476
   2_occ:    1.170    0.020    0.476
   3_bss:    1.170    0.020    0.476
   3_xyz:    1.181    0.025    0.523
   3_adp:    1.181    0.025    0.523
   3_occ:    1.181    0.025    0.523
   4_bss:    1.181    0.025    0.523
   4_xyz:    1.202    0.022    0.540
   4_adp:    1.202    0.022    0.540
   4_occ:    1.202    0.022    0.540
   5_bss:    1.202    0.022    0.540
   5_xyz:    1.221    0.037    0.545
   5_adp:    1.221    0.037    0.545
   5_occ:    1.221    0.037    0.545
   5_bss:    1.221    0.037    0.545
------------------------------------------------------------------------

CPU time actual refinement: 286.74


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/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_1145/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1145/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.62 
  Macro-tasks:
    bulk solvent and scale       = 32.56  
    individual site refinement   = 122.81 
    weights calculation          = 24.46  
    collect and process          = 5.50   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 185.42 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 93.29  
    alpha_beta                      = 6.94   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 101.50 
    fmodel                         = 5.50   
    r_factors                      = 0.20   
    phase_errors                   = 8.99   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 219.15 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.007 micro seconds
Total CPU time: 4.97 minutes
from_scatterers_fft:    655 calls, 93.01 s
gradients_fft:          600 calls, 89.45 s

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

# Date 2008-01-16 Time 06:31:18 PST -0800 (1200493878.09 s)
Start R-work = 0.3959, R-free = 0.4027 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1801 (no bulk solvent and anisotropic scale)

Start R-work = 0.3836, R-free = 0.3918
Final R-work = 0.1144, R-free = 0.1584