# Date 2008-01-16 Time 05:45:07 PST -0800 (1200491107.25 s)
#phil __OFF__

Command line arguments: "../864.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30360
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 864

-------------------------------------------------------------------------------
  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, 45.9914, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.96355
Completeness in resolution range: 0.938575
Completeness with d_max=infinity: 0.935885

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1235
                             d_min =   1.9636

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, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1235 1.96355
Completeness in resolution range: 0.938575
Completeness with d_max=infinity: 0.935885

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1239 -  4.2029 [2197/2224]  1976   221  10.1%
  bin  2:  4.2029 -  3.3479 [2109/2129]  1899   210  10.0%
  bin  3:  3.3479 -  2.9282 [2076/2095]  1870   206   9.9%
  bin  4:  2.9282 -  2.6620 [2058/2088]  1849   209  10.2%
  bin  5:  2.6620 -  2.4721 [2043/2062]  1847   196   9.6%
  bin  6:  2.4721 -  2.3269 [2044/2069]  1830   214  10.5%
  bin  7:  2.3269 -  2.2108 [2027/2055]  1821   206  10.2%
  bin  8:  2.2108 -  2.1148 [2006/2042]  1808   198   9.9%
  bin  9:  2.1148 -  2.0336 [2021/2063]  1825   196   9.7%
  bin 10:  2.0336 -  1.9636 [1008/2044]   905   103  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 32
        2.42 -     3.04: 2205
        3.04 -     3.66: 4735
        3.66 -     4.28: 9049
        4.28 -     4.90: 12316
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.854 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28332 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_864/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 45.9914 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4081   r_free= 0.4048   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.218706                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.3407 0.3315      6.4907      6.4637|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.3416 0.3115      6.7066      6.6186|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.3591 0.3480       6.562      6.5908|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.3961 0.4149       6.446      6.4926|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.4292 0.4027      6.2995      6.2729|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.4283 0.4569      6.2013      6.1707|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.4413 0.4091      6.1837      6.1167|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.4524 0.4509      6.1189      6.1459|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.4415 0.4832       6.072      6.1201|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.4635 0.4564      6.0492      6.0132|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.4540 0.4630      5.9931      6.0193|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.4642 0.4894      5.9119      5.9621|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.4648 0.4540      5.8415      5.7806|
| 14:  2.0125 -  1.9636 0.31    416   47 0.5266 0.5417      5.8626      5.8659|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.6884  1421   158  0.75  29.88   0.84     0.80      56901.01|
|  2:  4.6884 -  3.7398  1373   155  0.78  28.47   0.93     0.88      75285.71|
|  3:  3.7398 -  3.2726  1342   142  0.69  36.13   0.97     0.87      81668.11|
|  4:  3.2726 -  2.9758  1331   155  0.62  42.00   0.94     0.82      75883.79|
|  5:  2.9758 -  2.7639  1338   149  0.55  48.04   0.92     0.76      62734.97|
|  6:  2.7639 -  2.6018  1327   146  0.54  48.94   0.93     0.73      54082.35|
|  7:  2.6018 -  2.4721  1309   137  0.51  51.41   0.95     0.69      50846.70|
|  8:  2.4721 -  2.3649  1299   152  0.48  53.65   0.94     0.67      47066.67|
|  9:  2.3649 -  2.2742  1307   148  0.48  53.40   0.98     0.68      43666.65|
| 10:  2.2742 -  2.1960  1298   147  0.49  52.60   0.97     0.70      38646.05|
| 11:  2.1960 -  2.1275  1316   137  0.47  54.38   1.00     0.70      38788.04|
| 12:  2.1275 -  2.0668  1288   144  0.43  57.35   0.97     0.66      36154.76|
| 13:  2.0668 -  2.0125  1265   142  0.40  60.31   0.97     0.63      33107.42|
| 14:  2.0125 -  1.9636   416    47  0.43  57.58   0.97     0.62      26620.02|
|alpha:            min =        0.62 max =            0.88 mean =         0.74|
|beta:             min =    26620.02 max =        81668.11 mean =     53093.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        47.41|
|phase err.(test): min =        0.00 max =           89.89 mean =        47.64|
|-----------------------------------------------------------------------------|

============================== 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 = 6.218091              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.122   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.620519              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.012   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      201 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2004 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1880 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2855 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4642 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4407 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5626 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6690 |
|-----------------------------------------------------------------------------|
|-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 |        0.171 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.310 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4081   r_free= 0.4048   ksol= 0.00   Bsol= 0.00   scale= 0.927    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.218706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3966   r_free= 0.3980   ksol= 0.34   Bsol= 42.68   scale= 0.954   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,3.17,-1.22,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.205350                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.465802              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.178   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.841079              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.751   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3966      final r-factor (work) = 0.3037          |
| start r-factor (free) = 0.3980      final r-factor (free) = 0.3379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1285 = 5.47 * 0.50 * 6.2048 + 1.00 * 0.1713                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6829 = 5.47 * 0.50 * 6.0696 + 1.00 * 0.0952                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3037      final r-factor (work) = 0.2766          |
| start r-factor (free) = 0.3379      final r-factor (free) = 0.3509          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1111 = 0.84 * 1.00 * 6.0696 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0174 = 0.84 * 1.00 * 5.9473 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.79   18.17    None  None   None       |
|    all(noH): 2823   0      0.00    99.79   18.17    None  None   None       |
|    Sol.    : 438    0      1.77    99.79   37.71    None  None   None       |
|    Mac.    : 2385   0      0.00    61.54   14.58    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 -   9.979:  883   |   5:    49.893 -  59.872:   74        |
|      1:     9.979 -  19.957: 1025   |   6:    59.872 -  69.850:   29        |
|      2:    19.957 -  29.936:  449   |   7:    69.850 -  79.829:   14        |
|      3:    29.936 -  39.914:  217   |   8:    79.829 -  89.807:    0        |
|      4:    39.914 -  49.893:  131   |   9:    89.807 -  99.786:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2766 r_free = 0.3509             target_work(ml) = 5.959         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2760 r_free = 0.3510             target_work(ml) = 5.958         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2760   r_free= 0.3510   ksol= 0.34   Bsol= 42.68   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,3.17,-1.22,0.00,-0.00,-0.00); trace/3= 0.05                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.958052                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2755   r_free= 0.3475   ksol= 0.33   Bsol= 60.37   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,0.14,-0.93,0.00,-0.00,-0.00); trace/3= -0.85                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.956114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.306153              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.498   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329252              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.825  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2755      final r-factor (work) = 0.2079          |
| start r-factor (free) = 0.3475      final r-factor (free) = 0.2647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8737 = 5.31 * 0.50 * 5.9472 + 1.00 * 0.0952                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5794 = 5.31 * 0.50 * 5.8407 + 1.00 * 0.0834                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2079      final r-factor (work) = 0.1884          |
| start r-factor (free) = 0.2647      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9382 = 0.33 * 1.00 * 5.8407 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8669 = 0.33 * 1.00 * 5.6411 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.69   17.63    None  None   None       |
|    all(noH): 2823   0      0.00    97.69   17.63    None  None   None       |
|    Sol.    : 438    0      5.39    97.69   39.94    None  None   None       |
|    Mac.    : 2385   0      0.00    73.08   13.53    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 -   9.769:  936   |   5:    48.843 -  58.612:  100        |
|      1:     9.769 -  19.537: 1119   |   6:    58.612 -  68.380:   36        |
|      2:    19.537 -  29.306:  299   |   7:    68.380 -  78.149:   13        |
|      3:    29.306 -  39.075:  181   |   8:    78.149 -  87.918:    0        |
|      4:    39.075 -  48.843:  138   |   9:    87.918 -  97.686:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1884 r_free = 0.2436             target_work(ml) = 5.603         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1883 r_free = 0.2431             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1883   r_free= 0.2431   ksol= 0.33   Bsol= 60.37   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,0.14,-0.93,0.00,-0.00,-0.00); trace/3= -0.85                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.602190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1876   r_free= 0.2416   ksol= 0.34   Bsol= 60.37   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.51,-0.77,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.598044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.033819              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.368   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.859811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.832  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1876      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2416      final r-factor (free) = 0.2019          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8195 = 2.03 * 0.50 * 5.6407 + 1.00 * 0.0834                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6458 = 2.03 * 0.50 * 5.5043 + 1.00 * 0.0484                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1528      final r-factor (work) = 0.1427          |
| start r-factor (free) = 0.2019      final r-factor (free) = 0.1992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7506 = 2.86 * 1.00 * 5.5043 + 1.00 * 0.0095                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.4032 = 2.86 * 1.00 * 5.3815 + 1.00 * 0.0131                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.54  18.44    None  None   None       |
|    all(noH): 2823   0      0.00    105.54  18.44    None  None   None       |
|    Sol.    : 438    0      6.69    105.54  46.01    None  None   None       |
|    Mac.    : 2385   0      0.00    93.05   13.38    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 -  10.554: 1165   |   5:    52.770 -  63.323:  100        |
|      1:    10.554 -  21.108:  995   |   6:    63.323 -  73.877:   60        |
|      2:    21.108 -  31.662:  216   |   7:    73.877 -  84.431:   35        |
|      3:    31.662 -  42.216:  136   |   8:    84.431 -  94.985:    7        |
|      4:    42.216 -  52.770:  107   |   9:    94.985 - 105.539:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1427 r_free = 0.1992             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1427 r_free = 0.1991             target_work(ml) = 5.375         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1427   r_free= 0.1991   ksol= 0.34   Bsol= 60.37   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-1.51,-0.77,-0.00,-0.00,-0.00); trace/3= -1.41                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.374857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1427   r_free= 0.1987   ksol= 0.31   Bsol= 60.37   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.26,-1.00,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.372124                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.805362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.685  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330041              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.823  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1427      final r-factor (work) = 0.1225          |
| start r-factor (free) = 0.1987      final r-factor (free) = 0.1782          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2896 = 3.81 * 0.50 * 5.3825 + 1.00 * 0.0484                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1666 = 3.81 * 0.50 * 5.3099 + 1.00 * 0.0637                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1782      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7654 = 0.33 * 1.00 * 5.3099 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7363 = 0.33 * 1.00 * 5.2314 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.21    97.88   17.52    None  None   None       |
|    all(noH): 2823   0      0.21    97.88   17.52    None  None   None       |
|    Sol.    : 438    0      6.30    97.88   42.62    None  None   None       |
|    Mac.    : 2385   0      0.21    96.78   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.210 -   9.977: 1054   |   5:    49.046 -  58.813:   91        |
|      1:     9.977 -  19.744: 1098   |   6:    58.813 -  68.580:   53        |
|      2:    19.744 -  29.512:  230   |   7:    68.580 -  78.347:   31        |
|      3:    29.512 -  39.279:  136   |   8:    78.347 -  88.115:   11        |
|      4:    39.279 -  49.046:  115   |   9:    88.115 -  97.882:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1190 r_free = 0.1687             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1189 r_free = 0.1687             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1687   ksol= 0.31   Bsol= 60.37   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-2.26,-1.00,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1688   ksol= 0.32   Bsol= 55.10   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.41,-0.90,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.202753                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.218563              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.175  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.517  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8664 = 2.22 * 0.50 * 5.2310 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8136 = 2.22 * 0.50 * 5.1923 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1600          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8476 = 0.16 * 1.00 * 5.1923 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8433 = 0.16 * 1.00 * 5.1779 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.11    93.66   16.72    None  None   None       |
|    all(noH): 2823   0      1.11    93.66   16.72    None  None   None       |
|    Sol.    : 438    0      6.11    87.62   39.03    None  None   None       |
|    Mac.    : 2385   0      1.11    93.66   12.63    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:     1.111 -  10.366: 1153   |   5:    47.385 -  56.640:   78        |
|      1:    10.366 -  19.621: 1032   |   6:    56.640 -  65.894:   50        |
|      2:    19.621 -  28.875:  219   |   7:    65.894 -  75.149:   15        |
|      3:    28.875 -  38.130:  146   |   8:    75.149 -  84.404:    8        |
|      4:    38.130 -  47.385:  119   |   9:    84.404 -  93.658:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1600             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1600             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1600   ksol= 0.32   Bsol= 55.10   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.41,-0.90,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.0990 0.1301      5.3816      5.5792|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.0882 0.1128      5.4626      5.6495|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.1120 0.1607      5.5133      5.8497|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.1288 0.1700      5.4828      5.6305|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.1402 0.1775       5.354      5.5704|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.1251 0.1931      5.2136      5.4761|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.1284 0.1583       5.186      5.3264|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.1214 0.1737      5.0821      5.3493|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.1220 0.1817      5.0606      5.3404|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.1144 0.1629      4.9527      5.1754|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.1129 0.1865      4.9563      5.3512|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.1193 0.1657      4.8899      5.1034|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.1142 0.1738      4.7882      5.0467|
| 14:  2.0125 -  1.9636 0.31    416   47 0.1019 0.1388      4.6594      4.7959|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.6884  1421   158  0.94   8.88   0.98     0.95       6801.47|
|  2:  4.6884 -  3.7398  1373   155  0.95   8.03   1.01     1.00       9344.39|
|  3:  3.7398 -  3.2726  1342   142  0.93  11.83   1.02     1.02      11067.82|
|  4:  3.2726 -  2.9758  1331   155  0.91  14.61   1.01     0.98      10858.55|
|  5:  2.9758 -  2.7639  1338   149  0.90  16.21   1.00     0.98       8517.15|
|  6:  2.7639 -  2.6018  1327   146  0.90  16.33   0.99     0.97       7063.31|
|  7:  2.6018 -  2.4721  1309   137  0.90  15.71   1.00     0.97       6401.78|
|  8:  2.4721 -  2.3649  1299   152  0.90  15.77   0.99     0.96       5400.22|
|  9:  2.3649 -  2.2742  1307   148  0.90  15.92   1.00     0.96       5191.12|
| 10:  2.2742 -  2.1960  1298   147  0.90  16.01   1.01     0.97       4404.33|
| 11:  2.1960 -  2.1275  1316   137  0.90  15.90   0.99     0.95       4408.41|
| 12:  2.1275 -  2.0668  1288   144  0.90  16.36   1.01     1.01       4060.20|
| 13:  2.0668 -  2.0125  1265   142  0.90  16.50   1.00     0.98       3374.57|
| 14:  2.0125 -  1.9636   416    47  0.92  14.14   0.99     0.96       2582.15|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2582.15 max =        11067.82 mean =      6627.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.39|
|phase err.(test): min =        0.00 max =           88.76 mean =        13.89|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1593   ksol= 0.32   Bsol= 49.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.51,-0.89,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1153   r_free= 0.1593   ksol= 0.32   Bsol= 49.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-2.51,-0.89,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170715                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1239 -  4.6884 0.99   1421  158 0.0989 0.1269       5.369      5.5546|
|  2:  4.6884 -  3.7398 0.99   1373  155 0.0873 0.1105      5.4559      5.6457|
|  3:  3.7398 -  3.2726 0.99   1342  142 0.1121 0.1588      5.5117      5.8425|
|  4:  3.2726 -  2.9758 0.99   1331  155 0.1285 0.1711      5.4844      5.6378|
|  5:  2.9758 -  2.7639 0.99   1338  149 0.1403 0.1780      5.3571      5.5736|
|  6:  2.7639 -  2.6018 0.99   1327  146 0.1252 0.1933      5.2161      5.4788|
|  7:  2.6018 -  2.4721 0.99   1309  137 0.1286 0.1586      5.1873      5.3274|
|  8:  2.4721 -  2.3649 0.98   1299  152 0.1213 0.1741      5.0817      5.3495|
|  9:  2.3649 -  2.2742 0.98   1307  148 0.1220 0.1816      5.0609      5.3397|
| 10:  2.2742 -  2.1960 1.00   1298  147 0.1144 0.1637      4.9535      5.1801|
| 11:  2.1960 -  2.1275 0.98   1316  137 0.1128 0.1864      4.9573      5.3508|
| 12:  2.1275 -  2.0668 0.98   1288  144 0.1193 0.1661      4.8905      5.1058|
| 13:  2.0668 -  2.0125 0.98   1265  142 0.1143 0.1736      4.7885       5.046|
| 14:  2.0125 -  1.9636 0.31    416   47 0.1017 0.1389      4.6579      4.7942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1239 -  4.6884  1421   158  0.94   8.56   0.97     0.95       6406.91|
|  2:  4.6884 -  3.7398  1373   155  0.95   7.86   1.01     1.00       9037.37|
|  3:  3.7398 -  3.2726  1342   142  0.93  11.76   1.02     1.02      11006.36|
|  4:  3.2726 -  2.9758  1331   155  0.91  14.65   1.01     0.98      10917.32|
|  5:  2.9758 -  2.7639  1338   149  0.90  16.31   0.99     0.97       8605.39|
|  6:  2.7639 -  2.6018  1327   146  0.90  16.38   0.98     0.97       7099.64|
|  7:  2.6018 -  2.4721  1309   137  0.90  15.73   1.00     0.96       6421.33|
|  8:  2.4721 -  2.3649  1299   152  0.90  15.77   0.99     0.96       5398.83|
|  9:  2.3649 -  2.2742  1307   148  0.90  15.92   1.00     0.96       5194.53|
| 10:  2.2742 -  2.1960  1298   147  0.90  16.04   1.00     0.97       4417.68|
| 11:  2.1960 -  2.1275  1316   137  0.90  15.94   0.99     0.94       4432.42|
| 12:  2.1275 -  2.0668  1288   144  0.90  16.41   1.01     1.01       4077.79|
| 13:  2.0668 -  2.0125  1265   142  0.90  16.51   1.00     0.98       3378.81|
| 14:  2.0125 -  1.9636   416    47  0.92  14.11   0.98     0.96       2572.61|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2572.61 max =        11006.36 mean =      6586.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.37|
|phase err.(test): min =        0.00 max =           88.91 mean =        13.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.819)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    93.62   16.69    None  None   None       |
|    all(noH): 2823   0      1.07    93.62   16.69    None  None   None       |
|    Sol.    : 438    0      6.07    87.58   38.99    None  None   None       |
|    Mac.    : 2385   0      1.07    93.62   12.59    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:     1.073 -  10.327: 1153   |   5:    47.346 -  56.601:   78        |
|      1:    10.327 -  19.582: 1032   |   6:    56.601 -  65.856:   50        |
|      2:    19.582 -  28.837:  219   |   7:    65.856 -  75.110:   15        |
|      3:    28.837 -  38.091:  146   |   8:    75.110 -  84.365:    8        |
|      4:    38.091 -  47.346:  119   |   9:    84.365 -  93.620:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.606 - 4.739
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 336
   mapped sites are within: 0.727 - 4.739

peak=    6.338 closest distance to " NE2 GLN A  11 " =    1.318
peak=    5.454 closest distance to " NH2 ARG A  56 " =    2.090
peak=    5.376 closest distance to " CG  PRO A  54 " =    1.402
peak=    5.320 closest distance to " O   HOH Z 417 " =    1.842
peak=    5.319 closest distance to " O   HOH Z 144 " =    1.821
peak=    5.253 closest distance to " O   HOH Z 126 " =    2.080
peak=    5.237 closest distance to " O   HOH Z  63 " =    1.651
peak=    5.190 closest distance to " O   HOH Z   7 " =    1.450
peak=    4.970 closest distance to " CB  GLN A 223 " =    1.476
peak=    4.939 closest distance to " CB  PRO A  54 " =    1.006
peak=    4.912 closest distance to " O   HOH Z 423 " =    1.878
peak=    4.892 closest distance to " O   HOH Z 287 " =    2.133
peak=    4.854 closest distance to " O   HOH Z 232 " =    2.221
peak=    4.831 closest distance to " O   HOH Z 427 " =    2.274
peak=    4.826 closest distance to " CB  SER A  63 " =    1.264
peak=    4.712 closest distance to " O   HOH Z  78 " =    1.656
peak=    4.688 closest distance to " O   HOH Z 369 " =    2.183
peak=    4.673 closest distance to " O   HOH Z 298 " =    2.028
peak=    4.669 closest distance to " O   HOH Z 380 " =    1.807
peak=    4.662 closest distance to " O   HOH Z  57 " =    2.315
peak=    4.526 closest distance to " CB  ARG A 275 " =    0.945
peak=    4.506 closest distance to " ND2 ASN A 187 " =    1.550
peak=    4.437 closest distance to " O   HOH Z 425 " =    1.469
peak=    4.417 closest distance to " CG  PRO A 198 " =    1.295
peak=    4.389 closest distance to " CG  PRO A 213 " =    1.310
peak=    4.386 closest distance to " CB  ASN A 148 " =    1.352
peak=    4.385 closest distance to " CG  PRO A  90 " =    1.289
peak=    4.361 closest distance to " CB  GLU A 128 " =    0.994
peak=    4.343 closest distance to " O   HOH Z   9 " =    1.464
peak=    4.310 closest distance to " CB  SER A   3 " =    1.485
peak=    4.306 closest distance to " O   HOH Z   1 " =    1.895
peak=    4.281 closest distance to " CB  ARG A 190 " =    1.638
peak=    4.247 closest distance to " CB  ASN A 187 " =    0.997
peak=    4.236 closest distance to " O   HOH Z 133 " =    2.336
peak=    4.228 closest distance to " CG  PRO A 280 " =    0.803
peak=    4.220 closest distance to " CB  GLN A 183 " =    1.177
peak=    4.214 closest distance to " O   HOH Z   1 " =    1.716
peak=    4.194 closest distance to " O   HOH Z   2 " =    1.814
peak=    4.174 closest distance to " OG ASER A 258 " =    3.088
peak=    4.163 closest distance to " O   HOH Z  68 " =    2.065
peak=    4.155 closest distance to " CD  ARG A 159 " =    0.807
peak=    4.141 closest distance to " O   HOH Z  61 " =    1.614
peak=    4.130 closest distance to " CG  TRP A 179 " =    2.162
peak=    4.119 closest distance to " CB  ASN A  39 " =    0.869
peak=    4.110 closest distance to " CG2 VAL A 257 " =    0.956
peak=    4.099 closest distance to " O   HOH Z 225 " =    1.522
peak=    4.095 closest distance to " O   HOH Z  78 " =    1.850
peak=    4.092 closest distance to " CB  SER A 216 " =    0.856
peak=    4.078 closest distance to " O   HOH Z 236 " =    1.571
peak=    4.054 closest distance to " O   HOH Z 209 " =    2.265
peak=    4.033 closest distance to " CZ  PHE A 218 " =    1.070
peak=    4.032 closest distance to " CB  TYR A 169 " =    0.878
peak=    4.026 closest distance to " CB  GLU A 152 " =    1.267
peak=    4.000 closest distance to " O   HOH Z 392 " =    1.279
peak=    3.991 closest distance to " CG  LEU A 167 " =    1.281
peak=    3.971 closest distance to " O   HOH Z 437 " =    1.878
peak=    3.970 closest distance to " CA  TYR A  30 " =    1.034
peak=    3.968 closest distance to " O   HOH Z 214 " =    2.142
peak=    3.950 closest distance to " O   HOH Z 403 " =    1.456
peak=    3.939 closest distance to " O   HOH Z 144 " =    2.276
peak=    3.937 closest distance to " CD  ARG A  66 " =    2.123
peak=    3.929 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.919 closest distance to " O   HOH Z 195 " =    1.366
peak=    3.893 closest distance to " C   PRO A 198 " =    1.545
peak=    3.871 closest distance to " CG  PRO A 243 " =    1.135
peak=    3.852 closest distance to " O   HOH Z 365 " =    2.683
peak=    3.837 closest distance to " O   HOH Z 116 " =    2.920
peak=    3.836 closest distance to " O   HOH Z 427 " =    1.146
peak=    3.821 closest distance to " CB  TRP A 266 " =    0.997
peak=    3.814 closest distance to " CB  LEU A 228 " =    1.057
peak=    3.807 closest distance to " CB  ARG A  79 " =    1.224
peak=    3.806 closest distance to " O   HOH Z  10 " =    1.802
peak=    3.804 closest distance to " O   HOH Z 183 " =    1.426
peak=    3.803 closest distance to " ND1 HIS A  86 " =    1.717
peak=    3.800 closest distance to " NH1AARG A 145 " =    1.215
peak=    3.799 closest distance to " O   ASN A 209 " =    1.459
peak=    3.791 closest distance to " N   PHE A 130 " =    1.215
peak=    3.785 closest distance to " O   HOH Z 272 " =    1.846
peak=    3.784 closest distance to " OD1 ASN A  69 " =    2.593
peak=    3.784 closest distance to " O   HOH Z 132 " =    2.491
peak=    3.782 closest distance to " O   HOH Z 158 " =    2.765
peak=    3.773 closest distance to " O   HOH Z 368 " =    3.694
peak=    3.772 closest distance to " CG1 ILE A 151 " =    1.075
peak=    3.768 closest distance to " O   HOH Z 394 " =    1.724
peak=    3.765 closest distance to " CB  ASN A 142 " =    0.943
peak=    3.753 closest distance to " O   HOH Z 193 " =    1.658
peak=    3.749 closest distance to " O   HOH Z 175 " =    2.123
peak=    3.734 closest distance to " CB  ASP A 124 " =    0.862
peak=    3.734 closest distance to " O   HOH Z 145 " =    1.518
peak=    3.721 closest distance to " O   SER A  87 " =    2.304
peak=    3.716 closest distance to " CB  THR A 157 " =    1.120
peak=    3.704 closest distance to " CB  LYS A 117 " =    1.231
peak=    3.697 closest distance to " O   TYR A 116 " =    1.348
peak=    3.694 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.693 closest distance to " O   HOH Z 362 " =    1.997
peak=    3.692 closest distance to " CA  ALA A 233 " =    1.249
peak=    3.691 closest distance to " O   HOH Z 405 " =    1.493
peak=    3.687 closest distance to " O   HOH Z 258 " =    2.184
peak=    3.679 closest distance to " CD1 LEU A 300 " =    1.178
peak=    3.679 closest distance to " CB  GLU A 277 " =    3.561
peak=    3.677 closest distance to " CA  ARG A 195 " =    1.270
peak=    3.674 closest distance to " CE3 TRP A 274 " =    1.309
peak=    3.674 closest distance to " O   HOH Z  21 " =    1.700
peak=    3.669 closest distance to " CE  LYS A  76 " =    0.839
peak=    3.655 closest distance to " CA  ILE A 234 " =    0.982
peak=    3.646 closest distance to " O   HOH Z 352 " =    1.647
peak=    3.644 closest distance to " CB  SER A 212 " =    1.274
peak=    3.639 closest distance to " O   HOH Z 371 " =    2.688
peak=    3.638 closest distance to " CB  ARG A 139 " =    1.100
peak=    3.636 closest distance to " O   HOH Z 272 " =    2.015
peak=    3.624 closest distance to " CA  SER A  87 " =    0.986
peak=    3.624 closest distance to " O   HOH Z  40 " =    2.103
peak=    3.620 closest distance to " O   HOH Z 139 " =    1.172
peak=    3.618 closest distance to " ND2 ASN A 249 " =    1.886
peak=    3.614 closest distance to " O   HOH Z  44 " =    2.827
peak=    3.610 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.607 closest distance to " OE2 GLU A  53 " =    2.027
peak=    3.604 closest distance to " O   HOH Z  30 " =    1.759
peak=    3.603 closest distance to " NH1BARG A 145 " =    1.297
peak=    3.601 closest distance to " CG1BVAL A  72 " =    1.254
peak=    3.594 closest distance to " CG2 THR A 221 " =    1.046
peak=    3.593 closest distance to " CB  ILE A 120 " =    1.302
peak=    3.593 closest distance to " O   HOH Z 289 " =    1.627
peak=    3.584 closest distance to " O   HOH Z  88 " =    4.027
peak=    3.582 closest distance to " O   HOH Z 234 " =    3.813
peak=    3.571 closest distance to " CA  THR A 264 " =    0.837
peak=    3.564 closest distance to " CA  SER A  95 " =    1.001
peak=    3.557 closest distance to " CA  ASN A 127 " =    1.032
peak=    3.556 closest distance to " NE AARG A 275 " =    1.485
peak=    3.554 closest distance to " CD  PRO A 243 " =    1.727
peak=    3.553 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.551 closest distance to " O   HOH Z 171 " =    2.891
peak=    3.547 closest distance to " O   HOH Z 327 " =    1.767
peak=    3.545 closest distance to " N   SER A  97 " =    0.905
peak=    3.542 closest distance to " O   HOH Z 184 " =    1.541
peak=    3.529 closest distance to " CB  ALA A   1 " =    4.739
peak=    3.529 closest distance to " O   HOH Z 411 " =    3.743
peak=    3.520 closest distance to " O   HOH Z 368 " =    1.768
peak=    3.518 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.518 closest distance to " CB  SER A 210 " =    0.770
peak=    3.492 closest distance to " O   HOH Z  44 " =    1.648
peak=    3.488 closest distance to " O   HOH Z 126 " =    1.409
peak=    3.485 closest distance to " CB  SER A 276 " =    1.210
peak=    3.482 closest distance to " CB  GLN A  88 " =    1.241
peak=    3.479 closest distance to " O   HOH Z 217 " =    3.075
peak=    3.474 closest distance to " CB  LEU A 143 " =    1.142
peak=    3.471 closest distance to " CB  VAL A 202 " =    1.640
peak=    3.467 closest distance to " CA  ASN A 215 " =    1.163
peak=    3.465 closest distance to " O   HOH Z  59 " =    2.105
peak=    3.463 closest distance to " CG1 ILE A  33 " =    1.282
peak=    3.461 closest distance to " O   HOH Z 146 " =    1.584
peak=    3.459 closest distance to " CB  GLU A  46 " =    0.964
peak=    3.457 closest distance to " CA  ALA A  51 " =    1.006
peak=    3.456 closest distance to " CA  TYR A 116 " =    1.341
peak=    3.456 closest distance to " CA  LEU A 101 " =    1.599
peak=    3.452 closest distance to " O   HOH Z   3 " =    2.022
peak=    3.451 closest distance to " CB  SER A  62 " =    1.120
peak=    3.449 closest distance to " O   HOH Z 135 " =    1.763
peak=    3.448 closest distance to " O   HOH Z 265 " =    2.090
peak=    3.443 closest distance to " O   HOH Z 172 " =    2.627
peak=    3.441 closest distance to " CD  ARG A  66 " =    2.486
peak=    3.440 closest distance to " O   HOH Z 425 " =    1.879
peak=    3.440 closest distance to " O   HOH Z 188 " =    2.083
peak=    3.437 closest distance to " N   CYS A 260 " =    0.737
peak=    3.435 closest distance to " O   HOH Z 180 " =    2.161
peak=    3.434 closest distance to " N   GLU A   2 " =    1.332
peak=    3.431 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.429 closest distance to " O   HOH Z 414 " =    1.344
peak=    3.429 closest distance to " O   HOH Z   9 " =    1.638
peak=    3.425 closest distance to " O   HOH Z 219 " =    2.152
peak=    3.423 closest distance to " NE2 GLN A 278 " =    3.621
peak=    3.420 closest distance to " CA  ALA A 299 " =    0.861
peak=    3.389 closest distance to " O   HOH Z 422 " =    2.791
peak=    3.386 closest distance to " CB  ALA A 114 " =    0.981
peak=    3.386 closest distance to " O   HOH Z 306 " =    3.653
peak=    3.385 closest distance to " OG  SER A  62 " =    3.003
peak=    3.382 closest distance to " O   ASN A  74 " =    1.512
peak=    3.379 closest distance to " CE3 TRP A  85 " =    0.947
peak=    3.376 closest distance to " O   HOH Z  58 " =    1.773
peak=    3.369 closest distance to " O   HOH Z 222 " =    2.459
peak=    3.368 closest distance to " N   TYR A 116 " =    1.278
peak=    3.365 closest distance to " CB  ARG A 138 " =    0.980
peak=    3.364 closest distance to " CA  ALA A 291 " =    0.883
peak=    3.364 closest distance to " N   VAL A 296 " =    1.676
peak=    3.359 closest distance to " OG BSER A 164 " =    2.292
peak=    3.357 closest distance to " O   HOH Z 154 " =    1.987
peak=    3.355 closest distance to " O   HOH Z 255 " =    1.756
peak=    3.355 closest distance to " CB  PRO A 243 " =    1.127
peak=    3.352 closest distance to " O   HOH Z  49 " =    1.379
peak=    3.350 closest distance to " O   HOH Z 371 " =    1.921
peak=    3.350 closest distance to " CD  LYS A 166 " =    1.350
peak=    3.346 closest distance to " NE2 HIS A 207 " =    1.182
peak=    3.339 closest distance to " CB  TYR A 116 " =    0.895
peak=    3.338 closest distance to " O   HOH Z  51 " =    1.844
peak=    3.337 closest distance to " O   HOH Z 189 " =    2.344
peak=    3.337 closest distance to " N   GLN A 278 " =    1.134
peak=    3.331 closest distance to " N   ALA A   1 " =    2.162
peak=    3.330 closest distance to " O   HOH Z  20 " =    1.738
peak=    3.329 closest distance to " NH2AARG A 190 " =    1.661
peak=    3.327 closest distance to " CD2 TRP A 179 " =    1.213
peak=    3.322 closest distance to " CA  ALA A 154 " =    0.917
peak=    3.322 closest distance to " O   HOH Z 181 " =    2.111
peak=    3.321 closest distance to " N   ARG A 156 " =    1.323
peak=    3.321 closest distance to " CA  ALA A 180 " =    1.364
peak=    3.321 closest distance to " CG AARG A 275 " =    1.130
peak=    3.313 closest distance to " O   HOH Z 291 " =    1.544
peak=    3.311 closest distance to " OD2 ASP A 286 " =    2.788
peak=    3.305 closest distance to " CB  ALA A 291 " =    1.243
peak=    3.305 closest distance to " NE2 GLN A  73 " =    3.779
peak=    3.305 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.304 closest distance to " CZ3 TRP A 123 " =    1.475
peak=    3.303 closest distance to " O   HOH Z 213 " =    2.105
peak=    3.302 closest distance to " CB  ALA A  43 " =    0.833
peak=    3.301 closest distance to " OD1BASN A 224 " =    2.299
peak=    3.297 closest distance to " CZ  PHE A 192 " =    0.890
peak=    3.297 closest distance to " O   HOH Z 244 " =    1.668
peak=    3.294 closest distance to " CZ  PHE A  38 " =    1.292
peak=    3.290 closest distance to " CB  ALA A  10 " =    0.793
peak=    3.290 closest distance to " O   HOH Z 435 " =    1.931
peak=    3.287 closest distance to " CA  ASN A 217 " =    1.146
peak=    3.285 closest distance to " O   HOH Z 227 " =    1.950
peak=    3.282 closest distance to " O   HOH Z 409 " =    2.123
peak=    3.280 closest distance to " O   HOH Z 310 " =    2.403
peak=    3.280 closest distance to " CD1 ILE A 263 " =    1.307
peak=    3.277 closest distance to " O   HOH Z   3 " =    2.394
peak=    3.272 closest distance to " O   HOH Z 302 " =    1.665
peak=    3.269 closest distance to " CZ3 TRP A 266 " =    1.128
peak=    3.268 closest distance to " O   HOH Z 393 " =    1.256
peak=    3.266 closest distance to " O   HOH Z 313 " =    1.687
peak=    3.263 closest distance to " NZ BLYS A 290 " =    0.845
peak=    3.262 closest distance to " O   HOH Z 145 " =    2.168
peak=    3.261 closest distance to " O   HOH Z 303 " =    2.878
peak=    3.260 closest distance to " O   HOH Z 158 " =    1.757
peak=    3.258 closest distance to " CA  TYR A  30 " =    1.059
peak=    3.257 closest distance to " CA  ARG A 102 " =    1.176
peak=    3.246 closest distance to " ND2 ASN A 249 " =    0.835
peak=    3.244 closest distance to " O   HOH Z 130 " =    3.762
peak=    3.242 closest distance to " CA  MET A 105 " =    0.881
peak=    3.241 closest distance to " O   HOH Z  97 " =    2.101
peak=    3.239 closest distance to " CD BLYS A 290 " =    1.048
peak=    3.236 closest distance to " O   HOH Z 345 " =    1.819
peak=    3.229 closest distance to " O   HOH Z 148 " =    3.364
peak=    3.229 closest distance to " OG BSER A  99 " =    2.280
peak=    3.228 closest distance to " CG BARG A 102 " =    1.896
peak=    3.226 closest distance to " CB  TYR A  30 " =    1.300
peak=    3.225 closest distance to " CB  GLU A 152 " =    1.340
peak=    3.223 closest distance to " CA  THR A 221 " =    0.948
peak=    3.221 closest distance to " NH1 ARG A  14 " =    1.011
peak=    3.220 closest distance to " CD  ARG A 138 " =    0.727
peak=    3.220 closest distance to " CG1 VAL A 189 " =    1.759
peak=    3.218 closest distance to " O   HOH Z 286 " =    2.252
peak=    3.217 closest distance to " O   HOH Z 344 " =    3.080
peak=    3.215 closest distance to " N   TYR A  15 " =    0.869
peak=    3.211 closest distance to " O   HOH Z 273 " =    2.810
peak=    3.211 closest distance to " O   HOH Z 325 " =    3.724
peak=    3.210 closest distance to " O   HOH Z 153 " =    3.729
peak=    3.210 closest distance to " O   HOH Z 432 " =    1.880
peak=    3.210 closest distance to " CA  ALA A 160 " =    0.963
peak=    3.208 closest distance to " CB  GLU A 236 " =    1.221
peak=    3.208 closest distance to " O   HOH Z 207 " =    2.222
peak=    3.207 closest distance to " CB  LEU A 300 " =    0.942
peak=    3.207 closest distance to " CG  MET A 113 " =    1.252
peak=    3.205 closest distance to " NZ  LYS A 119 " =    1.382
peak=    3.202 closest distance to " CA  GLU A  46 " =    0.878
peak=    3.201 closest distance to " CG BARG A 275 " =    1.439
peak=    3.200 closest distance to " CA  GLY A 267 " =    1.209
peak=    3.200 closest distance to " CA  GLY A 136 " =    1.021
peak=    3.199 closest distance to " CB  ALA A 114 " =    1.453
peak=    3.196 closest distance to " O   HOH Z  88 " =    2.698
peak=    3.195 closest distance to " O   HOH Z 386 " =    2.903
peak=    3.194 closest distance to " O   HOH Z 406 " =    1.617
peak=    3.194 closest distance to " O   CYS A 168 " =    1.374
peak=    3.192 closest distance to " O   HOH Z  85 " =    2.038
peak=    3.192 closest distance to " CB  PHE A 204 " =    0.746
peak=    3.190 closest distance to " CG1 VAL A 153 " =    0.850
peak=    3.189 closest distance to " CG  GLN A 278 " =    1.288
peak=    3.185 closest distance to " N   SER A 271 " =    0.969
peak=    3.180 closest distance to " O   HOH Z 359 " =    1.376
peak=    3.176 closest distance to " O   HOH Z 147 " =    1.719
peak=    3.176 closest distance to " O   HOH Z 217 " =    1.606
peak=    3.175 closest distance to " O   HOH Z 288 " =    2.000
peak=    3.174 closest distance to " CD1 ILE A  33 " =    1.672
peak=    3.172 closest distance to " O   HOH Z 122 " =    1.722
peak=    3.171 closest distance to " CG  LEU A 101 " =    1.140
peak=    3.170 closest distance to " O   HOH Z 357 " =    1.997
peak=    3.167 closest distance to " NE2 GLN A  58 " =    3.951
peak=    3.166 closest distance to " CA  ILE A 263 " =    1.101
peak=    3.164 closest distance to " N   ASN A 127 " =    1.407
peak=    3.164 closest distance to " CB  LEU A  83 " =    0.782
peak=    3.160 closest distance to " O   GLY A 302 " =    1.683
peak=    3.159 closest distance to " CB  ALA A 291 " =    0.798
peak=    3.157 closest distance to " O   HOH Z 109 " =    2.471
peak=    3.148 closest distance to " O   HOH Z 343 " =    3.289
peak=    3.146 closest distance to " O   HOH Z  59 " =    1.622
peak=    3.146 closest distance to " CB  TRP A 179 " =    1.461
peak=    3.146 closest distance to " O   HOH Z 238 " =    4.011
peak=    3.143 closest distance to " O   HOH Z  42 " =    1.679
peak=    3.141 closest distance to " CA  ALA A 158 " =    1.115
peak=    3.139 closest distance to " O   HOH Z  17 " =    1.815
peak=    3.138 closest distance to " O   HOH Z 426 " =    1.936
peak=    3.138 closest distance to " O   HOH Z 115 " =    1.643
peak=    3.137 closest distance to " N   SER A 134 " =    1.329
peak=    3.131 closest distance to " O   HOH Z 153 " =    1.721
peak=    3.130 closest distance to " CA  ALA A  21 " =    1.253
peak=    3.125 closest distance to " CD2 LEU A 255 " =    1.543
peak=    3.124 closest distance to " O   PRO A 198 " =    1.256
peak=    3.123 closest distance to " CB  ALA A 160 " =    1.405
peak=    3.123 closest distance to " O   HOH Z 329 " =    3.891
peak=    3.119 closest distance to " CD2 TYR A 186 " =    1.057
peak=    3.119 closest distance to " O   HOH Z 140 " =    2.833
peak=    3.118 closest distance to " O   HOH Z 245 " =    1.277
peak=    3.117 closest distance to " O   HOH Z  50 " =    1.597
peak=    3.106 closest distance to " O   HOH Z 295 " =    1.587
peak=    3.103 closest distance to " O   HOH Z 438 " =    2.030
peak=    3.098 closest distance to " NH2 ARG A 219 " =    1.778
peak=    3.096 closest distance to " ND1 HIS A  81 " =    1.753
peak=    3.094 closest distance to " O   HOH Z 368 " =    4.316
peak=    3.087 closest distance to " O   HOH Z 274 " =    1.980
peak=    3.085 closest distance to " CD2 PHE A  59 " =    1.652
peak=    3.084 closest distance to " O   HOH Z 284 " =    1.424
peak=    3.083 closest distance to " CB  TRP A 150 " =    1.131
peak=    3.080 closest distance to " O   HOH Z 373 " =    1.536
peak=    3.078 closest distance to " O   HOH Z 113 " =    1.997
peak=    3.078 closest distance to " N   MET A 188 " =    1.778
peak=    3.074 closest distance to " CA  ILE A 106 " =    0.755
peak=    3.071 closest distance to " O   PRO A  90 " =    1.563
peak=    3.068 closest distance to " O   HOH Z 128 " =    1.988
peak=    3.066 closest distance to " CA  ALA A 129 " =    1.311
peak=    3.062 closest distance to " OG  SER A  22 " =    2.885
peak=    3.061 closest distance to " O   MET A 105 " =    1.754
peak=    3.044 closest distance to " CA  ALA A 100 " =    1.155

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.468 - 5.387
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 199
   mapped sites are within: 0.708 - 5.387

peak=   -4.767 closest distance to " CB  PRO A 243 " =    2.536
peak=   -4.601 closest distance to " O   HOH Z  65 " =    0.985
peak=   -4.521 closest distance to " O   PRO A 198 " =    1.241
peak=   -4.511 closest distance to " O   HOH Z 290 " =    0.976
peak=   -4.461 closest distance to " CD  ARG A  14 " =    3.417
peak=   -4.178 closest distance to " O   HOH Z 231 " =    1.902
peak=   -4.165 closest distance to " O   HOH Z 377 " =    1.692
peak=   -4.130 closest distance to " CD1 LEU A 255 " =    2.957
peak=   -4.107 closest distance to " O   HOH Z 351 " =    1.493
peak=   -4.103 closest distance to " CA  GLY A  98 " =    1.789
peak=   -4.074 closest distance to " CD  ARG A 156 " =    2.124
peak=   -4.067 closest distance to " N   THR A 157 " =    1.589
peak=   -4.029 closest distance to " O   HOH Z 185 " =    2.097
peak=   -3.998 closest distance to " CZ3 TRP A 179 " =    1.190
peak=   -3.989 closest distance to " O   SER A  22 " =    2.657
peak=   -3.983 closest distance to " O   HOH Z 231 " =    0.916
peak=   -3.959 closest distance to " C   ALA A 158 " =    1.626
peak=   -3.933 closest distance to " CB  ALA A  43 " =    2.402
peak=   -3.909 closest distance to " O   VAL A  67 " =    2.577
peak=   -3.897 closest distance to " CA  GLY A 241 " =    2.263
peak=   -3.888 closest distance to " O   HOH Z 266 " =    4.948
peak=   -3.877 closest distance to " O   HOH Z 407 " =    3.189
peak=   -3.874 closest distance to " O   HOH Z 313 " =    1.644
peak=   -3.840 closest distance to " O   HOH Z  52 " =    1.046
peak=   -3.837 closest distance to " CB  ALA A 291 " =    2.174
peak=   -3.830 closest distance to " O   TYR A 247 " =    2.837
peak=   -3.817 closest distance to " OG BSER A 134 " =    1.462
peak=   -3.788 closest distance to " O   HOH Z 372 " =    2.440
peak=   -3.784 closest distance to " CB  ALA A 248 " =    2.081
peak=   -3.765 closest distance to " ND2 ASN A 249 " =    2.285
peak=   -3.764 closest distance to " O   HOH Z 316 " =    1.900
peak=   -3.763 closest distance to " O   HOH Z 211 " =    1.437
peak=   -3.754 closest distance to " CG  MET A 105 " =    0.981
peak=   -3.724 closest distance to " CD2 TYR A 293 " =    1.932
peak=   -3.709 closest distance to " O   HOH Z 385 " =    2.073
peak=   -3.707 closest distance to " O   HOH Z 298 " =    1.058
peak=   -3.704 closest distance to " O   PRO A 243 " =    2.350
peak=   -3.699 closest distance to " CA  GLY A 203 " =    2.281
peak=   -3.699 closest distance to " CE2 PHE A 218 " =    2.387
peak=   -3.691 closest distance to " CB  ASP A  27 " =    2.387
peak=   -3.683 closest distance to " N   ASP A 171 " =    2.583
peak=   -3.674 closest distance to " O   HOH Z 384 " =    3.000
peak=   -3.663 closest distance to " O   ILE A  49 " =    1.652
peak=   -3.663 closest distance to " O   HOH Z 114 " =    0.757
peak=   -3.662 closest distance to " O   SER A 135 " =    1.443
peak=   -3.648 closest distance to " O   HOH Z 389 " =    2.048
peak=   -3.626 closest distance to " O   HOH Z 282 " =    4.553
peak=   -3.623 closest distance to " O   HOH Z 131 " =    4.076
peak=   -3.613 closest distance to " ND2 ASN A 285 " =    2.142
peak=   -3.611 closest distance to " O   HOH Z   1 " =    1.337
peak=   -3.610 closest distance to " O   PRO A 163 " =    1.863
peak=   -3.601 closest distance to " CG1 VAL A 112 " =    3.110
peak=   -3.588 closest distance to " CG  GLN A  88 " =    0.759
peak=   -3.580 closest distance to " CZ2 TRP A 274 " =    0.961
peak=   -3.575 closest distance to " O   HOH Z 140 " =    1.315
peak=   -3.574 closest distance to " CE3 TRP A 123 " =    1.362
peak=   -3.567 closest distance to " O   HOH Z  60 " =    1.648
peak=   -3.559 closest distance to " O   HOH Z  24 " =    1.069
peak=   -3.554 closest distance to " OG  SER A  97 " =    2.153
peak=   -3.545 closest distance to " CE2 TYR A  30 " =    2.543
peak=   -3.537 closest distance to " N   ALA A  43 " =    2.542
peak=   -3.535 closest distance to " O   HOH Z  28 " =    1.583
peak=   -3.526 closest distance to " C   ALA A 114 " =    2.324
peak=   -3.521 closest distance to " O   HOH Z  90 " =    2.730
peak=   -3.518 closest distance to " CG  PHE A 283 " =    2.661
peak=   -3.513 closest distance to " OG BSER A 134 " =    1.717
peak=   -3.512 closest distance to " C   HIS A 108 " =    1.153
peak=   -3.510 closest distance to " O   HOH Z 298 " =    2.587
peak=   -3.509 closest distance to " O   HOH Z  51 " =    0.912
peak=   -3.504 closest distance to " CB  ASP A 132 " =    2.388
peak=   -3.496 closest distance to " O   ASP A 162 " =    2.219
peak=   -3.489 closest distance to " O   HOH Z 111 " =    1.828
peak=   -3.485 closest distance to " O   HOH Z  11 " =    1.846
peak=   -3.476 closest distance to " CB  ASN A  39 " =    2.283
peak=   -3.474 closest distance to " OE1 GLN A  88 " =    1.214
peak=   -3.465 closest distance to " O   HOH Z  39 " =    1.047
peak=   -3.465 closest distance to " CE  MET A 105 " =    2.559
peak=   -3.457 closest distance to " CB  TYR A  15 " =    2.179
peak=   -3.454 closest distance to " CB  PHE A 192 " =    1.777
peak=   -3.450 closest distance to " CG  ASN A  39 " =    1.704
peak=   -3.450 closest distance to " O   HOH Z  38 " =    1.526
peak=   -3.446 closest distance to " CE BMET A  47 " =    1.352
peak=   -3.444 closest distance to " CD2 LEU A 143 " =    2.567
peak=   -3.440 closest distance to " CB  PRO A  54 " =    2.493
peak=   -3.438 closest distance to " CG2 THR A  18 " =    2.826
peak=   -3.438 closest distance to " CD1 LEU A 101 " =    2.225
peak=   -3.433 closest distance to " CD  GLU A 277 " =    0.961
peak=   -3.428 closest distance to " CD  GLN A  58 " =    0.900
peak=   -3.419 closest distance to " CB  CYS A 254 " =    2.105
peak=   -3.411 closest distance to " CB  TRP A  85 " =    2.524
peak=   -3.410 closest distance to " N   GLN A  58 " =    1.763
peak=   -3.404 closest distance to " CG  GLN A 240 " =    2.395
peak=   -3.392 closest distance to " ND2 ASN A  45 " =    1.142
peak=   -3.383 closest distance to " O   HOH Z 191 " =    5.387
peak=   -3.378 closest distance to " C   LEU A 143 " =    1.267
peak=   -3.376 closest distance to " O   HOH Z 429 " =    1.781
peak=   -3.369 closest distance to " ND2 ASN A 187 " =    1.323
peak=   -3.364 closest distance to " ND2 ASN A 209 " =    1.947
peak=   -3.364 closest distance to " CE  LYS A  76 " =    2.845
peak=   -3.364 closest distance to " O   HOH Z 286 " =    1.716
peak=   -3.364 closest distance to " O   HOH Z 317 " =    1.443
peak=   -3.362 closest distance to " CG  GLN A 223 " =    2.170
peak=   -3.361 closest distance to " O   HOH Z 152 " =    4.830
peak=   -3.351 closest distance to " O   HOH Z 166 " =    1.663
peak=   -3.351 closest distance to " N   ASP A 270 " =    1.366
peak=   -3.340 closest distance to " O   PRO A 198 " =    1.297
peak=   -3.334 closest distance to " OXT GLY A 302 " =    3.168
peak=   -3.331 closest distance to " CG  GLN A 223 " =    0.992
peak=   -3.330 closest distance to " C   GLU A 236 " =    0.779
peak=   -3.314 closest distance to " NH2 ARG A  79 " =    1.964
peak=   -3.313 closest distance to " O   HOH Z 359 " =    3.252
peak=   -3.312 closest distance to " O   HOH Z 102 " =    1.539
peak=   -3.311 closest distance to " O   HOH Z 198 " =    1.887
peak=   -3.311 closest distance to " ND2 ASN A  60 " =    4.123
peak=   -3.311 closest distance to " CG  LEU A  83 " =    2.020
peak=   -3.310 closest distance to " O   HOH Z 222 " =    0.909
peak=   -3.307 closest distance to " O   HOH Z 414 " =    1.762
peak=   -3.304 closest distance to " O   HOH Z  60 " =    1.028
peak=   -3.303 closest distance to " O   HOH Z 218 " =    3.677
peak=   -3.303 closest distance to " OG  SER A  87 " =    1.287
peak=   -3.302 closest distance to " CG1 VAL A  78 " =    2.508
peak=   -3.301 closest distance to " CG2 ILE A 151 " =    2.597
peak=   -3.299 closest distance to " ND2 ASN A  45 " =    1.926
peak=   -3.297 closest distance to " CG  ASP A 231 " =    0.708
peak=   -3.296 closest distance to " CG2 THR A 178 " =    2.215
peak=   -3.296 closest distance to " O   GLN A 240 " =    2.112
peak=   -3.295 closest distance to " ND2BASN A 224 " =    1.605
peak=   -3.290 closest distance to " O   HOH Z 166 " =    1.254
peak=   -3.287 closest distance to " CD1 ILE A 239 " =    2.295
peak=   -3.279 closest distance to " CE  MET A  93 " =    1.155
peak=   -3.274 closest distance to " O   HOH Z  76 " =    1.172
peak=   -3.271 closest distance to " CA  GLY A 133 " =    1.967
peak=   -3.270 closest distance to " OD2 ASP A  27 " =    1.664
peak=   -3.269 closest distance to " O   HOH Z 253 " =    4.016
peak=   -3.268 closest distance to " O   VAL A 189 " =    2.390
peak=   -3.266 closest distance to " O   PHE A 218 " =    1.418
peak=   -3.266 closest distance to " CB  ALA A   9 " =    2.409
peak=   -3.258 closest distance to " CA  GLY A  57 " =    2.289
peak=   -3.258 closest distance to " O   HOH Z  15 " =    1.517
peak=   -3.255 closest distance to " O   HOH Z  49 " =    1.288
peak=   -3.252 closest distance to " O   ALA A   1 " =    1.702
peak=   -3.249 closest distance to " CG1 VAL A 197 " =    2.277
peak=   -3.249 closest distance to " CB  CYS A 201 " =    2.383
peak=   -3.246 closest distance to " O   ALA A  10 " =    1.652
peak=   -3.245 closest distance to " OD2 ASP A 191 " =    1.473
peak=   -3.245 closest distance to " CG1 VAL A 230 " =    2.062
peak=   -3.244 closest distance to " O   ARG A 145 " =    1.420
peak=   -3.229 closest distance to " OD1 ASN A 148 " =    1.600
peak=   -3.228 closest distance to " CD  GLU A 152 " =    0.771
peak=   -3.222 closest distance to " N   GLN A 122 " =    1.405
peak=   -3.222 closest distance to " O   HOH Z 174 " =    2.739
peak=   -3.222 closest distance to " O   HOH Z 152 " =    0.841
peak=   -3.220 closest distance to " CA  ILE A 263 " =    0.986
peak=   -3.218 closest distance to " CD  LYS A 289 " =    2.369
peak=   -3.218 closest distance to " O   ALA A 180 " =    1.240
peak=   -3.214 closest distance to " O   VAL A  67 " =    2.917
peak=   -3.209 closest distance to " O   HOH Z 251 " =    1.002
peak=   -3.202 closest distance to " C   LEU A 222 " =    0.735
peak=   -3.201 closest distance to " CG2 VAL A 232 " =    2.052
peak=   -3.198 closest distance to " NZ  LYS A 166 " =    1.108
peak=   -3.196 closest distance to " OD2 ASP A 171 " =    2.092
peak=   -3.192 closest distance to " O   HOH Z 281 " =    2.807
peak=   -3.191 closest distance to " CA  GLY A  57 " =    2.122
peak=   -3.184 closest distance to " CD2 PHE A  61 " =    2.009
peak=   -3.183 closest distance to " OH  TYR A 172 " =    1.872
peak=   -3.180 closest distance to " O   ALA A   1 " =    1.190
peak=   -3.179 closest distance to " O   HOH Z 432 " =    3.621
peak=   -3.176 closest distance to " O   GLY A  17 " =    1.142
peak=   -3.173 closest distance to " CB  PRO A 163 " =    2.471
peak=   -3.171 closest distance to " O   HOH Z 412 " =    4.219
peak=   -3.171 closest distance to " CE3 TRP A 274 " =    2.538
peak=   -3.149 closest distance to " NE2 GLN A 278 " =    1.828
peak=   -3.145 closest distance to " CG  PRO A 163 " =    2.530
peak=   -3.143 closest distance to " O   HOH Z 346 " =    1.678
peak=   -3.121 closest distance to " O   SER A  95 " =    1.476
peak=   -3.121 closest distance to " O   HOH Z 275 " =    1.657
peak=   -3.109 closest distance to " O   HOH Z 250 " =    1.385
peak=   -3.108 closest distance to " O   HOH Z  47 " =    1.129
peak=   -3.104 closest distance to " C   MET A 188 " =    1.695
peak=   -3.104 closest distance to " O   HOH Z 348 " =    1.724
peak=   -3.102 closest distance to " OG  SER A 245 " =    1.265
peak=   -3.100 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.096 closest distance to " N   ASN A 127 " =    1.579
peak=   -3.096 closest distance to " CB  GLN A  55 " =    1.371
peak=   -3.088 closest distance to " NH2 ARG A 219 " =    1.778
peak=   -3.081 closest distance to " O   HOH Z   9 " =    1.741
peak=   -3.079 closest distance to " CZ  PHE A  59 " =    1.438
peak=   -3.059 closest distance to " CD1 ILE A 199 " =    2.642
peak=   -3.059 closest distance to " O   HOH Z 147 " =    1.367
peak=   -3.055 closest distance to " CE1 PHE A  59 " =    2.182
peak=   -3.053 closest distance to " CD1 ILE A 263 " =    2.670
peak=   -3.053 closest distance to " O   GLU A 152 " =    1.457
peak=   -3.037 closest distance to " OG  SER A 206 " =    1.844
peak=   -3.021 closest distance to " N   ARG A 159 " =    2.070

================= 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    :  0.4081 0.4048   6.218706e+00   6.210592e+00
   1_bss:  0.3966 0.3980   6.205350e+00   6.197605e+00
   1_xyz:  0.3037 0.3379   6.007031e+00   6.066928e+00
   1_adp:  0.2766 0.3509   5.958713e+00   6.090250e+00
   1_occ:  0.2760 0.3510   5.958052e+00   6.090379e+00
   2_bss:  0.2755 0.3475   5.956114e+00   6.087057e+00
   2_xyz:  0.2079 0.2647   5.689095e+00   5.856558e+00
   2_adp:  0.1884 0.2436   5.602932e+00   5.788133e+00
   2_occ:  0.1883 0.2431   5.602190e+00   5.787139e+00
   3_bss:  0.1876 0.2416   5.598044e+00   5.781864e+00
   3_xyz:  0.1528 0.2019   5.413812e+00   5.622974e+00
   3_adp:  0.1427 0.1992   5.374942e+00   5.603370e+00
   3_occ:  0.1427 0.1991   5.374857e+00   5.603328e+00
   4_bss:  0.1427 0.1987   5.372124e+00   5.600230e+00
   4_xyz:  0.1225 0.1782   5.239746e+00   5.490440e+00
   4_adp:  0.1190 0.1687   5.203487e+00   5.445600e+00
   4_occ:  0.1189 0.1687   5.203136e+00   5.445183e+00
   5_bss:  0.1188 0.1688   5.202753e+00   5.444545e+00
   5_xyz:  0.1154 0.1628   5.175497e+00   5.417161e+00
   5_adp:  0.1153 0.1600   5.172150e+00   5.408523e+00
   5_occ:  0.1152 0.1600   5.171582e+00   5.407901e+00
   5_bss:  0.1153 0.1593   5.170715e+00   5.406570e+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:  0.341  42.675  -1.786   3.168  -1.223   0.000  -0.000  -0.000
   1_xyz:  0.341  42.675  -1.786   3.168  -1.223   0.000  -0.000  -0.000
   1_adp:  0.341  42.675  -1.786   3.168  -1.223   0.000  -0.000  -0.000
   1_occ:  0.341  42.675  -1.786   3.168  -1.223   0.000  -0.000  -0.000
   2_bss:  0.331  60.371  -1.757   0.140  -0.926   0.000  -0.000  -0.000
   2_xyz:  0.331  60.371  -1.757   0.140  -0.926   0.000  -0.000  -0.000
   2_adp:  0.331  60.371  -1.757   0.140  -0.926   0.000  -0.000  -0.000
   2_occ:  0.331  60.371  -1.757   0.140  -0.926   0.000  -0.000  -0.000
   3_bss:  0.337  60.371  -1.955  -1.515  -0.767  -0.000  -0.000  -0.000
   3_xyz:  0.337  60.371  -1.955  -1.515  -0.767  -0.000  -0.000  -0.000
   3_adp:  0.337  60.371  -1.955  -1.515  -0.767  -0.000  -0.000  -0.000
   3_occ:  0.337  60.371  -1.955  -1.515  -0.767  -0.000  -0.000  -0.000
   4_bss:  0.312  60.371  -2.114  -2.257  -1.003  -0.000  -0.000  -0.000
   4_xyz:  0.312  60.371  -2.114  -2.257  -1.003  -0.000  -0.000  -0.000
   4_adp:  0.312  60.371  -2.114  -2.257  -1.003  -0.000  -0.000  -0.000
   4_occ:  0.312  60.371  -2.114  -2.257  -1.003  -0.000  -0.000  -0.000
   5_bss:  0.317  55.098  -2.091  -2.408  -0.904  -0.000  -0.000  -0.000
   5_xyz:  0.317  55.098  -2.091  -2.408  -0.904  -0.000  -0.000  -0.000
   5_adp:  0.317  55.098  -2.091  -2.408  -0.904  -0.000  -0.000  -0.000
   5_occ:  0.317  55.098  -2.091  -2.408  -0.904  -0.000  -0.000  -0.000
   5_bss:  0.317  49.451  -2.134  -2.513  -0.895  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.436 0.5534  0.7369    53092.485
   1_bss:  46.943 0.5582  0.7480    51175.000
   1_xyz:  36.096 0.6894  0.8897    32666.876
   1_adp:  37.821 0.6680  0.8707    34982.907
   1_occ:  37.855 0.6676  0.8699    35019.159
   2_bss:  37.324 0.6738  0.8522    34298.096
   2_xyz:  26.827 0.7910  0.9652    18164.151
   2_adp:  24.012 0.8215  0.9764    15259.108
   2_occ:  23.985 0.8217  0.9763    15213.144
   3_bss:  23.767 0.8238  0.9593    14962.870
   3_xyz:  19.450 0.8664  0.9865    10409.221
   3_adp:  18.947 0.8716  0.9809    10105.260
   3_occ:  18.949 0.8716  0.9806    10102.562
   4_bss:  18.852 0.8724  0.9681    10002.639
   4_xyz:  16.384 0.8944  0.9800     7864.846
   4_adp:  15.301 0.9041  0.9796     7210.079
   4_occ:  15.295 0.9042  0.9795     7199.869
   5_bss:  15.293 0.9042  0.9792     7192.074
   5_xyz:  14.605 0.9101  0.9803     6727.112
   5_adp:  14.354 0.9124  0.9772     6642.945
   5_occ:  14.341 0.9125  0.9772     6627.223
   5_bss:  14.321 0.9126  0.9741     6586.426
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7127e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7127e-01
   1_xyz:   1.304  0.010  0.088 15.502  0.006  4.106   9.5223e-02
   1_adp:   1.304  0.010  0.088 15.502  0.006  4.106   9.5223e-02
   1_occ:   1.304  0.010  0.088 15.502  0.006  4.106   9.5223e-02
   2_bss:   1.304  0.010  0.088 15.502  0.006  4.106   9.5223e-02
   2_xyz:   1.224  0.009  0.087 14.796  0.004  4.109   8.3436e-02
   2_adp:   1.224  0.009  0.087 14.796  0.004  4.109   8.3436e-02
   2_occ:   1.224  0.009  0.087 14.796  0.004  4.109   8.3436e-02
   3_bss:   1.224  0.009  0.087 14.796  0.004  4.109   8.3436e-02
   3_xyz:   0.883  0.005  0.063 14.212  0.003  4.113   4.8427e-02
   3_adp:   0.883  0.005  0.063 14.212  0.003  4.113   4.8427e-02
   3_occ:   0.883  0.005  0.063 14.212  0.003  4.113   4.8427e-02
   4_bss:   0.883  0.005  0.063 14.212  0.003  4.113   4.8427e-02
   4_xyz:   1.047  0.008  0.075 14.454  0.004  4.118   6.3672e-02
   4_adp:   1.047  0.008  0.075 14.454  0.004  4.118   6.3672e-02
   4_occ:   1.047  0.008  0.075 14.454  0.004  4.118   6.3672e-02
   5_bss:   1.047  0.008  0.075 14.454  0.004  4.118   6.3672e-02
   5_xyz:   0.942  0.006  0.071 14.274  0.004  4.111   5.3890e-02
   5_adp:   0.942  0.006  0.071 14.274  0.004  4.111   5.3890e-02
   5_occ:   0.942  0.006  0.071 14.274  0.004  4.111   5.3890e-02
   5_bss:   0.942  0.006  0.071 14.274  0.004  4.111   5.3890e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4088e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4088e-01
   1_xyz:   8.396  0.054  0.310 84.872  0.048  2.145   8.9462e-02
   1_adp:   8.396  0.054  0.310 84.872  0.048  2.145   8.9462e-02
   1_occ:   8.396  0.054  0.310 84.872  0.048  2.145   8.9462e-02
   2_bss:   8.396  0.054  0.310 84.872  0.048  2.145   8.9462e-02
   2_xyz:   7.413  0.048  0.238 81.092  0.030  2.086   1.2976e-01
   2_adp:   7.413  0.048  0.238 81.092  0.030  2.086   1.2976e-01
   2_occ:   7.413  0.048  0.238 81.092  0.030  2.086   1.2976e-01
   3_bss:   7.413  0.048  0.238 81.092  0.030  2.086   1.2976e-01
   3_xyz:   6.787  0.033  0.205 80.795  0.023  2.336   5.6823e-02
   3_adp:   6.787  0.033  0.205 80.795  0.023  2.336   5.6823e-02
   3_occ:   6.787  0.033  0.205 80.795  0.023  2.336   5.6823e-02
   4_bss:   6.787  0.033  0.205 80.795  0.023  2.336   5.6823e-02
   4_xyz:   7.453  0.040  0.246 82.206  0.029  2.297   5.2918e-02
   4_adp:   7.453  0.040  0.246 82.206  0.029  2.297   5.2918e-02
   4_occ:   7.453  0.040  0.246 82.206  0.029  2.297   5.2918e-02
   5_bss:   7.453  0.040  0.246 82.206  0.029  2.297   5.2918e-02
   5_xyz:   7.678  0.044  0.234 83.651  0.029  2.315   3.8902e-02
   5_adp:   7.678  0.044  0.234 83.651  0.029  2.315   3.8902e-02
   5_occ:   7.678  0.044  0.234 83.651  0.029  2.315   3.8902e-02
   5_bss:   7.678  0.044  0.234 83.651  0.029  2.315   3.8902e-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:  99.79   0.00  18.17  61.54   0.00  14.58  99.79   1.77  37.71
   1_occ:  99.79   0.00  18.17  61.54   0.00  14.58  99.79   1.77  37.71
   2_bss:  99.79   0.00  18.17  61.54   0.00  14.58  99.79   1.77  37.71
   2_xyz:  99.79   0.00  18.17  61.54   0.00  14.58  99.79   1.77  37.71
   2_adp:  97.69   0.00  17.63  73.08   0.00  13.53  97.69   5.39  39.94
   2_occ:  97.69   0.00  17.63  73.08   0.00  13.53  97.69   5.39  39.94
   3_bss:  97.69   0.00  17.63  73.08   0.00  13.53  97.69   5.39  39.94
   3_xyz:  97.69   0.00  17.63  73.08   0.00  13.53  97.69   5.39  39.94
   3_adp: 105.54   0.00  18.44  93.05   0.00  13.38 105.54   6.69  46.01
   3_occ: 105.54   0.00  18.44  93.05   0.00  13.38 105.54   6.69  46.01
   4_bss: 105.54   0.00  18.44  93.05   0.00  13.38 105.54   6.69  46.01
   4_xyz: 105.54   0.00  18.44  93.05   0.00  13.38 105.54   6.69  46.01
   4_adp:  97.88   0.21  17.52  96.78   0.21  12.92  97.88   6.30  42.62
   4_occ:  97.88   0.21  17.52  96.78   0.21  12.92  97.88   6.30  42.62
   5_bss:  97.88   0.21  17.52  96.78   0.21  12.92  97.88   6.30  42.62
   5_xyz:  97.88   0.21  17.52  96.78   0.21  12.92  97.88   6.30  42.62
   5_adp:  93.66   1.11  16.72  93.66   1.11  12.63  87.62   6.11  39.03
   5_occ:  93.66   1.11  16.72  93.66   1.11  12.63  87.62   6.11  39.03
   5_bss:  93.62   1.07  16.69  93.62   1.07  12.59  87.58   6.07  38.99
------------------------------------------------------------------------
 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:    1.609    0.013    0.291
   1_adp:    1.609    0.013    0.291
   1_occ:    1.609    0.013    0.291
   2_bss:    1.609    0.013    0.291
   2_xyz:    1.429    0.028    0.504
   2_adp:    1.429    0.028    0.504
   2_occ:    1.429    0.028    0.504
   3_bss:    1.429    0.028    0.504
   3_xyz:    1.343    0.041    0.574
   3_adp:    1.343    0.041    0.574
   3_occ:    1.343    0.041    0.574
   4_bss:    1.343    0.041    0.574
   4_xyz:    1.285    0.038    0.618
   4_adp:    1.285    0.038    0.618
   4_occ:    1.285    0.038    0.618
   5_bss:    1.285    0.038    0.618
   5_xyz:    1.390    0.061    0.638
   5_adp:    1.390    0.061    0.638
   5_occ:    1.390    0.061    0.638
   5_bss:    1.390    0.061    0.638
------------------------------------------------------------------------

CPU time actual refinement: 341.51


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/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_864/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_864/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.36 
  Macro-tasks:
    bulk solvent and scale       = 36.85  
    individual site refinement   = 137.50 
    weights calculation          = 29.98  
    collect and process          = 6.55   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 210.98 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 113.01 
    alpha_beta                      = 8.11   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 119.20 
    fmodel                         = 6.33   
    r_factors                      = 0.20   
    phase_errors                   = 10.89  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 261.60 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.921 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    632 calls, 112.63 s
gradients_fft:          577 calls, 106.68 s

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

# Date 2008-01-16 Time 05:51:01 PST -0800 (1200491461.22 s)
Start R-work = 0.4081, R-free = 0.4048 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.3966, R-free = 0.3980
Final R-work = 0.1153, R-free = 0.1593