# Date 2008-01-16 Time 00:39:18 PST -0800 (1200472758.21 s)
#phil __OFF__

Command line arguments: "../92.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15129
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 92

-------------------------------------------------------------------------------
  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, 47.6339, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.95078
Completeness in resolution range: 0.929137
Completeness with d_max=infinity: 0.926369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8941
                             d_min =   1.9508

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, 47.6339, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8941 1.95078
Completeness in resolution range: 0.929137
Completeness with d_max=infinity: 0.926369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8945 -  4.1749 [2212/2241]  1986   226  10.2%
  bin  2:  4.1749 -  3.3258 [2122/2145]  1912   210   9.9%
  bin  3:  3.3258 -  2.9090 [2093/2118]  1885   208   9.9%
  bin  4:  2.9090 -  2.6446 [2066/2084]  1857   209  10.1%
  bin  5:  2.6446 -  2.4560 [2056/2098]  1852   204   9.9%
  bin  6:  2.4560 -  2.3117 [2060/2088]  1858   202   9.8%
  bin  7:  2.3117 -  2.1964 [2036/2072]  1835   201   9.9%
  bin  8:  2.1964 -  2.1010 [2024/2066]  1824   200   9.9%
  bin  9:  2.1010 -  2.0203 [2036/2096]  1832   204  10.0%
  bin 10:  2.0203 -  1.9508 [ 884/2075]   789    95  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/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:
        0.94 -     1.73: 10
        1.73 -     2.52: 56
        2.52 -     3.32: 3861
        3.32 -     4.11: 9518
        4.11 -     4.90: 15182
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  0.938 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.279 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.468 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.539 3.040 -x+1,y-1/2,-z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.548 3.270 -x+1,y-1/2,-z+1/2
  ... (remaining 28622 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_92/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 47.63395 85.95805 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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4947   r_free= 0.4805   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293093                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.4092 0.3993      6.6165      6.6488|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.4142 0.4092      6.8005      6.8199|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.4688 0.4245      6.6875      6.7229|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.4787 0.4611      6.5189      6.4836|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.5290 0.5014      6.3794      6.4038|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.5196 0.5516      6.2839      6.1788|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.5253 0.4797      6.2396      6.1901|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.5354 0.5122      6.1834      6.1983|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.5338 0.5423      6.1214      6.1676|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.5343 0.5507      6.1046      6.0976|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.5614 0.5532      6.0336      6.0389|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.5401 0.5350      5.9515      5.9774|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.5505 0.5304      5.8768      5.8443|
| 14:  1.9995 -  1.9508 0.29    385   47 0.5623 0.5033       5.924      5.7142|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.6567  1434   159  0.65  38.86   0.80     0.66      85185.63|
|  2:  4.6567 -  3.7151  1393   155  0.66  38.59   0.88     0.72     120263.64|
|  3:  3.7151 -  3.2510  1349   148  0.56  47.10   0.83     0.68     124483.54|
|  4:  3.2510 -  2.9563  1335   144  0.49  52.77   0.79     0.59     103603.04|
|  5:  2.9563 -  2.7458  1339   152  0.38  61.19   0.72     0.48      87440.46|
|  6:  2.7458 -  2.5848  1347   154  0.35  64.01   0.71     0.40      75546.84|
|  7:  2.5848 -  2.4560  1295   145  0.31  66.87   0.73     0.37      70280.54|
|  8:  2.4560 -  2.3495  1331   139  0.32  65.98   0.72     0.38      60718.99|
|  9:  2.3495 -  2.2594  1314   150  0.33  65.72   0.73     0.40      57649.46|
| 10:  2.2594 -  2.1817  1319   143  0.31  66.51   0.75     0.38      51631.89|
| 11:  2.1817 -  2.1136  1310   147  0.25  71.78   0.73     0.33      51732.75|
| 12:  2.1136 -  2.0534  1286   151  0.22  73.71   0.74     0.30      48421.51|
| 13:  2.0534 -  1.9995  1193   125  0.24  72.14   0.72     0.32      40444.01|
| 14:  1.9995 -  1.9508   385    47  0.39  60.61   0.75     0.42      25844.28|
|alpha:            min =        0.30 max =            0.72 mean =         0.47|
|beta:             min =    25844.28 max =       124483.54 mean =     74798.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.03|
|phase err.(test): min =        0.00 max =           89.96 mean =        60.06|
|-----------------------------------------------------------------------------|

============================== 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 = 17.270468             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.366   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.433060              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.629   (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 |  0.682 -  1.104:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.104 -  1.526:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.526 -  1.947:       33 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.947 -  2.369:      266 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.369 -  2.791:     1002 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.791 -  3.213:     2204 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.213 -  3.635:     3811 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.635 -  4.056:     5396 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.056 -  4.478:     7206 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.478 -  4.900:     8713 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.350 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.682 |       3.271 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    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 = 11.606)------------------------------------------|
|    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 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4996   r_free= 0.4878   ksol= 0.00   Bsol= 0.00   scale= 0.759    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.293931                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4867   r_free= 0.4766   ksol= 0.34   Bsol= 6.58   scale= 0.991    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.12,10.34,7.57,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.286438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.969881             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.773   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.505412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4867      final r-factor (work) = 0.4087          |
| start r-factor (free) = 0.4766      final r-factor (free) = 0.4331          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.6000 = 15.97 * 0.50 * 6.2932 + 1.00 * 53.3495                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.8102 = 15.97 * 0.50 * 6.2179 + 1.00 * 0.1605                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4087      final r-factor (work) = 0.3616          |
| start r-factor (free) = 0.4331      final r-factor (free) = 0.4154          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3749 = 1.51 * 1.00 * 6.2179 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2715 = 1.51 * 1.00 * 6.1460 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.04   14.44    None  None   None       |
|    all(noH): 2823   0      0.00    91.04   14.44    None  None   None       |
|    Sol.    : 438    0      0.00    91.04   27.08    None  None   None       |
|    Mac.    : 2385   0      0.00    77.85   12.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.104: 1256   |   5:    45.522 -  54.626:   48        |
|      1:     9.104 -  18.209:  734   |   6:    54.626 -  63.730:   32        |
|      2:    18.209 -  27.313:  414   |   7:    63.730 -  72.835:   15        |
|      3:    27.313 -  36.417:  211   |   8:    72.835 -  81.939:    8        |
|      4:    36.417 -  45.522:  104   |   9:    81.939 -  91.044:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3616 r_free = 0.4154             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3610 r_free = 0.4146             target_work(ml) = 6.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3610   r_free= 0.4146   ksol= 0.34   Bsol= 6.58   scale= 1.111    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.12,10.34,7.57,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.125160                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3594   r_free= 0.4082   ksol= 0.31   Bsol= 20.00   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.69,6.39,4.80,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.125149                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.547664              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.469   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552511              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.078  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3594      final r-factor (work) = 0.2846          |
| start r-factor (free) = 0.4082      final r-factor (free) = 0.3334          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2707 = 6.55 * 0.50 * 6.1427 + 1.00 * 0.1605                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8179 = 6.55 * 0.50 * 6.0271 + 1.00 * 0.0862                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2846      final r-factor (work) = 0.2650          |
| start r-factor (free) = 0.3334      final r-factor (free) = 0.3196          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3496 = 0.55 * 1.00 * 6.0271 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2733 = 0.55 * 1.00 * 5.9006 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.61   14.25    None  None   None       |
|    all(noH): 2823   0      0.00    85.61   14.25    None  None   None       |
|    Sol.    : 438    0      0.00    84.37   31.27    None  None   None       |
|    Mac.    : 2385   0      0.00    85.61   11.12    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 -   8.562: 1240   |   5:    42.807 -  51.369:   80        |
|      1:     8.562 -  17.123:  798   |   6:    51.369 -  59.930:   21        |
|      2:    17.123 -  25.685:  336   |   7:    59.930 -  68.492:   20        |
|      3:    25.685 -  34.246:  178   |   8:    68.492 -  77.053:    8        |
|      4:    34.246 -  42.807:  135   |   9:    77.053 -  85.615:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2650 r_free = 0.3196             target_work(ml) = 5.880         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2650 r_free = 0.3196             target_work(ml) = 5.880         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2650   r_free= 0.3196   ksol= 0.31   Bsol= 20.00   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.69,6.39,4.80,0.00,0.00,0.00); trace/3= 5.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.879990                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2619   r_free= 0.3172   ksol= 0.32   Bsol= 37.42   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,3.66,3.10,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.877069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.200208              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.221098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.953  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2619      final r-factor (work) = 0.1923          |
| start r-factor (free) = 0.3172      final r-factor (free) = 0.2384          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4850 = 4.20 * 0.50 * 5.9039 + 1.00 * 0.0862                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1667 = 4.20 * 0.50 * 5.7589 + 1.00 * 0.0724                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1923      final r-factor (work) = 0.1782          |
| start r-factor (free) = 0.2384      final r-factor (free) = 0.2200          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2871 = 0.22 * 1.00 * 5.7589 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2485 = 0.22 * 1.00 * 5.5648 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.80   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    94.80   14.02    None  None   None       |
|    Sol.    : 438    0      3.16    82.82   33.20    None  None   None       |
|    Mac.    : 2385   0      0.00    94.80   10.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.480: 1491   |   5:    47.398 -  56.877:   47        |
|      1:     9.480 -  18.959:  694   |   6:    56.877 -  66.357:   24        |
|      2:    18.959 -  28.439:  231   |   7:    66.357 -  75.837:   10        |
|      3:    28.439 -  37.918:  192   |   8:    75.837 -  85.316:    5        |
|      4:    37.918 -  47.398:  127   |   9:    85.316 -  94.796:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1782 r_free = 0.2200             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1779 r_free = 0.2200             target_work(ml) = 5.529         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1779   r_free= 0.2200   ksol= 0.32   Bsol= 37.42   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,3.66,3.10,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.528917                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1769   r_free= 0.2189   ksol= 0.32   Bsol= 37.42   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,2.19,2.09,0.00,0.00,0.00); trace/3= 1.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.528373                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.415214              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.510  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1769      final r-factor (work) = 0.1402          |
| start r-factor (free) = 0.2189      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5902 = 3.42 * 0.50 * 5.5738 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3356 = 3.42 * 0.50 * 5.4271 + 1.00 * 0.0683                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1296          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5809 = 0.28 * 1.00 * 5.4271 + 1.00 * 0.0405                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5116 = 0.28 * 1.00 * 5.2931 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.01   14.10    None  None   None       |
|    all(noH): 2823   0      0.00    87.01   14.10    None  None   None       |
|    Sol.    : 438    0      3.12    74.43   36.41    None  None   None       |
|    Mac.    : 2385   0      0.00    87.01   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:     0.000 -   8.701: 1400   |   5:    43.504 -  52.205:  107        |
|      1:     8.701 -  17.402:  796   |   6:    52.205 -  60.906:   50        |
|      2:    17.402 -  26.102:  196   |   7:    60.906 -  69.606:   19        |
|      3:    26.102 -  34.803:  126   |   8:    69.606 -  78.307:    9        |
|      4:    34.803 -  43.504:  117   |   9:    78.307 -  87.008:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1296 r_free = 0.1722             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1295 r_free = 0.1721             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1295   r_free= 0.1721   ksol= 0.32   Bsol= 37.42   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,2.19,2.09,0.00,0.00,0.00); trace/3= 1.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.260574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1717   ksol= 0.31   Bsol= 41.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,1.47,1.75,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.260141                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.697842              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.005  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392290              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.120  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8588 = 3.70 * 0.50 * 5.2953 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7199 = 3.70 * 0.50 * 5.2139 + 1.00 * 0.0798                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0545 = 0.39 * 1.00 * 5.2139 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0384 = 0.39 * 1.00 * 5.1713 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.53   14.00    None  None   None       |
|    all(noH): 2823   0      0.00    86.53   14.00    None  None   None       |
|    Sol.    : 438    0      2.67    76.06   36.82    None  None   None       |
|    Mac.    : 2385   0      0.00    86.53   9.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.654: 1410   |   5:    43.267 -  51.921:   97        |
|      1:     8.654 -  17.307:  811   |   6:    51.921 -  60.574:   62        |
|      2:    17.307 -  25.960:  178   |   7:    60.574 -  69.227:   21        |
|      3:    25.960 -  34.614:  119   |   8:    69.227 -  77.881:    8        |
|      4:    34.614 -  43.267:  112   |   9:    77.881 -  86.534:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1606             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1129 r_free = 0.1606             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1606   ksol= 0.31   Bsol= 41.18   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,1.47,1.75,0.00,0.00,0.00); trace/3= 1.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166532                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.0982 0.1329      5.3884      5.5708|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.0853 0.1069      5.4438        5.64|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.1082 0.1528      5.4764      5.8497|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.1234 0.1623      5.4555      5.6402|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.1349 0.1628      5.3401      5.5105|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.1265 0.2153       5.235      5.5255|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.1233 0.1638      5.1678      5.3631|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.1183 0.1664      5.1006      5.3172|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.1192 0.1997      5.0427      5.3905|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.1146 0.1695      4.9879      5.1823|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.1134 0.1837      4.9363      5.2501|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.1130 0.1646      4.8589      5.1137|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.1135 0.1822      4.7763      5.0518|
| 14:  1.9995 -  1.9508 0.29    385   47 0.1024 0.1648      4.6847      4.8968|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.6567  1434   159  0.94   9.42   0.98     0.96       7654.93|
|  2:  4.6567 -  3.7151  1393   155  0.95   8.42   1.02     1.01       9458.46|
|  3:  3.7151 -  3.2510  1349   148  0.93  11.79   1.03     1.02      10710.17|
|  4:  3.2510 -  2.9563  1335   144  0.91  14.21   1.01     1.01      10556.19|
|  5:  2.9563 -  2.7458  1339   152  0.89  16.65   1.00     0.96       8679.41|
|  6:  2.7458 -  2.5848  1347   154  0.89  17.04   0.98     0.94       7416.13|
|  7:  2.5848 -  2.4560  1295   145  0.90  16.11   0.98     0.94       6382.72|
|  8:  2.4560 -  2.3495  1331   139  0.90  16.40   1.01     0.98       5966.36|
|  9:  2.3495 -  2.2594  1314   150  0.90  16.52   1.01     0.97       5330.18|
| 10:  2.2594 -  2.1817  1319   143  0.89  16.83   1.00     0.97       4932.93|
| 11:  2.1817 -  2.1136  1310   147  0.90  16.72   1.01     0.97       4544.58|
| 12:  2.1136 -  2.0534  1286   151  0.91  15.94   1.01     0.99       3891.70|
| 13:  2.0534 -  1.9995  1193   125  0.90  16.53   1.00     0.99       3329.52|
| 14:  1.9995 -  1.9508   385    47  0.91  14.88   0.98     0.94       2662.65|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2662.65 max =        10710.17 mean =      6805.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.66 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.14|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1606   ksol= 0.32   Bsol= 42.25   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,0.35,0.76,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1129   r_free= 0.1606   ksol= 0.32   Bsol= 42.25   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.11,0.35,0.76,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166821                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8945 -  4.6567 0.99   1434  159 0.0982 0.1329      5.3914      5.5735|
|  2:  4.6567 -  3.7151 0.99   1393  155 0.0851 0.1067      5.4433      5.6385|
|  3:  3.7151 -  3.2510 0.99   1349  148 0.1083 0.1528      5.4761      5.8503|
|  4:  3.2510 -  2.9563 0.99   1335  144 0.1234 0.1623      5.4555      5.6401|
|  5:  2.9563 -  2.7458 0.99   1339  152 0.1350 0.1628      5.3403      5.5105|
|  6:  2.7458 -  2.5848 0.99   1347  154 0.1265 0.2151      5.2348      5.5253|
|  7:  2.5848 -  2.4560 0.98   1295  145 0.1233 0.1640       5.168      5.3639|
|  8:  2.4560 -  2.3495 0.98   1331  139 0.1182 0.1664      5.1007      5.3172|
|  9:  2.3495 -  2.2594 0.99   1314  150 0.1191 0.1998       5.043      5.3911|
| 10:  2.2594 -  2.1817 0.98   1319  143 0.1145 0.1696      4.9878      5.1831|
| 11:  2.1817 -  2.1136 0.97   1310  147 0.1134 0.1835      4.9367      5.2496|
| 12:  2.1136 -  2.0534 0.98   1286  151 0.1131 0.1647      4.8594      5.1146|
| 13:  2.0534 -  1.9995 0.90   1193  125 0.1136 0.1819      4.7764      5.0506|
| 14:  1.9995 -  1.9508 0.29    385   47 0.1023 0.1649      4.6842       4.897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8945 -  4.6567  1434   159  0.94   9.45   0.98     0.96       7726.43|
|  2:  4.6567 -  3.7151  1393   155  0.95   8.42   1.02     1.01       9471.91|
|  3:  3.7151 -  3.2510  1349   148  0.93  11.78   1.03     1.02      10691.72|
|  4:  3.2510 -  2.9563  1335   144  0.91  14.22   1.02     1.01      10560.69|
|  5:  2.9563 -  2.7458  1339   152  0.89  16.64   1.00     0.96       8676.60|
|  6:  2.7458 -  2.5848  1347   154  0.89  17.04   0.98     0.94       7416.18|
|  7:  2.5848 -  2.4560  1295   145  0.90  16.11   0.99     0.94       6385.87|
|  8:  2.4560 -  2.3495  1331   139  0.90  16.41   1.01     0.98       5972.39|
|  9:  2.3495 -  2.2594  1314   150  0.90  16.53   1.01     0.97       5337.79|
| 10:  2.2594 -  2.1817  1319   143  0.89  16.83   1.00     0.97       4934.69|
| 11:  2.1817 -  2.1136  1310   147  0.90  16.73   1.01     0.97       4548.41|
| 12:  2.1136 -  2.0534  1286   151  0.91  15.95   1.01     0.99       3896.53|
| 13:  2.0534 -  1.9995  1193   125  0.90  16.53   1.01     0.99       3328.18|
| 14:  1.9995 -  1.9508   385    47  0.91  14.84   0.98     0.94       2655.14|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2655.14 max =        10691.72 mean =      6812.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.606)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    87.60   15.06    None  None   None       |
|    all(noH): 2823   0      1.06    87.60   15.06    None  None   None       |
|    Sol.    : 438    0      3.74    77.12   37.88    None  None   None       |
|    Mac.    : 2385   0      1.06    87.60   10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.063 -   9.717: 1410   |   5:    44.330 -  52.984:   97        |
|      1:     9.717 -  18.370:  811   |   6:    52.984 -  61.637:   62        |
|      2:    18.370 -  27.023:  178   |   7:    61.637 -  70.291:   21        |
|      3:    27.023 -  35.677:  119   |   8:    70.291 -  78.944:    8        |
|      4:    35.677 -  44.330:  112   |   9:    78.944 -  87.597:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.531 - 4.955
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 325
   mapped sites are within: 0.740 - 4.955

peak=   10.883 closest distance to " CB  VAL A 230 " =    1.412
peak=    6.561 closest distance to " CB  VAL A 296 " =    1.159
peak=    5.970 closest distance to " CG  LEU A   5 " =    1.241
peak=    5.667 closest distance to " CD1AILE A 234 " =    1.097
peak=    5.370 closest distance to " O   HOH Z 124 " =    1.505
peak=    5.326 closest distance to " O   HOH Z 193 " =    1.905
peak=    5.219 closest distance to " O   HOH Z 209 " =    2.259
peak=    5.214 closest distance to " O   HOH Z  85 " =    1.884
peak=    5.195 closest distance to " O   HOH Z 403 " =    1.868
peak=    5.147 closest distance to " CB  SER A  63 " =    1.157
peak=    5.122 closest distance to " O   HOH Z 102 " =    1.382
peak=    5.004 closest distance to " O   HOH Z 402 " =    1.585
peak=    5.004 closest distance to " NE2 GLN A  11 " =    1.037
peak=    4.982 closest distance to " CB  ARG A 275 " =    0.961
peak=    4.924 closest distance to " O   HOH Z 154 " =    1.847
peak=    4.902 closest distance to " O   HOH Z  80 " =    1.989
peak=    4.878 closest distance to " NH2 ARG A  56 " =    2.173
peak=    4.837 closest distance to " O   HOH Z 327 " =    1.769
peak=    4.825 closest distance to " O   HOH Z 272 " =    1.938
peak=    4.783 closest distance to " O   HOH Z  43 " =    1.601
peak=    4.724 closest distance to " CG  LEU A 228 " =    1.160
peak=    4.699 closest distance to " O   HOH Z 248 " =    1.393
peak=    4.668 closest distance to " O   HOH Z 126 " =    1.820
peak=    4.645 closest distance to " CG  PRO A  54 " =    1.187
peak=    4.638 closest distance to " CB  GLN A 183 " =    1.344
peak=    4.634 closest distance to " CA  TYR A  30 " =    0.996
peak=    4.609 closest distance to " O   HOH Z 142 " =    1.638
peak=    4.597 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.581 closest distance to " C   PRO A 198 " =    1.485
peak=    4.556 closest distance to " CB  GLN A 223 " =    1.420
peak=    4.554 closest distance to " O   HOH Z  63 " =    2.348
peak=    4.550 closest distance to " O   SER A  87 " =    2.224
peak=    4.489 closest distance to " O   HOH Z 357 " =    1.982
peak=    4.460 closest distance to " O   HOH Z 414 " =    2.050
peak=    4.430 closest distance to " CD2 LEU A   5 " =    1.205
peak=    4.425 closest distance to " CB  VAL A 230 " =    1.157
peak=    4.413 closest distance to " CG2 VAL A 296 " =    1.015
peak=    4.409 closest distance to " CB  SER A  26 " =    1.771
peak=    4.398 closest distance to " O   HOH Z 346 " =    1.537
peak=    4.375 closest distance to " CG  PRO A 213 " =    1.170
peak=    4.371 closest distance to " O   HOH Z 368 " =    2.183
peak=    4.366 closest distance to " O   HOH Z 130 " =    2.563
peak=    4.333 closest distance to " OE1 GLU A   2 " =    2.115
peak=    4.331 closest distance to " O   HOH Z 406 " =    1.294
peak=    4.304 closest distance to " CG1 VAL A 296 " =    1.140
peak=    4.273 closest distance to " O   HOH Z  54 " =    2.302
peak=    4.269 closest distance to " CB  PRO A  54 " =    0.916
peak=    4.258 closest distance to " O   HOH Z 236 " =    1.532
peak=    4.229 closest distance to " O   HOH Z 126 " =    1.923
peak=    4.206 closest distance to " O   HOH Z 423 " =    1.791
peak=    4.203 closest distance to " O   HOH Z 404 " =    1.534
peak=    4.190 closest distance to " O   HOH Z 394 " =    1.550
peak=    4.187 closest distance to " O   HOH Z  54 " =    1.643
peak=    4.156 closest distance to " CB  ASN A 148 " =    1.268
peak=    4.154 closest distance to " CD2 TRP A 179 " =    1.406
peak=    4.145 closest distance to " O   HOH Z 234 " =    3.449
peak=    4.130 closest distance to " O   HOH Z 203 " =    1.685
peak=    4.119 closest distance to " NZ  LYS A 117 " =    2.940
peak=    4.110 closest distance to " O   HOH Z 130 " =    1.116
peak=    4.083 closest distance to " O   HOH Z 419 " =    1.839
peak=    4.075 closest distance to " O   HOH Z 238 " =    1.141
peak=    4.065 closest distance to " O   HOH Z 369 " =    2.416
peak=    4.063 closest distance to " CB  TRP A 179 " =    1.135
peak=    4.062 closest distance to " O   HOH Z 137 " =    1.658
peak=    4.059 closest distance to " O   HOH Z 128 " =    1.575
peak=    4.057 closest distance to " CB  SER A   3 " =    1.260
peak=    4.056 closest distance to " CG1 ILE A  33 " =    1.191
peak=    4.032 closest distance to " O   HOH Z 298 " =    1.878
peak=    4.028 closest distance to " O   HOH Z 389 " =    1.872
peak=    4.027 closest distance to " O   HOH Z  97 " =    1.912
peak=    4.024 closest distance to " O   HOH Z 134 " =    1.731
peak=    4.021 closest distance to " CG  ARG A  66 " =    1.018
peak=    4.010 closest distance to " O   HOH Z 128 " =    2.445
peak=    4.009 closest distance to " O   HOH Z 426 " =    1.456
peak=    4.003 closest distance to " O   HOH Z 316 " =    2.768
peak=    4.002 closest distance to " O   HOH Z 345 " =    2.449
peak=    3.994 closest distance to " O   HOH Z 189 " =    2.658
peak=    3.982 closest distance to " CB  GLU A 277 " =    3.551
peak=    3.968 closest distance to " O   HOH Z 227 " =    1.580
peak=    3.959 closest distance to " CB  ARG A  79 " =    1.345
peak=    3.937 closest distance to " O   HOH Z  61 " =    1.599
peak=    3.929 closest distance to " O   HOH Z 421 " =    2.081
peak=    3.928 closest distance to " O   HOH Z 345 " =    1.796
peak=    3.923 closest distance to " CA  ALA A  51 " =    1.071
peak=    3.909 closest distance to " O   HOH Z 253 " =    1.687
peak=    3.894 closest distance to " NH1AARG A 275 " =    1.069
peak=    3.875 closest distance to " CB  GLU A 152 " =    1.127
peak=    3.869 closest distance to " O   HOH Z 128 " =    1.952
peak=    3.869 closest distance to " O   HOH Z 245 " =    1.467
peak=    3.851 closest distance to " O   HOH Z 247 " =    1.271
peak=    3.847 closest distance to " O   HOH Z 303 " =    2.275
peak=    3.845 closest distance to " N   ASN A  39 " =    1.276
peak=    3.837 closest distance to " O   HOH Z  44 " =    2.092
peak=    3.827 closest distance to " O   HOH Z 156 " =    3.301
peak=    3.825 closest distance to " O   HOH Z  97 " =    2.287
peak=    3.817 closest distance to " O   HOH Z 250 " =    1.562
peak=    3.815 closest distance to " CB  THR A  52 " =    0.945
peak=    3.814 closest distance to " NH2BARG A 145 " =    2.179
peak=    3.809 closest distance to " CA  VAL A  41 " =    0.846
peak=    3.807 closest distance to " ND2 ASN A 187 " =    1.723
peak=    3.804 closest distance to " O   HOH Z 406 " =    1.388
peak=    3.801 closest distance to " O   HOH Z 109 " =    1.551
peak=    3.795 closest distance to " CB BVAL A  41 " =    1.054
peak=    3.791 closest distance to " O   ASP A 124 " =    1.537
peak=    3.789 closest distance to " O   HOH Z  59 " =    2.054
peak=    3.786 closest distance to " CB  ALA A   9 " =    1.672
peak=    3.780 closest distance to " CG AARG A 275 " =    1.207
peak=    3.773 closest distance to " CG2 THR A 294 " =    1.453
peak=    3.770 closest distance to " CA  ASN A 176 " =    1.048
peak=    3.765 closest distance to " O   HOH Z  47 " =    1.692
peak=    3.765 closest distance to " O   HOH Z 359 " =    1.584
peak=    3.758 closest distance to " CA  ALA A  21 " =    1.175
peak=    3.757 closest distance to " O   HOH Z 380 " =    2.041
peak=    3.756 closest distance to " O   HOH Z 422 " =    2.496
peak=    3.748 closest distance to " O   HOH Z  78 " =    1.637
peak=    3.744 closest distance to " CG2 ILE A  20 " =    1.442
peak=    3.744 closest distance to " O   GLY A  23 " =    2.296
peak=    3.738 closest distance to " CD  LYS A 166 " =    1.395
peak=    3.732 closest distance to " CD2 LEU A 228 " =    1.251
peak=    3.710 closest distance to " O   HOH Z 280 " =    2.579
peak=    3.696 closest distance to " O   HOH Z 408 " =    1.742
peak=    3.695 closest distance to " O   HOH Z 130 " =    2.474
peak=    3.689 closest distance to " O   HOH Z 120 " =    0.966
peak=    3.670 closest distance to " O   HOH Z 411 " =    3.559
peak=    3.666 closest distance to " CG  PRO A 243 " =    1.140
peak=    3.663 closest distance to " CB  ALA A 100 " =    1.144
peak=    3.662 closest distance to " CB  ARG A 139 " =    0.997
peak=    3.661 closest distance to " CB  ARG A 190 " =    1.768
peak=    3.661 closest distance to " CG2AVAL A 121 " =    2.020
peak=    3.659 closest distance to " O   HOH Z 315 " =    1.812
peak=    3.654 closest distance to " O   HOH Z 193 " =    2.093
peak=    3.653 closest distance to " NH1BARG A 190 " =    2.117
peak=    3.646 closest distance to " O   HOH Z 173 " =    2.269
peak=    3.646 closest distance to " CE1 HIS A 108 " =    1.115
peak=    3.614 closest distance to " CB  THR A  31 " =    1.538
peak=    3.613 closest distance to " O   HOH Z  56 " =    2.126
peak=    3.613 closest distance to " O   HOH Z 365 " =    2.853
peak=    3.610 closest distance to " CG2 THR A 221 " =    1.191
peak=    3.609 closest distance to " O   HOH Z 287 " =    1.772
peak=    3.607 closest distance to " O   HOH Z 361 " =    2.957
peak=    3.604 closest distance to " O   HOH Z  68 " =    1.847
peak=    3.597 closest distance to " O   HOH Z 406 " =    1.510
peak=    3.591 closest distance to " O   HOH Z  40 " =    1.847
peak=    3.589 closest distance to " O   HOH Z 409 " =    1.881
peak=    3.583 closest distance to " O   HOH Z 425 " =    1.997
peak=    3.576 closest distance to " O   HOH Z 284 " =    2.922
peak=    3.574 closest distance to " CD  ARG A 269 " =    1.097
peak=    3.571 closest distance to " O   HOH Z 261 " =    2.009
peak=    3.570 closest distance to " O   HOH Z 197 " =    2.503
peak=    3.567 closest distance to " O   HOH Z 412 " =    3.638
peak=    3.565 closest distance to " O   HOH Z  15 " =    2.090
peak=    3.559 closest distance to " CB  ARG A 259 " =    1.875
peak=    3.554 closest distance to " OG BSER A 212 " =    2.693
peak=    3.549 closest distance to " O   HOH Z 244 " =    1.548
peak=    3.547 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.544 closest distance to " O   HOH Z 417 " =    3.403
peak=    3.541 closest distance to " O   HOH Z 250 " =    1.339
peak=    3.540 closest distance to " CB  GLU A 128 " =    1.125
peak=    3.538 closest distance to " O   HOH Z 130 " =    2.442
peak=    3.537 closest distance to " CD  LYS A  76 " =    1.846
peak=    3.527 closest distance to " O   HOH Z 425 " =    1.377
peak=    3.518 closest distance to " O   HOH Z 214 " =    1.492
peak=    3.515 closest distance to " CB  VAL A 265 " =    1.318
peak=    3.513 closest distance to " CZ2 TRP A 150 " =    1.056
peak=    3.511 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.502 closest distance to " CZ  PHE A 218 " =    1.152
peak=    3.500 closest distance to " O   HOH Z 249 " =    0.997
peak=    3.498 closest distance to " CZ AARG A 102 " =    1.724
peak=    3.486 closest distance to " O   HOH Z 344 " =    1.858
peak=    3.476 closest distance to " CZ  PHE A  38 " =    1.266
peak=    3.467 closest distance to " O   HOH Z 367 " =    3.450
peak=    3.465 closest distance to " O   HOH Z 162 " =    2.123
peak=    3.462 closest distance to " O   HOH Z 420 " =    2.109
peak=    3.454 closest distance to " CB  ASN A  39 " =    0.740
peak=    3.450 closest distance to " CZ3 TRP A  85 " =    1.035
peak=    3.450 closest distance to " O   HOH Z 273 " =    2.870
peak=    3.449 closest distance to " CG1BVAL A  72 " =    1.756
peak=    3.440 closest distance to " O   HOH Z 263 " =    1.721
peak=    3.438 closest distance to " O   HOH Z 298 " =    2.194
peak=    3.435 closest distance to " CB  VAL A 202 " =    1.449
peak=    3.429 closest distance to " O   HOH Z 257 " =    2.239
peak=    3.426 closest distance to " O   HOH Z 301 " =    1.850
peak=    3.424 closest distance to " O   HOH Z  88 " =    3.360
peak=    3.417 closest distance to " O   HOH Z 147 " =    1.834
peak=    3.417 closest distance to " OG1 THR A 294 " =    2.255
peak=    3.417 closest distance to " CD  ARG A  79 " =    1.864
peak=    3.416 closest distance to " CG  GLN A  77 " =    2.327
peak=    3.416 closest distance to " CA  ALA A 291 " =    0.894
peak=    3.413 closest distance to " O   HOH Z 155 " =    3.139
peak=    3.412 closest distance to " CG  PRO A 198 " =    1.192
peak=    3.408 closest distance to " OG BSER A 164 " =    2.204
peak=    3.407 closest distance to " O   HOH Z 189 " =    2.401
peak=    3.406 closest distance to " OH  TYR A 116 " =    1.199
peak=    3.398 closest distance to " O   HOH Z 163 " =    1.313
peak=    3.398 closest distance to " O   HOH Z 383 " =    1.904
peak=    3.396 closest distance to " OE1 GLN A  11 " =    1.741
peak=    3.394 closest distance to " CB  ALA A  71 " =    1.266
peak=    3.394 closest distance to " O   HOH Z 215 " =    1.426
peak=    3.389 closest distance to " CD  PRO A  54 " =    1.042
peak=    3.381 closest distance to " O   HOH Z 214 " =    2.481
peak=    3.379 closest distance to " O   HOH Z 427 " =    2.635
peak=    3.379 closest distance to " CA  SER A  32 " =    1.661
peak=    3.377 closest distance to " O   HOH Z   1 " =    2.039
peak=    3.377 closest distance to " CB  SER A 141 " =    1.075
peak=    3.375 closest distance to " O   HOH Z 128 " =    1.703
peak=    3.373 closest distance to " O   HOH Z  96 " =    1.936
peak=    3.371 closest distance to " O   HOH Z 435 " =    1.864
peak=    3.368 closest distance to " CD BLYS A 290 " =    1.151
peak=    3.366 closest distance to " O   HOH Z 353 " =    2.874
peak=    3.363 closest distance to " CE  LYS A 119 " =    1.030
peak=    3.362 closest distance to " CA  ARG A 275 " =    1.829
peak=    3.359 closest distance to " OG BSER A 210 " =    1.366
peak=    3.355 closest distance to " CB  PRO A 198 " =    1.042
peak=    3.355 closest distance to " CB  ASN A  45 " =    1.075
peak=    3.354 closest distance to " O   HOH Z 162 " =    1.866
peak=    3.348 closest distance to " O   HOH Z 416 " =    2.780
peak=    3.346 closest distance to " OD1 ASN A  60 " =    1.690
peak=    3.345 closest distance to " OG  SER A  62 " =    2.790
peak=    3.337 closest distance to " O   HOH Z 364 " =    2.282
peak=    3.331 closest distance to " O   HOH Z 337 " =    3.563
peak=    3.329 closest distance to " CB  TYR A 247 " =    0.977
peak=    3.327 closest distance to " CB  ALA A 248 " =    1.402
peak=    3.326 closest distance to " O   HOH Z 183 " =    1.825
peak=    3.321 closest distance to " O   HOH Z 227 " =    1.659
peak=    3.317 closest distance to " O   HOH Z 271 " =    2.538
peak=    3.316 closest distance to " CD  LYS A 119 " =    1.895
peak=    3.309 closest distance to " CG  LYS A 119 " =    1.149
peak=    3.307 closest distance to " CG2 ILE A 120 " =    1.367
peak=    3.305 closest distance to " O   GLY A  91 " =    1.421
peak=    3.303 closest distance to " CB  TRP A 266 " =    1.151
peak=    3.299 closest distance to " NH2AARG A 145 " =    2.274
peak=    3.295 closest distance to " O   HOH Z 116 " =    2.415
peak=    3.295 closest distance to " CD2 LEU A 297 " =    0.991
peak=    3.294 closest distance to " O   HOH Z 136 " =    1.265
peak=    3.294 closest distance to " CG AARG A 275 " =    1.245
peak=    3.292 closest distance to " O   HOH Z   4 " =    1.494
peak=    3.289 closest distance to " CH2 TRP A 274 " =    2.100
peak=    3.289 closest distance to " CA  ARG A  36 " =    0.982
peak=    3.288 closest distance to " CB  MET A  47 " =    1.147
peak=    3.286 closest distance to " O   HOH Z 281 " =    4.370
peak=    3.285 closest distance to " O   HOH Z 313 " =    1.703
peak=    3.283 closest distance to " O   HOH Z 438 " =    2.156
peak=    3.282 closest distance to " NH2 ARG A 156 " =    1.023
peak=    3.282 closest distance to " CA  LYS A 117 " =    1.318
peak=    3.281 closest distance to " O   HOH Z 155 " =    1.463
peak=    3.267 closest distance to " CB  LEU A   5 " =    1.282
peak=    3.265 closest distance to " CG  MET A 185 " =    1.131
peak=    3.259 closest distance to " O   HOH Z  71 " =    2.126
peak=    3.257 closest distance to " O   HOH Z 148 " =    3.170
peak=    3.256 closest distance to " O   HOH Z 197 " =    2.061
peak=    3.254 closest distance to " O   HOH Z 261 " =    1.936
peak=    3.252 closest distance to " O   HOH Z 158 " =    3.025
peak=    3.241 closest distance to " O   HOH Z   9 " =    2.341
peak=    3.241 closest distance to " CE1 TYR A 186 " =    1.280
peak=    3.237 closest distance to " OD1 ASN A  69 " =    2.522
peak=    3.234 closest distance to " OD2 ASP A 298 " =    3.919
peak=    3.233 closest distance to " CA  ASP A 162 " =    1.099
peak=    3.232 closest distance to " O   HOH Z  66 " =    2.127
peak=    3.230 closest distance to " CD1 ILE A 106 " =    1.085
peak=    3.227 closest distance to " NH2 ARG A  79 " =    1.332
peak=    3.220 closest distance to " O   HOH Z 411 " =    1.829
peak=    3.216 closest distance to " O   HOH Z  11 " =    1.406
peak=    3.214 closest distance to " N   PHE A 130 " =    1.408
peak=    3.214 closest distance to " O   HOH Z 313 " =    1.676
peak=    3.212 closest distance to " O   HOH Z 427 " =    3.077
peak=    3.211 closest distance to " CD  GLN A 194 " =    1.578
peak=    3.208 closest distance to " ND1 HIS A  81 " =    1.555
peak=    3.207 closest distance to " O   HOH Z 344 " =    2.853
peak=    3.207 closest distance to " CA  TYR A 116 " =    1.561
peak=    3.207 closest distance to " O   HOH Z 126 " =    1.516
peak=    3.205 closest distance to " CB  LYS A 290 " =    1.022
peak=    3.204 closest distance to " O   HOH Z 387 " =    1.999
peak=    3.198 closest distance to " O   HOH Z 403 " =    1.499
peak=    3.197 closest distance to " O   HOH Z 145 " =    2.201
peak=    3.190 closest distance to " CD  ARG A 195 " =    0.898
peak=    3.188 closest distance to " CA  ARG A  66 " =    0.866
peak=    3.183 closest distance to " O   THR A  82 " =    2.000
peak=    3.177 closest distance to " CG  GLN A  58 " =    2.682
peak=    3.170 closest distance to " O   HOH Z 163 " =    1.851
peak=    3.168 closest distance to " O   HOH Z 423 " =    3.057
peak=    3.168 closest distance to " CA  GLY A   6 " =    1.532
peak=    3.166 closest distance to " CB  ASN A 110 " =    1.057
peak=    3.159 closest distance to " CG1 ILE A  49 " =    1.479
peak=    3.157 closest distance to " O   HOH Z  83 " =    1.527
peak=    3.157 closest distance to " CD2 TYR A 186 " =    1.023
peak=    3.155 closest distance to " CB  ILE A 120 " =    1.499
peak=    3.155 closest distance to " O   HOH Z 293 " =    1.600
peak=    3.153 closest distance to " O   HOH Z 234 " =    1.875
peak=    3.152 closest distance to " O   HOH Z 185 " =    1.647
peak=    3.152 closest distance to " O   HOH Z 326 " =    1.466
peak=    3.146 closest distance to " O   ILE A  33 " =    1.200
peak=    3.143 closest distance to " OG  SER A 245 " =    1.490
peak=    3.141 closest distance to " NZ  LYS A 119 " =    1.706
peak=    3.141 closest distance to " O   HOH Z  40 " =    2.292
peak=    3.140 closest distance to " O   HOH Z 355 " =    1.884
peak=    3.138 closest distance to " CG  LYS A  76 " =    1.118
peak=    3.136 closest distance to " CB  ASN A 215 " =    1.077
peak=    3.135 closest distance to " CA  SER A  87 " =    0.931
peak=    3.133 closest distance to " O   HOH Z  49 " =    1.108
peak=    3.131 closest distance to " O   HOH Z 191 " =    4.830
peak=    3.128 closest distance to " CA  ARG A 195 " =    1.166
peak=    3.119 closest distance to " O   HOH Z 336 " =    4.330
peak=    3.105 closest distance to " O   HOH Z 156 " =    2.328
peak=    3.104 closest distance to " O   HOH Z 112 " =    1.810
peak=    3.102 closest distance to " CE BMET A  47 " =    1.319
peak=    3.101 closest distance to " O  BHOH Z  74 " =    1.408
peak=    3.099 closest distance to " O   HOH Z 158 " =    3.415
peak=    3.092 closest distance to " OD1 ASP A 286 " =    1.717
peak=    3.089 closest distance to " O   HOH Z 298 " =    4.955
peak=    3.083 closest distance to " O   GLU A   2 " =    1.596
peak=    3.081 closest distance to " N   CYS A 260 " =    0.851
peak=    3.070 closest distance to " CA  LYS A 290 " =    1.111
peak=    3.065 closest distance to " NZ  LYS A 117 " =    1.446
peak=    3.061 closest distance to " CD1 LEU A 228 " =    1.654
peak=    3.057 closest distance to " N   ASP A 162 " =    1.287
peak=    3.055 closest distance to " CZ2 TRP A 179 " =    1.928
peak=    3.048 closest distance to " CG2 VAL A 197 " =    1.048
peak=    3.047 closest distance to " CD1 LEU A   5 " =    1.519
peak=    3.045 closest distance to " CB  THR A 235 " =    1.134
peak=    3.021 closest distance to " CG2 ILE A 234 " =    1.088
peak=    3.020 closest distance to " CG  MET A 185 " =    0.934
peak=    3.003 closest distance to " CG  ARG A  66 " =    2.892

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.773 - 5.709
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 216
   mapped sites are within: 0.773 - 5.709

peak=   -4.948 closest distance to " CG2 VAL A 230 " =    0.773
peak=   -4.677 closest distance to " CD  ARG A  14 " =    3.222
peak=   -4.667 closest distance to " CD  ARG A 156 " =    2.042
peak=   -4.481 closest distance to " O   PRO A 163 " =    2.104
peak=   -4.464 closest distance to " O   HOH Z 266 " =    4.682
peak=   -4.304 closest distance to " CD  GLN A  58 " =    1.257
peak=   -4.283 closest distance to " OXT GLY A 302 " =    2.830
peak=   -4.283 closest distance to " OG BSER A 134 " =    1.462
peak=   -4.237 closest distance to " C   HIS A 108 " =    1.209
peak=   -4.217 closest distance to " CD1 LEU A 101 " =    2.550
peak=   -4.168 closest distance to " O   HOH Z 166 " =    1.678
peak=   -4.168 closest distance to " O   VAL A  67 " =    2.753
peak=   -4.159 closest distance to " O   HOH Z 120 " =    0.960
peak=   -4.087 closest distance to " O   HOH Z 290 " =    1.022
peak=   -4.086 closest distance to " O   HOH Z  13 " =    1.803
peak=   -4.085 closest distance to " O   HOH Z 351 " =    1.481
peak=   -3.933 closest distance to " CB  ALA A 291 " =    2.208
peak=   -3.897 closest distance to " O   ASN A  45 " =    1.764
peak=   -3.862 closest distance to " O   VAL A  67 " =    2.233
peak=   -3.850 closest distance to " CH2 TRP A 179 " =    1.358
peak=   -3.819 closest distance to " CB  PHE A 208 " =    2.275
peak=   -3.817 closest distance to " CB  ALA A 248 " =    2.235
peak=   -3.798 closest distance to " CG  ARG A 219 " =    2.440
peak=   -3.784 closest distance to " O   ASN A 187 " =    1.511
peak=   -3.781 closest distance to " O   HOH Z 426 " =    1.775
peak=   -3.762 closest distance to " OG  SER A  97 " =    2.318
peak=   -3.747 closest distance to " O   HOH Z  37 " =    1.906
peak=   -3.744 closest distance to " O   PHE A 218 " =    1.485
peak=   -3.742 closest distance to " O   HOH Z 109 " =    5.709
peak=   -3.737 closest distance to " O   GLY A  80 " =    2.481
peak=   -3.736 closest distance to " C   THR A 279 " =    1.200
peak=   -3.732 closest distance to " CD2 LEU A 237 " =    2.685
peak=   -3.728 closest distance to " O   ALA A 256 " =    1.540
peak=   -3.726 closest distance to " NE2 GLN A  88 " =    1.095
peak=   -3.723 closest distance to " O   HOH Z 165 " =    2.084
peak=   -3.716 closest distance to " CB  ALA A 161 " =    2.387
peak=   -3.693 closest distance to " CB  PRO A 163 " =    2.635
peak=   -3.691 closest distance to " N   ALA A 248 " =    1.859
peak=   -3.679 closest distance to " CD1 PHE A 130 " =    2.294
peak=   -3.679 closest distance to " CG1 VAL A 112 " =    2.606
peak=   -3.674 closest distance to " N   ALA A 226 " =    1.886
peak=   -3.673 closest distance to " CZ  TYR A 169 " =    1.835
peak=   -3.668 closest distance to " O   HOH Z 136 " =    2.287
peak=   -3.667 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.646 closest distance to " CB  PRO A 280 " =    2.216
peak=   -3.644 closest distance to " CA  GLY A 203 " =    2.389
peak=   -3.642 closest distance to " ND2 ASN A 187 " =    1.530
peak=   -3.629 closest distance to " CD2 PHE A 192 " =    2.019
peak=   -3.616 closest distance to " ND2 ASN A  69 " =    1.675
peak=   -3.613 closest distance to " CD1 PHE A  59 " =    2.041
peak=   -3.599 closest distance to " CB  SER A 210 " =    1.309
peak=   -3.584 closest distance to " CD2 TYR A  30 " =    2.741
peak=   -3.584 closest distance to " O  BHOH Z 338 " =    1.386
peak=   -3.583 closest distance to " O   VAL A 174 " =    2.168
peak=   -3.582 closest distance to " CE BMET A  47 " =    1.295
peak=   -3.578 closest distance to " ND2 ASN A  39 " =    1.056
peak=   -3.576 closest distance to " O   GLY A 241 " =    2.382
peak=   -3.568 closest distance to " O   HOH Z 423 " =    2.101
peak=   -3.558 closest distance to " O   HOH Z  15 " =    1.510
peak=   -3.557 closest distance to " O   HOH Z 388 " =    1.978
peak=   -3.556 closest distance to " O   HOH Z 174 " =    2.226
peak=   -3.553 closest distance to " CD2 TYR A 293 " =    1.941
peak=   -3.549 closest distance to " O   HOH Z 407 " =    2.949
peak=   -3.543 closest distance to " O   HOH Z  92 " =    1.657
peak=   -3.540 closest distance to " OG BSER A 212 " =    1.676
peak=   -3.539 closest distance to " O   HOH Z 174 " =    4.095
peak=   -3.526 closest distance to " O   HOH Z  11 " =    1.785
peak=   -3.524 closest distance to " CD1 TYR A 247 " =    2.444
peak=   -3.523 closest distance to " NH2 ARG A  79 " =    2.052
peak=   -3.513 closest distance to " O   HOH Z 131 " =    4.068
peak=   -3.510 closest distance to " OD2 ASP A  50 " =    1.389
peak=   -3.510 closest distance to " CG2 THR A 182 " =    2.264
peak=   -3.508 closest distance to " O   TRP A  92 " =    1.976
peak=   -3.504 closest distance to " O   HOH Z 196 " =    2.155
peak=   -3.493 closest distance to " C   ALA A 158 " =    1.299
peak=   -3.475 closest distance to " CA  ASP A 298 " =    1.069
peak=   -3.473 closest distance to " CE  LYS A 166 " =    2.998
peak=   -3.473 closest distance to " O   ALA A   1 " =    1.981
peak=   -3.472 closest distance to " O   HOH Z  78 " =    1.799
peak=   -3.468 closest distance to " CD2 LEU A 300 " =    2.755
peak=   -3.465 closest distance to " OD1 ASN A 301 " =    1.869
peak=   -3.458 closest distance to " CD1 PHE A  59 " =    2.039
peak=   -3.451 closest distance to " O   HOH Z 193 " =    1.572
peak=   -3.448 closest distance to " O   HOH Z 139 " =    5.089
peak=   -3.448 closest distance to " ND2 ASN A  45 " =    1.095
peak=   -3.448 closest distance to " CB  ALA A 248 " =    1.999
peak=   -3.447 closest distance to " O   SER A 210 " =    1.843
peak=   -3.442 closest distance to " O   HOH Z 114 " =    3.452
peak=   -3.439 closest distance to " O   HOH Z 397 " =    1.231
peak=   -3.433 closest distance to " O   HOH Z  71 " =    1.775
peak=   -3.414 closest distance to " CG2 VAL A 189 " =    2.019
peak=   -3.410 closest distance to " C   ILE A 234 " =    1.346
peak=   -3.405 closest distance to " O   HOH Z 313 " =    1.238
peak=   -3.404 closest distance to " O   SER A 146 " =    1.039
peak=   -3.403 closest distance to " O   HOH Z 166 " =    1.625
peak=   -3.403 closest distance to " N   GLN A  58 " =    2.065
peak=   -3.398 closest distance to " CB  ASP A 132 " =    2.345
peak=   -3.397 closest distance to " N   SER A 206 " =    1.821
peak=   -3.393 closest distance to " NH2AARG A 275 " =    4.570
peak=   -3.392 closest distance to " O   MET A  40 " =    2.817
peak=   -3.390 closest distance to " O   HOH Z 244 " =    1.367
peak=   -3.390 closest distance to " OG BSER A 134 " =    1.655
peak=   -3.381 closest distance to " O   HOH Z  17 " =    1.105
peak=   -3.378 closest distance to " CD  ARG A 139 " =    1.690
peak=   -3.377 closest distance to " CD  GLN A 223 " =    0.818
peak=   -3.376 closest distance to " CE3 TRP A 150 " =    2.202
peak=   -3.364 closest distance to " O   HOH Z 126 " =    1.799
peak=   -3.362 closest distance to " ND2 ASN A 209 " =    1.792
peak=   -3.360 closest distance to " O   HOH Z 191 " =    5.696
peak=   -3.356 closest distance to " O   HOH Z 422 " =    1.687
peak=   -3.353 closest distance to " O   GLY A 196 " =    1.012
peak=   -3.352 closest distance to " O   MET A 188 " =    1.898
peak=   -3.352 closest distance to " NH1 ARG A  66 " =    1.002
peak=   -3.347 closest distance to " N   ARG A  66 " =    1.817
peak=   -3.344 closest distance to " CG  ASP A 132 " =    2.326
peak=   -3.340 closest distance to " N   SER A 276 " =    1.411
peak=   -3.334 closest distance to " O   HOH Z 340 " =    1.031
peak=   -3.329 closest distance to " C   GLY A  91 " =    1.337
peak=   -3.322 closest distance to " OG  SER A  26 " =    1.270
peak=   -3.322 closest distance to " CD  GLN A 103 " =    1.481
peak=   -3.321 closest distance to " O   SER A 273 " =    1.245
peak=   -3.317 closest distance to " O   HOH Z 137 " =    1.809
peak=   -3.316 closest distance to " O   HOH Z  56 " =    2.173
peak=   -3.303 closest distance to " CA  GLY A 133 " =    1.984
peak=   -3.301 closest distance to " CG  ASP A  50 " =    2.303
peak=   -3.301 closest distance to " O   HOH Z   6 " =    1.870
peak=   -3.299 closest distance to " OG BSER A 210 " =    1.437
peak=   -3.297 closest distance to " NH1 ARG A 195 " =    2.520
peak=   -3.297 closest distance to " N   VAL A 189 " =    1.581
peak=   -3.295 closest distance to " CB  TYR A  15 " =    2.175
peak=   -3.295 closest distance to " CG  ASP A 231 " =    0.836
peak=   -3.294 closest distance to " O   HOH Z 172 " =    5.245
peak=   -3.284 closest distance to " CE2 PHE A 218 " =    2.694
peak=   -3.276 closest distance to " O   HOH Z  61 " =    1.466
peak=   -3.266 closest distance to " O   HOH Z 369 " =    2.069
peak=   -3.266 closest distance to " O   HOH Z 310 " =    3.457
peak=   -3.264 closest distance to " CD2 LEU A 237 " =    2.775
peak=   -3.263 closest distance to " O   HOH Z 166 " =    2.098
peak=   -3.260 closest distance to " OXT GLY A 302 " =    3.372
peak=   -3.250 closest distance to " O   HOH Z 250 " =    1.325
peak=   -3.249 closest distance to " CD2 LEU A 167 " =    1.771
peak=   -3.247 closest distance to " O   HOH Z 431 " =    2.211
peak=   -3.245 closest distance to " O   GLY A  75 " =    1.668
peak=   -3.244 closest distance to " NH2 ARG A  66 " =    1.493
peak=   -3.244 closest distance to " ND2 ASN A 173 " =    1.286
peak=   -3.243 closest distance to " N   SER A   3 " =    2.088
peak=   -3.241 closest distance to " CD2 PHE A 225 " =    1.299
peak=   -3.235 closest distance to " O   HOH Z 387 " =    2.471
peak=   -3.234 closest distance to " N   THR A 220 " =    2.146
peak=   -3.234 closest distance to " CG2 THR A 178 " =    2.252
peak=   -3.233 closest distance to " OG1 THR A  82 " =    1.291
peak=   -3.232 closest distance to " CG  GLU A 152 " =    1.099
peak=   -3.232 closest distance to " NE2 GLN A  11 " =    1.929
peak=   -3.227 closest distance to " CG2 VAL A 296 " =    1.358
peak=   -3.227 closest distance to " CG1 VAL A 296 " =    1.053
peak=   -3.225 closest distance to " OD2 ASP A 191 " =    1.473
peak=   -3.224 closest distance to " O   HOH Z 377 " =    1.520
peak=   -3.221 closest distance to " CD1 LEU A 228 " =    2.170
peak=   -3.217 closest distance to " CB  ALA A  43 " =    2.323
peak=   -3.214 closest distance to " OG  SER A   3 " =    1.434
peak=   -3.213 closest distance to " OD1 ASN A 148 " =    1.478
peak=   -3.204 closest distance to " CG2 ILE A 263 " =    2.243
peak=   -3.202 closest distance to " O   HOH Z 435 " =    2.595
peak=   -3.200 closest distance to " CG  GLU A  53 " =    1.554
peak=   -3.199 closest distance to " CG  GLU A 277 " =    1.084
peak=   -3.199 closest distance to " O   HOH Z  20 " =    1.498
peak=   -3.199 closest distance to " O   HOH Z 252 " =    3.984
peak=   -3.198 closest distance to " O   GLN A 144 " =    0.920
peak=   -3.197 closest distance to " C   SER A 206 " =    1.605
peak=   -3.195 closest distance to " NE2 GLN A  88 " =    1.784
peak=   -3.184 closest distance to " CH2 TRP A 150 " =    1.029
peak=   -3.178 closest distance to " O   HOH Z 307 " =    1.926
peak=   -3.175 closest distance to " O   HOH Z 183 " =    1.473
peak=   -3.175 closest distance to " CD1 LEU A  83 " =    2.264
peak=   -3.171 closest distance to " O   ASP A 171 " =    1.813
peak=   -3.171 closest distance to " N   TYR A  68 " =    3.146
peak=   -3.171 closest distance to " OD1 ASN A 249 " =    2.145
peak=   -3.163 closest distance to " O   SER A 141 " =    1.861
peak=   -3.162 closest distance to " OD1 ASN A  69 " =    2.094
peak=   -3.162 closest distance to " N   LEU A 281 " =    1.970
peak=   -3.162 closest distance to " O   HOH Z 234 " =    3.856
peak=   -3.161 closest distance to " CE  MET A 105 " =    2.101
peak=   -3.160 closest distance to " O   HOH Z 208 " =    1.419
peak=   -3.158 closest distance to " OD2 ASP A 171 " =    2.316
peak=   -3.154 closest distance to " O   HOH Z 243 " =    1.935
peak=   -3.153 closest distance to " O   ARG A  24 " =    1.960
peak=   -3.149 closest distance to " CG  MET A 105 " =    0.822
peak=   -3.146 closest distance to " O   HOH Z 313 " =    2.123
peak=   -3.144 closest distance to " N   THR A  52 " =    1.672
peak=   -3.144 closest distance to " CD  GLN A  88 " =    0.915
peak=   -3.141 closest distance to " O   ALA A  34 " =    2.370
peak=   -3.139 closest distance to " O   HOH Z 339 " =    1.752
peak=   -3.139 closest distance to " O   ALA A  10 " =    1.854
peak=   -3.139 closest distance to " CA  GLY A 133 " =    2.237
peak=   -3.137 closest distance to " CG  GLU A   2 " =    1.832
peak=   -3.132 closest distance to " O   HOH Z 193 " =    1.641
peak=   -3.130 closest distance to " O   HOH Z  60 " =    2.116
peak=   -3.130 closest distance to " NE2 GLN A 194 " =    1.763
peak=   -3.130 closest distance to " CD  GLN A  11 " =    0.856
peak=   -3.129 closest distance to " CG  ARG A 269 " =    2.147
peak=   -3.129 closest distance to " O   GLY A  80 " =    2.632
peak=   -3.123 closest distance to " O   VAL A 197 " =    1.347
peak=   -3.118 closest distance to " N   ALA A 248 " =    2.256
peak=   -3.109 closest distance to " CA  TYR A  68 " =    2.876
peak=   -3.101 closest distance to " CZ  ARG A 259 " =    0.810
peak=   -3.098 closest distance to " O   HOH Z 123 " =    2.329
peak=   -3.096 closest distance to " OD1 ASP A 171 " =    1.516
peak=   -3.090 closest distance to " O   LYS A 117 " =    1.642
peak=   -3.086 closest distance to " CA  GLY A  23 " =    1.786
peak=   -3.085 closest distance to " O   HOH Z  77 " =    2.132
peak=   -3.084 closest distance to " CD2 HIS A 115 " =    0.966
peak=   -3.068 closest distance to " C   ASN A 148 " =    1.524
peak=   -3.056 closest distance to " O   HOH Z 139 " =    3.263
peak=   -3.041 closest distance to " CB  TYR A 172 " =    2.401
peak=   -3.029 closest distance to " O   HOH Z 110 " =    1.499
peak=   -3.006 closest distance to " CG1 VAL A  78 " =    2.500

================= 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    :  0.4947 0.4805   6.293093e+00   6.285564e+00
   1_bss:  0.4867 0.4766   6.286438e+00   6.281130e+00
   1_xyz:  0.4087 0.4331   6.194620e+00   6.229703e+00
   1_adp:  0.3616 0.4154   6.126399e+00   6.207821e+00
   1_occ:  0.3610 0.4146   6.125160e+00   6.207284e+00
   2_bss:  0.3594 0.4082   6.125149e+00   6.205479e+00
   2_xyz:  0.2846 0.3334   5.930578e+00   6.067177e+00
   2_adp:  0.2650 0.3196   5.880444e+00   6.026680e+00
   2_occ:  0.2650 0.3196   5.879990e+00   6.026259e+00
   3_bss:  0.2619 0.3172   5.877069e+00   6.022893e+00
   3_xyz:  0.1923 0.2384   5.604884e+00   5.782008e+00
   3_adp:  0.1782 0.2200   5.529851e+00   5.707218e+00
   3_occ:  0.1779 0.2200   5.528917e+00   5.707291e+00
   4_bss:  0.1769 0.2189   5.528373e+00   5.705131e+00
   4_xyz:  0.1402 0.1830   5.329301e+00   5.536059e+00
   4_adp:  0.1296 0.1722   5.261002e+00   5.474668e+00
   4_occ:  0.1295 0.1721   5.260574e+00   5.474600e+00
   5_bss:  0.1294 0.1717   5.260141e+00   5.473379e+00
   5_xyz:  0.1158 0.1615   5.181021e+00   5.418544e+00
   5_adp:  0.1130 0.1606   5.166897e+00   5.410258e+00
   5_occ:  0.1129 0.1606   5.166532e+00   5.410082e+00
   5_bss:  0.1129 0.1606   5.166821e+00   5.410334e+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:  0.340   6.582   8.119  10.338   7.568   0.000   0.000   0.000
   1_xyz:  0.340   6.582   8.119  10.338   7.568   0.000   0.000   0.000
   1_adp:  0.340   6.582   8.119  10.338   7.568   0.000   0.000   0.000
   1_occ:  0.340   6.582   8.119  10.338   7.568   0.000   0.000   0.000
   2_bss:  0.309  20.002   4.688   6.385   4.796   0.000   0.000   0.000
   2_xyz:  0.309  20.002   4.688   6.385   4.796   0.000   0.000   0.000
   2_adp:  0.309  20.002   4.688   6.385   4.796   0.000   0.000   0.000
   2_occ:  0.309  20.002   4.688   6.385   4.796   0.000   0.000   0.000
   3_bss:  0.322  37.418   1.927   3.658   3.097   0.000   0.000   0.000
   3_xyz:  0.322  37.418   1.927   3.658   3.097   0.000   0.000   0.000
   3_adp:  0.322  37.418   1.927   3.658   3.097   0.000   0.000   0.000
   3_occ:  0.322  37.418   1.927   3.658   3.097   0.000   0.000   0.000
   4_bss:  0.322  37.418   0.413   2.193   2.086   0.000   0.000   0.000
   4_xyz:  0.322  37.418   0.413   2.193   2.086   0.000   0.000   0.000
   4_adp:  0.322  37.418   0.413   2.193   2.086   0.000   0.000   0.000
   4_occ:  0.322  37.418   0.413   2.193   2.086   0.000   0.000   0.000
   5_bss:  0.313  41.185  -0.118   1.473   1.748   0.000   0.000   0.000
   5_xyz:  0.313  41.185  -0.118   1.473   1.748   0.000   0.000   0.000
   5_adp:  0.313  41.185  -0.118   1.473   1.748   0.000   0.000   0.000
   5_occ:  0.313  41.185  -0.118   1.473   1.748   0.000   0.000   0.000
   5_bss:  0.321  42.248  -1.112   0.350   0.762   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.033 0.3937  0.4658    74786.405
   1_bss:  60.756 0.3826  0.5798    73653.872
   1_xyz:  52.404 0.4881  0.7280    57300.342
   1_adp:  47.358 0.5526  0.8832    51556.845
   1_occ:  47.235 0.5541  0.8841    51347.594
   2_bss:  46.831 0.5592  0.7952    50654.298
   2_xyz:  36.630 0.6813  0.9438    31682.448
   2_adp:  34.186 0.7101  0.9862    28416.966
   2_occ:  34.159 0.7104  0.9868    28387.117
   3_bss:  33.890 0.7133  0.9096    27983.657
   3_xyz:  24.075 0.8202  1.0013    14997.542
   3_adp:  21.728 0.8449  1.0196    12883.511
   3_occ:  21.722 0.8450  1.0196    12878.982
   4_bss:  21.621 0.8459  0.9720    12775.423
   4_xyz:  17.424 0.8855  0.9939     8795.864
   4_adp:  16.093 0.8975  0.9981     7807.580
   4_occ:  16.090 0.8975  0.9979     7802.847
   5_bss:  16.079 0.8976  0.9789     7795.067
   5_xyz:  14.906 0.9075  0.9816     6929.373
   5_adp:  14.688 0.9095  0.9773     6806.765
   5_occ:  14.677 0.9096  0.9773     6804.008
   5_bss:  14.680 0.9096  0.9785     6811.372
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3350e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3350e+01
   1_xyz:   1.802  0.015  0.112 18.316  0.007  4.106   1.6045e-01
   1_adp:   1.802  0.015  0.112 18.316  0.007  4.106   1.6045e-01
   1_occ:   1.802  0.015  0.112 18.316  0.007  4.106   1.6045e-01
   2_bss:   1.802  0.015  0.112 18.316  0.007  4.106   1.6045e-01
   2_xyz:   1.233  0.009  0.080 16.418  0.005  4.123   8.6174e-02
   2_adp:   1.233  0.009  0.080 16.418  0.005  4.123   8.6174e-02
   2_occ:   1.233  0.009  0.080 16.418  0.005  4.123   8.6174e-02
   3_bss:   1.233  0.009  0.080 16.418  0.005  4.123   8.6174e-02
   3_xyz:   1.124  0.007  0.079 15.994  0.004  4.121   7.2416e-02
   3_adp:   1.124  0.007  0.079 15.994  0.004  4.121   7.2416e-02
   3_occ:   1.124  0.007  0.079 15.994  0.004  4.121   7.2416e-02
   4_bss:   1.124  0.007  0.079 15.994  0.004  4.121   7.2416e-02
   4_xyz:   1.096  0.007  0.081 15.573  0.004  4.110   6.8282e-02
   4_adp:   1.096  0.007  0.081 15.573  0.004  4.110   6.8282e-02
   4_occ:   1.096  0.007  0.081 15.573  0.004  4.110   6.8282e-02
   5_bss:   1.096  0.007  0.081 15.573  0.004  4.110   6.8282e-02
   5_xyz:   1.189  0.009  0.090 15.761  0.005  4.114   7.9826e-02
   5_adp:   1.189  0.009  0.090 15.761  0.005  4.114   7.9826e-02
   5_occ:   1.189  0.009  0.090 15.761  0.005  4.114   7.9826e-02
   5_bss:   1.189  0.009  0.090 15.761  0.005  4.114   7.9826e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.682   6.9047e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.682   6.9047e+00
   1_xyz:  16.874  0.182  0.572 85.831  0.044  2.082   1.1069e-01
   1_adp:  16.874  0.182  0.572 85.831  0.044  2.082   1.1069e-01
   1_occ:  16.874  0.182  0.572 85.831  0.044  2.082   1.1069e-01
   2_bss:  16.874  0.182  0.572 85.831  0.044  2.082   1.1069e-01
   2_xyz:   7.992  0.105  0.314 81.133  0.043  2.270   7.5046e-02
   2_adp:   7.992  0.105  0.314 81.133  0.043  2.270   7.5046e-02
   2_occ:   7.992  0.105  0.314 81.133  0.043  2.270   7.5046e-02
   3_bss:   7.992  0.105  0.314 81.133  0.043  2.270   7.5046e-02
   3_xyz:   6.831  0.061  0.301 83.913  0.039  2.233   5.5497e-02
   3_adp:   6.831  0.061  0.301 83.913  0.039  2.233   5.5497e-02
   3_occ:   6.831  0.061  0.301 83.913  0.039  2.233   5.5497e-02
   4_bss:   6.831  0.061  0.301 83.913  0.039  2.233   5.5497e-02
   4_xyz:   7.737  0.048  0.434 82.548  0.037  2.126   4.4442e-02
   4_adp:   7.737  0.048  0.434 82.548  0.037  2.126   4.4442e-02
   4_occ:   7.737  0.048  0.434 82.548  0.037  2.126   4.4442e-02
   5_bss:   7.737  0.048  0.434 82.548  0.037  2.126   4.4442e-02
   5_xyz:   7.900  0.053  0.537 82.985  0.038  2.199   5.9908e-02
   5_adp:   7.900  0.053  0.537 82.985  0.038  2.199   5.9908e-02
   5_occ:   7.900  0.053  0.537 82.985  0.038  2.199   5.9908e-02
   5_bss:   7.900  0.053  0.537 82.985  0.038  2.199   5.9908e-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:  91.04   0.00  14.44  77.85   0.00  12.12  91.04   0.00  27.08
   1_occ:  91.04   0.00  14.44  77.85   0.00  12.12  91.04   0.00  27.08
   2_bss:  91.04   0.00  14.44  77.85   0.00  12.12  91.04   0.00  27.08
   2_xyz:  91.04   0.00  14.44  77.85   0.00  12.12  91.04   0.00  27.08
   2_adp:  85.61   0.00  14.25  85.61   0.00  11.12  84.37   0.00  31.27
   2_occ:  85.61   0.00  14.25  85.61   0.00  11.12  84.37   0.00  31.27
   3_bss:  85.61   0.00  14.25  85.61   0.00  11.12  84.37   0.00  31.27
   3_xyz:  85.61   0.00  14.25  85.61   0.00  11.12  84.37   0.00  31.27
   3_adp:  94.80   0.00  14.02  94.80   0.00  10.50  82.82   3.16  33.20
   3_occ:  94.80   0.00  14.02  94.80   0.00  10.50  82.82   3.16  33.20
   4_bss:  94.80   0.00  14.02  94.80   0.00  10.50  82.82   3.16  33.20
   4_xyz:  94.80   0.00  14.02  94.80   0.00  10.50  82.82   3.16  33.20
   4_adp:  87.01   0.00  14.10  87.01   0.00  10.00  74.43   3.12  36.41
   4_occ:  87.01   0.00  14.10  87.01   0.00  10.00  74.43   3.12  36.41
   5_bss:  87.01   0.00  14.10  87.01   0.00  10.00  74.43   3.12  36.41
   5_xyz:  87.01   0.00  14.10  87.01   0.00  10.00  74.43   3.12  36.41
   5_adp:  86.53   0.00  14.00  86.53   0.00   9.81  76.06   2.67  36.82
   5_occ:  86.53   0.00  14.00  86.53   0.00   9.81  76.06   2.67  36.82
   5_bss:  87.60   1.06  15.06  87.60   1.06  10.87  77.12   3.74  37.88
------------------------------------------------------------------------
 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:    1.186    0.020    0.423
   1_adp:    1.186    0.020    0.423
   1_occ:    1.186    0.020    0.423
   2_bss:    1.186    0.020    0.423
   2_xyz:    1.767    0.014    0.584
   2_adp:    1.767    0.014    0.584
   2_occ:    1.767    0.014    0.584
   3_bss:    1.767    0.014    0.584
   3_xyz:    1.764    0.009    0.695
   3_adp:    1.764    0.009    0.695
   3_occ:    1.764    0.009    0.695
   4_bss:    1.764    0.009    0.695
   4_xyz:    1.898    0.034    0.766
   4_adp:    1.898    0.034    0.766
   4_occ:    1.898    0.034    0.766
   5_bss:    1.898    0.034    0.766
   5_xyz:    1.929    0.041    0.792
   5_adp:    1.929    0.041    0.792
   5_occ:    1.929    0.041    0.792
   5_bss:    1.929    0.041    0.792
------------------------------------------------------------------------

CPU time actual refinement: 347.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/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_92/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_92/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.83 
  Macro-tasks:
    bulk solvent and scale       = 46.22  
    individual site refinement   = 142.43 
    weights calculation          = 32.75  
    collect and process          = 6.47   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 227.99 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 108.04 
    alpha_beta                      = 8.00   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 117.17 
    fmodel                         = 7.93   
    r_factors                      = 0.30   
    phase_errors                   = 10.34  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 255.69 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.868 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    642 calls, 107.76 s
gradients_fft:          586 calls, 103.84 s

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

# Date 2008-01-16 Time 00:45:21 PST -0800 (1200473121.87 s)
Start R-work = 0.4947, R-free = 0.4805 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.4867, R-free = 0.4766
Final R-work = 0.1129, R-free = 0.1606