# Date 2008-01-16 Time 01:45:01 PST -0800 (1200476701.39 s)
#phil __OFF__

Command line arguments: "../544.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4948
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 544

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 86.39, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (69.8988, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99053
Completeness in resolution range: 0.977007
Completeness with d_max=infinity: 0.973899

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9392
                             d_min =   1.9905

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: (69.8988, 46.93, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9392 1.99053
Completeness in resolution range: 0.977007
Completeness with d_max=infinity: 0.973899

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9396 -  4.2585 [2105/2129]  1894   211  10.0%
  bin  2:  4.2585 -  3.3931 [2028/2047]  1826   202  10.0%
  bin  3:  3.3931 -  2.9680 [1994/2013]  1795   199  10.0%
  bin  4:  2.9680 -  2.6984 [1972/2002]  1774   198  10.0%
  bin  5:  2.6984 -  2.5059 [1977/1996]  1781   196   9.9%
  bin  6:  2.5059 -  2.3588 [1946/1971]  1747   199  10.2%
  bin  7:  2.3588 -  2.2411 [1948/1976]  1756   192   9.9%
  bin  8:  2.2411 -  2.1438 [1953/1989]  1758   195  10.0%
  bin  9:  2.1438 -  2.0615 [1906/1948]  1713   193  10.1%
  bin 10:  2.0615 -  1.9905 [1760/1979]  1586   174   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/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: 10
        2.42 -     3.04: 2214
        3.04 -     3.66: 4643
        3.66 -     4.28: 9094
        4.28 -     4.90: 12363
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.274 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.298 3.040 -x+1,y+1/2,-z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 28319 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_544/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 86.39 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4046   r_free= 0.3927   ksol= 0.00   Bsol= 0.00   scale= 0.839    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.186483                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.3470 0.3251      6.4817      6.4308|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.2939 0.3029      6.5466      6.5637|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.3352 0.3229      6.4812      6.4831|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.3784 0.3482      6.3982      6.3002|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.4115 0.4404      6.2643      6.3332|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.4250 0.4818      6.1944      6.1839|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.4493 0.4436      6.1799      6.1117|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.4537 0.4426      6.1261      6.1256|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.4564 0.4610      6.0661      6.0528|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.4742 0.4283      6.0923      5.9809|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.4650 0.3686      6.0171      5.9011|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.4687 0.4499      5.9519      6.0046|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.4699 0.4813      5.8698      5.8569|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.4761 0.4351      5.8239      5.7106|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1375   153  0.75  30.11   0.82     0.77      55186.97|
|  2:  4.7493 -  3.7899  1306   146  0.80  25.85   0.93     0.84      61728.73|
|  3:  3.7899 -  3.3168  1294   143  0.76  30.41   0.90     0.83      61840.78|
|  4:  3.3168 -  3.0163  1285   139  0.70  35.14   0.85     0.75      55517.19|
|  5:  3.0163 -  2.8016  1266   144  0.61  43.45   0.80     0.67      53543.72|
|  6:  2.8016 -  2.6374  1277   141  0.57  46.26   0.77     0.63      50262.34|
|  7:  2.6374 -  2.5059  1267   140  0.55  48.10   0.78     0.62      47756.55|
|  8:  2.5059 -  2.3973  1248   140  0.56  47.72   0.79     0.63      41803.81|
|  9:  2.3973 -  2.3054  1253   142  0.58  45.45   0.76     0.65      35437.52|
| 10:  2.3054 -  2.2261  1247   136  0.60  43.92   0.79     0.68      30150.94|
| 11:  2.2261 -  2.1567  1254   137  0.61  43.66   0.79     0.68      27874.91|
| 12:  2.1567 -  2.0952  1241   142  0.56  47.73   0.81     0.65      28668.28|
| 13:  2.0952 -  2.0402  1248   136  0.53  50.10   0.79     0.60      26222.43|
| 14:  2.0402 -  1.9905  1069   120  0.55  48.43   0.76     0.58      20558.19|
|alpha:            min =        0.58 max =            0.84 mean =         0.69|
|beta:             min =    20558.19 max =        61840.78 mean =     43094.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.63|
|phase err.(work): min =        0.00 max =           89.95 mean =        41.65|
|phase err.(test): min =        0.00 max =           89.91 mean =        41.87|
|-----------------------------------------------------------------------------|

============================== 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 = 5.944933              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 71.737   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.447633              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.993   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2632 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3936 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5084 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6576 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7749 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.657 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.691 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4147   r_free= 0.4015   ksol= 0.00   Bsol= 0.00   scale= 0.806    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.195878                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3971   r_free= 0.3834   ksol= 0.35   Bsol= 18.50   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.38,8.25,8.26,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.180967                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.550680              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.851   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.722   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3971      final r-factor (work) = 0.2798          |
| start r-factor (free) = 0.3834      final r-factor (free) = 0.2982          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 70.9010 = 5.55 * 0.50 * 6.2135 + 1.00 * 53.6565                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7182 = 5.55 * 0.50 * 5.9867 + 1.00 * 0.1030                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2798      final r-factor (work) = 0.1990          |
| start r-factor (free) = 0.2982      final r-factor (free) = 0.2255          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7640 = 0.46 * 1.00 * 5.9867 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6409 = 0.46 * 1.00 * 5.7282 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    47.67   9.72     None  None   None       |
|    all(noH): 2823   0      0.00    47.67   9.72     None  None   None       |
|    Sol.    : 438    0      0.00    47.67   26.43    None  None   None       |
|    Mac.    : 2385   0      0.00    43.08   6.65     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 -   4.767: 1132   |   5:    23.835 -  28.602:   96        |
|      1:     4.767 -   9.534:  800   |   6:    28.602 -  33.369:  107        |
|      2:     9.534 -  14.301:  296   |   7:    33.369 -  38.136:   92        |
|      3:    14.301 -  19.068:  143   |   8:    38.136 -  42.902:   44        |
|      4:    19.068 -  23.835:  101   |   9:    42.902 -  47.669:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1990 r_free = 0.2255             target_work(ml) = 5.588         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1984 r_free = 0.2251             target_work(ml) = 5.585         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1984   r_free= 0.2251   ksol= 0.35   Bsol= 18.50   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.38,8.25,8.26,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.585417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1922   r_free= 0.2186   ksol= 0.36   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.97,4.43,5.29,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.582889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.721216              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.245   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.215636              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.140  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1922      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.2186      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0542 = 1.72 * 0.50 * 5.7537 + 1.00 * 0.1025                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7268 = 1.72 * 0.50 * 5.4292 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1433      final r-factor (work) = 0.1347          |
| start r-factor (free) = 0.1743      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1877 = 0.22 * 1.00 * 5.4292 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1855 = 0.22 * 1.00 * 5.2848 + 1.00 * 0.0459                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.93   10.12    None  None   None       |
|    all(noH): 2823   0      0.00    76.93   10.12    None  None   None       |
|    Sol.    : 438    0      0.96    48.63   28.66    None  None   None       |
|    Mac.    : 2385   0      0.00    76.93   6.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.693: 1740   |   5:    38.466 -  46.159:   78        |
|      1:     7.693 -  15.387:  524   |   6:    46.159 -  53.853:   13        |
|      2:    15.387 -  23.080:  159   |   7:    53.853 -  61.546:    0        |
|      3:    23.080 -  30.773:  135   |   8:    61.546 -  69.239:    0        |
|      4:    30.773 -  38.466:  173   |   9:    69.239 -  76.932:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1347 r_free = 0.1677             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1346 r_free = 0.1677             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1346   r_free= 0.1677   ksol= 0.36   Bsol= 50.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.97,4.43,5.29,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.266022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1344   r_free= 0.1680   ksol= 0.33   Bsol= 39.86   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.77,4.73,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.266516                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.983050              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.213  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.691106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.362   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9398 = 2.98 * 0.50 * 5.2868 + 1.00 * 0.0544                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8179 = 2.98 * 0.50 * 5.1943 + 1.00 * 0.0704                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1565      final r-factor (free) = 0.1538          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6051 = 0.69 * 1.00 * 5.1943 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5663 = 0.69 * 1.00 * 5.1411 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.67   10.94    None  None   None       |
|    all(noH): 2823   0      0.00    67.67   10.94    None  None   None       |
|    Sol.    : 438    0      0.17    65.21   32.79    None  None   None       |
|    Mac.    : 2385   0      0.00    67.67   6.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.767: 1613   |   5:    33.834 -  40.601:   80        |
|      1:     6.767 -  13.534:  570   |   6:    40.601 -  47.367:   73        |
|      2:    13.534 -  20.300:  173   |   7:    47.367 -  54.134:   67        |
|      3:    20.300 -  27.067:  105   |   8:    54.134 -  60.901:   27        |
|      4:    27.067 -  33.834:  105   |   9:    60.901 -  67.668:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1538             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1538             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1538   ksol= 0.33   Bsol= 39.86   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.23,3.77,4.73,0.00,0.00,0.00); trace/3= 3.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1537   ksol= 0.32   Bsol= 42.04   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,3.77,4.78,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132555                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.458036              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.961  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.197577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.407  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1114      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8182 = 1.46 * 0.50 * 5.1407 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8021 = 1.46 * 0.50 * 5.1412 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0306 = 0.20 * 1.00 * 5.1412 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0359 = 0.20 * 1.00 * 5.1498 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.81   10.51    None  None   None       |
|    all(noH): 2823   0      0.00    68.81   10.51    None  None   None       |
|    Sol.    : 438    0      0.76    62.16   30.75    None  None   None       |
|    Mac.    : 2385   0      0.00    68.81   6.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.881: 1642   |   5:    34.406 -  41.287:   85        |
|      1:     6.881 -  13.762:  571   |   6:    41.287 -  48.168:   80        |
|      2:    13.762 -  20.643:  160   |   7:    48.168 -  55.049:   34        |
|      3:    20.643 -  27.524:  107   |   8:    55.049 -  61.930:   10        |
|      4:    27.524 -  34.406:  128   |   9:    61.930 -  68.811:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1544             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1544             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1544   ksol= 0.32   Bsol= 42.04   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,3.77,4.78,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1544   ksol= 0.33   Bsol= 42.04   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,3.77,4.78,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.147954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.105621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.718  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.779116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.957   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1544      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0501 = 3.11 * 0.50 * 5.1493 + 1.00 * 0.0541                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0329 = 3.11 * 0.50 * 5.1254 + 1.00 * 0.0741                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0221 = 0.78 * 1.00 * 5.1254 + 1.00 * 0.0288                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9956 = 0.78 * 1.00 * 5.1130 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.55   10.73    None  None   None       |
|    all(noH): 2823   0      0.00    71.55   10.73    None  None   None       |
|    Sol.    : 438    0      0.43    63.63   32.00    None  None   None       |
|    Mac.    : 2385   0      0.00    71.55   6.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.155: 1673   |   5:    35.775 -  42.930:   87        |
|      1:     7.155 -  14.310:  541   |   6:    42.930 -  50.085:   80        |
|      2:    14.310 -  21.465:  158   |   7:    50.085 -  57.241:   33        |
|      3:    21.465 -  28.620:  109   |   8:    57.241 -  64.396:   13        |
|      4:    28.620 -  35.775:  124   |   9:    64.396 -  71.551:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1075 r_free = 0.1544             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1544             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1544   ksol= 0.33   Bsol= 42.04   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.27,3.77,4.78,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117210                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.1004 0.1282      5.3858      5.5178|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.0843 0.1135      5.4301      5.6382|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.1031 0.1488      5.4615      5.8443|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.1155 0.1460      5.4174      5.5612|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.1242 0.1644      5.2985      5.5262|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.1152 0.1835      5.1789      5.4558|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.1189 0.1595      5.1365      5.3307|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.1121 0.1718      5.0598      5.3679|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.1128 0.1782      5.0202      5.2719|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.1065 0.1692      4.9481      5.2056|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.1067 0.1667       4.906       5.214|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.1068 0.1634      4.8495       5.201|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.1075 0.1636      4.7701       5.025|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.1001 0.1758      4.6425       4.949|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1375   153  0.94   9.02   0.98     0.96       7161.47|
|  2:  4.7493 -  3.7899  1306   146  0.95   7.80   1.02     1.00       8987.05|
|  3:  3.7899 -  3.3168  1294   143  0.94  10.94   1.02     1.02      10158.73|
|  4:  3.3168 -  3.0163  1285   139  0.93  12.79   1.00     0.99       9665.09|
|  5:  3.0163 -  2.8016  1266   144  0.91  15.22   0.99     0.96       7964.05|
|  6:  2.8016 -  2.6374  1277   141  0.91  15.40   0.98     0.95       6700.27|
|  7:  2.6374 -  2.5059  1267   140  0.91  15.12   0.99     0.96       5931.48|
|  8:  2.5059 -  2.3973  1248   140  0.91  14.45   0.99     0.96       5201.13|
|  9:  2.3973 -  2.3054  1253   142  0.91  15.47   1.01     0.99       5028.61|
| 10:  2.3054 -  2.2261  1247   136  0.90  15.62   1.00     0.96       4369.37|
| 11:  2.2261 -  2.1567  1254   137  0.91  15.53   1.00     0.97       4204.05|
| 12:  2.1567 -  2.0952  1241   142  0.91  14.79   1.02     1.00       3750.02|
| 13:  2.0952 -  2.0402  1248   136  0.91  14.83   1.01     0.99       3196.10|
| 14:  2.0402 -  1.9905  1069   120  0.92  14.42   0.98     0.94       2472.36|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2472.36 max =        10158.73 mean =      6131.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.61|
|phase err.(test): min =        0.00 max =           88.35 mean =        13.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1544   ksol= 0.32   Bsol= 46.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.19,0.85,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117133                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1544   ksol= 0.32   Bsol= 46.03   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.19,0.85,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117133                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9396 -  4.7493 0.99   1375  153 0.1003 0.1283      5.3849      5.5168|
|  2:  4.7493 -  3.7899 0.99   1306  146 0.0844 0.1136      5.4304      5.6387|
|  3:  3.7899 -  3.3168 0.99   1294  143 0.1031 0.1488      5.4616      5.8443|
|  4:  3.3168 -  3.0163 0.99   1285  139 0.1155 0.1460      5.4174      5.5611|
|  5:  3.0163 -  2.8016 0.99   1266  144 0.1242 0.1644      5.2983       5.526|
|  6:  2.8016 -  2.6374 0.99   1277  141 0.1152 0.1834      5.1788      5.4555|
|  7:  2.6374 -  2.5059 0.99   1267  140 0.1189 0.1595      5.1364      5.3306|
|  8:  2.5059 -  2.3973 0.98   1248  140 0.1121 0.1718      5.0597      5.3678|
|  9:  2.3973 -  2.3054 0.98   1253  142 0.1128 0.1782      5.0202      5.2718|
| 10:  2.3054 -  2.2261 0.99   1247  136 0.1065 0.1692      4.9482      5.2056|
| 11:  2.2261 -  2.1567 0.98   1254  137 0.1067 0.1667       4.906      5.2142|
| 12:  2.1567 -  2.0952 0.97   1241  142 0.1068 0.1634      4.8496      5.2011|
| 13:  2.0952 -  2.0402 1.00   1248  136 0.1075 0.1636      4.7701      5.0249|
| 14:  2.0402 -  1.9905 0.84   1069  120 0.1001 0.1758      4.6424      4.9487|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9396 -  4.7493  1375   153  0.94   9.01   0.98     0.96       7143.59|
|  2:  4.7493 -  3.7899  1306   146  0.95   7.80   1.02     1.01       8983.08|
|  3:  3.7899 -  3.3168  1294   143  0.94  10.94   1.03     1.02      10162.77|
|  4:  3.3168 -  3.0163  1285   139  0.93  12.79   1.01     0.99       9662.56|
|  5:  3.0163 -  2.8016  1266   144  0.91  15.22   1.00     0.97       7960.37|
|  6:  2.8016 -  2.6374  1277   141  0.91  15.40   0.98     0.95       6697.99|
|  7:  2.6374 -  2.5059  1267   140  0.91  15.12   0.99     0.96       5929.56|
|  8:  2.5059 -  2.3973  1248   140  0.91  14.44   0.99     0.97       5199.86|
|  9:  2.3973 -  2.3054  1253   142  0.91  15.47   1.01     0.99       5028.30|
| 10:  2.3054 -  2.2261  1247   136  0.90  15.62   1.01     0.97       4369.80|
| 11:  2.2261 -  2.1567  1254   137  0.91  15.54   1.00     0.97       4205.00|
| 12:  2.1567 -  2.0952  1241   142  0.91  14.80   1.02     1.01       3750.60|
| 13:  2.0952 -  2.0402  1248   136  0.91  14.83   1.01     1.00       3195.82|
| 14:  2.0402 -  1.9905  1069   120  0.92  14.42   0.99     0.95       2471.36|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2471.36 max =        10162.77 mean =      6129.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.61|
|phase err.(test): min =        0.00 max =           88.35 mean =        13.16|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.848)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.99    75.54   14.72    None  None   None       |
|    all(noH): 2823   0      3.99    75.54   14.72    None  None   None       |
|    Sol.    : 438    0      4.42    67.62   35.99    None  None   None       |
|    Mac.    : 2385   0      3.99    75.54   10.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.990 -  11.145: 1673   |   5:    39.765 -  46.920:   87        |
|      1:    11.145 -  18.300:  541   |   6:    46.920 -  54.075:   80        |
|      2:    18.300 -  25.455:  158   |   7:    54.075 -  61.231:   33        |
|      3:    25.455 -  32.610:  109   |   8:    61.231 -  68.386:   13        |
|      4:    32.610 -  39.765:  124   |   9:    68.386 -  75.541:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.279 - 4.745
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 286 from: 294
   mapped sites are within: 0.754 - 4.745

peak=   10.320 closest distance to " CG2 VAL A 230 " =    1.319
peak=    6.378 closest distance to " CG  LEU A   5 " =    1.187
peak=    5.986 closest distance to " CG2 VAL A 296 " =    1.062
peak=    5.907 closest distance to " CG  LEU A 228 " =    1.152
peak=    5.777 closest distance to " CB  VAL A 296 " =    1.091
peak=    5.374 closest distance to " NH2 ARG A  56 " =    2.208
peak=    5.353 closest distance to " CD2 LEU A   5 " =    1.182
peak=    5.349 closest distance to " CG  PRO A  54 " =    1.228
peak=    5.297 closest distance to " CB  VAL A 230 " =    1.187
peak=    5.274 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.228 closest distance to " CB  GLN A 223 " =    1.464
peak=    5.189 closest distance to " O   HOH Z 142 " =    1.699
peak=    5.052 closest distance to " CB  GLN A 183 " =    1.288
peak=    4.940 closest distance to " CB  ARG A 275 " =    0.928
peak=    4.915 closest distance to " O   HOH Z 126 " =    1.917
peak=    4.886 closest distance to " CB  SER A  63 " =    1.242
peak=    4.866 closest distance to " O   HOH Z 232 " =    2.414
peak=    4.591 closest distance to " CB  GLU A 152 " =    1.220
peak=    4.564 closest distance to " O   HOH Z  61 " =    1.684
peak=    4.521 closest distance to " O   HOH Z 209 " =    2.305
peak=    4.508 closest distance to " O   HOH Z 272 " =    1.902
peak=    4.502 closest distance to " O   HOH Z 427 " =    2.960
peak=    4.425 closest distance to " O   SER A  87 " =    2.228
peak=    4.419 closest distance to " O   HOH Z  43 " =    2.052
peak=    4.380 closest distance to " O   HOH Z 193 " =    1.726
peak=    4.375 closest distance to " CB  PRO A  54 " =    0.925
peak=    4.351 closest distance to " C   PRO A 198 " =    1.452
peak=    4.346 closest distance to " O   HOH Z 346 " =    1.611
peak=    4.343 closest distance to " O   HOH Z 402 " =    1.451
peak=    4.288 closest distance to " O   HOH Z 236 " =    1.929
peak=    4.272 closest distance to " CB  ASN A 148 " =    1.387
peak=    4.255 closest distance to " O   HOH Z 316 " =    3.035
peak=    4.252 closest distance to " O   HOH Z 303 " =    2.057
peak=    4.233 closest distance to " CB  ARG A  79 " =    1.424
peak=    4.223 closest distance to " O   HOH Z 298 " =    1.821
peak=    4.211 closest distance to " O   HOH Z 203 " =    1.570
peak=    4.194 closest distance to " O   HOH Z 423 " =    1.813
peak=    4.187 closest distance to " O   HOH Z 158 " =    3.145
peak=    4.169 closest distance to " O   HOH Z 369 " =    2.299
peak=    4.110 closest distance to " O   HOH Z 248 " =    1.596
peak=    4.087 closest distance to " O   HOH Z 234 " =    3.576
peak=    4.075 closest distance to " CG  PRO A 213 " =    1.176
peak=    4.040 closest distance to " O   HOH Z 126 " =    2.093
peak=    4.031 closest distance to " OD1 ASN A  69 " =    2.604
peak=    4.029 closest distance to " CB  SER A   3 " =    1.237
peak=    4.028 closest distance to " O   HOH Z  15 " =    2.137
peak=    4.027 closest distance to " ND2 ASN A 187 " =    1.488
peak=    4.025 closest distance to " CB  ASP A 140 " =    1.031
peak=    4.011 closest distance to " O   HOH Z 280 " =    2.909
peak=    3.998 closest distance to " CB  VAL A 265 " =    1.315
peak=    3.993 closest distance to " O   HOH Z 197 " =    3.154
peak=    3.992 closest distance to " O   HOH Z  59 " =    2.094
peak=    3.992 closest distance to " O   HOH Z 368 " =    2.188
peak=    3.974 closest distance to " CG1BVAL A  72 " =    1.632
peak=    3.949 closest distance to " CB  GLU A 277 " =    3.563
peak=    3.946 closest distance to " CA  TYR A  30 " =    0.970
peak=    3.914 closest distance to " O   HOH Z  97 " =    2.461
peak=    3.913 closest distance to " CD2 TRP A 179 " =    1.385
peak=    3.911 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.911 closest distance to " CB  TRP A 266 " =    0.981
peak=    3.907 closest distance to " CB  ARG A 190 " =    1.638
peak=    3.902 closest distance to " O   HOH Z 371 " =    3.089
peak=    3.902 closest distance to " O   HOH Z  97 " =    1.968
peak=    3.901 closest distance to " CB  TRP A 179 " =    1.339
peak=    3.889 closest distance to " O   HOH Z 147 " =    1.763
peak=    3.888 closest distance to " O   HOH Z 411 " =    3.765
peak=    3.887 closest distance to " O   HOH Z  78 " =    1.688
peak=    3.870 closest distance to " O   HOH Z 250 " =    1.353
peak=    3.868 closest distance to " O   HOH Z 403 " =    1.716
peak=    3.863 closest distance to " CZ  PHE A 218 " =    1.154
peak=    3.855 closest distance to " O   HOH Z 425 " =    2.123
peak=    3.847 closest distance to " O   HOH Z 193 " =    1.956
peak=    3.821 closest distance to " CB  GLU A 128 " =    1.013
peak=    3.818 closest distance to " O   HOH Z 265 " =    2.382
peak=    3.812 closest distance to " CG  PRO A 243 " =    1.105
peak=    3.810 closest distance to " CB  ARG A 139 " =    0.946
peak=    3.804 closest distance to " CB  ASN A 148 " =    1.917
peak=    3.796 closest distance to " CB  ASN A  39 " =    0.900
peak=    3.787 closest distance to " O   HOH Z 189 " =    2.711
peak=    3.782 closest distance to " O   HOH Z 130 " =    2.260
peak=    3.768 closest distance to " O   HOH Z 261 " =    2.011
peak=    3.759 closest distance to " O   HOH Z 245 " =    1.382
peak=    3.746 closest distance to " O   HOH Z 407 " =    2.462
peak=    3.742 closest distance to " CD2 LEU A 228 " =    1.105
peak=    3.739 closest distance to " CG1 ILE A  49 " =    1.452
peak=    3.723 closest distance to " OG BSER A 164 " =    2.189
peak=    3.700 closest distance to " CG  ARG A  66 " =    2.716
peak=    3.696 closest distance to " O   HOH Z 389 " =    1.845
peak=    3.673 closest distance to " O   HOH Z 417 " =    3.329
peak=    3.666 closest distance to " CA  ASN A 215 " =    1.153
peak=    3.666 closest distance to " O   HOH Z 261 " =    1.681
peak=    3.655 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.652 closest distance to " CB  THR A  31 " =    1.614
peak=    3.649 closest distance to " CB  HIS A 108 " =    0.827
peak=    3.647 closest distance to " CB  SER A  26 " =    1.690
peak=    3.625 closest distance to " CA  ALA A  21 " =    1.162
peak=    3.624 closest distance to " O   HOH Z 263 " =    1.646
peak=    3.617 closest distance to " CB AVAL A  41 " =    1.127
peak=    3.607 closest distance to " O   HOH Z 145 " =    2.145
peak=    3.607 closest distance to " O   HOH Z 172 " =    3.698
peak=    3.604 closest distance to " O   HOH Z  40 " =    1.589
peak=    3.602 closest distance to " CB  VAL A 202 " =    1.543
peak=    3.584 closest distance to " O   HOH Z 344 " =    3.038
peak=    3.580 closest distance to " O   HOH Z 313 " =    1.816
peak=    3.578 closest distance to " CA  ALA A 158 " =    1.311
peak=    3.576 closest distance to " CB  ASN A 142 " =    1.118
peak=    3.572 closest distance to " CG2 VAL A 257 " =    0.826
peak=    3.571 closest distance to " O   HOH Z 128 " =    2.088
peak=    3.568 closest distance to " O   HOH Z 214 " =    2.273
peak=    3.564 closest distance to " O   HOH Z 187 " =    2.244
peak=    3.559 closest distance to " O   HOH Z 273 " =    2.749
peak=    3.551 closest distance to " CA  ALA A  51 " =    0.916
peak=    3.549 closest distance to " CA  PHE A 283 " =    1.258
peak=    3.539 closest distance to " NH1BARG A 190 " =    2.077
peak=    3.529 closest distance to " O   HOH Z 299 " =    4.281
peak=    3.527 closest distance to " N   ASN A  39 " =    1.212
peak=    3.513 closest distance to " CG  MET A 185 " =    1.162
peak=    3.511 closest distance to " CG  GLN A  77 " =    2.071
peak=    3.510 closest distance to " O   HOH Z  88 " =    2.921
peak=    3.508 closest distance to " O   HOH Z 112 " =    1.666
peak=    3.508 closest distance to " O   HOH Z  54 " =    1.565
peak=    3.500 closest distance to " CD BLYS A 290 " =    1.155
peak=    3.500 closest distance to " O   TRP A 274 " =    1.860
peak=    3.499 closest distance to " NH1AARG A 145 " =    1.100
peak=    3.495 closest distance to " O   HOH Z  19 " =    2.284
peak=    3.494 closest distance to " O   HOH Z 291 " =    1.564
peak=    3.494 closest distance to " CB  ASN A 110 " =    1.121
peak=    3.492 closest distance to " CG2 ILE A  20 " =    1.429
peak=    3.492 closest distance to " O   HOH Z 128 " =    2.120
peak=    3.490 closest distance to " CB  GLU A  46 " =    1.061
peak=    3.489 closest distance to " O   HOH Z 154 " =    2.022
peak=    3.479 closest distance to " O   HOH Z  10 " =    1.754
peak=    3.478 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.478 closest distance to " N   SER A 135 " =    1.316
peak=    3.474 closest distance to " CA  ALA A 291 " =    0.918
peak=    3.472 closest distance to " O   MET A 105 " =    1.854
peak=    3.472 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.463 closest distance to " NZ  LYS A 117 " =    3.199
peak=    3.462 closest distance to " NH2 ARG A 156 " =    1.101
peak=    3.458 closest distance to " CB  TRP A 150 " =    1.394
peak=    3.458 closest distance to " CB  ASN A 224 " =    1.011
peak=    3.450 closest distance to " O   HOH Z 305 " =    3.624
peak=    3.450 closest distance to " CA  ARG A  36 " =    0.994
peak=    3.448 closest distance to " OD2 ASP A 286 " =    2.757
peak=    3.448 closest distance to " NE2 GLN A  77 " =    3.178
peak=    3.445 closest distance to " CA  ARG A 195 " =    1.207
peak=    3.434 closest distance to " CG2 THR A 221 " =    1.269
peak=    3.426 closest distance to " CB  ALA A 291 " =    1.403
peak=    3.426 closest distance to " O   HOH Z 422 " =    2.604
peak=    3.424 closest distance to " O   HOH Z 148 " =    3.296
peak=    3.419 closest distance to " O   HOH Z 145 " =    3.797
peak=    3.418 closest distance to " O   HOH Z   1 " =    1.924
peak=    3.410 closest distance to " CG  MET A 185 " =    1.061
peak=    3.405 closest distance to " CD  LYS A 166 " =    1.332
peak=    3.402 closest distance to " N   PHE A 130 " =    1.276
peak=    3.398 closest distance to " O   ASP A 124 " =    1.131
peak=    3.396 closest distance to " CG2 ILE A 120 " =    1.197
peak=    3.392 closest distance to " CD  LYS A 119 " =    1.554
peak=    3.391 closest distance to " O   HOH Z   9 " =    2.038
peak=    3.387 closest distance to " O   HOH Z 423 " =    2.957
peak=    3.384 closest distance to " O   HOH Z  48 " =    1.583
peak=    3.379 closest distance to " CA  ASP A 162 " =    1.045
peak=    3.379 closest distance to " NZ  LYS A  48 " =    1.276
peak=    3.377 closest distance to " N   ASP A 162 " =    1.269
peak=    3.374 closest distance to " O   HOH Z  44 " =    1.707
peak=    3.373 closest distance to " O   HOH Z  66 " =    2.220
peak=    3.373 closest distance to " CB  LEU A 228 " =    1.297
peak=    3.372 closest distance to " CE  LYS A  76 " =    0.939
peak=    3.371 closest distance to " O   HOH Z 193 " =    1.624
peak=    3.367 closest distance to " CG  PRO A 198 " =    1.164
peak=    3.367 closest distance to " O   HOH Z 421 " =    1.731
peak=    3.358 closest distance to " CB  THR A 157 " =    1.173
peak=    3.356 closest distance to " O   HOH Z  80 " =    1.593
peak=    3.343 closest distance to " CD1 LEU A 228 " =    2.006
peak=    3.341 closest distance to " O   HOH Z  85 " =    2.200
peak=    3.339 closest distance to " O   HOH Z 368 " =    3.524
peak=    3.338 closest distance to " O   ARG A  56 " =    2.831
peak=    3.334 closest distance to " O   HOH Z 175 " =    2.112
peak=    3.333 closest distance to " O   HOH Z 426 " =    1.541
peak=    3.333 closest distance to " O   LYS A 290 " =    2.396
peak=    3.328 closest distance to " O   HOH Z 435 " =    1.992
peak=    3.325 closest distance to " O   HOH Z 366 " =    2.940
peak=    3.318 closest distance to " OG  SER A  22 " =    2.733
peak=    3.318 closest distance to " CA  THR A 264 " =    0.801
peak=    3.315 closest distance to " O   HOH Z 329 " =    3.979
peak=    3.311 closest distance to " CD1 LEU A 300 " =    1.273
peak=    3.309 closest distance to " O   GLN A 278 " =    1.187
peak=    3.308 closest distance to " CG  GLN A  88 " =    1.036
peak=    3.307 closest distance to " CB  LEU A 143 " =    1.139
peak=    3.305 closest distance to " CD1 ILE A 106 " =    1.055
peak=    3.305 closest distance to " CB  ALA A 295 " =    1.178
peak=    3.304 closest distance to " O   HOH Z 251 " =    1.495
peak=    3.304 closest distance to " CD1 ILE A  33 " =    1.653
peak=    3.299 closest distance to " CA  TYR A  30 " =    1.045
peak=    3.298 closest distance to " O   HOH Z 298 " =    4.745
peak=    3.294 closest distance to " O   HOH Z 337 " =    3.553
peak=    3.292 closest distance to " CA  ALA A  84 " =    1.375
peak=    3.290 closest distance to " O   HOH Z 180 " =    2.093
peak=    3.289 closest distance to " O   HOH Z 132 " =    2.614
peak=    3.283 closest distance to " O   HOH Z 124 " =    1.251
peak=    3.283 closest distance to " O   HOH Z 285 " =    2.942
peak=    3.280 closest distance to " CB  VAL A 268 " =    0.823
peak=    3.278 closest distance to " CG1 VAL A 296 " =    1.209
peak=    3.278 closest distance to " O   HOH Z 189 " =    2.622
peak=    3.277 closest distance to " CB  ILE A  20 " =    1.469
peak=    3.275 closest distance to " CA  VAL A  41 " =    0.806
peak=    3.273 closest distance to " O   HOH Z 302 " =    1.959
peak=    3.273 closest distance to " ND1 HIS A  81 " =    1.701
peak=    3.272 closest distance to " CB  GLN A  88 " =    1.167
peak=    3.271 closest distance to " O   HOH Z 359 " =    3.730
peak=    3.271 closest distance to " NH2 ARG A  79 " =    1.353
peak=    3.267 closest distance to " O   HOH Z 325 " =    2.180
peak=    3.265 closest distance to " CB  GLN A 278 " =    0.844
peak=    3.261 closest distance to " O   HOH Z 282 " =    2.003
peak=    3.261 closest distance to " O   HOH Z  90 " =    2.220
peak=    3.259 closest distance to " CA  ALA A 233 " =    1.278
peak=    3.256 closest distance to " N   ARG A 156 " =    1.335
peak=    3.256 closest distance to " CA  SER A 146 " =    1.725
peak=    3.253 closest distance to " CG1 ILE A  33 " =    1.264
peak=    3.252 closest distance to " CB  GLN A 205 " =    1.183
peak=    3.251 closest distance to " CG1 VAL A 153 " =    0.950
peak=    3.247 closest distance to " N   VAL A 126 " =    1.341
peak=    3.246 closest distance to " O   HOH Z  35 " =    2.437
peak=    3.243 closest distance to " CA  ASP A 140 " =    1.226
peak=    3.241 closest distance to " CG BARG A 275 " =    1.389
peak=    3.236 closest distance to " CG2AVAL A 121 " =    2.399
peak=    3.234 closest distance to " CB  ASN A 215 " =    1.183
peak=    3.233 closest distance to " OG1 THR A 294 " =    1.706
peak=    3.229 closest distance to " CB  SER A 212 " =    1.176
peak=    3.227 closest distance to " OE2 GLU A   2 " =    1.747
peak=    3.226 closest distance to " O   HOH Z 123 " =    2.203
peak=    3.226 closest distance to " O   HOH Z 185 " =    1.801
peak=    3.220 closest distance to " ND2 ASN A 110 " =    1.633
peak=    3.216 closest distance to " O   HOH Z  21 " =    1.709
peak=    3.214 closest distance to " CB  ALA A 248 " =    1.007
peak=    3.214 closest distance to " CE  LYS A  48 " =    1.163
peak=    3.213 closest distance to " CA  THR A 221 " =    0.946
peak=    3.208 closest distance to " CG  LEU A 167 " =    1.224
peak=    3.207 closest distance to " CB  LYS A 290 " =    0.961
peak=    3.207 closest distance to " O   HOH Z 171 " =    2.228
peak=    3.204 closest distance to " O   SER A 164 " =    1.053
peak=    3.203 closest distance to " CB  SER A 216 " =    0.754
peak=    3.201 closest distance to " CG AARG A 275 " =    1.161
peak=    3.191 closest distance to " OG BSER A 134 " =    3.081
peak=    3.186 closest distance to " O   HOH Z 213 " =    1.691
peak=    3.183 closest distance to " OE1 GLU A   2 " =    2.110
peak=    3.181 closest distance to " O   HOH Z 258 " =    1.616
peak=    3.179 closest distance to " O   HOH Z 409 " =    3.340
peak=    3.174 closest distance to " O   HOH Z 345 " =    3.234
peak=    3.173 closest distance to " CA  TYR A 116 " =    1.415
peak=    3.169 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.161 closest distance to " CD1 ILE A 263 " =    1.294
peak=    3.157 closest distance to " CG2 THR A 220 " =    0.846
peak=    3.155 closest distance to " O   HOH Z 227 " =    2.142
peak=    3.154 closest distance to " O   HOH Z 412 " =    2.047
peak=    3.150 closest distance to " CA  VAL A 126 " =    0.913
peak=    3.150 closest distance to " OE2 GLU A  53 " =    1.969
peak=    3.147 closest distance to " CD  ARG A  79 " =    1.991
peak=    3.145 closest distance to " N   ASN A 127 " =    1.269
peak=    3.130 closest distance to " O   HOH Z 425 " =    1.291
peak=    3.123 closest distance to " NZ  LYS A  76 " =    1.492
peak=    3.118 closest distance to " CB  LEU A 255 " =    0.779
peak=    3.116 closest distance to " CG2 VAL A 197 " =    0.993
peak=    3.114 closest distance to " O   HOH Z 256 " =    2.450
peak=    3.113 closest distance to " O   HOH Z  85 " =    1.331
peak=    3.113 closest distance to " CA  LYS A 290 " =    1.250
peak=    3.112 closest distance to " CB  ILE A 120 " =    1.355
peak=    3.111 closest distance to " CA  ASN A 176 " =    1.105
peak=    3.109 closest distance to " O   HOH Z 406 " =    1.503
peak=    3.105 closest distance to " CD2 LEU A 255 " =    1.563
peak=    3.099 closest distance to " O   HOH Z 222 " =    2.507
peak=    3.097 closest distance to " CB  ALA A 248 " =    1.523
peak=    3.088 closest distance to " CZ3 TRP A  85 " =    0.916
peak=    3.081 closest distance to " O   HOH Z  40 " =    2.465
peak=    3.079 closest distance to " CA  MET A 105 " =    0.953
peak=    3.079 closest distance to " CD2 TYR A  30 " =    0.967
peak=    3.077 closest distance to " O   HOH Z 116 " =    1.744
peak=    3.075 closest distance to " O   HOH Z 336 " =    1.746
peak=    3.074 closest distance to " O   HOH Z 420 " =    1.886
peak=    3.053 closest distance to " O   ALA A 158 " =    1.376
peak=    3.039 closest distance to " O   HOH Z 371 " =    3.310
peak=    3.038 closest distance to " O   HOH Z 141 " =    1.577
peak=    3.034 closest distance to " O   HOH Z  47 " =    1.707
peak=    3.033 closest distance to " O   HOH Z 353 " =    2.685
peak=    3.031 closest distance to " CA  SER A  87 " =    1.008
peak=    3.018 closest distance to " O   HOH Z  43 " =    2.894

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.559 - 5.449
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 206
   mapped sites are within: 0.785 - 5.449

peak=   -5.528 closest distance to " CG2 VAL A 230 " =    0.785
peak=   -4.667 closest distance to " CG2BVAL A  41 " =    2.594
peak=   -4.577 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.510 closest distance to " SG  CYS A 254 " =    3.273
peak=   -4.371 closest distance to " O   HOH Z 266 " =    5.105
peak=   -4.331 closest distance to " CB  PRO A 243 " =    2.626
peak=   -4.263 closest distance to " OG BSER A 134 " =    1.212
peak=   -4.254 closest distance to " CD  GLN A  58 " =    1.092
peak=   -4.249 closest distance to " C   HIS A 108 " =    1.214
peak=   -4.230 closest distance to " CG  GLN A 223 " =    2.034
peak=   -4.117 closest distance to " CD1 ILE A 199 " =    2.487
peak=   -4.100 closest distance to " CB  PHE A 192 " =    1.956
peak=   -4.070 closest distance to " CA  VAL A  67 " =    2.768
peak=   -4.047 closest distance to " CG2 VAL A 296 " =    1.185
peak=   -4.036 closest distance to " CB  ALA A 161 " =    2.584
peak=   -4.028 closest distance to " O   PRO A 163 " =    2.121
peak=   -4.012 closest distance to " O   HOH Z 290 " =    1.183
peak=   -3.995 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.957 closest distance to " O   HOH Z 389 " =    1.926
peak=   -3.925 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.906 closest distance to " O   HOH Z 114 " =    3.079
peak=   -3.882 closest distance to " O   HOH Z 231 " =    2.050
peak=   -3.877 closest distance to " CZ3 TRP A 179 " =    1.212
peak=   -3.865 closest distance to " OXT GLY A 302 " =    2.768
peak=   -3.829 closest distance to " CB  ALA A 248 " =    2.157
peak=   -3.819 closest distance to " CB  PRO A 163 " =    2.521
peak=   -3.811 closest distance to " OG  SER A  97 " =    2.249
peak=   -3.808 closest distance to " OD1 ASN A 187 " =    1.698
peak=   -3.806 closest distance to " CG1 VAL A 112 " =    2.764
peak=   -3.793 closest distance to " O   HOH Z 166 " =    1.873
peak=   -3.782 closest distance to " CD1 LEU A 101 " =    2.376
peak=   -3.769 closest distance to " NE2 GLN A  88 " =    1.923
peak=   -3.761 closest distance to " N   ALA A  43 " =    2.485
peak=   -3.749 closest distance to " O   HOH Z 196 " =    2.147
peak=   -3.741 closest distance to " CE2 PHE A 218 " =    2.533
peak=   -3.721 closest distance to " ND2 ASN A  45 " =    1.654
peak=   -3.716 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.701 closest distance to " N   ALA A 226 " =    2.012
peak=   -3.694 closest distance to " N   GLN A  58 " =    1.629
peak=   -3.679 closest distance to " O   HOH Z 211 " =    1.636
peak=   -3.672 closest distance to " O   HOH Z 166 " =    1.494
peak=   -3.655 closest distance to " OD2 ASP A 171 " =    2.317
peak=   -3.653 closest distance to " O   HOH Z  44 " =    2.245
peak=   -3.651 closest distance to " O   HOH Z 185 " =    2.372
peak=   -3.639 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.622 closest distance to " CB  ASP A 132 " =    2.379
peak=   -3.618 closest distance to " CB  PRO A 280 " =    2.166
peak=   -3.608 closest distance to " CG1 VAL A 250 " =    2.742
peak=   -3.608 closest distance to " O   HOH Z 407 " =    3.028
peak=   -3.604 closest distance to " O   HOH Z 394 " =    1.521
peak=   -3.601 closest distance to " CG  ASP A 231 " =    0.800
peak=   -3.589 closest distance to " O   HOH Z 435 " =    2.817
peak=   -3.586 closest distance to " CD1 LEU A 101 " =    2.835
peak=   -3.556 closest distance to " OD1 ASN A 148 " =    1.480
peak=   -3.555 closest distance to " CZ  TYR A 169 " =    1.689
peak=   -3.550 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.547 closest distance to " O   HOH Z  11 " =    1.840
peak=   -3.543 closest distance to " ND2 ASN A  45 " =    1.180
peak=   -3.541 closest distance to " NH2AARG A 275 " =    5.121
peak=   -3.541 closest distance to " N   THR A 235 " =    1.345
peak=   -3.538 closest distance to " N   THR A 157 " =    1.481
peak=   -3.535 closest distance to " CE  MET A 105 " =    2.076
peak=   -3.531 closest distance to " CD  ARG A 139 " =    1.619
peak=   -3.527 closest distance to " N   HIS A 115 " =    2.042
peak=   -3.523 closest distance to " CB  ASP A 132 " =    2.316
peak=   -3.518 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.514 closest distance to " O   MET A  40 " =    2.720
peak=   -3.510 closest distance to " CB  ALA A 248 " =    2.325
peak=   -3.505 closest distance to " CZ  PHE A  59 " =    1.498
peak=   -3.501 closest distance to " C   MET A 188 " =    1.398
peak=   -3.483 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.482 closest distance to " O   HOH Z  52 " =    1.475
peak=   -3.482 closest distance to " O   HOH Z 103 " =    1.768
peak=   -3.481 closest distance to " O   VAL A 189 " =    2.594
peak=   -3.481 closest distance to " CA  GLY A  98 " =    1.910
peak=   -3.479 closest distance to " CG2 ILE A 263 " =    2.295
peak=   -3.477 closest distance to " N   ALA A 248 " =    1.811
peak=   -3.470 closest distance to " CE BMET A  47 " =    1.675
peak=   -3.468 closest distance to " CG  TRP A 266 " =    1.898
peak=   -3.440 closest distance to " CG1 VAL A 230 " =    1.836
peak=   -3.430 closest distance to " NZ  LYS A 119 " =    3.524
peak=   -3.418 closest distance to " CA  GLY A 241 " =    3.057
peak=   -3.412 closest distance to " CG1 VAL A 197 " =    2.221
peak=   -3.407 closest distance to " OG  SER A  62 " =    1.582
peak=   -3.399 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.398 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.394 closest distance to " NH2 ARG A  79 " =    1.968
peak=   -3.389 closest distance to " CB  ALA A 291 " =    2.130
peak=   -3.384 closest distance to " O   HOH Z 353 " =    2.047
peak=   -3.377 closest distance to " O   HOH Z 102 " =    1.596
peak=   -3.375 closest distance to " O   HOH Z 198 " =    2.199
peak=   -3.375 closest distance to " O   HOH Z 313 " =    1.630
peak=   -3.372 closest distance to " C   ASN A 187 " =    1.913
peak=   -3.372 closest distance to " N   SER A 276 " =    1.297
peak=   -3.370 closest distance to " O   HOH Z 262 " =    2.772
peak=   -3.370 closest distance to " C   LEU A 143 " =    1.008
peak=   -3.367 closest distance to " O   HOH Z  13 " =    1.598
peak=   -3.360 closest distance to " O   HOH Z  38 " =    1.676
peak=   -3.359 closest distance to " O   ALA A 161 " =    1.706
peak=   -3.355 closest distance to " CD  LYS A 289 " =    2.444
peak=   -3.354 closest distance to " O   HOH Z 134 " =    2.981
peak=   -3.353 closest distance to " C   ALA A 158 " =    1.276
peak=   -3.351 closest distance to " NE2 GLN A  58 " =    2.877
peak=   -3.350 closest distance to " CB  ALA A  43 " =    2.392
peak=   -3.341 closest distance to " C   ASP A 231 " =    2.471
peak=   -3.339 closest distance to " CE3 TRP A 150 " =    2.032
peak=   -3.338 closest distance to " CG  PHE A 283 " =    2.671
peak=   -3.338 closest distance to " O   GLY A 196 " =    1.123
peak=   -3.335 closest distance to " NE2 GLN A 194 " =    1.787
peak=   -3.333 closest distance to " CB  ASN A  39 " =    2.246
peak=   -3.323 closest distance to " OG BSER A 134 " =    1.673
peak=   -3.321 closest distance to " OG  SER A  26 " =    1.152
peak=   -3.319 closest distance to " O   HOH Z 139 " =    3.168
peak=   -3.317 closest distance to " O   HOH Z 175 " =    4.273
peak=   -3.312 closest distance to " O   HOH Z  43 " =    1.764
peak=   -3.311 closest distance to " O   HOH Z 295 " =    1.589
peak=   -3.306 closest distance to " O   HOH Z 191 " =    5.449
peak=   -3.304 closest distance to " CB  VAL A 296 " =    1.031
peak=   -3.301 closest distance to " CB  ASN A  69 " =    1.150
peak=   -3.298 closest distance to " O   HOH Z 309 " =    2.554
peak=   -3.298 closest distance to " CD1 LEU A 228 " =    2.055
peak=   -3.297 closest distance to " CG  LEU A 228 " =    1.038
peak=   -3.297 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.280 closest distance to " CB  GLN A  11 " =    1.927
peak=   -3.279 closest distance to " OD2 ASP A  50 " =    2.206
peak=   -3.278 closest distance to " O   SER A 271 " =    2.092
peak=   -3.272 closest distance to " OG  SER A  87 " =    1.408
peak=   -3.270 closest distance to " O   SER A  95 " =    1.614
peak=   -3.268 closest distance to " O   HOH Z  47 " =    1.649
peak=   -3.268 closest distance to " O   SER A  22 " =    2.255
peak=   -3.264 closest distance to " O   HOH Z  88 " =    4.485
peak=   -3.264 closest distance to " O   HOH Z 385 " =    2.195
peak=   -3.262 closest distance to " CB  LEU A  83 " =    2.343
peak=   -3.260 closest distance to " O   HOH Z 339 " =    1.763
peak=   -3.255 closest distance to " CB  ASN A 252 " =    1.799
peak=   -3.254 closest distance to " O   HOH Z 313 " =    1.088
peak=   -3.243 closest distance to " CG2 THR A 221 " =    2.069
peak=   -3.239 closest distance to " O   HOH Z 426 " =    1.682
peak=   -3.238 closest distance to " N   ALA A 248 " =    2.210
peak=   -3.238 closest distance to " O   HOH Z  10 " =    1.410
peak=   -3.237 closest distance to " C   GLN A 205 " =    1.929
peak=   -3.234 closest distance to " O   ALA A  51 " =    1.326
peak=   -3.226 closest distance to " CG  ARG A 269 " =    2.282
peak=   -3.225 closest distance to " O   PHE A 218 " =    1.701
peak=   -3.223 closest distance to " O   HOH Z 369 " =    2.236
peak=   -3.220 closest distance to " O   SER A 210 " =    1.879
peak=   -3.218 closest distance to " O   LEU A 167 " =    1.532
peak=   -3.217 closest distance to " O   GLY A  75 " =    1.887
peak=   -3.214 closest distance to " N   GLN A  77 " =    1.605
peak=   -3.214 closest distance to " N   ASP A 171 " =    2.255
peak=   -3.211 closest distance to " C   SER A 206 " =    1.519
peak=   -3.210 closest distance to " O   HOH Z 139 " =    5.159
peak=   -3.205 closest distance to " CG  PRO A 163 " =    2.652
peak=   -3.203 closest distance to " CG1 VAL A 296 " =    1.318
peak=   -3.202 closest distance to " O   HOH Z  73 " =    2.246
peak=   -3.202 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.200 closest distance to " CD2 TYR A 293 " =    2.040
peak=   -3.199 closest distance to " SG BCYS A 201 " =    2.098
peak=   -3.196 closest distance to " CB  ALA A  64 " =    2.634
peak=   -3.196 closest distance to " O   HOH Z 281 " =    2.782
peak=   -3.196 closest distance to " O   HOH Z 123 " =    2.397
peak=   -3.195 closest distance to " N   ASN A  60 " =    1.278
peak=   -3.186 closest distance to " NE2 GLN A 278 " =    1.900
peak=   -3.185 closest distance to " OXT GLY A 302 " =    3.516
peak=   -3.184 closest distance to " OE2 GLU A 152 " =    1.278
peak=   -3.184 closest distance to " O   PRO A 198 " =    1.333
peak=   -3.183 closest distance to " O   HOH Z 165 " =    1.941
peak=   -3.182 closest distance to " O   SER A 276 " =    1.634
peak=   -3.173 closest distance to " O   LYS A 117 " =    1.655
peak=   -3.172 closest distance to " O   ALA A  10 " =    1.740
peak=   -3.171 closest distance to " ND2 ASN A 252 " =    1.877
peak=   -3.165 closest distance to " O   HOH Z 372 " =    2.315
peak=   -3.163 closest distance to " CB  TYR A  15 " =    2.196
peak=   -3.160 closest distance to " CA  GLY A 133 " =    1.984
peak=   -3.157 closest distance to " OG ASER A 134 " =    1.196
peak=   -3.155 closest distance to " CG1 VAL A  67 " =    3.157
peak=   -3.153 closest distance to " CB  ASP A 132 " =    2.265
peak=   -3.151 closest distance to " O   GLN A 240 " =    2.135
peak=   -3.150 closest distance to " O   HOH Z 421 " =    3.119
peak=   -3.149 closest distance to " CA  PRO A 243 " =    2.235
peak=   -3.142 closest distance to " CD1 TYR A 247 " =    2.708
peak=   -3.141 closest distance to " ND2 ASN A 249 " =    2.389
peak=   -3.139 closest distance to " CE1 HIS A  81 " =    1.453
peak=   -3.135 closest distance to " O   HOH Z 371 " =    1.944
peak=   -3.134 closest distance to " O   HOH Z   6 " =    1.614
peak=   -3.128 closest distance to " O   HOH Z 389 " =    4.858
peak=   -3.116 closest distance to " N   SER A   3 " =    2.016
peak=   -3.115 closest distance to " O   HOH Z 311 " =    3.767
peak=   -3.106 closest distance to " O   HOH Z 131 " =    4.053
peak=   -3.101 closest distance to " N   VAL A 230 " =    1.148
peak=   -3.100 closest distance to " OH  TYR A 214 " =    1.237
peak=   -3.099 closest distance to " O   HOH Z 234 " =    4.051
peak=   -3.087 closest distance to " O   HOH Z  41 " =    2.308
peak=   -3.087 closest distance to " CG  GLU A 152 " =    1.524
peak=   -3.079 closest distance to " O   HOH Z 407 " =    3.145
peak=   -3.077 closest distance to " CD2 TYR A 247 " =    2.362
peak=   -3.067 closest distance to " OG  SER A 206 " =    1.681
peak=   -3.066 closest distance to " OD1 ASP A 171 " =    1.639
peak=   -3.057 closest distance to " O   HOH Z 193 " =    1.837
peak=   -3.041 closest distance to " O   HOH Z 350 " =    1.782
peak=   -3.039 closest distance to " O   HOH Z 210 " =    1.193
peak=   -3.031 closest distance to " C   ASP A 270 " =    1.212
peak=   -2.963 closest distance to " NE2 GLN A  58 " =    2.562

================= 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    :  0.4046 0.3927   6.186483e+00   6.155170e+00
   1_bss:  0.3971 0.3834   6.180967e+00   6.137604e+00
   1_xyz:  0.2798 0.2982   5.908896e+00   5.956593e+00
   1_adp:  0.1990 0.2255   5.587647e+00   5.710407e+00
   1_occ:  0.1984 0.2251   5.585417e+00   5.710062e+00
   2_bss:  0.1922 0.2186   5.582889e+00   5.703470e+00
   2_xyz:  0.1433 0.1743   5.319615e+00   5.489407e+00
   2_adp:  0.1347 0.1677   5.266205e+00   5.446600e+00
   2_occ:  0.1346 0.1677   5.266022e+00   5.446704e+00
   3_bss:  0.1344 0.1680   5.266516e+00   5.446990e+00
   3_xyz:  0.1163 0.1565   5.160366e+00   5.388511e+00
   3_adp:  0.1115 0.1538   5.133737e+00   5.372754e+00
   3_occ:  0.1114 0.1538   5.133375e+00   5.372395e+00
   4_bss:  0.1114 0.1537   5.132555e+00   5.371554e+00
   4_xyz:  0.1131 0.1546   5.143449e+00   5.377445e+00
   4_adp:  0.1144 0.1544   5.148256e+00   5.376330e+00
   4_occ:  0.1143 0.1544   5.147920e+00   5.376429e+00
   5_bss:  0.1143 0.1544   5.147954e+00   5.376474e+00
   5_xyz:  0.1089 0.1537   5.119724e+00   5.368334e+00
   5_adp:  0.1075 0.1544   5.117330e+00   5.373090e+00
   5_occ:  0.1075 0.1544   5.117210e+00   5.372996e+00
   5_bss:  0.1075 0.1544   5.117133e+00   5.372899e+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:  0.349  18.499   7.378   8.254   8.260   0.000   0.000   0.000
   1_xyz:  0.349  18.499   7.378   8.254   8.260   0.000   0.000   0.000
   1_adp:  0.349  18.499   7.378   8.254   8.260   0.000   0.000   0.000
   1_occ:  0.349  18.499   7.378   8.254   8.260   0.000   0.000   0.000
   2_bss:  0.356  50.000   3.968   4.432   5.289   0.000   0.000   0.000
   2_xyz:  0.356  50.000   3.968   4.432   5.289   0.000   0.000   0.000
   2_adp:  0.356  50.000   3.968   4.432   5.289   0.000   0.000   0.000
   2_occ:  0.356  50.000   3.968   4.432   5.289   0.000   0.000   0.000
   3_bss:  0.333  39.858   3.231   3.770   4.729   0.000   0.000   0.000
   3_xyz:  0.333  39.858   3.231   3.770   4.729   0.000   0.000   0.000
   3_adp:  0.333  39.858   3.231   3.770   4.729   0.000   0.000   0.000
   3_occ:  0.333  39.858   3.231   3.770   4.729   0.000   0.000   0.000
   4_bss:  0.325  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   4_xyz:  0.325  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   4_adp:  0.325  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   4_occ:  0.325  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   5_bss:  0.326  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   5_xyz:  0.326  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   5_adp:  0.326  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   5_occ:  0.326  42.040   3.274   3.768   4.784   0.000   0.000   0.000
   5_bss:  0.323  46.030  -0.669  -0.186   0.855   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.671 0.6255  0.6857    43093.325
   1_bss:  41.784 0.6215  0.8676    40715.083
   1_xyz:  31.236 0.7432  1.0042    23617.219
   1_adp:  21.349 0.8496  1.0876    12554.642
   1_occ:  21.315 0.8500  1.0874    12517.097
   2_bss:  21.092 0.8522  0.9626    12305.187
   2_xyz:  16.119 0.8973  0.9924     7792.745
   2_adp:  15.137 0.9059  1.0005     7213.121
   2_occ:  15.145 0.9059  1.0004     7207.331
   3_bss:  15.159 0.9058  0.9755     7209.708
   3_xyz:  13.953 0.9154  0.9789     6358.795
   3_adp:  13.676 0.9176  0.9784     6130.550
   3_occ:  13.666 0.9177  0.9784     6125.238
   4_bss:  13.649 0.9178  0.9796     6109.789
   4_xyz:  13.662 0.9180  0.9791     6182.691
   4_adp:  13.590 0.9187  0.9785     6170.131
   4_occ:  13.590 0.9187  0.9784     6171.764
   5_bss:  13.591 0.9187  0.9784     6172.743
   5_xyz:  13.443 0.9198  0.9794     6094.449
   5_adp:  13.568 0.9188  0.9767     6131.494
   5_occ:  13.565 0.9188  0.9766     6131.148
   5_bss:  13.564 0.9188  0.9783     6128.950
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3657e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3657e+01
   1_xyz:   1.399  0.010  0.097 17.702  0.006  4.121   1.0304e-01
   1_adp:   1.399  0.010  0.097 17.702  0.006  4.121   1.0304e-01
   1_occ:   1.399  0.010  0.097 17.702  0.006  4.121   1.0304e-01
   2_bss:   1.399  0.010  0.097 17.702  0.006  4.121   1.0304e-01
   2_xyz:   0.916  0.006  0.072 15.892  0.003  4.121   5.4381e-02
   2_adp:   0.916  0.006  0.072 15.892  0.003  4.121   5.4381e-02
   2_occ:   0.916  0.006  0.072 15.892  0.003  4.121   5.4381e-02
   3_bss:   0.916  0.006  0.072 15.892  0.003  4.121   5.4381e-02
   3_xyz:   1.091  0.008  0.090 15.829  0.004  4.128   7.0396e-02
   3_adp:   1.091  0.008  0.090 15.829  0.004  4.128   7.0396e-02
   3_occ:   1.091  0.008  0.090 15.829  0.004  4.128   7.0396e-02
   4_bss:   1.091  0.008  0.090 15.829  0.004  4.128   7.0396e-02
   4_xyz:   0.922  0.006  0.076 15.401  0.003  4.116   5.4149e-02
   4_adp:   0.922  0.006  0.076 15.401  0.003  4.116   5.4149e-02
   4_occ:   0.922  0.006  0.076 15.401  0.003  4.116   5.4149e-02
   5_bss:   0.922  0.006  0.076 15.401  0.003  4.116   5.4149e-02
   5_xyz:   1.112  0.009  0.093 15.733  0.004  4.118   7.4136e-02
   5_adp:   1.112  0.009  0.093 15.733  0.004  4.118   7.4136e-02
   5_occ:   1.112  0.009  0.093 15.733  0.004  4.118   7.4136e-02
   5_bss:   1.112  0.009  0.093 15.733  0.004  4.118   7.4136e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9570e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9570e+00
   1_xyz:  10.936  0.117  0.431 87.891  0.036  2.251   7.4412e-02
   1_adp:  10.936  0.117  0.431 87.891  0.036  2.251   7.4412e-02
   1_occ:  10.936  0.117  0.431 87.891  0.036  2.251   7.4412e-02
   2_bss:  10.936  0.117  0.431 87.891  0.036  2.251   7.4412e-02
   2_xyz:   6.794  0.048  0.394 84.460  0.032  2.327   3.4728e-02
   2_adp:   6.794  0.048  0.394 84.460  0.032  2.327   3.4728e-02
   2_occ:   6.794  0.048  0.394 84.460  0.032  2.327   3.4728e-02
   3_bss:   6.794  0.048  0.394 84.460  0.032  2.327   3.4728e-02
   3_xyz:   6.845  0.050  0.675 83.852  0.039  2.303   5.2006e-02
   3_adp:   6.845  0.050  0.675 83.852  0.039  2.303   5.2006e-02
   3_occ:   6.845  0.050  0.675 83.852  0.039  2.303   5.2006e-02
   4_bss:   6.845  0.050  0.675 83.852  0.039  2.303   5.2006e-02
   4_xyz:   6.211  0.042  0.491 83.028  0.037  2.393   3.0464e-02
   4_adp:   6.211  0.042  0.491 83.028  0.037  2.393   3.0464e-02
   4_occ:   6.211  0.042  0.491 83.028  0.037  2.393   3.0464e-02
   5_bss:   6.211  0.042  0.491 83.028  0.037  2.393   3.0464e-02
   5_xyz:   7.085  0.050  0.700 83.408  0.040  2.251   5.7555e-02
   5_adp:   7.085  0.050  0.700 83.408  0.040  2.251   5.7555e-02
   5_occ:   7.085  0.050  0.700 83.408  0.040  2.251   5.7555e-02
   5_bss:   7.085  0.050  0.700 83.408  0.040  2.251   5.7555e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  47.67   0.00   9.72  43.08   0.00   6.65  47.67   0.00  26.43
   1_occ:  47.67   0.00   9.72  43.08   0.00   6.65  47.67   0.00  26.43
   2_bss:  47.67   0.00   9.72  43.08   0.00   6.65  47.67   0.00  26.43
   2_xyz:  47.67   0.00   9.72  43.08   0.00   6.65  47.67   0.00  26.43
   2_adp:  76.93   0.00  10.12  76.93   0.00   6.71  48.63   0.96  28.66
   2_occ:  76.93   0.00  10.12  76.93   0.00   6.71  48.63   0.96  28.66
   3_bss:  76.93   0.00  10.12  76.93   0.00   6.71  48.63   0.96  28.66
   3_xyz:  76.93   0.00  10.12  76.93   0.00   6.71  48.63   0.96  28.66
   3_adp:  67.67   0.00  10.94  67.67   0.00   6.93  65.21   0.17  32.79
   3_occ:  67.67   0.00  10.94  67.67   0.00   6.93  65.21   0.17  32.79
   4_bss:  67.67   0.00  10.94  67.67   0.00   6.93  65.21   0.17  32.79
   4_xyz:  67.67   0.00  10.94  67.67   0.00   6.93  65.21   0.17  32.79
   4_adp:  68.81   0.00  10.51  68.81   0.00   6.79  62.16   0.76  30.75
   4_occ:  68.81   0.00  10.51  68.81   0.00   6.79  62.16   0.76  30.75
   5_bss:  68.81   0.00  10.51  68.81   0.00   6.79  62.16   0.76  30.75
   5_xyz:  68.81   0.00  10.51  68.81   0.00   6.79  62.16   0.76  30.75
   5_adp:  71.55   0.00  10.73  71.55   0.00   6.82  63.63   0.43  32.00
   5_occ:  71.55   0.00  10.73  71.55   0.00   6.82  63.63   0.43  32.00
   5_bss:  75.54   3.99  14.72  75.54   3.99  10.81  67.62   4.42  35.99
------------------------------------------------------------------------
 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:    1.156    0.019    0.394
   1_adp:    1.156    0.019    0.394
   1_occ:    1.156    0.019    0.394
   2_bss:    1.156    0.019    0.394
   2_xyz:    1.421    0.037    0.453
   2_adp:    1.421    0.037    0.453
   2_occ:    1.421    0.037    0.453
   3_bss:    1.421    0.037    0.453
   3_xyz:    1.325    0.033    0.478
   3_adp:    1.325    0.033    0.478
   3_occ:    1.325    0.033    0.478
   4_bss:    1.325    0.033    0.478
   4_xyz:    1.424    0.054    0.482
   4_adp:    1.424    0.054    0.482
   4_occ:    1.424    0.054    0.482
   5_bss:    1.424    0.054    0.482
   5_xyz:    1.362    0.052    0.488
   5_adp:    1.362    0.052    0.488
   5_occ:    1.362    0.052    0.488
   5_bss:    1.362    0.052    0.488
------------------------------------------------------------------------

CPU time actual refinement: 331.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/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/trial/run_544/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_544/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.09 
  Macro-tasks:
    bulk solvent and scale       = 42.27  
    individual site refinement   = 137.95 
    weights calculation          = 32.45  
    collect and process          = 6.62   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 219.44 
  Micro-tasks:
    mask                            = 1.16   
    f_calc                          = 100.13 
    alpha_beta                      = 8.00   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.18 
    fmodel                         = 7.52   
    r_factors                      = 0.28   
    phase_errors                   = 11.08  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 241.73 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.600 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    656 calls, 99.81 s
gradients_fft:          600 calls, 98.28 s

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

# Date 2008-01-16 Time 01:50:46 PST -0800 (1200477046.01 s)
Start R-work = 0.4046, R-free = 0.3927 (no bulk solvent and anisotropic scale)
Final R-work = 0.1257, R-free = 0.1703 (no bulk solvent and anisotropic scale)

Start R-work = 0.3971, R-free = 0.3834
Final R-work = 0.1075, R-free = 0.1544