# Date 2008-01-16 Time 02:32:03 PST -0800 (1200479523.26 s)
#phil __OFF__

Command line arguments: "../868.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28764
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 868

-------------------------------------------------------------------------------
  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: (70.9525, 45.9914, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.96386
Completeness in resolution range: 0.921142
Completeness with d_max=infinity: 0.918507

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   1.9639

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: (70.9525, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 1.96386
Completeness in resolution range: 0.921142
Completeness with d_max=infinity: 0.918507

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2044 -  4.2040 [2227/2253]  2004   223  10.0%
  bin  2:  4.2040 -  3.3486 [2155/2175]  1942   213   9.9%
  bin  3:  3.3486 -  2.9287 [2113/2132]  1901   212  10.0%
  bin  4:  2.9287 -  2.6625 [2099/2129]  1882   217  10.3%
  bin  5:  2.6625 -  2.4725 [2100/2119]  1890   210  10.0%
  bin  6:  2.4725 -  2.3273 [2070/2095]  1864   206  10.0%
  bin  7:  2.3273 -  2.2111 [2080/2108]  1872   208  10.0%
  bin  8:  2.2111 -  2.1151 [2041/2077]  1833   208  10.2%
  bin  9:  2.1151 -  2.0339 [2018/2094]  1829   189   9.4%
  bin 10:  2.0339 -  1.9639 [ 686/2084]   613    73  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 39
        2.42 -     3.04: 2203
        3.04 -     3.66: 4671
        3.66 -     4.28: 8972
        4.28 -     4.90: 12235
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.862 3.040 -x+1,y+1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.897 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.935 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28115 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_868/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 70.9525 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5151   r_free= 0.5074   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.313567                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6898 0.99   1447  160 0.4421 0.4187      6.6765      6.6576|
|  2:  4.6898 -  3.7407 0.99   1396  157 0.4573 0.4509      6.8831       6.868|
|  3:  3.7407 -  3.2732 0.99   1370  152 0.4860 0.4483      6.7149      6.6809|
|  4:  3.2732 -  2.9764 0.99   1365  152 0.5206 0.4884      6.5625      6.5105|
|  5:  2.9764 -  2.7644 0.99   1346  151 0.5500 0.5478      6.3848      6.4042|
|  6:  2.7644 -  2.6023 0.99   1361  148 0.5470 0.5624      6.2882      6.2288|
|  7:  2.6023 -  2.4725 0.99   1334  155 0.5452 0.5068      6.2462      6.1835|
|  8:  2.4725 -  2.3653 0.98   1323  148 0.5607 0.5425      6.1836      6.1694|
|  9:  2.3653 -  2.2746 0.98   1330  141 0.5400 0.5621      6.1311      6.2276|
| 10:  2.2746 -  2.1963 1.00   1347  148 0.5360 0.5700      6.0859      6.0912|
| 11:  2.1963 -  2.1278 0.98   1322  149 0.5246 0.5438      6.0258      6.0463|
| 12:  2.1278 -  2.0672 0.98   1312  143 0.5574 0.5550      5.9372      5.9351|
| 13:  2.0672 -  2.0129 0.83   1113  126 0.5547 0.5626      5.8998      5.8031|
| 14:  2.0129 -  1.9639 0.20    264   29 0.5299 0.4534      5.8389      5.8759|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6898  1447   160  0.66  37.96   0.76     0.71      86623.63|
|  2:  4.6898 -  3.7407  1396   157  0.66  38.92   0.83     0.74     129963.44|
|  3:  3.7407 -  3.2732  1370   152  0.52  50.48   0.81     0.66     138042.22|
|  4:  3.2732 -  2.9764  1365   152  0.42  58.52   0.74     0.52     122763.13|
|  5:  2.9764 -  2.7644  1346   151  0.32  65.87   0.70     0.41      96151.05|
|  6:  2.7644 -  2.6023  1361   148  0.29  68.56   0.69     0.35      82364.00|
|  7:  2.6023 -  2.4725  1334   155  0.24  72.05   0.72     0.29      75126.09|
|  8:  2.4725 -  2.3653  1323   148  0.20  74.87   0.70     0.25      69249.62|
|  9:  2.3653 -  2.2746  1330   141  0.15  78.74   0.70     0.19      67074.75|
| 10:  2.2746 -  2.1963  1347   148  0.14  79.30   0.72     0.18      59254.20|
| 11:  2.1963 -  2.1278  1322   149  0.13  80.45   0.75     0.17      56474.07|
| 12:  2.1278 -  2.0672  1312   143  0.17  77.18   0.71     0.23      48892.86|
| 13:  2.0672 -  2.0129  1113   126  0.21  74.15   0.70     0.29      42125.32|
| 14:  2.0129 -  1.9639   264    29  0.32  65.96   0.73     0.36      31740.95|
|alpha:            min =        0.17 max =            0.74 mean =         0.39|
|beta:             min =    31740.95 max =       138042.22 mean =     82808.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.49|
|phase err.(test): min =        0.00 max =           89.95 mean =        65.72|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.668410             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.881   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.290963              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.582   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      692 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3898 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5045 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6512 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7666 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.994 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.028 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    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: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5193   r_free= 0.5081   ksol= 0.00   Bsol= 0.00   scale= 0.733    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.313965                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5074   r_free= 0.4966   ksol= 0.33   Bsol= 6.34   scale= 0.957    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,8.14,11.07,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.309453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.107735             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.514   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.855962              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.301   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5074      final r-factor (work) = 0.4438          |
| start r-factor (free) = 0.4966      final r-factor (free) = 0.4724          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 120.5421 = 21.11 * 0.50 * 6.3056 + 1.00 * 53.9936                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 66.2028 = 21.11 * 0.50 * 6.2565 + 1.00 * 0.1729                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4438      final r-factor (work) = 0.4103          |
| start r-factor (free) = 0.4724      final r-factor (free) = 0.4721          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6263 = 1.86 * 1.00 * 6.2565 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5508 = 1.86 * 1.00 * 6.2126 + 1.00 * 0.0205                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.26   17.27    None  None   None       |
|    all(noH): 2823   0      0.00    81.26   17.27    None  None   None       |
|    Sol.    : 438    0      0.00    80.24   24.47    None  None   None       |
|    Mac.    : 2385   0      0.00    81.26   15.95    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 -   8.126:  787   |   5:    40.630 -  48.756:   94        |
|      1:     8.126 -  16.252:  772   |   6:    48.756 -  56.882:   44        |
|      2:    16.252 -  24.378:  576   |   7:    56.882 -  65.008:   22        |
|      3:    24.378 -  32.504:  330   |   8:    65.008 -  73.134:    8        |
|      4:    32.504 -  40.630:  180   |   9:    73.134 -  81.259:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4103 r_free = 0.4721             target_work(ml) = 6.207         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4101 r_free = 0.4720             target_work(ml) = 6.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4101   r_free= 0.4720   ksol= 0.33   Bsol= 6.34   scale= 1.130    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,8.14,11.07,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.206267                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4078   r_free= 0.4686   ksol= 0.35   Bsol= 50.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,4.25,6.74,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.208910                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 22.359749             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.128  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.833891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.038  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4078      final r-factor (work) = 0.3354          |
| start r-factor (free) = 0.4686      final r-factor (free) = 0.4111          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 69.6045 = 22.36 * 0.50 * 6.2104 + 1.00 * 0.1729                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 68.8010 = 22.36 * 0.50 * 6.1416 + 1.00 * 0.1391                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3354      final r-factor (work) = 0.3100          |
| start r-factor (free) = 0.4111      final r-factor (free) = 0.3956          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1422 = 0.83 * 1.00 * 6.1416 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0487 = 0.83 * 1.00 * 6.0370 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.27   16.55    None  None   None       |
|    all(noH): 2823   0      0.00    82.27   16.55    None  None   None       |
|    Sol.    : 438    0      0.00    82.27   31.39    None  None   None       |
|    Mac.    : 2385   0      0.00    68.31   13.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.227:  823   |   5:    41.137 -  49.364:   82        |
|      1:     8.227 -  16.455:  878   |   6:    49.364 -  57.592:   41        |
|      2:    16.455 -  24.682:  543   |   7:    57.592 -  65.819:   19        |
|      3:    24.682 -  32.909:  272   |   8:    65.819 -  74.046:    9        |
|      4:    32.909 -  41.137:  151   |   9:    74.046 -  82.274:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3100 r_free = 0.3956             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3098 r_free = 0.3955             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3098   r_free= 0.3955   ksol= 0.35   Bsol= 50.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,4.25,6.74,0.00,0.00,0.00); trace/3= 4.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.018029                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3081   r_free= 0.3934   ksol= 0.34   Bsol= 54.74   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.38,3.77,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.017902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.524031              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.841  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.185063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.409  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2516          |
| start r-factor (free) = 0.3934      final r-factor (free) = 0.3233          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8515 = 7.52 * 0.50 * 6.0373 + 1.00 * 0.1391                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4769 = 7.52 * 0.50 * 5.9528 + 1.00 * 0.0825                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2516      final r-factor (work) = 0.2257          |
| start r-factor (free) = 0.3233      final r-factor (free) = 0.3025          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0690 = 1.19 * 1.00 * 5.9528 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9099 = 1.19 * 1.00 * 5.8070 + 1.00 * 0.0282                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.77  17.13    None  None   None       |
|    all(noH): 2823   0      0.00    102.77  17.13    None  None   None       |
|    Sol.    : 438    0      0.00    90.95   40.80    None  None   None       |
|    Mac.    : 2385   0      0.00    102.77  12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.277: 1239   |   5:    51.387 -  61.664:   91        |
|      1:    10.277 -  20.555:  807   |   6:    61.664 -  71.941:   48        |
|      2:    20.555 -  30.832:  335   |   7:    71.941 -  82.219:   13        |
|      3:    30.832 -  41.109:  160   |   8:    82.219 -  92.496:    6        |
|      4:    41.109 -  51.387:  123   |   9:    92.496 - 102.773:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2257 r_free = 0.3025             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2255 r_free = 0.3016             target_work(ml) = 5.775         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2255   r_free= 0.3016   ksol= 0.34   Bsol= 54.74   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,1.38,3.77,0.00,0.00,0.00); trace/3= 2.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.775143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2253   r_free= 0.3020   ksol= 0.32   Bsol= 60.36   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.35,0.33,2.53,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.774622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.462316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.469  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.424542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.324  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2253      final r-factor (work) = 0.1785          |
| start r-factor (free) = 0.3020      final r-factor (free) = 0.2442          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9449 = 5.46 * 0.50 * 5.8080 + 1.00 * 0.0825                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6121 = 5.46 * 0.50 * 5.6871 + 1.00 * 0.0797                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1785      final r-factor (work) = 0.1670          |
| start r-factor (free) = 0.2442      final r-factor (free) = 0.2287          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4348 = 0.42 * 1.00 * 5.6871 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3658 = 0.42 * 1.00 * 5.5400 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.74   16.55    None  None   None       |
|    all(noH): 2823   0      0.00    90.74   16.55    None  None   None       |
|    Sol.    : 438    0      2.10    90.74   41.30    None  None   None       |
|    Mac.    : 2385   0      0.00    78.62   12.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.074: 1191   |   5:    45.372 -  54.446:  110        |
|      1:     9.074 -  18.149:  849   |   6:    54.446 -  63.520:   57        |
|      2:    18.149 -  27.223:  274   |   7:    63.520 -  72.594:   43        |
|      3:    27.223 -  36.297:  166   |   8:    72.594 -  81.669:   10        |
|      4:    36.297 -  45.372:  117   |   9:    81.669 -  90.743:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1670 r_free = 0.2287             target_work(ml) = 5.505         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1669 r_free = 0.2283             target_work(ml) = 5.504         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2283   ksol= 0.32   Bsol= 60.36   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.35,0.33,2.53,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.503749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2274   ksol= 0.32   Bsol= 56.58   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.02,-0.29,2.00,-0.00,0.00,0.00); trace/3= 0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.500789                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.952767              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.193  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 57.505377             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.994   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1472          |
| start r-factor (free) = 0.2274      final r-factor (free) = 0.2042          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0296 = 3.95 * 0.50 * 5.5403 + 1.00 * 0.0797                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8504 = 3.95 * 0.50 * 5.4540 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1472      final r-factor (work) = 0.1363          |
| start r-factor (free) = 0.2042      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 313.6460 = 57.51 * 1.00 * 5.4540 + 1.00 * 0.0136                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 308.4819 = 57.51 * 1.00 * 5.3641 + 1.00 * 0.0197                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.46  16.74    None  None   None       |
|    all(noH): 2823   0      0.00    100.46  16.74    None  None   None       |
|    Sol.    : 438    0      3.82    100.46  45.95    None  None   None       |
|    Mac.    : 2385   0      0.00    86.28   11.38    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.046: 1428   |   5:    50.229 -  60.275:   85        |
|      1:    10.046 -  20.092:  754   |   6:    60.275 -  70.321:   78        |
|      2:    20.092 -  30.138:  202   |   7:    70.321 -  80.367:   29        |
|      3:    30.138 -  40.184:  118   |   8:    80.367 -  90.413:   24        |
|      4:    40.184 -  50.229:   96   |   9:    90.413 - 100.459:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1363 r_free = 0.1946             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1362 r_free = 0.1945             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1945   ksol= 0.32   Bsol= 56.58   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.02,-0.29,2.00,-0.00,0.00,0.00); trace/3= 0.58                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333795                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6898 0.99   1447  160 0.0991 0.1348      5.4103      5.6193|
|  2:  4.6898 -  3.7407 0.99   1396  157 0.0905 0.1275      5.5045      5.7495|
|  3:  3.7407 -  3.2732 0.99   1370  152 0.1243 0.1845      5.6072      5.9696|
|  4:  3.2732 -  2.9764 0.99   1365  152 0.1579 0.2103      5.6568      5.8141|
|  5:  2.9764 -  2.7644 0.99   1346  151 0.1649 0.2282      5.5364      5.7979|
|  6:  2.7644 -  2.6023 0.99   1361  148 0.1613 0.2490      5.4352       5.691|
|  7:  2.6023 -  2.4725 0.99   1334  155 0.1564 0.1917      5.3636      5.4986|
|  8:  2.4725 -  2.3653 0.98   1323  148 0.1545 0.2387      5.3053      5.6023|
|  9:  2.3653 -  2.2746 0.98   1330  141 0.1564 0.2218      5.2543      5.4802|
| 10:  2.2746 -  2.1963 1.00   1347  148 0.1406 0.1915       5.145      5.3368|
| 11:  2.1963 -  2.1278 0.98   1322  149 0.1435 0.2262      5.1275       5.521|
| 12:  2.1278 -  2.0672 0.98   1312  143 0.1417 0.2306      5.0586      5.3226|
| 13:  2.0672 -  2.0129 0.83   1113  126 0.1296 0.1963      4.9373       5.107|
| 14:  2.0129 -  1.9639 0.20    264   29 0.1162 0.2012      4.7948      5.2065|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6898  1447   160  0.93  10.03   0.97     0.94       8153.29|
|  2:  4.6898 -  3.7407  1396   157  0.94   9.32   1.03     1.01      10947.58|
|  3:  3.7407 -  3.2732  1370   152  0.91  14.38   1.05     1.05      13964.62|
|  4:  3.2732 -  2.9764  1365   152  0.87  19.12   1.03     1.00      16439.40|
|  5:  2.9764 -  2.7644  1346   151  0.85  21.03   1.00     0.98      13653.67|
|  6:  2.7644 -  2.6023  1361   148  0.84  22.16   0.98     0.94      11670.15|
|  7:  2.6023 -  2.4725  1334   155  0.86  20.93   1.00     0.95       9991.15|
|  8:  2.4725 -  2.3653  1323   148  0.85  21.29   1.00     0.96       9002.96|
|  9:  2.3653 -  2.2746  1330   141  0.85  21.54   1.00     0.94       8034.88|
| 10:  2.2746 -  2.1963  1347   148  0.86  20.29   1.00     0.97       6819.85|
| 11:  2.1963 -  2.1278  1322   149  0.85  21.37   1.00     0.93       6720.32|
| 12:  2.1278 -  2.0672  1312   143  0.86  20.98   1.00     0.98       6076.28|
| 13:  2.0672 -  2.0129  1113   126  0.85  21.37   1.00     0.96       4973.31|
| 14:  2.0129 -  1.9639   264    29  0.90  16.30   0.99     0.97       3491.74|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3491.74 max =        16439.40 mean =      9718.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.96 mean =        18.59|
|phase err.(test): min =        0.00 max =           89.44 mean =        17.81|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1945   ksol= 0.31   Bsol= 57.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.87,1.42,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333811                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1945   ksol= 0.31   Bsol= 57.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.87,1.42,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333811                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2044 -  4.6898 0.99   1447  160 0.0988 0.1328      5.4062      5.6146|
|  2:  4.6898 -  3.7407 0.99   1396  157 0.0919 0.1271      5.5093      5.7462|
|  3:  3.7407 -  3.2732 0.99   1370  152 0.1253 0.1848      5.6085      5.9725|
|  4:  3.2732 -  2.9764 0.99   1365  152 0.1582 0.2110      5.6582      5.8153|
|  5:  2.9764 -  2.7644 0.99   1346  151 0.1649 0.2288      5.5367      5.7968|
|  6:  2.7644 -  2.6023 0.99   1361  148 0.1613 0.2487       5.435      5.6903|
|  7:  2.6023 -  2.4725 0.99   1334  155 0.1563 0.1916      5.3628      5.4973|
|  8:  2.4725 -  2.3653 0.98   1323  148 0.1543 0.2380      5.3042      5.6006|
|  9:  2.3653 -  2.2746 0.98   1330  141 0.1563 0.2221      5.2536      5.4816|
| 10:  2.2746 -  2.1963 1.00   1347  148 0.1404 0.1916      5.1448      5.3372|
| 11:  2.1963 -  2.1278 0.98   1322  149 0.1434 0.2260      5.1276      5.5202|
| 12:  2.1278 -  2.0672 0.98   1312  143 0.1416 0.2307      5.0583      5.3224|
| 13:  2.0672 -  2.0129 0.83   1113  126 0.1296 0.1962      4.9371      5.1069|
| 14:  2.0129 -  1.9639 0.20    264   29 0.1163 0.2011      4.7947      5.2063|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2044 -  4.6898  1447   160  0.93   9.94   0.96     0.93       8141.03|
|  2:  4.6898 -  3.7407  1396   157  0.94   9.26   1.03     1.01      10865.26|
|  3:  3.7407 -  3.2732  1370   152  0.91  14.34   1.05     1.05      13878.13|
|  4:  3.2732 -  2.9764  1365   152  0.87  19.15   1.03     1.00      16493.38|
|  5:  2.9764 -  2.7644  1346   151  0.85  21.04   1.00     0.98      13674.57|
|  6:  2.7644 -  2.6023  1361   148  0.84  22.13   0.99     0.94      11654.73|
|  7:  2.6023 -  2.4725  1334   155  0.86  20.92   1.00     0.95       9977.35|
|  8:  2.4725 -  2.3653  1323   148  0.85  21.27   1.00     0.96       8981.14|
|  9:  2.3653 -  2.2746  1330   141  0.85  21.53   1.00     0.94       8026.01|
| 10:  2.2746 -  2.1963  1347   148  0.86  20.29   1.00     0.97       6819.45|
| 11:  2.1963 -  2.1278  1322   149  0.85  21.37   1.00     0.93       6724.43|
| 12:  2.1278 -  2.0672  1312   143  0.86  20.98   1.00     0.98       6074.83|
| 13:  2.0672 -  2.0129  1113   126  0.85  21.36   1.00     0.96       4971.41|
| 14:  2.0129 -  1.9639   264    29  0.90  16.29   0.99     0.97       3488.89|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3488.89 max =        16493.38 mean =      9705.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.99 mean =        18.57|
|phase err.(test): min =        0.00 max =           89.79 mean =        17.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.978)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    101.04  17.32    None  None   None       |
|    all(noH): 2823   0      0.58    101.04  17.32    None  None   None       |
|    Sol.    : 438    0      4.40    101.04  46.53    None  None   None       |
|    Mac.    : 2385   0      0.58    86.86   11.95    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:     0.579 -  10.625: 1428   |   5:    50.809 -  60.855:   85        |
|      1:    10.625 -  20.671:  754   |   6:    60.855 -  70.901:   78        |
|      2:    20.671 -  30.717:  202   |   7:    70.901 -  80.946:   29        |
|      3:    30.717 -  40.763:  118   |   8:    80.946 -  90.992:   24        |
|      4:    40.763 -  50.809:   96   |   9:    90.992 - 101.038:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.486 - 5.049
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 339
   mapped sites are within: 0.737 - 5.049

peak=    9.131 closest distance to " CB  VAL A 230 " =    1.431
peak=    7.799 closest distance to " O   HOH Z 130 " =    1.837
peak=    7.749 closest distance to " O   HOH Z 103 " =    1.184
peak=    7.507 closest distance to " CG2 VAL A 296 " =    1.543
peak=    6.586 closest distance to " CD2 LEU A   5 " =    1.384
peak=    6.028 closest distance to " CD1AILE A 234 " =    1.041
peak=    5.742 closest distance to " O   HOH Z 246 " =    1.739
peak=    5.479 closest distance to " O   HOH Z  70 " =    1.047
peak=    5.438 closest distance to " O   HOH Z 255 " =    1.075
peak=    5.392 closest distance to " O   HOH Z  65 " =    1.836
peak=    5.290 closest distance to " O   HOH Z 222 " =    1.709
peak=    5.222 closest distance to " CB  SER A  63 " =    1.388
peak=    5.180 closest distance to " O   HOH Z 375 " =    1.194
peak=    5.127 closest distance to " CG  PRO A  54 " =    1.467
peak=    5.069 closest distance to " NE2 GLN A  11 " =    1.128
peak=    5.047 closest distance to " O   HOH Z  69 " =    1.653
peak=    5.039 closest distance to " O   HOH Z 425 " =    1.801
peak=    5.025 closest distance to " O   HOH Z  63 " =    1.643
peak=    5.012 closest distance to " O   HOH Z 258 " =    1.317
peak=    4.954 closest distance to " O   HOH Z 427 " =    2.259
peak=    4.928 closest distance to " O   HOH Z 414 " =    1.820
peak=    4.921 closest distance to " O   HOH Z 417 " =    1.960
peak=    4.909 closest distance to " O   HOH Z 424 " =    2.088
peak=    4.856 closest distance to " CB  VAL A 230 " =    1.310
peak=    4.818 closest distance to " O   HOH Z  46 " =    1.141
peak=    4.798 closest distance to " OD1 ASN A  69 " =    1.134
peak=    4.756 closest distance to " O   HOH Z 385 " =    1.055
peak=    4.734 closest distance to " O   HOH Z 427 " =    1.318
peak=    4.731 closest distance to " O   HOH Z 287 " =    1.821
peak=    4.707 closest distance to " O   HOH Z 127 " =    1.249
peak=    4.695 closest distance to " CB  PRO A  54 " =    1.194
peak=    4.637 closest distance to " O   HOH Z 245 " =    1.230
peak=    4.572 closest distance to " O   HOH Z  24 " =    2.025
peak=    4.552 closest distance to " CG  LEU A 228 " =    1.082
peak=    4.444 closest distance to " O   HOH Z 278 " =    1.257
peak=    4.422 closest distance to " NH1 ARG A 138 " =    1.064
peak=    4.413 closest distance to " O   HOH Z 331 " =    1.083
peak=    4.400 closest distance to " CG  PRO A 243 " =    1.165
peak=    4.395 closest distance to " O   HOH Z 117 " =    0.940
peak=    4.382 closest distance to " O   HOH Z 143 " =    2.047
peak=    4.363 closest distance to " CB  GLN A 223 " =    1.635
peak=    4.360 closest distance to " O   HOH Z 105 " =    1.169
peak=    4.352 closest distance to " O   HOH Z 369 " =    2.188
peak=    4.302 closest distance to " CD2 LEU A 228 " =    1.330
peak=    4.299 closest distance to " O   HOH Z 360 " =    1.406
peak=    4.297 closest distance to " O   HOH Z 110 " =    0.937
peak=    4.279 closest distance to " O   HOH Z  49 " =    1.269
peak=    4.271 closest distance to " CB  MET A  40 " =    0.933
peak=    4.250 closest distance to " O   HOH Z 411 " =    3.300
peak=    4.236 closest distance to " O   HOH Z  39 " =    1.328
peak=    4.206 closest distance to " CB  ASN A 148 " =    1.414
peak=    4.201 closest distance to " CZ3 TRP A 266 " =    1.179
peak=    4.189 closest distance to " O   HOH Z 298 " =    1.956
peak=    4.167 closest distance to " O   HOH Z 359 " =    1.426
peak=    4.165 closest distance to " O   HOH Z 232 " =    2.262
peak=    4.142 closest distance to " O   PRO A 198 " =    1.389
peak=    4.135 closest distance to " O   HOH Z 126 " =    2.136
peak=    4.135 closest distance to " O   HOH Z 207 " =    1.112
peak=    4.128 closest distance to " O   HOH Z 389 " =    1.866
peak=    4.123 closest distance to " O   HOH Z  61 " =    1.477
peak=    4.117 closest distance to " CG1 VAL A 296 " =    1.207
peak=    4.090 closest distance to " CA  ALA A  51 " =    1.069
peak=    4.075 closest distance to " O   HOH Z 380 " =    1.946
peak=    4.056 closest distance to " O   HOH Z 257 " =    1.247
peak=    4.053 closest distance to " CG2 THR A 221 " =    1.227
peak=    4.034 closest distance to " CG2 ILE A 234 " =    1.042
peak=    4.032 closest distance to " CB  SER A 216 " =    1.139
peak=    4.028 closest distance to " CE  LYS A  76 " =    0.911
peak=    4.017 closest distance to " CE3 TRP A 274 " =    1.251
peak=    4.017 closest distance to " O   HOH Z 193 " =    1.734
peak=    3.993 closest distance to " O   HOH Z 225 " =    1.762
peak=    3.976 closest distance to " O   HOH Z 147 " =    1.315
peak=    3.973 closest distance to " N   TYR A  15 " =    1.098
peak=    3.964 closest distance to " O   HOH Z 238 " =    1.302
peak=    3.951 closest distance to " O   HOH Z  59 " =    1.965
peak=    3.947 closest distance to " CG  GLN A  58 " =    1.282
peak=    3.937 closest distance to " O   HOH Z  28 " =    1.343
peak=    3.926 closest distance to " O   HOH Z 437 " =    2.261
peak=    3.919 closest distance to " O   HOH Z 410 " =    1.535
peak=    3.912 closest distance to " CG  PRO A 198 " =    1.258
peak=    3.900 closest distance to " O   HOH Z 182 " =    1.149
peak=    3.888 closest distance to " O   HOH Z  52 " =    1.014
peak=    3.888 closest distance to " NZ  LYS A 119 " =    3.182
peak=    3.887 closest distance to " O   HOH Z 153 " =    3.729
peak=    3.872 closest distance to " CB  MET A  47 " =    1.233
peak=    3.870 closest distance to " O   HOH Z 424 " =    1.191
peak=    3.869 closest distance to " O   HOH Z 139 " =    1.102
peak=    3.862 closest distance to " O   HOH Z 422 " =    1.171
peak=    3.860 closest distance to " O   HOH Z 112 " =    0.917
peak=    3.857 closest distance to " CD1 LEU A   5 " =    1.390
peak=    3.856 closest distance to " O   HOH Z 293 " =    1.353
peak=    3.851 closest distance to " C   GLN A  73 " =    1.118
peak=    3.850 closest distance to " O   HOH Z 350 " =    1.558
peak=    3.820 closest distance to " O   HOH Z  92 " =    1.319
peak=    3.818 closest distance to " O   HOH Z 316 " =    2.954
peak=    3.813 closest distance to " O   HOH Z   9 " =    2.708
peak=    3.796 closest distance to " O   HOH Z  97 " =    1.428
peak=    3.792 closest distance to " CG  LEU A   5 " =    1.062
peak=    3.789 closest distance to " CG BARG A 275 " =    1.400
peak=    3.778 closest distance to " O   HOH Z  80 " =    1.901
peak=    3.759 closest distance to " O   HOH Z 361 " =    1.404
peak=    3.752 closest distance to " O   HOH Z  68 " =    2.183
peak=    3.751 closest distance to " O   HOH Z 373 " =    1.652
peak=    3.745 closest distance to " CB  VAL A 265 " =    1.337
peak=    3.740 closest distance to " O   HOH Z 330 " =    1.058
peak=    3.734 closest distance to " O   HOH Z  30 " =    1.363
peak=    3.731 closest distance to " CB  SER A   3 " =    1.568
peak=    3.730 closest distance to " CD  GLN A  77 " =    1.297
peak=    3.727 closest distance to " O   HOH Z 193 " =    1.445
peak=    3.722 closest distance to " CG2 ILE A  20 " =    1.697
peak=    3.719 closest distance to " ND2BASN A 224 " =    0.988
peak=    3.717 closest distance to " CB  ALA A  43 " =    0.823
peak=    3.709 closest distance to " O   HOH Z  88 " =    3.450
peak=    3.701 closest distance to " O   HOH Z 236 " =    1.505
peak=    3.698 closest distance to " O   HOH Z 392 " =    1.149
peak=    3.687 closest distance to " O   HOH Z 303 " =    2.177
peak=    3.685 closest distance to " CB  VAL A 202 " =    1.566
peak=    3.684 closest distance to " CZ  PHE A 218 " =    1.161
peak=    3.681 closest distance to " CD  LYS A  76 " =    1.766
peak=    3.673 closest distance to " CB  ASN A 142 " =    0.896
peak=    3.665 closest distance to " O   HOH Z  91 " =    2.516
peak=    3.664 closest distance to " ND1 HIS A  86 " =    1.845
peak=    3.664 closest distance to " NE1 TRP A 266 " =    1.820
peak=    3.659 closest distance to " O   HOH Z  76 " =    1.522
peak=    3.656 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.655 closest distance to " CG  GLN A  89 " =    1.504
peak=    3.648 closest distance to " O   HOH Z 111 " =    2.102
peak=    3.648 closest distance to " O   HOH Z   2 " =    1.710
peak=    3.636 closest distance to " CB  THR A  52 " =    0.994
peak=    3.632 closest distance to " OG  SER A 135 " =    1.206
peak=    3.624 closest distance to " O   HOH Z  26 " =    1.530
peak=    3.623 closest distance to " NE1 TRP A 274 " =    0.927
peak=    3.617 closest distance to " CG  ARG A 138 " =    1.178
peak=    3.614 closest distance to " O   HOH Z 374 " =    1.257
peak=    3.596 closest distance to " CB  GLU A 277 " =    3.649
peak=    3.592 closest distance to " CD2 TRP A 179 " =    1.302
peak=    3.590 closest distance to " CB  SER A 141 " =    1.103
peak=    3.589 closest distance to " O   HOH Z 353 " =    2.337
peak=    3.584 closest distance to " CB  GLU A 128 " =    1.082
peak=    3.583 closest distance to " NH1AARG A 145 " =    1.213
peak=    3.582 closest distance to " O   HOH Z   4 " =    2.230
peak=    3.580 closest distance to " O   HOH Z 403 " =    1.475
peak=    3.577 closest distance to " OG ASER A 212 " =    1.566
peak=    3.574 closest distance to " O   HOH Z 180 " =    2.200
peak=    3.569 closest distance to " CB  ALA A  10 " =    0.934
peak=    3.563 closest distance to " O   HOH Z 101 " =    0.849
peak=    3.562 closest distance to " CB  PHE A 225 " =    1.451
peak=    3.559 closest distance to " O   HOH Z  20 " =    1.623
peak=    3.554 closest distance to " NZ  LYS A 117 " =    2.984
peak=    3.550 closest distance to " O   HOH Z 425 " =    2.090
peak=    3.546 closest distance to " NH2AARG A 190 " =    1.833
peak=    3.544 closest distance to " O   HOH Z 329 " =    4.295
peak=    3.530 closest distance to " O   HOH Z 240 " =    2.214
peak=    3.520 closest distance to " O   HOH Z 368 " =    3.445
peak=    3.520 closest distance to " CA  ILE A 234 " =    1.120
peak=    3.516 closest distance to " CB  ILE A  33 " =    1.911
peak=    3.512 closest distance to " O   HOH Z 422 " =    2.523
peak=    3.509 closest distance to " CA  ALA A 160 " =    1.110
peak=    3.505 closest distance to " N   ALA A   1 " =    1.637
peak=    3.504 closest distance to " CD  ARG A 269 " =    0.923
peak=    3.504 closest distance to " CE  MET A  93 " =    1.549
peak=    3.502 closest distance to " CG  LEU A 167 " =    1.354
peak=    3.500 closest distance to " O   HOH Z 154 " =    2.340
peak=    3.495 closest distance to " O   HOH Z 148 " =    1.556
peak=    3.494 closest distance to " O   HOH Z 403 " =    1.361
peak=    3.493 closest distance to " O   HOH Z 342 " =    0.978
peak=    3.490 closest distance to " O   HOH Z 356 " =    1.397
peak=    3.490 closest distance to " O   HOH Z 145 " =    2.791
peak=    3.488 closest distance to " NH2AARG A 190 " =    1.933
peak=    3.486 closest distance to " CG2 VAL A 257 " =    0.836
peak=    3.485 closest distance to " O   HOH Z 203 " =    1.895
peak=    3.482 closest distance to " O   HOH Z 357 " =    2.109
peak=    3.472 closest distance to " O   HOH Z 211 " =    1.485
peak=    3.470 closest distance to " OE1 GLN A 240 " =    1.620
peak=    3.470 closest distance to " O   HOH Z  71 " =    1.307
peak=    3.467 closest distance to " CB  ASN A  39 " =    0.941
peak=    3.466 closest distance to " CB  PRO A  90 " =    1.108
peak=    3.460 closest distance to " CB  GLN A 183 " =    1.216
peak=    3.459 closest distance to " CE  LYS A 119 " =    1.018
peak=    3.457 closest distance to " O   HOH Z 343 " =    2.703
peak=    3.453 closest distance to " CG  PRO A 213 " =    1.249
peak=    3.451 closest distance to " CA  TYR A  30 " =    1.231
peak=    3.450 closest distance to " C   PRO A  54 " =    0.767
peak=    3.445 closest distance to " NE2 GLN A  58 " =    4.724
peak=    3.440 closest distance to " CA  ASN A 127 " =    1.269
peak=    3.438 closest distance to " O   HOH Z  57 " =    1.529
peak=    3.437 closest distance to " O   HOH Z  21 " =    1.447
peak=    3.432 closest distance to " NZ  LYS A 117 " =    1.310
peak=    3.432 closest distance to " CB  GLN A  88 " =    1.422
peak=    3.431 closest distance to " OG  SER A  62 " =    2.724
peak=    3.430 closest distance to " O   HOH Z 362 " =    1.763
peak=    3.425 closest distance to " CA  SER A  12 " =    1.699
peak=    3.423 closest distance to " O   HOH Z 423 " =    1.908
peak=    3.423 closest distance to " O   HOH Z  43 " =    1.188
peak=    3.420 closest distance to " O   HOH Z 181 " =    2.389
peak=    3.405 closest distance to " O   HOH Z 274 " =    2.542
peak=    3.395 closest distance to " O   HOH Z   1 " =    1.872
peak=    3.393 closest distance to " OD1 ASP A  65 " =    1.851
peak=    3.383 closest distance to " CE3 TRP A 150 " =    1.101
peak=    3.383 closest distance to " O   HOH Z 423 " =    1.540
peak=    3.382 closest distance to " CZ3 TRP A 123 " =    1.688
peak=    3.369 closest distance to " CB  GLU A 175 " =    1.039
peak=    3.367 closest distance to " O   HOH Z 172 " =    5.049
peak=    3.360 closest distance to " O   HOH Z 357 " =    2.376
peak=    3.357 closest distance to " CD  ARG A 195 " =    3.576
peak=    3.353 closest distance to " O   THR A 294 " =    1.074
peak=    3.352 closest distance to " N   CYS A 260 " =    0.995
peak=    3.346 closest distance to " CA  ASP A 124 " =    0.745
peak=    3.344 closest distance to " CB  SER A 276 " =    1.110
peak=    3.341 closest distance to " O   HOH Z 325 " =    1.907
peak=    3.340 closest distance to " CA  ARG A 195 " =    1.342
peak=    3.337 closest distance to " O   HOH Z 132 " =    2.381
peak=    3.336 closest distance to " O   HOH Z 201 " =    1.640
peak=    3.336 closest distance to " CB  VAL A 250 " =    1.171
peak=    3.331 closest distance to " C   ASN A 209 " =    1.769
peak=    3.330 closest distance to " CB  ASP A 124 " =    0.823
peak=    3.330 closest distance to " N   ALA A 256 " =    0.968
peak=    3.328 closest distance to " O   HOH Z 291 " =    1.566
peak=    3.324 closest distance to " O   HOH Z 409 " =    4.868
peak=    3.323 closest distance to " O   HOH Z 143 " =    1.607
peak=    3.322 closest distance to " CA  VAL A 112 " =    1.260
peak=    3.321 closest distance to " CB  ALA A 160 " =    1.360
peak=    3.319 closest distance to " CD BLYS A 290 " =    0.945
peak=    3.318 closest distance to " CD  ARG A  66 " =    2.159
peak=    3.317 closest distance to " CB  TRP A 150 " =    1.260
peak=    3.315 closest distance to " CG  GLN A  11 " =    2.161
peak=    3.311 closest distance to " NH2AARG A 145 " =    1.102
peak=    3.311 closest distance to " O   HOH Z 419 " =    1.770
peak=    3.304 closest distance to " CB  ARG A 275 " =    1.129
peak=    3.304 closest distance to " CB  LYS A 117 " =    1.168
peak=    3.301 closest distance to " O   MET A 105 " =    1.846
peak=    3.296 closest distance to " CB  ALA A 114 " =    1.613
peak=    3.296 closest distance to " NE2 HIS A 207 " =    0.986
peak=    3.294 closest distance to " CB  LEU A 237 " =    0.930
peak=    3.294 closest distance to " O   HOH Z 213 " =    1.906
peak=    3.292 closest distance to " CB  TRP A 266 " =    1.048
peak=    3.290 closest distance to " N   ARG A 156 " =    1.288
peak=    3.290 closest distance to " CE3 TRP A  85 " =    1.106
peak=    3.290 closest distance to " CE AMET A  47 " =    1.387
peak=    3.289 closest distance to " CB  TYR A  30 " =    1.321
peak=    3.286 closest distance to " OE2 GLU A   2 " =    2.192
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.261
peak=    3.280 closest distance to " O   HOH Z 285 " =    1.832
peak=    3.278 closest distance to " N   ASP A 231 " =    1.714
peak=    3.278 closest distance to " O   HOH Z  56 " =    2.070
peak=    3.265 closest distance to " O   ASP A 124 " =    0.862
peak=    3.260 closest distance to " O   HOH Z  27 " =    1.132
peak=    3.258 closest distance to " NH2BARG A 190 " =    1.346
peak=    3.256 closest distance to " CG  ARG A 138 " =    1.211
peak=    3.255 closest distance to " CB  THR A  31 " =    1.569
peak=    3.254 closest distance to " N   ASN A 127 " =    1.342
peak=    3.250 closest distance to " O   HOH Z 145 " =    1.886
peak=    3.249 closest distance to " O   HOH Z 218 " =    1.727
peak=    3.249 closest distance to " O   GLN A 278 " =    1.292
peak=    3.248 closest distance to " N   PHE A 208 " =    0.923
peak=    3.245 closest distance to " CB  ASN A  60 " =    0.955
peak=    3.243 closest distance to " OE2 GLU A  53 " =    1.042
peak=    3.242 closest distance to " CD2 TYR A 186 " =    1.053
peak=    3.240 closest distance to " CB  TRP A 179 " =    1.444
peak=    3.238 closest distance to " O   HOH Z 268 " =    1.016
peak=    3.233 closest distance to " N   PHE A 130 " =    1.300
peak=    3.232 closest distance to " CG  ARG A 159 " =    0.970
peak=    3.230 closest distance to " CB  GLU A 236 " =    1.356
peak=    3.229 closest distance to " CA  THR A 221 " =    0.948
peak=    3.227 closest distance to " CD  LYS A 119 " =    1.804
peak=    3.226 closest distance to " CZ3 TRP A  92 " =    1.088
peak=    3.222 closest distance to " OE2 GLU A  53 " =    1.804
peak=    3.221 closest distance to " O   HOH Z 353 " =    1.721
peak=    3.219 closest distance to " CB  ASP A 191 " =    1.337
peak=    3.218 closest distance to " CB  ASN A 176 " =    0.881
peak=    3.215 closest distance to " O   HOH Z  85 " =    2.703
peak=    3.214 closest distance to " CZ  PHE A  38 " =    1.280
peak=    3.209 closest distance to " CA  ARG A 139 " =    1.165
peak=    3.209 closest distance to " O   HOH Z  59 " =    2.352
peak=    3.206 closest distance to " O   HOH Z  33 " =    1.387
peak=    3.204 closest distance to " CA  VAL A 125 " =    1.141
peak=    3.204 closest distance to " O   HOH Z 368 " =    2.150
peak=    3.203 closest distance to " CA  GLY A 267 " =    1.301
peak=    3.203 closest distance to " OG BSER A 212 " =    2.361
peak=    3.203 closest distance to " CA  ARG A 156 " =    0.964
peak=    3.201 closest distance to " CB  ARG A 156 " =    1.198
peak=    3.201 closest distance to " O   HOH Z  51 " =    2.007
peak=    3.199 closest distance to " ND2 ASN A  60 " =    3.009
peak=    3.198 closest distance to " O   HOH Z 214 " =    2.735
peak=    3.197 closest distance to " CG  ARG A 156 " =    1.243
peak=    3.195 closest distance to " O   HOH Z 417 " =    1.888
peak=    3.195 closest distance to " CA  TRP A 150 " =    1.088
peak=    3.194 closest distance to " O   HOH Z 193 " =    1.580
peak=    3.191 closest distance to " CB  GLU A 152 " =    1.145
peak=    3.191 closest distance to " CG  ASN A  60 " =    1.014
peak=    3.190 closest distance to " O   TYR A 116 " =    1.264
peak=    3.186 closest distance to " O   HOH Z 233 " =    1.367
peak=    3.184 closest distance to " CG2 ILE A 120 " =    1.068
peak=    3.177 closest distance to " O   HOH Z  10 " =    1.640
peak=    3.171 closest distance to " O   HOH Z 186 " =    2.900
peak=    3.168 closest distance to " CA  LEU A 222 " =    1.096
peak=    3.165 closest distance to " O   HOH Z 128 " =    2.009
peak=    3.163 closest distance to " O   ASN A  69 " =    1.296
peak=    3.163 closest distance to " NH2 ARG A  56 " =    0.902
peak=    3.161 closest distance to " CG2 VAL A 202 " =    1.308
peak=    3.160 closest distance to " N   GLN A 122 " =    0.745
peak=    3.158 closest distance to " O   HOH Z 176 " =    1.402
peak=    3.156 closest distance to " N   PHE A  16 " =    1.421
peak=    3.153 closest distance to " O   HOH Z 328 " =    1.715
peak=    3.151 closest distance to " CG  PRO A  90 " =    1.775
peak=    3.149 closest distance to " O   HOH Z 104 " =    1.826
peak=    3.144 closest distance to " NH2 ARG A 159 " =    1.234
peak=    3.134 closest distance to " O   THR A 182 " =    1.651
peak=    3.130 closest distance to " O   HOH Z 265 " =    1.701
peak=    3.123 closest distance to " CG  LEU A 281 " =    0.920
peak=    3.121 closest distance to " O   HOH Z 272 " =    1.902
peak=    3.119 closest distance to " CB  ALA A 233 " =    1.042
peak=    3.113 closest distance to " O   HOH Z 218 " =    1.628
peak=    3.112 closest distance to " O   HOH Z 424 " =    2.838
peak=    3.112 closest distance to " CA  GLY A  80 " =    0.889
peak=    3.109 closest distance to " O   HOH Z 158 " =    2.872
peak=    3.106 closest distance to " O   HOH Z 133 " =    1.054
peak=    3.093 closest distance to " CB  ASP A 140 " =    1.060
peak=    3.087 closest distance to " CE2 TYR A 169 " =    1.250
peak=    3.086 closest distance to " CA  ASN A 284 " =    0.876
peak=    3.084 closest distance to " O   HOH Z 359 " =    4.206
peak=    3.079 closest distance to " CB  ARG A  79 " =    0.805
peak=    3.076 closest distance to " O   HOH Z 378 " =    1.023
peak=    3.074 closest distance to " CA  ALA A 129 " =    1.388
peak=    3.064 closest distance to " CB  ALA A 184 " =    1.113
peak=    3.062 closest distance to " OG  SER A  26 " =    1.421
peak=    3.059 closest distance to " NH1 ARG A  56 " =    1.262
peak=    3.034 closest distance to " CB  THR A 235 " =    1.034
peak=    3.032 closest distance to " O   HOH Z 213 " =    1.689
peak=    3.029 closest distance to " C   ALA A 299 " =    0.964
peak=    3.023 closest distance to " CA  ASN A 142 " =    1.264
peak=    3.021 closest distance to " OD1 ASN A 148 " =    1.883

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.376 - 5.438
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 223
   mapped sites are within: 0.759 - 5.438

peak=   -4.970 closest distance to " O   PRO A 198 " =    1.341
peak=   -4.434 closest distance to " CA  ASP A  27 " =    2.540
peak=   -4.427 closest distance to " O   HOH Z 147 " =    1.982
peak=   -4.363 closest distance to " CZ2 TRP A  92 " =    2.813
peak=   -4.290 closest distance to " CG  ARG A 219 " =    2.314
peak=   -4.245 closest distance to " CG2 VAL A 230 " =    0.997
peak=   -4.226 closest distance to " OG  SER A  97 " =    2.158
peak=   -4.020 closest distance to " CG1 VAL A 125 " =    2.373
peak=   -4.001 closest distance to " CB  VAL A 230 " =    0.981
peak=   -3.986 closest distance to " O   HOH Z 165 " =    2.376
peak=   -3.980 closest distance to " CB  GLN A  55 " =    1.144
peak=   -3.967 closest distance to " CD  ARG A  14 " =    3.173
peak=   -3.962 closest distance to " CD2 TYR A 116 " =    2.305
peak=   -3.923 closest distance to " O   HOH Z 216 " =    1.485
peak=   -3.917 closest distance to " OE1 GLU A 277 " =    2.391
peak=   -3.883 closest distance to " CB  ALA A   9 " =    2.565
peak=   -3.881 closest distance to " CG  ARG A 138 " =    1.144
peak=   -3.879 closest distance to " CB  ALA A  43 " =    2.730
peak=   -3.875 closest distance to " O   HOH Z 163 " =    1.654
peak=   -3.868 closest distance to " OG  SER A  28 " =    1.921
peak=   -3.857 closest distance to " N   THR A 157 " =    1.544
peak=   -3.857 closest distance to " CB  PHE A 130 " =    1.207
peak=   -3.856 closest distance to " O   SER A  22 " =    2.640
peak=   -3.849 closest distance to " NE2 GLN A 223 " =    1.495
peak=   -3.845 closest distance to " O   HOH Z 131 " =    3.917
peak=   -3.836 closest distance to " O   HOH Z  69 " =    1.998
peak=   -3.835 closest distance to " CD2 TYR A 293 " =    1.928
peak=   -3.835 closest distance to " O   HOH Z  22 " =    2.993
peak=   -3.834 closest distance to " CD  LYS A 166 " =    2.461
peak=   -3.832 closest distance to " O   HOH Z 110 " =    1.173
peak=   -3.829 closest distance to " O   HOH Z 275 " =    1.825
peak=   -3.822 closest distance to " O   HOH Z 128 " =    2.499
peak=   -3.815 closest distance to " O   HOH Z  39 " =    0.759
peak=   -3.813 closest distance to " CB  ALA A 291 " =    2.144
peak=   -3.810 closest distance to " OG BSER A 134 " =    1.600
peak=   -3.782 closest distance to " O   HOH Z 100 " =    0.942
peak=   -3.775 closest distance to " CG2AVAL A  41 " =    2.775
peak=   -3.749 closest distance to " CB  ALA A 129 " =    2.565
peak=   -3.748 closest distance to " CG2 ILE A 151 " =    2.646
peak=   -3.743 closest distance to " CB  ALA A 161 " =    1.503
peak=   -3.738 closest distance to " CA  GLY A 203 " =    2.552
peak=   -3.731 closest distance to " CD  PRO A 213 " =    2.110
peak=   -3.721 closest distance to " CD  LYS A 289 " =    2.309
peak=   -3.717 closest distance to " O   HOH Z  24 " =    1.246
peak=   -3.711 closest distance to " O   HOH Z 155 " =    1.105
peak=   -3.694 closest distance to " O   HOH Z 245 " =    0.982
peak=   -3.687 closest distance to " O   HOH Z 111 " =    1.702
peak=   -3.683 closest distance to " O   ALA A  10 " =    1.686
peak=   -3.669 closest distance to " O   HOH Z 415 " =    1.140
peak=   -3.647 closest distance to " C   ILE A 239 " =    2.030
peak=   -3.644 closest distance to " OE2 GLU A 152 " =    1.234
peak=   -3.644 closest distance to " O   HOH Z 246 " =    1.677
peak=   -3.634 closest distance to " CE2 TYR A  30 " =    2.503
peak=   -3.626 closest distance to " O   HOH Z 231 " =    0.796
peak=   -3.625 closest distance to " O   HOH Z 177 " =    2.466
peak=   -3.619 closest distance to " CB  ALA A 114 " =    2.460
peak=   -3.612 closest distance to " CA  HIS A 207 " =    1.081
peak=   -3.606 closest distance to " OD1 ASP A 191 " =    1.932
peak=   -3.602 closest distance to " CA  GLY A 133 " =    2.037
peak=   -3.602 closest distance to " CB  ALA A 160 " =    2.167
peak=   -3.600 closest distance to " CG  ARG A 259 " =    2.471
peak=   -3.600 closest distance to " O   SER A 135 " =    1.615
peak=   -3.596 closest distance to " O   HOH Z 411 " =    5.193
peak=   -3.592 closest distance to " CB  ASP A 132 " =    2.670
peak=   -3.592 closest distance to " O   HOH Z 245 " =    1.607
peak=   -3.592 closest distance to " O   HOH Z 165 " =    1.760
peak=   -3.585 closest distance to " O   HOH Z  60 " =    1.613
peak=   -3.581 closest distance to " CB  PRO A 243 " =    2.773
peak=   -3.574 closest distance to " N   ALA A  43 " =    2.678
peak=   -3.567 closest distance to " CD1 TYR A 247 " =    2.717
peak=   -3.566 closest distance to " C   GLU A   2 " =    1.955
peak=   -3.559 closest distance to " CD2 LEU A   5 " =    0.996
peak=   -3.548 closest distance to " O   HOH Z 149 " =    1.502
peak=   -3.537 closest distance to " O   ALA A  84 " =    1.670
peak=   -3.533 closest distance to " OG  SER A  87 " =    1.541
peak=   -3.526 closest distance to " O   HOH Z 134 " =    4.039
peak=   -3.522 closest distance to " O   HOH Z 385 " =    1.397
peak=   -3.516 closest distance to " ND2 ASN A 285 " =    2.061
peak=   -3.516 closest distance to " O   GLY A 203 " =    2.611
peak=   -3.511 closest distance to " O   HOH Z 276 " =    1.127
peak=   -3.510 closest distance to " C   HIS A 108 " =    1.444
peak=   -3.504 closest distance to " CD  ARG A 156 " =    1.851
peak=   -3.500 closest distance to " O   HOH Z 118 " =    0.805
peak=   -3.499 closest distance to " OH  TYR A 247 " =    1.479
peak=   -3.494 closest distance to " O   HOH Z 438 " =    1.080
peak=   -3.494 closest distance to " CB  TRP A  85 " =    2.403
peak=   -3.492 closest distance to " CG2 VAL A 189 " =    2.602
peak=   -3.492 closest distance to " O   HOH Z 198 " =    2.063
peak=   -3.486 closest distance to " CG  GLN A  88 " =    0.812
peak=   -3.482 closest distance to " N   PRO A  54 " =    1.042
peak=   -3.474 closest distance to " CB  ALA A 248 " =    2.041
peak=   -3.473 closest distance to " O   HOH Z 389 " =    2.598
peak=   -3.467 closest distance to " O   HOH Z 292 " =    1.667
peak=   -3.466 closest distance to " CG  LEU A 281 " =    1.916
peak=   -3.457 closest distance to " CG2 ILE A  20 " =    2.613
peak=   -3.453 closest distance to " CB  TYR A  68 " =    1.083
peak=   -3.452 closest distance to " O   HOH Z 134 " =    1.736
peak=   -3.444 closest distance to " O   ALA A  51 " =    1.323
peak=   -3.442 closest distance to " OD2 ASP A 171 " =    1.727
peak=   -3.434 closest distance to " O   HOH Z 257 " =    1.252
peak=   -3.429 closest distance to " CE BMET A  47 " =    1.275
peak=   -3.424 closest distance to " CG2 VAL A 230 " =    2.796
peak=   -3.419 closest distance to " O   HOH Z 275 " =    1.671
peak=   -3.409 closest distance to " NE2 GLN A  55 " =    1.265
peak=   -3.409 closest distance to " NH2AARG A 275 " =    5.438
peak=   -3.404 closest distance to " O   GLY A  80 " =    2.523
peak=   -3.404 closest distance to " O   PRO A 163 " =    1.654
peak=   -3.393 closest distance to " O   ASP A 253 " =    1.782
peak=   -3.393 closest distance to " CB  HIS A  86 " =    1.143
peak=   -3.392 closest distance to " O   HOH Z  68 " =    1.606
peak=   -3.390 closest distance to " O   HOH Z 298 " =    2.780
peak=   -3.387 closest distance to " O   HOH Z 300 " =    1.185
peak=   -3.386 closest distance to " CG  MET A 105 " =    0.892
peak=   -3.385 closest distance to " OE1 GLN A  88 " =    1.069
peak=   -3.383 closest distance to " CB  ALA A   7 " =    1.927
peak=   -3.378 closest distance to " CA  GLY A 241 " =    2.366
peak=   -3.378 closest distance to " O   HOH Z  32 " =    1.912
peak=   -3.373 closest distance to " CD1 TRP A  85 " =    1.019
peak=   -3.371 closest distance to " CG2 THR A  31 " =    2.442
peak=   -3.367 closest distance to " CG  LEU A   5 " =    1.035
peak=   -3.365 closest distance to " O   HOH Z 103 " =    1.735
peak=   -3.363 closest distance to " O   HOH Z 404 " =    1.105
peak=   -3.361 closest distance to " CG  GLU A 277 " =    1.178
peak=   -3.361 closest distance to " CZ  PHE A  38 " =    2.417
peak=   -3.356 closest distance to " OD1 ASN A  69 " =    0.811
peak=   -3.349 closest distance to " O   HOH Z 255 " =    1.124
peak=   -3.347 closest distance to " CZ3 TRP A 179 " =    1.282
peak=   -3.342 closest distance to " O   HOH Z 368 " =    1.795
peak=   -3.342 closest distance to " CB  PRO A  54 " =    2.398
peak=   -3.341 closest distance to " C   VAL A  72 " =    0.883
peak=   -3.338 closest distance to " O   HOH Z 283 " =    2.371
peak=   -3.337 closest distance to " O   HOH Z 139 " =    5.303
peak=   -3.335 closest distance to " C   ARG A 269 " =    1.408
peak=   -3.333 closest distance to " O   HOH Z 133 " =    1.249
peak=   -3.331 closest distance to " CG2 THR A 178 " =    2.260
peak=   -3.323 closest distance to " O   HOH Z 407 " =    2.939
peak=   -3.309 closest distance to " O   HOH Z 368 " =    1.437
peak=   -3.305 closest distance to " OG  SER A 141 " =    1.839
peak=   -3.296 closest distance to " NE2 GLN A 194 " =    1.926
peak=   -3.295 closest distance to " O   LEU A 300 " =    2.334
peak=   -3.294 closest distance to " O   HOH Z   9 " =    1.839
peak=   -3.293 closest distance to " NZ  LYS A 166 " =    1.667
peak=   -3.291 closest distance to " N   ALA A 244 " =    1.265
peak=   -3.289 closest distance to " OG  SER A 245 " =    1.519
peak=   -3.289 closest distance to " ND2 ASN A  60 " =    4.016
peak=   -3.287 closest distance to " CA  ASN A 127 " =    1.388
peak=   -3.286 closest distance to " O   GLU A  44 " =    1.595
peak=   -3.283 closest distance to " O   HOH Z 297 " =    3.884
peak=   -3.282 closest distance to " O   HOH Z  10 " =    1.538
peak=   -3.282 closest distance to " O   HOH Z 389 " =    1.264
peak=   -3.280 closest distance to " O   HOH Z 193 " =    1.040
peak=   -3.277 closest distance to " O   ILE A  49 " =    1.527
peak=   -3.276 closest distance to " O   SER A 245 " =    1.327
peak=   -3.262 closest distance to " O   HOH Z 313 " =    1.580
peak=   -3.261 closest distance to " CA  GLY A  98 " =    1.952
peak=   -3.261 closest distance to " CD2 LEU A 237 " =    2.136
peak=   -3.258 closest distance to " SG BCYS A 201 " =    2.334
peak=   -3.258 closest distance to " O   HOH Z  15 " =    1.271
peak=   -3.256 closest distance to " O   HOH Z   1 " =    3.521
peak=   -3.253 closest distance to " OD1 ASP A 107 " =    1.203
peak=   -3.252 closest distance to " CD1 LEU A 282 " =    2.586
peak=   -3.248 closest distance to " O   HOH Z 140 " =    1.184
peak=   -3.242 closest distance to " CG2 THR A  52 " =    2.805
peak=   -3.237 closest distance to " OE1 GLN A 278 " =    1.206
peak=   -3.235 closest distance to " O   HOH Z 286 " =    1.803
peak=   -3.235 closest distance to " O   ASP A 298 " =    1.807
peak=   -3.230 closest distance to " O   HOH Z 364 " =    2.517
peak=   -3.229 closest distance to " CA  ASN A 110 " =    0.932
peak=   -3.228 closest distance to " O   HOH Z 202 " =    1.816
peak=   -3.225 closest distance to " O   GLN A  73 " =    1.365
peak=   -3.222 closest distance to " O   HOH Z 359 " =    3.224
peak=   -3.222 closest distance to " O   GLN A 240 " =    3.181
peak=   -3.213 closest distance to " CG  GLN A  88 " =    0.783
peak=   -3.210 closest distance to " CA  GLY A  91 " =    2.260
peak=   -3.206 closest distance to " O   VAL A 189 " =    2.702
peak=   -3.204 closest distance to " CB  ASN A  39 " =    2.203
peak=   -3.198 closest distance to " ND2 ASN A 173 " =    1.735
peak=   -3.197 closest distance to " NE2 GLN A 240 " =    1.191
peak=   -3.196 closest distance to " CD  GLU A  44 " =    1.088
peak=   -3.194 closest distance to " O   HOH Z 179 " =    1.713
peak=   -3.194 closest distance to " OE1 GLU A  44 " =    1.839
peak=   -3.194 closest distance to " CD1 PHE A  59 " =    1.412
peak=   -3.193 closest distance to " ND2 ASN A  39 " =    1.387
peak=   -3.185 closest distance to " O   HOH Z 133 " =    1.500
peak=   -3.184 closest distance to " O   ARG A 219 " =    2.093
peak=   -3.181 closest distance to " O   SER A 276 " =    1.813
peak=   -3.166 closest distance to " OD2 ASP A 272 " =    1.421
peak=   -3.165 closest distance to " CE2 PHE A 218 " =    2.523
peak=   -3.164 closest distance to " OD2 ASP A  50 " =    1.732
peak=   -3.160 closest distance to " CD1 LEU A 297 " =    2.269
peak=   -3.156 closest distance to " OG ASER A 134 " =    1.126
peak=   -3.153 closest distance to " O   HOH Z 300 " =    2.173
peak=   -3.151 closest distance to " NH2 ARG A  79 " =    2.265
peak=   -3.139 closest distance to " O   LYS A  76 " =    1.460
peak=   -3.139 closest distance to " O   PRO A 243 " =    1.945
peak=   -3.138 closest distance to " NH2 ARG A  56 " =    1.192
peak=   -3.137 closest distance to " N   ALA A  19 " =    2.206
peak=   -3.136 closest distance to " O   HOH Z 281 " =    2.481
peak=   -3.135 closest distance to " O   HOH Z 251 " =    0.995
peak=   -3.122 closest distance to " CZ  TYR A 169 " =    1.820
peak=   -3.119 closest distance to " O   HOH Z 339 " =    1.798
peak=   -3.119 closest distance to " O   HOH Z 111 " =    4.904
peak=   -3.116 closest distance to " O   ASP A  27 " =    1.943
peak=   -3.104 closest distance to " O   HOH Z  52 " =    2.206
peak=   -3.102 closest distance to " CD1 TYR A 214 " =    1.623
peak=   -3.099 closest distance to " CE  MET A 105 " =    2.391
peak=   -3.097 closest distance to " CA  GLY A 133 " =    2.186
peak=   -3.093 closest distance to " CB  ASP A 132 " =    2.491
peak=   -3.088 closest distance to " CD1 LEU A 101 " =    2.233
peak=   -3.082 closest distance to " CD1 ILE A  33 " =    2.001
peak=   -3.075 closest distance to " O   HOH Z 136 " =    3.289
peak=   -3.072 closest distance to " O   THR A  52 " =    1.067
peak=   -3.071 closest distance to " CB  ASP A  50 " =    2.513
peak=   -3.071 closest distance to " O   PRO A 243 " =    2.451
peak=   -3.063 closest distance to " CE3 TRP A 150 " =    2.449
peak=   -3.050 closest distance to " CA  ARG A 156 " =    1.155
peak=   -3.045 closest distance to " O   HOH Z 139 " =    0.998
peak=   -3.041 closest distance to " C   ASN A 285 " =    2.327
peak=   -3.034 closest distance to " O   HOH Z 189 " =    4.030
peak=   -3.034 closest distance to " CD  GLN A  55 " =    1.247
peak=   -3.032 closest distance to " CG2BVAL A  72 " =    1.872

================= 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    :  0.5151 0.5074   6.313567e+00   6.299026e+00
   1_bss:  0.5074 0.4966   6.309453e+00   6.294679e+00
   1_xyz:  0.4438 0.4724   6.244954e+00   6.270723e+00
   1_adp:  0.4103 0.4721   6.206521e+00   6.269895e+00
   1_occ:  0.4101 0.4720   6.206267e+00   6.270027e+00
   2_bss:  0.4078 0.4686   6.208910e+00   6.270490e+00
   2_xyz:  0.3354 0.4111   6.062946e+00   6.182194e+00
   2_adp:  0.3100 0.3956   6.018216e+00   6.155627e+00
   2_occ:  0.3098 0.3955   6.018029e+00   6.155946e+00
   3_bss:  0.3081 0.3934   6.017902e+00   6.154881e+00
   3_xyz:  0.2516 0.3233   5.848783e+00   6.021878e+00
   3_adp:  0.2257 0.3025   5.776405e+00   5.973744e+00
   3_occ:  0.2255 0.3016   5.775143e+00   5.973013e+00
   4_bss:  0.2253 0.3020   5.774622e+00   5.972734e+00
   4_xyz:  0.1785 0.2442   5.566406e+00   5.791004e+00
   4_adp:  0.1670 0.2287   5.505000e+00   5.731222e+00
   4_occ:  0.1669 0.2283   5.503749e+00   5.730230e+00
   5_bss:  0.1671 0.2274   5.500789e+00   5.726368e+00
   5_xyz:  0.1472 0.2042   5.395741e+00   5.634214e+00
   5_adp:  0.1363 0.1946   5.334073e+00   5.580975e+00
   5_occ:  0.1362 0.1945   5.333795e+00   5.580831e+00
   5_bss:  0.1366 0.1945   5.333811e+00   5.580175e+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:  0.331   6.337   6.819   8.141  11.066   0.000   0.000   0.000
   1_xyz:  0.331   6.337   6.819   8.141  11.066   0.000   0.000   0.000
   1_adp:  0.331   6.337   6.819   8.141  11.066   0.000   0.000   0.000
   1_occ:  0.331   6.337   6.819   8.141  11.066   0.000   0.000   0.000
   2_bss:  0.354  50.001   3.439   4.245   6.743   0.000   0.000   0.000
   2_xyz:  0.354  50.001   3.439   4.245   6.743   0.000   0.000   0.000
   2_adp:  0.354  50.001   3.439   4.245   6.743   0.000   0.000   0.000
   2_occ:  0.354  50.001   3.439   4.245   6.743   0.000   0.000   0.000
   3_bss:  0.339  54.744   1.370   1.378   3.771   0.000   0.000   0.000
   3_xyz:  0.339  54.744   1.370   1.378   3.771   0.000   0.000   0.000
   3_adp:  0.339  54.744   1.370   1.378   3.771   0.000   0.000   0.000
   3_occ:  0.339  54.744   1.370   1.378   3.771   0.000   0.000   0.000
   4_bss:  0.316  60.365   0.348   0.328   2.532   0.000   0.000   0.000
   4_xyz:  0.316  60.365   0.348   0.328   2.532   0.000   0.000   0.000
   4_adp:  0.316  60.365   0.348   0.328   2.532   0.000   0.000   0.000
   4_occ:  0.316  60.365   0.348   0.328   2.532   0.000   0.000   0.000
   5_bss:  0.324  56.580   0.024  -0.290   2.004  -0.000   0.000   0.000
   5_xyz:  0.324  56.580   0.024  -0.290   2.004  -0.000   0.000   0.000
   5_adp:  0.324  56.580   0.024  -0.290   2.004  -0.000   0.000   0.000
   5_occ:  0.324  56.580   0.024  -0.290   2.004  -0.000   0.000   0.000
   5_bss:  0.314  57.159  -0.555  -0.869   1.425  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.510 0.3213  0.3885    82815.943
   1_bss:  63.770 0.3441  0.5338    81770.657
   1_xyz:  59.027 0.4042  0.6109    70888.691
   1_adp:  58.092 0.4161  0.7110    70346.352
   1_occ:  58.159 0.4153  0.7091    70505.831
   2_bss:  58.103 0.4159  0.6291    70362.335
   2_xyz:  46.693 0.5596  0.8393    48627.668
   2_adp:  43.930 0.5941  0.8834    44507.035
   2_occ:  43.966 0.5936  0.8823    44516.042
   3_bss:  43.751 0.5962  0.8093    44209.612
   3_xyz:  34.269 0.7082  0.9330    28628.934
   3_adp:  31.453 0.7406  0.9458    24916.747
   3_occ:  31.405 0.7411  0.9451    24781.775
   4_bss:  31.376 0.7413  0.9097    24778.531
   4_xyz:  24.757 0.8126  0.9672    15664.291
   4_adp:  22.733 0.8340  0.9773    13821.749
   4_occ:  22.695 0.8344  0.9771    13757.225
   5_bss:  22.557 0.8354  0.9609    13555.421
   5_xyz:  19.860 0.8623  0.9732    10971.474
   5_adp:  18.515 0.8752  0.9686     9728.857
   5_occ:  18.509 0.8752  0.9686     9719.392
   5_bss:  18.492 0.8754  0.9685     9706.385
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3994e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3994e+01
   1_xyz:   1.887  0.015  0.117 18.805  0.007  4.106   1.7292e-01
   1_adp:   1.887  0.015  0.117 18.805  0.007  4.106   1.7292e-01
   1_occ:   1.887  0.015  0.117 18.805  0.007  4.106   1.7292e-01
   2_bss:   1.887  0.015  0.117 18.805  0.007  4.106   1.7292e-01
   2_xyz:   1.500  0.012  0.102 17.865  0.006  4.107   1.3912e-01
   2_adp:   1.500  0.012  0.102 17.865  0.006  4.107   1.3912e-01
   2_occ:   1.500  0.012  0.102 17.865  0.006  4.107   1.3912e-01
   3_bss:   1.500  0.012  0.102 17.865  0.006  4.107   1.3912e-01
   3_xyz:   1.180  0.009  0.090 16.181  0.004  4.109   8.2462e-02
   3_adp:   1.180  0.009  0.090 16.181  0.004  4.109   8.2462e-02
   3_occ:   1.180  0.009  0.090 16.181  0.004  4.109   8.2462e-02
   4_bss:   1.180  0.009  0.090 16.181  0.004  4.109   8.2462e-02
   4_xyz:   1.151  0.009  0.085 15.956  0.005  4.123   7.9718e-02
   4_adp:   1.151  0.009  0.085 15.956  0.005  4.123   7.9718e-02
   4_occ:   1.151  0.009  0.085 15.956  0.005  4.123   7.9718e-02
   5_bss:   1.151  0.009  0.085 15.956  0.005  4.123   7.9718e-02
   5_xyz:   1.072  0.009  0.079 15.571  0.004  4.112   7.1224e-02
   5_adp:   1.072  0.009  0.079 15.571  0.004  4.112   7.1224e-02
   5_occ:   1.072  0.009  0.079 15.571  0.004  4.112   7.1224e-02
   5_bss:   1.072  0.009  0.079 15.571  0.004  4.112   7.1224e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9981e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9981e+00
   1_xyz:  14.883  0.208  0.472 85.142  0.034  2.075   1.1605e-01
   1_adp:  14.883  0.208  0.472 85.142  0.034  2.075   1.1605e-01
   1_occ:  14.883  0.208  0.472 85.142  0.034  2.075   1.1605e-01
   2_bss:  14.883  0.208  0.472 85.142  0.034  2.075   1.1605e-01
   2_xyz:   7.970  0.121  0.319 87.362  0.039  1.858   8.4737e-02
   2_adp:   7.970  0.121  0.319 87.362  0.039  1.858   8.4737e-02
   2_occ:   7.970  0.121  0.319 87.362  0.039  1.858   8.4737e-02
   3_bss:   7.970  0.121  0.319 87.362  0.039  1.858   8.4737e-02
   3_xyz:   7.310  0.062  0.310 83.504  0.030  2.266   6.6430e-02
   3_adp:   7.310  0.062  0.310 83.504  0.030  2.266   6.6430e-02
   3_occ:   7.310  0.062  0.310 83.504  0.030  2.266   6.6430e-02
   4_bss:   7.310  0.062  0.310 83.504  0.030  2.266   6.6430e-02
   4_xyz:   8.164  0.058  0.310 83.332  0.051  2.216   5.5075e-02
   4_adp:   8.164  0.058  0.310 83.332  0.051  2.216   5.5075e-02
   4_occ:   8.164  0.058  0.310 83.332  0.051  2.216   5.5075e-02
   5_bss:   8.164  0.058  0.310 83.332  0.051  2.216   5.5075e-02
   5_xyz:   7.363  0.051  0.313 80.581  0.046  2.279   5.0593e-02
   5_adp:   7.363  0.051  0.313 80.581  0.046  2.279   5.0593e-02
   5_occ:   7.363  0.051  0.313 80.581  0.046  2.279   5.0593e-02
   5_bss:   7.363  0.051  0.313 80.581  0.046  2.279   5.0593e-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:  81.26   0.00  17.27  81.26   0.00  15.95  80.24   0.00  24.47
   1_occ:  81.26   0.00  17.27  81.26   0.00  15.95  80.24   0.00  24.47
   2_bss:  81.26   0.00  17.27  81.26   0.00  15.95  80.24   0.00  24.47
   2_xyz:  81.26   0.00  17.27  81.26   0.00  15.95  80.24   0.00  24.47
   2_adp:  82.27   0.00  16.55  68.31   0.00  13.82  82.27   0.00  31.39
   2_occ:  82.27   0.00  16.55  68.31   0.00  13.82  82.27   0.00  31.39
   3_bss:  82.27   0.00  16.55  68.31   0.00  13.82  82.27   0.00  31.39
   3_xyz:  82.27   0.00  16.55  68.31   0.00  13.82  82.27   0.00  31.39
   3_adp: 102.77   0.00  17.13 102.77   0.00  12.78  90.95   0.00  40.80
   3_occ: 102.77   0.00  17.13 102.77   0.00  12.78  90.95   0.00  40.80
   4_bss: 102.77   0.00  17.13 102.77   0.00  12.78  90.95   0.00  40.80
   4_xyz: 102.77   0.00  17.13 102.77   0.00  12.78  90.95   0.00  40.80
   4_adp:  90.74   0.00  16.55  78.62   0.00  12.01  90.74   2.10  41.30
   4_occ:  90.74   0.00  16.55  78.62   0.00  12.01  90.74   2.10  41.30
   5_bss:  90.74   0.00  16.55  78.62   0.00  12.01  90.74   2.10  41.30
   5_xyz:  90.74   0.00  16.55  78.62   0.00  12.01  90.74   2.10  41.30
   5_adp: 100.46   0.00  16.74  86.28   0.00  11.38 100.46   3.82  45.95
   5_occ: 100.46   0.00  16.74  86.28   0.00  11.38 100.46   3.82  45.95
   5_bss: 101.04   0.58  17.32  86.86   0.58  11.95 101.04   4.40  46.53
------------------------------------------------------------------------
 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:    1.321    0.010    0.423
   1_adp:    1.321    0.010    0.423
   1_occ:    1.321    0.010    0.423
   2_bss:    1.321    0.010    0.423
   2_xyz:    1.811    0.031    0.658
   2_adp:    1.811    0.031    0.658
   2_occ:    1.811    0.031    0.658
   3_bss:    1.811    0.031    0.658
   3_xyz:    1.909    0.023    0.764
   3_adp:    1.909    0.023    0.764
   3_occ:    1.909    0.023    0.764
   4_bss:    1.909    0.023    0.764
   4_xyz:    1.833    0.055    0.873
   4_adp:    1.833    0.055    0.873
   4_occ:    1.833    0.055    0.873
   5_bss:    1.833    0.055    0.873
   5_xyz:    1.902    0.061    0.901
   5_adp:    1.902    0.061    0.901
   5_occ:    1.902    0.061    0.901
   5_bss:    1.902    0.061    0.901
------------------------------------------------------------------------

CPU time actual refinement: 348.70


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/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_868/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_868/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 348.53 
  Macro-tasks:
    bulk solvent and scale       = 42.47  
    individual site refinement   = 143.50 
    weights calculation          = 32.63  
    collect and process          = 6.46   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 225.20 
  Micro-tasks:
    mask                            = 3.12   
    f_calc                          = 109.97 
    alpha_beta                      = 8.54   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 118.18 
    fmodel                         = 7.30   
    r_factors                      = 0.21   
    phase_errors                   = 9.95   
    foms                           = 0.23   
    TOTAL for micro-tasks          = 258.69 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.985 micro seconds
Total CPU time: 6.04 minutes
from_scatterers_fft:    617 calls, 109.61 s
gradients_fft:          562 calls, 105.81 s

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

# Date 2008-01-16 Time 02:38:05 PST -0800 (1200479885.23 s)
Start R-work = 0.5151, R-free = 0.5074 (no bulk solvent and anisotropic scale)
Final R-work = 0.1527, R-free = 0.2101 (no bulk solvent and anisotropic scale)

Start R-work = 0.5074, R-free = 0.4966
Final R-work = 0.1366, R-free = 0.1945