# Date 2008-01-16 Time 05:47:33 PST -0800 (1200491253.87 s)
#phil __OFF__

Command line arguments: "../880.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32673
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 880

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.4607, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95118
Completeness in resolution range: 0.939656
Completeness with d_max=infinity: 0.936869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9961
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9961 1.95118
Completeness in resolution range: 0.939656
Completeness with d_max=infinity: 0.936869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9965 -  4.1763 [2186/2215]  1971   215   9.8%
  bin  2:  4.1763 -  3.3267 [2102/2118]  1888   214  10.2%
  bin  3:  3.3267 -  2.9097 [2061/2080]  1854   207  10.0%
  bin  4:  2.9097 -  2.6452 [2072/2102]  1875   197   9.5%
  bin  5:  2.6452 -  2.4565 [2042/2061]  1835   207  10.1%
  bin  6:  2.4565 -  2.3122 [2041/2077]  1831   210  10.3%
  bin  7:  2.3122 -  2.1968 [2021/2054]  1818   203  10.0%
  bin  8:  2.1968 -  2.1015 [2018/2052]  1819   199   9.9%
  bin  9:  2.1015 -  2.0208 [2001/2029]  1801   200  10.0%
  bin 10:  2.0208 -  1.9512 [1045/2059]   938   107  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/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:
        1.67 -     2.32: 25
        2.32 -     2.96: 1758
        2.96 -     3.61: 4624
        3.61 -     4.25: 9283
        4.25 -     4.90: 12962
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.670 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.743 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.785 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28647 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_880/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/model_refine_001.geo

CPU time processing inputs: 9.32


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.4607 84.23025 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4297   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.230588                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6586 0.99   1418  159 0.3439 0.3412       6.491      6.4919|
|  2:  4.6586 -  3.7162 0.99   1374  146 0.3576 0.3272      6.7094        6.68|
|  3:  3.7162 -  3.2519 0.99   1336  155 0.3997 0.4099      6.5922      6.6932|
|  4:  3.2519 -  2.9570 0.99   1337  148 0.4010 0.4203      6.4514      6.4366|
|  5:  2.9570 -  2.7465 0.99   1318  146 0.4466 0.4182      6.3095      6.2726|
|  6:  2.7465 -  2.5854 0.99   1320  149 0.4621 0.4874      6.2354      6.2415|
|  7:  2.5854 -  2.4565 0.99   1320  137 0.4538 0.4415      6.1925        6.16|
|  8:  2.4565 -  2.3500 0.98   1296  152 0.4729 0.4552      6.1286      6.1482|
|  9:  2.3500 -  2.2599 0.98   1310  147 0.4654 0.4329      6.0886      6.0174|
| 10:  2.2599 -  2.1821 0.98   1298  142 0.4816 0.5220      6.0517      6.1123|
| 11:  2.1821 -  2.1141 1.00   1303  139 0.4809 0.5654      6.0137      6.0442|
| 12:  2.1141 -  2.0538 0.97   1284  146 0.4865 0.5183      5.9274      5.9764|
| 13:  2.0538 -  1.9999 0.93   1228  142 0.4984 0.4807      5.8708       5.813|
| 14:  1.9999 -  1.9512 0.37    488   51 0.5262 0.4623      5.8176      5.7642|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6586  1418   159  0.74  30.56   0.85     0.78      56813.71|
|  2:  4.6586 -  3.7162  1374   146  0.75  30.55   0.94     0.87      83499.96|
|  3:  3.7162 -  3.2519  1336   155  0.66  38.53   0.94     0.86      91153.31|
|  4:  3.2519 -  2.9570  1337   148  0.59  44.90   0.97     0.80      84606.74|
|  5:  2.9570 -  2.7465  1318   146  0.51  50.85   0.92     0.71      68071.43|
|  6:  2.7465 -  2.5854  1320   149  0.49  52.80   0.92     0.68      59973.13|
|  7:  2.5854 -  2.4565  1320   137  0.50  52.44   0.96     0.66      52094.10|
|  8:  2.4565 -  2.3500  1296   152  0.49  53.16   0.93     0.70      47285.86|
|  9:  2.3500 -  2.2599  1310   147  0.49  52.71   0.98     0.70      42558.38|
| 10:  2.2599 -  2.1821  1298   142  0.45  55.82   0.97     0.67      42770.78|
| 11:  2.1821 -  2.1141  1303   139  0.41  59.43   0.99     0.62      42427.50|
| 12:  2.1141 -  2.0538  1284   146  0.38  61.66   0.99     0.60      39561.03|
| 13:  2.0538 -  1.9999  1228   142  0.37  62.08   0.96     0.59      34237.47|
| 14:  1.9999 -  1.9512   488    51  0.36  63.08   0.94     0.54      29419.18|
|alpha:            min =        0.54 max =            0.87 mean =         0.71|
|beta:             min =    29419.18 max =        91153.31 mean =     56884.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.97 mean =        49.73|
|phase err.(test): min =        0.00 max =           89.93 mean =        49.91|
|-----------------------------------------------------------------------------|

============================== 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 = 6.806824              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.182   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.813633              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.559   (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 |  1.670 -  1.993:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.993 -  2.316:       15 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.316 -  2.639:       76 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.639 -  2.962:     1682 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.962 -  3.285:     1945 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.285 -  3.608:     2679 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.608 -  3.931:     4790 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.931 -  4.254:     4493 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.254 -  4.577:     5937 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.577 -  4.900:     7025 |
|-----------------------------------------------------------------------------|
|-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 |        0.177 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.670 |       0.410 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4297   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.230588                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4167   r_free= 0.4194   ksol= 0.33   Bsol= 30.65   scale= 0.953   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.02,2.72,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.225975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.217427              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.362   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.820556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.431   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4167      final r-factor (work) = 0.2996          |
| start r-factor (free) = 0.4194      final r-factor (free) = 0.3275          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.4013 = 5.22 * 0.50 * 6.2194 + 1.00 * 0.1765                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9082 = 5.22 * 0.50 * 6.0608 + 1.00 * 0.0973                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2996      final r-factor (work) = 0.2740          |
| start r-factor (free) = 0.3275      final r-factor (free) = 0.3340          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9792 = 0.82 * 1.00 * 6.0608 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8705 = 0.82 * 1.00 * 5.9176 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.53   18.12    None  None   None       |
|    all(noH): 2823   0      0.00    86.53   18.12    None  None   None       |
|    Sol.    : 438    0      0.00    84.12   40.05    None  None   None       |
|    Mac.    : 2385   0      0.00    86.53   14.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.653:  773   |   5:    43.265 -  51.918:   93        |
|      1:     8.653 -  17.306: 1019   |   6:    51.918 -  60.571:   76        |
|      2:    17.306 -  25.959:  429   |   7:    60.571 -  69.224:   37        |
|      3:    25.959 -  34.612:  224   |   8:    69.224 -  77.878:   18        |
|      4:    34.612 -  43.265:  148   |   9:    77.878 -  86.531:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2740 r_free = 0.3340             target_work(ml) = 5.923         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2737 r_free = 0.3346             target_work(ml) = 5.922         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2737   r_free= 0.3346   ksol= 0.33   Bsol= 30.65   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.02,2.72,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.921869                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2733   r_free= 0.3336   ksol= 0.33   Bsol= 46.90   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.59,0.69,-0.00,0.00,0.00); trace/3= -0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.921408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.820258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.450   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273883              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2733      final r-factor (work) = 0.1912          |
| start r-factor (free) = 0.3336      final r-factor (free) = 0.2450          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3201 = 5.82 * 0.50 * 5.9182 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9327 = 5.82 * 0.50 * 5.7890 + 1.00 * 0.0861                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1912      final r-factor (work) = 0.1695          |
| start r-factor (free) = 0.2450      final r-factor (free) = 0.2226          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6001 = 0.27 * 1.00 * 5.7890 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5294 = 0.27 * 1.00 * 5.5543 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.95    80.77   17.33    None  None   None       |
|    all(noH): 2823   0      0.95    80.77   17.33    None  None   None       |
|    Sol.    : 438    0      4.50    79.11   39.84    None  None   None       |
|    Mac.    : 2385   0      0.95    80.77   13.19    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:     0.948 -   8.929:  770   |   5:    40.857 -  48.838:  114        |
|      1:     8.929 -  16.911: 1195   |   6:    48.838 -  56.820:   75        |
|      2:    16.911 -  24.893:  316   |   7:    56.820 -  64.802:   45        |
|      3:    24.893 -  32.875:  155   |   8:    64.802 -  72.784:   19        |
|      4:    32.875 -  40.857:  128   |   9:    72.784 -  80.765:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1695 r_free = 0.2226             target_work(ml) = 5.506         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1692 r_free = 0.2222             target_work(ml) = 5.504         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1692   r_free= 0.2222   ksol= 0.33   Bsol= 46.90   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.66,-1.59,0.69,-0.00,0.00,0.00); trace/3= -0.85                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.504299                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1684   r_free= 0.2203   ksol= 0.32   Bsol= 44.21   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.14,-1.03,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.497825                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.159502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.107   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.268212              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.627  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1684      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.2203      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8621 = 3.16 * 0.50 * 5.5553 + 1.00 * 0.0861                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5973 = 3.16 * 0.50 * 5.4072 + 1.00 * 0.0553                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1693          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4584 = 0.27 * 1.00 * 5.4072 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4190 = 0.27 * 1.00 * 5.2611 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    84.14   17.26    None  None   None       |
|    all(noH): 2823   0      1.70    84.14   17.26    None  None   None       |
|    Sol.    : 438    0      3.79    76.90   40.50    None  None   None       |
|    Mac.    : 2385   0      1.70    84.14   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.695 -   9.940:  985   |   5:    42.920 -  51.165:  112        |
|      1:     9.940 -  18.185: 1104   |   6:    51.165 -  59.410:   72        |
|      2:    18.185 -  26.430:  260   |   7:    59.410 -  67.654:   40        |
|      3:    26.430 -  34.675:  119   |   8:    67.654 -  75.899:   15        |
|      4:    34.675 -  42.920:  112   |   9:    75.899 -  84.144:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1693             target_work(ml) = 5.235         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1270 r_free = 0.1691             target_work(ml) = 5.234         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1691   ksol= 0.32   Bsol= 44.21   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.14,-1.03,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.234224                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1692   ksol= 0.32   Bsol= 44.21   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.65,-1.87,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.234568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.560468              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.775  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.321902              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.132  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1692      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1644 = 1.56 * 0.50 * 5.2665 + 1.00 * 0.0553                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1109 = 1.56 * 0.50 * 5.2052 + 1.00 * 0.0496                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1604      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6835 = 0.32 * 1.00 * 5.2052 + 1.00 * 0.0079                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6730 = 0.32 * 1.00 * 5.1716 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.73    89.57   17.19    None  None   None       |
|    all(noH): 2823   0      1.73    89.57   17.19    None  None   None       |
|    Sol.    : 438    0      3.84    83.07   40.32    None  None   None       |
|    Mac.    : 2385   0      1.73    89.57   12.95    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.733 -  10.517: 1133   |   5:    45.653 -  54.437:  106        |
|      1:    10.517 -  19.301: 1028   |   6:    54.437 -  63.221:   56        |
|      2:    19.301 -  28.085:  219   |   7:    63.221 -  72.005:   30        |
|      3:    28.085 -  36.869:  126   |   8:    72.005 -  80.789:   11        |
|      4:    36.869 -  45.653:  110   |   9:    80.789 -  89.573:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1592             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1590             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1590   ksol= 0.32   Bsol= 44.21   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.65,-1.87,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1589   ksol= 0.32   Bsol= 44.21   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.58,-1.95,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165018                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.248223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.775  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.318622              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.195  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2771 = 1.25 * 0.50 * 5.1713 + 1.00 * 0.0496                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2659 = 1.25 * 0.50 * 5.1578 + 1.00 * 0.0469                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6516 = 0.32 * 1.00 * 5.1578 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6487 = 0.32 * 1.00 * 5.1487 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    90.73   17.08    None  None   None       |
|    all(noH): 2823   0      1.35    90.73   17.08    None  None   None       |
|    Sol.    : 438    0      5.39    84.27   39.98    None  None   None       |
|    Mac.    : 2385   0      1.35    90.73   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:     1.347 -  10.285: 1085   |   5:    46.037 -  54.975:  108        |
|      1:    10.285 -  19.223: 1074   |   6:    54.975 -  63.913:   55        |
|      2:    19.223 -  28.161:  227   |   7:    63.913 -  72.851:   26        |
|      3:    28.161 -  37.099:  125   |   8:    72.851 -  81.789:    8        |
|      4:    37.099 -  46.037:  111   |   9:    81.789 -  90.727:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1569             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1568             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1568   ksol= 0.32   Bsol= 44.21   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-2.58,-1.95,-0.00,-0.00,-0.00); trace/3= -2.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150244                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6586 0.99   1418  159 0.0995 0.1268       5.384      5.5348|
|  2:  4.6586 -  3.7162 0.99   1374  146 0.0878 0.1120      5.4468      5.6516|
|  3:  3.7162 -  3.2519 0.99   1336  155 0.1088 0.1566      5.4832      5.8372|
|  4:  3.2519 -  2.9570 0.99   1337  148 0.1266 0.1580      5.4714      5.5909|
|  5:  2.9570 -  2.7465 0.99   1318  146 0.1322 0.1715      5.3032      5.4811|
|  6:  2.7465 -  2.5854 0.99   1320  149 0.1225 0.1642       5.186      5.3902|
|  7:  2.5854 -  2.4565 0.99   1320  137 0.1270 0.1619      5.1605      5.3334|
|  8:  2.4565 -  2.3500 0.98   1296  152 0.1151 0.1710      5.0332      5.3577|
|  9:  2.3500 -  2.2599 0.98   1310  147 0.1202 0.1875      5.0261      5.2893|
| 10:  2.2599 -  2.1821 0.98   1298  142 0.1131 0.1669      4.9352      5.2116|
| 11:  2.1821 -  2.1141 1.00   1303  139 0.1173 0.1842      4.9478      5.2895|
| 12:  2.1141 -  2.0538 0.97   1284  146 0.1132 0.1623      4.8817      5.0837|
| 13:  2.0538 -  1.9999 0.93   1228  142 0.1209 0.1802      4.8066      5.0458|
| 14:  1.9999 -  1.9512 0.37    488   51 0.1019 0.1600      4.6347       4.942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6586  1418   159  0.94   8.45   0.98     0.96       6560.99|
|  2:  4.6586 -  3.7162  1374   146  0.95   7.87   1.02     1.01       8729.81|
|  3:  3.7162 -  3.2519  1336   155  0.93  11.52   1.03     1.03      10389.83|
|  4:  3.2519 -  2.9570  1337   148  0.92  13.83   1.01     0.99      10233.25|
|  5:  2.9570 -  2.7465  1318   146  0.90  15.31   0.99     0.97       7651.25|
|  6:  2.7465 -  2.5854  1320   149  0.91  15.30   0.99     0.97       6468.90|
|  7:  2.5854 -  2.4565  1320   137  0.91  15.04   0.99     0.97       5961.95|
|  8:  2.4565 -  2.3500  1296   152  0.91  14.90   0.99     0.96       4842.55|
|  9:  2.3500 -  2.2599  1310   147  0.91  15.21   1.01     0.99       4791.05|
| 10:  2.2599 -  2.1821  1298   142  0.91  14.78   1.00     0.96       4023.12|
| 11:  2.1821 -  2.1141  1303   139  0.90  16.36   1.00     0.96       4368.29|
| 12:  2.1141 -  2.0538  1284   146  0.91  15.97   1.01     1.00       4069.16|
| 13:  2.0538 -  1.9999  1228   142  0.90  16.09   1.00     0.98       3341.57|
| 14:  1.9999 -  1.9512   488    51  0.91  14.77   0.99     0.96       2410.93|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2410.93 max =        10389.83 mean =      6201.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.85|
|phase err.(test): min =        0.00 max =           88.91 mean =        13.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1569   ksol= 0.32   Bsol= 44.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.41,-1.83,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1569   ksol= 0.32   Bsol= 44.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,-2.41,-1.83,-0.00,-0.00,-0.00); trace/3= -2.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150327                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9965 -  4.6586 0.99   1418  159 0.0996 0.1269      5.3847      5.5359|
|  2:  4.6586 -  3.7162 0.99   1374  146 0.0878 0.1120       5.447      5.6516|
|  3:  3.7162 -  3.2519 0.99   1336  155 0.1088 0.1566      5.4832      5.8373|
|  4:  3.2519 -  2.9570 0.99   1337  148 0.1266 0.1580      5.4714      5.5908|
|  5:  2.9570 -  2.7465 0.99   1318  146 0.1321 0.1716      5.3032       5.481|
|  6:  2.7465 -  2.5854 0.99   1320  149 0.1225 0.1643      5.1862      5.3906|
|  7:  2.5854 -  2.4565 0.99   1320  137 0.1270 0.1618      5.1608      5.3336|
|  8:  2.4565 -  2.3500 0.98   1296  152 0.1151 0.1709      5.0334      5.3581|
|  9:  2.3500 -  2.2599 0.98   1310  147 0.1202 0.1875      5.0262      5.2893|
| 10:  2.2599 -  2.1821 0.98   1298  142 0.1131 0.1670      4.9353      5.2114|
| 11:  2.1821 -  2.1141 1.00   1303  139 0.1173 0.1841      4.9478      5.2893|
| 12:  2.1141 -  2.0538 0.97   1284  146 0.1131 0.1623      4.8813      5.0835|
| 13:  2.0538 -  1.9999 0.93   1228  142 0.1209 0.1801      4.8065      5.0452|
| 14:  1.9999 -  1.9512 0.37    488   51 0.1019 0.1602      4.6349      4.9433|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9965 -  4.6586  1418   159  0.94   8.46   0.98     0.96       6572.21|
|  2:  4.6586 -  3.7162  1374   146  0.95   7.87   1.02     1.01       8737.22|
|  3:  3.7162 -  3.2519  1336   155  0.93  11.52   1.03     1.03      10390.09|
|  4:  3.2519 -  2.9570  1337   148  0.92  13.83   1.01     0.99      10230.67|
|  5:  2.9570 -  2.7465  1318   146  0.90  15.31   1.00     0.97       7653.06|
|  6:  2.7465 -  2.5854  1320   149  0.91  15.31   0.99     0.97       6471.13|
|  7:  2.5854 -  2.4565  1320   137  0.91  15.04   1.00     0.98       5966.39|
|  8:  2.4565 -  2.3500  1296   152  0.91  14.90   0.99     0.96       4844.19|
|  9:  2.3500 -  2.2599  1310   147  0.91  15.21   1.01     0.99       4791.43|
| 10:  2.2599 -  2.1821  1298   142  0.91  14.78   1.00     0.97       4023.60|
| 11:  2.1821 -  2.1141  1303   139  0.90  16.36   1.00     0.97       4367.32|
| 12:  2.1141 -  2.0538  1284   146  0.91  15.97   1.01     1.01       4065.88|
| 13:  2.0538 -  1.9999  1228   142  0.90  16.09   1.00     0.99       3340.80|
| 14:  1.9999 -  1.9512   488    51  0.91  14.77   1.00     0.97       2412.40|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2412.40 max =        10390.09 mean =      6202.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.86 mean =        13.85|
|phase err.(test): min =        0.00 max =           88.91 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    90.68   17.03    None  None   None       |
|    all(noH): 2823   0      1.30    90.68   17.03    None  None   None       |
|    Sol.    : 438    0      5.34    84.23   39.93    None  None   None       |
|    Mac.    : 2385   0      1.30    90.68   12.83    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:     1.300 -  10.238: 1085   |   5:    45.990 -  54.928:  108        |
|      1:    10.238 -  19.176: 1074   |   6:    54.928 -  63.866:   55        |
|      2:    19.176 -  28.114:  227   |   7:    63.866 -  72.804:   26        |
|      3:    28.114 -  37.052:  125   |   8:    72.804 -  81.742:    8        |
|      4:    37.052 -  45.990:  111   |   9:    81.742 -  90.680:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.700 - 5.713
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 307
   mapped sites are within: 0.700 - 5.713

peak=    5.926 closest distance to " NE2 GLN A  11 " =    1.218
peak=    5.609 closest distance to " NH2 ARG A  56 " =    2.100
peak=    5.502 closest distance to " CG  PRO A  54 " =    1.260
peak=    5.390 closest distance to " CG  PRO A 213 " =    1.275
peak=    5.343 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.316 closest distance to " CG  PRO A  90 " =    1.138
peak=    5.235 closest distance to " O   HOH Z 278 " =    1.113
peak=    5.232 closest distance to " O   HOH Z 144 " =    1.760
peak=    5.228 closest distance to " CG  PRO A 198 " =    1.356
peak=    5.135 closest distance to " O   HOH Z 126 " =    1.952
peak=    5.101 closest distance to " CB  SER A  63 " =    1.330
peak=    5.096 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.778 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.768 closest distance to " O   HOH Z 193 " =    1.857
peak=    4.752 closest distance to " O   HOH Z 232 " =    2.194
peak=    4.735 closest distance to " CB  PRO A  54 " =    0.953
peak=    4.658 closest distance to " O   HOH Z 260 " =    1.253
peak=    4.626 closest distance to " O   HOH Z 108 " =    1.652
peak=    4.607 closest distance to " CB  GLN A 183 " =    1.183
peak=    4.560 closest distance to " CB  SER A   3 " =    1.410
peak=    4.534 closest distance to " O   HOH Z 236 " =    1.445
peak=    4.528 closest distance to " O   HOH Z 427 " =    2.721
peak=    4.522 closest distance to " CB  GLU A 128 " =    1.064
peak=    4.498 closest distance to " OD2 ASP A 286 " =    2.728
peak=    4.487 closest distance to " O   HOH Z 214 " =    1.160
peak=    4.440 closest distance to " OD1 ASN A  69 " =    2.603
peak=    4.406 closest distance to " CB  TYR A 169 " =    0.820
peak=    4.400 closest distance to " O   HOH Z 134 " =    1.434
peak=    4.385 closest distance to " ND2 ASN A 187 " =    1.612
peak=    4.368 closest distance to " O   HOH Z 132 " =    1.063
peak=    4.366 closest distance to " C   PRO A 198 " =    1.543
peak=    4.346 closest distance to " O   HOH Z  78 " =    1.871
peak=    4.257 closest distance to " O   HOH Z 423 " =    1.541
peak=    4.240 closest distance to " O   HOH Z 207 " =    1.634
peak=    4.239 closest distance to " CB  LEU A 228 " =    1.128
peak=    4.232 closest distance to " O   HOH Z 316 " =    3.015
peak=    4.200 closest distance to " CA  ALA A  21 " =    1.097
peak=    4.186 closest distance to " CB  GLU A 152 " =    1.269
peak=    4.179 closest distance to " CA  TYR A  30 " =    0.981
peak=    4.167 closest distance to " O   HOH Z 298 " =    1.878
peak=    4.148 closest distance to " CB  TRP A 266 " =    0.999
peak=    4.147 closest distance to " O   HOH Z 368 " =    1.887
peak=    4.144 closest distance to " O   HOH Z  10 " =    1.862
peak=    4.143 closest distance to " O   HOH Z 344 " =    3.010
peak=    4.142 closest distance to " O   HOH Z 234 " =    3.826
peak=    4.136 closest distance to " O   HOH Z  59 " =    1.833
peak=    4.115 closest distance to " O   HOH Z 352 " =    1.769
peak=    4.107 closest distance to " O   HOH Z 282 " =    1.771
peak=    4.104 closest distance to " CB  PRO A 198 " =    0.954
peak=    4.078 closest distance to " O   HOH Z  48 " =    1.464
peak=    4.039 closest distance to " O   HOH Z 287 " =    1.925
peak=    4.034 closest distance to " O   HOH Z 425 " =    1.336
peak=    4.027 closest distance to " CD BLYS A 290 " =    1.203
peak=    4.024 closest distance to " O   HOH Z 369 " =    2.025
peak=    4.011 closest distance to " O   HOH Z 124 " =    1.363
peak=    3.995 closest distance to " CB  TRP A 179 " =    1.328
peak=    3.989 closest distance to " CA  GLY A 241 " =    3.679
peak=    3.984 closest distance to " O   HOH Z 263 " =    2.221
peak=    3.969 closest distance to " O   HOH Z  15 " =    2.308
peak=    3.968 closest distance to " O   HOH Z  21 " =    1.656
peak=    3.951 closest distance to " O   SER A  87 " =    2.239
peak=    3.933 closest distance to " CG1 ILE A  33 " =    1.249
peak=    3.929 closest distance to " O   HOH Z   3 " =    1.898
peak=    3.922 closest distance to " NH2BARG A 102 " =    1.016
peak=    3.914 closest distance to " CG2 VAL A 257 " =    0.935
peak=    3.909 closest distance to " CA  THR A 264 " =    0.827
peak=    3.905 closest distance to " O   HOH Z 247 " =    1.254
peak=    3.895 closest distance to " O   HOH Z  97 " =    1.973
peak=    3.887 closest distance to " O   HOH Z 371 " =    3.214
peak=    3.882 closest distance to " O   HOH Z 126 " =    1.532
peak=    3.873 closest distance to " CG  PRO A 243 " =    1.146
peak=    3.868 closest distance to " CB  VAL A 265 " =    1.262
peak=    3.863 closest distance to " O   HOH Z 135 " =    1.677
peak=    3.862 closest distance to " O   HOH Z  44 " =    1.712
peak=    3.841 closest distance to " O   HOH Z 217 " =    3.261
peak=    3.838 closest distance to " O   HOH Z 132 " =    2.205
peak=    3.834 closest distance to " CB  SER A 216 " =    0.765
peak=    3.833 closest distance to " O   HOH Z 272 " =    1.871
peak=    3.823 closest distance to " NH1AARG A 145 " =    1.008
peak=    3.822 closest distance to " O   HOH Z  88 " =    3.236
peak=    3.820 closest distance to " CG  PRO A 280 " =    0.747
peak=    3.816 closest distance to " O   HOH Z 134 " =    3.226
peak=    3.815 closest distance to " CA  ASN A 215 " =    1.220
peak=    3.810 closest distance to " OE1 GLU A   2 " =    2.116
peak=    3.799 closest distance to " CA  VAL A  41 " =    0.941
peak=    3.790 closest distance to " CG  LEU A 167 " =    1.171
peak=    3.788 closest distance to " O   HOH Z 189 " =    1.945
peak=    3.776 closest distance to " O   HOH Z 389 " =    1.809
peak=    3.776 closest distance to " CE  LYS A  76 " =    0.867
peak=    3.770 closest distance to " CB  ARG A 139 " =    0.983
peak=    3.757 closest distance to " CA  THR A 221 " =    0.937
peak=    3.755 closest distance to " O   HOH Z 261 " =    1.634
peak=    3.744 closest distance to " O   HOH Z  73 " =    1.603
peak=    3.738 closest distance to " O   HOH Z 403 " =    1.381
peak=    3.737 closest distance to " O   HOH Z 128 " =    2.020
peak=    3.730 closest distance to " CB  VAL A 202 " =    1.649
peak=    3.727 closest distance to " O   HOH Z 106 " =    2.188
peak=    3.715 closest distance to " O   HOH Z 202 " =    1.134
peak=    3.700 closest distance to " O   MET A 105 " =    1.728
peak=    3.691 closest distance to " O   HOH Z 303 " =    2.313
peak=    3.682 closest distance to " N   ASN A  39 " =    1.292
peak=    3.679 closest distance to " O   HOH Z 284 " =    2.901
peak=    3.674 closest distance to " O   HOH Z 334 " =    1.405
peak=    3.669 closest distance to " O   HOH Z  61 " =    1.624
peak=    3.667 closest distance to " O   HOH Z 108 " =    1.780
peak=    3.666 closest distance to " OD1BASN A 224 " =    2.246
peak=    3.665 closest distance to " O   HOH Z 346 " =    1.635
peak=    3.660 closest distance to " CG2 THR A 221 " =    1.085
peak=    3.658 closest distance to " O   HOH Z 409 " =    2.529
peak=    3.658 closest distance to " O   HOH Z 295 " =    1.531
peak=    3.649 closest distance to " O   HOH Z 193 " =    1.590
peak=    3.647 closest distance to " CB  ASN A 187 " =    1.363
peak=    3.632 closest distance to " O   ASP A 132 " =    3.907
peak=    3.624 closest distance to " O   HOH Z   1 " =    1.727
peak=    3.623 closest distance to " N   PHE A 130 " =    1.297
peak=    3.622 closest distance to " CB  ALA A 291 " =    1.496
peak=    3.619 closest distance to " O   HOH Z 227 " =    1.694
peak=    3.616 closest distance to " CD  LYS A 119 " =    1.153
peak=    3.616 closest distance to " NE AARG A 275 " =    1.474
peak=    3.610 closest distance to " O   HOH Z 374 " =    2.586
peak=    3.600 closest distance to " NH1 ARG A  14 " =    1.081
peak=    3.596 closest distance to " O   HOH Z  66 " =    2.155
peak=    3.586 closest distance to " O   HOH Z 163 " =    1.902
peak=    3.584 closest distance to " CA  LEU A 282 " =    1.086
peak=    3.582 closest distance to " CB  GLU A 152 " =    1.453
peak=    3.575 closest distance to " O   HOH Z 271 " =    2.247
peak=    3.565 closest distance to " ND1 HIS A  86 " =    1.807
peak=    3.555 closest distance to " CD1 LEU A 300 " =    1.211
peak=    3.549 closest distance to " O   HOH Z 227 " =    2.075
peak=    3.541 closest distance to " CD  LYS A 166 " =    1.324
peak=    3.540 closest distance to " O   HOH Z 281 " =    4.381
peak=    3.538 closest distance to " CD  ARG A 159 " =    0.748
peak=    3.537 closest distance to " CA  LYS A 290 " =    1.301
peak=    3.534 closest distance to " CB  ILE A 234 " =    0.948
peak=    3.533 closest distance to " O   HOH Z 153 " =    1.719
peak=    3.529 closest distance to " O   HOH Z 371 " =    1.618
peak=    3.525 closest distance to " CA  ASP A 124 " =    0.700
peak=    3.521 closest distance to " O   HOH Z  40 " =    2.065
peak=    3.512 closest distance to " O   HOH Z 366 " =    2.846
peak=    3.512 closest distance to " O   HOH Z 407 " =    2.088
peak=    3.510 closest distance to " N   ARG A 156 " =    1.293
peak=    3.509 closest distance to " C   ALA A 299 " =    0.977
peak=    3.507 closest distance to " O   HOH Z 193 " =    2.014
peak=    3.502 closest distance to " NH1BARG A 145 " =    1.350
peak=    3.502 closest distance to " O   HOH Z 276 " =    1.271
peak=    3.498 closest distance to " O   HOH Z 280 " =    1.743
peak=    3.496 closest distance to " O   HOH Z 423 " =    2.520
peak=    3.492 closest distance to " CD2 LEU A 255 " =    1.438
peak=    3.489 closest distance to " O   HOH Z 291 " =    1.921
peak=    3.489 closest distance to " O   HOH Z   1 " =    1.706
peak=    3.487 closest distance to " O   HOH Z   2 " =    1.564
peak=    3.486 closest distance to " N   GLN A 278 " =    0.925
peak=    3.485 closest distance to " CG  GLU A 277 " =    2.120
peak=    3.481 closest distance to " CE BMET A  47 " =    1.559
peak=    3.477 closest distance to " O   HOH Z 172 " =    3.383
peak=    3.475 closest distance to " O   HOH Z 133 " =    1.542
peak=    3.472 closest distance to " CA  ALA A  51 " =    1.064
peak=    3.464 closest distance to " CG  MET A 113 " =    1.117
peak=    3.460 closest distance to " OD1 ASP A 231 " =    1.784
peak=    3.455 closest distance to " O   HOH Z 180 " =    2.114
peak=    3.454 closest distance to " NH2 ARG A 156 " =    1.272
peak=    3.448 closest distance to " CB  MET A  47 " =    1.065
peak=    3.432 closest distance to " CA  LYS A  48 " =    1.359
peak=    3.432 closest distance to " O   HOH Z 128 " =    1.617
peak=    3.432 closest distance to " NH2AARG A 190 " =    1.361
peak=    3.427 closest distance to " O   HOH Z  63 " =    2.099
peak=    3.425 closest distance to " N   TYR A  15 " =    0.901
peak=    3.422 closest distance to " CE1 TYR A 186 " =    1.282
peak=    3.421 closest distance to " O   ALA A 165 " =    1.372
peak=    3.421 closest distance to " O   HOH Z  61 " =    1.617
peak=    3.420 closest distance to " CG  ARG A  66 " =    2.370
peak=    3.417 closest distance to " CG1BVAL A  72 " =    1.457
peak=    3.412 closest distance to " O   HOH Z 353 " =    2.548
peak=    3.411 closest distance to " OG  SER A  22 " =    2.759
peak=    3.411 closest distance to " CB  ARG A 102 " =    0.804
peak=    3.409 closest distance to " O   HOH Z 258 " =    1.786
peak=    3.401 closest distance to " CG2 VAL A 174 " =    1.357
peak=    3.396 closest distance to " CB  TYR A 116 " =    0.888
peak=    3.390 closest distance to " O   HOH Z 250 " =    1.485
peak=    3.388 closest distance to " OG BSER A 164 " =    2.410
peak=    3.384 closest distance to " O   HOH Z 183 " =    1.397
peak=    3.384 closest distance to " O   HOH Z 188 " =    2.017
peak=    3.382 closest distance to " O   HOH Z  68 " =    1.553
peak=    3.376 closest distance to " CB  ARG A  79 " =    1.302
peak=    3.373 closest distance to " CG  GLN A  88 " =    1.010
peak=    3.373 closest distance to " CA  ALA A  43 " =    1.226
peak=    3.369 closest distance to " O   ALA A   1 " =    1.557
peak=    3.366 closest distance to " CA  SER A  87 " =    0.925
peak=    3.362 closest distance to " CB  GLU A 236 " =    1.235
peak=    3.358 closest distance to " NZ ALYS A 290 " =    1.085
peak=    3.354 closest distance to " O   HOH Z 209 " =    2.488
peak=    3.351 closest distance to " O   HOH Z  43 " =    2.107
peak=    3.347 closest distance to " CA  VAL A 126 " =    1.042
peak=    3.346 closest distance to " O   HOH Z 261 " =    1.411
peak=    3.342 closest distance to " CG  GLN A  55 " =    2.013
peak=    3.342 closest distance to " O   HOH Z 214 " =    1.758
peak=    3.335 closest distance to " CG1 VAL A 153 " =    1.029
peak=    3.335 closest distance to " CB  ARG A 190 " =    1.752
peak=    3.330 closest distance to " CA  ALA A 154 " =    1.027
peak=    3.322 closest distance to " O   HOH Z  64 " =    2.073
peak=    3.320 closest distance to " O   GLY A  57 " =    2.484
peak=    3.319 closest distance to " O   HOH Z 368 " =    3.593
peak=    3.318 closest distance to " CB  ASP A 171 " =    0.903
peak=    3.318 closest distance to " O   HOH Z 394 " =    1.492
peak=    3.312 closest distance to " O   HOH Z 357 " =    1.717
peak=    3.311 closest distance to " CA  TYR A 186 " =    1.481
peak=    3.311 closest distance to " O   HOH Z  54 " =    1.538
peak=    3.306 closest distance to " O   HOH Z  93 " =    2.326
peak=    3.305 closest distance to " O   HOH Z 313 " =    1.691
peak=    3.305 closest distance to " CB  THR A  31 " =    1.709
peak=    3.304 closest distance to " O   HOH Z 419 " =    1.940
peak=    3.299 closest distance to " O   HOH Z 380 " =    2.065
peak=    3.299 closest distance to " O   GLY A 229 " =    1.552
peak=    3.298 closest distance to " O   HOH Z 158 " =    2.870
peak=    3.298 closest distance to " C   TYR A 214 " =    1.543
peak=    3.293 closest distance to " CB  LEU A 143 " =    1.114
peak=    3.285 closest distance to " NE2 GLN A  73 " =    3.498
peak=    3.277 closest distance to " CB  LEU A 255 " =    0.750
peak=    3.274 closest distance to " O   HOH Z 391 " =    2.991
peak=    3.272 closest distance to " O   HOH Z 125 " =    2.167
peak=    3.265 closest distance to " O   GLY A 147 " =    1.474
peak=    3.263 closest distance to " O   HOH Z 425 " =    1.955
peak=    3.263 closest distance to " CG  ARG A 159 " =    0.880
peak=    3.261 closest distance to " NH2AARG A 275 " =    3.755
peak=    3.256 closest distance to " O   HOH Z 273 " =    3.114
peak=    3.255 closest distance to " O   HOH Z 284 " =    1.548
peak=    3.254 closest distance to " CD1 LEU A  96 " =    0.837
peak=    3.253 closest distance to " O   HOH Z  66 " =    2.083
peak=    3.252 closest distance to " O   HOH Z 437 " =    1.817
peak=    3.248 closest distance to " O   HOH Z 410 " =    1.781
peak=    3.247 closest distance to " O   HOH Z  63 " =    2.399
peak=    3.245 closest distance to " CZ3 TRP A 123 " =    1.215
peak=    3.245 closest distance to " CG2BVAL A  41 " =    0.935
peak=    3.244 closest distance to " O   HOH Z 285 " =    1.621
peak=    3.239 closest distance to " O   HOH Z  44 " =    3.248
peak=    3.239 closest distance to " O   HOH Z  40 " =    2.100
peak=    3.238 closest distance to " O   HOH Z 329 " =    3.434
peak=    3.237 closest distance to " CA  MET A  40 " =    1.059
peak=    3.237 closest distance to " CB  ALA A  21 " =    1.767
peak=    3.237 closest distance to " N   ASN A 127 " =    1.245
peak=    3.233 closest distance to " CB  SER A 212 " =    1.052
peak=    3.231 closest distance to " CA  ALA A 158 " =    1.118
peak=    3.228 closest distance to " CB  THR A 157 " =    1.029
peak=    3.228 closest distance to " O   HOH Z 263 " =    1.543
peak=    3.226 closest distance to " OD1 ASN A 217 " =    1.684
peak=    3.226 closest distance to " O   THR A 220 " =    1.351
peak=    3.220 closest distance to " CA  ASP A 140 " =    1.128
peak=    3.205 closest distance to " O   HOH Z 211 " =    2.173
peak=    3.200 closest distance to " O   HOH Z 116 " =    1.648
peak=    3.199 closest distance to " O   HOH Z 175 " =    2.102
peak=    3.198 closest distance to " OE1 GLN A  11 " =    1.974
peak=    3.198 closest distance to " OD1 ASP A 238 " =    0.997
peak=    3.196 closest distance to " CB  ALA A  34 " =    1.144
peak=    3.193 closest distance to " CB  HIS A 108 " =    0.909
peak=    3.188 closest distance to " O   HOH Z 115 " =    2.030
peak=    3.187 closest distance to " O   HOH Z 173 " =    1.883
peak=    3.186 closest distance to " O   HOH Z 345 " =    3.432
peak=    3.183 closest distance to " O   HOH Z 217 " =    1.306
peak=    3.181 closest distance to " O   HOH Z 286 " =    2.251
peak=    3.176 closest distance to " CB  SER A  62 " =    1.305
peak=    3.173 closest distance to " CB  MET A  40 " =    0.774
peak=    3.173 closest distance to " O   HOH Z  49 " =    2.030
peak=    3.172 closest distance to " CA  ILE A 263 " =    1.053
peak=    3.170 closest distance to " O   HOH Z 327 " =    1.715
peak=    3.170 closest distance to " NH2 ARG A 219 " =    1.860
peak=    3.169 closest distance to " CA  GLY A 267 " =    1.279
peak=    3.169 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.166 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.160 closest distance to " CA  ARG A  56 " =    1.912
peak=    3.160 closest distance to " O   HOH Z  59 " =    1.919
peak=    3.155 closest distance to " NZ  LYS A  76 " =    1.268
peak=    3.154 closest distance to " O   HOH Z 269 " =    3.451
peak=    3.153 closest distance to " O   HOH Z 194 " =    2.088
peak=    3.150 closest distance to " N   SER A 210 " =    1.032
peak=    3.147 closest distance to " CB  ALA A  71 " =    1.489
peak=    3.147 closest distance to " O   HOH Z 387 " =    3.082
peak=    3.143 closest distance to " O   HOH Z 388 " =    1.981
peak=    3.137 closest distance to " O   HOH Z 277 " =    2.538
peak=    3.130 closest distance to " CG2 VAL A  67 " =    1.003
peak=    3.127 closest distance to " CD1 LEU A 228 " =    1.999
peak=    3.123 closest distance to " O   HOH Z 244 " =    1.662
peak=    3.123 closest distance to " O   HOH Z 365 " =    5.662
peak=    3.122 closest distance to " CD2 HIS A  81 " =    1.252
peak=    3.121 closest distance to " CA  ILE A  20 " =    0.797
peak=    3.101 closest distance to " NH2BARG A 145 " =    2.012
peak=    3.100 closest distance to " CD1AILE A 234 " =    1.055
peak=    3.095 closest distance to " O   HOH Z 409 " =    3.581
peak=    3.094 closest distance to " NZ  LYS A 117 " =    1.123
peak=    3.092 closest distance to " CB  SER A 276 " =    1.107
peak=    3.089 closest distance to " CB  ARG A 138 " =    0.965
peak=    3.087 closest distance to " O   HOH Z 213 " =    1.906
peak=    3.086 closest distance to " CB  TRP A 179 " =    1.704
peak=    3.084 closest distance to " O   HOH Z 134 " =    2.307
peak=    3.076 closest distance to " CB  PRO A 243 " =    1.228
peak=    3.070 closest distance to " CG BARG A 275 " =    1.493
peak=    3.069 closest distance to " CG1 ILE A 151 " =    0.880
peak=    3.064 closest distance to " O   HOH Z 248 " =    1.761
peak=    3.059 closest distance to " CA  PHE A 283 " =    1.109
peak=    3.059 closest distance to " O   HOH Z 163 " =    1.637
peak=    3.056 closest distance to " O   HOH Z 151 " =    2.161
peak=    3.050 closest distance to " O   HOH Z 286 " =    2.440
peak=    3.040 closest distance to " OG  SER A 206 " =    1.308
peak=    3.034 closest distance to " NE2 GLN A  58 " =    5.713
peak=    3.032 closest distance to " CB  LYS A 193 " =    1.047
peak=    3.029 closest distance to " O   HOH Z  97 " =    1.230
peak=    3.001 closest distance to " O   HOH Z 172 " =    3.204

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.810 - 5.496
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.810 - 5.496

peak=   -4.534 closest distance to " O   HOH Z 377 " =    1.683
peak=   -4.490 closest distance to " CB  PRO A 243 " =    2.565
peak=   -4.475 closest distance to " O   PRO A 198 " =    1.240
peak=   -4.381 closest distance to " O   HOH Z 290 " =    0.996
peak=   -4.330 closest distance to " O   HOH Z 198 " =    2.171
peak=   -4.219 closest distance to " O   HOH Z  98 " =    1.818
peak=   -4.144 closest distance to " SG  CYS A 254 " =    3.273
peak=   -4.125 closest distance to " O   HOH Z 388 " =    1.905
peak=   -4.118 closest distance to " O   HOH Z 266 " =    4.280
peak=   -4.095 closest distance to " CB  TYR A  15 " =    2.132
peak=   -4.081 closest distance to " C   ALA A 158 " =    1.283
peak=   -4.064 closest distance to " N   GLN A  58 " =    1.805
peak=   -4.045 closest distance to " CG  LYS A 193 " =    2.335
peak=   -4.000 closest distance to " O   HOH Z  92 " =    1.762
peak=   -3.968 closest distance to " CD  ARG A 156 " =    1.944
peak=   -3.948 closest distance to " ND2 ASN A  45 " =    0.938
peak=   -3.936 closest distance to " CG  MET A 105 " =    0.961
peak=   -3.932 closest distance to " OXT GLY A 302 " =    2.880
peak=   -3.914 closest distance to " O   VAL A  67 " =    2.821
peak=   -3.895 closest distance to " CZ  PHE A  59 " =    1.546
peak=   -3.893 closest distance to " CB  ALA A 291 " =    2.182
peak=   -3.862 closest distance to " O   HOH Z  13 " =    1.282
peak=   -3.856 closest distance to " CG  ASP A 231 " =    0.810
peak=   -3.854 closest distance to " N   ASP A 286 " =    2.531
peak=   -3.829 closest distance to " CB  CYS A 201 " =    2.476
peak=   -3.826 closest distance to " O   HOH Z 407 " =    3.226
peak=   -3.823 closest distance to " O   HOH Z  43 " =    1.623
peak=   -3.811 closest distance to " O   GLY A 211 " =    1.329
peak=   -3.764 closest distance to " O   ALA A 161 " =    1.546
peak=   -3.751 closest distance to " CE2 TYR A  30 " =    2.945
peak=   -3.745 closest distance to " CD  GLN A 223 " =    1.702
peak=   -3.736 closest distance to " CZ  TYR A 169 " =    1.741
peak=   -3.736 closest distance to " O   HOH Z  93 " =    2.094
peak=   -3.722 closest distance to " CB  ASN A  39 " =    2.159
peak=   -3.717 closest distance to " O   TRP A  70 " =    1.512
peak=   -3.709 closest distance to " CB  PHE A 283 " =    2.663
peak=   -3.692 closest distance to " O   HOH Z 185 " =    2.099
peak=   -3.679 closest distance to " OE1 GLN A  88 " =    1.048
peak=   -3.677 closest distance to " O   HOH Z  24 " =    1.405
peak=   -3.661 closest distance to " OD1 ASP A 191 " =    1.793
peak=   -3.651 closest distance to " O   HOH Z 231 " =    1.796
peak=   -3.647 closest distance to " O   ALA A  51 " =    1.553
peak=   -3.636 closest distance to " O   PRO A 163 " =    1.897
peak=   -3.628 closest distance to " CA  SER A 146 " =    2.258
peak=   -3.618 closest distance to " CE  MET A 105 " =    2.171
peak=   -3.615 closest distance to " C   HIS A 108 " =    1.134
peak=   -3.608 closest distance to " CZ3 TRP A 179 " =    1.290
peak=   -3.605 closest distance to " O   SER A 135 " =    1.486
peak=   -3.603 closest distance to " OD1 ASN A 187 " =    1.663
peak=   -3.601 closest distance to " CB  ASP A  27 " =    2.395
peak=   -3.594 closest distance to " O   HOH Z 152 " =    5.136
peak=   -3.592 closest distance to " O   VAL A 153 " =    2.352
peak=   -3.579 closest distance to " N   ALA A  43 " =    2.373
peak=   -3.572 closest distance to " C   LEU A 143 " =    1.410
peak=   -3.572 closest distance to " O   ILE A 109 " =    2.559
peak=   -3.568 closest distance to " O   HOH Z 213 " =    1.114
peak=   -3.567 closest distance to " CD  GLN A  88 " =    0.846
peak=   -3.563 closest distance to " O   HOH Z 438 " =    1.112
peak=   -3.555 closest distance to " NH1 ARG A 195 " =    2.615
peak=   -3.546 closest distance to " O   HOH Z 351 " =    1.454
peak=   -3.543 closest distance to " CD1 LEU A 228 " =    2.275
peak=   -3.538 closest distance to " OG BSER A 134 " =    1.147
peak=   -3.532 closest distance to " O   VAL A  67 " =    2.544
peak=   -3.528 closest distance to " CB  ALA A 248 " =    1.932
peak=   -3.515 closest distance to " O   HOH Z  11 " =    1.897
peak=   -3.511 closest distance to " CD2 LEU A 300 " =    2.955
peak=   -3.510 closest distance to " N   THR A 157 " =    1.561
peak=   -3.504 closest distance to " N   MET A 188 " =    1.824
peak=   -3.502 closest distance to " OG  SER A  97 " =    2.056
peak=   -3.486 closest distance to " CE2 PHE A 218 " =    2.505
peak=   -3.481 closest distance to " O   HOH Z  88 " =    2.227
peak=   -3.479 closest distance to " CB  ALA A  43 " =    2.375
peak=   -3.474 closest distance to " CE3 TRP A 274 " =    2.456
peak=   -3.467 closest distance to " OD1 ASP A 200 " =    1.311
peak=   -3.466 closest distance to " O   HOH Z 353 " =    2.102
peak=   -3.437 closest distance to " N   GLN A 122 " =    1.532
peak=   -3.434 closest distance to " O   HOH Z 435 " =    2.682
peak=   -3.431 closest distance to " O   HOH Z 148 " =    1.925
peak=   -3.428 closest distance to " CG  GLU A 152 " =    2.308
peak=   -3.425 closest distance to " O   HOH Z 166 " =    1.289
peak=   -3.424 closest distance to " CE  MET A  93 " =    1.158
peak=   -3.421 closest distance to " O   HOH Z  11 " =    2.019
peak=   -3.419 closest distance to " O   ALA A 180 " =    1.190
peak=   -3.418 closest distance to " O   HOH Z 385 " =    1.997
peak=   -3.415 closest distance to " O   HOH Z  97 " =    1.979
peak=   -3.415 closest distance to " O   HOH Z 298 " =    1.230
peak=   -3.413 closest distance to " O   HOH Z 266 " =    4.499
peak=   -3.413 closest distance to " CD  ARG A 139 " =    1.596
peak=   -3.412 closest distance to " OH  TYR A 214 " =    1.226
peak=   -3.409 closest distance to " O   HOH Z  47 " =    1.516
peak=   -3.408 closest distance to " OXT GLY A 302 " =    3.385
peak=   -3.405 closest distance to " O   HOH Z 168 " =    1.854
peak=   -3.404 closest distance to " CD1 PHE A  59 " =    1.852
peak=   -3.398 closest distance to " CA  ARG A 139 " =    1.046
peak=   -3.396 closest distance to " O   SER A  62 " =    2.140
peak=   -3.391 closest distance to " CG  LEU A  83 " =    1.880
peak=   -3.389 closest distance to " O   HOH Z 389 " =    1.831
peak=   -3.383 closest distance to " O   HOH Z  71 " =    1.061
peak=   -3.378 closest distance to " CA  GLY A 203 " =    2.142
peak=   -3.377 closest distance to " CB  CYS A 254 " =    2.221
peak=   -3.376 closest distance to " OG ASER A 134 " =    1.169
peak=   -3.374 closest distance to " O   HOH Z  52 " =    1.247
peak=   -3.368 closest distance to " O   HOH Z 281 " =    3.042
peak=   -3.368 closest distance to " N   HIS A 115 " =    2.006
peak=   -3.358 closest distance to " O   HOH Z  63 " =    1.386
peak=   -3.357 closest distance to " NH2 ARG A  79 " =    1.774
peak=   -3.356 closest distance to " O   SER A  22 " =    2.458
peak=   -3.355 closest distance to " CD2 LEU A 237 " =    2.527
peak=   -3.354 closest distance to " CB  ALA A 291 " =    2.320
peak=   -3.352 closest distance to " O   HOH Z 222 " =    1.071
peak=   -3.347 closest distance to " OD1 ASN A 148 " =    1.769
peak=   -3.345 closest distance to " NH1AARG A 275 " =    1.784
peak=   -3.344 closest distance to " O   GLN A 183 " =    1.393
peak=   -3.339 closest distance to " O   HOH Z 436 " =    1.187
peak=   -3.338 closest distance to " OD2 ASP A 171 " =    2.104
peak=   -3.338 closest distance to " N   SER A 276 " =    1.151
peak=   -3.335 closest distance to " O   ALA A   7 " =    1.710
peak=   -3.334 closest distance to " O   HOH Z  28 " =    2.090
peak=   -3.332 closest distance to " O   GLY A 196 " =    1.057
peak=   -3.331 closest distance to " CE3 TRP A 150 " =    1.972
peak=   -3.330 closest distance to " O   HOH Z  60 " =    1.669
peak=   -3.324 closest distance to " CG2 ILE A 263 " =    2.345
peak=   -3.314 closest distance to " CG  PRO A 163 " =    2.416
peak=   -3.314 closest distance to " O   HOH Z 385 " =    2.061
peak=   -3.310 closest distance to " CB  ASP A 132 " =    2.207
peak=   -3.305 closest distance to " NH2AARG A 275 " =    5.496
peak=   -3.301 closest distance to " O   HOH Z 313 " =    1.986
peak=   -3.298 closest distance to " CD1 TRP A 274 " =    1.684
peak=   -3.267 closest distance to " O   HOH Z 423 " =    1.160
peak=   -3.263 closest distance to " CE  LYS A  76 " =    2.814
peak=   -3.251 closest distance to " NH2BARG A 275 " =    1.977
peak=   -3.245 closest distance to " OG ASER A 216 " =    1.035
peak=   -3.245 closest distance to " O   HOH Z 137 " =    1.505
peak=   -3.240 closest distance to " CA  GLY A 241 " =    2.164
peak=   -3.240 closest distance to " O   HOH Z 317 " =    2.702
peak=   -3.237 closest distance to " N   SER A 212 " =    1.782
peak=   -3.229 closest distance to " CB  SER A 245 " =    2.485
peak=   -3.223 closest distance to " CE3 TRP A 123 " =    1.269
peak=   -3.223 closest distance to " N   GLN A  58 " =    1.383
peak=   -3.220 closest distance to " O   ASP A 231 " =    2.504
peak=   -3.220 closest distance to " CB  PRO A 163 " =    2.583
peak=   -3.218 closest distance to " SG BCYS A 201 " =    2.241
peak=   -3.218 closest distance to " O   HOH Z 193 " =    1.967
peak=   -3.216 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.215 closest distance to " O   HOH Z 417 " =    2.658
peak=   -3.208 closest distance to " O   VAL A 197 " =    1.150
peak=   -3.204 closest distance to " CG1 VAL A 112 " =    2.909
peak=   -3.204 closest distance to " N   ALA A 248 " =    1.657
peak=   -3.195 closest distance to " O   HOH Z  97 " =    1.273
peak=   -3.195 closest distance to " CD2 TYR A 293 " =    2.048
peak=   -3.192 closest distance to " O   HOH Z 323 " =    1.402
peak=   -3.189 closest distance to " O   HOH Z 298 " =    2.576
peak=   -3.187 closest distance to " NH1 ARG A  56 " =    2.469
peak=   -3.186 closest distance to " O   HOH Z 417 " =    2.433
peak=   -3.181 closest distance to " N   GLY A  23 " =    2.100
peak=   -3.181 closest distance to " SG ACYS A 201 " =    2.167
peak=   -3.180 closest distance to " O   HOH Z 263 " =    2.956
peak=   -3.179 closest distance to " O   HOH Z 234 " =    4.162
peak=   -3.175 closest distance to " OH  TYR A 169 " =    0.938
peak=   -3.172 closest distance to " O   HOH Z 120 " =    2.746
peak=   -3.170 closest distance to " CB  TRP A  85 " =    2.446
peak=   -3.165 closest distance to " O   THR A  29 " =    2.847
peak=   -3.162 closest distance to " O   TYR A 247 " =    2.773
peak=   -3.160 closest distance to " O   HOH Z 359 " =    3.246
peak=   -3.158 closest distance to " CD  LYS A 289 " =    2.550
peak=   -3.157 closest distance to " O   ILE A  49 " =    1.787
peak=   -3.151 closest distance to " ND2 ASN A 252 " =    1.501
peak=   -3.148 closest distance to " O   HOH Z 210 " =    1.023
peak=   -3.139 closest distance to " OD1 ASN A 301 " =    1.902
peak=   -3.137 closest distance to " O   PHE A 218 " =    1.317
peak=   -3.133 closest distance to " O   HOH Z 378 " =    2.050
peak=   -3.132 closest distance to " ND2 ASN A  60 " =    1.658
peak=   -3.126 closest distance to " CD  GLN A  88 " =    2.218
peak=   -3.123 closest distance to " OG BSER A 134 " =    1.621
peak=   -3.117 closest distance to " O   HOH Z 377 " =    0.815
peak=   -3.113 closest distance to " O   VAL A 174 " =    1.979
peak=   -3.109 closest distance to " CD2 LEU A 143 " =    2.573
peak=   -3.108 closest distance to " O   HOH Z 198 " =    1.548
peak=   -3.106 closest distance to " O   HOH Z 166 " =    1.947
peak=   -3.104 closest distance to " O   MET A  40 " =    2.673
peak=   -3.102 closest distance to " CE1 TYR A 169 " =    2.435
peak=   -3.090 closest distance to " N   ALA A 226 " =    2.148
peak=   -3.088 closest distance to " CB  ALA A 131 " =    1.925
peak=   -3.074 closest distance to " N   ALA A 114 " =    2.552
peak=   -3.071 closest distance to " CG  GLN A 278 " =    2.239
peak=   -3.069 closest distance to " CA  GLY A 133 " =    1.913
peak=   -3.068 closest distance to " O   HOH Z 410 " =    2.214
peak=   -3.068 closest distance to " CD2 LEU A 300 " =    2.872
peak=   -3.064 closest distance to " O   ASP A 162 " =    2.205
peak=   -3.063 closest distance to " O   HOH Z 275 " =    1.573
peak=   -3.060 closest distance to " CG1 VAL A 197 " =    2.223
peak=   -3.039 closest distance to " O   HOH Z 207 " =    1.986
peak=   -3.015 closest distance to " O   ASN A 249 " =    1.522
peak=   -3.013 closest distance to " CB  ASP A 132 " =    1.975
peak=   -3.007 closest distance to " CD1 ILE A 199 " =    2.498

================= 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    :  0.4275 0.4297   6.230588e+00   6.230932e+00
   1_bss:  0.4167 0.4194   6.225975e+00   6.213803e+00
   1_xyz:  0.2996 0.3275   5.975846e+00   6.053775e+00
   1_adp:  0.2740 0.3340   5.922589e+00   6.066907e+00
   1_occ:  0.2737 0.3346   5.921869e+00   6.066083e+00
   2_bss:  0.2733 0.3336   5.921408e+00   6.064480e+00
   2_xyz:  0.1912 0.2450   5.607565e+00   5.793504e+00
   2_adp:  0.1695 0.2226   5.505564e+00   5.708153e+00
   2_occ:  0.1692 0.2222   5.504299e+00   5.706830e+00
   3_bss:  0.1684 0.2203   5.497825e+00   5.700784e+00
   3_xyz:  0.1344 0.1773   5.286781e+00   5.507045e+00
   3_adp:  0.1271 0.1693   5.235089e+00   5.458965e+00
   3_occ:  0.1270 0.1691   5.234224e+00   5.458093e+00
   4_bss:  0.1270 0.1692   5.234568e+00   5.458760e+00
   4_xyz:  0.1187 0.1604   5.179808e+00   5.407180e+00
   4_adp:  0.1166 0.1592   5.165868e+00   5.396313e+00
   4_occ:  0.1165 0.1590   5.165043e+00   5.395683e+00
   5_bss:  0.1165 0.1589   5.165018e+00   5.395702e+00
   5_xyz:  0.1142 0.1567   5.150556e+00   5.382290e+00
   5_adp:  0.1138 0.1569   5.150562e+00   5.385203e+00
   5_occ:  0.1137 0.1568   5.150244e+00   5.385090e+00
   5_bss:  0.1137 0.1569   5.150327e+00   5.385177e+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:  0.326  30.649  -1.895  -1.018   2.720  -0.000   0.000   0.000
   1_xyz:  0.326  30.649  -1.895  -1.018   2.720  -0.000   0.000   0.000
   1_adp:  0.326  30.649  -1.895  -1.018   2.720  -0.000   0.000   0.000
   1_occ:  0.326  30.649  -1.895  -1.018   2.720  -0.000   0.000   0.000
   2_bss:  0.333  46.899  -1.664  -1.594   0.695  -0.000   0.000   0.000
   2_xyz:  0.333  46.899  -1.664  -1.594   0.695  -0.000   0.000   0.000
   2_adp:  0.333  46.899  -1.664  -1.594   0.695  -0.000   0.000   0.000
   2_occ:  0.333  46.899  -1.664  -1.594   0.695  -0.000   0.000   0.000
   3_bss:  0.325  44.209  -1.803  -2.144  -1.026  -0.000  -0.000  -0.000
   3_xyz:  0.325  44.209  -1.803  -2.144  -1.026  -0.000  -0.000  -0.000
   3_adp:  0.325  44.209  -1.803  -2.144  -1.026  -0.000  -0.000  -0.000
   3_occ:  0.325  44.209  -1.803  -2.144  -1.026  -0.000  -0.000  -0.000
   4_bss:  0.325  44.209  -2.393  -2.649  -1.875  -0.000  -0.000  -0.000
   4_xyz:  0.325  44.209  -2.393  -2.649  -1.875  -0.000  -0.000  -0.000
   4_adp:  0.325  44.209  -2.393  -2.649  -1.875  -0.000  -0.000  -0.000
   4_occ:  0.325  44.209  -2.393  -2.649  -1.875  -0.000  -0.000  -0.000
   5_bss:  0.325  44.209  -2.323  -2.577  -1.950  -0.000  -0.000  -0.000
   5_xyz:  0.325  44.209  -2.323  -2.577  -1.950  -0.000  -0.000  -0.000
   5_adp:  0.325  44.209  -2.323  -2.577  -1.950  -0.000  -0.000  -0.000
   5_occ:  0.325  44.209  -2.323  -2.577  -1.950  -0.000  -0.000  -0.000
   5_bss:  0.325  44.161  -2.148  -2.407  -1.827  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.750 0.5244  0.7089    56884.290
   1_bss:  48.252 0.5409  0.7310    52687.720
   1_xyz:  35.174 0.6996  0.9052    30709.153
   1_adp:  36.080 0.6880  0.8929    31555.683
   1_occ:  36.105 0.6876  0.8914    31513.374
   2_bss:  35.899 0.6900  0.8720    31365.658
   2_xyz:  24.708 0.8140  0.9902    15695.740
   2_adp:  21.712 0.8455  1.0080    12945.271
   2_occ:  21.678 0.8458  1.0076    12896.563
   3_bss:  21.438 0.8480  0.9800    12600.511
   3_xyz:  16.595 0.8926  1.0031     8051.944
   3_adp:  15.405 0.9032  1.0049     7339.322
   3_occ:  15.375 0.9035  1.0049     7319.885
   4_bss:  15.380 0.9034  0.9815     7340.795
   4_xyz:  14.341 0.9120  0.9842     6509.356
   4_adp:  14.076 0.9144  0.9816     6388.284
   4_occ:  14.052 0.9146  0.9815     6373.529
   5_bss:  14.052 0.9146  0.9823     6375.234
   5_xyz:  13.773 0.9168  0.9830     6174.130
   5_adp:  13.805 0.9167  0.9798     6205.102
   5_occ:  13.799 0.9168  0.9797     6201.220
   5_bss:  13.802 0.9167  0.9836     6203.016
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7653e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7653e-01
   1_xyz:   1.299  0.010  0.082 15.688  0.005  4.107   9.7312e-02
   1_adp:   1.299  0.010  0.082 15.688  0.005  4.107   9.7312e-02
   1_occ:   1.299  0.010  0.082 15.688  0.005  4.107   9.7312e-02
   2_bss:   1.299  0.010  0.082 15.688  0.005  4.107   9.7312e-02
   2_xyz:   1.191  0.009  0.077 14.475  0.004  4.109   8.6091e-02
   2_adp:   1.191  0.009  0.077 14.475  0.004  4.109   8.6091e-02
   2_occ:   1.191  0.009  0.077 14.475  0.004  4.109   8.6091e-02
   3_bss:   1.191  0.009  0.077 14.475  0.004  4.109   8.6091e-02
   3_xyz:   0.972  0.006  0.068 14.375  0.004  4.113   5.5307e-02
   3_adp:   0.972  0.006  0.068 14.375  0.004  4.113   5.5307e-02
   3_occ:   0.972  0.006  0.068 14.375  0.004  4.113   5.5307e-02
   4_bss:   0.972  0.006  0.068 14.375  0.004  4.113   5.5307e-02
   4_xyz:   0.911  0.005  0.066 14.251  0.003  4.115   4.9634e-02
   4_adp:   0.911  0.005  0.066 14.251  0.003  4.115   4.9634e-02
   4_occ:   0.911  0.005  0.066 14.251  0.003  4.115   4.9634e-02
   5_bss:   0.911  0.005  0.066 14.251  0.003  4.115   4.9634e-02
   5_xyz:   0.875  0.005  0.063 14.143  0.003  4.116   4.6860e-02
   5_adp:   0.875  0.005  0.063 14.143  0.003  4.116   4.6860e-02
   5_occ:   0.875  0.005  0.063 14.143  0.003  4.116   4.6860e-02
   5_bss:   0.875  0.005  0.063 14.143  0.003  4.116   4.6860e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.670   2.3923e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.670   2.3923e-01
   1_xyz:   9.407  0.055  0.353 86.045  0.030  2.169   8.9743e-02
   1_adp:   9.407  0.055  0.353 86.045  0.030  2.169   8.9743e-02
   1_occ:   9.407  0.055  0.353 86.045  0.030  2.169   8.9743e-02
   2_bss:   9.407  0.055  0.353 86.045  0.030  2.169   8.9743e-02
   2_xyz:   7.304  0.102  0.250 82.633  0.027  2.333   2.4256e-01
   2_adp:   7.304  0.102  0.250 82.633  0.027  2.333   2.4256e-01
   2_occ:   7.304  0.102  0.250 82.633  0.027  2.333   2.4256e-01
   3_bss:   7.304  0.102  0.250 82.633  0.027  2.333   2.4256e-01
   3_xyz:   7.578  0.032  0.298 83.921  0.032  2.330   4.4367e-02
   3_adp:   7.578  0.032  0.298 83.921  0.032  2.330   4.4367e-02
   3_occ:   7.578  0.032  0.298 83.921  0.032  2.330   4.4367e-02
   4_bss:   7.578  0.032  0.298 83.921  0.032  2.330   4.4367e-02
   4_xyz:   6.948  0.051  0.201 84.172  0.034  2.374   3.2285e-02
   4_adp:   6.948  0.051  0.201 84.172  0.034  2.374   3.2285e-02
   4_occ:   6.948  0.051  0.201 84.172  0.034  2.374   3.2285e-02
   5_bss:   6.948  0.051  0.201 84.172  0.034  2.374   3.2285e-02
   5_xyz:   7.120  0.034  0.192 84.476  0.031  2.362   2.8309e-02
   5_adp:   7.120  0.034  0.192 84.476  0.031  2.362   2.8309e-02
   5_occ:   7.120  0.034  0.192 84.476  0.031  2.362   2.8309e-02
   5_bss:   7.120  0.034  0.192 84.476  0.031  2.362   2.8309e-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:  86.53   0.00  18.12  86.53   0.00  14.09  84.12   0.00  40.05
   1_occ:  86.53   0.00  18.12  86.53   0.00  14.09  84.12   0.00  40.05
   2_bss:  86.53   0.00  18.12  86.53   0.00  14.09  84.12   0.00  40.05
   2_xyz:  86.53   0.00  18.12  86.53   0.00  14.09  84.12   0.00  40.05
   2_adp:  80.77   0.95  17.33  80.77   0.95  13.19  79.11   4.50  39.84
   2_occ:  80.77   0.95  17.33  80.77   0.95  13.19  79.11   4.50  39.84
   3_bss:  80.77   0.95  17.33  80.77   0.95  13.19  79.11   4.50  39.84
   3_xyz:  80.77   0.95  17.33  80.77   0.95  13.19  79.11   4.50  39.84
   3_adp:  84.14   1.70  17.26  84.14   1.70  12.99  76.90   3.79  40.50
   3_occ:  84.14   1.70  17.26  84.14   1.70  12.99  76.90   3.79  40.50
   4_bss:  84.14   1.70  17.26  84.14   1.70  12.99  76.90   3.79  40.50
   4_xyz:  84.14   1.70  17.26  84.14   1.70  12.99  76.90   3.79  40.50
   4_adp:  89.57   1.73  17.19  89.57   1.73  12.95  83.07   3.84  40.32
   4_occ:  89.57   1.73  17.19  89.57   1.73  12.95  83.07   3.84  40.32
   5_bss:  89.57   1.73  17.19  89.57   1.73  12.95  83.07   3.84  40.32
   5_xyz:  89.57   1.73  17.19  89.57   1.73  12.95  83.07   3.84  40.32
   5_adp:  90.73   1.35  17.08  90.73   1.35  12.88  84.27   5.39  39.98
   5_occ:  90.73   1.35  17.08  90.73   1.35  12.88  84.27   5.39  39.98
   5_bss:  90.68   1.30  17.03  90.68   1.30  12.83  84.23   5.34  39.93
------------------------------------------------------------------------
 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:    1.820    0.006    0.313
   1_adp:    1.820    0.006    0.313
   1_occ:    1.820    0.006    0.313
   2_bss:    1.820    0.006    0.313
   2_xyz:    1.278    0.048    0.532
   2_adp:    1.278    0.048    0.532
   2_occ:    1.278    0.048    0.532
   3_bss:    1.278    0.048    0.532
   3_xyz:    1.179    0.058    0.585
   3_adp:    1.179    0.058    0.585
   3_occ:    1.179    0.058    0.585
   4_bss:    1.179    0.058    0.585
   4_xyz:    1.295    0.022    0.613
   4_adp:    1.295    0.022    0.613
   4_occ:    1.295    0.022    0.613
   5_bss:    1.295    0.022    0.613
   5_xyz:    1.322    0.057    0.622
   5_adp:    1.322    0.057    0.622
   5_occ:    1.322    0.057    0.622
   5_bss:    1.322    0.057    0.622
------------------------------------------------------------------------

CPU time actual refinement: 340.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/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_880/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_880/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.00 
  Macro-tasks:
    bulk solvent and scale       = 36.11  
    individual site refinement   = 141.02 
    weights calculation          = 29.75  
    collect and process          = 6.53   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 213.50 
  Micro-tasks:
    mask                            = 1.87   
    f_calc                          = 112.67 
    alpha_beta                      = 8.12   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 120.33 
    fmodel                         = 6.56   
    r_factors                      = 0.25   
    phase_errors                   = 10.70  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 261.98 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.836 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    646 calls, 112.43 s
gradients_fft:          591 calls, 107.04 s

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

# Date 2008-01-16 Time 05:53:27 PST -0800 (1200491607.75 s)
Start R-work = 0.4275, R-free = 0.4297 (no bulk solvent and anisotropic scale)
Final R-work = 0.1386, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.4167, R-free = 0.4194
Final R-work = 0.1137, R-free = 0.1569