# Date 2008-01-16 Time 00:27:24 PST -0800 (1200472044.38 s)
#phil __OFF__

Command line arguments: "../24.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25286
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 24

-------------------------------------------------------------------------------
  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: (68.4938, 46.2261, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6593 1.95058
Completeness in resolution range: 0.967693
Completeness with d_max=infinity: 0.964643

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6593
                             d_min =   1.9506

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: (68.4938, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6593 1.95058
Completeness in resolution range: 0.967693
Completeness with d_max=infinity: 0.964643

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6597 -  4.1731 [2132/2159]  1917   215  10.1%
  bin  2:  4.1731 -  3.3250 [2036/2052]  1834   202   9.9%
  bin  3:  3.3250 -  2.9085 [2030/2049]  1827   203  10.0%
  bin  4:  2.9085 -  2.6442 [1984/2014]  1782   202  10.2%
  bin  5:  2.6442 -  2.4557 [1993/2012]  1797   196   9.8%
  bin  6:  2.4557 -  2.3115 [1975/2000]  1780   195   9.9%
  bin  7:  2.3115 -  2.1961 [1970/2004]  1773   197  10.0%
  bin  8:  2.1961 -  2.1008 [1941/1972]  1743   198  10.2%
  bin  9:  2.1008 -  2.0201 [1947/1988]  1753   194  10.0%
  bin 10:  2.0201 -  1.9506 [1581/1993]  1424   157   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/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:
        0.93 -     1.72: 10
        1.72 -     2.52: 99
        2.52 -     3.31: 3917
        3.31 -     4.11: 9736
        4.11 -     4.90: 15474
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.929 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.935 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.488 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.604 3.040 -x+1/2,-y+1,z+1/2
  " OE1 GLN A  55 " - " CB  ASN A 285 "  1.609 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 29231 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_24/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/model_refine_001.geo

CPU time processing inputs: 11.17


============================ 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 = 68.49375 46.22605 85.09415 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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5075   r_free= 0.5009   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.299540                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1383  153 0.4184 0.4210      6.6228      6.6536|
|  2:  4.6542 -  3.7139 0.99   1320  150 0.4466 0.4330      6.8389        6.85|
|  3:  3.7139 -  3.2503 0.99   1315  144 0.4823 0.4636      6.7251      6.7801|
|  4:  3.2503 -  2.9558 0.99   1293  139 0.4935 0.4572      6.5658      6.4947|
|  5:  2.9558 -  2.7454 0.99   1285  143 0.5412 0.5398      6.4003      6.4164|
|  6:  2.7454 -  2.5845 0.99   1277  145 0.5443 0.5625       6.306      6.2356|
|  7:  2.5845 -  2.4557 0.99   1284  144 0.5360 0.5004      6.2658      6.2001|
|  8:  2.4557 -  2.3492 0.98   1278  139 0.5522 0.5449      6.2029      6.2045|
|  9:  2.3492 -  2.2591 0.98   1245  141 0.5314 0.5649      6.1178      6.1656|
| 10:  2.2591 -  2.1814 0.98   1269  139 0.5440 0.5188      6.1333      6.1141|
| 11:  2.1814 -  2.1134 0.99   1266  143 0.5410 0.5810      6.0481        6.11|
| 12:  2.1134 -  2.0532 0.97   1244  136 0.5386 0.5297      5.9865       6.038|
| 13:  2.0532 -  1.9992 0.99   1282  140 0.5574 0.5013      5.9044      5.8506|
| 14:  1.9992 -  1.9506 0.71    889  103 0.5481 0.5198      5.8693      5.7716|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1383   153  0.62  40.89   0.79     0.67      94238.48|
|  2:  4.6542 -  3.7139  1320   150  0.63  40.95   0.86     0.72     135213.51|
|  3:  3.7139 -  3.2503  1315   144  0.52  50.33   0.85     0.66     141015.07|
|  4:  3.2503 -  2.9558  1293   139  0.44  56.22   0.80     0.56     119985.00|
|  5:  2.9558 -  2.7454  1285   143  0.34  64.11   0.72     0.43      94149.04|
|  6:  2.7454 -  2.5845  1277   145  0.30  67.39   0.71     0.36      81057.30|
|  7:  2.5845 -  2.4557  1284   144  0.22  73.24   0.74     0.27      76766.27|
|  8:  2.4557 -  2.3492  1278   139  0.20  75.06   0.73     0.25      70426.08|
|  9:  2.3492 -  2.2591  1245   141  0.18  76.49   0.72     0.23      66082.28|
| 10:  2.2591 -  2.1814  1269   139  0.23  73.12   0.78     0.28      57111.75|
| 11:  2.1814 -  2.1134  1266   143  0.19  75.78   0.76     0.25      54393.92|
| 12:  2.1134 -  2.0532  1244   136  0.19  75.82   0.76     0.24      49529.67|
| 13:  2.0532 -  1.9992  1282   140  0.16  78.49   0.75     0.21      43229.29|
| 14:  1.9992 -  1.9506   889   103  0.20  75.17   0.74     0.23      33369.30|
|alpha:            min =        0.21 max =            0.72 mean =         0.39|
|beta:             min =    33369.30 max =       141015.07 mean =     81268.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.99 mean =        65.44|
|phase err.(test): min =        0.00 max =           89.97 mean =        65.72|
|-----------------------------------------------------------------------------|

============================== 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 = 24.152980             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.766   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.445389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.430   (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 |  0.942 -  1.338:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.338 -  1.734:       14 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.734 -  2.130:      100 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.130 -  2.525:      487 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.525 -  2.921:     1281 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.921 -  3.317:     2490 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.317 -  3.713:     4057 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.713 -  4.108:     5368 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.108 -  4.504:     7024 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.504 -  4.900:     8394 |
|-----------------------------------------------------------------------------|
|-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 |       52.530 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  0.942 |       3.628 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    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 = 11.208)------------------------------------------|
|    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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5105   r_free= 0.5038   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.300331                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4977   r_free= 0.4903   ksol= 0.38   Bsol= 0.00   scale= 0.975    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,8.75,7.53,0.00,0.00,0.00); trace/3= 7.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.292591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.281627             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.733   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.985291              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.041   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4977      final r-factor (work) = 0.4324          |
| start r-factor (free) = 0.4903      final r-factor (free) = 0.4521          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.0852 = 18.28 * 0.50 * 6.2965 + 1.00 * 52.5296                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.1741 = 18.28 * 0.50 * 6.2366 + 1.00 * 0.1661                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4324      final r-factor (work) = 0.3894          |
| start r-factor (free) = 0.4521      final r-factor (free) = 0.4393          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3959 = 1.99 * 1.00 * 6.2366 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2940 = 1.99 * 1.00 * 6.1805 + 1.00 * 0.0240                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.36   15.50    None  None   None       |
|    all(noH): 2823   0      0.00    84.36   15.50    None  None   None       |
|    Sol.    : 438    0      0.00    84.36   25.94    None  None   None       |
|    Mac.    : 2385   0      0.00    77.46   13.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.436: 1019   |   5:    42.182 -  50.618:   82        |
|      1:     8.436 -  16.873:  780   |   6:    50.618 -  59.054:   38        |
|      2:    16.873 -  25.309:  477   |   7:    59.054 -  67.490:   20        |
|      3:    25.309 -  33.745:  262   |   8:    67.490 -  75.927:    5        |
|      4:    33.745 -  42.182:  136   |   9:    75.927 -  84.363:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3894 r_free = 0.4393             target_work(ml) = 6.166         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3890 r_free = 0.4381             target_work(ml) = 6.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3890   r_free= 0.4381   ksol= 0.38   Bsol= 0.00   scale= 1.107    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.15,8.75,7.53,0.00,0.00,0.00); trace/3= 7.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.164605                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3872   r_free= 0.4327   ksol= 0.34   Bsol= 20.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.29,5.09,5.31,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.163866                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.627668              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.709   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.742610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.561  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3872      final r-factor (work) = 0.3173          |
| start r-factor (free) = 0.4327      final r-factor (free) = 0.3769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7199 = 7.63 * 0.50 * 6.1759 + 1.00 * 0.1661                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3087 = 7.63 * 0.50 * 6.0873 + 1.00 * 0.0927                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3173      final r-factor (work) = 0.2995          |
| start r-factor (free) = 0.3769      final r-factor (free) = 0.3599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5534 = 0.74 * 1.00 * 6.0873 + 1.00 * 0.0329                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5005 = 0.74 * 1.00 * 5.9949 + 1.00 * 0.0486                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.25   15.00    None  None   None       |
|    all(noH): 2823   0      0.00    86.25   15.00    None  None   None       |
|    Sol.    : 438    0      0.00    86.25   30.63    None  None   None       |
|    Mac.    : 2385   0      0.00    84.56   12.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.625: 1127   |   5:    43.123 -  51.747:   62        |
|      1:     8.625 -  17.249:  810   |   6:    51.747 -  60.372:   32        |
|      2:    17.249 -  25.874:  413   |   7:    60.372 -  68.996:    9        |
|      3:    25.874 -  34.498:  208   |   8:    68.996 -  77.621:    8        |
|      4:    34.498 -  43.123:  151   |   9:    77.621 -  86.246:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2995 r_free = 0.3599             target_work(ml) = 5.976         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2991 r_free = 0.3602             target_work(ml) = 5.976         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2991   r_free= 0.3602   ksol= 0.34   Bsol= 20.00   scale= 1.089   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.29,5.09,5.31,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.975557                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2963   r_free= 0.3593   ksol= 0.34   Bsol= 37.50   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,2.55,2.94,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.973335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.133526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.587  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.283194              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.099   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2963      final r-factor (work) = 0.2280          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2874          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4808 = 4.13 * 0.50 * 5.9940 + 1.00 * 0.0927                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2014 = 4.13 * 0.50 * 5.8690 + 1.00 * 0.0717                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2280      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.2874      final r-factor (free) = 0.2696          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5496 = 1.28 * 1.00 * 5.8690 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3292 = 1.28 * 1.00 * 5.6987 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.61  15.92    None  None   None       |
|    all(noH): 2823   0      0.00    112.61  15.92    None  None   None       |
|    Sol.    : 438    0      2.36    90.12   40.09    None  None   None       |
|    Mac.    : 2385   0      0.00    112.61  11.48    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 -  11.261: 1566   |   5:    56.303 -  67.563:   76        |
|      1:    11.261 -  22.521:  650   |   6:    67.563 -  78.824:   25        |
|      2:    22.521 -  33.782:  223   |   7:    78.824 -  90.084:   12        |
|      3:    33.782 -  45.042:  156   |   8:    90.084 - 101.345:    2        |
|      4:    45.042 -  56.303:  111   |   9:   101.345 - 112.605:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2035 r_free = 0.2696             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2029 r_free = 0.2690             target_work(ml) = 5.668         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2029   r_free= 0.2690   ksol= 0.34   Bsol= 37.50   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.90,2.55,2.94,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.668336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2028   r_free= 0.2685   ksol= 0.33   Bsol= 33.39   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.90,1.43,2.10,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.666951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.338293              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.345   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.145028              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.840  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2028      final r-factor (work) = 0.1654          |
| start r-factor (free) = 0.2685      final r-factor (free) = 0.2247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7363 = 2.34 * 0.50 * 5.7004 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5795 = 2.34 * 0.50 * 5.5821 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1654      final r-factor (work) = 0.1614          |
| start r-factor (free) = 0.2247      final r-factor (free) = 0.2087          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8260 = 0.15 * 1.00 * 5.5821 + 1.00 * 0.0165                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8370 = 0.15 * 1.00 * 5.4814 + 1.00 * 0.0420                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.03  14.36    None  None   None       |
|    all(noH): 2823   0      0.00    101.03  14.36    None  None   None       |
|    Sol.    : 438    0      3.73    83.52   36.00    None  None   None       |
|    Mac.    : 2385   0      0.00    101.03  10.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.103: 1572   |   5:    50.514 -  60.617:   57        |
|      1:    10.103 -  20.206:  690   |   6:    60.617 -  70.720:   19        |
|      2:    20.206 -  30.308:  194   |   7:    70.720 -  80.822:    6        |
|      3:    30.308 -  40.411:  159   |   8:    80.822 -  90.925:    5        |
|      4:    40.411 -  50.514:  120   |   9:    90.925 - 101.028:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1614 r_free = 0.2087             target_work(ml) = 5.443         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1610 r_free = 0.2082             target_work(ml) = 5.441         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1610   r_free= 0.2082   ksol= 0.33   Bsol= 33.39   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.90,1.43,2.10,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.440933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1610   r_free= 0.2076   ksol= 0.33   Bsol= 33.39   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,0.67,1.54,0.00,0.00,0.00); trace/3= 0.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.440648                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.629345              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.178  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.755891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.291   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1610      final r-factor (work) = 0.1373          |
| start r-factor (free) = 0.2076      final r-factor (free) = 0.1777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5204 = 1.63 * 0.50 * 5.4834 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4240 = 1.63 * 0.50 * 5.3646 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1373      final r-factor (work) = 0.1338          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1772          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.7997 = 2.76 * 1.00 * 5.3646 + 1.00 * 0.0155                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.5861 = 2.76 * 1.00 * 5.2784 + 1.00 * 0.0393                              |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.16  14.37    None  None   None       |
|    all(noH): 2823   0      0.00    101.16  14.37    None  None   None       |
|    Sol.    : 438    0      2.14    83.86   36.60    None  None   None       |
|    Mac.    : 2385   0      0.00    101.16  10.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.116: 1593   |   5:    50.581 -  60.697:   59        |
|      1:    10.116 -  20.232:  670   |   6:    60.697 -  70.813:   21        |
|      2:    20.232 -  30.349:  187   |   7:    70.813 -  80.930:    6        |
|      3:    30.349 -  40.465:  158   |   8:    80.930 -  91.046:    5        |
|      4:    40.465 -  50.581:  123   |   9:    91.046 - 101.162:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1338 r_free = 0.1772             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1336 r_free = 0.1771             target_work(ml) = 5.276         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1771   ksol= 0.33   Bsol= 33.39   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.07,0.67,1.54,0.00,0.00,0.00); trace/3= 0.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.276373                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1383  153 0.1111 0.1364      5.4793      5.6014|
|  2:  4.6542 -  3.7139 0.99   1320  150 0.1014 0.1345      5.5752      5.8174|
|  3:  3.7139 -  3.2503 0.99   1315  144 0.1307 0.1536      5.6491      5.8456|
|  4:  3.2503 -  2.9558 0.99   1293  139 0.1455 0.2101      5.5948      5.8357|
|  5:  2.9558 -  2.7454 0.99   1285  143 0.1550 0.1791      5.4599      5.5903|
|  6:  2.7454 -  2.5845 0.99   1277  145 0.1484 0.1968      5.3488      5.4899|
|  7:  2.5845 -  2.4557 0.99   1284  144 0.1465 0.1944      5.2762      5.4973|
|  8:  2.4557 -  2.3492 0.98   1278  139 0.1460 0.1959      5.2437      5.4743|
|  9:  2.3492 -  2.2591 0.98   1245  141 0.1435 0.2036       5.168      5.3762|
| 10:  2.2591 -  2.1814 0.98   1269  139 0.1356 0.1937      5.1071      5.3057|
| 11:  2.1814 -  2.1134 0.99   1266  143 0.1356 0.1943      5.0615      5.3936|
| 12:  2.1134 -  2.0532 0.97   1244  136 0.1377 0.1806      5.0265      5.2965|
| 13:  2.0532 -  1.9992 0.99   1282  140 0.1335 0.1954      4.9141      5.1749|
| 14:  1.9992 -  1.9506 0.71    889  103 0.1173 0.1898      4.7519      5.0118|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1383   153  0.93  10.32   0.99     0.97       8671.71|
|  2:  4.6542 -  3.7139  1320   150  0.94   9.45   1.04     1.02      11095.89|
|  3:  3.7139 -  3.2503  1315   144  0.92  13.71   1.06     1.05      13686.01|
|  4:  3.2503 -  2.9558  1293   139  0.91  15.37   1.02     1.02      12711.57|
|  5:  2.9558 -  2.7454  1285   143  0.88  17.97   1.01     0.97      10146.75|
|  6:  2.7454 -  2.5845  1277   145  0.89  17.63   0.99     0.96       8515.39|
|  7:  2.5845 -  2.4557  1284   144  0.88  17.95   1.00     0.97       7498.77|
|  8:  2.4557 -  2.3492  1278   139  0.89  17.53   1.02     1.00       7086.36|
|  9:  2.3492 -  2.2591  1245   141  0.89  17.69   1.02     0.99       6294.23|
| 10:  2.2591 -  2.1814  1269   139  0.88  18.01   1.02     0.97       5684.33|
| 11:  2.1814 -  2.1134  1266   143  0.88  18.32   1.03     0.99       5463.20|
| 12:  2.1134 -  2.0532  1244   136  0.88  18.41   1.04     1.02       5237.78|
| 13:  2.0532 -  1.9992  1282   140  0.89  17.90   1.04     1.02       4148.27|
| 14:  1.9992 -  1.9506   889   103  0.90  15.75   1.02     0.98       2862.99|
|alpha:            min =        0.96 max =            1.05 mean =         0.99|
|beta:             min =     2862.99 max =        13686.01 mean =      7941.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.09|
|phase err.(test): min =        0.00 max =           88.77 mean =        15.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1769   ksol= 0.33   Bsol= 34.02   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.14,0.80,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275030                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1769   ksol= 0.33   Bsol= 34.02   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,-0.14,0.80,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.275030                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1383  153 0.1098 0.1358      5.4651      5.5896|
|  2:  4.6542 -  3.7139 0.99   1320  150 0.1021 0.1356      5.5799      5.8326|
|  3:  3.7139 -  3.2503 0.99   1315  144 0.1307 0.1533      5.6523      5.8416|
|  4:  3.2503 -  2.9558 0.99   1293  139 0.1456 0.2097      5.5935      5.8329|
|  5:  2.9558 -  2.7454 0.99   1285  143 0.1551 0.1770      5.4597      5.5833|
|  6:  2.7454 -  2.5845 0.99   1277  145 0.1482 0.1970      5.3475      5.4917|
|  7:  2.5845 -  2.4557 0.99   1284  144 0.1461 0.1933      5.2738      5.4938|
|  8:  2.4557 -  2.3492 0.98   1278  139 0.1458 0.1958      5.2418      5.4727|
|  9:  2.3492 -  2.2591 0.98   1245  141 0.1435 0.2035      5.1664      5.3771|
| 10:  2.2591 -  2.1814 0.98   1269  139 0.1351 0.1925      5.1053      5.3037|
| 11:  2.1814 -  2.1134 0.99   1266  143 0.1354 0.1943      5.0611      5.3937|
| 12:  2.1134 -  2.0532 0.97   1244  136 0.1376 0.1807      5.0258      5.2962|
| 13:  2.0532 -  1.9992 0.99   1282  140 0.1333 0.1951      4.9138      5.1726|
| 14:  1.9992 -  1.9506 0.71    889  103 0.1172 0.1901      4.7526      5.0139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1383   153  0.93  10.13   0.99     0.97       8410.11|
|  2:  4.6542 -  3.7139  1320   150  0.94   9.48   1.04     1.02      11084.75|
|  3:  3.7139 -  3.2503  1315   144  0.92  13.74   1.06     1.04      13828.21|
|  4:  3.2503 -  2.9558  1293   139  0.91  15.26   1.02     1.01      12613.39|
|  5:  2.9558 -  2.7454  1285   143  0.88  17.88   1.01     0.96      10057.23|
|  6:  2.7454 -  2.5845  1277   145  0.89  17.60   0.99     0.95       8487.68|
|  7:  2.5845 -  2.4557  1284   144  0.88  17.92   1.00     0.96       7476.70|
|  8:  2.4557 -  2.3492  1278   139  0.89  17.49   1.01     0.99       7051.25|
|  9:  2.3492 -  2.2591  1245   141  0.89  17.64   1.01     0.98       6263.99|
| 10:  2.2591 -  2.1814  1269   139  0.88  18.00   1.01     0.97       5670.80|
| 11:  2.1814 -  2.1134  1266   143  0.88  18.31   1.02     0.99       5461.57|
| 12:  2.1134 -  2.0532  1244   136  0.88  18.40   1.03     1.01       5235.19|
| 13:  2.0532 -  1.9992  1282   140  0.89  17.90   1.03     1.01       4148.21|
| 14:  1.9992 -  1.9506   889   103  0.90  15.80   1.01     0.97       2875.33|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2875.33 max =        13828.21 mean =      7908.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.85 mean =        16.05|
|phase err.(test): min =        0.00 max =           89.72 mean =        15.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.208)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.63    101.80  15.00    None  None   None       |
|    all(noH): 2823   0      0.63    101.80  15.00    None  None   None       |
|    Sol.    : 438    0      2.78    84.50   37.23    None  None   None       |
|    Mac.    : 2385   0      0.63    101.80  10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.634 -  10.750: 1593   |   5:    51.215 -  61.331:   59        |
|      1:    10.750 -  20.866:  670   |   6:    61.331 -  71.447:   21        |
|      2:    20.866 -  30.982:  187   |   7:    71.447 -  81.563:    6        |
|      3:    30.982 -  41.099:  158   |   8:    81.563 -  91.680:    5        |
|      4:    41.099 -  51.215:  123   |   9:    91.680 - 101.796:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 350         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 5.573
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 350
   mapped sites are within: 0.726 - 5.573

peak=   10.189 closest distance to " CB  VAL A 296 " =    1.550
peak=   10.090 closest distance to " CB  VAL A 230 " =    1.419
peak=    9.351 closest distance to " O   HOH Z 178 " =    1.481
peak=    6.899 closest distance to " CG  ARG A 138 " =    1.231
peak=    6.824 closest distance to " OD2 ASP A  50 " =    0.726
peak=    6.446 closest distance to " O   HOH Z 130 " =    1.642
peak=    6.436 closest distance to " CD1AILE A 234 " =    1.096
peak=    6.330 closest distance to " CD2 LEU A   5 " =    1.374
peak=    6.295 closest distance to " O   HOH Z 236 " =    1.814
peak=    5.828 closest distance to " O   HOH Z 142 " =    2.022
peak=    5.601 closest distance to " O   HOH Z  45 " =    1.035
peak=    5.510 closest distance to " O   HOH Z 193 " =    1.896
peak=    5.470 closest distance to " O   HOH Z 169 " =    0.862
peak=    5.448 closest distance to " O   HOH Z  65 " =    1.313
peak=    5.382 closest distance to " O   HOH Z  78 " =    1.625
peak=    5.359 closest distance to " O   HOH Z 124 " =    1.716
peak=    5.337 closest distance to " O   HOH Z 278 " =    1.434
peak=    5.321 closest distance to " CB  ARG A 275 " =    1.160
peak=    5.114 closest distance to " O   HOH Z   9 " =    1.295
peak=    5.111 closest distance to " O   HOH Z  28 " =    1.535
peak=    5.066 closest distance to " NH1 ARG A 138 " =    1.015
peak=    5.052 closest distance to " O   HOH Z 375 " =    1.376
peak=    5.029 closest distance to " O   HOH Z 126 " =    1.846
peak=    4.993 closest distance to " O   HOH Z  69 " =    1.514
peak=    4.845 closest distance to " NE2 GLN A  11 " =    1.161
peak=    4.832 closest distance to " O   HOH Z 424 " =    1.192
peak=    4.778 closest distance to " CB  SER A   3 " =    1.242
peak=    4.774 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.643 closest distance to " CB  GLN A 278 " =    0.846
peak=    4.635 closest distance to " O   HOH Z 369 " =    2.164
peak=    4.624 closest distance to " O   HOH Z 291 " =    1.613
peak=    4.618 closest distance to " NE2 GLN A  55 " =    1.481
peak=    4.601 closest distance to " O   HOH Z 178 " =    2.100
peak=    4.567 closest distance to " O   HOH Z 423 " =    1.587
peak=    4.566 closest distance to " NH2 ARG A  56 " =    1.887
peak=    4.562 closest distance to " O   HOH Z 344 " =    1.518
peak=    4.553 closest distance to " NE1 TRP A 274 " =    1.027
peak=    4.522 closest distance to " O   HOH Z 272 " =    1.805
peak=    4.509 closest distance to " O   HOH Z 148 " =    1.828
peak=    4.509 closest distance to " O   HOH Z 199 " =    1.212
peak=    4.508 closest distance to " CG2 ILE A 234 " =    0.963
peak=    4.505 closest distance to " O   PRO A 198 " =    1.333
peak=    4.445 closest distance to " O   HOH Z 385 " =    0.746
peak=    4.422 closest distance to " CB  VAL A 230 " =    1.136
peak=    4.372 closest distance to " O   HOH Z 414 " =    1.743
peak=    4.349 closest distance to " O   HOH Z 263 " =    1.573
peak=    4.338 closest distance to " CG  LEU A   5 " =    1.281
peak=    4.319 closest distance to " CB  VAL A 202 " =    1.647
peak=    4.314 closest distance to " O   HOH Z 146 " =    1.720
peak=    4.271 closest distance to " O   HOH Z 410 " =    1.338
peak=    4.263 closest distance to " CB  GLN A 223 " =    1.623
peak=    4.258 closest distance to " O   HOH Z  11 " =    1.930
peak=    4.256 closest distance to " O   HOH Z  59 " =    1.712
peak=    4.251 closest distance to " O   HOH Z   7 " =    1.564
peak=    4.250 closest distance to " O   HOH Z 419 " =    1.828
peak=    4.250 closest distance to " O   HOH Z  97 " =    1.650
peak=    4.248 closest distance to " CD2 LEU A 228 " =    1.238
peak=    4.247 closest distance to " O   HOH Z 238 " =    1.052
peak=    4.229 closest distance to " CG  GLN A  11 " =    2.198
peak=    4.223 closest distance to " NE BARG A 275 " =    1.221
peak=    4.222 closest distance to " O   HOH Z 406 " =    1.513
peak=    4.213 closest distance to " NH2BARG A 145 " =    1.571
peak=    4.209 closest distance to " O   HOH Z 249 " =    1.311
peak=    4.204 closest distance to " CG  PRO A 198 " =    1.322
peak=    4.194 closest distance to " O   HOH Z 423 " =    1.661
peak=    4.186 closest distance to " O   HOH Z 234 " =    1.930
peak=    4.182 closest distance to " O   HOH Z 132 " =    1.184
peak=    4.172 closest distance to " CD  ARG A 138 " =    0.888
peak=    4.156 closest distance to " CE AMET A  47 " =    1.050
peak=    4.150 closest distance to " O   HOH Z 276 " =    1.500
peak=    4.145 closest distance to " O   HOH Z  85 " =    1.413
peak=    4.140 closest distance to " NH1 ARG A  14 " =    0.998
peak=    4.134 closest distance to " O   HOH Z 427 " =    2.249
peak=    4.124 closest distance to " O   HOH Z 380 " =    1.839
peak=    4.110 closest distance to " O   SER A  87 " =    2.311
peak=    4.108 closest distance to " O   HOH Z 381 " =    1.222
peak=    4.107 closest distance to " O   HOH Z 123 " =    1.363
peak=    4.084 closest distance to " O   HOH Z 188 " =    1.009
peak=    4.081 closest distance to " O   HOH Z 422 " =    0.801
peak=    4.034 closest distance to " O   HOH Z 244 " =    1.809
peak=    4.029 closest distance to " NZ  LYS A 117 " =    3.275
peak=    4.024 closest distance to " O   HOH Z 222 " =    1.387
peak=    3.999 closest distance to " O   HOH Z 179 " =    0.774
peak=    3.991 closest distance to " CA  ASN A 284 " =    0.983
peak=    3.983 closest distance to " O   HOH Z  43 " =    1.433
peak=    3.976 closest distance to " CB  PRO A  54 " =    1.071
peak=    3.975 closest distance to " CG  PRO A 243 " =    1.162
peak=    3.936 closest distance to " CG  PRO A  54 " =    1.337
peak=    3.933 closest distance to " O   HOH Z 316 " =    2.604
peak=    3.910 closest distance to " O   HOH Z 234 " =    3.331
peak=    3.902 closest distance to " O   HOH Z 130 " =    1.909
peak=    3.889 closest distance to " O   HOH Z 137 " =    1.563
peak=    3.882 closest distance to " O   HOH Z  59 " =    2.005
peak=    3.875 closest distance to " O   HOH Z 371 " =    1.686
peak=    3.872 closest distance to " O   HOH Z  69 " =    2.228
peak=    3.869 closest distance to " O   HOH Z 250 " =    2.246
peak=    3.867 closest distance to " O   HOH Z  80 " =    1.458
peak=    3.865 closest distance to " O   HOH Z 233 " =    1.417
peak=    3.864 closest distance to " O   HOH Z  88 " =    2.684
peak=    3.862 closest distance to " O   HOH Z 222 " =    2.062
peak=    3.862 closest distance to " O   HOH Z  44 " =    1.956
peak=    3.850 closest distance to " O   HOH Z 213 " =    1.752
peak=    3.835 closest distance to " O   HOH Z 260 " =    1.504
peak=    3.824 closest distance to " OG ASER A 134 " =    1.685
peak=    3.819 closest distance to " O   HOH Z  47 " =    1.565
peak=    3.818 closest distance to " O   HOH Z  24 " =    1.681
peak=    3.817 closest distance to " O   HOH Z 192 " =    1.497
peak=    3.815 closest distance to " O   HOH Z  95 " =    1.688
peak=    3.813 closest distance to " O   HOH Z  51 " =    1.455
peak=    3.803 closest distance to " O   HOH Z 427 " =    1.133
peak=    3.794 closest distance to " OE1 GLU A  44 " =    1.088
peak=    3.792 closest distance to " O   HOH Z 214 " =    1.280
peak=    3.785 closest distance to " CB  TRP A 179 " =    1.094
peak=    3.777 closest distance to " O   HOH Z 390 " =    1.065
peak=    3.771 closest distance to " CA  PRO A 163 " =    0.926
peak=    3.757 closest distance to " CA  ARG A 275 " =    0.980
peak=    3.755 closest distance to " O   HOH Z  28 " =    2.096
peak=    3.749 closest distance to " CA  ILE A 234 " =    0.904
peak=    3.747 closest distance to " CB  ALA A   1 " =    1.058
peak=    3.743 closest distance to " O   HOH Z  97 " =    1.858
peak=    3.736 closest distance to " O   HOH Z 347 " =    1.048
peak=    3.730 closest distance to " CG2 VAL A 257 " =    0.926
peak=    3.728 closest distance to " NH1AARG A 275 " =    1.095
peak=    3.720 closest distance to " O   HOH Z 366 " =    2.010
peak=    3.714 closest distance to " O   HOH Z 293 " =    1.467
peak=    3.714 closest distance to " O   HOH Z 425 " =    2.120
peak=    3.705 closest distance to " OD1 ASP A 286 " =    1.019
peak=    3.697 closest distance to " CD  GLN A 194 " =    1.404
peak=    3.693 closest distance to " O   HOH Z 147 " =    1.646
peak=    3.678 closest distance to " O   HOH Z 334 " =    1.576
peak=    3.665 closest distance to " O   HOH Z 176 " =    1.808
peak=    3.658 closest distance to " NH2BARG A 190 " =    1.557
peak=    3.648 closest distance to " O   HOH Z 130 " =    1.921
peak=    3.640 closest distance to " CB  PHE A 130 " =    0.911
peak=    3.637 closest distance to " C   ALA A 299 " =    0.993
peak=    3.637 closest distance to " N   GLN A 278 " =    0.994
peak=    3.637 closest distance to " O   HOH Z  56 " =    1.883
peak=    3.632 closest distance to " CA  ALA A  21 " =    1.171
peak=    3.624 closest distance to " O   HOH Z 153 " =    3.277
peak=    3.621 closest distance to " O   HOH Z 120 " =    0.948
peak=    3.619 closest distance to " SD BMET A  47 " =    1.401
peak=    3.613 closest distance to " O   HOH Z 352 " =    1.364
peak=    3.610 closest distance to " CB  ASN A  69 " =    1.583
peak=    3.600 closest distance to " O   HOH Z 259 " =    2.085
peak=    3.600 closest distance to " CZ AARG A 102 " =    1.692
peak=    3.598 closest distance to " CE BMET A  47 " =    1.470
peak=    3.590 closest distance to " O   HOH Z 100 " =    1.172
peak=    3.588 closest distance to " O   HOH Z 425 " =    1.457
peak=    3.584 closest distance to " O   HOH Z 303 " =    1.734
peak=    3.581 closest distance to " CB  ASN A 142 " =    1.089
peak=    3.578 closest distance to " O   HOH Z 424 " =    2.165
peak=    3.577 closest distance to " CG  LEU A 228 " =    1.251
peak=    3.576 closest distance to " CE1 PHE A  38 " =    1.015
peak=    3.571 closest distance to " CB  ASN A 148 " =    1.287
peak=    3.571 closest distance to " NE2 GLN A  58 " =    5.573
peak=    3.568 closest distance to " CB  TYR A  30 " =    1.694
peak=    3.568 closest distance to " CB  PRO A  90 " =    1.185
peak=    3.567 closest distance to " NH1AARG A 145 " =    0.748
peak=    3.566 closest distance to " O   HOH Z 245 " =    1.418
peak=    3.563 closest distance to " O   HOH Z 145 " =    1.878
peak=    3.562 closest distance to " CD1 LEU A   5 " =    1.847
peak=    3.560 closest distance to " O   HOH Z   4 " =    1.437
peak=    3.559 closest distance to " CB  ALA A 248 " =    1.474
peak=    3.557 closest distance to " CA  TYR A  30 " =    0.956
peak=    3.556 closest distance to " NZ  LYS A  48 " =    1.957
peak=    3.556 closest distance to " O   HOH Z 364 " =    1.814
peak=    3.555 closest distance to " CB  GLU A 277 " =    1.075
peak=    3.551 closest distance to " O   HOH Z 366 " =    2.526
peak=    3.548 closest distance to " O   HOH Z 267 " =    2.021
peak=    3.545 closest distance to " OG1 THR A 246 " =    1.223
peak=    3.545 closest distance to " CG  ARG A  66 " =    1.120
peak=    3.539 closest distance to " O   HOH Z 344 " =    2.620
peak=    3.535 closest distance to " CB  GLN A 183 " =    1.174
peak=    3.532 closest distance to " O   HOH Z  35 " =    2.077
peak=    3.532 closest distance to " O   HOH Z 126 " =    1.475
peak=    3.519 closest distance to " O   HOH Z 118 " =    2.001
peak=    3.518 closest distance to " O   HOH Z 261 " =    2.217
peak=    3.514 closest distance to " CB BVAL A  41 " =    1.024
peak=    3.507 closest distance to " O   HOH Z 422 " =    2.179
peak=    3.502 closest distance to " O   HOH Z 185 " =    1.233
peak=    3.499 closest distance to " OD2 ASP A 286 " =    2.257
peak=    3.497 closest distance to " O   HOH Z 119 " =    1.369
peak=    3.493 closest distance to " O   HOH Z 368 " =    1.978
peak=    3.492 closest distance to " CG1AVAL A 121 " =    0.981
peak=    3.488 closest distance to " O   HOH Z 289 " =    1.554
peak=    3.487 closest distance to " O   HOH Z 189 " =    2.342
peak=    3.483 closest distance to " CB  LEU A 255 " =    0.952
peak=    3.482 closest distance to " NH1BARG A 145 " =    1.596
peak=    3.481 closest distance to " O   HOH Z 412 " =    1.594
peak=    3.479 closest distance to " O   HOH Z 326 " =    2.037
peak=    3.479 closest distance to " O   HOH Z 305 " =    3.124
peak=    3.473 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.472 closest distance to " CB  ALA A 233 " =    1.198
peak=    3.468 closest distance to " CA  PHE A 283 " =    1.129
peak=    3.467 closest distance to " O   HOH Z 143 " =    1.615
peak=    3.460 closest distance to " O   HOH Z 112 " =    1.377
peak=    3.460 closest distance to " O   HOH Z 356 " =    1.580
peak=    3.459 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.457 closest distance to " CG  LYS A 166 " =    1.426
peak=    3.451 closest distance to " O   HOH Z 223 " =    1.091
peak=    3.450 closest distance to " O   HOH Z 130 " =    2.422
peak=    3.445 closest distance to " CA  ASN A 127 " =    1.086
peak=    3.439 closest distance to " O   HOH Z 128 " =    1.930
peak=    3.436 closest distance to " CA  SER A 210 " =    1.551
peak=    3.434 closest distance to " O   HOH Z 404 " =    1.576
peak=    3.428 closest distance to " CB  ASP A 200 " =    0.932
peak=    3.428 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.422 closest distance to " CG2 THR A 221 " =    1.264
peak=    3.421 closest distance to " O   HOH Z 280 " =    1.537
peak=    3.416 closest distance to " NE2 GLN A  73 " =    1.915
peak=    3.414 closest distance to " O  BHOH Z  74 " =    1.175
peak=    3.400 closest distance to " CB  ARG A 102 " =    0.811
peak=    3.398 closest distance to " O   HOH Z 343 " =    2.993
peak=    3.398 closest distance to " O   HOH Z 203 " =    1.504
peak=    3.398 closest distance to " O   HOH Z 367 " =    3.859
peak=    3.395 closest distance to " O   HOH Z 128 " =    2.030
peak=    3.392 closest distance to " O   HOH Z 298 " =    1.753
peak=    3.391 closest distance to " O   HOH Z 196 " =    1.434
peak=    3.391 closest distance to " O   HOH Z 303 " =    2.237
peak=    3.389 closest distance to " CG2 ILE A  20 " =    1.198
peak=    3.389 closest distance to " CB  THR A  31 " =    1.488
peak=    3.388 closest distance to " CG  LYS A  76 " =    1.454
peak=    3.386 closest distance to " CB  ASN A 215 " =    1.233
peak=    3.375 closest distance to " O   HOH Z  71 " =    1.557
peak=    3.375 closest distance to " O   HOH Z 193 " =    1.911
peak=    3.373 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.369 closest distance to " O   HOH Z 134 " =    1.357
peak=    3.362 closest distance to " O   HOH Z 113 " =    1.962
peak=    3.361 closest distance to " O   HOH Z 118 " =    1.780
peak=    3.361 closest distance to " O   HOH Z  92 " =    1.198
peak=    3.360 closest distance to " N   ASN A 148 " =    1.068
peak=    3.354 closest distance to " CB  ASN A 148 " =    1.818
peak=    3.353 closest distance to " CG  LEU A 281 " =    1.068
peak=    3.353 closest distance to " CA  GLN A 194 " =    0.978
peak=    3.349 closest distance to " CB  SER A  26 " =    1.532
peak=    3.349 closest distance to " CE1 PHE A  61 " =    1.140
peak=    3.348 closest distance to " O   HOH Z 337 " =    1.762
peak=    3.347 closest distance to " CG1 VAL A 153 " =    0.937
peak=    3.345 closest distance to " O   HOH Z 358 " =    1.340
peak=    3.345 closest distance to " O   HOH Z 156 " =    2.701
peak=    3.342 closest distance to " CB  ASN A 110 " =    1.065
peak=    3.339 closest distance to " CB  GLU A 128 " =    1.095
peak=    3.336 closest distance to " CB  GLN A  88 " =    1.449
peak=    3.335 closest distance to " CA  ARG A 195 " =    1.372
peak=    3.328 closest distance to " O   HOH Z 402 " =    1.436
peak=    3.324 closest distance to " CG2 ILE A 120 " =    1.387
peak=    3.317 closest distance to " OG  SER A  62 " =    2.887
peak=    3.315 closest distance to " O   HOH Z 357 " =    1.717
peak=    3.304 closest distance to " O   HOH Z 411 " =    4.055
peak=    3.301 closest distance to " CA  ALA A  51 " =    1.087
peak=    3.301 closest distance to " O   HOH Z 227 " =    2.029
peak=    3.297 closest distance to " O   HOH Z 109 " =    2.085
peak=    3.293 closest distance to " CD1 LEU A 228 " =    1.615
peak=    3.293 closest distance to " SD  MET A  40 " =    1.075
peak=    3.292 closest distance to " CB  SER A  62 " =    1.103
peak=    3.291 closest distance to " CB  ALA A   9 " =    1.556
peak=    3.290 closest distance to " CG  GLN A  88 " =    1.038
peak=    3.284 closest distance to " N   GLU A 277 " =    0.981
peak=    3.279 closest distance to " O   HOH Z   8 " =    1.668
peak=    3.279 closest distance to " O   HOH Z 388 " =    1.056
peak=    3.277 closest distance to " CB  ALA A 114 " =    1.443
peak=    3.276 closest distance to " O   HOH Z  61 " =    1.416
peak=    3.275 closest distance to " O   HOH Z  35 " =    1.443
peak=    3.274 closest distance to " O   HOH Z 279 " =    0.975
peak=    3.274 closest distance to " CA  ASN A 217 " =    1.014
peak=    3.273 closest distance to " N   ALA A   1 " =    3.325
peak=    3.271 closest distance to " O   HOH Z  39 " =    1.454
peak=    3.269 closest distance to " O   GLN A  58 " =    1.412
peak=    3.267 closest distance to " CA  PRO A  90 " =    1.042
peak=    3.266 closest distance to " O   HOH Z 374 " =    2.277
peak=    3.258 closest distance to " O   HOH Z 261 " =    1.653
peak=    3.258 closest distance to " O   HOH Z 388 " =    1.712
peak=    3.257 closest distance to " O   HOH Z  37 " =    1.210
peak=    3.256 closest distance to " ND1 HIS A  81 " =    1.383
peak=    3.246 closest distance to " CB  SER A  63 " =    1.093
peak=    3.245 closest distance to " O   HOH Z 257 " =    1.324
peak=    3.244 closest distance to " CB  ARG A  79 " =    1.503
peak=    3.243 closest distance to " CB  SER A 276 " =    1.329
peak=    3.242 closest distance to " O   HOH Z 261 " =    2.262
peak=    3.240 closest distance to " ND1 HIS A  81 " =    1.089
peak=    3.236 closest distance to " O   ASP A 124 " =    1.247
peak=    3.234 closest distance to " CB  PHE A 204 " =    0.997
peak=    3.233 closest distance to " CG  LYS A 119 " =    1.008
peak=    3.232 closest distance to " O   HOH Z 418 " =    2.108
peak=    3.231 closest distance to " O   HOH Z 300 " =    2.177
peak=    3.231 closest distance to " O   HOH Z 251 " =    1.731
peak=    3.227 closest distance to " NH1BARG A 190 " =    2.010
peak=    3.224 closest distance to " N   GLU A   2 " =    1.372
peak=    3.224 closest distance to " O   HOH Z 248 " =    2.101
peak=    3.223 closest distance to " O   HOH Z  24 " =    1.550
peak=    3.219 closest distance to " O   HOH Z 281 " =    1.955
peak=    3.217 closest distance to " O   HOH Z 108 " =    1.147
peak=    3.216 closest distance to " O   HOH Z   6 " =    2.156
peak=    3.215 closest distance to " CD  LYS A 119 " =    1.623
peak=    3.211 closest distance to " CB  GLU A 175 " =    1.028
peak=    3.203 closest distance to " O   HOH Z 212 " =    1.568
peak=    3.202 closest distance to " O   HOH Z 158 " =    3.078
peak=    3.202 closest distance to " CB  ALA A  84 " =    1.599
peak=    3.200 closest distance to " O   HOH Z  51 " =    1.662
peak=    3.196 closest distance to " O   HOH Z 223 " =    1.758
peak=    3.191 closest distance to " O   HOH Z 153 " =    1.577
peak=    3.187 closest distance to " O   HOH Z 311 " =    1.375
peak=    3.187 closest distance to " O   HOH Z   6 " =    1.359
peak=    3.186 closest distance to " O   SER A 164 " =    1.288
peak=    3.185 closest distance to " O   HOH Z 250 " =    1.442
peak=    3.181 closest distance to " CA  GLY A  91 " =    1.522
peak=    3.178 closest distance to " O   HOH Z   9 " =    1.962
peak=    3.172 closest distance to " CA  LYS A 117 " =    1.136
peak=    3.171 closest distance to " O   TRP A 274 " =    0.898
peak=    3.169 closest distance to " OE1 GLN A  58 " =    3.886
peak=    3.168 closest distance to " O   ARG A 195 " =    1.414
peak=    3.166 closest distance to " O   HOH Z 426 " =    1.078
peak=    3.164 closest distance to " NH2AARG A 190 " =    1.835
peak=    3.162 closest distance to " O   HOH Z  41 " =    2.396
peak=    3.162 closest distance to " O   HOH Z 112 " =    2.334
peak=    3.159 closest distance to " O   HOH Z 435 " =    2.083
peak=    3.159 closest distance to " CB  GLU A 152 " =    1.319
peak=    3.153 closest distance to " N   TYR A  15 " =    1.145
peak=    3.146 closest distance to " CG2 THR A 220 " =    0.926
peak=    3.145 closest distance to " O   HOH Z 287 " =    1.492
peak=    3.144 closest distance to " CB  ASN A 187 " =    1.050
peak=    3.141 closest distance to " O   HOH Z 411 " =    1.984
peak=    3.140 closest distance to " CB  THR A  52 " =    1.183
peak=    3.140 closest distance to " O   HOH Z 365 " =    5.496
peak=    3.139 closest distance to " O   HOH Z 272 " =    2.132
peak=    3.138 closest distance to " NH1AARG A 145 " =    1.126
peak=    3.130 closest distance to " O   HOH Z 433 " =    2.073
peak=    3.129 closest distance to " CG1BVAL A  72 " =    1.271
peak=    3.126 closest distance to " CB  ARG A 138 " =    0.934
peak=    3.119 closest distance to " CD2 LEU A  25 " =    1.193
peak=    3.118 closest distance to " O   HOH Z 389 " =    1.483
peak=    3.117 closest distance to " CD2 LEU A 297 " =    1.055
peak=    3.117 closest distance to " CZ AARG A 275 " =    3.245
peak=    3.116 closest distance to " O   PHE A  59 " =    2.744
peak=    3.115 closest distance to " O   HOH Z   1 " =    1.592
peak=    3.113 closest distance to " CB  TRP A 266 " =    1.168
peak=    3.109 closest distance to " CG  ARG A  36 " =    1.019
peak=    3.100 closest distance to " O   HOH Z 365 " =    1.608
peak=    3.092 closest distance to " O   HOH Z 279 " =    2.614
peak=    3.090 closest distance to " CB  VAL A 126 " =    1.242
peak=    3.086 closest distance to " CB  HIS A 108 " =    0.889
peak=    3.076 closest distance to " O   HOH Z 183 " =    1.843
peak=    3.035 closest distance to " CG  LYS A  76 " =    0.966
peak=    3.033 closest distance to " CB  ASN A  39 " =    0.898

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 5.245
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 193
   mapped sites are within: 0.715 - 5.245

peak=   -4.942 closest distance to " O   HOH Z  69 " =    1.095
peak=   -4.793 closest distance to " CD  ARG A 138 " =    1.132
peak=   -4.358 closest distance to " O   SER A 135 " =    1.656
peak=   -4.330 closest distance to " C   HIS A 108 " =    1.232
peak=   -4.306 closest distance to " CA  VAL A  67 " =    2.801
peak=   -4.281 closest distance to " O   PRO A 198 " =    1.049
peak=   -4.168 closest distance to " O   HOH Z 429 " =    1.960
peak=   -4.130 closest distance to " NH2 ARG A  79 " =    1.998
peak=   -4.125 closest distance to " O   HOH Z 290 " =    0.821
peak=   -4.097 closest distance to " C   ASN A 285 " =    1.901
peak=   -4.060 closest distance to " O   HOH Z 385 " =    1.321
peak=   -4.045 closest distance to " O   HOH Z 377 " =    0.876
peak=   -4.016 closest distance to " OG BSER A 134 " =    1.236
peak=   -4.009 closest distance to " CG  ARG A 138 " =    0.935
peak=   -3.999 closest distance to " N   THR A  52 " =    1.715
peak=   -3.995 closest distance to " CG  PHE A 283 " =    2.434
peak=   -3.988 closest distance to " OG  SER A   3 " =    1.155
peak=   -3.946 closest distance to " O   HOH Z 419 " =    0.715
peak=   -3.879 closest distance to " O   HOH Z 125 " =    3.259
peak=   -3.876 closest distance to " CD  GLU A 277 " =    0.867
peak=   -3.876 closest distance to " O   HOH Z  56 " =    1.678
peak=   -3.870 closest distance to " CE3 TRP A 274 " =    2.162
peak=   -3.860 closest distance to " O   SER A  22 " =    2.284
peak=   -3.844 closest distance to " O   ALA A 161 " =    1.587
peak=   -3.843 closest distance to " OD2 ASP A  50 " =    1.548
peak=   -3.843 closest distance to " O   HOH Z  24 " =    1.034
peak=   -3.818 closest distance to " CE2 TYR A  30 " =    2.966
peak=   -3.809 closest distance to " CD1 LEU A 255 " =    2.742
peak=   -3.763 closest distance to " O   HOH Z 164 " =    5.245
peak=   -3.725 closest distance to " CG BARG A 275 " =    0.823
peak=   -3.709 closest distance to " O   HOH Z 234 " =    3.913
peak=   -3.698 closest distance to " CE2 PHE A 218 " =    2.550
peak=   -3.691 closest distance to " N   HIS A 115 " =    2.058
peak=   -3.676 closest distance to " O   HOH Z 111 " =    4.448
peak=   -3.662 closest distance to " CD  GLN A  88 " =    1.047
peak=   -3.648 closest distance to " O   HOH Z 123 " =    0.905
peak=   -3.644 closest distance to " OG ASER A 134 " =    1.250
peak=   -3.640 closest distance to " CG  PRO A 198 " =    1.657
peak=   -3.617 closest distance to " O   GLU A 152 " =    1.576
peak=   -3.615 closest distance to " O   HOH Z 423 " =    2.454
peak=   -3.614 closest distance to " OD2 ASP A  50 " =    1.508
peak=   -3.591 closest distance to " O   GLY A 118 " =    1.199
peak=   -3.583 closest distance to " O   HOH Z  79 " =    1.590
peak=   -3.571 closest distance to " OD1 ASN A  39 " =    1.913
peak=   -3.570 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.567 closest distance to " CD1 LEU A 101 " =    2.219
peak=   -3.553 closest distance to " O   HOH Z 427 " =    1.660
peak=   -3.552 closest distance to " CG  GLN A  58 " =    0.889
peak=   -3.549 closest distance to " O   HOH Z 203 " =    1.734
peak=   -3.546 closest distance to " O   HOH Z 414 " =    2.651
peak=   -3.543 closest distance to " O   LYS A 117 " =    1.429
peak=   -3.537 closest distance to " CG  ARG A 219 " =    2.083
peak=   -3.523 closest distance to " O   HOH Z 235 " =    0.988
peak=   -3.520 closest distance to " CA  GLY A  23 " =    1.769
peak=   -3.514 closest distance to " N   GLN A  58 " =    1.115
peak=   -3.506 closest distance to " CD  ARG A 156 " =    1.974
peak=   -3.506 closest distance to " CD  ARG A  14 " =    2.707
peak=   -3.501 closest distance to " N   GLN A 122 " =    1.318
peak=   -3.489 closest distance to " O   HOH Z 103 " =    1.569
peak=   -3.478 closest distance to " CG  GLU A 152 " =    2.392
peak=   -3.466 closest distance to " O   HOH Z 130 " =    1.759
peak=   -3.461 closest distance to " O   HOH Z 140 " =    1.762
peak=   -3.451 closest distance to " O   HOH Z 392 " =    2.484
peak=   -3.450 closest distance to " O   HOH Z 307 " =    1.971
peak=   -3.448 closest distance to " C   LEU A 143 " =    1.048
peak=   -3.442 closest distance to " O   MET A  40 " =    2.833
peak=   -3.442 closest distance to " O   HOH Z 388 " =    2.097
peak=   -3.427 closest distance to " CA  GLY A 133 " =    1.898
peak=   -3.417 closest distance to " O   HOH Z 266 " =    4.581
peak=   -3.411 closest distance to " CB  ALA A 248 " =    1.867
peak=   -3.411 closest distance to " O   HOH Z 359 " =    1.789
peak=   -3.409 closest distance to " CA  SER A 210 " =    1.265
peak=   -3.406 closest distance to " CD  LYS A 289 " =    2.549
peak=   -3.405 closest distance to " CB  GLN A  11 " =    1.921
peak=   -3.403 closest distance to " CZ  PHE A 130 " =    0.826
peak=   -3.396 closest distance to " O   HOH Z 147 " =    1.231
peak=   -3.394 closest distance to " O   HOH Z   9 " =    1.476
peak=   -3.393 closest distance to " O   ASP A 107 " =    1.322
peak=   -3.389 closest distance to " O   HOH Z 368 " =    2.652
peak=   -3.388 closest distance to " CD1 TRP A 179 " =    1.064
peak=   -3.383 closest distance to " CD2 LEU A 237 " =    2.466
peak=   -3.382 closest distance to " OG BSER A  99 " =    1.182
peak=   -3.381 closest distance to " CZ  PHE A  59 " =    1.552
peak=   -3.378 closest distance to " O   HOH Z 407 " =    2.228
peak=   -3.377 closest distance to " O   HOH Z  98 " =    1.783
peak=   -3.373 closest distance to " O   HOH Z 179 " =    1.334
peak=   -3.369 closest distance to " O   HOH Z 365 " =    1.688
peak=   -3.368 closest distance to " O   HOH Z  88 " =    1.897
peak=   -3.366 closest distance to " N   GLN A  58 " =    2.170
peak=   -3.361 closest distance to " O   SER A 245 " =    1.270
peak=   -3.358 closest distance to " O   HOH Z 336 " =    2.508
peak=   -3.357 closest distance to " OG  SER A 245 " =    1.228
peak=   -3.355 closest distance to " O   HOH Z 100 " =    1.084
peak=   -3.337 closest distance to " CD1 TYR A 169 " =    2.410
peak=   -3.333 closest distance to " O   HOH Z 404 " =    1.510
peak=   -3.332 closest distance to " O   HOH Z 372 " =    1.175
peak=   -3.332 closest distance to " CE1 TYR A 247 " =    2.418
peak=   -3.329 closest distance to " O   ALA A  51 " =    1.194
peak=   -3.328 closest distance to " CD1 PHE A  61 " =    2.905
peak=   -3.324 closest distance to " NE2 GLN A  58 " =    1.945
peak=   -3.323 closest distance to " CA  GLY A 203 " =    2.253
peak=   -3.317 closest distance to " O   HOH Z 113 " =    0.755
peak=   -3.316 closest distance to " CG  HIS A 108 " =    0.971
peak=   -3.316 closest distance to " CB  PHE A  59 " =    2.015
peak=   -3.313 closest distance to " CB  TRP A 274 " =    2.715
peak=   -3.313 closest distance to " O   HOH Z 220 " =    2.007
peak=   -3.307 closest distance to " O   HOH Z 131 " =    3.852
peak=   -3.297 closest distance to " O   HOH Z 184 " =    0.717
peak=   -3.294 closest distance to " OH  TYR A 214 " =    0.978
peak=   -3.293 closest distance to " N   ALA A 226 " =    1.881
peak=   -3.288 closest distance to " O   HOH Z 342 " =    2.123
peak=   -3.284 closest distance to " O   HOH Z 437 " =    1.900
peak=   -3.283 closest distance to " OE2 GLU A 152 " =    1.196
peak=   -3.283 closest distance to " O   HOH Z 308 " =    1.640
peak=   -3.279 closest distance to " OG  SER A 206 " =    1.444
peak=   -3.274 closest distance to " ND2 ASN A  39 " =    1.408
peak=   -3.269 closest distance to " C   ALA A 158 " =    1.149
peak=   -3.266 closest distance to " N   GLN A  77 " =    1.416
peak=   -3.264 closest distance to " O   HOH Z 265 " =    2.004
peak=   -3.264 closest distance to " CD  PRO A 243 " =    2.034
peak=   -3.263 closest distance to " CG  PHE A  59 " =    2.226
peak=   -3.256 closest distance to " CG  ARG A 219 " =    2.681
peak=   -3.256 closest distance to " CG2 THR A 264 " =    2.046
peak=   -3.256 closest distance to " O   HOH Z 169 " =    1.057
peak=   -3.255 closest distance to " CB  ALA A 244 " =    2.056
peak=   -3.254 closest distance to " O   HOH Z 397 " =    1.352
peak=   -3.251 closest distance to " O   HOH Z  28 " =    0.808
peak=   -3.250 closest distance to " N   PRO A 163 " =    1.574
peak=   -3.246 closest distance to " ND2 ASN A  69 " =    1.422
peak=   -3.245 closest distance to " C   ASP A 124 " =    1.093
peak=   -3.241 closest distance to " OE2 GLU A   2 " =    0.940
peak=   -3.241 closest distance to " O   HOH Z 220 " =    0.887
peak=   -3.240 closest distance to " CE  LYS A  76 " =    2.920
peak=   -3.240 closest distance to " OG1 THR A 178 " =    1.108
peak=   -3.239 closest distance to " CD2 LEU A 282 " =    2.143
peak=   -3.237 closest distance to " CB  ALA A   7 " =    1.977
peak=   -3.232 closest distance to " CA  ALA A 291 " =    2.539
peak=   -3.231 closest distance to " O   HOH Z  60 " =    2.183
peak=   -3.226 closest distance to " O   HOH Z 185 " =    1.467
peak=   -3.225 closest distance to " OE1 GLU A 277 " =    2.224
peak=   -3.218 closest distance to " O   HOH Z 431 " =    1.427
peak=   -3.213 closest distance to " N   VAL A  72 " =    1.865
peak=   -3.212 closest distance to " CB  VAL A 230 " =    1.082
peak=   -3.210 closest distance to " O   HOH Z  65 " =    0.825
peak=   -3.205 closest distance to " O   HOH Z 313 " =    1.245
peak=   -3.205 closest distance to " O   ALA A 100 " =    2.455
peak=   -3.204 closest distance to " CE3 TRP A 179 " =    2.251
peak=   -3.200 closest distance to " O   ARG A 145 " =    1.569
peak=   -3.195 closest distance to " O   HOH Z  77 " =    1.887
peak=   -3.195 closest distance to " O   HOH Z 134 " =    2.662
peak=   -3.192 closest distance to " C   LEU A 222 " =    1.345
peak=   -3.192 closest distance to " O   ARG A  24 " =    1.781
peak=   -3.190 closest distance to " CD  ARG A 219 " =    2.465
peak=   -3.189 closest distance to " O   THR A 182 " =    1.249
peak=   -3.189 closest distance to " C   GLN A 205 " =    1.922
peak=   -3.186 closest distance to " OXT GLY A 302 " =    2.789
peak=   -3.184 closest distance to " O   HOH Z 249 " =    0.817
peak=   -3.176 closest distance to " O   HOH Z 126 " =    1.853
peak=   -3.169 closest distance to " O   HOH Z 191 " =    5.230
peak=   -3.168 closest distance to " CB  ALA A  43 " =    2.006
peak=   -3.162 closest distance to " C   ASN A  69 " =    1.394
peak=   -3.159 closest distance to " O   HOH Z 102 " =    1.869
peak=   -3.157 closest distance to " OG1 THR A 246 " =    1.132
peak=   -3.155 closest distance to " CD2 LEU A   5 " =    0.971
peak=   -3.145 closest distance to " CH2 TRP A 123 " =    1.946
peak=   -3.133 closest distance to " O   HOH Z 137 " =    1.514
peak=   -3.130 closest distance to " O   HOH Z 137 " =    1.422
peak=   -3.129 closest distance to " O   HOH Z 197 " =    5.050
peak=   -3.128 closest distance to " ND2 ASN A 127 " =    1.500
peak=   -3.127 closest distance to " OG  SER A  87 " =    1.548
peak=   -3.123 closest distance to " ND2 ASN A  45 " =    1.584
peak=   -3.119 closest distance to " O   HOH Z  51 " =    0.815
peak=   -3.118 closest distance to " CE  LYS A 166 " =    1.169
peak=   -3.114 closest distance to " CB  PRO A 163 " =    2.715
peak=   -3.106 closest distance to " O   HOH Z 424 " =    1.972
peak=   -3.100 closest distance to " O   MET A 188 " =    1.612
peak=   -3.099 closest distance to " O   ALA A   1 " =    1.629
peak=   -3.092 closest distance to " O   HOH Z  63 " =    1.224
peak=   -3.091 closest distance to " O   VAL A  67 " =    2.634
peak=   -3.089 closest distance to " O   HOH Z 385 " =    1.572
peak=   -3.076 closest distance to " ND2 ASN A 209 " =    1.942
peak=   -3.049 closest distance to " CZ  PHE A  16 " =    1.402
peak=   -3.047 closest distance to " O   ASN A 301 " =    1.615
peak=   -3.044 closest distance to " O   HOH Z 145 " =    2.475

================= 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    :  0.5075 0.5009   6.299540e+00   6.293640e+00
   1_bss:  0.4977 0.4903   6.292591e+00   6.283576e+00
   1_xyz:  0.4324 0.4521   6.219788e+00   6.244906e+00
   1_adp:  0.3894 0.4393   6.165621e+00   6.231972e+00
   1_occ:  0.3890 0.4381   6.164605e+00   6.231915e+00
   2_bss:  0.3872 0.4327   6.163866e+00   6.228936e+00
   2_xyz:  0.3173 0.3769   6.019506e+00   6.135289e+00
   2_adp:  0.2995 0.3599   5.975635e+00   6.101139e+00
   2_occ:  0.2991 0.3602   5.975557e+00   6.101771e+00
   3_bss:  0.2963 0.3593   5.973335e+00   6.101433e+00
   3_xyz:  0.2280 0.2874   5.751793e+00   5.927792e+00
   3_adp:  0.2035 0.2696   5.669867e+00   5.875159e+00
   3_occ:  0.2029 0.2690   5.668336e+00   5.873703e+00
   4_bss:  0.2028 0.2685   5.666951e+00   5.872234e+00
   4_xyz:  0.1654 0.2247   5.488085e+00   5.713361e+00
   4_adp:  0.1614 0.2087   5.443301e+00   5.639343e+00
   4_occ:  0.1610 0.2082   5.440933e+00   5.635681e+00
   5_bss:  0.1610 0.2076   5.440648e+00   5.633330e+00
   5_xyz:  0.1373 0.1777   5.292959e+00   5.494118e+00
   5_adp:  0.1338 0.1772   5.278027e+00   5.493630e+00
   5_occ:  0.1336 0.1771   5.276373e+00   5.491775e+00
   5_bss:  0.1335 0.1769   5.275030e+00   5.490630e+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:  0.381   0.000   7.150   8.748   7.533   0.000   0.000   0.000
   1_xyz:  0.381   0.000   7.150   8.748   7.533   0.000   0.000   0.000
   1_adp:  0.381   0.000   7.150   8.748   7.533   0.000   0.000   0.000
   1_occ:  0.381   0.000   7.150   8.748   7.533   0.000   0.000   0.000
   2_bss:  0.342  20.000   4.293   5.089   5.314   0.000   0.000   0.000
   2_xyz:  0.342  20.000   4.293   5.089   5.314   0.000   0.000   0.000
   2_adp:  0.342  20.000   4.293   5.089   5.314   0.000   0.000   0.000
   2_occ:  0.342  20.000   4.293   5.089   5.314   0.000   0.000   0.000
   3_bss:  0.342  37.498   1.897   2.554   2.942   0.000   0.000   0.000
   3_xyz:  0.342  37.498   1.897   2.554   2.942   0.000   0.000   0.000
   3_adp:  0.342  37.498   1.897   2.554   2.942   0.000   0.000   0.000
   3_occ:  0.342  37.498   1.897   2.554   2.942   0.000   0.000   0.000
   4_bss:  0.326  33.387   0.898   1.426   2.099   0.000   0.000   0.000
   4_xyz:  0.326  33.387   0.898   1.426   2.099   0.000   0.000   0.000
   4_adp:  0.326  33.387   0.898   1.426   2.099   0.000   0.000   0.000
   4_occ:  0.326  33.387   0.898   1.426   2.099   0.000   0.000   0.000
   5_bss:  0.326  33.387   0.073   0.668   1.543   0.000   0.000   0.000
   5_xyz:  0.326  33.387   0.073   0.668   1.543   0.000   0.000   0.000
   5_adp:  0.326  33.387   0.073   0.668   1.543   0.000   0.000   0.000
   5_occ:  0.326  33.387   0.073   0.668   1.543   0.000   0.000   0.000
   5_bss:  0.326  34.020  -0.656  -0.139   0.795   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.464 0.3225  0.3888    81258.243
   1_bss:  64.260 0.3368  0.4993    77408.744
   1_xyz:  55.258 0.4528  0.6663    63356.201
   1_adp:  50.978 0.5082  0.8109    59418.437
   1_occ:  50.932 0.5088  0.8102    59268.722
   2_bss:  50.553 0.5132  0.7418    58348.339
   2_xyz:  40.920 0.6318  0.9024    40380.548
   2_adp:  38.138 0.6651  0.9580    35965.365
   2_occ:  38.170 0.6647  0.9569    36058.455
   3_bss:  37.979 0.6668  0.8784    35792.696
   3_xyz:  28.785 0.7706  0.9852    21180.534
   3_adp:  26.430 0.7966  1.0017    18632.584
   3_occ:  26.356 0.7974  1.0020    18526.088
   4_bss:  26.282 0.7981  0.9667    18424.849
   4_xyz:  21.510 0.8470  0.9998    12814.046
   4_adp:  19.292 0.8695  1.0131    11027.282
   4_occ:  19.196 0.8704  1.0134    10924.064
   5_bss:  19.132 0.8709  0.9865    10853.438
   5_xyz:  16.124 0.8978  0.9988     8017.166
   5_adp:  16.054 0.8985  0.9944     7971.176
   5_occ:  16.019 0.8988  0.9949     7940.255
   5_bss:  15.987 0.8990  0.9903     7906.844
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2530e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2530e+01
   1_xyz:   1.835  0.015  0.112 18.327  0.007  4.103   1.6606e-01
   1_adp:   1.835  0.015  0.112 18.327  0.007  4.103   1.6606e-01
   1_occ:   1.835  0.015  0.112 18.327  0.007  4.103   1.6606e-01
   2_bss:   1.835  0.015  0.112 18.327  0.007  4.103   1.6606e-01
   2_xyz:   1.240  0.009  0.080 16.323  0.005  4.116   9.2692e-02
   2_adp:   1.240  0.009  0.080 16.323  0.005  4.116   9.2692e-02
   2_occ:   1.240  0.009  0.080 16.323  0.005  4.116   9.2692e-02
   3_bss:   1.240  0.009  0.080 16.323  0.005  4.116   9.2692e-02
   3_xyz:   1.080  0.008  0.074 15.689  0.004  4.108   7.1704e-02
   3_adp:   1.080  0.008  0.074 15.689  0.004  4.108   7.1704e-02
   3_occ:   1.080  0.008  0.074 15.689  0.004  4.108   7.1704e-02
   4_bss:   1.080  0.008  0.074 15.689  0.004  4.108   7.1704e-02
   4_xyz:   0.896  0.005  0.064 15.351  0.003  4.108   5.3218e-02
   4_adp:   0.896  0.005  0.064 15.351  0.003  4.108   5.3218e-02
   4_occ:   0.896  0.005  0.064 15.351  0.003  4.108   5.3218e-02
   5_bss:   0.896  0.005  0.064 15.351  0.003  4.108   5.3218e-02
   5_xyz:   0.916  0.005  0.064 15.335  0.003  4.108   5.3572e-02
   5_adp:   0.916  0.005  0.064 15.335  0.003  4.108   5.3572e-02
   5_occ:   0.916  0.005  0.064 15.335  0.003  4.108   5.3572e-02
   5_bss:   0.916  0.005  0.064 15.335  0.003  4.108   5.3572e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.942   6.7957e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.942   6.7957e+00
   1_xyz:  15.926  0.175  0.516 88.541  0.040  2.130   1.0786e-01
   1_adp:  15.926  0.175  0.516 88.541  0.040  2.130   1.0786e-01
   1_occ:  15.926  0.175  0.516 88.541  0.040  2.130   1.0786e-01
   2_bss:  15.926  0.175  0.516 88.541  0.040  2.130   1.0786e-01
   2_xyz:   7.757  0.105  0.385 79.084  0.040  2.114   6.6163e-02
   2_adp:   7.757  0.105  0.385 79.084  0.040  2.114   6.6163e-02
   2_occ:   7.757  0.105  0.385 79.084  0.040  2.114   6.6163e-02
   3_bss:   7.757  0.105  0.385 79.084  0.040  2.114   6.6163e-02
   3_xyz:   7.244  0.097  0.260 85.531  0.028  2.358   7.0038e-02
   3_adp:   7.244  0.097  0.260 85.531  0.028  2.358   7.0038e-02
   3_occ:   7.244  0.097  0.260 85.531  0.028  2.358   7.0038e-02
   4_bss:   7.244  0.097  0.260 85.531  0.028  2.358   7.0038e-02
   4_xyz:   7.965  0.031  0.232 88.482  0.022  2.372   3.6448e-02
   4_adp:   7.965  0.031  0.232 88.482  0.022  2.372   3.6448e-02
   4_occ:   7.965  0.031  0.232 88.482  0.022  2.372   3.6448e-02
   5_bss:   7.965  0.031  0.232 88.482  0.022  2.372   3.6448e-02
   5_xyz:   7.118  0.034  0.191 88.744  0.026  2.391   3.3847e-02
   5_adp:   7.118  0.034  0.191 88.744  0.026  2.391   3.3847e-02
   5_occ:   7.118  0.034  0.191 88.744  0.026  2.391   3.3847e-02
   5_bss:   7.118  0.034  0.191 88.744  0.026  2.391   3.3847e-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:  84.36   0.00  15.50  77.46   0.00  13.58  84.36   0.00  25.94
   1_occ:  84.36   0.00  15.50  77.46   0.00  13.58  84.36   0.00  25.94
   2_bss:  84.36   0.00  15.50  77.46   0.00  13.58  84.36   0.00  25.94
   2_xyz:  84.36   0.00  15.50  77.46   0.00  13.58  84.36   0.00  25.94
   2_adp:  86.25   0.00  15.00  84.56   0.00  12.13  86.25   0.00  30.63
   2_occ:  86.25   0.00  15.00  84.56   0.00  12.13  86.25   0.00  30.63
   3_bss:  86.25   0.00  15.00  84.56   0.00  12.13  86.25   0.00  30.63
   3_xyz:  86.25   0.00  15.00  84.56   0.00  12.13  86.25   0.00  30.63
   3_adp: 112.61   0.00  15.92 112.61   0.00  11.48  90.12   2.36  40.09
   3_occ: 112.61   0.00  15.92 112.61   0.00  11.48  90.12   2.36  40.09
   4_bss: 112.61   0.00  15.92 112.61   0.00  11.48  90.12   2.36  40.09
   4_xyz: 112.61   0.00  15.92 112.61   0.00  11.48  90.12   2.36  40.09
   4_adp: 101.03   0.00  14.36 101.03   0.00  10.39  83.52   3.73  36.00
   4_occ: 101.03   0.00  14.36 101.03   0.00  10.39  83.52   3.73  36.00
   5_bss: 101.03   0.00  14.36 101.03   0.00  10.39  83.52   3.73  36.00
   5_xyz: 101.03   0.00  14.36 101.03   0.00  10.39  83.52   3.73  36.00
   5_adp: 101.16   0.00  14.37 101.16   0.00  10.29  83.86   2.14  36.60
   5_occ: 101.16   0.00  14.37 101.16   0.00  10.29  83.86   2.14  36.60
   5_bss: 101.80   0.63  15.00 101.80   0.63  10.92  84.50   2.78  37.23
------------------------------------------------------------------------
 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:    1.266    0.010    0.425
   1_adp:    1.266    0.010    0.425
   1_occ:    1.266    0.010    0.425
   2_bss:    1.266    0.010    0.425
   2_xyz:    1.576    0.015    0.574
   2_adp:    1.576    0.015    0.574
   2_occ:    1.576    0.015    0.574
   3_bss:    1.576    0.015    0.574
   3_xyz:    1.717    0.037    0.692
   3_adp:    1.717    0.037    0.692
   3_occ:    1.717    0.037    0.692
   4_bss:    1.717    0.037    0.692
   4_xyz:    1.767    0.042    0.762
   4_adp:    1.767    0.042    0.762
   4_occ:    1.767    0.042    0.762
   5_bss:    1.767    0.042    0.762
   5_xyz:    1.779    0.066    0.812
   5_adp:    1.779    0.066    0.812
   5_occ:    1.779    0.066    0.812
   5_bss:    1.779    0.066    0.812
------------------------------------------------------------------------

CPU time actual refinement: 354.92


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/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_24/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_24/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.76 
  Macro-tasks:
    bulk solvent and scale       = 45.93  
    individual site refinement   = 148.00 
    weights calculation          = 32.47  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 233.00 
  Micro-tasks:
    mask                            = 3.10   
    f_calc                          = 110.45 
    alpha_beta                      = 8.54   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 120.52 
    fmodel                         = 7.93   
    r_factors                      = 0.30   
    phase_errors                   = 9.90   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 262.14 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.043 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    637 calls, 110.16 s
gradients_fft:          583 calls, 107.77 s

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

# Date 2008-01-16 Time 00:33:34 PST -0800 (1200472414.11 s)
Start R-work = 0.5075, R-free = 0.5009 (no bulk solvent and anisotropic scale)
Final R-work = 0.1501, R-free = 0.1920 (no bulk solvent and anisotropic scale)

Start R-work = 0.4977, R-free = 0.4903
Final R-work = 0.1335, R-free = 0.1769