# Date 2008-01-16 Time 05:53:27 PST -0800 (1200491607.19 s)
#phil __OFF__

Command line arguments: "../921.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3322
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 921

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.01196
Completeness in resolution range: 0.974383
Completeness with d_max=infinity: 0.971339

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0120

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.01196
Completeness in resolution range: 0.974383
Completeness with d_max=infinity: 0.971339

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1646 -  4.3047 [2112/2136]  1899   213  10.1%
  bin  2:  4.3047 -  3.4297 [2031/2051]  1829   202   9.9%
  bin  3:  3.4297 -  3.0000 [2000/2019]  1802   198   9.9%
  bin  4:  3.0000 -  2.7275 [1981/2011]  1780   201  10.1%
  bin  5:  2.7275 -  2.5329 [1977/1996]  1779   198  10.0%
  bin  6:  2.5329 -  2.3842 [1964/1989]  1765   199  10.1%
  bin  7:  2.3842 -  2.2652 [1938/1966]  1749   189   9.8%
  bin  8:  2.2652 -  2.1669 [1950/1986]  1754   196  10.1%
  bin  9:  2.1669 -  2.0837 [1940/1982]  1746   194  10.0%
  bin 10:  2.0837 -  2.0120 [1696/1968]  1527   169  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2162
        3.04 -     3.66: 4580
        3.66 -     4.28: 8878
        4.28 -     4.90: 12239
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.007 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.087 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.228 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27865 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_921/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3317   r_free= 0.3195   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.051751                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.2803 0.2682      6.3343      6.2445|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.2533 0.2407      6.4345       6.425|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.2894 0.2553      6.3707      6.3311|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.3011 0.3292      6.2426        6.26|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.3407 0.2936      6.1287      6.0603|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.3426 0.3552      6.0337      5.9955|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.3640 0.3504      6.0226      6.0437|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.3673 0.3393      6.0008      5.9757|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.3670 0.3494      5.9314      5.9017|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.3865 0.3328      5.9473      5.8426|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.3951 0.3935      5.8935      5.9275|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.3957 0.4120      5.8394      5.9511|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.3919 0.3643      5.7369       5.689|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.3788 0.3989      5.6738      5.6578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.80  24.85   0.86     0.82      38837.84|
|  2:  4.8010 -  3.8309  1315   148  0.85  21.48   0.96     0.90      43526.81|
|  3:  3.8309 -  3.3526  1294   144  0.81  25.27   0.97     0.92      42417.12|
|  4:  3.3526 -  3.0488  1285   142  0.78  28.11   0.98     0.89      37800.38|
|  5:  3.0488 -  2.8318  1270   141  0.73  33.01   0.98     0.87      31585.67|
|  6:  2.8318 -  2.6658  1285   141  0.71  34.55   0.97     0.86      29071.73|
|  7:  2.6658 -  2.5329  1264   144  0.69  36.52   0.98     0.86      27546.55|
|  8:  2.5329 -  2.4231  1260   136  0.70  35.79   0.98     0.88      25745.93|
|  9:  2.4231 -  2.3302  1259   141  0.70  35.73   1.00     0.89      23164.31|
| 10:  2.3302 -  2.2501  1252   141  0.69  36.69   1.03     0.88      21387.42|
| 11:  2.2501 -  2.1799  1258   137  0.67  38.13   1.00     0.88      21471.57|
| 12:  2.1799 -  2.1178  1246   139  0.66  38.95   1.00     0.89      21216.13|
| 13:  2.1178 -  2.0622  1251   139  0.65  40.50   1.01     0.88      18939.85|
| 14:  2.0622 -  2.0120  1015   114  0.66  39.62   1.02     0.84      15295.23|
|alpha:            min =        0.82 max =            0.92 mean =         0.88|
|beta:             min =    15295.23 max =        43526.81 mean =     28784.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.97 mean =        33.31|
|phase err.(test): min =        0.00 max =           89.42 mean =        32.65|
|-----------------------------------------------------------------------------|

============================== 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 = 4.591565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.163   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.673783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.849   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      175 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1987 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1817 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2763 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4576 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4302 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5584 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6655 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.143 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3317   r_free= 0.3195   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.051751                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3192   r_free= 0.3087   ksol= 0.32   Bsol= 65.46   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.18,2.26,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 6.028769                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.171942              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.017   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.620   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3192      final r-factor (work) = 0.1801          |
| start r-factor (free) = 0.3087      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7481 = 4.17 * 0.50 * 6.0337 + 1.00 * 0.1620                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0325 = 4.17 * 0.50 * 5.7353 + 1.00 * 0.0688                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1801      final r-factor (work) = 0.1656          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.2049          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2396 = 0.39 * 1.00 * 5.7353 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1489 = 0.39 * 1.00 * 5.4470 + 1.00 * 0.0280                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.33   16.80    None  None   None       |
|    all(noH): 2823   0      0.00    65.33   16.80    None  None   None       |
|    Sol.    : 438    0      6.03    65.33   38.10    None  None   None       |
|    Mac.    : 2385   0      0.00    57.98   12.88    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 -   6.533:  279   |   5:    32.663 -  39.196:   98        |
|      1:     6.533 -  13.065: 1228   |   6:    39.196 -  45.728:  111        |
|      2:    13.065 -  19.598:  624   |   7:    45.728 -  52.261:   81        |
|      3:    19.598 -  26.131:  221   |   8:    52.261 -  58.794:   55        |
|      4:    26.131 -  32.663:  115   |   9:    58.794 -  65.326:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1656 r_free = 0.2049             target_work(ml) = 5.454         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1651 r_free = 0.2047             target_work(ml) = 5.452         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1651   r_free= 0.2047   ksol= 0.32   Bsol= 65.46   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.18,2.26,-0.00,0.00,0.00); trace/3= -0.65                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.452270                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1635   r_free= 0.2026   ksol= 0.34   Bsol= 71.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.51,-0.32,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.447738                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.768488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.716  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279672              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.269   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1635      final r-factor (work) = 0.1333          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8951 = 1.77 * 0.50 * 5.4582 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7887 = 1.77 * 0.50 * 5.3535 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1333      final r-factor (work) = 0.1266          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5183 = 0.28 * 1.00 * 5.3535 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4743 = 0.28 * 1.00 * 5.2403 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.12    77.11   17.04    None  None   None       |
|    all(noH): 2823   0      1.12    77.11   17.04    None  None   None       |
|    Sol.    : 438    0      6.10    72.05   39.51    None  None   None       |
|    Mac.    : 2385   0      1.12    77.11   12.92    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:     1.120 -   8.720:  711   |   5:    39.117 -  46.717:   99        |
|      1:     8.720 -  16.319: 1239   |   6:    46.717 -  54.316:   93        |
|      2:    16.319 -  23.919:  354   |   7:    54.316 -  61.915:   67        |
|      3:    23.919 -  31.518:  130   |   8:    61.915 -  69.515:   23        |
|      4:    31.518 -  39.117:  102   |   9:    69.515 -  77.114:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1266 r_free = 0.1652             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1265 r_free = 0.1650             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1650   ksol= 0.34   Bsol= 71.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,-2.51,-0.32,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.226435                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1264   r_free= 0.1651   ksol= 0.34   Bsol= 71.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.36,-0.67,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.225863                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.893607              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.199  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.320716              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6355 = 2.89 * 0.50 * 5.2396 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5654 = 2.89 * 0.50 * 5.1768 + 1.00 * 0.0756                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6689 = 0.32 * 1.00 * 5.1768 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6603 = 0.32 * 1.00 * 5.1499 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    79.37   16.85    None  None   None       |
|    all(noH): 2823   0      0.91    79.37   16.85    None  None   None       |
|    Sol.    : 438    0      1.89    74.21   39.22    None  None   None       |
|    Mac.    : 2385   0      0.91    79.37   12.74    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:     0.908 -   8.754:  742   |   5:    40.139 -  47.985:   97        |
|      1:     8.754 -  16.601: 1257   |   6:    47.985 -  55.832:   91        |
|      2:    16.601 -  24.447:  317   |   7:    55.832 -  63.678:   54        |
|      3:    24.447 -  32.293:  126   |   8:    63.678 -  71.524:   19        |
|      4:    32.293 -  40.139:  115   |   9:    71.524 -  79.370:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1577             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1577             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1577   ksol= 0.34   Bsol= 71.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.36,-0.67,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1576   ksol= 0.32   Bsol= 62.03   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.10,-0.61,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.113548              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.967  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.782832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.357  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5185 = 2.11 * 0.50 * 5.1505 + 1.00 * 0.0756                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5061 = 2.11 * 0.50 * 5.1492 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0395 = 0.78 * 1.00 * 5.1492 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0420 = 0.78 * 1.00 * 5.1510 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    84.10   16.83    None  None   None       |
|    all(noH): 2823   0      0.24    84.10   16.83    None  None   None       |
|    Sol.    : 438    0      1.76    77.92   39.69    None  None   None       |
|    Mac.    : 2385   0      0.24    84.10   12.64    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:     0.242 -   8.628:  772   |   5:    42.172 -  50.558:   93        |
|      1:     8.628 -  17.014: 1262   |   6:    50.558 -  58.943:   83        |
|      2:    17.014 -  25.400:  294   |   7:    58.943 -  67.329:   41        |
|      3:    25.400 -  33.786:  133   |   8:    67.329 -  75.715:   17        |
|      4:    33.786 -  42.172:  122   |   9:    75.715 -  84.101:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1128 r_free = 0.1598             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1598             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1598   ksol= 0.32   Bsol= 62.03   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.10,-0.61,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.155048                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1597   ksol= 0.32   Bsol= 62.03   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.89,-0.45,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.154982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.556713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.904  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.994414              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.520  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1127      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6500 = 2.56 * 0.50 * 5.1515 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6513 = 2.56 * 0.50 * 5.1467 + 1.00 * 0.0720                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1105      final r-factor (work) = 0.1106          |
| start r-factor (free) = 0.1601      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2742 = 1.99 * 1.00 * 5.1467 + 1.00 * 0.0096                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2725 = 1.99 * 1.00 * 5.1455 + 1.00 * 0.0102                              |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.59   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    84.59   16.66    None  None   None       |
|    Sol.    : 438    0      3.39    78.41   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    84.59   12.42    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 -   8.459:  800   |   5:    42.295 -  50.754:   93        |
|      1:     8.459 -  16.918: 1231   |   6:    50.754 -  59.213:   84        |
|      2:    16.918 -  25.377:  302   |   7:    59.213 -  67.672:   41        |
|      3:    25.377 -  33.836:  134   |   8:    67.672 -  76.131:   17        |
|      4:    33.836 -  42.295:  115   |   9:    76.131 -  84.590:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1106 r_free = 0.1609             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1105 r_free = 0.1609             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1105   r_free= 0.1609   ksol= 0.32   Bsol= 62.03   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.08,-1.89,-0.45,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.148522                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.1003 0.1361      5.4178      5.5555|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.0845 0.1129       5.442      5.6548|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.1029 0.1469      5.4687      5.8413|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.1181 0.1602      5.4401      5.5933|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.1321 0.1730      5.3407      5.5626|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.1190 0.2020      5.2289      5.5165|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.1262 0.1644      5.1743      5.3523|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.1136 0.1716      5.0724      5.3724|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.1129 0.1786      5.0301      5.2993|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.1114 0.1751      4.9714      5.2499|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.1135 0.1781      4.9518      5.2338|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.1124 0.1741      4.9007      5.2386|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.1106 0.1768      4.8076      5.0893|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.1023 0.1819      4.6797      4.9836|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.93   9.91   0.97     0.93       8111.55|
|  2:  4.8010 -  3.8309  1315   148  0.95   8.30   1.00     0.98       9536.01|
|  3:  3.8309 -  3.3526  1294   144  0.94  11.07   1.01     1.01      10336.08|
|  4:  3.3526 -  3.0488  1285   142  0.92  13.47   1.00     0.98      10151.97|
|  5:  3.0488 -  2.8318  1270   141  0.90  15.81   0.99     0.96       8634.26|
|  6:  2.8318 -  2.6658  1285   141  0.90  16.44   0.98     0.95       7526.62|
|  7:  2.6658 -  2.5329  1264   144  0.90  16.05   0.98     0.96       6474.55|
|  8:  2.5329 -  2.4231  1260   136  0.91  15.06   0.98     0.95       5411.94|
|  9:  2.4231 -  2.3302  1259   141  0.91  15.29   0.98     0.94       5054.31|
| 10:  2.3302 -  2.2501  1252   141  0.90  15.79   0.98     0.94       4550.02|
| 11:  2.2501 -  2.1799  1258   137  0.90  16.50   0.97     0.93       4547.51|
| 12:  2.1799 -  2.1178  1246   139  0.91  15.76   0.98     0.97       4164.07|
| 13:  2.1178 -  2.0622  1251   139  0.90  16.21   0.97     0.95       3535.55|
| 14:  2.0622 -  2.0120  1015   114  0.92  14.60   0.94     0.91       2682.69|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2682.69 max =        10336.08 mean =      6572.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.58 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1607   ksol= 0.32   Bsol= 62.04   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.59,-0.19,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.148646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1607   ksol= 0.32   Bsol= 62.04   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-1.59,-0.19,-0.00,-0.00,-0.00); trace/3= -1.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.148646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1646 -  4.8010 0.99   1376  152 0.1003 0.1363      5.4185      5.5568|
|  2:  4.8010 -  3.8309 0.99   1315  148 0.0845 0.1129      5.4425      5.6546|
|  3:  3.8309 -  3.3526 0.99   1294  144 0.1030 0.1470      5.4686      5.8417|
|  4:  3.3526 -  3.0488 0.99   1285  142 0.1181 0.1602      5.4401      5.5934|
|  5:  3.0488 -  2.8318 0.99   1270  141 0.1321 0.1729      5.3407      5.5625|
|  6:  2.8318 -  2.6658 0.99   1285  141 0.1190 0.2021       5.229      5.5167|
|  7:  2.6658 -  2.5329 0.99   1264  144 0.1262 0.1644      5.1745      5.3523|
|  8:  2.5329 -  2.4231 0.98   1260  136 0.1136 0.1715      5.0726      5.3723|
|  9:  2.4231 -  2.3302 0.98   1259  141 0.1129 0.1786      5.0302      5.2995|
| 10:  2.3302 -  2.2501 1.00   1252  141 0.1115 0.1751      4.9714      5.2496|
| 11:  2.2501 -  2.1799 0.97   1258  137 0.1135 0.1780      4.9517      5.2333|
| 12:  2.1799 -  2.1178 0.98   1246  139 0.1124 0.1740      4.9005      5.2384|
| 13:  2.1178 -  2.0622 0.99   1251  139 0.1106 0.1769      4.8076      5.0893|
| 14:  2.0622 -  2.0120 0.81   1015  114 0.1023 0.1820        4.68       4.984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1646 -  4.8010  1376   152  0.93   9.93   0.97     0.94       8130.61|
|  2:  4.8010 -  3.8309  1315   148  0.95   8.31   1.00     0.99       9545.83|
|  3:  3.8309 -  3.3526  1294   144  0.94  11.07   1.02     1.01      10335.31|
|  4:  3.3526 -  3.0488  1285   142  0.92  13.47   1.00     0.98      10151.19|
|  5:  3.0488 -  2.8318  1270   141  0.90  15.81   1.00     0.97       8634.95|
|  6:  2.8318 -  2.6658  1285   141  0.90  16.44   0.99     0.96       7525.99|
|  7:  2.6658 -  2.5329  1264   144  0.90  16.05   0.99     0.97       6475.52|
|  8:  2.5329 -  2.4231  1260   136  0.91  15.07   0.99     0.96       5412.92|
|  9:  2.4231 -  2.3302  1259   141  0.91  15.30   1.00     0.95       5055.38|
| 10:  2.3302 -  2.2501  1252   141  0.90  15.79   0.99     0.95       4548.99|
| 11:  2.2501 -  2.1799  1258   137  0.90  16.50   0.99     0.95       4544.92|
| 12:  2.1799 -  2.1178  1246   139  0.91  15.76   1.00     0.99       4162.30|
| 13:  2.1178 -  2.0622  1251   139  0.90  16.21   0.98     0.96       3535.52|
| 14:  2.0622 -  2.0120  1015   114  0.92  14.61   0.96     0.92       2684.54|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2684.54 max =        10335.31 mean =      6574.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.58 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.255)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.59   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    84.59   16.66    None  None   None       |
|    Sol.    : 438    0      3.39    78.41   39.73    None  None   None       |
|    Mac.    : 2385   0      0.00    84.59   12.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   8.462:  800   |   5:    42.298 -  50.757:   93        |
|      1:     8.462 -  16.921: 1231   |   6:    50.757 -  59.216:   84        |
|      2:    16.921 -  25.380:  302   |   7:    59.216 -  67.675:   41        |
|      3:    25.380 -  33.839:  134   |   8:    67.675 -  76.134:   17        |
|      4:    33.839 -  42.298:  115   |   9:    76.134 -  84.593:    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)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.483 - 4.853
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 297
   mapped sites are within: 0.706 - 4.853

peak=    5.769 closest distance to " NH2 ARG A  56 " =    2.266
peak=    5.390 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.143 closest distance to " CG  PRO A  54 " =    1.333
peak=    4.875 closest distance to " O   HOH Z 232 " =    2.312
peak=    4.780 closest distance to " CB  SER A  63 " =    1.183
peak=    4.762 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.718 closest distance to " CB  ARG A  79 " =    1.337
peak=    4.666 closest distance to " CB  ARG A 190 " =    1.668
peak=    4.640 closest distance to " NE2 GLN A  11 " =    1.091
peak=    4.627 closest distance to " O   HOH Z 298 " =    2.005
peak=    4.554 closest distance to " O   HOH Z 126 " =    1.844
peak=    4.499 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.481 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.479 closest distance to " CG  PRO A 198 " =    1.263
peak=    4.472 closest distance to " CG  PRO A 213 " =    1.162
peak=    4.426 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.419 closest distance to " O   HOH Z  53 " =    2.490
peak=    4.370 closest distance to " CB  PRO A  54 " =    0.911
peak=    4.364 closest distance to " CZ  PHE A 218 " =    1.095
peak=    4.357 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.317 closest distance to " CA  TYR A  30 " =    0.963
peak=    4.204 closest distance to " O   HOH Z  15 " =    2.163
peak=    4.192 closest distance to " O   HOH Z 303 " =    2.162
peak=    4.175 closest distance to " CB  TYR A 169 " =    0.772
peak=    4.154 closest distance to " C   PRO A 198 " =    1.462
peak=    4.133 closest distance to " O   HOH Z 287 " =    2.143
peak=    4.077 closest distance to " O   HOH Z 142 " =    1.634
peak=    4.065 closest distance to " CB  ASN A 148 " =    1.505
peak=    4.058 closest distance to " O   HOH Z 158 " =    3.050
peak=    4.058 closest distance to " CB  GLU A 152 " =    1.144
peak=    4.052 closest distance to " CB  ASP A 124 " =    0.706
peak=    4.044 closest distance to " O   HOH Z 368 " =    2.152
peak=    4.042 closest distance to " NH1AARG A 145 " =    1.358
peak=    4.037 closest distance to " CE  LYS A  76 " =    0.855
peak=    4.034 closest distance to " O   HOH Z 189 " =    2.778
peak=    4.028 closest distance to " CA  ALA A  51 " =    0.936
peak=    4.008 closest distance to " CB  GLU A 277 " =    3.718
peak=    4.006 closest distance to " O   HOH Z 234 " =    3.808
peak=    4.001 closest distance to " O   HOH Z 427 " =    3.124
peak=    3.995 closest distance to " CA  ARG A 195 " =    1.232
peak=    3.985 closest distance to " CD1 LEU A 300 " =    1.194
peak=    3.982 closest distance to " O   HOH Z 180 " =    2.117
peak=    3.980 closest distance to " CB  TRP A 266 " =    1.000
peak=    3.965 closest distance to " ND2 ASN A 187 " =    1.437
peak=    3.962 closest distance to " CB  ASP A 140 " =    1.082
peak=    3.950 closest distance to " O   HOH Z 392 " =    3.007
peak=    3.943 closest distance to " O   HOH Z 423 " =    1.909
peak=    3.934 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.925 closest distance to " NH2 ARG A 156 " =    1.210
peak=    3.922 closest distance to " O   HOH Z 316 " =    3.153
peak=    3.906 closest distance to " CD  ARG A 159 " =    0.783
peak=    3.890 closest distance to " O   HOH Z  78 " =    2.176
peak=    3.867 closest distance to " O   HOH Z 313 " =    1.946
peak=    3.866 closest distance to " CB  GLU A 128 " =    0.969
peak=    3.864 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.852 closest distance to " O   HOH Z 250 " =    1.486
peak=    3.851 closest distance to " CG2 VAL A 257 " =    0.842
peak=    3.848 closest distance to " OD1 ASN A  69 " =    2.623
peak=    3.841 closest distance to " O   HOH Z 346 " =    1.651
peak=    3.839 closest distance to " O  BHOH Z 338 " =    2.411
peak=    3.831 closest distance to " O   HOH Z 126 " =    1.970
peak=    3.821 closest distance to " CD2 TRP A 179 " =    1.338
peak=    3.798 closest distance to " NZ  LYS A 117 " =    3.297
peak=    3.798 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.797 closest distance to " CB  GLU A  46 " =    0.963
peak=    3.788 closest distance to " O   HOH Z 265 " =    2.323
peak=    3.766 closest distance to " CA  ARG A  36 " =    1.102
peak=    3.764 closest distance to " CD2 LEU A 297 " =    0.874
peak=    3.740 closest distance to " CD  LYS A 166 " =    1.288
peak=    3.734 closest distance to " CB  VAL A 265 " =    1.273
peak=    3.732 closest distance to " CA  PRO A  54 " =    1.372
peak=    3.731 closest distance to " C   ILE A 106 " =    1.900
peak=    3.730 closest distance to " O   HOH Z  40 " =    1.815
peak=    3.727 closest distance to " CD1 LEU A  96 " =    0.718
peak=    3.726 closest distance to " CG  PRO A 243 " =    1.075
peak=    3.724 closest distance to " O   HOH Z 214 " =    2.178
peak=    3.715 closest distance to " O   HOH Z 133 " =    2.461
peak=    3.708 closest distance to " CB  ASN A 187 " =    1.437
peak=    3.695 closest distance to " O   HOH Z 403 " =    1.469
peak=    3.693 closest distance to " CB  ASN A 142 " =    1.043
peak=    3.685 closest distance to " O   HOH Z  61 " =    1.613
peak=    3.685 closest distance to " CG  LEU A 167 " =    1.256
peak=    3.684 closest distance to " O   HOH Z 285 " =    2.453
peak=    3.668 closest distance to " O   HOH Z 185 " =    1.865
peak=    3.667 closest distance to " CA  ASN A 215 " =    1.187
peak=    3.651 closest distance to " O   HOH Z 209 " =    2.317
peak=    3.651 closest distance to " O   HOH Z 203 " =    1.748
peak=    3.648 closest distance to " CB  TYR A 116 " =    0.776
peak=    3.639 closest distance to " O   HOH Z 280 " =    2.960
peak=    3.639 closest distance to " O   HOH Z 261 " =    1.887
peak=    3.635 closest distance to " O   HOH Z 406 " =    1.637
peak=    3.631 closest distance to " ND2 ASN A 249 " =    1.926
peak=    3.629 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.623 closest distance to " O   HOH Z   1 " =    2.196
peak=    3.621 closest distance to " O   HOH Z 291 " =    1.594
peak=    3.617 closest distance to " CD BLYS A 290 " =    0.979
peak=    3.611 closest distance to " CA  THR A 221 " =    0.987
peak=    3.605 closest distance to " O   HOH Z  21 " =    1.834
peak=    3.603 closest distance to " O   HOH Z 411 " =    3.825
peak=    3.598 closest distance to " CB  MET A  40 " =    0.793
peak=    3.593 closest distance to " O   SER A  87 " =    2.233
peak=    3.591 closest distance to " O   HOH Z 371 " =    3.157
peak=    3.589 closest distance to " CG2 ILE A 120 " =    1.123
peak=    3.585 closest distance to " NH2BARG A 145 " =    2.267
peak=    3.580 closest distance to " O   HOH Z 403 " =    1.612
peak=    3.570 closest distance to " O   HOH Z 147 " =    1.852
peak=    3.566 closest distance to " CA  MET A 105 " =    1.025
peak=    3.561 closest distance to " CD  ARG A  66 " =    2.431
peak=    3.560 closest distance to " CG2AVAL A  72 " =    1.764
peak=    3.553 closest distance to " CG1 VAL A 153 " =    0.987
peak=    3.549 closest distance to " CB  SER A   3 " =    1.332
peak=    3.549 closest distance to " N   ASN A 127 " =    1.283
peak=    3.547 closest distance to " CG2 THR A 221 " =    1.145
peak=    3.546 closest distance to " O   HOH Z  10 " =    1.786
peak=    3.542 closest distance to " O   HOH Z 368 " =    3.671
peak=    3.540 closest distance to " CA  VAL A 125 " =    1.185
peak=    3.540 closest distance to " CA  ALA A 158 " =    1.221
peak=    3.535 closest distance to " CB  SER A 212 " =    1.156
peak=    3.534 closest distance to " O   HOH Z 172 " =    3.621
peak=    3.529 closest distance to " ND2 ASN A 249 " =    0.838
peak=    3.523 closest distance to " O   HOH Z  43 " =    1.918
peak=    3.522 closest distance to " CB  TRP A 179 " =    1.512
peak=    3.520 closest distance to " CB  PRO A  90 " =    1.171
peak=    3.514 closest distance to " N   ARG A 156 " =    1.389
peak=    3.501 closest distance to " O   HOH Z 148 " =    3.360
peak=    3.499 closest distance to " O   ASN A  74 " =    1.508
peak=    3.495 closest distance to " O   HOH Z 305 " =    3.683
peak=    3.495 closest distance to " CZ3 TRP A 266 " =    1.148
peak=    3.489 closest distance to " CA  THR A 264 " =    0.895
peak=    3.485 closest distance to " CG  MET A 185 " =    1.172
peak=    3.485 closest distance to " CE1 PHE A 218 " =    1.008
peak=    3.485 closest distance to " O   HOH Z 383 " =    2.245
peak=    3.479 closest distance to " O   HOH Z 271 " =    2.734
peak=    3.476 closest distance to " O   HOH Z 353 " =    2.642
peak=    3.468 closest distance to " CG2 ILE A 234 " =    0.813
peak=    3.465 closest distance to " O   HOH Z 272 " =    1.841
peak=    3.460 closest distance to " CA  ALA A 154 " =    1.013
peak=    3.459 closest distance to " O   HOH Z  59 " =    2.322
peak=    3.454 closest distance to " CA  TYR A  30 " =    1.051
peak=    3.449 closest distance to " O   HOH Z 425 " =    1.937
peak=    3.441 closest distance to " O   HOH Z 359 " =    1.478
peak=    3.441 closest distance to " O   HOH Z 245 " =    1.248
peak=    3.439 closest distance to " OG BSER A 164 " =    2.367
peak=    3.436 closest distance to " O   THR A 220 " =    1.222
peak=    3.434 closest distance to " O   HOH Z 166 " =    3.882
peak=    3.431 closest distance to " CB  GLN A  89 " =    1.254
peak=    3.424 closest distance to " CA  SER A  87 " =    1.072
peak=    3.419 closest distance to " OD1 ASN A 217 " =    1.854
peak=    3.419 closest distance to " CA  ALA A 160 " =    0.947
peak=    3.414 closest distance to " O   THR A 251 " =    1.190
peak=    3.412 closest distance to " O   HOH Z 213 " =    2.004
peak=    3.410 closest distance to " O   HOH Z 426 " =    1.847
peak=    3.402 closest distance to " CB  ALA A 104 " =    0.736
peak=    3.401 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.399 closest distance to " NZ  LYS A  48 " =    1.328
peak=    3.396 closest distance to " CB  THR A  82 " =    1.440
peak=    3.395 closest distance to " CZ2 TRP A 179 " =    1.712
peak=    3.393 closest distance to " CA  ALA A 295 " =    1.060
peak=    3.388 closest distance to " CB  GLN A 103 " =    0.822
peak=    3.385 closest distance to " CB  ARG A 138 " =    0.977
peak=    3.382 closest distance to " O   HOH Z 273 " =    2.858
peak=    3.382 closest distance to " N   ASN A  39 " =    1.375
peak=    3.378 closest distance to " O   HOH Z  88 " =    3.782
peak=    3.377 closest distance to " CB  ASN A 110 " =    1.125
peak=    3.377 closest distance to " O   HOH Z 193 " =    1.772
peak=    3.375 closest distance to " O   HOH Z 294 " =    1.535
peak=    3.372 closest distance to " O   TYR A 116 " =    1.309
peak=    3.371 closest distance to " O   HOH Z 421 " =    2.114
peak=    3.369 closest distance to " O   HOH Z 128 " =    2.485
peak=    3.366 closest distance to " CB  THR A  31 " =    1.662
peak=    3.366 closest distance to " CB  SER A 141 " =    1.042
peak=    3.362 closest distance to " O   HOH Z 422 " =    2.732
peak=    3.362 closest distance to " CB  ALA A   9 " =    1.588
peak=    3.354 closest distance to " O   HOH Z 126 " =    1.641
peak=    3.351 closest distance to " CA  GLY A 241 " =    0.733
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.815
peak=    3.348 closest distance to " O   HOH Z 325 " =    2.400
peak=    3.345 closest distance to " CB  GLN A  88 " =    1.208
peak=    3.344 closest distance to " O   HOH Z 417 " =    3.241
peak=    3.344 closest distance to " CB  ILE A 120 " =    1.249
peak=    3.344 closest distance to " O   HOH Z 329 " =    4.063
peak=    3.341 closest distance to " CB  ALA A 248 " =    0.950
peak=    3.337 closest distance to " OG1 THR A 294 " =    2.489
peak=    3.330 closest distance to " CG2 ILE A  20 " =    1.268
peak=    3.328 closest distance to " CG1 ILE A  33 " =    1.217
peak=    3.327 closest distance to " CB  LEU A  83 " =    0.783
peak=    3.327 closest distance to " OG  SER A  22 " =    2.779
peak=    3.325 closest distance to " O   HOH Z 391 " =    2.917
peak=    3.319 closest distance to " CB  MET A  47 " =    0.971
peak=    3.314 closest distance to " OD2 ASP A 286 " =    2.897
peak=    3.313 closest distance to " NE  ARG A  79 " =    1.135
peak=    3.310 closest distance to " CZ  PHE A  38 " =    1.250
peak=    3.309 closest distance to " O   HOH Z 227 " =    1.771
peak=    3.306 closest distance to " CA  MET A  40 " =    1.185
peak=    3.306 closest distance to " CD  ARG A  66 " =    2.415
peak=    3.305 closest distance to " CB  ALA A  34 " =    0.976
peak=    3.304 closest distance to " NE2 HIS A 207 " =    1.248
peak=    3.300 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.299 closest distance to " CB  ALA A   1 " =    4.853
peak=    3.297 closest distance to " O   HOH Z 299 " =    4.494
peak=    3.283 closest distance to " O   HOH Z 344 " =    3.229
peak=    3.281 closest distance to " CA  ASN A 217 " =    1.228
peak=    3.278 closest distance to " CA  ALA A 233 " =    1.513
peak=    3.277 closest distance to " O   HOH Z 128 " =    2.191
peak=    3.276 closest distance to " O   HOH Z 234 " =    1.797
peak=    3.274 closest distance to " NH2AARG A 275 " =    3.622
peak=    3.274 closest distance to " O   HOH Z  80 " =    1.588
peak=    3.273 closest distance to " ND1 HIS A  81 " =    1.626
peak=    3.268 closest distance to " CB  ARG A 139 " =    0.964
peak=    3.266 closest distance to " O   HOH Z 132 " =    2.784
peak=    3.258 closest distance to " CB  ALA A 248 " =    1.298
peak=    3.256 closest distance to " O   HOH Z 365 " =    2.904
peak=    3.256 closest distance to " CB  HIS A 108 " =    0.787
peak=    3.256 closest distance to " O   ALA A 158 " =    1.259
peak=    3.254 closest distance to " NE2 GLN A  77 " =    3.370
peak=    3.254 closest distance to " CB  ALA A 291 " =    1.251
peak=    3.240 closest distance to " CB  ASP A 298 " =    1.198
peak=    3.240 closest distance to " O   HOH Z 248 " =    1.617
peak=    3.236 closest distance to " O   HOH Z 402 " =    1.373
peak=    3.234 closest distance to " CA  ALA A  21 " =    1.200
peak=    3.230 closest distance to " O   HOH Z  62 " =    2.154
peak=    3.229 closest distance to " CD  ARG A 219 " =    1.125
peak=    3.227 closest distance to " O   HOH Z  66 " =    2.222
peak=    3.223 closest distance to " O   HOH Z 285 " =    1.810
peak=    3.223 closest distance to " CD1 ILE A 106 " =    0.773
peak=    3.220 closest distance to " O   HOH Z 302 " =    2.042
peak=    3.214 closest distance to " O   HOH Z 171 " =    3.943
peak=    3.213 closest distance to " C   TYR A 214 " =    1.552
peak=    3.213 closest distance to " O   HOH Z 394 " =    4.026
peak=    3.212 closest distance to " CG  GLN A  11 " =    1.619
peak=    3.212 closest distance to " OG BSER A 134 " =    2.927
peak=    3.210 closest distance to " CG  GLU A  37 " =    0.857
peak=    3.205 closest distance to " CE  LYS A  48 " =    1.078
peak=    3.201 closest distance to " N   GLY A  98 " =    1.138
peak=    3.198 closest distance to " O   ASP A 191 " =    1.489
peak=    3.196 closest distance to " CA  GLU A  46 " =    0.786
peak=    3.196 closest distance to " CD  LYS A  76 " =    2.040
peak=    3.195 closest distance to " O   HOH Z   9 " =    2.075
peak=    3.194 closest distance to " CB  ALA A 227 " =    1.067
peak=    3.191 closest distance to " CB  PHE A 204 " =    0.916
peak=    3.191 closest distance to " O   HOH Z 425 " =    1.269
peak=    3.189 closest distance to " O   HOH Z  20 " =    1.625
peak=    3.189 closest distance to " CG  PHE A 204 " =    0.844
peak=    3.187 closest distance to " O   HOH Z 248 " =    1.659
peak=    3.182 closest distance to " O   HOH Z 258 " =    1.644
peak=    3.180 closest distance to " CB  LYS A 117 " =    1.190
peak=    3.176 closest distance to " CG2 VAL A 197 " =    1.110
peak=    3.173 closest distance to " O   HOH Z 419 " =    1.973
peak=    3.167 closest distance to " CA  TYR A 116 " =    1.383
peak=    3.165 closest distance to " CG BARG A 102 " =    1.859
peak=    3.161 closest distance to " O   HOH Z 290 " =    0.980
peak=    3.161 closest distance to " O   HOH Z 282 " =    1.885
peak=    3.159 closest distance to " O   HOH Z 132 " =    3.318
peak=    3.157 closest distance to " CB  LEU A  96 " =    1.305
peak=    3.154 closest distance to " O   HOH Z  97 " =    1.917
peak=    3.153 closest distance to " CG1 ILE A 151 " =    0.978
peak=    3.153 closest distance to " O   HOH Z  88 " =    3.132
peak=    3.150 closest distance to " CA  LEU A  83 " =    1.419
peak=    3.141 closest distance to " CG2 ILE A 151 " =    0.989
peak=    3.135 closest distance to " CB  ALA A 100 " =    1.147
peak=    3.131 closest distance to " ND2 ASN A 110 " =    1.554
peak=    3.127 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.124 closest distance to " O   HOH Z  88 " =    3.511
peak=    3.123 closest distance to " CA  ARG A 159 " =    1.273
peak=    3.123 closest distance to " CA  ILE A 234 " =    0.976
peak=    3.121 closest distance to " CG1 ILE A  49 " =    1.500
peak=    3.119 closest distance to " CA  ASP A 162 " =    1.077
peak=    3.117 closest distance to " CB  LYS A 193 " =    0.924
peak=    3.116 closest distance to " O   HOH Z 135 " =    1.692
peak=    3.113 closest distance to " O   HOH Z 409 " =    3.165
peak=    3.113 closest distance to " CB  THR A 235 " =    1.210
peak=    3.112 closest distance to " O   THR A 182 " =    1.405
peak=    3.110 closest distance to " O   TRP A 274 " =    1.740
peak=    3.107 closest distance to " CG BARG A 275 " =    1.397
peak=    3.106 closest distance to " CB  SER A 216 " =    0.853
peak=    3.102 closest distance to " CG  ARG A 159 " =    0.874
peak=    3.098 closest distance to " CB  ALA A 114 " =    1.049
peak=    3.098 closest distance to " O   SER A 164 " =    1.412
peak=    3.096 closest distance to " O   HOH Z 430 " =    1.514
peak=    3.095 closest distance to " O   HOH Z 167 " =    1.775
peak=    3.095 closest distance to " O   HOH Z 384 " =    2.987
peak=    3.094 closest distance to " CA  ARG A 102 " =    1.111
peak=    3.094 closest distance to " O   HOH Z 124 " =    1.723
peak=    3.093 closest distance to " N   ALA A 158 " =    1.494
peak=    3.090 closest distance to " O   HOH Z 188 " =    1.990
peak=    3.086 closest distance to " CB  GLU A 236 " =    1.121
peak=    3.081 closest distance to " CB  PHE A 204 " =    0.743
peak=    3.075 closest distance to " N   PHE A 130 " =    1.254
peak=    3.037 closest distance to " CB  ALA A  43 " =    0.828
peak=    3.018 closest distance to " OG BSER A  99 " =    2.284
peak=    3.018 closest distance to " CA  ASP A 191 " =    0.901
peak=    3.013 closest distance to " O   HOH Z 383 " =    1.607

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.920 - 5.785
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 211
   mapped sites are within: 0.920 - 5.785

peak=   -4.644 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -4.625 closest distance to " CD  GLN A  58 " =    0.920
peak=   -4.515 closest distance to " CB  PRO A 243 " =    2.644
peak=   -4.494 closest distance to " CD  ARG A  14 " =    3.476
peak=   -4.472 closest distance to " CD  ARG A 156 " =    2.103
peak=   -4.390 closest distance to " O   HOH Z 266 " =    5.397
peak=   -4.383 closest distance to " O   HOH Z 231 " =    2.299
peak=   -4.319 closest distance to " O   VAL A  67 " =    2.720
peak=   -4.278 closest distance to " O   HOH Z  73 " =    2.232
peak=   -4.251 closest distance to " O   HOH Z 377 " =    2.050
peak=   -4.181 closest distance to " N   ALA A  43 " =    2.685
peak=   -4.150 closest distance to " C   HIS A 108 " =    1.093
peak=   -4.104 closest distance to " CG  GLN A 223 " =    2.088
peak=   -4.081 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -4.072 closest distance to " OG BSER A 134 " =    1.329
peak=   -4.036 closest distance to " O   PRO A 198 " =    1.325
peak=   -4.008 closest distance to " O   HOH Z  10 " =    1.536
peak=   -3.988 closest distance to " OG  SER A  97 " =    2.297
peak=   -3.972 closest distance to " CG1 VAL A 250 " =    2.679
peak=   -3.962 closest distance to " CE2 PHE A  61 " =    2.678
peak=   -3.948 closest distance to " CD1 PHE A  59 " =    1.962
peak=   -3.940 closest distance to " CG1 VAL A 112 " =    2.885
peak=   -3.933 closest distance to " O   HOH Z 198 " =    2.147
peak=   -3.923 closest distance to " OD1 ASN A 148 " =    1.502
peak=   -3.909 closest distance to " CB  ALA A 161 " =    2.625
peak=   -3.896 closest distance to " CE2 TYR A  30 " =    2.748
peak=   -3.893 closest distance to " CD2 TYR A 293 " =    2.058
peak=   -3.888 closest distance to " O   HOH Z 196 " =    1.997
peak=   -3.828 closest distance to " O   HOH Z 290 " =    1.253
peak=   -3.795 closest distance to " OXT GLY A 302 " =    3.008
peak=   -3.794 closest distance to " CA  VAL A  67 " =    2.940
peak=   -3.754 closest distance to " NH2AARG A 275 " =    5.432
peak=   -3.751 closest distance to " CB  PHE A 192 " =    2.087
peak=   -3.746 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.725 closest distance to " CA  GLY A 241 " =    3.265
peak=   -3.710 closest distance to " O   HOH Z 372 " =    2.382
peak=   -3.708 closest distance to " O   HOH Z 394 " =    1.525
peak=   -3.702 closest distance to " O   HOH Z 389 " =    1.983
peak=   -3.688 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.679 closest distance to " O   HOH Z 114 " =    3.172
peak=   -3.675 closest distance to " CB  ASN A  39 " =    2.342
peak=   -3.668 closest distance to " CB  ALA A  43 " =    2.666
peak=   -3.668 closest distance to " O   HOH Z  51 " =    1.703
peak=   -3.658 closest distance to " CG  ARG A 269 " =    2.541
peak=   -3.648 closest distance to " NE2 GLN A 194 " =    1.851
peak=   -3.640 closest distance to " O   HOH Z  60 " =    1.980
peak=   -3.609 closest distance to " CE3 TRP A 150 " =    2.198
peak=   -3.608 closest distance to " CB  ALA A 291 " =    2.335
peak=   -3.605 closest distance to " CG2 ILE A  49 " =    2.771
peak=   -3.605 closest distance to " CG2 ILE A 263 " =    2.363
peak=   -3.602 closest distance to " CE  MET A 105 " =    2.474
peak=   -3.599 closest distance to " NE2 GLN A  88 " =    1.916
peak=   -3.598 closest distance to " O   HOH Z  43 " =    1.596
peak=   -3.592 closest distance to " ND2 ASN A 249 " =    2.445
peak=   -3.591 closest distance to " O   PHE A 218 " =    1.492
peak=   -3.569 closest distance to " ND2 ASN A  45 " =    1.910
peak=   -3.563 closest distance to " ND2 ASN A  45 " =    1.140
peak=   -3.561 closest distance to " CA  GLY A 203 " =    2.416
peak=   -3.554 closest distance to " CD1 LEU A 101 " =    2.450
peak=   -3.551 closest distance to " CB  ALA A 291 " =    2.369
peak=   -3.544 closest distance to " CD1 ILE A 151 " =    2.457
peak=   -3.532 closest distance to " O   PRO A 163 " =    2.157
peak=   -3.526 closest distance to " O   HOH Z   6 " =    1.504
peak=   -3.521 closest distance to " O   HOH Z 128 " =    2.664
peak=   -3.516 closest distance to " ND2BASN A 224 " =    1.784
peak=   -3.514 closest distance to " O   HOH Z 211 " =    1.567
peak=   -3.511 closest distance to " OD1 ASP A 171 " =    1.642
peak=   -3.500 closest distance to " CG1 VAL A 125 " =    1.971
peak=   -3.489 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.478 closest distance to " O   HOH Z 407 " =    3.254
peak=   -3.477 closest distance to " O   HOH Z 353 " =    2.154
peak=   -3.477 closest distance to " N   THR A  52 " =    1.674
peak=   -3.475 closest distance to " O   HOH Z  71 " =    1.897
peak=   -3.474 closest distance to " O   HOH Z 348 " =    2.223
peak=   -3.472 closest distance to " O   HOH Z 351 " =    1.471
peak=   -3.468 closest distance to " O   HOH Z  38 " =    1.425
peak=   -3.461 closest distance to " O   HOH Z 435 " =    2.840
peak=   -3.457 closest distance to " N   ALA A 248 " =    1.668
peak=   -3.454 closest distance to " O   HOH Z 166 " =    1.832
peak=   -3.451 closest distance to " CE BMET A  47 " =    1.711
peak=   -3.443 closest distance to " C   ASN A 285 " =    2.468
peak=   -3.442 closest distance to " O   HOH Z  52 " =    1.444
peak=   -3.440 closest distance to " CA  GLY A 241 " =    2.334
peak=   -3.430 closest distance to " CG  HIS A  86 " =    1.092
peak=   -3.427 closest distance to " O   ALA A  10 " =    1.682
peak=   -3.425 closest distance to " O   HOH Z 426 " =    1.618
peak=   -3.424 closest distance to " NH2 ARG A  79 " =    1.494
peak=   -3.424 closest distance to " C   LEU A 143 " =    1.135
peak=   -3.423 closest distance to " NH2 ARG A 159 " =    2.387
peak=   -3.421 closest distance to " N   THR A 157 " =    1.625
peak=   -3.417 closest distance to " CG  PHE A 283 " =    2.674
peak=   -3.413 closest distance to " O   HOH Z 295 " =    1.572
peak=   -3.413 closest distance to " CG  ARG A  66 " =    2.324
peak=   -3.409 closest distance to " O   HOH Z 357 " =    2.123
peak=   -3.407 closest distance to " C   ASN A 187 " =    1.944
peak=   -3.395 closest distance to " O   HOH Z   6 " =    2.322
peak=   -3.394 closest distance to " CG  GLU A 277 " =    1.114
peak=   -3.393 closest distance to " ND2 ASN A  60 " =    1.294
peak=   -3.389 closest distance to " C   SER A 206 " =    1.457
peak=   -3.385 closest distance to " CG  GLN A  11 " =    1.776
peak=   -3.385 closest distance to " OD2 ASP A 171 " =    1.851
peak=   -3.375 closest distance to " CB  TRP A  85 " =    2.455
peak=   -3.372 closest distance to " O   HOH Z 311 " =    3.806
peak=   -3.362 closest distance to " O   HOH Z 393 " =    1.373
peak=   -3.357 closest distance to " O   HOH Z 396 " =    1.839
peak=   -3.347 closest distance to " CD  ARG A 195 " =    5.119
peak=   -3.337 closest distance to " O   HOH Z 243 " =    2.015
peak=   -3.336 closest distance to " O   HOH Z 193 " =    1.684
peak=   -3.335 closest distance to " O   HOH Z 313 " =    1.969
peak=   -3.334 closest distance to " CG  MET A 105 " =    0.977
peak=   -3.330 closest distance to " O   HOH Z  37 " =    1.857
peak=   -3.326 closest distance to " CG  LYS A 193 " =    2.626
peak=   -3.321 closest distance to " CG2 VAL A 189 " =    2.214
peak=   -3.320 closest distance to " O   GLY A 211 " =    1.408
peak=   -3.317 closest distance to " NE2 GLN A 103 " =    1.750
peak=   -3.312 closest distance to " O   HOH Z 134 " =    2.897
peak=   -3.300 closest distance to " O   HOH Z 216 " =    1.651
peak=   -3.299 closest distance to " CD2 PHE A  61 " =    2.109
peak=   -3.279 closest distance to " O   HOH Z 322 " =    1.624
peak=   -3.278 closest distance to " O   HOH Z 275 " =    1.859
peak=   -3.278 closest distance to " O   HOH Z  44 " =    2.308
peak=   -3.277 closest distance to " CB  PRO A  54 " =    2.531
peak=   -3.277 closest distance to " O   HOH Z 102 " =    1.567
peak=   -3.275 closest distance to " O   HOH Z 111 " =    1.524
peak=   -3.272 closest distance to " O   HOH Z 106 " =    1.866
peak=   -3.271 closest distance to " N   THR A 264 " =    1.309
peak=   -3.271 closest distance to " CB  ASP A 286 " =    2.118
peak=   -3.270 closest distance to " OG  SER A  62 " =    1.802
peak=   -3.267 closest distance to " SG ACYS A 201 " =    1.944
peak=   -3.266 closest distance to " CG  LEU A  83 " =    1.993
peak=   -3.265 closest distance to " O   HOH Z 198 " =    1.506
peak=   -3.262 closest distance to " C   GLY A  17 " =    1.163
peak=   -3.259 closest distance to " O   HOH Z 265 " =    2.367
peak=   -3.258 closest distance to " O   SER A 135 " =    1.500
peak=   -3.255 closest distance to " CD1 LEU A  83 " =    2.633
peak=   -3.254 closest distance to " ND2 ASN A  69 " =    1.794
peak=   -3.252 closest distance to " CD  ARG A 139 " =    1.582
peak=   -3.250 closest distance to " O   HOH Z 253 " =    4.050
peak=   -3.245 closest distance to " C   MET A 188 " =    1.387
peak=   -3.245 closest distance to " CG  PRO A 243 " =    1.838
peak=   -3.241 closest distance to " CD1 ILE A 239 " =    2.104
peak=   -3.241 closest distance to " C   ALA A 158 " =    1.319
peak=   -3.239 closest distance to " CD2 PHE A 225 " =    1.125
peak=   -3.238 closest distance to " O   HOH Z 275 " =    1.569
peak=   -3.235 closest distance to " O   SER A 210 " =    1.991
peak=   -3.235 closest distance to " O   HOH Z 232 " =    1.691
peak=   -3.233 closest distance to " CD1 LEU A 228 " =    2.365
peak=   -3.228 closest distance to " CA  GLY A 241 " =    2.888
peak=   -3.227 closest distance to " ND2 ASN A  60 " =    4.105
peak=   -3.227 closest distance to " O   HOH Z 174 " =    3.049
peak=   -3.227 closest distance to " CG1 VAL A 112 " =    2.811
peak=   -3.224 closest distance to " OG BSER A 134 " =    1.854
peak=   -3.223 closest distance to " O   HOH Z 234 " =    4.397
peak=   -3.219 closest distance to " O   HOH Z 421 " =    3.124
peak=   -3.218 closest distance to " O   ALA A  34 " =    2.129
peak=   -3.215 closest distance to " CD2 TYR A 247 " =    2.375
peak=   -3.215 closest distance to " O   GLN A 240 " =    2.516
peak=   -3.213 closest distance to " CG1AVAL A  41 " =    2.837
peak=   -3.212 closest distance to " CE3 TRP A 274 " =    2.470
peak=   -3.212 closest distance to " CA  GLY A 133 " =    2.306
peak=   -3.210 closest distance to " O   HOH Z  70 " =    2.222
peak=   -3.205 closest distance to " CG  ASN A 252 " =    1.620
peak=   -3.205 closest distance to " O   SER A  95 " =    1.674
peak=   -3.204 closest distance to " O   HOH Z 322 " =    1.315
peak=   -3.204 closest distance to " O   HOH Z 350 " =    2.058
peak=   -3.202 closest distance to " O   HOH Z 266 " =    5.211
peak=   -3.201 closest distance to " OE1 GLN A  88 " =    1.175
peak=   -3.201 closest distance to " O   VAL A 189 " =    1.597
peak=   -3.198 closest distance to " CB  PHE A  16 " =    2.579
peak=   -3.196 closest distance to " O   HOH Z 298 " =    2.528
peak=   -3.195 closest distance to " O   HOH Z 409 " =    4.679
peak=   -3.192 closest distance to " O   HOH Z 264 " =    1.766
peak=   -3.191 closest distance to " CB  ALA A 248 " =    2.442
peak=   -3.191 closest distance to " CB  TYR A  15 " =    2.238
peak=   -3.191 closest distance to " O   HOH Z 177 " =    1.810
peak=   -3.188 closest distance to " OD2 ASP A 191 " =    1.545
peak=   -3.185 closest distance to " OH  TYR A 247 " =    1.817
peak=   -3.183 closest distance to " CG1 VAL A 197 " =    2.249
peak=   -3.176 closest distance to " CD1 LEU A   5 " =    2.577
peak=   -3.176 closest distance to " CD  ARG A  79 " =    1.161
peak=   -3.173 closest distance to " CE2 PHE A 218 " =    2.396
peak=   -3.168 closest distance to " CE3 TRP A  70 " =    1.862
peak=   -3.167 closest distance to " CA  SER A 135 " =    1.300
peak=   -3.163 closest distance to " CG  GLU A  53 " =    1.508
peak=   -3.161 closest distance to " O   TRP A  70 " =    1.438
peak=   -3.159 closest distance to " O   HOH Z 278 " =    1.659
peak=   -3.151 closest distance to " OD1 ASN A 187 " =    1.579
peak=   -3.150 closest distance to " N   ALA A 226 " =    2.134
peak=   -3.145 closest distance to " CD  GLU A 236 " =    1.107
peak=   -3.143 closest distance to " CG  PRO A 163 " =    2.312
peak=   -3.135 closest distance to " ND2 ASN A 249 " =    2.203
peak=   -3.133 closest distance to " O   ILE A 106 " =    1.937
peak=   -3.131 closest distance to " O   ALA A  34 " =    2.559
peak=   -3.129 closest distance to " CG  TRP A 266 " =    1.794
peak=   -3.127 closest distance to " SD  MET A 188 " =    2.240
peak=   -3.126 closest distance to " O   HOH Z 114 " =    1.515
peak=   -3.124 closest distance to " O   HOH Z 189 " =    1.923
peak=   -3.121 closest distance to " O   HOH Z 191 " =    5.785
peak=   -3.113 closest distance to " N   ASP A 171 " =    2.309
peak=   -3.112 closest distance to " CD2 LEU A 300 " =    2.680
peak=   -3.111 closest distance to " CG1BVAL A  41 " =    2.852
peak=   -3.109 closest distance to " O   HOH Z 166 " =    1.656
peak=   -3.102 closest distance to " CD2 PHE A  59 " =    2.531
peak=   -3.101 closest distance to " O   PRO A 198 " =    1.412
peak=   -3.100 closest distance to " O   HOH Z 281 " =    2.645
peak=   -3.095 closest distance to " N   SER A 276 " =    1.358
peak=   -3.095 closest distance to " CD1 TRP A  70 " =    1.108
peak=   -3.088 closest distance to " N   SER A   3 " =    2.131
peak=   -3.079 closest distance to " NH2BARG A 275 " =    1.955
peak=   -3.076 closest distance to " NH2 ARG A  66 " =    2.272
peak=   -3.026 closest distance to " CD1 ILE A 199 " =    2.555

================= 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    :  0.3317 0.3195   6.051751e+00   6.030873e+00
   1_bss:  0.3192 0.3087   6.028769e+00   6.004277e+00
   1_xyz:  0.1801 0.2006   5.509392e+00   5.599738e+00
   1_adp:  0.1656 0.2049   5.453903e+00   5.624398e+00
   1_occ:  0.1651 0.2047   5.452270e+00   5.623727e+00
   2_bss:  0.1635 0.2026   5.447738e+00   5.619582e+00
   2_xyz:  0.1333 0.1694   5.266913e+00   5.459496e+00
   2_adp:  0.1266 0.1652   5.227026e+00   5.430636e+00
   2_occ:  0.1265 0.1650   5.226435e+00   5.430404e+00
   3_bss:  0.1264 0.1651   5.225863e+00   5.429149e+00
   3_xyz:  0.1138 0.1590   5.155827e+00   5.392284e+00
   3_adp:  0.1125 0.1577   5.145485e+00   5.384614e+00
   3_occ:  0.1124 0.1577   5.145494e+00   5.384967e+00
   4_bss:  0.1123 0.1576   5.145508e+00   5.385287e+00
   4_xyz:  0.1132 0.1591   5.155096e+00   5.395855e+00
   4_adp:  0.1128 0.1598   5.154920e+00   5.399721e+00
   4_occ:  0.1127 0.1598   5.155048e+00   5.400131e+00
   5_bss:  0.1127 0.1597   5.154982e+00   5.400093e+00
   5_xyz:  0.1105 0.1601   5.147565e+00   5.401952e+00
   5_adp:  0.1106 0.1609   5.148464e+00   5.404876e+00
   5_occ:  0.1105 0.1609   5.148522e+00   5.405032e+00
   5_bss:  0.1104 0.1607   5.148646e+00   5.405124e+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:  0.318  65.461  -2.021  -2.177   2.261  -0.000   0.000   0.000
   1_xyz:  0.318  65.461  -2.021  -2.177   2.261  -0.000   0.000   0.000
   1_adp:  0.318  65.461  -2.021  -2.177   2.261  -0.000   0.000   0.000
   1_occ:  0.318  65.461  -2.021  -2.177   2.261  -0.000   0.000   0.000
   2_bss:  0.336  70.999  -2.620  -2.514  -0.320  -0.000  -0.000  -0.000
   2_xyz:  0.336  70.999  -2.620  -2.514  -0.320  -0.000  -0.000  -0.000
   2_adp:  0.336  70.999  -2.620  -2.514  -0.320  -0.000  -0.000  -0.000
   2_occ:  0.336  70.999  -2.620  -2.514  -0.320  -0.000  -0.000  -0.000
   3_bss:  0.336  70.999  -2.540  -2.359  -0.669  -0.000  -0.000  -0.000
   3_xyz:  0.336  70.999  -2.540  -2.359  -0.669  -0.000  -0.000  -0.000
   3_adp:  0.336  70.999  -2.540  -2.359  -0.669  -0.000  -0.000  -0.000
   3_occ:  0.336  70.999  -2.540  -2.359  -0.669  -0.000  -0.000  -0.000
   4_bss:  0.325  62.034  -2.277  -2.102  -0.608  -0.000  -0.000  -0.000
   4_xyz:  0.325  62.034  -2.277  -2.102  -0.608  -0.000  -0.000  -0.000
   4_adp:  0.325  62.034  -2.277  -2.102  -0.608  -0.000  -0.000  -0.000
   4_occ:  0.325  62.034  -2.277  -2.102  -0.608  -0.000  -0.000  -0.000
   5_bss:  0.320  62.034  -2.076  -1.892  -0.453  -0.000  -0.000  -0.000
   5_xyz:  0.320  62.034  -2.076  -1.892  -0.453  -0.000  -0.000  -0.000
   5_adp:  0.320  62.034  -2.076  -1.892  -0.453  -0.000  -0.000  -0.000
   5_occ:  0.320  62.034  -2.076  -1.892  -0.453  -0.000  -0.000  -0.000
   5_bss:  0.320  62.037  -1.772  -1.595  -0.192  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.240 0.7247  0.8756    28784.831
   1_bss:  32.196 0.7350  0.8740    26372.189
   1_xyz:  18.566 0.8765  0.9955    10064.129
   1_adp:  19.216 0.8699  0.9919    10512.837
   1_occ:  19.200 0.8700  0.9916    10476.455
   2_bss:  19.001 0.8721  0.9532    10396.135
   2_xyz:  15.503 0.9026  0.9679     7319.452
   2_adp:  14.814 0.9085  0.9627     6890.336
   2_occ:  14.807 0.9086  0.9626     6884.281
   3_bss:  14.787 0.9088  0.9612     6865.844
   3_xyz:  14.034 0.9148  0.9663     6401.976
   3_adp:  13.842 0.9165  0.9609     6307.444
   3_occ:  13.847 0.9165  0.9608     6309.395
   4_bss:  13.853 0.9164  0.9674     6310.051
   4_xyz:  14.016 0.9152  0.9659     6456.662
   4_adp:  14.099 0.9146  0.9575     6495.626
   4_occ:  14.105 0.9145  0.9574     6499.933
   5_bss:  14.105 0.9145  0.9638     6498.630
   5_xyz:  14.146 0.9142  0.9641     6548.340
   5_adp:  14.194 0.9138  0.9552     6571.204
   5_occ:  14.199 0.9138  0.9551     6572.633
   5_bss:  14.202 0.9138  0.9650     6574.680
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6201e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6201e-01
   1_xyz:   1.104  0.009  0.072 15.216  0.004  4.115   6.8774e-02
   1_adp:   1.104  0.009  0.072 15.216  0.004  4.115   6.8774e-02
   1_occ:   1.104  0.009  0.072 15.216  0.004  4.115   6.8774e-02
   2_bss:   1.104  0.009  0.072 15.216  0.004  4.115   6.8774e-02
   2_xyz:   0.963  0.007  0.073 14.746  0.003  4.128   5.4840e-02
   2_adp:   0.963  0.007  0.073 14.746  0.003  4.128   5.4840e-02
   2_occ:   0.963  0.007  0.073 14.746  0.003  4.128   5.4840e-02
   3_bss:   0.963  0.007  0.073 14.746  0.003  4.128   5.4840e-02
   3_xyz:   1.103  0.011  0.083 15.002  0.004  4.116   7.5564e-02
   3_adp:   1.103  0.011  0.083 15.002  0.004  4.116   7.5564e-02
   3_occ:   1.103  0.011  0.083 15.002  0.004  4.116   7.5564e-02
   4_bss:   1.103  0.011  0.083 15.002  0.004  4.116   7.5564e-02
   4_xyz:   1.016  0.009  0.078 14.786  0.004  4.117   6.4540e-02
   4_adp:   1.016  0.009  0.078 14.786  0.004  4.117   6.4540e-02
   4_occ:   1.016  0.009  0.078 14.786  0.004  4.117   6.4540e-02
   5_bss:   1.016  0.009  0.078 14.786  0.004  4.117   6.4540e-02
   5_xyz:   1.077  0.010  0.083 14.874  0.004  4.119   7.2019e-02
   5_adp:   1.077  0.010  0.083 14.874  0.004  4.119   7.2019e-02
   5_occ:   1.077  0.010  0.083 14.874  0.004  4.119   7.2019e-02
   5_bss:   1.077  0.010  0.083 14.874  0.004  4.119   7.2019e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4380e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4380e-01
   1_xyz:   8.645  0.049  0.229 82.967  0.039  2.359   6.2653e-02
   1_adp:   8.645  0.049  0.229 82.967  0.039  2.359   6.2653e-02
   1_occ:   8.645  0.049  0.229 82.967  0.039  2.359   6.2653e-02
   2_bss:   8.645  0.049  0.229 82.967  0.039  2.359   6.2653e-02
   2_xyz:   6.695  0.033  0.222 82.368  0.040  2.394   3.6946e-02
   2_adp:   6.695  0.033  0.222 82.368  0.040  2.394   3.6946e-02
   2_occ:   6.695  0.033  0.222 82.368  0.040  2.394   3.6946e-02
   3_bss:   6.695  0.033  0.222 82.368  0.040  2.394   3.6946e-02
   3_xyz:   7.695  0.051  0.289 83.097  0.038  2.349   5.6428e-02
   3_adp:   7.695  0.051  0.289 83.097  0.038  2.349   5.6428e-02
   3_occ:   7.695  0.051  0.289 83.097  0.038  2.349   5.6428e-02
   4_bss:   7.695  0.051  0.289 83.097  0.038  2.349   5.6428e-02
   4_xyz:   7.052  0.048  0.248 81.807  0.036  2.388   4.4167e-02
   4_adp:   7.052  0.048  0.248 81.807  0.036  2.388   4.4167e-02
   4_occ:   7.052  0.048  0.248 81.807  0.036  2.388   4.4167e-02
   5_bss:   7.052  0.048  0.248 81.807  0.036  2.388   4.4167e-02
   5_xyz:   7.351  0.051  0.273 82.437  0.036  2.349   5.2490e-02
   5_adp:   7.351  0.051  0.273 82.437  0.036  2.349   5.2490e-02
   5_occ:   7.351  0.051  0.273 82.437  0.036  2.349   5.2490e-02
   5_bss:   7.351  0.051  0.273 82.437  0.036  2.349   5.2490e-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:  65.33   0.00  16.80  57.98   0.00  12.88  65.33   6.03  38.10
   1_occ:  65.33   0.00  16.80  57.98   0.00  12.88  65.33   6.03  38.10
   2_bss:  65.33   0.00  16.80  57.98   0.00  12.88  65.33   6.03  38.10
   2_xyz:  65.33   0.00  16.80  57.98   0.00  12.88  65.33   6.03  38.10
   2_adp:  77.11   1.12  17.04  77.11   1.12  12.92  72.05   6.10  39.51
   2_occ:  77.11   1.12  17.04  77.11   1.12  12.92  72.05   6.10  39.51
   3_bss:  77.11   1.12  17.04  77.11   1.12  12.92  72.05   6.10  39.51
   3_xyz:  77.11   1.12  17.04  77.11   1.12  12.92  72.05   6.10  39.51
   3_adp:  79.37   0.91  16.85  79.37   0.91  12.74  74.21   1.89  39.22
   3_occ:  79.37   0.91  16.85  79.37   0.91  12.74  74.21   1.89  39.22
   4_bss:  79.37   0.91  16.85  79.37   0.91  12.74  74.21   1.89  39.22
   4_xyz:  79.37   0.91  16.85  79.37   0.91  12.74  74.21   1.89  39.22
   4_adp:  84.10   0.24  16.83  84.10   0.24  12.64  77.92   1.76  39.69
   4_occ:  84.10   0.24  16.83  84.10   0.24  12.64  77.92   1.76  39.69
   5_bss:  84.10   0.24  16.83  84.10   0.24  12.64  77.92   1.76  39.69
   5_xyz:  84.10   0.24  16.83  84.10   0.24  12.64  77.92   1.76  39.69
   5_adp:  84.59   0.00  16.66  84.59   0.00  12.42  78.41   3.39  39.73
   5_occ:  84.59   0.00  16.66  84.59   0.00  12.42  78.41   3.39  39.73
   5_bss:  84.59   0.00  16.66  84.59   0.00  12.42  78.41   3.39  39.73
------------------------------------------------------------------------
 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:    0.985    0.025    0.310
   1_adp:    0.985    0.025    0.310
   1_occ:    0.985    0.025    0.310
   2_bss:    0.985    0.025    0.310
   2_xyz:    0.906    0.006    0.350
   2_adp:    0.906    0.006    0.350
   2_occ:    0.906    0.006    0.350
   3_bss:    0.906    0.006    0.350
   3_xyz:    1.013    0.017    0.388
   3_adp:    1.013    0.017    0.388
   3_occ:    1.013    0.017    0.388
   4_bss:    1.013    0.017    0.388
   4_xyz:    1.236    0.033    0.395
   4_adp:    1.236    0.033    0.395
   4_occ:    1.236    0.033    0.395
   5_bss:    1.236    0.033    0.395
   5_xyz:    1.272    0.011    0.403
   5_adp:    1.272    0.011    0.403
   5_occ:    1.272    0.011    0.403
   5_bss:    1.272    0.011    0.403
------------------------------------------------------------------------

CPU time actual refinement: 318.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/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_921/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_921/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.94 
  Macro-tasks:
    bulk solvent and scale       = 38.51  
    individual site refinement   = 130.02 
    weights calculation          = 28.91  
    collect and process          = 6.62   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 204.16 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 99.57  
    alpha_beta                      = 8.25   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 108.67 
    fmodel                         = 6.55   
    r_factors                      = 0.19   
    phase_errors                   = 11.32  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 237.14 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.517 micro seconds
Total CPU time: 5.52 minutes
from_scatterers_fft:    644 calls, 99.21 s
gradients_fft:          589 calls, 95.23 s

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

# Date 2008-01-16 Time 05:58:57 PST -0800 (1200491937.54 s)
Start R-work = 0.3317, R-free = 0.3195 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1766 (no bulk solvent and anisotropic scale)

Start R-work = 0.3192, R-free = 0.3087
Final R-work = 0.1104, R-free = 0.1607