# Date 2008-01-16 Time 01:15:22 PST -0800 (1200474922.53 s)
#phil __OFF__

Command line arguments: "../339.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 = 24324
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 339

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.6339, 88.1178, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.97088
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9376
                             d_min =   1.9709

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9376 1.97088
Completeness in resolution range: 0.926106
Completeness with d_max=infinity: 0.923313

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9380 -  4.2173 [2218/2246]  1995   223  10.1%
  bin  2:  4.2173 -  3.3599 [2130/2153]  1913   217  10.2%
  bin  3:  3.3599 -  2.9389 [2102/2127]  1898   204   9.7%
  bin  4:  2.9389 -  2.6718 [2089/2105]  1878   211  10.1%
  bin  5:  2.6718 -  2.4813 [2063/2101]  1851   212  10.3%
  bin  6:  2.4813 -  2.3355 [2057/2090]  1852   205  10.0%
  bin  7:  2.3355 -  2.2190 [2054/2091]  1858   196   9.5%
  bin  8:  2.2190 -  2.1227 [2051/2093]  1840   211  10.3%
  bin  9:  2.1227 -  2.0412 [2031/2070]  1836   195   9.6%
  bin 10:  2.0412 -  1.9709 [ 794/2076]   709    85  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/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:
        1.58 -     2.24: 19
        2.24 -     2.91: 1409
        2.91 -     3.57: 4421
        3.57 -     4.24: 9113
        4.24 -     4.90: 13106
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.578 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.593 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.647 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.723 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.732 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28063 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_339/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/model_refine_001.geo

CPU time processing inputs: 9.21


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.63395 88.1178 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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5017   r_free= 0.4892   ksol= 0.00   Bsol= 0.00   scale= 0.773    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.298618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.4009 0.3985      6.6168      6.6352|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.4294 0.4778      6.8168      6.9244|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.4773 0.4405      6.7011      6.6735|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.4944 0.4695      6.5251      6.5081|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.5373 0.4992      6.3769      6.4011|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.5277 0.5528      6.2901      6.2127|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.5258 0.4642       6.241      6.1552|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.5514 0.4893      6.1898      6.1388|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.5512 0.5782      6.1336      6.1979|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.5531 0.4881      6.0982      6.0947|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.5421 0.5800      6.0303      6.0338|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.5477 0.5063      5.9455      5.9346|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.5454 0.5557      5.8793      5.8631|
| 14:  2.0201 -  1.9709 0.23    293   38 0.5440 0.4009      5.9344      5.6977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.7038  1442   159  0.67  36.74   0.79     0.68      78736.35|
|  2:  4.7038 -  3.7530  1395   155  0.65  39.35   0.87     0.71     124546.89|
|  3:  3.7530 -  3.2843  1359   152  0.54  48.36   0.79     0.66     130477.23|
|  4:  3.2843 -  2.9867  1352   144  0.45  56.03   0.78     0.55     111138.74|
|  5:  2.9867 -  2.7741  1334   153  0.38  61.67   0.71     0.46      86880.40|
|  6:  2.7741 -  2.6114  1340   149  0.35  63.55   0.71     0.42      75703.65|
|  7:  2.6114 -  2.4813  1313   155  0.36  62.78   0.73     0.42      66560.85|
|  8:  2.4813 -  2.3737  1341   138  0.37  62.01   0.70     0.44      57471.07|
|  9:  2.3737 -  2.2826  1330   147  0.35  63.52   0.69     0.43      55421.56|
| 10:  2.2826 -  2.2041  1320   144  0.31  66.70   0.72     0.38      50808.57|
| 11:  2.2041 -  2.1354  1283   156  0.26  70.98   0.74     0.33      52054.09|
| 12:  2.1354 -  2.0745  1339   144  0.25  71.67   0.72     0.33      46520.16|
| 13:  2.0745 -  2.0201  1189   125  0.25  71.17   0.70     0.33      40695.96|
| 14:  2.0201 -  1.9709   293    38  0.31  66.84   0.77     0.32      30422.84|
|alpha:            min =        0.32 max =            0.71 mean =         0.47|
|beta:             min =    30422.84 max =       130477.23 mean =     75088.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.34|
|phase err.(test): min =        0.00 max =           89.91 mean =        59.69|
|-----------------------------------------------------------------------------|

============================== 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 = 18.120837             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.835   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.594943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.714   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      178 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1500 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2613 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3884 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5014 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6537 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7697 |
|-----------------------------------------------------------------------------|
|-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 |       54.019 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       2.062 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    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 = 12.010)------------------------------------------|
|    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: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5062   r_free= 0.4912   ksol= 0.00   Bsol= 0.00   scale= 0.745    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.299463                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4924   r_free= 0.4836   ksol= 0.32   Bsol= 1.07   scale= 0.989    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,10.16,10.96,0.00,0.00,0.00); trace/3= 9.43                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.291708                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.104967             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.131   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.491274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.540   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4924      final r-factor (work) = 0.4181          |
| start r-factor (free) = 0.4836      final r-factor (free) = 0.4408          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.7209 = 16.10 * 0.50 * 6.2965 + 1.00 * 54.0187                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.2808 = 16.10 * 0.50 * 6.2248 + 1.00 * 0.1557                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4181      final r-factor (work) = 0.3742          |
| start r-factor (free) = 0.4408      final r-factor (free) = 0.4335          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2973 = 1.49 * 1.00 * 6.2248 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1961 = 1.49 * 1.00 * 6.1528 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.38   14.65    None  None   None       |
|    all(noH): 2823   0      0.00    72.38   14.65    None  None   None       |
|    Sol.    : 438    0      0.00    72.38   25.29    None  None   None       |
|    Mac.    : 2385   0      0.00    67.69   12.70    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.238:  906   |   5:    36.191 -  43.429:   96        |
|      1:     7.238 -  14.476:  731   |   6:    43.429 -  50.667:   51        |
|      2:    14.476 -  21.714:  527   |   7:    50.667 -  57.905:   22        |
|      3:    21.714 -  28.953:  307   |   8:    57.905 -  65.143:    8        |
|      4:    28.953 -  36.191:  167   |   9:    65.143 -  72.381:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3742 r_free = 0.4335             target_work(ml) = 6.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3737 r_free = 0.4336             target_work(ml) = 6.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3737   r_free= 0.4336   ksol= 0.32   Bsol= 1.07   scale= 1.119    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,10.16,10.96,0.00,0.00,0.00); trace/3= 9.43                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.140265                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3706   r_free= 0.4270   ksol= 0.31   Bsol= 31.34   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,5.72,6.68,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.140959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.538394             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.243  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.602821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.570  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3706      final r-factor (work) = 0.2698          |
| start r-factor (free) = 0.4270      final r-factor (free) = 0.3256          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.8573 = 14.54 * 0.50 * 6.1495 + 1.00 * 0.1557                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.8953 = 14.54 * 0.50 * 6.0216 + 1.00 * 0.1234                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2698      final r-factor (work) = 0.2383          |
| start r-factor (free) = 0.3256      final r-factor (free) = 0.2941          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6506 = 0.60 * 1.00 * 6.0216 + 1.00 * 0.0207                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5265 = 0.60 * 1.00 * 5.8296 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.21   14.04    None  None   None       |
|    all(noH): 2823   0      0.00    72.21   14.04    None  None   None       |
|    Sol.    : 438    0      0.00    70.78   33.13    None  None   None       |
|    Mac.    : 2385   0      0.00    72.21   10.53    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 -   7.221: 1045   |   5:    36.105 -  43.326:   96        |
|      1:     7.221 -  14.442:  840   |   6:    43.326 -  50.547:   65        |
|      2:    14.442 -  21.663:  375   |   7:    50.547 -  57.767:   44        |
|      3:    21.663 -  28.884:  212   |   8:    57.767 -  64.988:   20        |
|      4:    28.884 -  36.105:  116   |   9:    64.988 -  72.209:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2383 r_free = 0.2941             target_work(ml) = 5.783         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2378 r_free = 0.2939             target_work(ml) = 5.783         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2378   r_free= 0.2939   ksol= 0.31   Bsol= 31.34   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,5.72,6.68,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.782805                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2348   r_free= 0.2934   ksol= 0.33   Bsol= 53.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,3.15,4.01,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.781567                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.388814              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.165   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.226587              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.778  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2348      final r-factor (work) = 0.1849          |
| start r-factor (free) = 0.2934      final r-factor (free) = 0.2296          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0115 = 3.39 * 0.50 * 5.8357 + 1.00 * 0.1234                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7094 = 3.39 * 0.50 * 5.6931 + 1.00 * 0.0629                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1849      final r-factor (work) = 0.1746          |
| start r-factor (free) = 0.2296      final r-factor (free) = 0.2168          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3023 = 0.23 * 1.00 * 5.6931 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2648 = 0.23 * 1.00 * 5.5410 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.90   13.64    None  None   None       |
|    all(noH): 2823   0      0.00    71.90   13.64    None  None   None       |
|    Sol.    : 438    0      2.86    71.85   34.71    None  None   None       |
|    Mac.    : 2385   0      0.00    71.90   9.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.191: 1144   |   5:    35.952 -  43.143:  108        |
|      1:     7.191 -  14.381:  878   |   6:    43.143 -  50.333:   78        |
|      2:    14.381 -  21.572:  285   |   7:    50.333 -  57.524:   44        |
|      3:    21.572 -  28.762:  131   |   8:    57.524 -  64.714:   20        |
|      4:    28.762 -  35.952:  125   |   9:    64.714 -  71.905:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1746 r_free = 0.2168             target_work(ml) = 5.516         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1744 r_free = 0.2168             target_work(ml) = 5.516         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1744   r_free= 0.2168   ksol= 0.33   Bsol= 53.34   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,3.15,4.01,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.515597                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1737   r_free= 0.2163   ksol= 0.33   Bsol= 53.34   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.98,3.07,0.00,0.00,0.00); trace/3= 1.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.514133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.824187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.858  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.726360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.278  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1737      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.2163      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6662 = 3.82 * 0.50 * 5.5453 + 1.00 * 0.0631                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4321 = 3.82 * 0.50 * 5.4172 + 1.00 * 0.0739                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1377      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9440 = 0.73 * 1.00 * 5.4172 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8656 = 0.73 * 1.00 * 5.2857 + 1.00 * 0.0263                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.48   14.34    None  None   None       |
|    all(noH): 2823   0      0.00    83.48   14.34    None  None   None       |
|    Sol.    : 438    0      2.14    83.48   39.56    None  None   None       |
|    Mac.    : 2385   0      0.00    83.33   9.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.349: 1373   |   5:    41.743 -  50.091:   98        |
|      1:     8.349 -  16.697:  797   |   6:    50.091 -  58.440:   73        |
|      2:    16.697 -  25.046:  199   |   7:    58.440 -  66.788:   44        |
|      3:    25.046 -  33.394:  111   |   8:    66.788 -  75.137:   26        |
|      4:    33.394 -  41.743:   90   |   9:    75.137 -  83.485:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1297 r_free = 0.1751             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1296 r_free = 0.1750             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1296   r_free= 0.1750   ksol= 0.33   Bsol= 53.34   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.98,3.07,0.00,0.00,0.00); trace/3= 1.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1753   ksol= 0.33   Bsol= 62.35   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.66,2.87,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.272961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.384088              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653761              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.331   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3746 = 2.38 * 0.50 * 5.2856 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3265 = 2.38 * 0.50 * 5.2514 + 1.00 * 0.0666                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1688          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4485 = 0.65 * 1.00 * 5.2514 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4519 = 0.65 * 1.00 * 5.2315 + 1.00 * 0.0317                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.69   14.20    None  None   None       |
|    all(noH): 2823   0      0.00    85.69   14.20    None  None   None       |
|    Sol.    : 438    0      2.23    85.69   39.32    None  None   None       |
|    Mac.    : 2385   0      0.00    84.96   9.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.569: 1435   |   5:    42.844 -  51.412:  103        |
|      1:     8.569 -  17.138:  764   |   6:    51.412 -  59.981:   58        |
|      2:    17.138 -  25.706:  182   |   7:    59.981 -  68.550:   41        |
|      3:    25.706 -  34.275:  116   |   8:    68.550 -  77.119:   27        |
|      4:    34.275 -  42.844:   89   |   9:    77.119 -  85.687:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1218 r_free = 0.1688             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1216 r_free = 0.1688             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1688   ksol= 0.33   Bsol= 62.35   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.33,1.66,2.87,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228201                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.0995 0.1332      5.4187      5.5873|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.0882 0.1066       5.459      5.6456|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.1142 0.1597      5.5219      5.8769|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.1344 0.1750      5.5158      5.6883|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.1471 0.1759      5.4233      5.5807|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.1398 0.2388      5.3186      5.6269|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.1389 0.1673      5.2676      5.4169|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.1290 0.1940       5.179      5.3954|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.1285 0.1983      5.0986      5.3988|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.1266 0.1747      5.0373       5.218|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.1244 0.2022      4.9758      5.3338|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.1224 0.1641      4.9216      5.1335|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.1201 0.1935      4.8397      5.0862|
| 14:  2.0201 -  1.9709 0.23    293   38 0.1075 0.1800      4.7808      4.9845|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.7038  1442   159  0.94   9.77   0.97     0.94       8133.90|
|  2:  4.7038 -  3.7530  1395   155  0.95   8.54   1.01     1.00       9545.69|
|  3:  3.7530 -  3.2843  1359   152  0.93  11.90   1.02     1.02      11052.45|
|  4:  3.2843 -  2.9867  1352   144  0.91  15.26   1.01     0.99      11677.85|
|  5:  2.9867 -  2.7741  1334   153  0.88  17.94   1.00     0.97      10351.35|
|  6:  2.7741 -  2.6114  1340   149  0.87  18.97   0.97     0.93       8986.67|
|  7:  2.6114 -  2.4813  1313   155  0.89  17.75   0.98     0.94       7719.04|
|  8:  2.4813 -  2.3737  1341   138  0.89  17.78   0.99     0.95       6904.57|
|  9:  2.3737 -  2.2826  1330   147  0.89  17.73   0.99     0.95       5831.65|
| 10:  2.2826 -  2.2041  1320   144  0.89  17.67   0.99     0.95       5291.02|
| 11:  2.2041 -  2.1354  1283   156  0.89  17.21   0.98     0.94       4733.59|
| 12:  2.1354 -  2.0745  1339   144  0.89  17.35   0.99     0.98       4401.65|
| 13:  2.0745 -  2.0201  1189   125  0.89  17.73   0.97     0.95       3812.71|
| 14:  2.0201 -  1.9709   293    38  0.90  15.68   0.96     0.91       3196.83|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3196.83 max =        11677.85 mean =      7559.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.72|
|phase err.(test): min =        0.00 max =           89.31 mean =        15.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1687   ksol= 0.33   Bsol= 60.23   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.00,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1687   ksol= 0.33   Bsol= 60.23   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.23,-0.00,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.228212                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9380 -  4.7038 0.99   1442  159 0.0992 0.1332      5.4164      5.5857|
|  2:  4.7038 -  3.7530 0.99   1395  155 0.0881 0.1064      5.4576      5.6438|
|  3:  3.7530 -  3.2843 0.99   1359  152 0.1142 0.1597      5.5216      5.8774|
|  4:  3.2843 -  2.9867 0.99   1352  144 0.1345 0.1751      5.5164      5.6888|
|  5:  2.9867 -  2.7741 0.98   1334  153 0.1472 0.1761      5.4241      5.5813|
|  6:  2.7741 -  2.6114 0.99   1340  149 0.1397 0.2388      5.3191      5.6274|
|  7:  2.6114 -  2.4813 0.99   1313  155 0.1390 0.1674      5.2685      5.4176|
|  8:  2.4813 -  2.3737 0.99   1341  138 0.1291 0.1940      5.1797      5.3959|
|  9:  2.3737 -  2.2826 0.99   1330  147 0.1286 0.1983       5.099      5.3996|
| 10:  2.2826 -  2.2041 0.98   1320  144 0.1265 0.1747      5.0374      5.2179|
| 11:  2.2041 -  2.1354 0.98   1283  156 0.1244 0.2020      4.9759      5.3338|
| 12:  2.1354 -  2.0745 1.00   1339  144 0.1224 0.1642      4.9216      5.1341|
| 13:  2.0745 -  2.0201 0.87   1189  125 0.1201 0.1932      4.8396       5.085|
| 14:  2.0201 -  1.9709 0.23    293   38 0.1075 0.1801      4.7822      4.9861|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9380 -  4.7038  1442   159  0.94   9.75   0.97     0.94       8102.25|
|  2:  4.7038 -  3.7530  1395   155  0.95   8.52   1.01     1.00       9516.83|
|  3:  3.7530 -  3.2843  1359   152  0.93  11.90   1.02     1.02      11034.11|
|  4:  3.2843 -  2.9867  1352   144  0.91  15.27   1.01     1.00      11684.61|
|  5:  2.9867 -  2.7741  1334   153  0.88  17.95   1.00     0.98      10368.04|
|  6:  2.7741 -  2.6114  1340   149  0.87  18.98   0.97     0.94       8998.45|
|  7:  2.6114 -  2.4813  1313   155  0.89  17.77   0.99     0.94       7732.57|
|  8:  2.4813 -  2.3737  1341   138  0.89  17.80   1.00     0.96       6914.90|
|  9:  2.3737 -  2.2826  1330   147  0.89  17.74   0.99     0.95       5840.29|
| 10:  2.2826 -  2.2041  1320   144  0.89  17.67   0.99     0.96       5293.11|
| 11:  2.2041 -  2.1354  1283   156  0.89  17.21   0.99     0.95       4732.60|
| 12:  2.1354 -  2.0745  1339   144  0.89  17.35   1.00     0.99       4401.24|
| 13:  2.0745 -  2.0201  1189   125  0.89  17.73   0.98     0.96       3811.22|
| 14:  2.0201 -  1.9709   293    38  0.90  15.70   0.97     0.92       3198.66|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3198.66 max =        11684.61 mean =      7558.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.73|
|phase err.(test): min =        0.00 max =           89.32 mean =        15.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.010)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    87.43   15.94    None  None   None       |
|    all(noH): 2823   0      1.74    87.43   15.94    None  None   None       |
|    Sol.    : 438    0      3.97    87.43   41.06    None  None   None       |
|    Mac.    : 2385   0      1.74    86.70   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:     1.742 -  10.311: 1435   |   5:    44.586 -  53.154:  103        |
|      1:    10.311 -  18.879:  764   |   6:    53.154 -  61.723:   58        |
|      2:    18.879 -  27.448:  182   |   7:    61.723 -  70.292:   41        |
|      3:    27.448 -  36.017:  116   |   8:    70.292 -  78.860:   27        |
|      4:    36.017 -  44.586:   89   |   9:    78.860 -  87.429:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.508 - 4.961
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 312
   mapped sites are within: 0.711 - 4.961

peak=   10.297 closest distance to " CB  VAL A 230 " =    1.452
peak=    6.390 closest distance to " CG1 VAL A 296 " =    1.201
peak=    5.867 closest distance to " O   HOH Z 210 " =    1.291
peak=    5.441 closest distance to " CG  LEU A   5 " =    1.280
peak=    5.333 closest distance to " CD1AILE A 234 " =    1.029
peak=    5.322 closest distance to " NH2 ARG A  56 " =    2.134
peak=    5.251 closest distance to " O   HOH Z 248 " =    1.428
peak=    5.226 closest distance to " O   HOH Z 403 " =    1.864
peak=    5.068 closest distance to " CB  GLN A 223 " =    1.474
peak=    4.998 closest distance to " CG  PRO A  54 " =    1.367
peak=    4.931 closest distance to " CD2 LEU A   5 " =    1.167
peak=    4.919 closest distance to " O   HOH Z  76 " =    1.232
peak=    4.833 closest distance to " O   HOH Z 404 " =    1.184
peak=    4.819 closest distance to " NE2 GLN A  11 " =    1.106
peak=    4.758 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.751 closest distance to " CD2 LEU A 228 " =    1.304
peak=    4.725 closest distance to " CB  VAL A 296 " =    1.074
peak=    4.697 closest distance to " O   HOH Z 238 " =    1.524
peak=    4.689 closest distance to " O   HOH Z 124 " =    1.279
peak=    4.574 closest distance to " O   HOH Z 130 " =    2.637
peak=    4.561 closest distance to " O   HOH Z 128 " =    1.636
peak=    4.549 closest distance to " CB  PRO A  54 " =    0.991
peak=    4.530 closest distance to " O   HOH Z 251 " =    1.705
peak=    4.491 closest distance to " CG  LEU A 228 " =    1.219
peak=    4.471 closest distance to " O   HOH Z 126 " =    1.616
peak=    4.466 closest distance to " CG2 VAL A 296 " =    1.006
peak=    4.457 closest distance to " CA  TYR A  30 " =    0.964
peak=    4.386 closest distance to " O   HOH Z 214 " =    1.428
peak=    4.355 closest distance to " CA  ALA A  51 " =    1.055
peak=    4.350 closest distance to " O   HOH Z 142 " =    1.636
peak=    4.333 closest distance to " O   HOH Z 402 " =    1.483
peak=    4.331 closest distance to " O   HOH Z 346 " =    1.483
peak=    4.300 closest distance to " O   HOH Z 232 " =    2.349
peak=    4.296 closest distance to " O   HOH Z 359 " =    1.916
peak=    4.293 closest distance to " CA  VAL A 230 " =    1.231
peak=    4.278 closest distance to " CB  ARG A  79 " =    1.468
peak=    4.265 closest distance to " O   HOH Z 193 " =    1.897
peak=    4.246 closest distance to " CB  GLN A 183 " =    1.281
peak=    4.246 closest distance to " O   HOH Z  49 " =    1.364
peak=    4.238 closest distance to " O   HOH Z  63 " =    2.030
peak=    4.228 closest distance to " O   HOH Z 117 " =    1.094
peak=    4.221 closest distance to " CB  SER A  63 " =    1.149
peak=    4.211 closest distance to " O   HOH Z 406 " =    1.503
peak=    4.209 closest distance to " O   PRO A 198 " =    1.505
peak=    4.208 closest distance to " CB  GLU A 277 " =    3.715
peak=    4.200 closest distance to " CZ  PHE A 218 " =    1.130
peak=    4.184 closest distance to " O   HOH Z 425 " =    1.506
peak=    4.184 closest distance to " CD2 TRP A 179 " =    1.304
peak=    4.181 closest distance to " CB  ASN A 148 " =    1.341
peak=    4.171 closest distance to " CB  TRP A 179 " =    1.348
peak=    4.155 closest distance to " CG  PRO A 198 " =    1.226
peak=    4.118 closest distance to " CB  SER A  26 " =    1.824
peak=    4.111 closest distance to " CB  ARG A 190 " =    1.809
peak=    4.110 closest distance to " O   HOH Z 209 " =    2.299
peak=    4.102 closest distance to " O   HOH Z 154 " =    1.827
peak=    4.096 closest distance to " CA  ALA A 295 " =    1.008
peak=    4.059 closest distance to " O   HOH Z 265 " =    1.984
peak=    4.034 closest distance to " CZ  PHE A  38 " =    1.161
peak=    4.030 closest distance to " CA  ARG A  36 " =    1.023
peak=    4.027 closest distance to " O   HOH Z  43 " =    2.206
peak=    4.026 closest distance to " O   HOH Z 162 " =    1.905
peak=    4.025 closest distance to " O   HOH Z  40 " =    1.920
peak=    4.015 closest distance to " CG  PRO A 243 " =    1.169
peak=    4.010 closest distance to " O   SER A  87 " =    2.375
peak=    4.004 closest distance to " O   HOH Z 412 " =    3.785
peak=    4.004 closest distance to " CZ3 TRP A 266 " =    1.062
peak=    3.994 closest distance to " O   HOH Z 365 " =    2.343
peak=    3.989 closest distance to " O   HOH Z 234 " =    3.709
peak=    3.986 closest distance to " CB  ASN A 142 " =    1.151
peak=    3.982 closest distance to " O   HOH Z 214 " =    3.187
peak=    3.962 closest distance to " O   HOH Z 188 " =    2.853
peak=    3.962 closest distance to " CD  ARG A 159 " =    0.786
peak=    3.948 closest distance to " O   HOH Z 261 " =    2.557
peak=    3.940 closest distance to " CB BVAL A  41 " =    1.354
peak=    3.937 closest distance to " O   ASP A 124 " =    1.370
peak=    3.935 closest distance to " O   ASN A  74 " =    1.727
peak=    3.904 closest distance to " O   HOH Z 422 " =    2.670
peak=    3.899 closest distance to " O   HOH Z  85 " =    1.569
peak=    3.893 closest distance to " O   HOH Z 369 " =    2.325
peak=    3.888 closest distance to " CB  GLU A 152 " =    1.143
peak=    3.887 closest distance to " O   HOH Z 126 " =    1.917
peak=    3.872 closest distance to " OG BSER A 164 " =    2.216
peak=    3.869 closest distance to " N   ASN A  39 " =    1.266
peak=    3.857 closest distance to " O   HOH Z 431 " =    1.155
peak=    3.853 closest distance to " ND2 ASN A 249 " =    0.910
peak=    3.852 closest distance to " CB  SER A   3 " =    1.248
peak=    3.851 closest distance to " CD  LYS A 166 " =    1.446
peak=    3.838 closest distance to " O   HOH Z 144 " =    1.701
peak=    3.833 closest distance to " CG  PHE A 204 " =    0.906
peak=    3.833 closest distance to " O   ALA A 165 " =    1.369
peak=    3.822 closest distance to " O   HOH Z 303 " =    2.244
peak=    3.811 closest distance to " O   HOH Z 316 " =    3.164
peak=    3.809 closest distance to " O   HOH Z 414 " =    1.549
peak=    3.804 closest distance to " CD1 LEU A  96 " =    0.829
peak=    3.804 closest distance to " CB  ASP A 124 " =    0.744
peak=    3.793 closest distance to " CA  VAL A  41 " =    0.731
peak=    3.785 closest distance to " CA  ARG A 195 " =    1.198
peak=    3.785 closest distance to " O   HOH Z  80 " =    1.983
peak=    3.776 closest distance to " O   HOH Z 433 " =    1.474
peak=    3.760 closest distance to " CD  ARG A 269 " =    1.075
peak=    3.753 closest distance to " O   HOH Z 417 " =    3.274
peak=    3.750 closest distance to " O   HOH Z 246 " =    1.279
peak=    3.747 closest distance to " CG  PRO A 213 " =    1.225
peak=    3.746 closest distance to " O   HOH Z 365 " =    2.665
peak=    3.735 closest distance to " O   HOH Z 272 " =    1.895
peak=    3.729 closest distance to " O   HOH Z 394 " =    1.571
peak=    3.728 closest distance to " O   HOH Z 130 " =    1.134
peak=    3.680 closest distance to " ND2 ASN A 249 " =    1.962
peak=    3.662 closest distance to " O   HOH Z 287 " =    1.727
peak=    3.658 closest distance to " O   HOH Z 427 " =    2.773
peak=    3.657 closest distance to " CB  THR A  52 " =    0.859
peak=    3.626 closest distance to " O   HOH Z   3 " =    1.899
peak=    3.622 closest distance to " CD1 ILE A 199 " =    1.206
peak=    3.601 closest distance to " CA  ASN A 217 " =    1.213
peak=    3.600 closest distance to " O   HOH Z 284 " =    3.011
peak=    3.598 closest distance to " O   ASP A 191 " =    1.588
peak=    3.598 closest distance to " CG  ARG A 138 " =    1.309
peak=    3.594 closest distance to " CZ3 TRP A  85 " =    0.915
peak=    3.587 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.584 closest distance to " CB  VAL A 265 " =    1.252
peak=    3.581 closest distance to " NH1AARG A 145 " =    1.400
peak=    3.579 closest distance to " O   HOH Z 203 " =    1.438
peak=    3.577 closest distance to " ND2 ASN A 187 " =    1.669
peak=    3.577 closest distance to " CD  LYS A 119 " =    1.838
peak=    3.568 closest distance to " CD  PRO A  54 " =    1.013
peak=    3.568 closest distance to " CG2 VAL A 197 " =    1.104
peak=    3.566 closest distance to " O   HOH Z 313 " =    1.676
peak=    3.565 closest distance to " CG1 ILE A  20 " =    1.263
peak=    3.564 closest distance to " CB  PRO A 243 " =    1.074
peak=    3.563 closest distance to " O   HOH Z 371 " =    2.801
peak=    3.561 closest distance to " CA  TYR A 116 " =    1.434
peak=    3.559 closest distance to " O   HOH Z 337 " =    1.945
peak=    3.558 closest distance to " O   HOH Z   4 " =    1.630
peak=    3.554 closest distance to " CA  ALA A 160 " =    0.984
peak=    3.551 closest distance to " O   HOH Z 313 " =    1.636
peak=    3.548 closest distance to " O   HOH Z 258 " =    2.170
peak=    3.547 closest distance to " CB  PRO A 198 " =    1.066
peak=    3.531 closest distance to " O  BHOH Z  74 " =    1.361
peak=    3.529 closest distance to " O   HOH Z 285 " =    2.361
peak=    3.527 closest distance to " CB  ALA A 248 " =    1.333
peak=    3.522 closest distance to " O   HOH Z 423 " =    1.794
peak=    3.521 closest distance to " CB  ASN A  39 " =    0.809
peak=    3.521 closest distance to " CD2 LEU A 297 " =    0.833
peak=    3.517 closest distance to " O   HOH Z 421 " =    2.074
peak=    3.513 closest distance to " CB  TRP A 266 " =    1.091
peak=    3.508 closest distance to " CB  GLU A 128 " =    1.056
peak=    3.491 closest distance to " CA  LYS A 117 " =    1.254
peak=    3.488 closest distance to " O   HOH Z 298 " =    4.354
peak=    3.486 closest distance to " CG  MET A 185 " =    1.223
peak=    3.485 closest distance to " OG  SER A 135 " =    1.338
peak=    3.482 closest distance to " CB  SER A 141 " =    1.217
peak=    3.482 closest distance to " OG  SER A 245 " =    1.514
peak=    3.476 closest distance to " O   THR A 182 " =    1.450
peak=    3.476 closest distance to " O   GLY A  91 " =    1.301
peak=    3.474 closest distance to " CA  ALA A  21 " =    1.080
peak=    3.471 closest distance to " O   HOH Z  83 " =    1.487
peak=    3.467 closest distance to " CG1 VAL A 153 " =    1.028
peak=    3.465 closest distance to " O   HOH Z  88 " =    2.703
peak=    3.463 closest distance to " CB  ALA A   9 " =    1.680
peak=    3.456 closest distance to " O   HOH Z 383 " =    2.001
peak=    3.453 closest distance to " O  BHOH Z 338 " =    2.216
peak=    3.445 closest distance to " O   HOH Z 357 " =    2.148
peak=    3.444 closest distance to " NH2 ARG A 156 " =    1.024
peak=    3.443 closest distance to " O   HOH Z 199 " =    1.666
peak=    3.441 closest distance to " CA  ALA A 158 " =    1.575
peak=    3.438 closest distance to " CB  PHE A 204 " =    1.063
peak=    3.435 closest distance to " O   ASP A 200 " =    1.632
peak=    3.434 closest distance to " O   HOH Z 146 " =    1.489
peak=    3.431 closest distance to " CD2 TYR A 186 " =    1.048
peak=    3.426 closest distance to " CB  GLN A  89 " =    1.226
peak=    3.424 closest distance to " CB  SER A  62 " =    0.954
peak=    3.418 closest distance to " O   HOH Z  78 " =    1.675
peak=    3.417 closest distance to " CA  ASP A 162 " =    1.020
peak=    3.416 closest distance to " O   HOH Z 154 " =    2.295
peak=    3.416 closest distance to " CB  VAL A 202 " =    1.447
peak=    3.415 closest distance to " O   HOH Z 403 " =    1.304
peak=    3.412 closest distance to " O   HOH Z 193 " =    1.755
peak=    3.411 closest distance to " CG2 ILE A 234 " =    1.178
peak=    3.410 closest distance to " O   HOH Z 173 " =    2.385
peak=    3.405 closest distance to " O   HOH Z  97 " =    2.033
peak=    3.405 closest distance to " O   HOH Z 327 " =    1.622
peak=    3.400 closest distance to " O   HOH Z 134 " =    1.354
peak=    3.399 closest distance to " CG  LEU A 167 " =    1.118
peak=    3.398 closest distance to " O   HOH Z 353 " =    2.807
peak=    3.397 closest distance to " CB  ASN A 215 " =    1.195
peak=    3.397 closest distance to " CA  ASP A 191 " =    1.194
peak=    3.396 closest distance to " O   HOH Z 361 " =    3.384
peak=    3.396 closest distance to " O   HOH Z 372 " =    0.951
peak=    3.395 closest distance to " CB  THR A  31 " =    1.362
peak=    3.392 closest distance to " O   HOH Z 132 " =    2.835
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.210
peak=    3.373 closest distance to " CA  ASN A 127 " =    1.117
peak=    3.369 closest distance to " CG2 ILE A  20 " =    1.434
peak=    3.368 closest distance to " O   LEU A 228 " =    1.750
peak=    3.362 closest distance to " O   HOH Z 155 " =    3.295
peak=    3.362 closest distance to " CG AARG A 275 " =    1.285
peak=    3.360 closest distance to " CB  ASP A 298 " =    1.128
peak=    3.357 closest distance to " O   HOH Z   1 " =    2.229
peak=    3.353 closest distance to " O   HOH Z  47 " =    2.789
peak=    3.352 closest distance to " CB  PRO A  90 " =    1.182
peak=    3.351 closest distance to " O   TRP A 274 " =    1.719
peak=    3.348 closest distance to " O   HOH Z  54 " =    1.650
peak=    3.342 closest distance to " CB  ARG A 190 " =    1.177
peak=    3.340 closest distance to " CB  THR A 235 " =    1.247
peak=    3.340 closest distance to " O   HOH Z  35 " =    2.345
peak=    3.337 closest distance to " CA  SER A  87 " =    0.996
peak=    3.332 closest distance to " O   HOH Z 298 " =    1.820
peak=    3.330 closest distance to " NZ  LYS A 117 " =    2.869
peak=    3.328 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.324 closest distance to " CG1 ILE A  49 " =    1.533
peak=    3.322 closest distance to " O   HOH Z 366 " =    2.424
peak=    3.316 closest distance to " CB  GLU A  46 " =    0.977
peak=    3.316 closest distance to " CG  GLN A  58 " =    1.033
peak=    3.315 closest distance to " CG  MET A 188 " =    0.865
peak=    3.311 closest distance to " CB  TYR A 169 " =    0.835
peak=    3.311 closest distance to " NZ  LYS A  48 " =    1.203
peak=    3.310 closest distance to " CA  LEU A 282 " =    1.162
peak=    3.305 closest distance to " CG2 THR A 221 " =    1.177
peak=    3.304 closest distance to " O   HOH Z 285 " =    2.038
peak=    3.304 closest distance to " CB  ASN A 285 " =    0.987
peak=    3.303 closest distance to " O   HOH Z 189 " =    2.748
peak=    3.301 closest distance to " CD1 LEU A   5 " =    1.485
peak=    3.301 closest distance to " CA  ASP A 140 " =    1.294
peak=    3.299 closest distance to " O   HOH Z 420 " =    4.961
peak=    3.298 closest distance to " CG2AVAL A 121 " =    2.092
peak=    3.289 closest distance to " O   HOH Z 136 " =    1.156
peak=    3.289 closest distance to " CA  ILE A 106 " =    0.737
peak=    3.288 closest distance to " O   HOH Z 329 " =    4.133
peak=    3.287 closest distance to " CD  ARG A 195 " =    0.949
peak=    3.282 closest distance to " CB  SER A 210 " =    0.870
peak=    3.281 closest distance to " O   HOH Z 129 " =    1.166
peak=    3.280 closest distance to " O   ASN A 284 " =    1.851
peak=    3.276 closest distance to " O   HOH Z 172 " =    3.729
peak=    3.271 closest distance to " CE1 HIS A 108 " =    1.164
peak=    3.264 closest distance to " O   HOH Z 345 " =    1.635
peak=    3.263 closest distance to " OE1 GLU A   2 " =    1.879
peak=    3.261 closest distance to " O   HOH Z 213 " =    1.607
peak=    3.257 closest distance to " OD1 ASN A  69 " =    2.375
peak=    3.249 closest distance to " NH1 ARG A  14 " =    1.135
peak=    3.248 closest distance to " O   HOH Z  67 " =    1.884
peak=    3.243 closest distance to " CA  ALA A 100 " =    0.904
peak=    3.237 closest distance to " CA  SER A  32 " =    1.794
peak=    3.237 closest distance to " O   THR A 220 " =    1.297
peak=    3.232 closest distance to " O   HOH Z 120 " =    2.540
peak=    3.227 closest distance to " O   HOH Z 299 " =    4.305
peak=    3.222 closest distance to " O   HOH Z 299 " =    2.432
peak=    3.216 closest distance to " O   HOH Z 293 " =    1.864
peak=    3.211 closest distance to " O   HOH Z 336 " =    1.773
peak=    3.211 closest distance to " CG2 ILE A 120 " =    1.483
peak=    3.209 closest distance to " O   HOH Z 419 " =    1.802
peak=    3.209 closest distance to " O   HOH Z 420 " =    1.875
peak=    3.208 closest distance to " OG BSER A 134 " =    2.795
peak=    3.208 closest distance to " CB  ASP A 107 " =    1.209
peak=    3.206 closest distance to " CB  ASN A  74 " =    1.422
peak=    3.204 closest distance to " NH2BARG A 190 " =    1.791
peak=    3.202 closest distance to " O   HOH Z 435 " =    1.990
peak=    3.199 closest distance to " N   ARG A 156 " =    1.628
peak=    3.198 closest distance to " O   HOH Z 428 " =    3.920
peak=    3.196 closest distance to " CB  GLN A 103 " =    0.957
peak=    3.196 closest distance to " OG  SER A  62 " =    2.772
peak=    3.194 closest distance to " CG BARG A 275 " =    1.299
peak=    3.194 closest distance to " CA  ARG A 139 " =    1.155
peak=    3.191 closest distance to " O   HOH Z 438 " =    2.387
peak=    3.183 closest distance to " O   HOH Z 227 " =    1.421
peak=    3.181 closest distance to " N   GLN A 205 " =    1.202
peak=    3.181 closest distance to " ND2AASN A 224 " =    0.878
peak=    3.172 closest distance to " CB  SER A 273 " =    0.971
peak=    3.171 closest distance to " O   GLN A  88 " =    1.626
peak=    3.168 closest distance to " CB  PHE A 283 " =    0.858
peak=    3.167 closest distance to " NH1 ARG A 269 " =    0.811
peak=    3.167 closest distance to " CB  SER A  62 " =    1.004
peak=    3.166 closest distance to " CB  ALA A 114 " =    0.721
peak=    3.163 closest distance to " CG  GLU A  37 " =    0.942
peak=    3.161 closest distance to " CB  PHE A  16 " =    1.023
peak=    3.158 closest distance to " CB  LYS A 117 " =    1.157
peak=    3.152 closest distance to " O   HOH Z 271 " =    2.368
peak=    3.151 closest distance to " CB  TYR A 247 " =    1.051
peak=    3.148 closest distance to " N   TYR A 247 " =    1.366
peak=    3.148 closest distance to " CE3 TRP A 150 " =    1.100
peak=    3.144 closest distance to " CG2AVAL A  72 " =    1.817
peak=    3.141 closest distance to " O   HOH Z 385 " =    2.798
peak=    3.138 closest distance to " CG  MET A 185 " =    1.001
peak=    3.137 closest distance to " CB  ARG A 145 " =    0.817
peak=    3.135 closest distance to " O   HOH Z 437 " =    1.774
peak=    3.135 closest distance to " O   HOH Z 236 " =    1.628
peak=    3.134 closest distance to " N   ALA A 256 " =    1.117
peak=    3.124 closest distance to " O   HOH Z 129 " =    3.309
peak=    3.123 closest distance to " O   HOH Z 148 " =    3.273
peak=    3.121 closest distance to " O   HOH Z 345 " =    3.204
peak=    3.121 closest distance to " O   HOH Z  44 " =    2.067
peak=    3.120 closest distance to " CA  ASN A 176 " =    1.228
peak=    3.116 closest distance to " O   HOH Z 371 " =    1.188
peak=    3.113 closest distance to " CG  GLN A  11 " =    1.507
peak=    3.097 closest distance to " O   HOH Z  19 " =    1.798
peak=    3.086 closest distance to " CE1 PHE A 218 " =    0.711
peak=    3.086 closest distance to " O   HOH Z 111 " =    1.541
peak=    3.081 closest distance to " NH2AARG A 145 " =    1.037
peak=    3.074 closest distance to " CG1 VAL A 296 " =    1.748
peak=    3.065 closest distance to " O   HOH Z 305 " =    3.514
peak=    3.065 closest distance to " O   HOH Z 109 " =    2.094
peak=    3.058 closest distance to " N   ASP A 162 " =    1.316
peak=    3.056 closest distance to " CD  ARG A  66 " =    2.485
peak=    3.045 closest distance to " CG2 ILE A 234 " =    0.716
peak=    3.022 closest distance to " O   HOH Z 423 " =    3.102
peak=    3.016 closest distance to " O   HOH Z 175 " =    3.670
peak=    3.006 closest distance to " O   GLU A   2 " =    1.474

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.689 - 5.827
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.780 - 5.827

peak=   -4.506 closest distance to " CG1 VAL A 296 " =    0.982
peak=   -4.418 closest distance to " CD  GLN A  58 " =    1.032
peak=   -4.296 closest distance to " CG2 ILE A  49 " =    2.873
peak=   -4.281 closest distance to " SG  CYS A 254 " =    3.348
peak=   -4.250 closest distance to " CD2 LEU A 237 " =    2.652
peak=   -4.250 closest distance to " O   HOH Z 193 " =    0.938
peak=   -4.210 closest distance to " CD  ARG A 156 " =    2.050
peak=   -4.167 closest distance to " O   PRO A 198 " =    1.329
peak=   -4.146 closest distance to " CD2 TYR A 293 " =    1.939
peak=   -4.125 closest distance to " CA  ASP A 298 " =    1.055
peak=   -4.074 closest distance to " O   HOH Z 411 " =    5.610
peak=   -4.063 closest distance to " CE2 TYR A  30 " =    2.735
peak=   -4.014 closest distance to " O   PRO A 163 " =    2.138
peak=   -4.009 closest distance to " O   HOH Z 196 " =    2.192
peak=   -3.959 closest distance to " O   HOH Z 166 " =    1.539
peak=   -3.954 closest distance to " O   SER A 271 " =    2.212
peak=   -3.916 closest distance to " CG1 VAL A 112 " =    2.659
peak=   -3.909 closest distance to " CG2BVAL A  41 " =    2.730
peak=   -3.902 closest distance to " CB  PHE A 208 " =    2.354
peak=   -3.898 closest distance to " OG BSER A 134 " =    1.447
peak=   -3.878 closest distance to " O   HOH Z 131 " =    4.180
peak=   -3.855 closest distance to " O   HOH Z  13 " =    1.762
peak=   -3.853 closest distance to " OE1 GLN A 223 " =    2.474
peak=   -3.847 closest distance to " CD1 LEU A 101 " =    2.411
peak=   -3.844 closest distance to " OXT GLY A 302 " =    2.900
peak=   -3.833 closest distance to " O   HOH Z 394 " =    1.740
peak=   -3.796 closest distance to " CD1 PHE A  59 " =    2.017
peak=   -3.783 closest distance to " O   HOH Z 423 " =    2.451
peak=   -3.782 closest distance to " C   HIS A 108 " =    1.141
peak=   -3.767 closest distance to " CG  GLN A  11 " =    1.664
peak=   -3.752 closest distance to " O   HOH Z 431 " =    2.312
peak=   -3.748 closest distance to " ND2BASN A 224 " =    1.846
peak=   -3.745 closest distance to " CB  ALA A 248 " =    2.207
peak=   -3.737 closest distance to " CG  GLN A 103 " =    2.516
peak=   -3.736 closest distance to " CE3 TRP A 150 " =    2.305
peak=   -3.736 closest distance to " O   HOH Z 154 " =    1.348
peak=   -3.733 closest distance to " ND2 ASN A  69 " =    1.922
peak=   -3.714 closest distance to " O   HOH Z 216 " =    1.152
peak=   -3.697 closest distance to " CB  ALA A 161 " =    2.429
peak=   -3.682 closest distance to " O   HOH Z 165 " =    1.941
peak=   -3.672 closest distance to " O   HOH Z 119 " =    2.045
peak=   -3.658 closest distance to " O   HOH Z 301 " =    2.561
peak=   -3.657 closest distance to " O   HOH Z 340 " =    1.694
peak=   -3.650 closest distance to " CZ  PHE A  38 " =    2.356
peak=   -3.650 closest distance to " CG2 VAL A 189 " =    2.028
peak=   -3.649 closest distance to " O   HOH Z 290 " =    0.984
peak=   -3.644 closest distance to " O   HOH Z 214 " =    2.422
peak=   -3.644 closest distance to " O   HOH Z 285 " =    1.887
peak=   -3.642 closest distance to " OG  SER A  97 " =    2.372
peak=   -3.629 closest distance to " CG  PRO A 243 " =    1.624
peak=   -3.616 closest distance to " CA  GLY A 241 " =    2.391
peak=   -3.606 closest distance to " CZ  TYR A 169 " =    1.868
peak=   -3.601 closest distance to " O   HOH Z 351 " =    1.684
peak=   -3.593 closest distance to " CE2 TRP A  70 " =    2.242
peak=   -3.592 closest distance to " O   HOH Z  37 " =    1.866
peak=   -3.589 closest distance to " CG  GLU A 277 " =    1.316
peak=   -3.584 closest distance to " NE2 GLN A  88 " =    1.102
peak=   -3.584 closest distance to " O   HOH Z 231 " =    2.244
peak=   -3.582 closest distance to " O   HOH Z 384 " =    2.099
peak=   -3.580 closest distance to " ND2 ASN A  45 " =    1.232
peak=   -3.574 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.554 closest distance to " CE3 TRP A 274 " =    2.417
peak=   -3.541 closest distance to " CH2 TRP A 179 " =    1.225
peak=   -3.533 closest distance to " O   HOH Z  10 " =    1.612
peak=   -3.523 closest distance to " ND2 ASN A 187 " =    1.693
peak=   -3.519 closest distance to " CB  SER A 210 " =    1.121
peak=   -3.493 closest distance to " CB  ALA A  10 " =    2.237
peak=   -3.492 closest distance to " O   HOH Z 136 " =    2.694
peak=   -3.481 closest distance to " CB  ALA A  43 " =    2.556
peak=   -3.469 closest distance to " O   HOH Z 145 " =    2.578
peak=   -3.465 closest distance to " N   SER A 276 " =    1.338
peak=   -3.465 closest distance to " O   HOH Z   6 " =    1.745
peak=   -3.464 closest distance to " O   HOH Z 111 " =    1.860
peak=   -3.459 closest distance to " O   GLY A  80 " =    2.648
peak=   -3.458 closest distance to " O   HOH Z 387 " =    2.731
peak=   -3.457 closest distance to " CG  ARG A 269 " =    2.197
peak=   -3.455 closest distance to " OG1 THR A  82 " =    1.434
peak=   -3.450 closest distance to " CD  PRO A 243 " =    1.942
peak=   -3.444 closest distance to " O   HOH Z 174 " =    2.156
peak=   -3.440 closest distance to " CA  VAL A  67 " =    3.013
peak=   -3.431 closest distance to " O   HOH Z 250 " =    1.983
peak=   -3.427 closest distance to " O   HOH Z 166 " =    1.628
peak=   -3.426 closest distance to " CD2 HIS A 207 " =    2.416
peak=   -3.424 closest distance to " CD  LYS A 289 " =    2.393
peak=   -3.423 closest distance to " O   HOH Z 426 " =    1.788
peak=   -3.420 closest distance to " CG  GLU A  53 " =    1.556
peak=   -3.418 closest distance to " O   ALA A   1 " =    1.638
peak=   -3.415 closest distance to " CE  LYS A  76 " =    2.635
peak=   -3.413 closest distance to " CD2 LEU A 167 " =    1.800
peak=   -3.399 closest distance to " O   HOH Z 275 " =    1.520
peak=   -3.394 closest distance to " O   HOH Z 191 " =    5.827
peak=   -3.390 closest distance to " O   HOH Z 283 " =    2.359
peak=   -3.388 closest distance to " CD1 ILE A 109 " =    2.867
peak=   -3.382 closest distance to " O   HOH Z  28 " =    2.367
peak=   -3.379 closest distance to " CB  ALA A  51 " =    1.928
peak=   -3.369 closest distance to " CG  TRP A 266 " =    1.941
peak=   -3.366 closest distance to " CE1 TYR A 247 " =    2.611
peak=   -3.365 closest distance to " C   ASN A 285 " =    2.198
peak=   -3.363 closest distance to " CG2 ILE A 263 " =    2.211
peak=   -3.362 closest distance to " O   HOH Z   2 " =    2.354
peak=   -3.361 closest distance to " O   HOH Z 107 " =    1.119
peak=   -3.358 closest distance to " CH2 TRP A 150 " =    1.147
peak=   -3.353 closest distance to " O   ASN A 187 " =    1.631
peak=   -3.353 closest distance to " O   HOH Z 128 " =    2.452
peak=   -3.352 closest distance to " O   ALA A 227 " =    1.276
peak=   -3.351 closest distance to " CG  LEU A   5 " =    0.970
peak=   -3.347 closest distance to " CE3 TRP A  70 " =    1.689
peak=   -3.343 closest distance to " O   PHE A 218 " =    1.505
peak=   -3.342 closest distance to " O   HOH Z 150 " =    2.099
peak=   -3.338 closest distance to " O   VAL A 174 " =    2.220
peak=   -3.336 closest distance to " O   TRP A  92 " =    2.101
peak=   -3.330 closest distance to " O   HOH Z 264 " =    1.775
peak=   -3.325 closest distance to " C   ILE A 239 " =    2.110
peak=   -3.321 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.318 closest distance to " O   HOH Z 407 " =    2.766
peak=   -3.318 closest distance to " O   HOH Z 252 " =    3.471
peak=   -3.316 closest distance to " CA  GLY A 203 " =    2.489
peak=   -3.314 closest distance to " NE  ARG A  66 " =    4.399
peak=   -3.313 closest distance to " O   SER A 210 " =    1.754
peak=   -3.313 closest distance to " O   HOH Z 210 " =    0.812
peak=   -3.313 closest distance to " N   ALA A 226 " =    2.000
peak=   -3.311 closest distance to " O   HOH Z  78 " =    1.884
peak=   -3.310 closest distance to " O   HOH Z  60 " =    1.950
peak=   -3.310 closest distance to " O   HOH Z  63 " =    1.149
peak=   -3.307 closest distance to " O   ILE A 106 " =    1.608
peak=   -3.307 closest distance to " CG2 VAL A 296 " =    1.302
peak=   -3.299 closest distance to " O   HOH Z 185 " =    2.459
peak=   -3.298 closest distance to " CD2 HIS A 115 " =    1.092
peak=   -3.298 closest distance to " O  BHOH Z 338 " =    1.128
peak=   -3.296 closest distance to " CD1 TRP A  70 " =    1.838
peak=   -3.292 closest distance to " OH  TYR A 172 " =    1.930
peak=   -3.291 closest distance to " O   HOH Z  19 " =    2.253
peak=   -3.283 closest distance to " O   HOH Z 136 " =    1.343
peak=   -3.279 closest distance to " O   GLY A 196 " =    1.108
peak=   -3.271 closest distance to " O   HOH Z 109 " =    0.946
peak=   -3.259 closest distance to " C   THR A 279 " =    1.144
peak=   -3.256 closest distance to " O   HOH Z 211 " =    1.388
peak=   -3.251 closest distance to " ND2 ASN A 249 " =    2.295
peak=   -3.250 closest distance to " O   HOH Z 244 " =    1.948
peak=   -3.249 closest distance to " CB  HIS A  86 " =    1.262
peak=   -3.243 closest distance to " O   HOH Z 198 " =    1.926
peak=   -3.239 closest distance to " O   HOH Z 148 " =    3.827
peak=   -3.239 closest distance to " OD1 ASN A 173 " =    1.509
peak=   -3.237 closest distance to " O   HOH Z 388 " =    2.150
peak=   -3.236 closest distance to " CG1 VAL A 112 " =    2.752
peak=   -3.235 closest distance to " O   ALA A  34 " =    1.974
peak=   -3.235 closest distance to " CB  TRP A  85 " =    2.609
peak=   -3.234 closest distance to " NH2 ARG A  79 " =    2.235
peak=   -3.230 closest distance to " CD  GLN A  73 " =    0.783
peak=   -3.229 closest distance to " O   HOH Z 140 " =    1.329
peak=   -3.224 closest distance to " OXT GLY A 302 " =    3.520
peak=   -3.222 closest distance to " CG1 VAL A  78 " =    2.422
peak=   -3.219 closest distance to " ND2 ASN A 249 " =    0.971
peak=   -3.212 closest distance to " O   HOH Z 251 " =    4.889
peak=   -3.204 closest distance to " CD  GLN A 223 " =    1.764
peak=   -3.202 closest distance to " C   VAL A 265 " =    0.899
peak=   -3.202 closest distance to " CE  LYS A  76 " =    0.829
peak=   -3.202 closest distance to " NH2 ARG A  24 " =    2.034
peak=   -3.199 closest distance to " CB  PRO A 163 " =    2.495
peak=   -3.196 closest distance to " O   HOH Z  90 " =    3.995
peak=   -3.194 closest distance to " C   LEU A 143 " =    1.023
peak=   -3.194 closest distance to " CG  LEU A  83 " =    2.151
peak=   -3.193 closest distance to " NE2 GLN A 194 " =    2.011
peak=   -3.192 closest distance to " N   ALA A 295 " =    0.950
peak=   -3.192 closest distance to " ND2 ASN A  45 " =    2.172
peak=   -3.188 closest distance to " O   HOH Z 101 " =    1.534
peak=   -3.181 closest distance to " O   MET A  40 " =    2.933
peak=   -3.181 closest distance to " CD2 TYR A 172 " =    2.031
peak=   -3.180 closest distance to " CB  ALA A 129 " =    2.413
peak=   -3.172 closest distance to " O   HOH Z  11 " =    1.889
peak=   -3.172 closest distance to " O   HOH Z  52 " =    1.973
peak=   -3.171 closest distance to " CG  ASP A 286 " =    1.483
peak=   -3.168 closest distance to " O   HOH Z 128 " =    1.186
peak=   -3.167 closest distance to " O   HOH Z 392 " =    1.962
peak=   -3.163 closest distance to " NH2 ARG A  79 " =    1.524
peak=   -3.157 closest distance to " O   HOH Z  17 " =    1.465
peak=   -3.153 closest distance to " O   HOH Z 149 " =    2.068
peak=   -3.148 closest distance to " O   HOH Z 166 " =    1.834
peak=   -3.140 closest distance to " O   HOH Z 238 " =    0.780
peak=   -3.137 closest distance to " O   HOH Z 177 " =    1.739
peak=   -3.136 closest distance to " OH  TYR A 169 " =    0.897
peak=   -3.134 closest distance to " O   HOH Z 156 " =    3.570
peak=   -3.133 closest distance to " O   HOH Z 200 " =    1.607
peak=   -3.127 closest distance to " CB  ALA A   9 " =    2.335
peak=   -3.127 closest distance to " O   HOH Z 329 " =    0.975
peak=   -3.124 closest distance to " O   HOH Z 106 " =    1.901
peak=   -3.122 closest distance to " O   HOH Z 378 " =    1.482
peak=   -3.122 closest distance to " CG1BVAL A  72 " =    2.425
peak=   -3.117 closest distance to " O   HOH Z 231 " =    2.311
peak=   -3.116 closest distance to " NE2 GLN A 278 " =    2.009
peak=   -3.114 closest distance to " O   SER A 276 " =    1.685
peak=   -3.112 closest distance to " O   HOH Z  64 " =    1.827
peak=   -3.110 closest distance to " CG  ASP A 231 " =    0.830
peak=   -3.109 closest distance to " ND2 ASN A  39 " =    1.212
peak=   -3.106 closest distance to " CG1BVAL A  72 " =    5.318
peak=   -3.099 closest distance to " O   GLY A 203 " =    2.482
peak=   -3.096 closest distance to " OD1 ASN A 148 " =    1.396
peak=   -3.092 closest distance to " NH2 ARG A  66 " =    1.878
peak=   -3.090 closest distance to " O   HOH Z 105 " =    2.226
peak=   -3.088 closest distance to " O   SER A   3 " =    1.082
peak=   -3.085 closest distance to " O   HOH Z 352 " =    1.697
peak=   -3.083 closest distance to " O   HOH Z 357 " =    2.063
peak=   -3.079 closest distance to " O   TRP A  70 " =    1.597
peak=   -3.073 closest distance to " CZ  ARG A  66 " =    1.230
peak=   -3.072 closest distance to " O   ARG A  24 " =    2.099
peak=   -3.069 closest distance to " O   HOH Z 265 " =    2.471
peak=   -3.067 closest distance to " OE1 GLN A  88 " =    0.932
peak=   -3.040 closest distance to " CA  ALA A 299 " =    2.238

================= 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    :  0.5017 0.4892   6.298618e+00   6.288969e+00
   1_bss:  0.4924 0.4836   6.291708e+00   6.287648e+00
   1_xyz:  0.4181 0.4408   6.202248e+00   6.233346e+00
   1_adp:  0.3742 0.4335   6.140796e+00   6.216722e+00
   1_occ:  0.3737 0.4336   6.140265e+00   6.217527e+00
   2_bss:  0.3706 0.4270   6.140959e+00   6.216747e+00
   2_xyz:  0.2698 0.3256   5.883442e+00   6.038360e+00
   2_adp:  0.2383 0.2941   5.783295e+00   5.956777e+00
   2_occ:  0.2378 0.2939   5.782805e+00   5.956650e+00
   3_bss:  0.2348 0.2934   5.781567e+00   5.954332e+00
   3_xyz:  0.1849 0.2296   5.566798e+00   5.752378e+00
   3_adp:  0.1746 0.2168   5.516008e+00   5.701274e+00
   3_occ:  0.1744 0.2168   5.515597e+00   5.701463e+00
   4_bss:  0.1737 0.2163   5.514133e+00   5.699536e+00
   4_xyz:  0.1377 0.1804   5.314429e+00   5.520784e+00
   4_adp:  0.1297 0.1751   5.273209e+00   5.493567e+00
   4_occ:  0.1296 0.1750   5.272879e+00   5.493314e+00
   5_bss:  0.1298 0.1753   5.272961e+00   5.493310e+00
   5_xyz:  0.1229 0.1696   5.235652e+00   5.465262e+00
   5_adp:  0.1218 0.1688   5.228552e+00   5.458492e+00
   5_occ:  0.1216 0.1688   5.228201e+00   5.458784e+00
   5_bss:  0.1215 0.1687   5.228212e+00   5.458834e+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:  0.316   1.067   7.155  10.161  10.963   0.000   0.000   0.000
   1_xyz:  0.316   1.067   7.155  10.161  10.963   0.000   0.000   0.000
   1_adp:  0.316   1.067   7.155  10.161  10.963   0.000   0.000   0.000
   1_occ:  0.316   1.067   7.155  10.161  10.963   0.000   0.000   0.000
   2_bss:  0.315  31.342   3.034   5.724   6.676   0.000   0.000   0.000
   2_xyz:  0.315  31.342   3.034   5.724   6.676   0.000   0.000   0.000
   2_adp:  0.315  31.342   3.034   5.724   6.676   0.000   0.000   0.000
   2_occ:  0.315  31.342   3.034   5.724   6.676   0.000   0.000   0.000
   3_bss:  0.326  53.340   1.302   3.148   4.007   0.000   0.000   0.000
   3_xyz:  0.326  53.340   1.302   3.148   4.007   0.000   0.000   0.000
   3_adp:  0.326  53.340   1.302   3.148   4.007   0.000   0.000   0.000
   3_occ:  0.326  53.340   1.302   3.148   4.007   0.000   0.000   0.000
   4_bss:  0.333  53.340   0.334   1.980   3.067   0.000   0.000   0.000
   4_xyz:  0.333  53.340   0.334   1.980   3.067   0.000   0.000   0.000
   4_adp:  0.333  53.340   0.334   1.980   3.067   0.000   0.000   0.000
   4_occ:  0.333  53.340   0.334   1.980   3.067   0.000   0.000   0.000
   5_bss:  0.333  62.345   0.330   1.662   2.873   0.000   0.000   0.000
   5_xyz:  0.333  62.345   0.330   1.662   2.873   0.000   0.000   0.000
   5_adp:  0.333  62.345   0.330   1.662   2.873   0.000   0.000   0.000
   5_occ:  0.333  62.345   0.330   1.662   2.873   0.000   0.000   0.000
   5_bss:  0.326  60.228  -1.226  -0.000   1.226   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.372 0.4024  0.4729    75084.241
   1_bss:  59.942 0.3936  0.6055    74819.950
   1_xyz:  51.292 0.5030  0.7588    57169.075
   1_adp:  48.875 0.5335  0.8639    54239.953
   1_occ:  48.921 0.5329  0.8614    54299.600
   2_bss:  48.396 0.5397  0.7592    53838.763
   2_xyz:  35.387 0.6957  0.9522    29642.299
   2_adp:  30.969 0.7469  0.9945    23921.322
   2_occ:  30.940 0.7473  0.9947    23920.563
   3_bss:  30.727 0.7497  0.9199    23721.752
   3_xyz:  23.201 0.8296  0.9785    14215.739
   3_adp:  21.438 0.8481  0.9886    12785.320
   3_occ:  21.441 0.8481  0.9886    12772.999
   4_bss:  21.363 0.8487  0.9541    12675.228
   4_xyz:  17.144 0.8881  0.9743     8593.393
   4_adp:  16.527 0.8937  0.9711     8168.989
   4_occ:  16.518 0.8938  0.9711     8162.458
   5_bss:  16.519 0.8938  0.9653     8179.195
   5_xyz:  15.822 0.9001  0.9675     7638.755
   5_adp:  15.670 0.9015  0.9623     7557.652
   5_occ:  15.673 0.9015  0.9620     7558.949
   5_bss:  15.677 0.9015  0.9660     7557.772
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4019e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4019e+01
   1_xyz:   1.789  0.014  0.111 18.322  0.007  4.109   1.5572e-01
   1_adp:   1.789  0.014  0.111 18.322  0.007  4.109   1.5572e-01
   1_occ:   1.789  0.014  0.111 18.322  0.007  4.109   1.5572e-01
   2_bss:   1.789  0.014  0.111 18.322  0.007  4.109   1.5572e-01
   2_xyz:   1.458  0.012  0.089 16.688  0.006  4.112   1.2344e-01
   2_adp:   1.458  0.012  0.089 16.688  0.006  4.112   1.2344e-01
   2_occ:   1.458  0.012  0.089 16.688  0.006  4.112   1.2344e-01
   3_bss:   1.458  0.012  0.089 16.688  0.006  4.112   1.2344e-01
   3_xyz:   0.998  0.007  0.073 15.710  0.004  4.132   6.2867e-02
   3_adp:   0.998  0.007  0.073 15.710  0.004  4.132   6.2867e-02
   3_occ:   0.998  0.007  0.073 15.710  0.004  4.132   6.2867e-02
   4_bss:   0.998  0.007  0.073 15.710  0.004  4.132   6.2867e-02
   4_xyz:   1.110  0.009  0.083 15.732  0.004  4.132   7.3924e-02
   4_adp:   1.110  0.009  0.083 15.732  0.004  4.132   7.3924e-02
   4_occ:   1.110  0.009  0.083 15.732  0.004  4.132   7.3924e-02
   5_bss:   1.110  0.009  0.083 15.732  0.004  4.132   7.3924e-02
   5_xyz:   1.055  0.008  0.082 15.597  0.004  4.137   6.6618e-02
   5_adp:   1.055  0.008  0.082 15.597  0.004  4.137   6.6618e-02
   5_occ:   1.055  0.008  0.082 15.597  0.004  4.137   6.6618e-02
   5_bss:   1.055  0.008  0.082 15.597  0.004  4.137   6.6618e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0008e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0008e+00
   1_xyz:  15.752  0.183  0.501 86.614  0.044  2.171   1.1170e-01
   1_adp:  15.752  0.183  0.501 86.614  0.044  2.171   1.1170e-01
   1_occ:  15.752  0.183  0.501 86.614  0.044  2.171   1.1170e-01
   2_bss:  15.752  0.183  0.501 86.614  0.044  2.171   1.1170e-01
   2_xyz:   9.513  0.163  0.332 83.221  0.060  2.059   1.7210e-01
   2_adp:   9.513  0.163  0.332 83.221  0.060  2.059   1.7210e-01
   2_occ:   9.513  0.163  0.332 83.221  0.060  2.059   1.7210e-01
   3_bss:   9.513  0.163  0.332 83.221  0.060  2.059   1.7210e-01
   3_xyz:   7.210  0.046  0.242 79.385  0.054  2.263   5.8874e-02
   3_adp:   7.210  0.046  0.242 79.385  0.054  2.263   5.8874e-02
   3_occ:   7.210  0.046  0.242 79.385  0.054  2.263   5.8874e-02
   4_bss:   7.210  0.046  0.242 79.385  0.054  2.263   5.8874e-02
   4_xyz:   7.742  0.046  0.405 82.373  0.046  2.237   5.1900e-02
   4_adp:   7.742  0.046  0.405 82.373  0.046  2.237   5.1900e-02
   4_occ:   7.742  0.046  0.405 82.373  0.046  2.237   5.1900e-02
   5_bss:   7.742  0.046  0.405 82.373  0.046  2.237   5.1900e-02
   5_xyz:   7.436  0.047  0.415 88.632  0.037  2.318   4.0836e-02
   5_adp:   7.436  0.047  0.415 88.632  0.037  2.318   4.0836e-02
   5_occ:   7.436  0.047  0.415 88.632  0.037  2.318   4.0836e-02
   5_bss:   7.436  0.047  0.415 88.632  0.037  2.318   4.0836e-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:  72.38   0.00  14.65  67.69   0.00  12.70  72.38   0.00  25.29
   1_occ:  72.38   0.00  14.65  67.69   0.00  12.70  72.38   0.00  25.29
   2_bss:  72.38   0.00  14.65  67.69   0.00  12.70  72.38   0.00  25.29
   2_xyz:  72.38   0.00  14.65  67.69   0.00  12.70  72.38   0.00  25.29
   2_adp:  72.21   0.00  14.04  72.21   0.00  10.53  70.78   0.00  33.13
   2_occ:  72.21   0.00  14.04  72.21   0.00  10.53  70.78   0.00  33.13
   3_bss:  72.21   0.00  14.04  72.21   0.00  10.53  70.78   0.00  33.13
   3_xyz:  72.21   0.00  14.04  72.21   0.00  10.53  70.78   0.00  33.13
   3_adp:  71.90   0.00  13.64  71.90   0.00   9.77  71.85   2.86  34.71
   3_occ:  71.90   0.00  13.64  71.90   0.00   9.77  71.85   2.86  34.71
   4_bss:  71.90   0.00  13.64  71.90   0.00   9.77  71.85   2.86  34.71
   4_xyz:  71.90   0.00  13.64  71.90   0.00   9.77  71.85   2.86  34.71
   4_adp:  83.48   0.00  14.34  83.33   0.00   9.71  83.48   2.14  39.56
   4_occ:  83.48   0.00  14.34  83.33   0.00   9.71  83.48   2.14  39.56
   5_bss:  83.48   0.00  14.34  83.33   0.00   9.71  83.48   2.14  39.56
   5_xyz:  83.48   0.00  14.34  83.33   0.00   9.71  83.48   2.14  39.56
   5_adp:  85.69   0.00  14.20  84.96   0.00   9.59  85.69   2.23  39.32
   5_occ:  85.69   0.00  14.20  84.96   0.00   9.59  85.69   2.23  39.32
   5_bss:  87.43   1.74  15.94  86.70   1.74  11.33  87.43   3.97  41.06
------------------------------------------------------------------------
 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:    1.302    0.021    0.418
   1_adp:    1.302    0.021    0.418
   1_occ:    1.302    0.021    0.418
   2_bss:    1.302    0.021    0.418
   2_xyz:    1.944    0.015    0.658
   2_adp:    1.944    0.015    0.658
   2_occ:    1.944    0.015    0.658
   3_bss:    1.944    0.015    0.658
   3_xyz:    1.954    0.060    0.716
   3_adp:    1.954    0.060    0.716
   3_occ:    1.954    0.060    0.716
   4_bss:    1.954    0.060    0.716
   4_xyz:    2.036    0.022    0.782
   4_adp:    2.036    0.022    0.782
   4_occ:    2.036    0.022    0.782
   5_bss:    2.036    0.022    0.782
   5_xyz:    2.160    0.058    0.801
   5_adp:    2.160    0.058    0.801
   5_occ:    2.160    0.058    0.801
   5_bss:    2.160    0.058    0.801
------------------------------------------------------------------------

CPU time actual refinement: 359.17


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/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_339/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_339/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.99 
  Macro-tasks:
    bulk solvent and scale       = 42.81  
    individual site refinement   = 151.77 
    weights calculation          = 33.43  
    collect and process          = 6.74   
    model show statistics        = 0.16   
    TOTAL for macro-tasks        = 234.91 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 112.30 
    alpha_beta                      = 8.41   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.89 
    fmodel                         = 8.09   
    r_factors                      = 0.30   
    phase_errors                   = 10.60  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 267.37 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.961 micro seconds
Total CPU time: 6.21 minutes
from_scatterers_fft:    679 calls, 111.97 s
gradients_fft:          623 calls, 109.94 s

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

# Date 2008-01-16 Time 01:21:35 PST -0800 (1200475295.10 s)
Start R-work = 0.5017, R-free = 0.4892 (no bulk solvent and anisotropic scale)
Final R-work = 0.1394, R-free = 0.1836 (no bulk solvent and anisotropic scale)

Start R-work = 0.4924, R-free = 0.4836
Final R-work = 0.1215, R-free = 0.1687