# Date 2008-01-16 Time 00:33:46 PST -0800 (1200472426.50 s)
#phil __OFF__

Command line arguments: "../76.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1361
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 76

-------------------------------------------------------------------------------
  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, 47.1647, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9229 1.95101
Completeness in resolution range: 0.912559
Completeness with d_max=infinity: 0.909847

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9229
                             d_min =   1.9510

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, 47.1647, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9229 1.95101
Completeness in resolution range: 0.912559
Completeness with d_max=infinity: 0.909847

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9233 -  4.1755 [2249/2277]  2019   230  10.2%
  bin  2:  4.1755 -  3.3263 [2164/2187]  1949   215   9.9%
  bin  3:  3.3263 -  2.9094 [2145/2170]  1937   208   9.7%
  bin  4:  2.9094 -  2.6450 [2111/2127]  1894   217  10.3%
  bin  5:  2.6450 -  2.4563 [2095/2135]  1875   220  10.5%
  bin  6:  2.4563 -  2.3120 [2105/2136]  1907   198   9.4%
  bin  7:  2.3120 -  2.1966 [2076/2113]  1870   206   9.9%
  bin  8:  2.1966 -  2.1013 [2083/2125]  1876   207   9.9%
  bin  9:  2.1013 -  2.0206 [1948/2091]  1761   187   9.6%
  bin 10:  2.0206 -  1.9510 [ 613/2105]   542    71  11.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/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: 0.15 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:
        0.88 -     1.68: 7
        1.68 -     2.49: 61
        2.49 -     3.29: 3663
        3.29 -     4.10: 9436
        4.10 -     4.90: 15247
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  0.878 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.056 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.264 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.294 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.339 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28409 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_76/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 47.16465 88.54975 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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5030   r_free= 0.4988   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.300094                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9233 -  4.6575 0.99   1460  161 0.4048 0.4053      6.6286      6.6448|
|  2:  4.6575 -  3.7156 0.99   1414  155 0.4180 0.4798      6.8031      6.9285|
|  3:  3.7156 -  3.2515 0.99   1387  159 0.4865 0.4576      6.7082      6.6985|
|  4:  3.2515 -  2.9567 0.99   1360  142 0.5035 0.4807      6.5242      6.5085|
|  5:  2.9567 -  2.7462 0.98   1373  158 0.5248 0.5377       6.371      6.4221|
|  6:  2.7462 -  2.5852 0.99   1349  151 0.5384 0.5463      6.2932      6.2003|
|  7:  2.5852 -  2.4563 0.99   1331  164 0.5426 0.4840      6.2265      6.1612|
|  8:  2.4563 -  2.3498 0.99   1371  142 0.5439 0.5014      6.1795        6.14|
|  9:  2.3498 -  2.2596 0.99   1347  144 0.5509 0.5052      6.1251      6.1901|
| 10:  2.2596 -  2.1819 0.98   1328  150 0.5444 0.5970      6.0884      6.1081|
| 11:  2.1819 -  2.1139 0.98   1322  149 0.5442 0.5350      6.0091       6.027|
| 12:  2.1139 -  2.0536 1.00   1346  150 0.5512 0.5325      5.9438      5.9225|
| 13:  2.0536 -  1.9997 0.73   1003  102 0.5491 0.5196      5.8832      5.8321|
| 14:  1.9997 -  1.9510 0.18    239   32 0.5420 0.5732      5.9354       5.732|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9233 -  4.6575  1460   161  0.67  36.80   0.78     0.69      79874.60|
|  2:  4.6575 -  3.7156  1414   155  0.64  40.22   0.87     0.71     130924.36|
|  3:  3.7156 -  3.2515  1387   159  0.52  50.20   0.80     0.65     138565.31|
|  4:  3.2515 -  2.9567  1360   142  0.40  60.00   0.77     0.51     122718.17|
|  5:  2.9567 -  2.7462  1373   158  0.31  67.05   0.72     0.38      96193.40|
|  6:  2.7462 -  2.5852  1349   151  0.25  71.19   0.71     0.31      85628.16|
|  7:  2.5852 -  2.4563  1331   164  0.28  68.74   0.71     0.33      71526.89|
|  8:  2.4563 -  2.3498  1371   142  0.34  64.75   0.71     0.41      60253.20|
|  9:  2.3498 -  2.2596  1347   144  0.36  63.08   0.70     0.45      54364.33|
| 10:  2.2596 -  2.1819  1328   150  0.31  66.77   0.73     0.38      49783.01|
| 11:  2.1819 -  2.1139  1322   149  0.18  76.73   0.72     0.23      53355.28|
| 12:  2.1139 -  2.0536  1346   150  0.11  81.49   0.73     0.16      50891.56|
| 13:  2.0536 -  1.9997  1003   102  0.15  79.14   0.72     0.20      43920.04|
| 14:  1.9997 -  1.9510   239    32  0.35  63.36   0.78     0.37      28446.57|
|alpha:            min =        0.16 max =            0.71 mean =         0.42|
|beta:             min =    28446.57 max =       138565.31 mean =     80286.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.93|
|phase err.(test): min =        0.00 max =           89.99 mean =        63.36|
|-----------------------------------------------------------------------------|

============================== 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 = 19.589410             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.818   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.778099              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.953   (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 |  0.996 -  1.386:        8 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.386 -  1.777:       17 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.777 -  2.167:       98 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.167 -  2.557:      505 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.557 -  2.948:     1320 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.948 -  3.338:     2424 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.338 -  3.729:     3944 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.729 -  4.119:     5185 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.119 -  4.510:     6858 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.510 -  4.900:     8103 |
|-----------------------------------------------------------------------------|
|-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 |       53.605 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  0.996 |       3.111 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    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 = 11.760)------------------------------------------|
|    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 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5079   r_free= 0.4989   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.300972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4937   r_free= 0.4909   ksol= 0.31   Bsol= 0.00   scale= 0.989    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,7.83,11.82,0.00,0.00,0.00); trace/3= 9.24                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.293727                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.073700             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.955   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.734593              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.607   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4937      final r-factor (work) = 0.4272          |
| start r-factor (free) = 0.4909      final r-factor (free) = 0.4507          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 107.3661 = 17.07 * 0.50 * 6.2975 + 1.00 * 53.6050                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.4230 = 17.07 * 0.50 * 6.2397 + 1.00 * 0.1552                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4272      final r-factor (work) = 0.3873          |
| start r-factor (free) = 0.4507      final r-factor (free) = 0.4413          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8379 = 1.73 * 1.00 * 6.2397 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.7364 = 1.73 * 1.00 * 6.1781 + 1.00 * 0.0199                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.25   15.51    None  None   None       |
|    all(noH): 2823   0      0.00    89.25   15.51    None  None   None       |
|    Sol.    : 438    0      0.00    89.25   26.26    None  None   None       |
|    Mac.    : 2385   0      0.00    77.56   13.53    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.925: 1077   |   5:    44.626 -  53.551:   54        |
|      1:     8.925 -  17.850:  776   |   6:    53.551 -  62.477:   27        |
|      2:    17.850 -  26.776:  473   |   7:    62.477 -  71.402:   11        |
|      3:    26.776 -  35.701:  266   |   8:    71.402 -  80.327:    8        |
|      4:    35.701 -  44.626:  129   |   9:    80.327 -  89.252:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3873 r_free = 0.4413             target_work(ml) = 6.164         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3875 r_free = 0.4403             target_work(ml) = 6.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3875   r_free= 0.4403   ksol= 0.31   Bsol= 0.00   scale= 1.122    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,7.83,11.82,0.00,0.00,0.00); trace/3= 9.24                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.163302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3841   r_free= 0.4376   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,3.85,7.45,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.164356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.633545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.481  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.692226              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.391  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3841      final r-factor (work) = 0.3093          |
| start r-factor (free) = 0.4376      final r-factor (free) = 0.3629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8967 = 9.63 * 0.50 * 6.1746 + 1.00 * 0.1552                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.4201 = 9.63 * 0.50 * 6.0841 + 1.00 * 0.1143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3093      final r-factor (work) = 0.2851          |
| start r-factor (free) = 0.3629      final r-factor (free) = 0.3464          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2316 = 0.69 * 1.00 * 6.0841 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1358 = 0.69 * 1.00 * 5.9531 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.38   15.67    None  None   None       |
|    all(noH): 2823   0      0.00    92.38   15.67    None  None   None       |
|    Sol.    : 438    0      0.00    92.38   33.49    None  None   None       |
|    Mac.    : 2385   0      0.00    83.33   12.40    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 -   9.238: 1154   |   5:    46.192 -  55.430:   80        |
|      1:     9.238 -  18.477:  816   |   6:    55.430 -  64.669:   34        |
|      2:    18.477 -  27.715:  398   |   7:    64.669 -  73.907:   15        |
|      3:    27.715 -  36.954:  206   |   8:    73.907 -  83.146:    4        |
|      4:    36.954 -  46.192:  114   |   9:    83.146 -  92.384:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2851 r_free = 0.3464             target_work(ml) = 5.932         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2849 r_free = 0.3463             target_work(ml) = 5.932         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2849   r_free= 0.3463   ksol= 0.34   Bsol= 50.00   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.62,3.85,7.45,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.931931                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2820   r_free= 0.3442   ksol= 0.33   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.01,4.33,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.931703                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.995101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.253   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.931  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2820      final r-factor (work) = 0.2173          |
| start r-factor (free) = 0.3442      final r-factor (free) = 0.2765          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.9881 = 5.00 * 0.50 * 5.9554 + 1.00 * 0.1143                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6455 = 5.00 * 0.50 * 5.8328 + 1.00 * 0.0779                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2173      final r-factor (work) = 0.2024          |
| start r-factor (free) = 0.2765      final r-factor (free) = 0.2581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7764 = 0.30 * 1.00 * 5.8328 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7263 = 0.30 * 1.00 * 5.6825 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.86   15.20    None  None   None       |
|    all(noH): 2823   0      0.00    87.86   15.20    None  None   None       |
|    Sol.    : 438    0      3.04    87.86   36.29    None  None   None       |
|    Mac.    : 2385   0      0.00    79.35   11.33    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 -   8.786: 1180   |   5:    43.929 -  52.715:   99        |
|      1:     8.786 -  17.572:  886   |   6:    52.715 -  61.501:   37        |
|      2:    17.572 -  26.357:  288   |   7:    61.501 -  70.286:   16        |
|      3:    26.357 -  35.143:  175   |   8:    70.286 -  79.072:    7        |
|      4:    35.143 -  43.929:  133   |   9:    79.072 -  87.858:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2024 r_free = 0.2581             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2019 r_free = 0.2577             target_work(ml) = 5.651         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2019   r_free= 0.2577   ksol= 0.33   Bsol= 50.00   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.01,4.33,0.00,0.00,0.00); trace/3= 2.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.650625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2006   r_free= 0.2565   ksol= 0.32   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,0.52,2.57,0.00,0.00,0.00); trace/3= 0.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.650074                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.699895              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.082   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.438055              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.352  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2006      final r-factor (work) = 0.1563          |
| start r-factor (free) = 0.2565      final r-factor (free) = 0.2048          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6056 = 3.70 * 0.50 * 5.6908 + 1.00 * 0.0779                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3393 = 3.70 * 0.50 * 5.5499 + 1.00 * 0.0722                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1563      final r-factor (work) = 0.1439          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4407 = 0.44 * 1.00 * 5.5499 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3728 = 0.44 * 1.00 * 5.3876 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.22   15.47    None  None   None       |
|    all(noH): 2823   0      0.00    90.22   15.47    None  None   None       |
|    Sol.    : 438    0      3.28    90.22   40.20    None  None   None       |
|    Mac.    : 2385   0      0.00    81.34   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.022: 1265   |   5:    45.111 -  54.134:  110        |
|      1:     9.022 -  18.045:  897   |   6:    54.134 -  63.156:   66        |
|      2:    18.045 -  27.067:  212   |   7:    63.156 -  72.178:   25        |
|      3:    27.067 -  36.089:  118   |   8:    72.178 -  81.200:    9        |
|      4:    36.089 -  45.111:  116   |   9:    81.200 -  90.222:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1439 r_free = 0.1942             target_work(ml) = 5.363         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1438 r_free = 0.1941             target_work(ml) = 5.363         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1438   r_free= 0.1941   ksol= 0.32   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.57,0.52,2.57,0.00,0.00,0.00); trace/3= 0.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.362670                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1439   r_free= 0.1943   ksol= 0.32   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.07,1.86,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.362892                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.068924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.679  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.497140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.675   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1439      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1943      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6485 = 2.07 * 0.50 * 5.3904 + 1.00 * 0.0722                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5739 = 2.07 * 0.50 * 5.3297 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1766          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6614 = 0.50 * 1.00 * 5.3297 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6380 = 0.50 * 1.00 * 5.2835 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.54   15.41    None  None   None       |
|    all(noH): 2823   0      0.00    91.54   15.41    None  None   None       |
|    Sol.    : 438    0      3.95    91.54   40.26    None  None   None       |
|    Mac.    : 2385   0      0.00    80.47   10.84    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 -   9.154: 1304   |   5:    45.769 -  54.922:  107        |
|      1:     9.154 -  18.307:  881   |   6:    54.922 -  64.076:   64        |
|      2:    18.307 -  27.461:  198   |   7:    64.076 -  73.230:   25        |
|      3:    27.461 -  36.615:  123   |   8:    73.230 -  82.383:   10        |
|      4:    36.615 -  45.769:  108   |   9:    82.383 -  91.537:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1766             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1299 r_free = 0.1765             target_work(ml) = 5.278         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1765   ksol= 0.32   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.07,1.86,0.00,0.00,0.00); trace/3= 0.28                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.277890                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9233 -  4.6575 0.99   1460  161 0.1061 0.1423      5.4731      5.6637|
|  2:  4.6575 -  3.7156 0.99   1414  155 0.0927 0.1218      5.5319      5.7444|
|  3:  3.7156 -  3.2515 0.99   1387  159 0.1262 0.1656      5.6207      5.8904|
|  4:  3.2515 -  2.9567 0.99   1360  142 0.1474 0.1950       5.563      5.7815|
|  5:  2.9567 -  2.7462 0.98   1373  158 0.1583 0.1748      5.4752      5.6052|
|  6:  2.7462 -  2.5852 0.99   1349  151 0.1475 0.2362      5.3415      5.6321|
|  7:  2.5852 -  2.4563 0.99   1331  164 0.1452 0.1827      5.2844      5.4317|
|  8:  2.4563 -  2.3498 0.99   1371  142 0.1406 0.1975       5.213      5.3986|
|  9:  2.3498 -  2.2596 0.99   1347  144 0.1388 0.1967       5.137      5.4084|
| 10:  2.2596 -  2.1819 0.98   1328  150 0.1285 0.1858      5.0458      5.2525|
| 11:  2.1819 -  2.1139 0.98   1322  149 0.1318 0.2088      5.0181      5.4111|
| 12:  2.1139 -  2.0536 1.00   1346  150 0.1312 0.1698      4.9717       5.159|
| 13:  2.0536 -  1.9997 0.73   1003  102 0.1269 0.1986      4.8701      5.0735|
| 14:  1.9997 -  1.9510 0.18    239   32 0.1118 0.1598      4.7712      4.9419|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9233 -  4.6575  1460   161  0.93  10.82   0.97     0.94       9283.95|
|  2:  4.6575 -  3.7156  1414   155  0.94   9.43   1.02     1.00      11208.41|
|  3:  3.7156 -  3.2515  1387   159  0.92  13.58   1.03     1.02      13533.76|
|  4:  3.2515 -  2.9567  1360   142  0.90  16.36   1.01     1.00      12478.83|
|  5:  2.9567 -  2.7462  1373   158  0.87  19.26   1.00     0.98      11588.96|
|  6:  2.7462 -  2.5852  1349   151  0.88  18.66   0.97     0.93       8710.19|
|  7:  2.5852 -  2.4563  1331   164  0.88  18.58   0.98     0.94       8135.14|
|  8:  2.4563 -  2.3498  1371   142  0.88  18.40   1.00     0.96       7036.14|
|  9:  2.3498 -  2.2596  1347   144  0.88  18.72   1.00     0.96       6319.38|
| 10:  2.2596 -  2.1819  1328   150  0.88  17.94   1.00     0.96       5393.51|
| 11:  2.1819 -  2.1139  1322   149  0.88  18.59   0.99     0.95       5218.14|
| 12:  2.1139 -  2.0536  1346   150  0.88  18.54   0.99     0.99       4852.68|
| 13:  2.0536 -  1.9997  1003   102  0.88  18.44   0.98     0.96       3991.97|
| 14:  1.9997 -  1.9510   239    32  0.92  14.39   0.96     0.92       2903.10|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2903.10 max =        13533.76 mean =      8342.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.58|
|phase err.(test): min =        0.00 max =           89.52 mean =        16.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1765   ksol= 0.32   Bsol= 51.60   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,-0.18,1.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.277939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1765   ksol= 0.32   Bsol= 51.60   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,-0.18,1.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.277939                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9233 -  4.6575 0.99   1460  161 0.1062 0.1424      5.4737      5.6647|
|  2:  4.6575 -  3.7156 0.99   1414  155 0.0928 0.1218      5.5326       5.745|
|  3:  3.7156 -  3.2515 0.99   1387  159 0.1263 0.1657       5.621      5.8906|
|  4:  3.2515 -  2.9567 0.99   1360  142 0.1473 0.1949      5.5628      5.7816|
|  5:  2.9567 -  2.7462 0.98   1373  158 0.1582 0.1747      5.4749      5.6049|
|  6:  2.7462 -  2.5852 0.99   1349  151 0.1475 0.2360      5.3414      5.6321|
|  7:  2.5852 -  2.4563 0.99   1331  164 0.1451 0.1826      5.2843      5.4315|
|  8:  2.4563 -  2.3498 0.99   1371  142 0.1406 0.1976       5.213      5.3988|
|  9:  2.3498 -  2.2596 0.99   1347  144 0.1388 0.1967      5.1368      5.4081|
| 10:  2.2596 -  2.1819 0.98   1328  150 0.1286 0.1858      5.0457      5.2522|
| 11:  2.1819 -  2.1139 0.98   1322  149 0.1318 0.2087      5.0179      5.4107|
| 12:  2.1139 -  2.0536 1.00   1346  150 0.1312 0.1699      4.9717      5.1597|
| 13:  2.0536 -  1.9997 0.73   1003  102 0.1269 0.1986      4.8699      5.0728|
| 14:  1.9997 -  1.9510 0.18    239   32 0.1119 0.1598      4.7714      4.9418|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9233 -  4.6575  1460   161  0.93  10.83   0.97     0.94       9297.41|
|  2:  4.6575 -  3.7156  1414   155  0.94   9.44   1.02     1.00      11225.43|
|  3:  3.7156 -  3.2515  1387   159  0.92  13.59   1.03     1.02      13550.90|
|  4:  3.2515 -  2.9567  1360   142  0.90  16.36   1.01     1.00      12478.55|
|  5:  2.9567 -  2.7462  1373   158  0.87  19.26   1.00     0.98      11585.84|
|  6:  2.7462 -  2.5852  1349   151  0.88  18.66   0.98     0.93       8703.76|
|  7:  2.5852 -  2.4563  1331   164  0.88  18.57   0.98     0.94       8133.02|
|  8:  2.4563 -  2.3498  1371   142  0.88  18.40   1.00     0.96       7035.68|
|  9:  2.3498 -  2.2596  1347   144  0.88  18.72   1.00     0.96       6317.93|
| 10:  2.2596 -  2.1819  1328   150  0.88  17.94   1.00     0.97       5389.80|
| 11:  2.1819 -  2.1139  1322   149  0.88  18.58   1.00     0.95       5211.76|
| 12:  2.1139 -  2.0536  1346   150  0.88  18.55   1.00     0.99       4852.81|
| 13:  2.0536 -  1.9997  1003   102  0.88  18.44   0.98     0.96       3992.25|
| 14:  1.9997 -  1.9510   239    32  0.92  14.39   0.97     0.92       2902.21|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2902.21 max =        13550.90 mean =      8344.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.58|
|phase err.(test): min =        0.00 max =           89.58 mean =        16.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    91.88   15.75    None  None   None       |
|    all(noH): 2823   0      0.34    91.88   15.75    None  None   None       |
|    Sol.    : 438    0      4.29    91.88   40.60    None  None   None       |
|    Mac.    : 2385   0      0.34    80.81   11.18    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:     0.339 -   9.492: 1304   |   5:    46.107 -  55.261:  107        |
|      1:     9.492 -  18.646:  881   |   6:    55.261 -  64.415:   64        |
|      2:    18.646 -  27.800:  198   |   7:    64.415 -  73.568:   25        |
|      3:    27.800 -  36.953:  123   |   8:    73.568 -  82.722:   10        |
|      4:    36.953 -  46.107:  108   |   9:    82.722 -  91.876:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.561 - 4.305
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 326
   mapped sites are within: 0.761 - 4.305

peak=   10.216 closest distance to " CB  VAL A 230 " =    1.471
peak=    8.907 closest distance to " O   HOH Z 203 " =    0.912
peak=    7.772 closest distance to " O   HOH Z 103 " =    1.094
peak=    7.439 closest distance to " O   HOH Z 255 " =    1.378
peak=    7.154 closest distance to " CG1 VAL A 296 " =    1.256
peak=    6.968 closest distance to " CD1AILE A 234 " =    1.300
peak=    6.926 closest distance to " O   HOH Z 169 " =    1.391
peak=    6.551 closest distance to " CD2 LEU A   5 " =    1.184
peak=    5.841 closest distance to " O   HOH Z 248 " =    1.373
peak=    5.726 closest distance to " O   HOH Z 188 " =    1.762
peak=    5.410 closest distance to " O   HOH Z 375 " =    1.298
peak=    5.150 closest distance to " NH2AARG A 145 " =    1.146
peak=    5.146 closest distance to " O   HOH Z 258 " =    1.340
peak=    5.105 closest distance to " O  BHOH Z  74 " =    1.102
peak=    5.096 closest distance to " O   HOH Z 124 " =    1.349
peak=    5.021 closest distance to " NE2 GLN A  11 " =    1.154
peak=    4.999 closest distance to " CG  PRO A  54 " =    1.459
peak=    4.910 closest distance to " CZ  PHE A 218 " =    1.177
peak=    4.817 closest distance to " O   HOH Z  43 " =    1.892
peak=    4.792 closest distance to " O   HOH Z 403 " =    1.721
peak=    4.770 closest distance to " CB  ARG A 275 " =    0.990
peak=    4.733 closest distance to " O   HOH Z 394 " =    1.520
peak=    4.725 closest distance to " O   HOH Z 117 " =    1.197
peak=    4.707 closest distance to " CD2 TRP A 179 " =    1.332
peak=    4.686 closest distance to " O   HOH Z 402 " =    1.432
peak=    4.672 closest distance to " O   HOH Z  95 " =    1.495
peak=    4.667 closest distance to " CB  GLN A 223 " =    1.562
peak=    4.652 closest distance to " NH2 ARG A  56 " =    2.064
peak=    4.618 closest distance to " CG  LEU A   5 " =    1.298
peak=    4.566 closest distance to " CB  ASN A 148 " =    1.293
peak=    4.561 closest distance to " CB  SER A  26 " =    1.780
peak=    4.531 closest distance to " CZ3 TRP A 266 " =    1.096
peak=    4.503 closest distance to " O   HOH Z  97 " =    1.504
peak=    4.493 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.489 closest distance to " O   HOH Z 232 " =    2.337
peak=    4.480 closest distance to " O   HOH Z 251 " =    1.825
peak=    4.467 closest distance to " O   HOH Z 107 " =    1.117
peak=    4.460 closest distance to " CB  ASN A 142 " =    1.151
peak=    4.439 closest distance to " O   HOH Z  76 " =    1.302
peak=    4.392 closest distance to " CG  LEU A 228 " =    1.252
peak=    4.388 closest distance to " O   HOH Z 425 " =    1.591
peak=    4.377 closest distance to " O   HOH Z 238 " =    1.772
peak=    4.365 closest distance to " CA  ALA A  51 " =    1.024
peak=    4.331 closest distance to " CA  TYR A  30 " =    0.988
peak=    4.313 closest distance to " O   HOH Z 236 " =    1.550
peak=    4.294 closest distance to " CG  PRO A 243 " =    1.117
peak=    4.265 closest distance to " O   HOH Z 193 " =    2.037
peak=    4.260 closest distance to " CB  VAL A 296 " =    1.032
peak=    4.257 closest distance to " O   SER A  87 " =    2.423
peak=    4.232 closest distance to " O   HOH Z 128 " =    1.573
peak=    4.230 closest distance to " CA  GLN A  58 " =    0.774
peak=    4.197 closest distance to " O   HOH Z 246 " =    1.230
peak=    4.190 closest distance to " CG2 VAL A 296 " =    1.067
peak=    4.157 closest distance to " CB  PRO A  54 " =    0.978
peak=    4.130 closest distance to " O   HOH Z 143 " =    1.478
peak=    4.121 closest distance to " O   HOH Z 126 " =    1.673
peak=    4.119 closest distance to " CB  GLN A  58 " =    1.184
peak=    4.102 closest distance to " NH1AARG A 102 " =    1.016
peak=    4.077 closest distance to " O   HOH Z 372 " =    1.069
peak=    4.051 closest distance to " O   HOH Z  30 " =    1.510
peak=    4.018 closest distance to " CG2 VAL A 257 " =    0.847
peak=    4.007 closest distance to " O   HOH Z   4 " =    1.598
peak=    4.005 closest distance to " O   HOH Z 411 " =    3.978
peak=    3.991 closest distance to " O   HOH Z 112 " =    1.080
peak=    3.971 closest distance to " O   HOH Z  85 " =    1.399
peak=    3.960 closest distance to " CB  ALA A 114 " =    0.855
peak=    3.947 closest distance to " CD2 LEU A 228 " =    1.171
peak=    3.940 closest distance to " CB  GLU A 277 " =    3.723
peak=    3.939 closest distance to " CD1 LEU A  96 " =    0.852
peak=    3.923 closest distance to " CA  ASP A 162 " =    1.092
peak=    3.920 closest distance to " O   HOH Z 249 " =    1.228
peak=    3.913 closest distance to " O   HOH Z  69 " =    0.835
peak=    3.912 closest distance to " O   HOH Z 369 " =    2.162
peak=    3.900 closest distance to " O   HOH Z 263 " =    1.813
peak=    3.884 closest distance to " CG  ARG A 138 " =    1.454
peak=    3.883 closest distance to " CD  LYS A  76 " =    1.727
peak=    3.878 closest distance to " CG AARG A 275 " =    1.310
peak=    3.870 closest distance to " O   HOH Z   3 " =    1.886
peak=    3.869 closest distance to " CB  ARG A  79 " =    1.135
peak=    3.860 closest distance to " NE AARG A 145 " =    0.899
peak=    3.859 closest distance to " CD  ARG A 159 " =    0.761
peak=    3.856 closest distance to " O   HOH Z 126 " =    1.499
peak=    3.855 closest distance to " O   HOH Z 234 " =    3.492
peak=    3.850 closest distance to " CB  TYR A 169 " =    0.902
peak=    3.850 closest distance to " NH1AARG A 145 " =    1.140
peak=    3.849 closest distance to " CA  ILE A 234 " =    0.998
peak=    3.848 closest distance to " CG2 ILE A 234 " =    1.087
peak=    3.847 closest distance to " CB  GLN A 183 " =    1.293
peak=    3.846 closest distance to " O   HOH Z 406 " =    1.695
peak=    3.835 closest distance to " O   HOH Z  80 " =    1.906
peak=    3.833 closest distance to " CB  GLU A 152 " =    1.301
peak=    3.832 closest distance to " O   HOH Z 261 " =    2.502
peak=    3.828 closest distance to " O   HOH Z 365 " =    2.341
peak=    3.824 closest distance to " O   HOH Z 346 " =    1.525
peak=    3.823 closest distance to " O   HOH Z 132 " =    2.623
peak=    3.822 closest distance to " O   HOH Z 214 " =    1.360
peak=    3.808 closest distance to " CG AARG A 102 " =    1.160
peak=    3.806 closest distance to " CB  ASN A 110 " =    1.134
peak=    3.802 closest distance to " O   HOH Z 359 " =    1.843
peak=    3.798 closest distance to " CG  GLN A  58 " =    1.289
peak=    3.797 closest distance to " CD  LYS A 166 " =    1.423
peak=    3.796 closest distance to " O   HOH Z 207 " =    1.344
peak=    3.795 closest distance to " CA  ARG A  36 " =    1.031
peak=    3.790 closest distance to " CE  LYS A  76 " =    0.866
peak=    3.769 closest distance to " O   PRO A 198 " =    1.566
peak=    3.766 closest distance to " O   HOH Z 295 " =    1.236
peak=    3.766 closest distance to " O   HOH Z 272 " =    1.833
peak=    3.759 closest distance to " NH2AARG A 190 " =    2.057
peak=    3.747 closest distance to " O   HOH Z 258 " =    1.487
peak=    3.743 closest distance to " CB  PRO A  90 " =    1.142
peak=    3.742 closest distance to " CG  LEU A 167 " =    1.175
peak=    3.741 closest distance to " O   HOH Z 365 " =    2.518
peak=    3.734 closest distance to " O   HOH Z 199 " =    1.327
peak=    3.732 closest distance to " O   HOH Z 209 " =    2.248
peak=    3.727 closest distance to " CB  LYS A 117 " =    1.203
peak=    3.719 closest distance to " O   HOH Z 126 " =    2.054
peak=    3.711 closest distance to " O   HOH Z 142 " =    1.568
peak=    3.706 closest distance to " O   HOH Z 303 " =    2.150
peak=    3.705 closest distance to " CB  ASP A 124 " =    0.986
peak=    3.687 closest distance to " O   HOH Z 130 " =    2.628
peak=    3.686 closest distance to " O   HOH Z 427 " =    2.755
peak=    3.678 closest distance to " O   HOH Z 188 " =    2.446
peak=    3.664 closest distance to " ND2 ASN A 249 " =    0.913
peak=    3.662 closest distance to " CD  PRO A  54 " =    0.911
peak=    3.660 closest distance to " ND2 ASN A 187 " =    1.693
peak=    3.651 closest distance to " O   HOH Z 265 " =    2.037
peak=    3.649 closest distance to " O   HOH Z  59 " =    2.119
peak=    3.647 closest distance to " CG  ARG A  56 " =    1.162
peak=    3.646 closest distance to " O   HOH Z 287 " =    1.710
peak=    3.642 closest distance to " CD2 LEU A 297 " =    0.955
peak=    3.636 closest distance to " O   HOH Z 129 " =    1.265
peak=    3.627 closest distance to " CG2AVAL A 121 " =    2.176
peak=    3.624 closest distance to " CB  GLN A  55 " =    0.891
peak=    3.622 closest distance to " NH2 ARG A  56 " =    1.145
peak=    3.618 closest distance to " O   HOH Z 404 " =    1.500
peak=    3.616 closest distance to " O   HOH Z 357 " =    2.106
peak=    3.603 closest distance to " O   HOH Z 423 " =    1.779
peak=    3.600 closest distance to " CG  MET A 185 " =    1.233
peak=    3.591 closest distance to " O   HOH Z  78 " =    1.683
peak=    3.588 closest distance to " CA  ASN A 217 " =    1.137
peak=    3.585 closest distance to " CB  SER A  63 " =    1.224
peak=    3.579 closest distance to " O   HOH Z 130 " =    1.109
peak=    3.577 closest distance to " NZ  LYS A 117 " =    2.978
peak=    3.574 closest distance to " O   HOH Z 403 " =    1.431
peak=    3.570 closest distance to " O   HOH Z 337 " =    2.073
peak=    3.570 closest distance to " CG  PHE A 204 " =    1.005
peak=    3.568 closest distance to " CB  VAL A 265 " =    1.224
peak=    3.567 closest distance to " O   HOH Z 422 " =    2.543
peak=    3.558 closest distance to " CB  ARG A 138 " =    0.931
peak=    3.555 closest distance to " CB  THR A 235 " =    1.291
peak=    3.548 closest distance to " CB  THR A  52 " =    0.844
peak=    3.539 closest distance to " CB  SER A 271 " =    1.429
peak=    3.538 closest distance to " CB  ASP A 191 " =    1.287
peak=    3.537 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.534 closest distance to " CB  ALA A 248 " =    1.444
peak=    3.532 closest distance to " CB  THR A  31 " =    1.556
peak=    3.530 closest distance to " CG1 ILE A  20 " =    1.276
peak=    3.518 closest distance to " O   HOH Z 371 " =    1.452
peak=    3.515 closest distance to " CG  PRO A 198 " =    1.225
peak=    3.509 closest distance to " CB BVAL A  41 " =    1.311
peak=    3.506 closest distance to " N   PHE A  59 " =    0.801
peak=    3.500 closest distance to " CD  ARG A 269 " =    1.055
peak=    3.498 closest distance to " O   HOH Z 172 " =    3.543
peak=    3.494 closest distance to " O   THR A 182 " =    1.458
peak=    3.494 closest distance to " CA  ALA A 295 " =    0.952
peak=    3.493 closest distance to " N   ASP A 162 " =    1.273
peak=    3.489 closest distance to " CZ  PHE A  38 " =    1.031
peak=    3.485 closest distance to " O   HOH Z 371 " =    2.707
peak=    3.483 closest distance to " O   HOH Z 156 " =    3.204
peak=    3.482 closest distance to " CE  LYS A 119 " =    1.108
peak=    3.480 closest distance to " CB  ARG A 145 " =    1.075
peak=    3.472 closest distance to " ND2BASN A 224 " =    0.776
peak=    3.471 closest distance to " CG2 ILE A 120 " =    1.436
peak=    3.466 closest distance to " OG BSER A 212 " =    2.478
peak=    3.462 closest distance to " O   HOH Z   9 " =    0.990
peak=    3.456 closest distance to " CB  ASP A 298 " =    1.156
peak=    3.453 closest distance to " OG  SER A 146 " =    0.772
peak=    3.452 closest distance to " O   HOH Z 171 " =    3.461
peak=    3.447 closest distance to " CB  GLN A  89 " =    1.175
peak=    3.442 closest distance to " CE3 TRP A 274 " =    1.310
peak=    3.437 closest distance to " O   HOH Z 140 " =    1.782
peak=    3.436 closest distance to " CB  ASN A 215 " =    1.079
peak=    3.434 closest distance to " CG  PRO A 213 " =    1.268
peak=    3.431 closest distance to " O   HOH Z 141 " =    1.670
peak=    3.424 closest distance to " CB  ARG A 219 " =    1.190
peak=    3.424 closest distance to " OG ASER A 258 " =    3.005
peak=    3.419 closest distance to " O   HOH Z 368 " =    3.357
peak=    3.415 closest distance to " CB  ARG A  79 " =    0.882
peak=    3.415 closest distance to " NE1 TRP A  92 " =    1.715
peak=    3.411 closest distance to " O   HOH Z 419 " =    1.830
peak=    3.411 closest distance to " CB  SER A  99 " =    0.780
peak=    3.409 closest distance to " CB  ARG A 190 " =    1.716
peak=    3.406 closest distance to " O   HOH Z  19 " =    1.676
peak=    3.396 closest distance to " O   HOH Z 116 " =    1.106
peak=    3.389 closest distance to " N   TYR A  15 " =    1.110
peak=    3.387 closest distance to " CA  ALA A 100 " =    0.920
peak=    3.387 closest distance to " O   HOH Z 252 " =    2.457
peak=    3.386 closest distance to " NE2 GLN A  77 " =    3.165
peak=    3.383 closest distance to " CE2 TYR A 169 " =    1.296
peak=    3.380 closest distance to " CD  LYS A 119 " =    1.741
peak=    3.379 closest distance to " CB  SER A  62 " =    0.900
peak=    3.376 closest distance to " O   HOH Z  49 " =    1.133
peak=    3.376 closest distance to " CA  PHE A 283 " =    1.177
peak=    3.375 closest distance to " CB  SER A  99 " =    1.177
peak=    3.373 closest distance to " CD1 ILE A 199 " =    1.228
peak=    3.362 closest distance to " O   HOH Z  40 " =    1.566
peak=    3.357 closest distance to " O   HOH Z 409 " =    1.574
peak=    3.356 closest distance to " CA  ASN A 215 " =    1.064
peak=    3.354 closest distance to " O   HOH Z 213 " =    1.837
peak=    3.350 closest distance to " CB  TRP A 266 " =    1.183
peak=    3.341 closest distance to " O   HOH Z 383 " =    1.706
peak=    3.340 closest distance to " CB  ARG A 156 " =    1.176
peak=    3.340 closest distance to " O  BHOH Z 338 " =    2.157
peak=    3.334 closest distance to " O   HOH Z 438 " =    2.707
peak=    3.334 closest distance to " O   HOH Z 298 " =    2.404
peak=    3.331 closest distance to " O   PRO A 213 " =    1.329
peak=    3.330 closest distance to " CE2 TRP A  70 " =    1.500
peak=    3.328 closest distance to " O   HOH Z 146 " =    1.436
peak=    3.326 closest distance to " CG2 VAL A 197 " =    1.153
peak=    3.323 closest distance to " O   HOH Z 200 " =    2.328
peak=    3.322 closest distance to " CG1 ILE A  49 " =    1.621
peak=    3.321 closest distance to " O   HOH Z 407 " =    2.640
peak=    3.320 closest distance to " CB  ASN A  45 " =    1.121
peak=    3.317 closest distance to " O   HOH Z 210 " =    0.976
peak=    3.305 closest distance to " O   HOH Z 191 " =    0.950
peak=    3.301 closest distance to " O   HOH Z 154 " =    1.704
peak=    3.298 closest distance to " O   HOH Z 280 " =    3.007
peak=    3.297 closest distance to " CG1 VAL A 153 " =    0.848
peak=    3.294 closest distance to " CB  SER A   3 " =    1.338
peak=    3.293 closest distance to " O   GLN A  88 " =    1.515
peak=    3.291 closest distance to " CG  LYS A 289 " =    1.490
peak=    3.290 closest distance to " O   HOH Z  85 " =    1.613
peak=    3.286 closest distance to " CG  GLN A  11 " =    1.891
peak=    3.285 closest distance to " CB  ALA A 291 " =    0.868
peak=    3.280 closest distance to " O   HOH Z 345 " =    1.622
peak=    3.280 closest distance to " O   HOH Z 433 " =    1.369
peak=    3.280 closest distance to " CB  SER A  95 " =    1.280
peak=    3.268 closest distance to " NH1AARG A 275 " =    1.032
peak=    3.268 closest distance to " O   ALA A 165 " =    1.532
peak=    3.268 closest distance to " O   HOH Z 301 " =    2.833
peak=    3.267 closest distance to " O   HOH Z 174 " =    2.249
peak=    3.266 closest distance to " CA  ILE A 239 " =    0.955
peak=    3.266 closest distance to " O   HOH Z 109 " =    1.823
peak=    3.258 closest distance to " O   HOH Z 410 " =    3.212
peak=    3.256 closest distance to " N   ASN A  39 " =    1.315
peak=    3.255 closest distance to " O   HOH Z 189 " =    2.566
peak=    3.254 closest distance to " O   ASP A 124 " =    1.114
peak=    3.254 closest distance to " NH1 ARG A  14 " =    1.147
peak=    3.253 closest distance to " CG  LEU A 237 " =    1.530
peak=    3.253 closest distance to " O   HOH Z 247 " =    1.623
peak=    3.248 closest distance to " CB  ALA A 295 " =    1.311
peak=    3.247 closest distance to " O   HOH Z   1 " =    2.254
peak=    3.244 closest distance to " CA  ALA A 129 " =    1.436
peak=    3.243 closest distance to " OE1 GLU A   2 " =    1.739
peak=    3.238 closest distance to " O   HOH Z 112 " =    1.332
peak=    3.235 closest distance to " O   HOH Z 214 " =    3.096
peak=    3.233 closest distance to " O   HOH Z  78 " =    2.055
peak=    3.233 closest distance to " CD1 ILE A  33 " =    1.742
peak=    3.231 closest distance to " N   PHE A 130 " =    1.407
peak=    3.231 closest distance to " O   HOH Z 350 " =    1.642
peak=    3.230 closest distance to " CG2 THR A  42 " =    1.085
peak=    3.229 closest distance to " O   HOH Z 343 " =    2.648
peak=    3.227 closest distance to " CA  LYS A 290 " =    1.166
peak=    3.227 closest distance to " CB  ASP A 140 " =    1.061
peak=    3.219 closest distance to " OG  SER A  22 " =    1.914
peak=    3.218 closest distance to " O   HOH Z 298 " =    4.305
peak=    3.216 closest distance to " O   HOH Z   9 " =    2.056
peak=    3.214 closest distance to " OG  SER A  22 " =    2.504
peak=    3.213 closest distance to " O   HOH Z 162 " =    1.777
peak=    3.211 closest distance to " CB  ASN A 173 " =    0.949
peak=    3.210 closest distance to " CG2 ILE A  20 " =    1.444
peak=    3.210 closest distance to " CG  ARG A 269 " =    1.818
peak=    3.209 closest distance to " O   HOH Z 132 " =    0.843
peak=    3.207 closest distance to " CB  TRP A 179 " =    1.351
peak=    3.200 closest distance to " CG  GLN A  55 " =    2.485
peak=    3.198 closest distance to " CG2 THR A 221 " =    1.300
peak=    3.197 closest distance to " O   HOH Z 366 " =    2.383
peak=    3.193 closest distance to " O   HOH Z 132 " =    2.561
peak=    3.189 closest distance to " O   HOH Z  61 " =    1.779
peak=    3.188 closest distance to " CB  ASP A 107 " =    1.159
peak=    3.184 closest distance to " OH  TYR A  30 " =    1.004
peak=    3.183 closest distance to " O   HOH Z 148 " =    3.433
peak=    3.183 closest distance to " CG1 ILE A 120 " =    0.938
peak=    3.180 closest distance to " O   HOH Z  32 " =    2.462
peak=    3.172 closest distance to " O   HOH Z 151 " =    1.588
peak=    3.171 closest distance to " CB  PRO A 243 " =    1.024
peak=    3.171 closest distance to " CA  TYR A 116 " =    1.412
peak=    3.171 closest distance to " CA  THR A 221 " =    1.047
peak=    3.167 closest distance to " O   HOH Z 173 " =    1.752
peak=    3.166 closest distance to " CB  SER A 273 " =    0.915
peak=    3.159 closest distance to " N   TYR A 247 " =    1.430
peak=    3.157 closest distance to " CB  GLN A  58 " =    1.285
peak=    3.154 closest distance to " O   PHE A 192 " =    1.256
peak=    3.153 closest distance to " O   THR A 220 " =    1.272
peak=    3.151 closest distance to " O   HOH Z 344 " =    1.742
peak=    3.145 closest distance to " O   HOH Z  50 " =    1.786
peak=    3.145 closest distance to " O   HOH Z 293 " =    1.927
peak=    3.142 closest distance to " CG1 VAL A 257 " =    1.267
peak=    3.139 closest distance to " N   ARG A 156 " =    1.446
peak=    3.137 closest distance to " O   HOH Z 162 " =    2.944
peak=    3.131 closest distance to " O   HOH Z   9 " =    1.976
peak=    3.131 closest distance to " CE3 TRP A 150 " =    1.160
peak=    3.117 closest distance to " CE1 TYR A  30 " =    1.214
peak=    3.116 closest distance to " CA  VAL A 153 " =    0.814
peak=    3.115 closest distance to " CB  SER A 141 " =    1.103
peak=    3.115 closest distance to " O   HOH Z 417 " =    1.157
peak=    3.109 closest distance to " O   HOH Z 380 " =    2.140
peak=    3.102 closest distance to " O   HOH Z  88 " =    3.663
peak=    3.099 closest distance to " O   THR A 157 " =    1.419
peak=    3.097 closest distance to " O   HOH Z  85 " =    2.035
peak=    3.096 closest distance to " CA  ASP A 149 " =    1.060
peak=    3.082 closest distance to " CA  TYR A 214 " =    1.111
peak=    3.076 closest distance to " CB  GLU A  46 " =    1.083
peak=    3.074 closest distance to " O   HOH Z 128 " =    2.684
peak=    3.072 closest distance to " CB  VAL A 202 " =    1.505
peak=    3.066 closest distance to " CG  LEU A 101 " =    1.144
peak=    3.066 closest distance to " CG1 VAL A 125 " =    0.971
peak=    3.064 closest distance to " O   HOH Z 214 " =    2.270
peak=    3.029 closest distance to " OG BSER A  99 " =    2.905
peak=    3.014 closest distance to " O   GLU A   2 " =    1.447

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 189         
Filter by distance & map next to the model:
   mapped sites are within: 0.485 - 5.924
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 189
   mapped sites are within: 0.728 - 5.924

peak=   -5.261 closest distance to " O   HOH Z 203 " =    1.115
peak=   -4.880 closest distance to " CG2 VAL A 230 " =    0.756
peak=   -4.671 closest distance to " O   PRO A 198 " =    1.294
peak=   -4.647 closest distance to " CG1 VAL A 250 " =    2.773
peak=   -4.542 closest distance to " CG  GLN A  58 " =    0.792
peak=   -4.384 closest distance to " O   HOH Z 116 " =    1.085
peak=   -4.384 closest distance to " OG BSER A 134 " =    1.468
peak=   -4.298 closest distance to " O   HOH Z 109 " =    0.872
peak=   -4.225 closest distance to " O   HOH Z  69 " =    1.482
peak=   -4.195 closest distance to " O   HOH Z 128 " =    1.103
peak=   -4.193 closest distance to " CD  ARG A  14 " =    3.100
peak=   -4.093 closest distance to " O   HOH Z 131 " =    4.226
peak=   -4.089 closest distance to " O   HOH Z 166 " =    1.684
peak=   -4.076 closest distance to " CD2 TYR A 293 " =    1.969
peak=   -4.062 closest distance to " CG2BVAL A  41 " =    2.481
peak=   -4.026 closest distance to " CG1 VAL A 296 " =    1.019
peak=   -4.002 closest distance to " CD  ARG A 156 " =    2.088
peak=   -3.989 closest distance to " CG  ARG A 219 " =    2.443
peak=   -3.955 closest distance to " CB  ALA A  43 " =    2.538
peak=   -3.945 closest distance to " O   ASP A 107 " =    1.963
peak=   -3.932 closest distance to " O   HOH Z 423 " =    2.666
peak=   -3.927 closest distance to " O   HOH Z 357 " =    2.311
peak=   -3.918 closest distance to " O   HOH Z 387 " =    2.724
peak=   -3.883 closest distance to " O   HOH Z 211 " =    1.090
peak=   -3.883 closest distance to " O   HOH Z 216 " =    0.920
peak=   -3.863 closest distance to " OG  SER A  97 " =    2.407
peak=   -3.841 closest distance to " CB  HIS A  86 " =    1.192
peak=   -3.790 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.778 closest distance to " CG2 ILE A  20 " =    2.969
peak=   -3.771 closest distance to " CA  GLY A 241 " =    2.419
peak=   -3.758 closest distance to " C   HIS A 108 " =    1.199
peak=   -3.743 closest distance to " O   PRO A 163 " =    2.071
peak=   -3.739 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.732 closest distance to " CB  ALA A  51 " =    1.818
peak=   -3.715 closest distance to " O   HOH Z 267 " =    5.692
peak=   -3.680 closest distance to " O   HOH Z 103 " =    1.236
peak=   -3.665 closest distance to " CA  GLN A  58 " =    1.105
peak=   -3.662 closest distance to " NH2BARG A 102 " =    0.930
peak=   -3.662 closest distance to " CZ2 TRP A  92 " =    2.836
peak=   -3.659 closest distance to " CZ  TYR A 172 " =    1.795
peak=   -3.656 closest distance to " OXT GLY A 302 " =    2.925
peak=   -3.656 closest distance to " CE1 PHE A 218 " =    1.513
peak=   -3.629 closest distance to " OG1 THR A  52 " =    2.498
peak=   -3.628 closest distance to " O   HOH Z 214 " =    2.640
peak=   -3.627 closest distance to " O   HOH Z 351 " =    1.775
peak=   -3.627 closest distance to " CE1 TYR A 247 " =    2.576
peak=   -3.625 closest distance to " O   HOH Z 111 " =    1.361
peak=   -3.614 closest distance to " O   HOH Z 252 " =    3.755
peak=   -3.602 closest distance to " CD2 HIS A 207 " =    2.006
peak=   -3.595 closest distance to " O   HOH Z 119 " =    2.175
peak=   -3.590 closest distance to " CE BMET A  47 " =    1.189
peak=   -3.589 closest distance to " O   THR A   4 " =    1.288
peak=   -3.589 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.588 closest distance to " O   VAL A 174 " =    2.213
peak=   -3.571 closest distance to " O   HOH Z 348 " =    2.270
peak=   -3.557 closest distance to " CZ  PHE A  38 " =    2.303
peak=   -3.555 closest distance to " O   HOH Z 154 " =    1.411
peak=   -3.549 closest distance to " CA  ASP A 286 " =    1.579
peak=   -3.544 closest distance to " O   ALA A 227 " =    1.354
peak=   -3.528 closest distance to " CG2 VAL A 296 " =    1.137
peak=   -3.522 closest distance to " O   HOH Z 174 " =    3.593
peak=   -3.519 closest distance to " O   ALA A 256 " =    1.883
peak=   -3.519 closest distance to " O   HOH Z 275 " =    1.756
peak=   -3.518 closest distance to " OG BSER A  99 " =    1.187
peak=   -3.515 closest distance to " O   HOH Z 221 " =    1.202
peak=   -3.514 closest distance to " O   HOH Z 359 " =    2.804
peak=   -3.513 closest distance to " CA  GLY A  23 " =    1.923
peak=   -3.500 closest distance to " O   HOH Z 100 " =    0.783
peak=   -3.500 closest distance to " O   HOH Z 201 " =    2.202
peak=   -3.467 closest distance to " OG  SER A  63 " =    1.105
peak=   -3.462 closest distance to " NE2 GLN A  88 " =    1.190
peak=   -3.460 closest distance to " O   HOH Z 278 " =    0.995
peak=   -3.460 closest distance to " O   GLY A  80 " =    2.592
peak=   -3.452 closest distance to " CD1 ILE A 239 " =    2.339
peak=   -3.451 closest distance to " O   HOH Z 281 " =    2.978
peak=   -3.449 closest distance to " NE2 GLN A  11 " =    1.571
peak=   -3.440 closest distance to " O   HOH Z 126 " =    1.859
peak=   -3.439 closest distance to " O   HOH Z  64 " =    1.652
peak=   -3.438 closest distance to " CB  ALA A 129 " =    2.403
peak=   -3.430 closest distance to " SG BCYS A 201 " =    2.512
peak=   -3.418 closest distance to " CE2 TRP A  70 " =    2.188
peak=   -3.415 closest distance to " N   THR A  52 " =    1.646
peak=   -3.410 closest distance to " OD2 ASP A 191 " =    1.490
peak=   -3.398 closest distance to " OG  SER A  87 " =    1.518
peak=   -3.395 closest distance to " CG2 VAL A 189 " =    1.958
peak=   -3.393 closest distance to " O   HOH Z 286 " =    1.920
peak=   -3.387 closest distance to " O   HOH Z 285 " =    2.089
peak=   -3.383 closest distance to " O   HOH Z 165 " =    1.841
peak=   -3.376 closest distance to " CG  ARG A 269 " =    2.163
peak=   -3.366 closest distance to " CD  GLN A  73 " =    0.728
peak=   -3.361 closest distance to " NH2 ARG A  79 " =    1.417
peak=   -3.358 closest distance to " CD  GLN A 223 " =    1.139
peak=   -3.356 closest distance to " NH2 ARG A  66 " =    5.924
peak=   -3.356 closest distance to " O   HOH Z 345 " =    2.514
peak=   -3.349 closest distance to " OE2 GLU A 128 " =    2.047
peak=   -3.343 closest distance to " N   ALA A  43 " =    2.742
peak=   -3.333 closest distance to " O   HOH Z 215 " =    1.927
peak=   -3.331 closest distance to " CE3 TRP A 150 " =    2.208
peak=   -3.327 closest distance to " CB  ALA A 248 " =    2.270
peak=   -3.319 closest distance to " O   HOH Z 136 " =    1.471
peak=   -3.312 closest distance to " N   GLY A 196 " =    1.788
peak=   -3.309 closest distance to " O   GLU A 152 " =    1.345
peak=   -3.308 closest distance to " CE  LYS A  76 " =    0.819
peak=   -3.307 closest distance to " O   HOH Z 290 " =    1.006
peak=   -3.303 closest distance to " CD1 ILE A 199 " =    2.257
peak=   -3.302 closest distance to " O   HOH Z 377 " =    2.062
peak=   -3.297 closest distance to " OH  TYR A 172 " =    1.717
peak=   -3.286 closest distance to " C   ASP A 200 " =    1.029
peak=   -3.282 closest distance to " N   ALA A 226 " =    1.920
peak=   -3.280 closest distance to " O   HOH Z 191 " =    5.534
peak=   -3.279 closest distance to " O   HOH Z 297 " =    2.622
peak=   -3.279 closest distance to " CZ2 TRP A 150 " =    1.196
peak=   -3.278 closest distance to " CG  PHE A  59 " =    1.885
peak=   -3.276 closest distance to " CD  GLN A 223 " =    1.717
peak=   -3.276 closest distance to " O   HOH Z 368 " =    1.943
peak=   -3.275 closest distance to " N   ASP A 191 " =    1.262
peak=   -3.270 closest distance to " CE1 HIS A 207 " =    2.568
peak=   -3.270 closest distance to " O   HOH Z 250 " =    2.046
peak=   -3.266 closest distance to " OG BSER A 210 " =    1.642
peak=   -3.264 closest distance to " O   HOH Z 214 " =    0.872
peak=   -3.263 closest distance to " O   HOH Z 265 " =    2.552
peak=   -3.262 closest distance to " O   HOH Z 107 " =    1.022
peak=   -3.259 closest distance to " O   HOH Z   6 " =    1.608
peak=   -3.258 closest distance to " O   HOH Z 210 " =    1.011
peak=   -3.256 closest distance to " O   HOH Z 162 " =    2.915
peak=   -3.254 closest distance to " CB  ALA A   9 " =    2.180
peak=   -3.252 closest distance to " CB  ALA A 100 " =    2.202
peak=   -3.250 closest distance to " CB  ASN A  39 " =    2.258
peak=   -3.249 closest distance to " CA  ALA A 114 " =    1.012
peak=   -3.247 closest distance to " N   ASP A 286 " =    2.150
peak=   -3.240 closest distance to " O   SER A 146 " =    1.329
peak=   -3.231 closest distance to " NE  ARG A  66 " =    4.460
peak=   -3.229 closest distance to " OG1 THR A  82 " =    1.122
peak=   -3.229 closest distance to " O   HOH Z 295 " =    1.734
peak=   -3.221 closest distance to " CG  HIS A 115 " =    1.075
peak=   -3.217 closest distance to " CG2 THR A  18 " =    2.825
peak=   -3.215 closest distance to " CB  TRP A  85 " =    2.640
peak=   -3.214 closest distance to " O   HOH Z  17 " =    1.523
peak=   -3.211 closest distance to " CG  PRO A 198 " =    1.726
peak=   -3.211 closest distance to " O  BHOH Z 338 " =    1.275
peak=   -3.211 closest distance to " CG  TRP A 266 " =    1.946
peak=   -3.209 closest distance to " CD2 LEU A   5 " =    1.073
peak=   -3.208 closest distance to " O   HOH Z 421 " =    3.437
peak=   -3.208 closest distance to " NH2 ARG A 159 " =    2.401
peak=   -3.208 closest distance to " OH  TYR A 169 " =    0.865
peak=   -3.205 closest distance to " CD2 PHE A 225 " =    1.052
peak=   -3.204 closest distance to " O   HOH Z 384 " =    1.112
peak=   -3.202 closest distance to " ND2 ASN A 249 " =    2.366
peak=   -3.199 closest distance to " O   HOH Z 139 " =    5.168
peak=   -3.199 closest distance to " CG1 VAL A 112 " =    2.654
peak=   -3.197 closest distance to " CG  TYR A 169 " =    2.161
peak=   -3.190 closest distance to " OE1 GLN A  88 " =    1.082
peak=   -3.190 closest distance to " O   ASN A 187 " =    1.558
peak=   -3.189 closest distance to " O   HOH Z 266 " =    1.480
peak=   -3.187 closest distance to " O   HOH Z 102 " =    1.688
peak=   -3.181 closest distance to " O   SER A 273 " =    1.161
peak=   -3.173 closest distance to " OXT GLY A 302 " =    3.520
peak=   -3.172 closest distance to " CD  GLU A  44 " =    1.165
peak=   -3.167 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.165 closest distance to " O   HOH Z 246 " =    1.552
peak=   -3.153 closest distance to " CD  PRO A 243 " =    1.674
peak=   -3.151 closest distance to " O   HOH Z 340 " =    2.111
peak=   -3.147 closest distance to " OD1 ASN A  39 " =    1.292
peak=   -3.143 closest distance to " O   HOH Z 179 " =    2.142
peak=   -3.142 closest distance to " CB  ALA A  10 " =    2.285
peak=   -3.133 closest distance to " CG  LEU A   5 " =    1.002
peak=   -3.128 closest distance to " CA  GLY A 133 " =    2.025
peak=   -3.125 closest distance to " O   HOH Z  71 " =    1.232
peak=   -3.124 closest distance to " O   HOH Z 431 " =    2.108
peak=   -3.123 closest distance to " O   HOH Z 357 " =    2.505
peak=   -3.117 closest distance to " O   HOH Z 429 " =    1.459
peak=   -3.113 closest distance to " CB  GLN A  55 " =    1.272
peak=   -3.113 closest distance to " NH2 ARG A  66 " =    1.072
peak=   -3.098 closest distance to " OG BSER A 134 " =    1.661
peak=   -3.097 closest distance to " O   HOH Z 398 " =    1.296
peak=   -3.093 closest distance to " CG1 VAL A  78 " =    2.437
peak=   -3.090 closest distance to " O   HOH Z 149 " =    1.517
peak=   -3.088 closest distance to " N   GLN A 223 " =    0.989
peak=   -3.088 closest distance to " O   HOH Z 196 " =    2.197
peak=   -3.057 closest distance to " O   VAL A 125 " =    2.299
peak=   -3.053 closest distance to " CG1BVAL A  72 " =    2.714
peak=   -3.053 closest distance to " CB  ALA A 248 " =    2.174
peak=   -3.051 closest distance to " O   HOH Z 407 " =    2.453
peak=   -3.050 closest distance to " N   ASP A 270 " =    1.416
peak=   -3.049 closest distance to " O   HOH Z 198 " =    0.966
peak=   -3.041 closest distance to " SG  CYS A 260 " =    1.698

================= 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    :  0.5030 0.4988   6.300094e+00   6.298389e+00
   1_bss:  0.4937 0.4909   6.293727e+00   6.295278e+00
   1_xyz:  0.4272 0.4507   6.219460e+00   6.257681e+00
   1_adp:  0.3873 0.4413   6.164396e+00   6.240818e+00
   1_occ:  0.3875 0.4403   6.163302e+00   6.241336e+00
   2_bss:  0.3841 0.4376   6.164356e+00   6.241590e+00
   2_xyz:  0.3093 0.3629   5.989632e+00   6.122021e+00
   2_adp:  0.2851 0.3464   5.932402e+00   6.082394e+00
   2_occ:  0.2849 0.3463   5.931931e+00   6.081724e+00
   3_bss:  0.2820 0.3442   5.931703e+00   6.080594e+00
   3_xyz:  0.2173 0.2765   5.715152e+00   5.899614e+00
   3_adp:  0.2024 0.2581   5.651372e+00   5.837111e+00
   3_occ:  0.2019 0.2577   5.650625e+00   5.837295e+00
   4_bss:  0.2006 0.2565   5.650074e+00   5.836359e+00
   4_xyz:  0.1563 0.2048   5.425771e+00   5.629889e+00
   4_adp:  0.1439 0.1942   5.363085e+00   5.581426e+00
   4_occ:  0.1438 0.1941   5.362670e+00   5.581415e+00
   5_bss:  0.1439 0.1943   5.362892e+00   5.581253e+00
   5_xyz:  0.1323 0.1785   5.291045e+00   5.511637e+00
   5_adp:  0.1301 0.1766   5.278297e+00   5.500466e+00
   5_occ:  0.1299 0.1765   5.277890e+00   5.500597e+00
   5_bss:  0.1299 0.1765   5.277939e+00   5.500662e+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:  0.314   0.000   8.065   7.826  11.815   0.000   0.000   0.000
   1_xyz:  0.314   0.000   8.065   7.826  11.815   0.000   0.000   0.000
   1_adp:  0.314   0.000   8.065   7.826  11.815   0.000   0.000   0.000
   1_occ:  0.314   0.000   8.065   7.826  11.815   0.000   0.000   0.000
   2_bss:  0.341  50.000   3.616   3.849   7.455   0.000   0.000   0.000
   2_xyz:  0.341  50.000   3.616   3.849   7.455   0.000   0.000   0.000
   2_adp:  0.341  50.000   3.616   3.849   7.455   0.000   0.000   0.000
   2_occ:  0.341  50.000   3.616   3.849   7.455   0.000   0.000   0.000
   3_bss:  0.327  50.000   1.071   2.012   4.328   0.000   0.000   0.000
   3_xyz:  0.327  50.000   1.071   2.012   4.328   0.000   0.000   0.000
   3_adp:  0.327  50.000   1.071   2.012   4.328   0.000   0.000   0.000
   3_occ:  0.327  50.000   1.071   2.012   4.328   0.000   0.000   0.000
   4_bss:  0.324  50.000  -0.573   0.521   2.571   0.000   0.000   0.000
   4_xyz:  0.324  50.000  -0.573   0.521   2.571   0.000   0.000   0.000
   4_adp:  0.324  50.000  -0.573   0.521   2.571   0.000   0.000   0.000
   4_occ:  0.324  50.000  -0.573   0.521   2.571   0.000   0.000   0.000
   5_bss:  0.318  50.000  -1.090   0.067   1.860   0.000   0.000   0.000
   5_xyz:  0.318  50.000  -1.090   0.067   1.860   0.000   0.000   0.000
   5_adp:  0.318  50.000  -1.090   0.067   1.860   0.000   0.000   0.000
   5_occ:  0.318  50.000  -1.090   0.067   1.860   0.000   0.000   0.000
   5_bss:  0.320  51.603  -1.357  -0.180   1.537  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.973 0.3548  0.4216    80287.325
   1_bss:  63.076 0.3524  0.5484    79744.080
   1_xyz:  54.909 0.4572  0.6988    64312.389
   1_adp:  51.656 0.4991  0.8340    60393.483
   1_occ:  51.613 0.4996  0.8321    60310.064
   2_bss:  51.154 0.5055  0.7333    60061.336
   2_xyz:  39.391 0.6494  0.9186    37695.103
   2_adp:  36.849 0.6796  0.9707    33694.407
   2_occ:  36.824 0.6799  0.9713    33662.347
   3_bss:  36.657 0.6819  0.8909    33539.528
   3_xyz:  27.938 0.7802  0.9824    20279.782
   3_adp:  25.523 0.8066  1.0058    17679.227
   3_occ:  25.528 0.8066  1.0059    17652.509
   4_bss:  25.434 0.8074  0.9500    17564.426
   4_xyz:  19.653 0.8652  0.9820    10878.014
   4_adp:  18.478 0.8764  0.9819     9950.774
   4_occ:  18.473 0.8765  0.9819     9951.891
   5_bss:  18.447 0.8767  0.9631     9946.292
   5_xyz:  16.779 0.8920  0.9705     8497.806
   5_adp:  16.529 0.8943  0.9677     8346.365
   5_occ:  16.530 0.8943  0.9676     8343.690
   5_bss:  16.531 0.8943  0.9697     8345.709
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3605e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3605e+01
   1_xyz:   1.771  0.014  0.108 18.489  0.007  4.107   1.5516e-01
   1_adp:   1.771  0.014  0.108 18.489  0.007  4.107   1.5516e-01
   1_occ:   1.771  0.014  0.108 18.489  0.007  4.107   1.5516e-01
   2_bss:   1.771  0.014  0.108 18.489  0.007  4.107   1.5516e-01
   2_xyz:   1.372  0.011  0.086 16.678  0.006  4.107   1.1425e-01
   2_adp:   1.372  0.011  0.086 16.678  0.006  4.107   1.1425e-01
   2_occ:   1.372  0.011  0.086 16.678  0.006  4.107   1.1425e-01
   3_bss:   1.372  0.011  0.086 16.678  0.006  4.107   1.1425e-01
   3_xyz:   1.165  0.008  0.081 15.968  0.004  4.111   7.7860e-02
   3_adp:   1.165  0.008  0.081 15.968  0.004  4.111   7.7860e-02
   3_occ:   1.165  0.008  0.081 15.968  0.004  4.111   7.7860e-02
   4_bss:   1.165  0.008  0.081 15.968  0.004  4.111   7.7860e-02
   4_xyz:   1.098  0.008  0.078 15.812  0.004  4.124   7.2244e-02
   4_adp:   1.098  0.008  0.078 15.812  0.004  4.124   7.2244e-02
   4_occ:   1.098  0.008  0.078 15.812  0.004  4.124   7.2244e-02
   5_bss:   1.098  0.008  0.078 15.812  0.004  4.124   7.2244e-02
   5_xyz:   1.004  0.007  0.076 15.447  0.004  4.112   6.0543e-02
   5_adp:   1.004  0.007  0.076 15.447  0.004  4.112   6.0543e-02
   5_occ:   1.004  0.007  0.076 15.447  0.004  4.112   6.0543e-02
   5_bss:   1.004  0.007  0.076 15.447  0.004  4.112   6.0543e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.996   6.9387e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.996   6.9387e+00
   1_xyz:  15.119  0.174  0.474 86.460  0.047  2.002   1.0449e-01
   1_adp:  15.119  0.174  0.474 86.460  0.047  2.002   1.0449e-01
   1_occ:  15.119  0.174  0.474 86.460  0.047  2.002   1.0449e-01
   2_bss:  15.119  0.174  0.474 86.460  0.047  2.002   1.0449e-01
   2_xyz:   9.746  0.136  0.264 87.921  0.059  2.153   1.8970e-01
   2_adp:   9.746  0.136  0.264 87.921  0.059  2.153   1.8970e-01
   2_occ:   9.746  0.136  0.264 87.921  0.059  2.153   1.8970e-01
   3_bss:   9.746  0.136  0.264 87.921  0.059  2.153   1.8970e-01
   3_xyz:   7.517  0.051  0.288 79.424  0.043  2.280   9.8231e-02
   3_adp:   7.517  0.051  0.288 79.424  0.043  2.280   9.8231e-02
   3_occ:   7.517  0.051  0.288 79.424  0.043  2.280   9.8231e-02
   4_bss:   7.517  0.051  0.288 79.424  0.043  2.280   9.8231e-02
   4_xyz:   8.663  0.048  0.306 84.501  0.045  2.252   8.5764e-02
   4_adp:   8.663  0.048  0.306 84.501  0.045  2.252   8.5764e-02
   4_occ:   8.663  0.048  0.306 84.501  0.045  2.252   8.5764e-02
   5_bss:   8.663  0.048  0.306 84.501  0.045  2.252   8.5764e-02
   5_xyz:   6.919  0.043  0.318 83.394  0.036  2.318   4.0098e-02
   5_adp:   6.919  0.043  0.318 83.394  0.036  2.318   4.0098e-02
   5_occ:   6.919  0.043  0.318 83.394  0.036  2.318   4.0098e-02
   5_bss:   6.919  0.043  0.318 83.394  0.036  2.318   4.0098e-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:  89.25   0.00  15.51  77.56   0.00  13.53  89.25   0.00  26.26
   1_occ:  89.25   0.00  15.51  77.56   0.00  13.53  89.25   0.00  26.26
   2_bss:  89.25   0.00  15.51  77.56   0.00  13.53  89.25   0.00  26.26
   2_xyz:  89.25   0.00  15.51  77.56   0.00  13.53  89.25   0.00  26.26
   2_adp:  92.38   0.00  15.67  83.33   0.00  12.40  92.38   0.00  33.49
   2_occ:  92.38   0.00  15.67  83.33   0.00  12.40  92.38   0.00  33.49
   3_bss:  92.38   0.00  15.67  83.33   0.00  12.40  92.38   0.00  33.49
   3_xyz:  92.38   0.00  15.67  83.33   0.00  12.40  92.38   0.00  33.49
   3_adp:  87.86   0.00  15.20  79.35   0.00  11.33  87.86   3.04  36.29
   3_occ:  87.86   0.00  15.20  79.35   0.00  11.33  87.86   3.04  36.29
   4_bss:  87.86   0.00  15.20  79.35   0.00  11.33  87.86   3.04  36.29
   4_xyz:  87.86   0.00  15.20  79.35   0.00  11.33  87.86   3.04  36.29
   4_adp:  90.22   0.00  15.47  81.34   0.00  10.92  90.22   3.28  40.20
   4_occ:  90.22   0.00  15.47  81.34   0.00  10.92  90.22   3.28  40.20
   5_bss:  90.22   0.00  15.47  81.34   0.00  10.92  90.22   3.28  40.20
   5_xyz:  90.22   0.00  15.47  81.34   0.00  10.92  90.22   3.28  40.20
   5_adp:  91.54   0.00  15.41  80.47   0.00  10.84  91.54   3.95  40.26
   5_occ:  91.54   0.00  15.41  80.47   0.00  10.84  91.54   3.95  40.26
   5_bss:  91.88   0.34  15.75  80.81   0.34  11.18  91.88   4.29  40.60
------------------------------------------------------------------------
 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:    1.305    0.032    0.415
   1_adp:    1.305    0.032    0.415
   1_occ:    1.305    0.032    0.415
   2_bss:    1.305    0.032    0.415
   2_xyz:    2.044    0.034    0.608
   2_adp:    2.044    0.034    0.608
   2_occ:    2.044    0.034    0.608
   3_bss:    2.044    0.034    0.608
   3_xyz:    1.784    0.010    0.694
   3_adp:    1.784    0.010    0.694
   3_occ:    1.784    0.010    0.694
   4_bss:    1.784    0.010    0.694
   4_xyz:    1.921    0.063    0.784
   4_adp:    1.921    0.063    0.784
   4_occ:    1.921    0.063    0.784
   5_bss:    1.921    0.063    0.784
   5_xyz:    1.916    0.043    0.799
   5_adp:    1.916    0.043    0.799
   5_occ:    1.916    0.043    0.799
   5_bss:    1.916    0.043    0.799
------------------------------------------------------------------------

CPU time actual refinement: 368.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/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_76/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_76/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.35 
  Macro-tasks:
    bulk solvent and scale       = 39.04  
    individual site refinement   = 163.20 
    weights calculation          = 32.22  
    collect and process          = 6.46   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 241.05 
  Micro-tasks:
    mask                            = 2.53   
    f_calc                          = 118.91 
    alpha_beta                      = 8.55   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 132.21 
    fmodel                         = 7.19   
    r_factors                      = 0.28   
    phase_errors                   = 10.31  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 281.42 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.091 micro seconds
Total CPU time: 6.37 minutes
from_scatterers_fft:    668 calls, 118.45 s
gradients_fft:          613 calls, 118.12 s

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

# Date 2008-01-16 Time 00:40:07 PST -0800 (1200472807.92 s)
Start R-work = 0.5030, R-free = 0.4988 (no bulk solvent and anisotropic scale)
Final R-work = 0.1479, R-free = 0.1910 (no bulk solvent and anisotropic scale)

Start R-work = 0.4937, R-free = 0.4909
Final R-work = 0.1299, R-free = 0.1765