# Date 2008-01-16 Time 06:10:56 PST -0800 (1200492656.04 s)
#phil __OFF__

Command line arguments: "../1035.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11408
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1035

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (71.3037, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96132
Completeness in resolution range: 0.930196
Completeness with d_max=infinity: 0.927422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9613

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96132
Completeness in resolution range: 0.930196
Completeness with d_max=infinity: 0.927422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1980 [2210/2239]  1991   219   9.9%
  bin  2:  4.1980 -  3.3440 [2115/2138]  1904   211  10.0%
  bin  3:  3.3440 -  2.9248 [2092/2114]  1876   216  10.3%
  bin  4:  2.9248 -  2.6590 [2082/2101]  1885   197   9.5%
  bin  5:  2.6590 -  2.4693 [2063/2092]  1849   214  10.4%
  bin  6:  2.4693 -  2.3243 [2038/2080]  1838   200   9.8%
  bin  7:  2.3243 -  2.2082 [2044/2080]  1838   206  10.1%
  bin  8:  2.2082 -  2.1124 [2016/2053]  1816   200   9.9%
  bin  9:  2.1124 -  2.0313 [2053/2085]  1848   205  10.0%
  bin 10:  2.0313 -  1.9613 [ 876/2077]   785    91  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/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:
        1.73 -     2.36: 28
        2.36 -     3.00: 1912
        3.00 -     3.63: 4603
        3.63 -     4.27: 9133
        4.27 -     4.90: 12653
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.992 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.012 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28324 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_1035/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3842   r_free= 0.3913   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.163939                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.3067 0.3065      6.4104      6.3976|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.3010 0.2913      6.5733      6.5736|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.3395 0.3391      6.4718      6.5417|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.3662 0.3661      6.3529      6.3512|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.3902 0.3851      6.2165      6.2402|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.4249 0.4209      6.1683      6.1137|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.4121 0.3793       6.137      6.0649|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.4250 0.4519      6.0648      6.1281|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.4357 0.4372      6.0489      5.9974|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.4460 0.5241      6.0161      6.0922|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.4515 0.5288      5.9556      6.0353|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.4529 0.4889      5.8996      5.9606|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.4588 0.4429      5.8285       5.778|
| 14:  2.0103 -  1.9613 0.27    368   35 0.5333 0.5097      5.8008      5.7727|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.78  27.16   0.86     0.79      46426.75|
|  2:  4.6828 -  3.7355  1388   150  0.80  26.43   0.96     0.88      61363.19|
|  3:  3.7355 -  3.2688  1355   156  0.73  32.59   0.96     0.89      66627.31|
|  4:  3.2688 -  2.9724  1343   148  0.66  38.52   0.97     0.86      62103.94|
|  5:  2.9724 -  2.7608  1325   146  0.60  44.13   0.94     0.79      52102.15|
|  6:  2.7608 -  2.5989  1325   152  0.59  45.03   0.95     0.79      45022.97|
|  7:  2.5989 -  2.4693  1342   146  0.61  43.65   0.97     0.78      39598.84|
|  8:  2.4693 -  2.3622  1312   146  0.58  45.68   0.95     0.81      38353.46|
|  9:  2.3622 -  2.2716  1312   149  0.55  47.85   0.99     0.77      36211.37|
| 10:  2.2716 -  2.1935  1312   147  0.50  52.21   0.99     0.72      39179.24|
| 11:  2.1935 -  2.1251  1315   138  0.46  55.62   0.99     0.67      37600.51|
| 12:  2.1251 -  2.0645  1308   144  0.43  57.55   0.98     0.67      36810.03|
| 13:  2.0645 -  2.0103  1198   143  0.44  57.08   0.98     0.66      30430.87|
| 14:  2.0103 -  1.9613   368    35  0.42  58.42   0.91     0.61      25533.27|
|alpha:            min =        0.61 max =            0.89 mean =         0.77|
|beta:             min =    25533.27 max =        66627.31 mean =     45355.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.10|
|phase err.(test): min =        0.00 max =           89.91 mean =        44.15|
|-----------------------------------------------------------------------------|

============================== 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 = 6.345341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.127   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.303107              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.279   (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 |  1.731 -  2.047:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.047 -  2.364:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.364 -  2.681:       88 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.681 -  2.998:     1824 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.998 -  3.315:     1896 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.315 -  3.632:     2707 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.632 -  3.949:     4730 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.949 -  4.266:     4403 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.266 -  4.583:     5794 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6859 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.731 |       0.294 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3842   r_free= 0.3913   ksol= 0.00   Bsol= 0.00   scale= 0.943    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.163939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3738   r_free= 0.3822   ksol= 0.32   Bsol= 39.71   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-1.98,2.08,-0.00,0.00,0.00); trace/3= -0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.154054                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.099093              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.330   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.628019              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.049   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3738      final r-factor (work) = 0.2360          |
| start r-factor (free) = 0.3822      final r-factor (free) = 0.2669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8529 = 5.10 * 0.50 * 6.1512 + 1.00 * 0.1702                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2270 = 5.10 * 0.50 * 5.9375 + 1.00 * 0.0892                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2360      final r-factor (work) = 0.2179          |
| start r-factor (free) = 0.2669      final r-factor (free) = 0.2734          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7353 = 0.63 * 1.00 * 5.9375 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6252 = 0.63 * 1.00 * 5.7136 + 1.00 * 0.0369                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.47   16.92    None  None   None       |
|    all(noH): 2823   0      0.00    72.47   16.92    None  None   None       |
|    Sol.    : 438    0      6.51    63.51   38.27    None  None   None       |
|    Mac.    : 2385   0      0.00    72.47   13.00    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 -   7.247:  452   |   5:    36.236 -  43.483:  119        |
|      1:     7.247 -  14.494: 1198   |   6:    43.483 -  50.730:   97        |
|      2:    14.494 -  21.741:  552   |   7:    50.730 -  57.977:   71        |
|      3:    21.741 -  28.989:  193   |   8:    57.977 -  65.224:   16        |
|      4:    28.989 -  36.236:  124   |   9:    65.224 -  72.471:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2179 r_free = 0.2734             target_work(ml) = 5.725         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2173 r_free = 0.2734             target_work(ml) = 5.723         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2173   r_free= 0.2734   ksol= 0.32   Bsol= 39.71   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-1.98,2.08,-0.00,0.00,0.00); trace/3= -0.09                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.723478                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2153   r_free= 0.2707   ksol= 0.33   Bsol= 53.66   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.45,-0.73,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.719037                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.758085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.392   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.434210              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.851   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2153      final r-factor (work) = 0.1530          |
| start r-factor (free) = 0.2707      final r-factor (free) = 0.1968          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8426 = 3.76 * 0.50 * 5.7228 + 1.00 * 0.0892                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5701 = 3.76 * 0.50 * 5.5922 + 1.00 * 0.0621                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1530      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.1968      final r-factor (free) = 0.1839          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4698 = 0.43 * 1.00 * 5.5922 + 1.00 * 0.0417                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3363 = 0.43 * 1.00 * 5.3597 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.77   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    75.77   17.37    None  None   None       |
|    Sol.    : 438    0      5.76    71.67   40.82    None  None   None       |
|    Mac.    : 2385   0      0.00    75.77   13.06    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 -   7.577:  453   |   5:    37.887 -  45.464:  103        |
|      1:     7.577 -  15.155: 1379   |   6:    45.464 -  53.042:  109        |
|      2:    15.155 -  22.732:  422   |   7:    53.042 -  60.619:   70        |
|      3:    22.732 -  30.310:  139   |   8:    60.619 -  68.196:   36        |
|      4:    30.310 -  37.887:  101   |   9:    68.196 -  75.774:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1378 r_free = 0.1839             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1836             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1836   ksol= 0.33   Bsol= 53.66   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.45,-0.73,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.320123                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1827   ksol= 0.33   Bsol= 53.66   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.29,-1.58,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.317891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.351136              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.385  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.312781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.377  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1376      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1827      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0428 = 3.35 * 0.50 * 5.3598 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8692 = 3.35 * 0.50 * 5.2531 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1616      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6521 = 0.31 * 1.00 * 5.2531 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6265 = 0.31 * 1.00 * 5.1735 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    80.76   17.10    None  None   None       |
|    all(noH): 2823   0      1.35    80.76   17.10    None  None   None       |
|    Sol.    : 438    0      4.18    75.46   39.81    None  None   None       |
|    Mac.    : 2385   0      1.35    80.76   12.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.346 -   9.287:  845   |   5:    41.054 -  48.996:  101        |
|      1:     9.287 -  17.229: 1181   |   6:    48.996 -  56.938:   89        |
|      2:    17.229 -  25.171:  303   |   7:    56.938 -  64.879:   44        |
|      3:    25.171 -  33.113:  119   |   8:    64.879 -  72.821:   20        |
|      4:    33.113 -  41.054:  115   |   9:    72.821 -  80.763:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1585             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1583             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1583   ksol= 0.33   Bsol= 53.66   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.29,-1.58,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1582   ksol= 0.33   Bsol= 53.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.27,-1.84,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.160123                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.567324              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.866  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.456787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.294  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1216 = 1.57 * 0.50 * 5.1732 + 1.00 * 0.0676                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0986 = 1.57 * 0.50 * 5.1629 + 1.00 * 0.0526                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1577      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3667 = 0.46 * 1.00 * 5.1629 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3646 = 0.46 * 1.00 * 5.1573 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.41    86.79   17.06    None  None   None       |
|    all(noH): 2823   0      1.41    86.79   17.06    None  None   None       |
|    Sol.    : 438    0      5.15    78.73   39.80    None  None   None       |
|    Mac.    : 2385   0      1.41    86.79   12.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.406 -   9.944: 1011   |   5:    44.097 -  52.636:  114        |
|      1:     9.944 -  18.482: 1105   |   6:    52.636 -  61.174:   56        |
|      2:    18.482 -  27.021:  245   |   7:    61.174 -  69.712:   35        |
|      3:    27.021 -  35.559:  123   |   8:    69.712 -  78.250:    9        |
|      4:    35.559 -  44.097:  119   |   9:    78.250 -  86.789:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1584             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1584             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1584   ksol= 0.33   Bsol= 53.66   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.27,-1.84,-0.00,-0.00,-0.00); trace/3= -2.11                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.160200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1583   ksol= 0.33   Bsol= 53.66   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.17,-1.83,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162199                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.863223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.333  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.957275              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.343  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1101          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8583 = 1.86 * 0.50 * 5.1584 + 1.00 * 0.0526                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8548 = 1.86 * 0.50 * 5.1495 + 1.00 * 0.0574                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9383 = 0.96 * 1.00 * 5.1495 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9351 = 0.96 * 1.00 * 5.1453 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    94.92   17.04    None  None   None       |
|    all(noH): 2823   0      0.58    94.92   17.04    None  None   None       |
|    Sol.    : 438    0      5.97    84.42   40.10    None  None   None       |
|    Mac.    : 2385   0      0.58    94.92   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.581 -  10.015: 1072   |   5:    47.748 -  57.182:  103        |
|      1:    10.015 -  19.448: 1092   |   6:    57.182 -  66.615:   44        |
|      2:    19.448 -  28.881:  215   |   7:    66.615 -  76.048:   22        |
|      3:    28.881 -  38.315:  144   |   8:    76.048 -  85.482:    8        |
|      4:    38.315 -  47.748:  118   |   9:    85.482 -  94.915:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1588             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1588             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1588   ksol= 0.33   Bsol= 53.66   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.17,-1.83,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149037                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.0966 0.1271      5.3707      5.5301|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.0831 0.1032      5.4044      5.6085|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.1034 0.1632      5.4453      5.8644|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.1205 0.1515      5.4442      5.5728|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.1290 0.1790      5.3115      5.5253|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.1226 0.1855      5.2125      5.4471|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.1213 0.1713      5.1598      5.3796|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.1118 0.1744      5.0445      5.2859|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.1156 0.1931      5.0221      5.3402|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.1108 0.1654      4.9681      5.2114|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.1133 0.1881       4.945       5.308|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.1117 0.1655      4.8854      5.0944|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.1131 0.1767       4.784      5.0422|
| 14:  2.0103 -  1.9613 0.27    368   35 0.1063 0.1759      4.6298      4.9222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.94   8.77   0.97     0.95       6902.73|
|  2:  4.6828 -  3.7355  1388   150  0.95   7.87   1.01     0.99       8452.38|
|  3:  3.7355 -  3.2688  1355   156  0.94  10.91   1.02     1.03       9794.44|
|  4:  3.2688 -  2.9724  1343   148  0.92  14.02   1.00     0.98      10348.54|
|  5:  2.9724 -  2.7608  1325   146  0.90  16.26   0.99     0.96       8360.74|
|  6:  2.7608 -  2.5989  1325   152  0.90  16.48   0.98     0.95       7246.84|
|  7:  2.5989 -  2.4693  1342   146  0.91  15.37   0.99     0.96       6282.99|
|  8:  2.4693 -  2.3622  1312   146  0.90  15.70   0.98     0.95       5305.68|
|  9:  2.3622 -  2.2716  1312   149  0.90  16.06   0.99     0.95       4988.66|
| 10:  2.2716 -  2.1935  1312   147  0.91  15.62   0.98     0.95       4617.49|
| 11:  2.1935 -  2.1251  1315   138  0.90  16.82   0.98     0.94       4554.08|
| 12:  2.1251 -  2.0645  1308   144  0.90  16.49   0.99     0.98       4229.40|
| 13:  2.0645 -  2.0103  1198   143  0.90  16.26   0.98     0.97       3379.79|
| 14:  2.0103 -  1.9613   368    35  0.90  15.88   0.98     0.94       2478.27|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2478.27 max =        10348.54 mean =      6461.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1588   ksol= 0.33   Bsol= 53.64   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.94,-1.62,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1096   r_free= 0.1588   ksol= 0.33   Bsol= 53.64   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-1.94,-1.62,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149161                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6828 0.99   1427  159 0.0967 0.1273      5.3718      5.5317|
|  2:  4.6828 -  3.7355 0.99   1388  150 0.0831 0.1032      5.4049      5.6084|
|  3:  3.7355 -  3.2688 0.99   1355  156 0.1034 0.1632      5.4451      5.8644|
|  4:  3.2688 -  2.9724 0.99   1343  148 0.1205 0.1515      5.4442      5.5729|
|  5:  2.9724 -  2.7608 0.99   1325  146 0.1290 0.1790      5.3115      5.5252|
|  6:  2.7608 -  2.5989 0.98   1325  152 0.1226 0.1855      5.2127      5.4472|
|  7:  2.5989 -  2.4693 0.99   1342  146 0.1213 0.1712        5.16      5.3798|
|  8:  2.4693 -  2.3622 0.99   1312  146 0.1118 0.1745      5.0447       5.286|
|  9:  2.3622 -  2.2716 0.98   1312  149 0.1156 0.1930      5.0222      5.3399|
| 10:  2.2716 -  2.1935 0.98   1312  147 0.1107 0.1653      4.9681      5.2112|
| 11:  2.1935 -  2.1251 0.98   1315  138 0.1133 0.1881      4.9451      5.3082|
| 12:  2.1251 -  2.0645 0.99   1308  144 0.1117 0.1654      4.8851      5.0942|
| 13:  2.0645 -  2.0103 0.91   1198  143 0.1131 0.1766      4.7839      5.0419|
| 14:  2.0103 -  1.9613 0.27    368   35 0.1063 0.1760      4.6299      4.9225|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6828  1427   159  0.94   8.79   0.98     0.95       6918.63|
|  2:  4.6828 -  3.7355  1388   150  0.95   7.87   1.01     1.00       8459.43|
|  3:  3.7355 -  3.2688  1355   156  0.94  10.91   1.03     1.03       9791.23|
|  4:  3.2688 -  2.9724  1343   148  0.92  14.02   1.01     0.99      10347.38|
|  5:  2.9724 -  2.7608  1325   146  0.90  16.26   0.99     0.97       8361.06|
|  6:  2.7608 -  2.5989  1325   152  0.90  16.49   0.99     0.96       7248.39|
|  7:  2.5989 -  2.4693  1342   146  0.91  15.38   0.99     0.97       6284.57|
|  8:  2.4693 -  2.3622  1312   146  0.90  15.71   0.99     0.96       5305.50|
|  9:  2.3622 -  2.2716  1312   149  0.90  16.06   1.00     0.96       4987.29|
| 10:  2.2716 -  2.1935  1312   147  0.91  15.62   0.99     0.96       4616.42|
| 11:  2.1935 -  2.1251  1315   138  0.90  16.82   0.99     0.95       4552.85|
| 12:  2.1251 -  2.0645  1308   144  0.90  16.49   1.00     0.99       4227.40|
| 13:  2.0645 -  2.0103  1198   143  0.90  16.26   0.99     0.98       3378.92|
| 14:  2.0103 -  1.9613   368    35  0.90  15.89   0.99     0.96       2478.95|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2478.95 max =        10347.38 mean =      6462.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.88 mean =        13.85|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.914)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.56    94.90   17.02    None  None   None       |
|    all(noH): 2823   0      0.56    94.90   17.02    None  None   None       |
|    Sol.    : 438    0      5.96    84.40   40.08    None  None   None       |
|    Mac.    : 2385   0      0.56    94.90   12.79    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:     0.562 -   9.996: 1072   |   5:    47.729 -  57.163:  103        |
|      1:     9.996 -  19.429: 1092   |   6:    57.163 -  66.596:   44        |
|      2:    19.429 -  28.863:  215   |   7:    66.596 -  76.030:   22        |
|      3:    28.863 -  38.296:  144   |   8:    76.030 -  85.463:    8        |
|      4:    38.296 -  47.729:  118   |   9:    85.463 -  94.896:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 299         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 5.890
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 299
   mapped sites are within: 0.702 - 5.890

peak=    6.018 closest distance to " NH2 ARG A  56 " =    2.203
peak=    5.886 closest distance to " CB  GLN A 223 " =    1.428
peak=    5.587 closest distance to " CG  PRO A  54 " =    1.211
peak=    5.301 closest distance to " CB  SER A  63 " =    1.274
peak=    5.175 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.959 closest distance to " O   HOH Z 232 " =    2.258
peak=    4.923 closest distance to " CB  GLN A 183 " =    1.263
peak=    4.920 closest distance to " CB  GLU A 128 " =    1.119
peak=    4.913 closest distance to " O   HOH Z 126 " =    1.977
peak=    4.864 closest distance to " CB  PRO A  54 " =    0.897
peak=    4.783 closest distance to " O   HOH Z 193 " =    1.918
peak=    4.718 closest distance to " CG  PRO A  90 " =    1.080
peak=    4.668 closest distance to " CG  PRO A 198 " =    1.281
peak=    4.649 closest distance to " NE2 GLN A  11 " =    1.074
peak=    4.589 closest distance to " O   HOH Z 298 " =    1.837
peak=    4.584 closest distance to " C   PRO A 198 " =    1.537
peak=    4.566 closest distance to " CB  ARG A 275 " =    0.895
peak=    4.552 closest distance to " CB  LEU A 228 " =    1.137
peak=    4.516 closest distance to " CA  TYR A  30 " =    0.960
peak=    4.505 closest distance to " O   HOH Z  15 " =    2.139
peak=    4.445 closest distance to " O   HOH Z 236 " =    1.984
peak=    4.431 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.412 closest distance to " CB  TYR A 169 " =    0.792
peak=    4.408 closest distance to " CB  SER A   3 " =    1.350
peak=    4.360 closest distance to " OD1 ASN A  69 " =    2.560
peak=    4.336 closest distance to " O   HOH Z 368 " =    1.981
peak=    4.331 closest distance to " OD2 ASP A 286 " =    2.881
peak=    4.262 closest distance to " O   HOH Z  78 " =    1.648
peak=    4.247 closest distance to " CB  VAL A 202 " =    1.661
peak=    4.235 closest distance to " O   HOH Z 344 " =    3.099
peak=    4.205 closest distance to " CB  TRP A 179 " =    1.434
peak=    4.203 closest distance to " O   HOH Z 427 " =    2.908
peak=    4.194 closest distance to " O   HOH Z 209 " =    2.282
peak=    4.180 closest distance to " O   HOH Z 135 " =    1.762
peak=    4.165 closest distance to " O   HOH Z 316 " =    3.045
peak=    4.153 closest distance to " CA  THR A 221 " =    0.975
peak=    4.135 closest distance to " CA  ALA A  21 " =    1.191
peak=    4.132 closest distance to " O   HOH Z 389 " =    1.940
peak=    4.123 closest distance to " CB  ASN A 148 " =    1.328
peak=    4.116 closest distance to " O   HOH Z 352 " =    1.896
peak=    4.109 closest distance to " NH2 ARG A 156 " =    1.201
peak=    4.100 closest distance to " O   HOH Z 144 " =    1.634
peak=    4.095 closest distance to " CG2 THR A 221 " =    1.021
peak=    4.088 closest distance to " O   HOH Z 234 " =    3.763
peak=    4.068 closest distance to " O   HOH Z 108 " =    1.431
peak=    4.050 closest distance to " O   HOH Z 369 " =    2.039
peak=    4.048 closest distance to " O   HOH Z 134 " =    1.391
peak=    4.023 closest distance to " CG  PRO A 243 " =    1.159
peak=    4.020 closest distance to " O   HOH Z 247 " =    1.310
peak=    4.009 closest distance to " CB  ARG A 190 " =    1.706
peak=    3.986 closest distance to " O   HOH Z 108 " =    1.979
peak=    3.983 closest distance to " CD BLYS A 290 " =    1.007
peak=    3.982 closest distance to " O   HOH Z 132 " =    2.603
peak=    3.981 closest distance to " O   HOH Z  68 " =    1.661
peak=    3.981 closest distance to " CB  ARG A  79 " =    1.400
peak=    3.968 closest distance to " O   HOH Z 425 " =    1.355
peak=    3.964 closest distance to " CD1 LEU A 300 " =    1.241
peak=    3.925 closest distance to " CA  MET A  40 " =    1.082
peak=    3.918 closest distance to " O   HOH Z 133 " =    2.333
peak=    3.915 closest distance to " CA  ASP A 124 " =    0.702
peak=    3.907 closest distance to " CG1 ILE A  33 " =    1.276
peak=    3.904 closest distance to " ND2 ASN A 187 " =    1.530
peak=    3.896 closest distance to " O   HOH Z  20 " =    1.741
peak=    3.885 closest distance to " O   HOH Z 371 " =    3.252
peak=    3.876 closest distance to " CB  VAL A 265 " =    1.184
peak=    3.875 closest distance to " O   HOH Z 303 " =    2.050
peak=    3.848 closest distance to " CB  ASN A 148 " =    1.673
peak=    3.847 closest distance to " O   HOH Z 180 " =    2.208
peak=    3.842 closest distance to " O   HOH Z 426 " =    1.508
peak=    3.827 closest distance to " O   HOH Z  88 " =    3.592
peak=    3.822 closest distance to " O   HOH Z 346 " =    1.659
peak=    3.821 closest distance to " O   HOH Z 214 " =    2.016
peak=    3.818 closest distance to " O   HOH Z  54 " =    2.299
peak=    3.813 closest distance to " O   HOH Z 189 " =    2.241
peak=    3.792 closest distance to " O   HOH Z 207 " =    1.895
peak=    3.791 closest distance to " O   HOH Z 403 " =    1.716
peak=    3.786 closest distance to " O   HOH Z  97 " =    1.876
peak=    3.785 closest distance to " O   HOH Z 193 " =    2.110
peak=    3.780 closest distance to " O   HOH Z 261 " =    2.013
peak=    3.779 closest distance to " O   MET A 105 " =    1.865
peak=    3.778 closest distance to " CD  ARG A 159 " =    0.826
peak=    3.778 closest distance to " CB  TRP A 266 " =    0.927
peak=    3.772 closest distance to " O   HOH Z  61 " =    1.595
peak=    3.771 closest distance to " NH1AARG A 145 " =    1.069
peak=    3.764 closest distance to " O   HOH Z 183 " =    1.482
peak=    3.759 closest distance to " CB  MET A  47 " =    1.000
peak=    3.758 closest distance to " O   HOH Z  40 " =    1.690
peak=    3.739 closest distance to " CB  GLU A 277 " =    3.626
peak=    3.739 closest distance to " O   HOH Z  21 " =    1.662
peak=    3.727 closest distance to " O   HOH Z 280 " =    3.070
peak=    3.725 closest distance to " O   HOH Z 411 " =    1.856
peak=    3.716 closest distance to " O   HOH Z 272 " =    1.865
peak=    3.712 closest distance to " NH2BARG A 145 " =    2.087
peak=    3.710 closest distance to " CD  ARG A  66 " =    2.440
peak=    3.708 closest distance to " O   HOH Z 411 " =    3.762
peak=    3.690 closest distance to " CD  ARG A 269 " =    0.905
peak=    3.689 closest distance to " CA  ASN A 215 " =    1.231
peak=    3.685 closest distance to " O   HOH Z  54 " =    1.689
peak=    3.680 closest distance to " O   ALA A 165 " =    1.387
peak=    3.674 closest distance to " CD  LYS A 119 " =    1.247
peak=    3.671 closest distance to " ND1 HIS A  86 " =    1.746
peak=    3.652 closest distance to " O   HOH Z 295 " =    1.486
peak=    3.648 closest distance to " CB  ARG A 139 " =    0.830
peak=    3.644 closest distance to " CA  ALA A  51 " =    0.966
peak=    3.638 closest distance to " O   HOH Z 133 " =    1.705
peak=    3.625 closest distance to " O   HOH Z  93 " =    2.584
peak=    3.625 closest distance to " CG2 VAL A 257 " =    0.946
peak=    3.621 closest distance to " O   HOH Z  43 " =    1.882
peak=    3.616 closest distance to " NZ  LYS A 117 " =    3.317
peak=    3.615 closest distance to " CB  SER A 141 " =    1.023
peak=    3.613 closest distance to " CG1 ILE A 151 " =    0.908
peak=    3.611 closest distance to " N   ASN A  39 " =    1.326
peak=    3.609 closest distance to " CB  SER A 216 " =    0.809
peak=    3.608 closest distance to " O   HOH Z 172 " =    3.846
peak=    3.601 closest distance to " CD2 LEU A 255 " =    1.406
peak=    3.597 closest distance to " O   SER A  87 " =    2.223
peak=    3.595 closest distance to " OG BSER A 164 " =    2.428
peak=    3.587 closest distance to " CB  SER A 212 " =    1.074
peak=    3.585 closest distance to " CG1 VAL A 202 " =    2.035
peak=    3.579 closest distance to " CB  ASP A 140 " =    0.920
peak=    3.578 closest distance to " N   ASN A 127 " =    1.241
peak=    3.575 closest distance to " CA  ASP A 140 " =    1.157
peak=    3.573 closest distance to " CB  TYR A 169 " =    0.838
peak=    3.563 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.553 closest distance to " CA  THR A 264 " =    0.879
peak=    3.548 closest distance to " O   HOH Z 193 " =    1.666
peak=    3.548 closest distance to " O   HOH Z   6 " =    2.172
peak=    3.547 closest distance to " OD1 ASN A 217 " =    1.694
peak=    3.545 closest distance to " O   HOH Z  48 " =    1.364
peak=    3.543 closest distance to " O   HOH Z 423 " =    1.863
peak=    3.540 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.539 closest distance to " O   HOH Z 245 " =    1.305
peak=    3.538 closest distance to " O   HOH Z 409 " =    3.100
peak=    3.536 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.534 closest distance to " CG  LEU A 167 " =    1.183
peak=    3.531 closest distance to " O   HOH Z 368 " =    3.727
peak=    3.526 closest distance to " ND1 HIS A  81 " =    1.564
peak=    3.521 closest distance to " O   HOH Z  61 " =    1.545
peak=    3.508 closest distance to " O   HOH Z  10 " =    1.868
peak=    3.504 closest distance to " CA  ARG A  36 " =    1.144
peak=    3.502 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.499 closest distance to " CA  ALA A 160 " =    0.817
peak=    3.497 closest distance to " N   ARG A 156 " =    1.357
peak=    3.492 closest distance to " CD1 ILE A 106 " =    0.927
peak=    3.487 closest distance to " O   HOH Z 374 " =    2.647
peak=    3.486 closest distance to " CG2BVAL A  41 " =    0.891
peak=    3.485 closest distance to " O   HOH Z 147 " =    1.669
peak=    3.484 closest distance to " CB  LEU A 143 " =    1.095
peak=    3.482 closest distance to " CA  ARG A 195 " =    1.253
peak=    3.479 closest distance to " O   HOH Z 163 " =    1.490
peak=    3.479 closest distance to " O   HOH Z 158 " =    2.968
peak=    3.475 closest distance to " O   HOH Z 128 " =    2.201
peak=    3.475 closest distance to " O   HOH Z 227 " =    1.648
peak=    3.474 closest distance to " O   HOH Z  40 " =    2.307
peak=    3.474 closest distance to " O   HOH Z 197 " =    2.778
peak=    3.467 closest distance to " O   HOH Z 427 " =    3.129
peak=    3.465 closest distance to " O   HOH Z 281 " =    4.356
peak=    3.462 closest distance to " CD2 LEU A 297 " =    0.889
peak=    3.452 closest distance to " CA  ALA A 154 " =    1.012
peak=    3.442 closest distance to " O   HOH Z  49 " =    2.290
peak=    3.441 closest distance to " O   HOH Z  80 " =    1.626
peak=    3.437 closest distance to " O   HOH Z 211 " =    2.577
peak=    3.433 closest distance to " CD  ARG A 219 " =    1.002
peak=    3.423 closest distance to " O   HOH Z 128 " =    2.162
peak=    3.423 closest distance to " CB  LEU A 255 " =    0.719
peak=    3.421 closest distance to " CA  ASP A 191 " =    0.796
peak=    3.421 closest distance to " CB  VAL A 265 " =    1.619
peak=    3.413 closest distance to " NZ  LYS A 166 " =    3.055
peak=    3.408 closest distance to " O   TRP A 274 " =    1.826
peak=    3.405 closest distance to " O   HOH Z 437 " =    1.562
peak=    3.404 closest distance to " O   HOH Z  44 " =    1.801
peak=    3.391 closest distance to " O   ALA A 158 " =    1.277
peak=    3.390 closest distance to " O   THR A 220 " =    1.353
peak=    3.388 closest distance to " CG2 VAL A  78 " =    0.938
peak=    3.387 closest distance to " CG1BVAL A  72 " =    1.632
peak=    3.385 closest distance to " O   HOH Z  59 " =    2.192
peak=    3.381 closest distance to " CE1 TYR A 186 " =    1.242
peak=    3.380 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.380 closest distance to " O   HOH Z 345 " =    3.400
peak=    3.378 closest distance to " CA  GLY A 267 " =    1.145
peak=    3.375 closest distance to " CB  ALA A 291 " =    1.382
peak=    3.369 closest distance to " NH2AARG A 190 " =    1.381
peak=    3.363 closest distance to " CB  GLU A 152 " =    1.554
peak=    3.362 closest distance to " CG2 VAL A 197 " =    1.119
peak=    3.361 closest distance to " O   HOH Z   1 " =    2.034
peak=    3.361 closest distance to " CD  PRO A 280 " =    0.982
peak=    3.358 closest distance to " CG2 VAL A 174 " =    1.349
peak=    3.355 closest distance to " O   HOH Z 327 " =    2.380
peak=    3.349 closest distance to " O   HOH Z  64 " =    2.275
peak=    3.349 closest distance to " O   HOH Z  63 " =    2.011
peak=    3.339 closest distance to " O   HOH Z 407 " =    2.651
peak=    3.335 closest distance to " CG  MET A 113 " =    1.397
peak=    3.335 closest distance to " CA  TYR A 186 " =    1.404
peak=    3.334 closest distance to " C   TYR A 214 " =    1.542
peak=    3.333 closest distance to " O   HOH Z 286 " =    2.207
peak=    3.333 closest distance to " O   HOH Z 112 " =    1.506
peak=    3.333 closest distance to " CG2 ILE A 120 " =    1.148
peak=    3.332 closest distance to " O   HOH Z 175 " =    2.145
peak=    3.327 closest distance to " O   HOH Z 273 " =    2.803
peak=    3.327 closest distance to " NH2 ARG A 219 " =    1.875
peak=    3.326 closest distance to " O   HOH Z 334 " =    1.542
peak=    3.324 closest distance to " CA  LYS A 290 " =    1.338
peak=    3.324 closest distance to " CG BARG A 102 " =    1.884
peak=    3.322 closest distance to " O   HOH Z 174 " =    2.602
peak=    3.319 closest distance to " OG1 THR A 294 " =    1.639
peak=    3.314 closest distance to " O   HOH Z 391 " =    2.927
peak=    3.312 closest distance to " O   HOH Z 171 " =    3.831
peak=    3.312 closest distance to " CB  TYR A 116 " =    0.931
peak=    3.311 closest distance to " O   HOH Z 250 " =    1.839
peak=    3.310 closest distance to " CB  ALA A 248 " =    0.974
peak=    3.309 closest distance to " CB  ALA A  71 " =    1.313
peak=    3.307 closest distance to " O   HOH Z  66 " =    2.064
peak=    3.305 closest distance to " O   HOH Z 250 " =    1.624
peak=    3.294 closest distance to " CB  PRO A 198 " =    0.972
peak=    3.293 closest distance to " CA  ALA A 158 " =    1.097
peak=    3.291 closest distance to " CB  PHE A  16 " =    0.968
peak=    3.290 closest distance to " CG  MET A 185 " =    1.244
peak=    3.289 closest distance to " OG  SER A  22 " =    2.820
peak=    3.287 closest distance to " O   HOH Z 116 " =    1.841
peak=    3.282 closest distance to " O   HOH Z 425 " =    1.982
peak=    3.280 closest distance to " O   HOH Z 406 " =    1.633
peak=    3.279 closest distance to " O   HOH Z 173 " =    1.857
peak=    3.279 closest distance to " O   THR A 251 " =    1.209
peak=    3.273 closest distance to " O   HOH Z  53 " =    2.498
peak=    3.272 closest distance to " O   HOH Z  66 " =    1.949
peak=    3.266 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.260 closest distance to " O   HOH Z 188 " =    2.115
peak=    3.259 closest distance to " OD1 ASP A 231 " =    1.855
peak=    3.256 closest distance to " O   HOH Z 329 " =    3.555
peak=    3.250 closest distance to " CA  ALA A 248 " =    1.175
peak=    3.244 closest distance to " O   HOH Z 118 " =    1.556
peak=    3.239 closest distance to " OE1 GLU A 152 " =    0.856
peak=    3.235 closest distance to " CG BARG A 275 " =    1.462
peak=    3.232 closest distance to " CA  LEU A 282 " =    1.117
peak=    3.230 closest distance to " O   HOH Z 313 " =    1.674
peak=    3.229 closest distance to " CG  GLN A  58 " =    2.618
peak=    3.228 closest distance to " CG2 THR A 220 " =    1.051
peak=    3.225 closest distance to " CB  MET A  40 " =    0.842
peak=    3.223 closest distance to " O   HOH Z 365 " =    2.850
peak=    3.222 closest distance to " CB  GLU A  46 " =    1.016
peak=    3.222 closest distance to " O   HOH Z  44 " =    3.407
peak=    3.213 closest distance to " O   HOH Z 368 " =    2.501
peak=    3.212 closest distance to " O   HOH Z   4 " =    1.861
peak=    3.204 closest distance to " OG  SER A  97 " =    3.518
peak=    3.204 closest distance to " CG1 VAL A 153 " =    1.008
peak=    3.203 closest distance to " CD1AILE A 234 " =    0.994
peak=    3.201 closest distance to " O   HOH Z 403 " =    1.329
peak=    3.201 closest distance to " CA  GLU A 152 " =    0.832
peak=    3.199 closest distance to " O   HOH Z 213 " =    1.673
peak=    3.198 closest distance to " CA  LEU A  83 " =    1.503
peak=    3.197 closest distance to " O   HOH Z 163 " =    1.641
peak=    3.192 closest distance to " CD2 HIS A  81 " =    1.111
peak=    3.191 closest distance to " O   HOH Z 388 " =    1.913
peak=    3.191 closest distance to " O   HOH Z 337 " =    3.730
peak=    3.184 closest distance to " CA  SER A  87 " =    0.973
peak=    3.184 closest distance to " O   HOH Z 279 " =    2.266
peak=    3.183 closest distance to " CB  ASN A  39 " =    0.890
peak=    3.181 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.176 closest distance to " CG  MET A 185 " =    1.084
peak=    3.172 closest distance to " CZ2 TRP A 179 " =    1.678
peak=    3.162 closest distance to " O   ALA A   1 " =    1.468
peak=    3.153 closest distance to " CA  LEU A 101 " =    1.556
peak=    3.151 closest distance to " ND2 ASN A 301 " =    1.455
peak=    3.151 closest distance to " C   SER A  32 " =    1.051
peak=    3.149 closest distance to " CA  VAL A 126 " =    1.199
peak=    3.148 closest distance to " OH  TYR A  30 " =    1.213
peak=    3.144 closest distance to " O   HOH Z 353 " =    2.763
peak=    3.144 closest distance to " CA  ILE A  33 " =    1.651
peak=    3.141 closest distance to " O   HOH Z 163 " =    1.827
peak=    3.137 closest distance to " O   HOH Z 368 " =    2.565
peak=    3.133 closest distance to " OG  SER A  62 " =    3.064
peak=    3.122 closest distance to " O   HOH Z 166 " =    3.632
peak=    3.119 closest distance to " O   ALA A 233 " =    1.810
peak=    3.109 closest distance to " CA  MET A 105 " =    1.052
peak=    3.108 closest distance to " O   HOH Z 301 " =    1.927
peak=    3.108 closest distance to " CB  THR A 157 " =    1.044
peak=    3.105 closest distance to " NE2 GLN A  58 " =    4.287
peak=    3.103 closest distance to " CD  GLN A  58 " =    5.890
peak=    3.101 closest distance to " CB  PRO A 243 " =    1.165
peak=    3.100 closest distance to " CZ  PHE A 208 " =    1.172
peak=    3.096 closest distance to " O   HOH Z 189 " =    1.391
peak=    3.093 closest distance to " O   HOH Z 207 " =    1.987
peak=    3.089 closest distance to " NZ  LYS A  76 " =    1.223
peak=    3.086 closest distance to " CA  GLN A 223 " =    0.956
peak=    3.086 closest distance to " O   HOH Z  64 " =    2.228
peak=    3.085 closest distance to " OE1 GLN A  11 " =    1.927
peak=    3.079 closest distance to " CA  ASP A 162 " =    1.212
peak=    3.078 closest distance to " O   HOH Z  88 " =    2.930
peak=    3.077 closest distance to " O   HOH Z 345 " =    1.658
peak=    3.077 closest distance to " O   HOH Z 410 " =    1.923
peak=    3.075 closest distance to " OG  SER A 206 " =    1.199
peak=    3.067 closest distance to " CA  ILE A 234 " =    0.922
peak=    3.031 closest distance to " CB  TYR A  30 " =    1.443
peak=    3.016 closest distance to " OG ASER A  99 " =    2.135

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.492
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.863 - 5.492

peak=   -4.792 closest distance to " O   HOH Z 266 " =    4.400
peak=   -4.451 closest distance to " O   HOH Z 377 " =    1.835
peak=   -4.326 closest distance to " O   ILE A 109 " =    2.636
peak=   -4.315 closest distance to " CB  PRO A 243 " =    2.584
peak=   -4.273 closest distance to " O   HOH Z 198 " =    2.269
peak=   -4.208 closest distance to " CD  ARG A 156 " =    1.963
peak=   -4.203 closest distance to " C   ASN A 187 " =    1.878
peak=   -4.125 closest distance to " O   HOH Z 372 " =    2.462
peak=   -4.121 closest distance to " N   ALA A  43 " =    2.539
peak=   -4.057 closest distance to " O   HOH Z 290 " =    1.163
peak=   -4.050 closest distance to " SG  CYS A 254 " =    3.385
peak=   -4.023 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -4.016 closest distance to " O   HOH Z  19 " =    2.363
peak=   -3.989 closest distance to " O   HOH Z 231 " =    2.091
peak=   -3.981 closest distance to " CD1 LEU A 228 " =    2.325
peak=   -3.974 closest distance to " O   HOH Z  43 " =    1.555
peak=   -3.934 closest distance to " C   ALA A 158 " =    1.246
peak=   -3.919 closest distance to " OE1 GLN A 223 " =    2.022
peak=   -3.901 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.901 closest distance to " O   HOH Z 407 " =    3.361
peak=   -3.884 closest distance to " O   HOH Z 353 " =    2.185
peak=   -3.876 closest distance to " ND2 ASN A  45 " =    0.967
peak=   -3.873 closest distance to " CG1 VAL A 250 " =    2.633
peak=   -3.865 closest distance to " CZ3 TRP A 179 " =    1.210
peak=   -3.839 closest distance to " O   VAL A  67 " =    2.821
peak=   -3.838 closest distance to " O   HOH Z  52 " =    1.404
peak=   -3.805 closest distance to " O   PRO A 198 " =    1.323
peak=   -3.796 closest distance to " O   HOH Z 118 " =    2.856
peak=   -3.793 closest distance to " SG ACYS A 201 " =    2.092
peak=   -3.788 closest distance to " O   HOH Z  11 " =    1.952
peak=   -3.776 closest distance to " CG  GLU A  53 " =    1.314
peak=   -3.775 closest distance to " O   PRO A 163 " =    2.058
peak=   -3.774 closest distance to " OG  SER A  97 " =    2.147
peak=   -3.767 closest distance to " NE2 GLN A  88 " =    2.060
peak=   -3.756 closest distance to " O   HOH Z  13 " =    1.481
peak=   -3.751 closest distance to " CD2 LEU A 300 " =    2.872
peak=   -3.748 closest distance to " O   HOH Z 388 " =    1.904
peak=   -3.738 closest distance to " C   HIS A 108 " =    1.047
peak=   -3.718 closest distance to " O   HOH Z 292 " =    4.499
peak=   -3.711 closest distance to " OXT GLY A 302 " =    2.927
peak=   -3.707 closest distance to " C   ASN A 285 " =    2.504
peak=   -3.707 closest distance to " NH2AARG A 275 " =    5.492
peak=   -3.693 closest distance to " NH1 ARG A 195 " =    2.622
peak=   -3.682 closest distance to " CB  ASN A  39 " =    2.183
peak=   -3.681 closest distance to " OG  SER A  62 " =    1.602
peak=   -3.676 closest distance to " CD  ARG A 195 " =    5.168
peak=   -3.656 closest distance to " CD1 PHE A  59 " =    1.846
peak=   -3.645 closest distance to " O   HOH Z  38 " =    1.454
peak=   -3.640 closest distance to " CD  LYS A 289 " =    2.535
peak=   -3.638 closest distance to " CD  ARG A 139 " =    1.615
peak=   -3.629 closest distance to " CB  CYS A 254 " =    2.341
peak=   -3.628 closest distance to " O   HOH Z  93 " =    1.844
peak=   -3.620 closest distance to " O   HOH Z 185 " =    2.318
peak=   -3.613 closest distance to " CG  ASP A 231 " =    0.863
peak=   -3.610 closest distance to " O   HOH Z  98 " =    2.227
peak=   -3.601 closest distance to " O   HOH Z 166 " =    1.798
peak=   -3.598 closest distance to " O   HOH Z 102 " =    1.717
peak=   -3.597 closest distance to " CZ  PHE A  59 " =    1.660
peak=   -3.585 closest distance to " O   HOH Z 266 " =    4.741
peak=   -3.578 closest distance to " CB  ALA A 291 " =    2.362
peak=   -3.574 closest distance to " O   HOH Z 283 " =    1.960
peak=   -3.569 closest distance to " OG BSER A 134 " =    1.198
peak=   -3.563 closest distance to " OD1 ASN A 148 " =    1.653
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.542
peak=   -3.558 closest distance to " CE  MET A  93 " =    1.221
peak=   -3.556 closest distance to " O   SER A 210 " =    2.001
peak=   -3.554 closest distance to " CG  PHE A 283 " =    2.701
peak=   -3.548 closest distance to " O   SER A 135 " =    1.552
peak=   -3.548 closest distance to " O   GLY A 211 " =    1.498
peak=   -3.544 closest distance to " CZ  TYR A 169 " =    1.732
peak=   -3.542 closest distance to " O   HOH Z 275 " =    1.541
peak=   -3.538 closest distance to " C   LEU A 143 " =    1.277
peak=   -3.533 closest distance to " OD1 ASP A 191 " =    1.674
peak=   -3.531 closest distance to " OG BSER A 134 " =    1.743
peak=   -3.530 closest distance to " CB  TYR A  15 " =    2.162
peak=   -3.521 closest distance to " O   HOH Z 389 " =    1.833
peak=   -3.520 closest distance to " NH2 ARG A  66 " =    1.965
peak=   -3.515 closest distance to " OG ASER A 134 " =    1.241
peak=   -3.504 closest distance to " O   HOH Z  11 " =    1.958
peak=   -3.497 closest distance to " CG  PRO A 163 " =    2.432
peak=   -3.494 closest distance to " N   SER A 276 " =    1.295
peak=   -3.489 closest distance to " O   HOH Z  98 " =    2.027
peak=   -3.479 closest distance to " O   HOH Z 148 " =    3.444
peak=   -3.474 closest distance to " N   GLN A  58 " =    1.753
peak=   -3.453 closest distance to " O   HOH Z  76 " =    1.922
peak=   -3.451 closest distance to " O   HOH Z 166 " =    1.507
peak=   -3.444 closest distance to " O   HOH Z 234 " =    4.155
peak=   -3.434 closest distance to " O   HOH Z 311 " =    3.645
peak=   -3.433 closest distance to " CG1 VAL A 112 " =    2.792
peak=   -3.422 closest distance to " OG  SER A  87 " =    1.421
peak=   -3.413 closest distance to " N   THR A 157 " =    1.668
peak=   -3.410 closest distance to " OD1 ASN A 187 " =    1.744
peak=   -3.405 closest distance to " CG  LEU A  83 " =    1.919
peak=   -3.405 closest distance to " O   VAL A  67 " =    2.766
peak=   -3.400 closest distance to " CB  ALA A 291 " =    2.234
peak=   -3.393 closest distance to " CE3 TRP A 150 " =    1.917
peak=   -3.387 closest distance to " CB  ALA A  43 " =    2.390
peak=   -3.386 closest distance to " O   HOH Z 385 " =    1.970
peak=   -3.385 closest distance to " O   HOH Z 436 " =    1.488
peak=   -3.380 closest distance to " O   HOH Z 243 " =    2.024
peak=   -3.379 closest distance to " CE2 PHE A 218 " =    2.490
peak=   -3.377 closest distance to " CB  PHE A 192 " =    1.963
peak=   -3.366 closest distance to " O   HOH Z 417 " =    2.566
peak=   -3.366 closest distance to " CB  ASP A 132 " =    2.294
peak=   -3.359 closest distance to " O   GLY A 196 " =    1.103
peak=   -3.357 closest distance to " NH2 ARG A  79 " =    1.845
peak=   -3.357 closest distance to " OE1 GLN A  88 " =    1.117
peak=   -3.355 closest distance to " O   HOH Z 396 " =    1.690
peak=   -3.351 closest distance to " OD2 ASP A 171 " =    1.782
peak=   -3.343 closest distance to " O   HOH Z 435 " =    2.733
peak=   -3.342 closest distance to " OE2 GLU A   2 " =    1.734
peak=   -3.329 closest distance to " CD2 TYR A 293 " =    2.034
peak=   -3.324 closest distance to " CE  MET A 105 " =    2.134
peak=   -3.322 closest distance to " O   PHE A 218 " =    1.498
peak=   -3.315 closest distance to " O   HOH Z  71 " =    1.309
peak=   -3.312 closest distance to " N   ALA A 226 " =    2.053
peak=   -3.307 closest distance to " CG2 ILE A 263 " =    2.340
peak=   -3.305 closest distance to " O   HOH Z  97 " =    1.819
peak=   -3.305 closest distance to " O   HOH Z  88 " =    2.385
peak=   -3.299 closest distance to " O   HOH Z 351 " =    1.522
peak=   -3.298 closest distance to " CA  GLY A 203 " =    2.186
peak=   -3.292 closest distance to " CG  TRP A 266 " =    1.666
peak=   -3.291 closest distance to " O   ASN A 249 " =    1.543
peak=   -3.288 closest distance to " CD2 PHE A  59 " =    2.533
peak=   -3.287 closest distance to " CD1 ILE A 239 " =    2.070
peak=   -3.284 closest distance to " OD2 ASP A  50 " =    2.579
peak=   -3.284 closest distance to " OD1 ASP A 191 " =    1.536
peak=   -3.283 closest distance to " O   HOH Z 252 " =    4.267
peak=   -3.282 closest distance to " OH  TYR A 169 " =    1.015
peak=   -3.280 closest distance to " CG  ARG A  66 " =    2.340
peak=   -3.276 closest distance to " CB  ALA A 248 " =    1.955
peak=   -3.276 closest distance to " O   HOH Z 211 " =    1.602
peak=   -3.275 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.274 closest distance to " CB  SER A 245 " =    2.406
peak=   -3.266 closest distance to " CG  GLN A  88 " =    0.872
peak=   -3.264 closest distance to " CG2 VAL A 189 " =    2.093
peak=   -3.262 closest distance to " O   HOH Z 399 " =    2.221
peak=   -3.259 closest distance to " O   HOH Z 350 " =    1.650
peak=   -3.257 closest distance to " O   HOH Z 361 " =    3.393
peak=   -3.256 closest distance to " ND2 ASN A 249 " =    2.136
peak=   -3.255 closest distance to " CE  LYS A  76 " =    2.643
peak=   -3.253 closest distance to " CG1 VAL A 197 " =    2.312
peak=   -3.250 closest distance to " CA  VAL A 232 " =    2.516
peak=   -3.242 closest distance to " CB  PHE A  16 " =    2.611
peak=   -3.242 closest distance to " O   HOH Z 298 " =    1.211
peak=   -3.240 closest distance to " OD1 ASP A 200 " =    1.387
peak=   -3.239 closest distance to " O   HOH Z 265 " =    1.985
peak=   -3.229 closest distance to " O   HOH Z  60 " =    2.395
peak=   -3.229 closest distance to " OG1 THR A 178 " =    1.274
peak=   -3.228 closest distance to " CB  PRO A 163 " =    2.556
peak=   -3.224 closest distance to " NH2 ARG A  66 " =    5.183
peak=   -3.223 closest distance to " CA  GLY A 241 " =    3.090
peak=   -3.221 closest distance to " NH2 ARG A 159 " =    2.434
peak=   -3.216 closest distance to " NE2 GLN A  58 " =    1.144
peak=   -3.212 closest distance to " CE3 TRP A 274 " =    2.526
peak=   -3.209 closest distance to " O   HOH Z 222 " =    1.247
peak=   -3.203 closest distance to " O   HOH Z 103 " =    1.857
peak=   -3.200 closest distance to " O   HOH Z 111 " =    1.350
peak=   -3.197 closest distance to " CE3 TRP A  70 " =    1.822
peak=   -3.196 closest distance to " O   GLY A 118 " =    2.189
peak=   -3.192 closest distance to " O   HOH Z 207 " =    2.077
peak=   -3.187 closest distance to " NE1 TRP A 266 " =    2.214
peak=   -3.178 closest distance to " C   MET A 188 " =    1.620
peak=   -3.177 closest distance to " O   ALA A 160 " =    1.586
peak=   -3.174 closest distance to " O   LEU A 167 " =    1.517
peak=   -3.174 closest distance to " CG1 VAL A 125 " =    1.999
peak=   -3.173 closest distance to " O   HOH Z 198 " =    1.508
peak=   -3.165 closest distance to " O   HOH Z 111 " =    2.324
peak=   -3.162 closest distance to " N   ALA A   9 " =    1.591
peak=   -3.160 closest distance to " O   HOH Z 409 " =    4.595
peak=   -3.160 closest distance to " O   VAL A 153 " =    2.311
peak=   -3.157 closest distance to " C   SER A 206 " =    1.460
peak=   -3.153 closest distance to " O   HOH Z 423 " =    2.229
peak=   -3.135 closest distance to " CB  LEU A 167 " =    2.137
peak=   -3.132 closest distance to " O   HOH Z  47 " =    1.516
peak=   -3.124 closest distance to " O   HOH Z 252 " =    3.797
peak=   -3.122 closest distance to " O   ASN A 301 " =    1.404
peak=   -3.117 closest distance to " O   VAL A 125 " =    2.277
peak=   -3.116 closest distance to " OD2 ASP A 171 " =    2.278
peak=   -3.115 closest distance to " OXT GLY A 302 " =    3.211
peak=   -3.112 closest distance to " O   HOH Z 184 " =    1.792
peak=   -3.110 closest distance to " CA  ARG A 139 " =    1.051
peak=   -3.100 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.098 closest distance to " O   PRO A 198 " =    2.065
peak=   -3.098 closest distance to " CG  ARG A 259 " =    2.888
peak=   -3.098 closest distance to " CG  ARG A 269 " =    2.469
peak=   -3.097 closest distance to " O   HOH Z  98 " =    1.439
peak=   -3.093 closest distance to " O   HOH Z 298 " =    2.648
peak=   -3.082 closest distance to " O   HOH Z 411 " =    3.526
peak=   -3.072 closest distance to " O   HOH Z 310 " =    3.529
peak=   -3.067 closest distance to " O   MET A  40 " =    2.812
peak=   -3.064 closest distance to " O   HOH Z 165 " =    2.005
peak=   -3.048 closest distance to " CA  SER A 135 " =    1.284
peak=   -3.046 closest distance to " O   HOH Z 119 " =    4.234
peak=   -3.044 closest distance to " CG  GLN A 278 " =    2.285
peak=   -3.019 closest distance to " O   HOH Z 139 " =    2.925

================= 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    :  0.3842 0.3913   6.163939e+00   6.173010e+00
   1_bss:  0.3738 0.3822   6.154054e+00   6.156223e+00
   1_xyz:  0.2360 0.2669   5.765178e+00   5.871983e+00
   1_adp:  0.2179 0.2734   5.725189e+00   5.896859e+00
   1_occ:  0.2173 0.2734   5.723478e+00   5.895382e+00
   2_bss:  0.2153 0.2707   5.719037e+00   5.889139e+00
   2_xyz:  0.1530 0.1968   5.405527e+00   5.607964e+00
   2_adp:  0.1378 0.1839   5.321226e+00   5.536308e+00
   2_occ:  0.1376 0.1836   5.320123e+00   5.535203e+00
   3_bss:  0.1376 0.1827   5.317891e+00   5.531756e+00
   3_xyz:  0.1176 0.1616   5.185692e+00   5.417561e+00
   3_adp:  0.1140 0.1585   5.160998e+00   5.395359e+00
   3_occ:  0.1139 0.1583   5.160411e+00   5.394869e+00
   4_bss:  0.1138 0.1582   5.160123e+00   5.394554e+00
   4_xyz:  0.1137 0.1577   5.160727e+00   5.391211e+00
   4_adp:  0.1129 0.1584   5.160392e+00   5.395356e+00
   4_occ:  0.1129 0.1584   5.160200e+00   5.395355e+00
   5_bss:  0.1134 0.1583   5.162199e+00   5.396526e+00
   5_xyz:  0.1101 0.1579   5.147940e+00   5.392432e+00
   5_adp:  0.1097 0.1588   5.149073e+00   5.397100e+00
   5_occ:  0.1097 0.1588   5.149037e+00   5.397234e+00
   5_bss:  0.1096 0.1588   5.149161e+00   5.397320e+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:  0.317  39.708  -0.353  -1.983   2.079  -0.000   0.000   0.000
   1_xyz:  0.317  39.708  -0.353  -1.983   2.079  -0.000   0.000   0.000
   1_adp:  0.317  39.708  -0.353  -1.983   2.079  -0.000   0.000   0.000
   1_occ:  0.317  39.708  -0.353  -1.983   2.079  -0.000   0.000   0.000
   2_bss:  0.332  53.660  -1.829  -2.447  -0.728  -0.000  -0.000  -0.000
   2_xyz:  0.332  53.660  -1.829  -2.447  -0.728  -0.000  -0.000  -0.000
   2_adp:  0.332  53.660  -1.829  -2.447  -0.728  -0.000  -0.000  -0.000
   2_occ:  0.332  53.660  -1.829  -2.447  -0.728  -0.000  -0.000  -0.000
   3_bss:  0.332  53.660  -2.127  -2.290  -1.578  -0.000  -0.000  -0.000
   3_xyz:  0.332  53.660  -2.127  -2.290  -1.578  -0.000  -0.000  -0.000
   3_adp:  0.332  53.660  -2.127  -2.290  -1.578  -0.000  -0.000  -0.000
   3_occ:  0.332  53.660  -2.127  -2.290  -1.578  -0.000  -0.000  -0.000
   4_bss:  0.332  53.660  -2.211  -2.272  -1.838  -0.000  -0.000  -0.000
   4_xyz:  0.332  53.660  -2.211  -2.272  -1.838  -0.000  -0.000  -0.000
   4_adp:  0.332  53.660  -2.211  -2.272  -1.838  -0.000  -0.000  -0.000
   4_occ:  0.332  53.660  -2.211  -2.272  -1.838  -0.000  -0.000  -0.000
   5_bss:  0.332  53.660  -2.132  -2.172  -1.833  -0.000  -0.000  -0.000
   5_xyz:  0.332  53.660  -2.132  -2.172  -1.833  -0.000  -0.000  -0.000
   5_adp:  0.332  53.660  -2.132  -2.172  -1.833  -0.000  -0.000  -0.000
   5_occ:  0.332  53.660  -2.132  -2.172  -1.833  -0.000  -0.000  -0.000
   5_bss:  0.332  53.641  -1.906  -1.936  -1.624  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.108 0.5939  0.7733    45357.629
   1_bss:  42.810 0.6073  0.7926    41882.914
   1_xyz:  26.809 0.7935  0.9810    18904.228
   1_adp:  28.066 0.7790  0.9680    20153.671
   1_occ:  28.030 0.7793  0.9679    20073.908
   2_bss:  27.703 0.7827  0.9191    19732.463
   2_xyz:  19.240 0.8683  0.9796    10092.088
   2_adp:  17.319 0.8867  0.9853     8748.233
   2_occ:  17.290 0.8869  0.9852     8717.936
   3_bss:  17.206 0.8877  0.9731     8637.944
   3_xyz:  14.846 0.9075  0.9820     6757.093
   3_adp:  14.308 0.9123  0.9804     6489.061
   3_occ:  14.294 0.9124  0.9803     6482.273
   4_bss:  14.288 0.9125  0.9764     6480.322
   4_xyz:  14.089 0.9144  0.9759     6361.267
   4_adp:  14.144 0.9141  0.9714     6412.696
   4_occ:  14.142 0.9142  0.9713     6413.195
   5_bss:  14.186 0.9138  0.9732     6445.980
   5_xyz:  14.168 0.9138  0.9731     6413.894
   5_adp:  14.260 0.9131  0.9673     6459.731
   5_occ:  14.261 0.9131  0.9672     6461.695
   5_bss:  14.265 0.9130  0.9742     6462.979
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7021e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7021e-01
   1_xyz:   1.262  0.010  0.078 15.298  0.005  4.113   8.9169e-02
   1_adp:   1.262  0.010  0.078 15.298  0.005  4.113   8.9169e-02
   1_occ:   1.262  0.010  0.078 15.298  0.005  4.113   8.9169e-02
   2_bss:   1.262  0.010  0.078 15.298  0.005  4.113   8.9169e-02
   2_xyz:   1.056  0.007  0.073 14.212  0.004  4.126   6.2136e-02
   2_adp:   1.056  0.007  0.073 14.212  0.004  4.126   6.2136e-02
   2_occ:   1.056  0.007  0.073 14.212  0.004  4.126   6.2136e-02
   3_bss:   1.056  0.007  0.073 14.212  0.004  4.126   6.2136e-02
   3_xyz:   1.080  0.008  0.077 14.575  0.004  4.130   6.7294e-02
   3_adp:   1.080  0.008  0.077 14.575  0.004  4.130   6.7294e-02
   3_occ:   1.080  0.008  0.077 14.575  0.004  4.130   6.7294e-02
   4_bss:   1.080  0.008  0.077 14.575  0.004  4.130   6.7294e-02
   4_xyz:   0.944  0.006  0.069 14.211  0.003  4.113   5.2614e-02
   4_adp:   0.944  0.006  0.069 14.211  0.003  4.113   5.2614e-02
   4_occ:   0.944  0.006  0.069 14.211  0.003  4.113   5.2614e-02
   5_bss:   0.944  0.006  0.069 14.211  0.003  4.113   5.2614e-02
   5_xyz:   0.996  0.007  0.072 14.339  0.004  4.114   5.7448e-02
   5_adp:   0.996  0.007  0.072 14.339  0.004  4.114   5.7448e-02
   5_occ:   0.996  0.007  0.072 14.339  0.004  4.114   5.7448e-02
   5_bss:   0.996  0.007  0.072 14.339  0.004  4.114   5.7448e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.731   2.4106e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.731   2.4106e-01
   1_xyz:   9.365  0.054  0.273 88.114  0.018  2.217   9.4182e-02
   1_adp:   9.365  0.054  0.273 88.114  0.018  2.217   9.4182e-02
   1_occ:   9.365  0.054  0.273 88.114  0.018  2.217   9.4182e-02
   2_bss:   9.365  0.054  0.273 88.114  0.018  2.217   9.4182e-02
   2_xyz:   7.128  0.045  0.245 83.004  0.042  2.353   8.4159e-02
   2_adp:   7.128  0.045  0.245 83.004  0.042  2.353   8.4159e-02
   2_occ:   7.128  0.045  0.245 83.004  0.042  2.353   8.4159e-02
   3_bss:   7.128  0.045  0.245 83.004  0.042  2.353   8.4159e-02
   3_xyz:   7.141  0.046  0.241 83.876  0.034  2.272   8.0811e-02
   3_adp:   7.141  0.046  0.241 83.876  0.034  2.272   8.0811e-02
   3_occ:   7.141  0.046  0.241 83.876  0.034  2.272   8.0811e-02
   4_bss:   7.141  0.046  0.241 83.876  0.034  2.272   8.0811e-02
   4_xyz:   7.382  0.040  0.223 82.993  0.030  2.380   3.5133e-02
   4_adp:   7.382  0.040  0.223 82.993  0.030  2.380   3.5133e-02
   4_occ:   7.382  0.040  0.223 82.993  0.030  2.380   3.5133e-02
   5_bss:   7.382  0.040  0.223 82.993  0.030  2.380   3.5133e-02
   5_xyz:   7.208  0.041  0.230 83.499  0.030  2.329   3.8390e-02
   5_adp:   7.208  0.041  0.230 83.499  0.030  2.329   3.8390e-02
   5_occ:   7.208  0.041  0.230 83.499  0.030  2.329   3.8390e-02
   5_bss:   7.208  0.041  0.230 83.499  0.030  2.329   3.8390e-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:  72.47   0.00  16.92  72.47   0.00  13.00  63.51   6.51  38.27
   1_occ:  72.47   0.00  16.92  72.47   0.00  13.00  63.51   6.51  38.27
   2_bss:  72.47   0.00  16.92  72.47   0.00  13.00  63.51   6.51  38.27
   2_xyz:  72.47   0.00  16.92  72.47   0.00  13.00  63.51   6.51  38.27
   2_adp:  75.77   0.00  17.37  75.77   0.00  13.06  71.67   5.76  40.82
   2_occ:  75.77   0.00  17.37  75.77   0.00  13.06  71.67   5.76  40.82
   3_bss:  75.77   0.00  17.37  75.77   0.00  13.06  71.67   5.76  40.82
   3_xyz:  75.77   0.00  17.37  75.77   0.00  13.06  71.67   5.76  40.82
   3_adp:  80.76   1.35  17.10  80.76   1.35  12.93  75.46   4.18  39.81
   3_occ:  80.76   1.35  17.10  80.76   1.35  12.93  75.46   4.18  39.81
   4_bss:  80.76   1.35  17.10  80.76   1.35  12.93  75.46   4.18  39.81
   4_xyz:  80.76   1.35  17.10  80.76   1.35  12.93  75.46   4.18  39.81
   4_adp:  86.79   1.41  17.06  86.79   1.41  12.88  78.73   5.15  39.80
   4_occ:  86.79   1.41  17.06  86.79   1.41  12.88  78.73   5.15  39.80
   5_bss:  86.79   1.41  17.06  86.79   1.41  12.88  78.73   5.15  39.80
   5_xyz:  86.79   1.41  17.06  86.79   1.41  12.88  78.73   5.15  39.80
   5_adp:  94.92   0.58  17.04  94.92   0.58  12.81  84.42   5.97  40.10
   5_occ:  94.92   0.58  17.04  94.92   0.58  12.81  84.42   5.97  40.10
   5_bss:  94.90   0.56  17.02  94.90   0.56  12.79  84.40   5.96  40.08
------------------------------------------------------------------------
 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:    1.795    0.022    0.343
   1_adp:    1.795    0.022    0.343
   1_occ:    1.795    0.022    0.343
   2_bss:    1.795    0.022    0.343
   2_xyz:    1.075    0.057    0.451
   2_adp:    1.075    0.057    0.451
   2_occ:    1.075    0.057    0.451
   3_bss:    1.075    0.057    0.451
   3_xyz:    1.124    0.065    0.501
   3_adp:    1.124    0.065    0.501
   3_occ:    1.124    0.065    0.501
   4_bss:    1.124    0.065    0.501
   4_xyz:    1.213    0.052    0.510
   4_adp:    1.213    0.052    0.510
   4_occ:    1.213    0.052    0.510
   5_bss:    1.213    0.052    0.510
   5_xyz:    1.211    0.049    0.522
   5_adp:    1.211    0.049    0.522
   5_occ:    1.211    0.049    0.522
   5_bss:    1.211    0.049    0.522
------------------------------------------------------------------------

CPU time actual refinement: 359.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/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_1035/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1035/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.20 
  Macro-tasks:
    bulk solvent and scale       = 38.05  
    individual site refinement   = 154.47 
    weights calculation          = 30.26  
    collect and process          = 6.60   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 229.47 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 119.42 
    alpha_beta                      = 8.09   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 129.09 
    fmodel                         = 6.57   
    r_factors                      = 0.15   
    phase_errors                   = 11.08  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 277.69 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.980 micro seconds
Total CPU time: 6.21 minutes
from_scatterers_fft:    678 calls, 119.08 s
gradients_fft:          623 calls, 114.90 s

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

# Date 2008-01-16 Time 06:17:07 PST -0800 (1200493027.67 s)
Start R-work = 0.3842, R-free = 0.3913 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.3738, R-free = 0.3822
Final R-work = 0.1096, R-free = 0.1588