# Date 2008-01-16 Time 05:29:56 PST -0800 (1200490196.40 s)
#phil __OFF__

Command line arguments: "../756.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23518
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 756

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.2261, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.9731
Completeness in resolution range: 0.94264
Completeness with d_max=infinity: 0.939836

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9731

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.9731
Completeness in resolution range: 0.94264
Completeness with d_max=infinity: 0.939836

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2229 [2181/2206]  1961   220  10.1%
  bin  2:  4.2229 -  3.3640 [2100/2120]  1893   207   9.9%
  bin  3:  3.3640 -  2.9423 [2078/2097]  1871   207  10.0%
  bin  4:  2.9423 -  2.6749 [2042/2072]  1834   208  10.2%
  bin  5:  2.6749 -  2.4841 [2038/2057]  1841   197   9.7%
  bin  6:  2.4841 -  2.3382 [2035/2060]  1828   207  10.2%
  bin  7:  2.3382 -  2.2215 [2019/2047]  1812   207  10.3%
  bin  8:  2.2215 -  2.1251 [1998/2034]  1798   200  10.0%
  bin  9:  2.1251 -  2.0435 [2020/2062]  1823   197   9.8%
  bin 10:  2.0435 -  1.9731 [1078/2026]   969   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/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: 33
        2.42 -     3.04: 2178
        3.04 -     3.66: 4693
        3.66 -     4.28: 9000
        4.28 -     4.90: 12345
  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  42 " - " O   HOH Z 183 "  2.016 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.064 3.040 -x+1,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.092 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28244 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_756/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.22605 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: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3986   r_free= 0.3942   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.197041                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.3245 0.2996      6.4693      6.3747|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.3208 0.3152      6.6412      6.5738|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.3444 0.3247      6.5207      6.5244|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.3855 0.4202      6.4186      6.4815|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.4208 0.3585      6.2622      6.2142|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.4176 0.4356      6.1606      6.1259|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.4228 0.4042      6.1631      6.1034|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.4531 0.4678       6.114      6.1483|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.4481 0.4439      6.0651      6.0689|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.4628 0.4568      6.0495      5.9999|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.4641 0.4972      5.9988      6.0355|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.4639 0.4539       5.917      5.9412|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.4607 0.4630      5.8264      5.7676|
| 14:  2.0223 -  1.9731 0.37    488   57 0.5025 0.5149      5.8743      5.8449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7104  1416   156  0.79  26.08   0.85     0.83      44362.55|
|  2:  4.7104 -  3.7577  1370   155  0.80  25.94   0.94     0.90      64047.33|
|  3:  3.7577 -  3.2883  1332   145  0.73  32.92   0.97     0.90      69671.91|
|  4:  3.2883 -  2.9902  1340   150  0.67  38.44   0.94     0.85      64705.38|
|  5:  2.9902 -  2.7773  1318   149  0.60  43.73   0.93     0.80      51935.47|
|  6:  2.7773 -  2.6144  1318   144  0.58  45.72   0.94     0.76      46350.77|
|  7:  2.6144 -  2.4841  1306   140  0.56  47.68   0.96     0.73      45055.25|
|  8:  2.4841 -  2.3764  1297   151  0.52  50.38   0.94     0.71      42883.33|
|  9:  2.3764 -  2.2852  1290   142  0.52  50.53   0.97     0.72      40037.07|
| 10:  2.2852 -  2.2066  1297   148  0.52  50.50   0.97     0.72      36001.46|
| 11:  2.2066 -  2.1378  1309   142  0.50  52.48   0.97     0.73      36618.64|
| 12:  2.1378 -  2.0769  1275   141  0.47  54.83   0.96     0.70      35083.61|
| 13:  2.0769 -  2.0223  1274   139  0.42  58.20   0.98     0.67      31796.87|
| 14:  2.0223 -  1.9731   488    57  0.47  54.99   0.97     0.64      25417.13|
|alpha:            min =        0.64 max =            0.90 mean =         0.77|
|beta:             min =    25417.13 max =        69671.91 mean =     46397.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           90.00 mean =        44.45|
|phase err.(test): min =        0.00 max =           89.93 mean =        44.65|
|-----------------------------------------------------------------------------|

============================== 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 = 7.287263              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.071   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.353816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.665   (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:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       28 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      191 |
| 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:     1864 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2829 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4614 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4386 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5623 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6722 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.228 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3986   r_free= 0.3942   ksol= 0.00   Bsol= 0.00   scale= 0.932    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.197041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3865   r_free= 0.3875   ksol= 0.33   Bsol= 48.13   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,1.63,2.01,0.00,0.00,0.00); trace/3= 0.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.185202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.177207              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.093   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.671292              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.448   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3865      final r-factor (work) = 0.2431          |
| start r-factor (free) = 0.3875      final r-factor (free) = 0.2745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2490 = 6.18 * 0.50 * 6.1785 + 1.00 * 0.1661                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5087 = 6.18 * 0.50 * 5.9612 + 1.00 * 0.0968                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2431      final r-factor (work) = 0.2224          |
| start r-factor (free) = 0.2745      final r-factor (free) = 0.2829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0081 = 0.67 * 1.00 * 5.9612 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8920 = 0.67 * 1.00 * 5.7314 + 1.00 * 0.0445                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.80   17.10    None  None   None       |
|    all(noH): 2823   0      0.00    69.80   17.10    None  None   None       |
|    Sol.    : 438    0      1.84    66.26   38.78    None  None   None       |
|    Mac.    : 2385   0      0.00    69.80   13.11    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 -   6.980:  492   |   5:    34.898 -  41.878:  114        |
|      1:     6.980 -  13.959: 1032   |   6:    41.878 -  48.857:  104        |
|      2:    13.959 -  20.939:  605   |   7:    48.857 -  55.837:   75        |
|      3:    20.939 -  27.918:  226   |   8:    55.837 -  62.816:   31        |
|      4:    27.918 -  34.898:  139   |   9:    62.816 -  69.796:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2224 r_free = 0.2829             target_work(ml) = 5.744         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2221 r_free = 0.2827             target_work(ml) = 5.743         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2221   r_free= 0.2827   ksol= 0.33   Bsol= 48.13   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,1.63,2.01,0.00,0.00,0.00); trace/3= 0.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.742684                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2197   r_free= 0.2798   ksol= 0.34   Bsol= 67.27   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.23,-0.14,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.738845                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.408640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.087   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.412439              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.465   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2197      final r-factor (work) = 0.1560          |
| start r-factor (free) = 0.2798      final r-factor (free) = 0.2034          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7508 = 4.41 * 0.50 * 5.7406 + 1.00 * 0.0966                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4171 = 4.41 * 0.50 * 5.6007 + 1.00 * 0.0713                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1560      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.2034      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3887 = 0.41 * 1.00 * 5.6007 + 1.00 * 0.0787                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2269 = 0.41 * 1.00 * 5.3760 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.44   17.42    None  None   None       |
|    all(noH): 2823   0      0.00    76.44   17.42    None  None   None       |
|    Sol.    : 438    0      5.82    76.44   41.53    None  None   None       |
|    Mac.    : 2385   0      0.00    73.09   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.644:  499   |   5:    38.219 -  45.862:   96        |
|      1:     7.644 -  15.287: 1346   |   6:    45.862 -  53.506:   90        |
|      2:    15.287 -  22.931:  413   |   7:    53.506 -  61.150:   79        |
|      3:    22.931 -  30.575:  141   |   8:    61.150 -  68.793:   42        |
|      4:    30.575 -  38.219:  102   |   9:    68.793 -  76.437:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1394 r_free = 0.1880             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1393 r_free = 0.1876             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1876   ksol= 0.34   Bsol= 67.27   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.23,-0.14,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.332711                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1392   r_free= 0.1870   ksol= 0.34   Bsol= 67.27   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.07,-0.52,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.328166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.999254              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.225  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.510955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.785  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1392      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1870      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1323 = 3.00 * 0.50 * 5.3753 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9620 = 3.00 * 0.50 * 5.2678 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7012 = 0.51 * 1.00 * 5.2678 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6619 = 0.51 * 1.00 * 5.1909 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.25   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    80.25   17.27    None  None   None       |
|    Sol.    : 438    0      0.00    80.18   41.47    None  None   None       |
|    Mac.    : 2385   0      0.00    80.25   12.82    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 -   8.025:  598   |   5:    40.124 -  48.148:   88        |
|      1:     8.025 -  16.049: 1349   |   6:    48.148 -  56.173:   90        |
|      2:    16.049 -  24.074:  348   |   7:    56.173 -  64.198:   65        |
|      3:    24.074 -  32.099:  143   |   8:    64.198 -  72.222:   35        |
|      4:    32.099 -  40.124:   95   |   9:    72.222 -  80.247:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1629             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1630             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1630   ksol= 0.34   Bsol= 67.27   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.07,-0.52,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.180205                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1628   ksol= 0.33   Bsol= 67.27   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.32,-0.58,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179360                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.230688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.713  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.437108              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.793  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8510 = 2.23 * 0.50 * 5.1900 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8234 = 2.23 * 0.50 * 5.1675 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2683 = 0.44 * 1.00 * 5.1675 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2631 = 0.44 * 1.00 * 5.1562 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.22    84.75   17.02    None  None   None       |
|    all(noH): 2823   0      0.22    84.75   17.02    None  None   None       |
|    Sol.    : 438    0      0.22    82.60   40.67    None  None   None       |
|    Mac.    : 2385   0      0.30    84.75   12.67    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:     0.222 -   8.674:  787   |   5:    42.485 -  50.937:   89        |
|      1:     8.674 -  17.127: 1263   |   6:    50.937 -  59.390:   77        |
|      2:    17.127 -  25.579:  292   |   7:    59.390 -  67.842:   47        |
|      3:    25.579 -  34.032:  128   |   8:    67.842 -  76.295:   27        |
|      4:    34.032 -  42.485:  108   |   9:    76.295 -  84.747:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1124 r_free = 0.1589             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1123 r_free = 0.1589             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1123   r_free= 0.1589   ksol= 0.33   Bsol= 67.27   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.42,-2.32,-0.58,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.153181                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1583   ksol= 0.32   Bsol= 59.73   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.34,-0.52,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.152521                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.948125              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.056  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.366  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1126      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0825 = 1.95 * 0.50 * 5.1564 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0725 = 1.95 * 0.50 * 5.1486 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1147 = 0.21 * 1.00 * 5.1486 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1141 = 0.21 * 1.00 * 5.1513 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    84.51   16.56    None  None   None       |
|    all(noH): 2823   0      0.84    84.51   16.56    None  None   None       |
|    Sol.    : 438    0      3.07    81.74   38.88    None  None   None       |
|    Mac.    : 2385   0      0.84    84.51   12.46    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:     0.836 -   9.203:  927   |   5:    42.672 -  51.039:   89        |
|      1:     9.203 -  17.570: 1164   |   6:    51.039 -  59.406:   82        |
|      2:    17.570 -  25.937:  267   |   7:    59.406 -  67.773:   26        |
|      3:    25.937 -  34.305:  134   |   8:    67.773 -  76.141:   19        |
|      4:    34.305 -  42.672:  111   |   9:    76.141 -  84.508:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1120 r_free = 0.1572             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1571             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1571   ksol= 0.32   Bsol= 59.73   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.34,-0.52,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148114                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.0960 0.1234      5.3599      5.5277|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.0857 0.1139      5.4336       5.628|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.1072 0.1532      5.4814      5.8288|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.1220 0.1705      5.4531      5.6194|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.1331 0.1709      5.3257      5.5629|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.1221 0.1875      5.1967      5.4677|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.1276 0.1581      5.1726      5.3062|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.1183 0.1564      5.0663      5.2936|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.1183 0.1826      5.0367      5.3105|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.1132 0.1705      4.9339      5.1995|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.1102 0.1755      4.9254       5.304|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.1151 0.1657      4.8624      5.1229|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.1111 0.1751      4.7821      5.0376|
| 14:  2.0223 -  1.9731 0.37    488   57 0.1032 0.1504      4.6889      4.8621|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7104  1416   156  0.94   8.67   0.97     0.94       6624.95|
|  2:  4.7104 -  3.7577  1370   155  0.95   7.77   1.01     1.00       8840.94|
|  3:  3.7577 -  3.2883  1332   145  0.93  11.45   1.02     1.01      10445.96|
|  4:  3.2883 -  2.9902  1340   150  0.92  14.07   1.00     0.97      10341.28|
|  5:  2.9902 -  2.7773  1318   149  0.90  15.65   0.99     0.98       8298.60|
|  6:  2.7773 -  2.6144  1318   144  0.90  16.15   0.98     0.95       6824.75|
|  7:  2.6144 -  2.4841  1306   140  0.91  15.40   0.99     0.96       6178.17|
|  8:  2.4841 -  2.3764  1297   151  0.91  15.37   0.98     0.96       5238.27|
|  9:  2.3764 -  2.2852  1290   142  0.91  15.45   1.00     0.96       5014.29|
| 10:  2.2852 -  2.2066  1297   148  0.91  15.19   1.00     0.97       4145.02|
| 11:  2.2066 -  2.1378  1309   142  0.91  15.44   0.98     0.93       4061.58|
| 12:  2.1378 -  2.0769  1275   141  0.91  15.42   1.00     1.00       3801.63|
| 13:  2.0769 -  2.0223  1274   139  0.90  16.67   0.99     0.97       3410.98|
| 14:  2.0223 -  1.9731   488    57  0.92  14.21   0.97     0.94       2731.31|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2731.31 max =        10445.96 mean =      6338.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.99|
|phase err.(test): min =        0.00 max =           88.60 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1571   ksol= 0.32   Bsol= 54.36   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.25,-0.38,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148231                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1571   ksol= 0.32   Bsol= 54.36   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.25,-0.38,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148231                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.0957 0.1231      5.3583      5.5257|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.0854 0.1136       5.431      5.6253|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.1070 0.1529      5.4799      5.8273|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.1220 0.1708      5.4539      5.6211|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.1333 0.1711      5.3269      5.5643|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.1223 0.1878      5.1979      5.4691|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.1278 0.1584       5.174       5.308|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.1184 0.1567      5.0671      5.2942|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.1183 0.1824      5.0373        5.31|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.1132 0.1709      4.9347      5.2016|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.1102 0.1756      4.9261      5.3046|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.1151 0.1657      4.8625      5.1229|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.1111 0.1749       4.782      5.0369|
| 14:  2.0223 -  1.9731 0.37    488   57 0.1033 0.1504      4.6888      4.8622|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.7104  1416   156  0.94   8.66   0.97     0.94       6591.88|
|  2:  4.7104 -  3.7577  1370   155  0.95   7.76   1.01     1.00       8803.59|
|  3:  3.7577 -  3.2883  1332   145  0.93  11.43   1.02     1.01      10416.72|
|  4:  3.2883 -  2.9902  1340   150  0.92  14.08   1.00     0.98      10348.44|
|  5:  2.9902 -  2.7773  1318   149  0.90  15.66   1.00     0.98       8319.00|
|  6:  2.7773 -  2.6144  1318   144  0.90  16.18   0.98     0.96       6844.40|
|  7:  2.6144 -  2.4841  1306   140  0.91  15.43   0.99     0.96       6199.08|
|  8:  2.4841 -  2.3764  1297   151  0.91  15.38   0.99     0.96       5245.38|
|  9:  2.3764 -  2.2852  1290   142  0.91  15.46   1.00     0.97       5021.11|
| 10:  2.2852 -  2.2066  1297   148  0.91  15.22   1.00     0.97       4152.39|
| 11:  2.2066 -  2.1378  1309   142  0.91  15.47   0.98     0.93       4072.68|
| 12:  2.1378 -  2.0769  1275   141  0.91  15.44   1.01     1.00       3806.14|
| 13:  2.0769 -  2.0223  1274   139  0.90  16.67   0.99     0.98       3410.86|
| 14:  2.0223 -  1.9731   488    57  0.92  14.21   0.97     0.95       2729.36|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2729.36 max =        10416.72 mean =      6338.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.00|
|phase err.(test): min =        0.00 max =           88.67 mean =        13.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    84.48   16.53    None  None   None       |
|    all(noH): 2823   0      0.81    84.48   16.53    None  None   None       |
|    Sol.    : 438    0      3.04    81.71   38.85    None  None   None       |
|    Mac.    : 2385   0      0.81    84.48   12.44    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:     0.807 -   9.175:  927   |   5:    42.643 -  51.011:   89        |
|      1:     9.175 -  17.542: 1164   |   6:    51.011 -  59.378:   82        |
|      2:    17.542 -  25.909:  267   |   7:    59.378 -  67.745:   26        |
|      3:    25.909 -  34.276:  134   |   8:    67.745 -  76.112:   19        |
|      4:    34.276 -  42.643:  111   |   9:    76.112 -  84.479:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.637 - 4.705
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 304
   mapped sites are within: 0.701 - 4.705

peak=    5.831 closest distance to " NE2 GLN A  11 " =    1.212
peak=    5.705 closest distance to " NH2 ARG A  56 " =    2.107
peak=    5.684 closest distance to " CG  PRO A  54 " =    1.342
peak=    5.468 closest distance to " O   HOH Z 144 " =    1.889
peak=    5.053 closest distance to " CB  PRO A  54 " =    1.040
peak=    4.990 closest distance to " O   HOH Z 232 " =    2.271
peak=    4.915 closest distance to " O   HOH Z 126 " =    1.887
peak=    4.908 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.907 closest distance to " O   HOH Z 423 " =    1.670
peak=    4.870 closest distance to " CB  GLN A 223 " =    1.453
peak=    4.748 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.721 closest distance to " CG  PRO A 280 " =    0.863
peak=    4.640 closest distance to " CB  SER A  63 " =    1.245
peak=    4.582 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.571 closest distance to " CB  ARG A 190 " =    1.590
peak=    4.560 closest distance to " ND2 ASN A 187 " =    1.598
peak=    4.521 closest distance to " CB  ASN A 148 " =    1.351
peak=    4.459 closest distance to " CG  PRO A 198 " =    1.334
peak=    4.437 closest distance to " O   HOH Z 287 " =    2.122
peak=    4.417 closest distance to " O   HOH Z 298 " =    1.961
peak=    4.407 closest distance to " O   HOH Z  63 " =    1.445
peak=    4.400 closest distance to " CB  GLN A 183 " =    1.172
peak=    4.397 closest distance to " O   HOH Z  78 " =    1.859
peak=    4.342 closest distance to " O   HOH Z 417 " =    1.381
peak=    4.309 closest distance to " CB  ARG A  79 " =    1.438
peak=    4.302 closest distance to " CZ  PHE A 218 " =    1.033
peak=    4.274 closest distance to " CG2 VAL A 257 " =    0.886
peak=    4.268 closest distance to " O   HOH Z 427 " =    2.826
peak=    4.253 closest distance to " C   PRO A 198 " =    1.510
peak=    4.197 closest distance to " CD  ARG A 159 " =    0.753
peak=    4.191 closest distance to " CG  TRP A 179 " =    2.176
peak=    4.185 closest distance to " CG  PRO A 243 " =    1.096
peak=    4.179 closest distance to " O   HOH Z   9 " =    1.396
peak=    4.173 closest distance to " O   HOH Z 419 " =    2.174
peak=    4.163 closest distance to " CB  VAL A 265 " =    1.374
peak=    4.149 closest distance to " O   HOH Z 133 " =    2.485
peak=    4.124 closest distance to " CB  TRP A 266 " =    1.044
peak=    4.122 closest distance to " CB  LEU A 228 " =    1.061
peak=    4.084 closest distance to " O   HOH Z 189 " =    2.718
peak=    4.061 closest distance to " CE  LYS A  76 " =    0.903
peak=    4.058 closest distance to " CG  LEU A 167 " =    1.234
peak=    4.038 closest distance to " CA  TYR A  30 " =    0.941
peak=    4.028 closest distance to " O   HOH Z 380 " =    1.707
peak=    4.027 closest distance to " CB  ASN A  39 " =    0.914
peak=    4.023 closest distance to " O   HOH Z  61 " =    1.631
peak=    4.021 closest distance to " CA  SER A  87 " =    0.939
peak=    3.997 closest distance to " O   HOH Z  10 " =    1.760
peak=    3.979 closest distance to " CD2 TRP A 179 " =    1.258
peak=    3.973 closest distance to " O   HOH Z   1 " =    1.920
peak=    3.972 closest distance to " O   HOH Z 180 " =    2.098
peak=    3.971 closest distance to " CB  GLU A 128 " =    0.932
peak=    3.969 closest distance to " O   HOH Z 261 " =    2.156
peak=    3.968 closest distance to " CB  ASN A 142 " =    0.884
peak=    3.963 closest distance to " CD  ARG A  66 " =    2.236
peak=    3.962 closest distance to " O   HOH Z 362 " =    2.510
peak=    3.938 closest distance to " O   HOH Z 406 " =    1.659
peak=    3.936 closest distance to " CB  ASN A 187 " =    1.125
peak=    3.931 closest distance to " CB  SER A 212 " =    1.208
peak=    3.918 closest distance to " O   HOH Z 158 " =    3.120
peak=    3.886 closest distance to " CA  ALA A 233 " =    1.121
peak=    3.881 closest distance to " O   HOH Z 234 " =    3.761
peak=    3.879 closest distance to " CB  SER A   3 " =    1.369
peak=    3.869 closest distance to " NH1AARG A 145 " =    1.273
peak=    3.868 closest distance to " O   HOH Z  21 " =    1.788
peak=    3.864 closest distance to " O   HOH Z 214 " =    2.192
peak=    3.851 closest distance to " O   HOH Z 371 " =    1.955
peak=    3.843 closest distance to " O   HOH Z 368 " =    3.637
peak=    3.824 closest distance to " O   HOH Z 209 " =    2.245
peak=    3.821 closest distance to " OD1 ASN A  69 " =    2.615
peak=    3.814 closest distance to " O   HOH Z 352 " =    1.782
peak=    3.811 closest distance to " O   SER A  87 " =    2.136
peak=    3.793 closest distance to " OG ASER A 258 " =    3.115
peak=    3.790 closest distance to " CB  GLU A 152 " =    1.287
peak=    3.779 closest distance to " O   HOH Z 272 " =    1.800
peak=    3.775 closest distance to " CD1 LEU A 300 " =    1.138
peak=    3.773 closest distance to " O   HOH Z   1 " =    1.772
peak=    3.746 closest distance to " CA  ASN A 215 " =    1.133
peak=    3.733 closest distance to " CB  TYR A 169 " =    0.767
peak=    3.733 closest distance to " CB  SER A 216 " =    0.863
peak=    3.729 closest distance to " NH2AARG A 190 " =    2.039
peak=    3.729 closest distance to " CB  ARG A  79 " =    0.906
peak=    3.729 closest distance to " O   HOH Z 172 " =    2.724
peak=    3.727 closest distance to " CB  GLU A  46 " =    0.999
peak=    3.722 closest distance to " O   HOH Z 346 " =    1.680
peak=    3.722 closest distance to " O   HOH Z 405 " =    1.333
peak=    3.721 closest distance to " NZ  LYS A 117 " =    3.194
peak=    3.718 closest distance to " CA  THR A 264 " =    0.875
peak=    3.717 closest distance to " N   PHE A 130 " =    1.225
peak=    3.713 closest distance to " NE2 HIS A 207 " =    1.195
peak=    3.708 closest distance to " O   HOH Z 265 " =    2.158
peak=    3.707 closest distance to " CZ3 TRP A 266 " =    1.129
peak=    3.704 closest distance to " O   HOH Z 325 " =    4.033
peak=    3.696 closest distance to " CA  ARG A 195 " =    1.227
peak=    3.692 closest distance to " O   HOH Z 327 " =    1.576
peak=    3.686 closest distance to " CB  GLU A 277 " =    3.650
peak=    3.683 closest distance to " CB  ASP A 124 " =    0.775
peak=    3.677 closest distance to " CB  SER A 210 " =    0.741
peak=    3.676 closest distance to " O   HOH Z 193 " =    1.667
peak=    3.662 closest distance to " O   HOH Z  68 " =    2.187
peak=    3.657 closest distance to " O   HOH Z  40 " =    2.006
peak=    3.652 closest distance to " ND2 ASN A 249 " =    0.879
peak=    3.646 closest distance to " OD1BASN A 224 " =    2.366
peak=    3.640 closest distance to " O   HOH Z 128 " =    2.192
peak=    3.639 closest distance to " O   HOH Z 437 " =    1.510
peak=    3.638 closest distance to " O   HOH Z 250 " =    1.534
peak=    3.638 closest distance to " CB  VAL A 202 " =    1.614
peak=    3.629 closest distance to " CA  TYR A 116 " =    1.363
peak=    3.627 closest distance to " CG2 THR A 221 " =    0.993
peak=    3.620 closest distance to " O   HOH Z 371 " =    2.908
peak=    3.618 closest distance to " OG BSER A 164 " =    2.361
peak=    3.612 closest distance to " O   HOH Z 132 " =    2.548
peak=    3.611 closest distance to " O   HOH Z   9 " =    1.993
peak=    3.610 closest distance to " O   TYR A 116 " =    1.324
peak=    3.604 closest distance to " O   HOH Z 126 " =    1.500
peak=    3.594 closest distance to " O   HOH Z 389 " =    1.873
peak=    3.588 closest distance to " O   HOH Z 116 " =    3.079
peak=    3.585 closest distance to " ND1 HIS A  86 " =    1.634
peak=    3.574 closest distance to " O   HOH Z 258 " =    2.165
peak=    3.560 closest distance to " CB  TYR A 116 " =    0.903
peak=    3.555 closest distance to " O   HOH Z  88 " =    3.877
peak=    3.539 closest distance to " CD  LYS A 166 " =    1.246
peak=    3.530 closest distance to " O   HOH Z 391 " =    2.841
peak=    3.520 closest distance to " CB  MET A  47 " =    1.086
peak=    3.519 closest distance to " O   ASN A  74 " =    1.491
peak=    3.519 closest distance to " CA  THR A 221 " =    0.967
peak=    3.517 closest distance to " O   HOH Z 425 " =    1.333
peak=    3.515 closest distance to " O   HOH Z  61 " =    1.509
peak=    3.514 closest distance to " CB  ASP A 140 " =    0.883
peak=    3.510 closest distance to " O   HOH Z 332 " =    1.548
peak=    3.505 closest distance to " CB  MET A  40 " =    0.821
peak=    3.504 closest distance to " CD BLYS A 290 " =    1.070
peak=    3.501 closest distance to " CA  ARG A 102 " =    1.130
peak=    3.497 closest distance to " CB  ALA A   1 " =    4.705
peak=    3.494 closest distance to " O   HOH Z 193 " =    1.848
peak=    3.493 closest distance to " O   HOH Z 291 " =    1.524
peak=    3.491 closest distance to " N   GLN A 278 " =    1.240
peak=    3.487 closest distance to " N   ASN A  39 " =    1.192
peak=    3.480 closest distance to " N   CYS A 260 " =    0.811
peak=    3.478 closest distance to " CE1 PHE A 218 " =    0.995
peak=    3.471 closest distance to " CB  ALA A 114 " =    0.834
peak=    3.471 closest distance to " O   HOH Z 411 " =    3.818
peak=    3.468 closest distance to " O   HOH Z  44 " =    2.872
peak=    3.465 closest distance to " CA  ALA A  51 " =    0.926
peak=    3.465 closest distance to " O   HOH Z 345 " =    1.822
peak=    3.455 closest distance to " CD  ARG A 269 " =    0.904
peak=    3.447 closest distance to " CD1 ILE A 263 " =    1.286
peak=    3.437 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.437 closest distance to " NH1 ARG A 138 " =    1.094
peak=    3.430 closest distance to " O   HOH Z 285 " =    2.287
peak=    3.430 closest distance to " O   HOH Z 359 " =    1.476
peak=    3.429 closest distance to " CB  ASN A 110 " =    1.029
peak=    3.422 closest distance to " O   HOH Z 426 " =    1.962
peak=    3.418 closest distance to " O   ASN A 209 " =    1.331
peak=    3.418 closest distance to " CB  PRO A  90 " =    1.160
peak=    3.417 closest distance to " CZ  PHE A  38 " =    1.214
peak=    3.411 closest distance to " N   ALA A   1 " =    2.142
peak=    3.404 closest distance to " CB  THR A  31 " =    1.702
peak=    3.403 closest distance to " CA  SER A  95 " =    0.979
peak=    3.398 closest distance to " CB  LYS A 117 " =    1.250
peak=    3.396 closest distance to " CB  ILE A 120 " =    1.257
peak=    3.393 closest distance to " O   HOH Z  88 " =    3.319
peak=    3.391 closest distance to " O   HOH Z 325 " =    2.430
peak=    3.384 closest distance to " CG2AVAL A  72 " =    1.510
peak=    3.380 closest distance to " CG  LYS A 119 " =    1.173
peak=    3.377 closest distance to " O   HOH Z 343 " =    3.349
peak=    3.372 closest distance to " CG  GLN A  11 " =    2.007
peak=    3.370 closest distance to " O   HOH Z 294 " =    1.527
peak=    3.370 closest distance to " O   HOH Z 403 " =    1.445
peak=    3.368 closest distance to " CB  SER A  62 " =    1.078
peak=    3.359 closest distance to " O   HOH Z 305 " =    3.624
peak=    3.357 closest distance to " O   HOH Z 365 " =    2.817
peak=    3.351 closest distance to " O   HOH Z 368 " =    4.246
peak=    3.351 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.348 closest distance to " O   HOH Z 188 " =    1.970
peak=    3.347 closest distance to " O   HOH Z 147 " =    1.780
peak=    3.346 closest distance to " O   HOH Z 310 " =    2.221
peak=    3.344 closest distance to " O   HOH Z 148 " =    3.448
peak=    3.343 closest distance to " O   HOH Z 386 " =    2.987
peak=    3.343 closest distance to " CB  VAL A 265 " =    1.951
peak=    3.342 closest distance to " CA  ARG A  36 " =    1.022
peak=    3.342 closest distance to " CG1 ILE A  33 " =    1.283
peak=    3.341 closest distance to " CA  ALA A 158 " =    1.170
peak=    3.334 closest distance to " O   HOH Z  28 " =    1.776
peak=    3.330 closest distance to " CB  ALA A  34 " =    1.034
peak=    3.330 closest distance to " CA  GLU A  46 " =    0.905
peak=    3.330 closest distance to " NE2 GLN A  73 " =    3.852
peak=    3.329 closest distance to " O   HOH Z 421 " =    2.220
peak=    3.325 closest distance to " CA  ALA A 299 " =    0.895
peak=    3.323 closest distance to " CB  ARG A 139 " =    1.028
peak=    3.322 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.322 closest distance to " CA  MET A 105 " =    0.894
peak=    3.317 closest distance to " CA  ASN A 127 " =    1.065
peak=    3.311 closest distance to " O   HOH Z  53 " =    2.563
peak=    3.310 closest distance to " CB  PHE A 204 " =    0.758
peak=    3.308 closest distance to " OG  SER A  62 " =    2.938
peak=    3.308 closest distance to " CB  GLN A  88 " =    1.211
peak=    3.306 closest distance to " O   HOH Z 368 " =    1.968
peak=    3.305 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.303 closest distance to " NH2BARG A 145 " =    1.974
peak=    3.301 closest distance to " O   HOH Z   7 " =    1.309
peak=    3.300 closest distance to " O   HOH Z 175 " =    2.193
peak=    3.292 closest distance to " CA  MET A  40 " =    1.190
peak=    3.290 closest distance to " O   HOH Z  44 " =    1.668
peak=    3.290 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.289 closest distance to " O   HOH Z 153 " =    4.350
peak=    3.286 closest distance to " O   HOH Z 128 " =    2.076
peak=    3.286 closest distance to " O   HOH Z 116 " =    1.761
peak=    3.285 closest distance to " CA  ASN A 217 " =    1.204
peak=    3.285 closest distance to " ND2 ASN A 110 " =    1.829
peak=    3.282 closest distance to " CG  GLN A  89 " =    1.547
peak=    3.280 closest distance to " CB  THR A 157 " =    1.133
peak=    3.277 closest distance to " CD1 ILE A 106 " =    0.923
peak=    3.274 closest distance to " O   HOH Z 213 " =    2.760
peak=    3.271 closest distance to " CB  LEU A  83 " =    0.738
peak=    3.271 closest distance to " O   HOH Z 402 " =    1.473
peak=    3.268 closest distance to " O   HOH Z 369 " =    1.745
peak=    3.267 closest distance to " CG2 ILE A 120 " =    1.393
peak=    3.266 closest distance to " NH2AARG A 275 " =    3.585
peak=    3.266 closest distance to " O   HOH Z 286 " =    2.268
peak=    3.266 closest distance to " CG1 VAL A 189 " =    1.871
peak=    3.264 closest distance to " CB  ALA A  43 " =    0.800
peak=    3.262 closest distance to " CB  ASN A 215 " =    1.063
peak=    3.261 closest distance to " O   ARG A 145 " =    1.624
peak=    3.258 closest distance to " CB  ALA A 248 " =    0.940
peak=    3.257 closest distance to " O  BHOH Z  74 " =    1.276
peak=    3.255 closest distance to " O   HOH Z 421 " =    2.899
peak=    3.255 closest distance to " O   HOH Z 145 " =    2.413
peak=    3.254 closest distance to " O   HOH Z 248 " =    1.552
peak=    3.253 closest distance to " O   HOH Z 213 " =    2.077
peak=    3.250 closest distance to " CB  ARG A 138 " =    0.997
peak=    3.248 closest distance to " CG1 ILE A 151 " =    1.077
peak=    3.247 closest distance to " O   HOH Z 409 " =    2.427
peak=    3.246 closest distance to " CG2 ILE A  20 " =    1.531
peak=    3.238 closest distance to " OG BSER A 134 " =    2.851
peak=    3.235 closest distance to " CG  ARG A 159 " =    0.828
peak=    3.235 closest distance to " CA  ASP A 162 " =    0.975
peak=    3.234 closest distance to " CG AARG A 275 " =    1.203
peak=    3.234 closest distance to " O   HOH Z   2 " =    1.453
peak=    3.232 closest distance to " O   HOH Z 287 " =    2.151
peak=    3.231 closest distance to " O   HOH Z 415 " =    3.808
peak=    3.231 closest distance to " CG1 ILE A 120 " =    1.090
peak=    3.230 closest distance to " O   HOH Z 128 " =    1.864
peak=    3.227 closest distance to " O   HOH Z 344 " =    3.121
peak=    3.223 closest distance to " O   HOH Z 340 " =    2.170
peak=    3.222 closest distance to " O  BHOH Z 338 " =    2.394
peak=    3.221 closest distance to " CA  VAL A 125 " =    1.115
peak=    3.220 closest distance to " N   ASN A 127 " =    1.278
peak=    3.219 closest distance to " CB  ALA A 114 " =    1.401
peak=    3.213 closest distance to " CA  ASP A 124 " =    0.734
peak=    3.212 closest distance to " CB  SER A 273 " =    0.889
peak=    3.208 closest distance to " O   PHE A 192 " =    1.369
peak=    3.207 closest distance to " O   HOH Z 183 " =    1.421
peak=    3.204 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.199 closest distance to " CD2 LEU A 297 " =    0.893
peak=    3.198 closest distance to " CA  GLY A 136 " =    0.991
peak=    3.197 closest distance to " CB  TRP A 150 " =    1.291
peak=    3.192 closest distance to " O   THR A 294 " =    1.060
peak=    3.192 closest distance to " CA  ALA A  84 " =    1.333
peak=    3.192 closest distance to " O   HOH Z 132 " =    3.652
peak=    3.191 closest distance to " O   HOH Z 329 " =    3.994
peak=    3.188 closest distance to " CD  PRO A 243 " =    1.615
peak=    3.187 closest distance to " O   HOH Z 218 " =    4.488
peak=    3.179 closest distance to " CB  ALA A 291 " =    1.324
peak=    3.178 closest distance to " O   HOH Z 274 " =    2.094
peak=    3.175 closest distance to " O   HOH Z 109 " =    2.564
peak=    3.173 closest distance to " CA  LYS A 290 " =    1.247
peak=    3.171 closest distance to " CA  GLY A 267 " =    1.136
peak=    3.171 closest distance to " O   HOH Z  43 " =    1.765
peak=    3.169 closest distance to " NH1BARG A 145 " =    1.226
peak=    3.166 closest distance to " O   HOH Z 233 " =    1.645
peak=    3.163 closest distance to " CG  MET A 113 " =    1.258
peak=    3.162 closest distance to " CA  ILE A 106 " =    0.805
peak=    3.160 closest distance to " N   ARG A 156 " =    1.311
peak=    3.156 closest distance to " CG2 ILE A 239 " =    0.701
peak=    3.152 closest distance to " CG  GLN A 144 " =    0.837
peak=    3.150 closest distance to " O   HOH Z 302 " =    1.808
peak=    3.148 closest distance to " CB  ALA A 160 " =    1.212
peak=    3.147 closest distance to " CA  ALA A 100 " =    1.033
peak=    3.146 closest distance to " CG  GLN A 278 " =    1.332
peak=    3.144 closest distance to " CB  LEU A 300 " =    0.922
peak=    3.140 closest distance to " O   HOH Z 227 " =    2.031
peak=    3.137 closest distance to " O   HOH Z 290 " =    1.070
peak=    3.132 closest distance to " O   SER A 164 " =    1.332
peak=    3.128 closest distance to " O   HOH Z 213 " =    2.182
peak=    3.123 closest distance to " O   HOH Z 273 " =    2.861
peak=    3.122 closest distance to " O   HOH Z 423 " =    2.230
peak=    3.112 closest distance to " O   HOH Z 272 " =    2.207
peak=    3.111 closest distance to " O   HOH Z 152 " =    2.375
peak=    3.111 closest distance to " O   HOH Z 219 " =    1.739
peak=    3.110 closest distance to " CB  ALA A 180 " =    1.289
peak=    3.104 closest distance to " O   HOH Z 394 " =    1.645
peak=    3.102 closest distance to " OE2 GLU A  53 " =    2.054
peak=    3.100 closest distance to " O   HOH Z  30 " =    1.749
peak=    3.098 closest distance to " CA  PRO A 280 " =    1.245
peak=    3.096 closest distance to " CB  GLN A 103 " =    0.867
peak=    3.094 closest distance to " O   HOH Z 271 " =    2.363
peak=    3.093 closest distance to " O   HOH Z 188 " =    1.388
peak=    3.092 closest distance to " CB  PRO A 243 " =    1.396
peak=    3.080 closest distance to " OG BSER A  99 " =    2.282
peak=    3.075 closest distance to " O   HOH Z  97 " =    1.980
peak=    3.062 closest distance to " O   HOH Z 245 " =    1.289

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.685 - 5.975
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.737 - 5.975

peak=   -4.457 closest distance to " CB  PRO A 243 " =    2.646
peak=   -4.342 closest distance to " CD  ARG A  14 " =    3.440
peak=   -4.322 closest distance to " O   HOH Z 377 " =    1.968
peak=   -4.257 closest distance to " O   PRO A 198 " =    1.209
peak=   -4.167 closest distance to " CD  ARG A 156 " =    2.092
peak=   -4.165 closest distance to " O   HOH Z 231 " =    2.206
peak=   -4.152 closest distance to " CB  ALA A  43 " =    2.558
peak=   -4.134 closest distance to " CZ3 TRP A 179 " =    1.238
peak=   -4.090 closest distance to " O   HOH Z 351 " =    1.487
peak=   -4.077 closest distance to " OG BSER A 134 " =    1.305
peak=   -4.052 closest distance to " O   VAL A  67 " =    2.661
peak=   -4.023 closest distance to " O   HOH Z 290 " =    1.153
peak=   -4.009 closest distance to " O   HOH Z 266 " =    5.215
peak=   -4.008 closest distance to " O   HOH Z 372 " =    2.554
peak=   -3.991 closest distance to " CB  ALA A 291 " =    2.257
peak=   -3.939 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.903 closest distance to " N   ALA A  43 " =    2.528
peak=   -3.888 closest distance to " O   TYR A 247 " =    2.857
peak=   -3.854 closest distance to " ND2 ASN A 249 " =    2.214
peak=   -3.848 closest distance to " CD2 PHE A 192 " =    2.046
peak=   -3.843 closest distance to " CG  GLN A 223 " =    1.941
peak=   -3.839 closest distance to " CG1 VAL A 112 " =    3.055
peak=   -3.830 closest distance to " CD1 LEU A 255 " =    2.927
peak=   -3.829 closest distance to " CD  GLN A  58 " =    0.990
peak=   -3.819 closest distance to " O   HOH Z  38 " =    1.539
peak=   -3.790 closest distance to " O   HOH Z 389 " =    2.049
peak=   -3.770 closest distance to " O   HOH Z 185 " =    2.251
peak=   -3.769 closest distance to " O   HOH Z 211 " =    1.513
peak=   -3.757 closest distance to " O   HOH Z  22 " =    2.487
peak=   -3.749 closest distance to " CE2 TYR A  30 " =    2.663
peak=   -3.737 closest distance to " CE  MET A 105 " =    2.522
peak=   -3.722 closest distance to " O   HOH Z 131 " =    4.149
peak=   -3.714 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.704 closest distance to " C   HIS A 108 " =    1.187
peak=   -3.695 closest distance to " CA  GLY A 241 " =    2.277
peak=   -3.692 closest distance to " CB  ASN A  39 " =    2.203
peak=   -3.692 closest distance to " O   HOH Z 407 " =    3.190
peak=   -3.690 closest distance to " O   HOH Z  60 " =    2.447
peak=   -3.667 closest distance to " ND2 ASN A  45 " =    1.215
peak=   -3.664 closest distance to " CB  TRP A  85 " =    2.462
peak=   -3.649 closest distance to " ND2 ASN A  45 " =    1.962
peak=   -3.628 closest distance to " N   THR A 157 " =    1.530
peak=   -3.618 closest distance to " O   PRO A 163 " =    2.002
peak=   -3.610 closest distance to " O   ALA A  10 " =    1.630
peak=   -3.603 closest distance to " O   HOH Z 140 " =    1.449
peak=   -3.600 closest distance to " O   HOH Z 198 " =    1.827
peak=   -3.599 closest distance to " CA  ASP A  27 " =    2.433
peak=   -3.597 closest distance to " CD2 TYR A 293 " =    1.952
peak=   -3.595 closest distance to " O   HOH Z  52 " =    1.210
peak=   -3.592 closest distance to " O   HOH Z 152 " =    5.122
peak=   -3.587 closest distance to " O   HOH Z 429 " =    2.149
peak=   -3.583 closest distance to " CG2 ILE A 263 " =    2.320
peak=   -3.571 closest distance to " ND2 ASN A  60 " =    4.128
peak=   -3.565 closest distance to " OD1 ASP A 171 " =    1.645
peak=   -3.559 closest distance to " CE BMET A  47 " =    1.393
peak=   -3.558 closest distance to " N   ASP A 171 " =    2.356
peak=   -3.553 closest distance to " O   ARG A 145 " =    1.533
peak=   -3.552 closest distance to " CA  GLY A 241 " =    3.168
peak=   -3.549 closest distance to " OG  SER A  97 " =    2.207
peak=   -3.539 closest distance to " O   HOH Z 359 " =    3.211
peak=   -3.528 closest distance to " O   HOH Z   9 " =    1.692
peak=   -3.527 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.520 closest distance to " CD1 PHE A  59 " =    2.063
peak=   -3.516 closest distance to " CE2 PHE A 218 " =    2.420
peak=   -3.516 closest distance to " O   PRO A 198 " =    1.342
peak=   -3.514 closest distance to " CB  ALA A 291 " =    1.952
peak=   -3.512 closest distance to " ND2 ASN A 187 " =    1.430
peak=   -3.509 closest distance to " CB  ALA A 248 " =    2.426
peak=   -3.508 closest distance to " NH2AARG A 275 " =    5.426
peak=   -3.505 closest distance to " O   HOH Z 166 " =    2.147
peak=   -3.499 closest distance to " O   VAL A 189 " =    2.559
peak=   -3.487 closest distance to " O   HOH Z  73 " =    2.088
peak=   -3.484 closest distance to " CB  ALA A 158 " =    1.674
peak=   -3.484 closest distance to " CG  MET A 105 " =    0.994
peak=   -3.470 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.467 closest distance to " O   ALA A 161 " =    1.609
peak=   -3.461 closest distance to " CG  PHE A 283 " =    2.642
peak=   -3.456 closest distance to " O   HOH Z 313 " =    1.938
peak=   -3.455 closest distance to " CB  PRO A 163 " =    2.531
peak=   -3.454 closest distance to " CA  GLY A 133 " =    2.061
peak=   -3.454 closest distance to " CB  TYR A  15 " =    2.276
peak=   -3.451 closest distance to " CG2 ILE A  20 " =    2.942
peak=   -3.450 closest distance to " C   ALA A 114 " =    2.349
peak=   -3.449 closest distance to " CD1 LEU A 101 " =    2.264
peak=   -3.448 closest distance to " CG2 THR A 178 " =    2.282
peak=   -3.444 closest distance to " O   HOH Z 384 " =    2.843
peak=   -3.436 closest distance to " O   PRO A 243 " =    2.533
peak=   -3.432 closest distance to " CG2 THR A  18 " =    2.846
peak=   -3.423 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.422 closest distance to " O   SER A  22 " =    2.555
peak=   -3.420 closest distance to " O   HOH Z 174 " =    2.606
peak=   -3.419 closest distance to " CD  GLU A 277 " =    1.192
peak=   -3.414 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.414 closest distance to " OD1 ASN A 148 " =    1.550
peak=   -3.411 closest distance to " NE2 GLN A 278 " =    1.631
peak=   -3.406 closest distance to " OH  TYR A 172 " =    1.812
peak=   -3.399 closest distance to " CG  TRP A 266 " =    1.799
peak=   -3.399 closest distance to " O   HOH Z 412 " =    4.397
peak=   -3.399 closest distance to " CA  GLY A 203 " =    2.390
peak=   -3.396 closest distance to " OD2 ASP A 171 " =    2.200
peak=   -3.396 closest distance to " O   HOH Z 377 " =    0.748
peak=   -3.393 closest distance to " OG BSER A 134 " =    1.823
peak=   -3.391 closest distance to " O   HOH Z 316 " =    1.771
peak=   -3.389 closest distance to " O   HOH Z 298 " =    2.504
peak=   -3.383 closest distance to " N   SER A 212 " =    1.935
peak=   -3.382 closest distance to " OXT GLY A 302 " =    3.046
peak=   -3.381 closest distance to " O   VAL A 189 " =    1.619
peak=   -3.377 closest distance to " O   HOH Z 111 " =    1.677
peak=   -3.376 closest distance to " O   HOH Z 191 " =    5.542
peak=   -3.372 closest distance to " CG1 VAL A 250 " =    2.706
peak=   -3.366 closest distance to " CB  PHE A 208 " =    2.316
peak=   -3.356 closest distance to " CB  ASP A 286 " =    2.146
peak=   -3.350 closest distance to " O   SER A 135 " =    1.433
peak=   -3.348 closest distance to " O   HOH Z 176 " =    0.767
peak=   -3.343 closest distance to " O   HOH Z 394 " =    1.444
peak=   -3.337 closest distance to " CE3 TRP A 274 " =    1.008
peak=   -3.332 closest distance to " CE2 PHE A  61 " =    2.673
peak=   -3.325 closest distance to " O   SER A  95 " =    1.498
peak=   -3.324 closest distance to " O   HOH Z 409 " =    5.975
peak=   -3.306 closest distance to " O   HOH Z 357 " =    2.028
peak=   -3.301 closest distance to " CB  ALA A 114 " =    2.534
peak=   -3.295 closest distance to " O   ILE A  49 " =    1.780
peak=   -3.293 closest distance to " NH2 ARG A  79 " =    2.142
peak=   -3.292 closest distance to " CG  GLN A  88 " =    0.815
peak=   -3.291 closest distance to " CG2 ILE A  49 " =    2.697
peak=   -3.290 closest distance to " ND2 ASN A 285 " =    2.196
peak=   -3.282 closest distance to " O   HOH Z 219 " =    4.577
peak=   -3.281 closest distance to " C   MET A 188 " =    1.452
peak=   -3.271 closest distance to " O   GLU A 152 " =    1.403
peak=   -3.270 closest distance to " CE  LYS A  76 " =    2.745
peak=   -3.264 closest distance to " CD  ARG A 139 " =    1.561
peak=   -3.262 closest distance to " O   HOH Z 368 " =    1.680
peak=   -3.261 closest distance to " CA  ASP A 298 " =    1.112
peak=   -3.260 closest distance to " CA  GLY A  57 " =    2.182
peak=   -3.257 closest distance to " CB  CYS A 254 " =    2.218
peak=   -3.256 closest distance to " O   ALA A   7 " =    1.589
peak=   -3.256 closest distance to " O   HOH Z 385 " =    1.911
peak=   -3.255 closest distance to " O   HOH Z 275 " =    1.697
peak=   -3.254 closest distance to " O   GLY A 229 " =    1.862
peak=   -3.254 closest distance to " OG  SER A  87 " =    1.304
peak=   -3.253 closest distance to " O   ALA A  34 " =    2.581
peak=   -3.253 closest distance to " CG  LEU A  83 " =    1.916
peak=   -3.252 closest distance to " O   HOH Z 281 " =    2.684
peak=   -3.251 closest distance to " O   HOH Z 184 " =    1.701
peak=   -3.249 closest distance to " O   HOH Z 102 " =    1.605
peak=   -3.244 closest distance to " N   SER A 276 " =    1.313
peak=   -3.244 closest distance to " NH2BARG A 275 " =    1.754
peak=   -3.241 closest distance to " O   HOH Z 174 " =    3.974
peak=   -3.239 closest distance to " CZ  TYR A 169 " =    1.645
peak=   -3.237 closest distance to " O   HOH Z  65 " =    1.199
peak=   -3.232 closest distance to " O   HOH Z  10 " =    1.388
peak=   -3.228 closest distance to " C   PHE A  59 " =    1.258
peak=   -3.226 closest distance to " OE1 GLN A  88 " =    1.149
peak=   -3.225 closest distance to " O   ILE A 106 " =    2.135
peak=   -3.223 closest distance to " ND2BASN A 224 " =    1.790
peak=   -3.217 closest distance to " CB  PRO A  54 " =    2.465
peak=   -3.214 closest distance to " CB  ALA A 100 " =    2.272
peak=   -3.211 closest distance to " O   HOH Z 421 " =    2.873
peak=   -3.208 closest distance to " O   GLN A 240 " =    2.059
peak=   -3.208 closest distance to " O   HOH Z 426 " =    1.617
peak=   -3.207 closest distance to " NH1AARG A 275 " =    1.881
peak=   -3.207 closest distance to " O   ALA A 292 " =    2.130
peak=   -3.205 closest distance to " NE2 GLN A  58 " =    3.029
peak=   -3.198 closest distance to " O   HOH Z  43 " =    1.678
peak=   -3.193 closest distance to " O   HOH Z 318 " =    1.813
peak=   -3.192 closest distance to " CB  GLN A  11 " =    1.791
peak=   -3.190 closest distance to " O   HOH Z 253 " =    3.879
peak=   -3.189 closest distance to " ND2 ASN A  60 " =    1.485
peak=   -3.187 closest distance to " N   MET A 105 " =    2.540
peak=   -3.187 closest distance to " C   LYS A  76 " =    1.602
peak=   -3.185 closest distance to " O   HOH Z 166 " =    1.309
peak=   -3.185 closest distance to " O   HOH Z  63 " =    2.061
peak=   -3.185 closest distance to " CD2 HIS A 207 " =    2.307
peak=   -3.184 closest distance to " O   HOH Z 353 " =    2.253
peak=   -3.180 closest distance to " OH  TYR A 247 " =    2.151
peak=   -3.177 closest distance to " CG  PRO A 163 " =    2.645
peak=   -3.167 closest distance to " O   HOH Z 390 " =    2.442
peak=   -3.166 closest distance to " O   HOH Z 281 " =    2.975
peak=   -3.165 closest distance to " CD  GLN A 223 " =    0.737
peak=   -3.164 closest distance to " CD2 TYR A 293 " =    2.125
peak=   -3.163 closest distance to " C   LEU A 222 " =    0.748
peak=   -3.159 closest distance to " O   HOH Z 252 " =    4.182
peak=   -3.156 closest distance to " CB  ALA A  10 " =    2.297
peak=   -3.156 closest distance to " O   HOH Z 231 " =    1.243
peak=   -3.152 closest distance to " CG  LEU A 167 " =    0.909
peak=   -3.147 closest distance to " CA  GLY A 241 " =    2.871
peak=   -3.133 closest distance to " O   HOH Z  51 " =    1.173
peak=   -3.128 closest distance to " OG  SER A  63 " =    1.172
peak=   -3.127 closest distance to " CD1 LEU A   5 " =    2.477
peak=   -3.108 closest distance to " SG BCYS A 201 " =    1.990
peak=   -3.108 closest distance to " C   GLY A  13 " =    0.907
peak=   -3.107 closest distance to " CG2 VAL A 189 " =    1.882
peak=   -3.106 closest distance to " O   HOH Z 198 " =    1.748
peak=   -3.102 closest distance to " CE1 TYR A 247 " =    2.931
peak=   -3.088 closest distance to " CD1 TRP A 179 " =    0.959
peak=   -3.080 closest distance to " O   HOH Z 352 " =    2.299
peak=   -3.079 closest distance to " O   TRP A  70 " =    1.460
peak=   -3.079 closest distance to " O   HOH Z 218 " =    3.874
peak=   -3.070 closest distance to " CG1 VAL A 197 " =    2.191
peak=   -3.045 closest distance to " O   HOH Z 288 " =    1.356
peak=   -3.043 closest distance to " O   HOH Z  28 " =    1.888
peak=   -3.038 closest distance to " CA  ASN A 110 " =    2.426
peak=   -3.023 closest distance to " CD1 ILE A 199 " =    2.563

================= 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    :  0.3986 0.3942   6.197041e+00   6.177618e+00
   1_bss:  0.3865 0.3875   6.185202e+00   6.162917e+00
   1_xyz:  0.2431 0.2745   5.793458e+00   5.874183e+00
   1_adp:  0.2224 0.2829   5.743713e+00   5.904878e+00
   1_occ:  0.2221 0.2827   5.742684e+00   5.904464e+00
   2_bss:  0.2197 0.2798   5.738845e+00   5.899064e+00
   2_xyz:  0.1560 0.2034   5.425233e+00   5.625129e+00
   2_adp:  0.1394 0.1880   5.333410e+00   5.548493e+00
   2_occ:  0.1393 0.1876   5.332711e+00   5.547825e+00
   3_bss:  0.1392 0.1870   5.328166e+00   5.543048e+00
   3_xyz:  0.1204 0.1666   5.204531e+00   5.434685e+00
   3_adp:  0.1165 0.1629   5.180397e+00   5.415463e+00
   3_occ:  0.1164 0.1630   5.180205e+00   5.415570e+00
   4_bss:  0.1163 0.1628   5.179360e+00   5.415086e+00
   4_xyz:  0.1132 0.1598   5.158925e+00   5.401164e+00
   4_adp:  0.1124 0.1589   5.153368e+00   5.396480e+00
   4_occ:  0.1123 0.1589   5.153181e+00   5.396389e+00
   5_bss:  0.1126 0.1583   5.152521e+00   5.393463e+00
   5_xyz:  0.1115 0.1580   5.149063e+00   5.393998e+00
   5_adp:  0.1120 0.1572   5.148321e+00   5.389457e+00
   5_occ:  0.1119 0.1571   5.148114e+00   5.389309e+00
   5_bss:  0.1118 0.1571   5.148231e+00   5.389461e+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:  0.328  48.127  -2.787   1.632   2.015   0.000   0.000   0.000
   1_xyz:  0.328  48.127  -2.787   1.632   2.015   0.000   0.000   0.000
   1_adp:  0.328  48.127  -2.787   1.632   2.015   0.000   0.000   0.000
   1_occ:  0.328  48.127  -2.787   1.632   2.015   0.000   0.000   0.000
   2_bss:  0.342  67.268  -2.749  -1.229  -0.139  -0.000  -0.000  -0.000
   2_xyz:  0.342  67.268  -2.749  -1.229  -0.139  -0.000  -0.000  -0.000
   2_adp:  0.342  67.268  -2.749  -1.229  -0.139  -0.000  -0.000  -0.000
   2_occ:  0.342  67.268  -2.749  -1.229  -0.139  -0.000  -0.000  -0.000
   3_bss:  0.342  67.268  -2.532  -2.071  -0.520  -0.000  -0.000  -0.000
   3_xyz:  0.342  67.268  -2.532  -2.071  -0.520  -0.000  -0.000  -0.000
   3_adp:  0.342  67.268  -2.532  -2.071  -0.520  -0.000  -0.000  -0.000
   3_occ:  0.342  67.268  -2.532  -2.071  -0.520  -0.000  -0.000  -0.000
   4_bss:  0.335  67.268  -2.416  -2.321  -0.579  -0.000  -0.000  -0.000
   4_xyz:  0.335  67.268  -2.416  -2.321  -0.579  -0.000  -0.000  -0.000
   4_adp:  0.335  67.268  -2.416  -2.321  -0.579  -0.000  -0.000  -0.000
   4_occ:  0.335  67.268  -2.416  -2.321  -0.579  -0.000  -0.000  -0.000
   5_bss:  0.325  59.725  -2.279  -2.341  -0.522  -0.000  -0.000  -0.000
   5_xyz:  0.325  59.725  -2.279  -2.341  -0.522  -0.000  -0.000  -0.000
   5_adp:  0.325  59.725  -2.279  -2.341  -0.522  -0.000  -0.000  -0.000
   5_occ:  0.325  59.725  -2.279  -2.341  -0.522  -0.000  -0.000  -0.000
   5_bss:  0.320  54.356  -2.121  -2.250  -0.384  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.467 0.5898  0.7665    46397.173
   1_bss:  43.607 0.5986  0.7895    44057.480
   1_xyz:  26.782 0.7940  0.9822    19001.973
   1_adp:  28.100 0.7787  0.9687    20341.670
   1_occ:  28.108 0.7785  0.9681    20290.919
   2_bss:  27.756 0.7826  0.9196    19991.255
   2_xyz:  19.656 0.8641  0.9804    10470.876
   2_adp:  17.639 0.8837  0.9845     8962.823
   2_occ:  17.619 0.8838  0.9844     8944.903
   3_bss:  17.481 0.8850  0.9735     8815.873
   3_xyz:  15.098 0.9055  0.9825     6970.838
   3_adp:  14.583 0.9102  0.9778     6714.549
   3_occ:  14.592 0.9101  0.9776     6715.010
   4_bss:  14.577 0.9103  0.9755     6707.099
   4_xyz:  14.219 0.9134  0.9768     6491.248
   4_adp:  14.070 0.9147  0.9714     6419.447
   4_occ:  14.073 0.9147  0.9713     6417.038
   5_bss:  14.033 0.9149  0.9734     6363.193
   5_xyz:  14.046 0.9149  0.9732     6391.700
   5_adp:  13.940 0.9157  0.9690     6343.432
   5_occ:  13.941 0.9157  0.9689     6338.214
   5_bss:  13.950 0.9156  0.9722     6338.185
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6612e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6612e-01
   1_xyz:   1.303  0.010  0.089 15.897  0.005  4.109   9.6845e-02
   1_adp:   1.303  0.010  0.089 15.897  0.005  4.109   9.6845e-02
   1_occ:   1.303  0.010  0.089 15.897  0.005  4.109   9.6845e-02
   2_bss:   1.303  0.010  0.089 15.897  0.005  4.109   9.6845e-02
   2_xyz:   1.109  0.008  0.081 14.986  0.004  4.111   7.1328e-02
   2_adp:   1.109  0.008  0.081 14.986  0.004  4.111   7.1328e-02
   2_occ:   1.109  0.008  0.081 14.986  0.004  4.111   7.1328e-02
   3_bss:   1.109  0.008  0.081 14.986  0.004  4.111   7.1328e-02
   3_xyz:   1.013  0.008  0.076 14.845  0.004  4.115   6.2294e-02
   3_adp:   1.013  0.008  0.076 14.845  0.004  4.115   6.2294e-02
   3_occ:   1.013  0.008  0.076 14.845  0.004  4.115   6.2294e-02
   4_bss:   1.013  0.008  0.076 14.845  0.004  4.115   6.2294e-02
   4_xyz:   0.992  0.008  0.076 14.727  0.003  4.117   5.9856e-02
   4_adp:   0.992  0.008  0.076 14.727  0.003  4.117   5.9856e-02
   4_occ:   0.992  0.008  0.076 14.727  0.003  4.117   5.9856e-02
   5_bss:   0.992  0.008  0.076 14.727  0.003  4.117   5.9856e-02
   5_xyz:   0.966  0.007  0.074 14.588  0.003  4.120   5.7510e-02
   5_adp:   0.966  0.007  0.074 14.588  0.003  4.120   5.7510e-02
   5_occ:   0.966  0.007  0.074 14.588  0.003  4.120   5.7510e-02
   5_bss:   0.966  0.007  0.074 14.588  0.003  4.120   5.7510e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4127e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4127e-01
   1_xyz:   8.926  0.060  0.289 84.502  0.046  1.999   9.8665e-02
   1_adp:   8.926  0.060  0.289 84.502  0.046  1.999   9.8665e-02
   1_occ:   8.926  0.060  0.289 84.502  0.046  1.999   9.8665e-02
   2_bss:   8.926  0.060  0.289 84.502  0.046  1.999   9.8665e-02
   2_xyz:   6.464  0.049  0.308 81.594  0.028  2.310   1.0591e-01
   2_adp:   6.464  0.049  0.308 81.594  0.028  2.310   1.0591e-01
   2_occ:   6.464  0.049  0.308 81.594  0.028  2.310   1.0591e-01
   3_bss:   6.464  0.049  0.308 81.594  0.028  2.310   1.0591e-01
   3_xyz:   6.766  0.041  0.255 83.055  0.026  2.338   4.7157e-02
   3_adp:   6.766  0.041  0.255 83.055  0.026  2.338   4.7157e-02
   3_occ:   6.766  0.041  0.255 83.055  0.026  2.338   4.7157e-02
   4_bss:   6.766  0.041  0.255 83.055  0.026  2.338   4.7157e-02
   4_xyz:   7.108  0.046  0.243 83.345  0.030  2.339   4.2272e-02
   4_adp:   7.108  0.046  0.243 83.345  0.030  2.339   4.2272e-02
   4_occ:   7.108  0.046  0.243 83.345  0.030  2.339   4.2272e-02
   5_bss:   7.108  0.046  0.243 83.345  0.030  2.339   4.2272e-02
   5_xyz:   6.955  0.042  0.244 84.022  0.028  2.361   3.8624e-02
   5_adp:   6.955  0.042  0.244 84.022  0.028  2.361   3.8624e-02
   5_occ:   6.955  0.042  0.244 84.022  0.028  2.361   3.8624e-02
   5_bss:   6.955  0.042  0.244 84.022  0.028  2.361   3.8624e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  69.80   0.00  17.10  69.80   0.00  13.11  66.26   1.84  38.78
   1_occ:  69.80   0.00  17.10  69.80   0.00  13.11  66.26   1.84  38.78
   2_bss:  69.80   0.00  17.10  69.80   0.00  13.11  66.26   1.84  38.78
   2_xyz:  69.80   0.00  17.10  69.80   0.00  13.11  66.26   1.84  38.78
   2_adp:  76.44   0.00  17.42  73.09   0.00  12.99  76.44   5.82  41.53
   2_occ:  76.44   0.00  17.42  73.09   0.00  12.99  76.44   5.82  41.53
   3_bss:  76.44   0.00  17.42  73.09   0.00  12.99  76.44   5.82  41.53
   3_xyz:  76.44   0.00  17.42  73.09   0.00  12.99  76.44   5.82  41.53
   3_adp:  80.25   0.00  17.27  80.25   0.00  12.82  80.18   0.00  41.47
   3_occ:  80.25   0.00  17.27  80.25   0.00  12.82  80.18   0.00  41.47
   4_bss:  80.25   0.00  17.27  80.25   0.00  12.82  80.18   0.00  41.47
   4_xyz:  80.25   0.00  17.27  80.25   0.00  12.82  80.18   0.00  41.47
   4_adp:  84.75   0.22  17.02  84.75   0.30  12.67  82.60   0.22  40.67
   4_occ:  84.75   0.22  17.02  84.75   0.30  12.67  82.60   0.22  40.67
   5_bss:  84.75   0.22  17.02  84.75   0.30  12.67  82.60   0.22  40.67
   5_xyz:  84.75   0.22  17.02  84.75   0.30  12.67  82.60   0.22  40.67
   5_adp:  84.51   0.84  16.56  84.51   0.84  12.46  81.74   3.07  38.88
   5_occ:  84.51   0.84  16.56  84.51   0.84  12.46  81.74   3.07  38.88
   5_bss:  84.48   0.81  16.53  84.48   0.81  12.44  81.71   3.04  38.85
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.381    0.020    0.400
   1_adp:    1.381    0.020    0.400
   1_occ:    1.381    0.020    0.400
   2_bss:    1.381    0.020    0.400
   2_xyz:    1.254    0.036    0.503
   2_adp:    1.254    0.036    0.503
   2_occ:    1.254    0.036    0.503
   3_bss:    1.254    0.036    0.503
   3_xyz:    1.221    0.075    0.550
   3_adp:    1.221    0.075    0.550
   3_occ:    1.221    0.075    0.550
   4_bss:    1.221    0.075    0.550
   4_xyz:    1.349    0.050    0.565
   4_adp:    1.349    0.050    0.565
   4_occ:    1.349    0.050    0.565
   5_bss:    1.349    0.050    0.565
   5_xyz:    1.452    0.077    0.577
   5_adp:    1.452    0.077    0.577
   5_occ:    1.452    0.077    0.577
   5_bss:    1.452    0.077    0.577
------------------------------------------------------------------------

CPU time actual refinement: 328.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/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_756/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_756/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.36 
  Macro-tasks:
    bulk solvent and scale       = 35.63  
    individual site refinement   = 138.58 
    weights calculation          = 29.02  
    collect and process          = 6.52   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 209.84 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 105.32 
    alpha_beta                      = 8.06   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 115.54 
    fmodel                         = 6.46   
    r_factors                      = 0.25   
    phase_errors                   = 11.03  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.85 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.611 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    662 calls, 104.98 s
gradients_fft:          607 calls, 101.58 s

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

# Date 2008-01-16 Time 05:35:36 PST -0800 (1200490536.81 s)
Start R-work = 0.3986, R-free = 0.3942 (no bulk solvent and anisotropic scale)
Final R-work = 0.1345, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.3865, R-free = 0.3875
Final R-work = 0.1118, R-free = 0.1571