# Date 2008-01-16 Time 03:01:37 PST -0800 (1200481297.23 s)
#phil __OFF__

Command line arguments: "../1068.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23150
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1068

-------------------------------------------------------------------------------
  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: (71.3037, 47.8686, 84.6622, 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: (71.3037, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96152
Completeness in resolution range: 0.917303
Completeness with d_max=infinity: 0.914605

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9615

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: (71.3037, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96152
Completeness in resolution range: 0.917303
Completeness with d_max=infinity: 0.914605

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1984 [2241/2270]  2018   223  10.0%
  bin  2:  4.1984 -  3.3443 [2149/2172]  1933   216  10.1%
  bin  3:  3.3443 -  2.9251 [2111/2136]  1898   213  10.1%
  bin  4:  2.9251 -  2.6593 [2104/2121]  1897   207   9.8%
  bin  5:  2.6593 -  2.4695 [2087/2130]  1882   205   9.8%
  bin  6:  2.4695 -  2.3245 [2082/2110]  1875   207   9.9%
  bin  7:  2.3245 -  2.2085 [2070/2106]  1857   213  10.3%
  bin  8:  2.2085 -  2.1126 [2057/2099]  1854   203   9.9%
  bin  9:  2.1126 -  2.0315 [2039/2106]  1833   206  10.1%
  bin 10:  2.0315 -  1.9615 [ 649/2105]   583    66  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/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:
        1.55 -     2.22: 20
        2.22 -     2.89: 1319
        2.89 -     3.56: 4414
        3.56 -     4.23: 9167
        4.23 -     4.90: 13277
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.546 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.556 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.586 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.646 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.700 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28192 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_1068/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/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 = 71.30375 47.8686 84.6622 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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5022   r_free= 0.4957   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.303796                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.4148 0.4152      6.6403       6.623|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.4305 0.4490      6.8487       6.924|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.4810 0.4139      6.7059      6.6607|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.4983 0.4795      6.5357      6.5185|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.5312 0.5540      6.3774      6.3725|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.5299 0.4951      6.2939      6.2006|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.5312 0.4606      6.2583      6.1854|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.5429 0.5750       6.156      6.2046|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.5526 0.5653      6.1475      6.1296|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.5229 0.5333      6.0801      6.1271|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.5342 0.5445      6.0355      5.9889|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.5527 0.5507      5.9366      5.9917|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.5496 0.5494       5.881      5.8285|
| 14:  2.0105 -  1.9615 0.20    282   28 0.5708 0.5356      5.7892      5.7774|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6832  1457   165  0.66  37.42   0.78     0.69      83496.59|
|  2:  4.6832 -  3.7358  1393   151  0.65  39.40   0.86     0.72     123691.86|
|  3:  3.7358 -  3.2691  1375   152  0.53  49.58   0.79     0.65     134084.59|
|  4:  3.2691 -  2.9727  1359   151  0.42  57.79   0.78     0.53     117938.04|
|  5:  2.9727 -  2.7610  1357   152  0.35  63.79   0.70     0.44      93705.33|
|  6:  2.7610 -  2.5991  1348   155  0.35  63.37   0.71     0.42      75558.75|
|  7:  2.5991 -  2.4695  1339   138  0.35  63.67   0.73     0.41      66503.68|
|  8:  2.4695 -  2.3625  1337   149  0.29  68.11   0.70     0.36      63941.63|
|  9:  2.3625 -  2.2718  1334   154  0.21  74.50   0.71     0.25      63091.93|
| 10:  2.2718 -  2.1937  1337   149  0.14  79.36   0.74     0.17      60563.74|
| 11:  2.1937 -  2.1253  1318   141  0.13  80.41   0.77     0.17      55384.93|
| 12:  2.1253 -  2.0647  1320   146  0.13  80.29   0.72     0.18      50548.82|
| 13:  2.0647 -  2.0105  1074   128  0.12  81.15   0.72     0.16      43346.43|
| 14:  2.0105 -  1.9615   282    28  0.06  85.64   0.65     0.08      37707.67|
|alpha:            min =        0.08 max =            0.72 mean =         0.40|
|beta:             min =    37707.67 max =       134084.59 mean =     79648.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.28|
|phase err.(test): min =        0.00 max =           89.99 mean =        64.49|
|-----------------------------------------------------------------------------|

============================== 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 = 20.054843             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.712   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.964189              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.980   (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 |  1.123 -  1.501:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.501 -  1.879:       19 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.879 -  2.256:      148 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.256 -  2.634:      615 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.634 -  3.012:     1412 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.012 -  3.389:     2534 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.389 -  3.767:     3938 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.767 -  4.145:     5046 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.145 -  4.522:     6644 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.522 -  4.900:     7849 |
|-----------------------------------------------------------------------------|
|-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 |       53.920 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.123 |       2.145 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    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 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5064   r_free= 0.5008   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.304426                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4950   r_free= 0.4852   ksol= 0.30   Bsol= 20.00   scale= 0.952   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,10.10,7.30,0.00,0.00,0.00); trace/3= 8.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.94 A                  |
| x-ray target function (ml) for work reflections: 6.209483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.211385             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.533   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.526903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.405   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4950      final r-factor (work) = 0.4400          |
| start r-factor (free) = 0.4852      final r-factor (free) = 0.4638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.9824 = 16.21 * 0.50 * 6.2996 + 1.00 * 53.9197                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.0107 = 16.21 * 0.50 * 6.1505 + 1.00 * 0.1565                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4400      final r-factor (work) = 0.4038          |
| start r-factor (free) = 0.4638      final r-factor (free) = 0.4549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4060 = 1.53 * 1.00 * 6.1505 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4871 = 1.53 * 1.00 * 6.2000 + 1.00 * 0.0203                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    135.93  15.97    None  None   None       |
|    all(noH): 2823   0      0.00    135.93  15.97    None  None   None       |
|    Sol.    : 438    0      0.00    135.93  27.12    None  None   None       |
|    Mac.    : 2385   0      0.00    86.07   13.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  13.593: 1493   |   5:    67.964 -  81.557:   25        |
|      1:    13.593 -  27.186:  871   |   6:    81.557 -  95.150:    3        |
|      2:    27.186 -  40.779:  308   |   7:    95.150 - 108.743:    1        |
|      3:    40.779 -  54.372:   91   |   8:   108.743 - 122.336:    1        |
|      4:    54.372 -  67.964:   29   |   9:   122.336 - 135.929:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4038 r_free = 0.4549             target_work(ml) = 6.191         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4036 r_free = 0.4558             target_work(ml) = 6.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4036   r_free= 0.4558   ksol= 0.30   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,10.10,7.30,0.00,0.00,0.00); trace/3= 8.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.190911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4025   r_free= 0.4505   ksol= 0.32   Bsol= 38.03   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,6.43,4.72,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.192040                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.902778             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.909  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.773783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4025      final r-factor (work) = 0.3372          |
| start r-factor (free) = 0.4505      final r-factor (free) = 0.4076          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.0389 = 11.90 * 0.50 * 6.1974 + 1.00 * 0.1560                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.5475 = 11.90 * 0.50 * 6.1235 + 1.00 * 0.1044                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3372      final r-factor (work) = 0.3211          |
| start r-factor (free) = 0.4076      final r-factor (free) = 0.3995          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7581 = 0.77 * 1.00 * 6.1235 + 1.00 * 0.0199                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7047 = 0.77 * 1.00 * 6.0622 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.74  15.39    None  None   None       |
|    all(noH): 2823   0      0.00    126.74  15.39    None  None   None       |
|    Sol.    : 438    0      0.00    126.74  29.96    None  None   None       |
|    Mac.    : 2385   0      0.00    84.30   12.72    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 -  12.675: 1508   |   5:    63.372 -  76.047:   15        |
|      1:    12.675 -  25.349:  815   |   6:    76.047 -  88.721:    3        |
|      2:    25.349 -  38.023:  332   |   7:    88.721 - 101.396:    1        |
|      3:    38.023 -  50.698:  102   |   8:   101.396 - 114.070:    0        |
|      4:    50.698 -  63.372:   46   |   9:   114.070 - 126.744:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3211 r_free = 0.3995             target_work(ml) = 6.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3210 r_free = 0.3995             target_work(ml) = 6.049         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3210   r_free= 0.3995   ksol= 0.32   Bsol= 38.03   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,6.43,4.72,0.00,0.00,0.00); trace/3= 4.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.049179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3196   r_free= 0.3976   ksol= 0.31   Bsol= 57.90   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,3.64,2.39,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.049458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.701727              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.177  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505413              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.925  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3196      final r-factor (work) = 0.2494          |
| start r-factor (free) = 0.3976      final r-factor (free) = 0.3117          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4828 = 8.70 * 0.50 * 6.0628 + 1.00 * 0.1044                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.0549 = 8.70 * 0.50 * 5.9679 + 1.00 * 0.0895                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2494      final r-factor (work) = 0.2270          |
| start r-factor (free) = 0.3117      final r-factor (free) = 0.2913          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0289 = 0.51 * 1.00 * 5.9679 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9393 = 0.51 * 1.00 * 5.7929 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    121.13  15.58    None  None   None       |
|    all(noH): 2823   0      0.00    121.13  15.58    None  None   None       |
|    Sol.    : 438    0      3.13    121.13  36.79    None  None   None       |
|    Mac.    : 2385   0      0.00    77.04   11.69    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 -  12.113: 1586   |   5:    60.566 -  72.680:   34        |
|      1:    12.113 -  24.227:  686   |   6:    72.680 -  84.793:    6        |
|      2:    24.227 -  36.340:  261   |   7:    84.793 -  96.906:    2        |
|      3:    36.340 -  48.453:  163   |   8:    96.906 - 109.019:    0        |
|      4:    48.453 -  60.566:   84   |   9:   109.019 - 121.133:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2270 r_free = 0.2913             target_work(ml) = 5.761         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2268 r_free = 0.2907             target_work(ml) = 5.760         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2268   r_free= 0.2907   ksol= 0.31   Bsol= 57.90   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,3.64,2.39,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.760346                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2257   r_free= 0.2893   ksol= 0.32   Bsol= 57.90   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,1.93,0.89,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.758776                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.248890              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.986   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.354500              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.738  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2257      final r-factor (work) = 0.1756          |
| start r-factor (free) = 0.2893      final r-factor (free) = 0.2278          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4030 = 4.25 * 0.50 * 5.7961 + 1.00 * 0.0895                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1074 = 4.25 * 0.50 * 5.6655 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1756      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2278      final r-factor (free) = 0.2138          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6855 = 1.35 * 1.00 * 5.6655 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4506 = 1.35 * 1.00 * 5.4888 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.20  16.64    None  None   None       |
|    all(noH): 2823   0      0.00    111.20  16.64    None  None   None       |
|    Sol.    : 438    0      2.88    107.85  45.50    None  None   None       |
|    Mac.    : 2385   0      0.00    111.20  11.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.120: 1579   |   5:    55.600 -  66.720:   75        |
|      1:    11.120 -  22.240:  664   |   6:    66.720 -  77.840:   53        |
|      2:    22.240 -  33.360:  175   |   7:    77.840 -  88.960:   27        |
|      3:    33.360 -  44.480:  129   |   8:    88.960 - 100.080:   13        |
|      4:    44.480 -  55.600:  104   |   9:   100.080 - 111.200:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1592 r_free = 0.2138             target_work(ml) = 5.457         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1591 r_free = 0.2136             target_work(ml) = 5.456         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1591   r_free= 0.2136   ksol= 0.32   Bsol= 57.90   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.68,1.93,0.89,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.456210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1594   r_free= 0.2144   ksol= 0.32   Bsol= 63.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,1.22,0.70,0.00,0.00,0.00); trace/3= 0.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.458881                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.464132              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.318573              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.729  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1594      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2144      final r-factor (free) = 0.1898          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8364 = 2.46 * 0.50 * 5.4907 + 1.00 * 0.0715                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7241 = 2.46 * 0.50 * 5.4048 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1363          |
| start r-factor (free) = 0.1898      final r-factor (free) = 0.1833          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7378 = 0.32 * 1.00 * 5.4048 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7137 = 0.32 * 1.00 * 5.3364 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.10  15.76    None  None   None       |
|    all(noH): 2823   0      0.00    110.10  15.76    None  None   None       |
|    Sol.    : 438    0      3.16    98.41   42.84    None  None   None       |
|    Mac.    : 2385   0      0.00    110.10  10.78    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 -  11.010: 1645   |   5:    55.051 -  66.061:   73        |
|      1:    11.010 -  22.020:  658   |   6:    66.061 -  77.071:   46        |
|      2:    22.020 -  33.031:  150   |   7:    77.071 -  88.082:   14        |
|      3:    33.031 -  44.041:  123   |   8:    88.082 -  99.092:   11        |
|      4:    44.041 -  55.051:   99   |   9:    99.092 - 110.102:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1363 r_free = 0.1833             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1361 r_free = 0.1831             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1361   r_free= 0.1831   ksol= 0.32   Bsol= 63.50   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.29,1.22,0.70,0.00,0.00,0.00); trace/3= 0.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.319213                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.1010 0.1297      5.4214      5.5984|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.0952 0.1194      5.5142      5.7506|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.1256 0.1855      5.6156      5.9706|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.1572 0.1830      5.6252      5.7819|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.1667 0.1894      5.5125      5.6451|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.1576 0.2472      5.4191      5.6725|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.1534 0.1937      5.3522      5.5254|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.1508 0.1954      5.2542       5.425|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.1446 0.2203      5.1833      5.4386|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.1441 0.2080      5.1523      5.4605|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.1444 0.2065      5.0945      5.3166|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.1444 0.2083      5.0404      5.2446|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.1440 0.2070      4.9539      5.1893|
| 14:  2.0105 -  1.9615 0.20    282   28 0.1330 0.1878      4.8334      5.1044|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6832  1457   165  0.93  10.16   0.96     0.94       8341.12|
|  2:  4.6832 -  3.7358  1393   151  0.94   9.27   1.01     0.99      10470.72|
|  3:  3.7358 -  3.2691  1375   152  0.91  14.00   1.03     1.03      13687.17|
|  4:  3.2691 -  2.9727  1359   151  0.89  17.45   1.01     0.98      13974.49|
|  5:  2.9727 -  2.7610  1357   152  0.86  20.75   1.00     0.98      12563.84|
|  6:  2.7610 -  2.5991  1348   155  0.86  20.31   0.99     0.96      10693.78|
|  7:  2.5991 -  2.4695  1339   138  0.87  19.64   0.99     0.95       9229.00|
|  8:  2.4695 -  2.3625  1337   149  0.87  20.04   1.00     0.96       7890.59|
|  9:  2.3625 -  2.2718  1334   154  0.87  19.13   1.01     0.97       6757.20|
| 10:  2.2718 -  2.1937  1337   149  0.87  19.18   0.99     0.94       6372.73|
| 11:  2.1937 -  2.1253  1318   141  0.87  19.67   0.99     0.95       5925.04|
| 12:  2.1253 -  2.0647  1320   146  0.87  20.16   0.99     0.97       5629.28|
| 13:  2.0647 -  2.0105  1074   128  0.86  20.34   0.99     0.98       4689.06|
| 14:  2.0105 -  1.9615   282    28  0.86  20.59   0.98     0.95       3870.27|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3870.27 max =        13974.49 mean =      8951.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.91 mean =        17.62|
|phase err.(test): min =        0.00 max =           88.61 mean =        16.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1834   ksol= 0.32   Bsol= 57.04   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,0.37,0.01,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321458                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1834   ksol= 0.32   Bsol= 57.04   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.38,0.37,0.01,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.321458                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.1026 0.1318      5.4366      5.6064|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.0956 0.1199      5.5192       5.753|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.1260 0.1852      5.6179      5.9673|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.1574 0.1830      5.6256      5.7794|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.1672 0.1891       5.514      5.6466|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.1577 0.2474      5.4193      5.6735|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.1534 0.1940      5.3532      5.5269|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.1507 0.1959      5.2556      5.4273|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.1444 0.2202      5.1838       5.439|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.1440 0.2080      5.1525      5.4616|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.1442 0.2064      5.0939      5.3158|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.1444 0.2087      5.0409      5.2459|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.1441 0.2069      4.9542      5.1892|
| 14:  2.0105 -  1.9615 0.20    282   28 0.1331 0.1878      4.8332      5.1028|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0715 -  4.6832  1457   165  0.93  10.35   0.96     0.94       8493.04|
|  2:  4.6832 -  3.7358  1393   151  0.94   9.33   1.01     0.99      10598.00|
|  3:  3.7358 -  3.2691  1375   152  0.91  14.04   1.03     1.03      13752.40|
|  4:  3.2691 -  2.9727  1359   151  0.89  17.39   1.00     0.97      13918.01|
|  5:  2.9727 -  2.7610  1357   152  0.86  20.73   1.00     0.97      12552.61|
|  6:  2.7610 -  2.5991  1348   155  0.86  20.32   0.99     0.95      10707.83|
|  7:  2.5991 -  2.4695  1339   138  0.87  19.67   0.99     0.94       9262.94|
|  8:  2.4695 -  2.3625  1337   149  0.87  20.08   1.00     0.95       7930.47|
|  9:  2.3625 -  2.2718  1334   154  0.87  19.16   1.00     0.96       6783.87|
| 10:  2.2718 -  2.1937  1337   149  0.87  19.20   0.98     0.93       6383.62|
| 11:  2.1937 -  2.1253  1318   141  0.87  19.65   0.98     0.94       5920.55|
| 12:  2.1253 -  2.0647  1320   146  0.87  20.16   0.98     0.96       5633.64|
| 13:  2.0647 -  2.0105  1074   128  0.86  20.34   0.98     0.97       4689.66|
| 14:  2.0105 -  1.9615   282    28  0.86  20.58   0.97     0.94       3866.08|
|alpha:            min =        0.93 max =            1.03 mean =         0.96|
|beta:             min =     3866.08 max =        13918.01 mean =      8983.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.65|
|phase err.(test): min =        0.00 max =           88.58 mean =        16.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.54    110.64  16.30    None  None   None       |
|    all(noH): 2823   0      0.54    110.64  16.30    None  None   None       |
|    Sol.    : 438    0      3.70    98.95   43.38    None  None   None       |
|    Mac.    : 2385   0      0.54    110.64  11.32    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:     0.540 -  11.551: 1645   |   5:    55.591 -  66.602:   73        |
|      1:    11.551 -  22.561:  658   |   6:    66.602 -  77.612:   46        |
|      2:    22.561 -  33.571:  150   |   7:    77.612 -  88.622:   14        |
|      3:    33.571 -  44.581:  123   |   8:    88.622 -  99.632:   11        |
|      4:    44.581 -  55.591:   99   |   9:    99.632 - 110.642:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 363         
Filter by distance & map next to the model:
   mapped sites are within: 0.630 - 5.826
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 361 from: 363
   mapped sites are within: 0.740 - 5.826

peak=    8.429 closest distance to " O   HOH Z 120 " =    2.146
peak=    7.614 closest distance to " CG2 VAL A 230 " =    1.380
peak=    7.408 closest distance to " CG2 VAL A 296 " =    1.315
peak=    6.848 closest distance to " O   HOH Z  37 " =    1.608
peak=    6.325 closest distance to " O   HOH Z 279 " =    1.365
peak=    6.324 closest distance to " CG  ARG A 138 " =    1.236
peak=    5.800 closest distance to " CG  LEU A   5 " =    1.399
peak=    5.704 closest distance to " O   HOH Z 111 " =    2.245
peak=    5.602 closest distance to " O   HOH Z 246 " =    1.685
peak=    5.507 closest distance to " O   HOH Z  11 " =    1.433
peak=    5.294 closest distance to " CD1AILE A 234 " =    1.197
peak=    5.273 closest distance to " O  BHOH Z 338 " =    1.341
peak=    5.186 closest distance to " O   HOH Z 221 " =    1.541
peak=    5.046 closest distance to " O   HOH Z  69 " =    1.647
peak=    5.029 closest distance to " O   HOH Z 277 " =    1.409
peak=    5.022 closest distance to " O   HOH Z 278 " =    1.138
peak=    4.971 closest distance to " CG  GLN A  77 " =    0.901
peak=    4.937 closest distance to " O   HOH Z 117 " =    1.183
peak=    4.907 closest distance to " O   HOH Z  49 " =    1.314
peak=    4.851 closest distance to " NH1 ARG A 138 " =    0.980
peak=    4.792 closest distance to " O   HOH Z 210 " =    1.535
peak=    4.786 closest distance to " CG  PRO A  54 " =    1.240
peak=    4.784 closest distance to " O   HOH Z 426 " =    1.375
peak=    4.724 closest distance to " O   HOH Z 400 " =    0.998
peak=    4.713 closest distance to " NH2BARG A 102 " =    1.019
peak=    4.694 closest distance to " O   HOH Z 182 " =    1.221
peak=    4.684 closest distance to " O   HOH Z 411 " =    3.053
peak=    4.646 closest distance to " O   HOH Z 431 " =    1.508
peak=    4.580 closest distance to " O   HOH Z 126 " =    1.987
peak=    4.579 closest distance to " CD2 LEU A   5 " =    1.226
peak=    4.565 closest distance to " O   HOH Z  47 " =    1.891
peak=    4.561 closest distance to " CG  PRO A 280 " =    0.925
peak=    4.488 closest distance to " O   HOH Z 394 " =    1.901
peak=    4.485 closest distance to " O   HOH Z 291 " =    1.431
peak=    4.464 closest distance to " CE  LYS A 119 " =    1.341
peak=    4.458 closest distance to " O   HOH Z 134 " =    2.179
peak=    4.448 closest distance to " O   HOH Z 124 " =    1.653
peak=    4.443 closest distance to " O   HOH Z 433 " =    1.939
peak=    4.440 closest distance to " CD2 LEU A 228 " =    1.231
peak=    4.409 closest distance to " CB  PRO A 198 " =    1.045
peak=    4.397 closest distance to " NE2 HIS A 115 " =    0.849
peak=    4.379 closest distance to " CA  TYR A  30 " =    1.050
peak=    4.352 closest distance to " CA  ALA A  21 " =    1.420
peak=    4.347 closest distance to " CB  GLN A 223 " =    1.441
peak=    4.339 closest distance to " O   HOH Z 416 " =    1.484
peak=    4.328 closest distance to " O   HOH Z 156 " =    3.319
peak=    4.321 closest distance to " O   HOH Z 395 " =    1.503
peak=    4.311 closest distance to " CB  VAL A 230 " =    1.345
peak=    4.310 closest distance to " O   HOH Z 132 " =    1.267
peak=    4.290 closest distance to " O   HOH Z 137 " =    2.137
peak=    4.290 closest distance to " CD  ARG A 269 " =    0.888
peak=    4.276 closest distance to " CB  PRO A  54 " =    0.819
peak=    4.264 closest distance to " OE1 GLN A  11 " =    1.967
peak=    4.252 closest distance to " CB  ARG A 275 " =    0.988
peak=    4.240 closest distance to " O   HOH Z 155 " =    1.794
peak=    4.217 closest distance to " OG ASER A 164 " =    0.899
peak=    4.192 closest distance to " O   HOH Z 389 " =    1.936
peak=    4.177 closest distance to " O   HOH Z 234 " =    3.790
peak=    4.169 closest distance to " CB  SER A  63 " =    1.372
peak=    4.148 closest distance to " O   HOH Z  61 " =    1.403
peak=    4.148 closest distance to " CD  ARG A 138 " =    1.239
peak=    4.145 closest distance to " CB  GLN A  58 " =    0.908
peak=    4.145 closest distance to " O   HOH Z   4 " =    1.396
peak=    4.136 closest distance to " O   HOH Z  80 " =    2.152
peak=    4.123 closest distance to " O   HOH Z  43 " =    1.811
peak=    4.120 closest distance to " O   PRO A 198 " =    1.573
peak=    4.105 closest distance to " CB  ALA A 100 " =    1.560
peak=    4.087 closest distance to " CA  ALA A 160 " =    0.957
peak=    4.076 closest distance to " O   HOH Z 225 " =    2.023
peak=    4.070 closest distance to " CG  PRO A 198 " =    1.321
peak=    4.070 closest distance to " O   HOH Z  97 " =    1.994
peak=    4.039 closest distance to " O   HOH Z 243 " =    1.107
peak=    4.025 closest distance to " CB  SER A  62 " =    0.957
peak=    4.015 closest distance to " O   HOH Z  88 " =    3.140
peak=    4.014 closest distance to " O   HOH Z 276 " =    1.532
peak=    4.007 closest distance to " O   HOH Z 402 " =    1.447
peak=    3.996 closest distance to " CA  ARG A  66 " =    1.032
peak=    3.989 closest distance to " O   HOH Z  47 " =    1.624
peak=    3.988 closest distance to " O   HOH Z  63 " =    1.815
peak=    3.987 closest distance to " O   HOH Z 193 " =    1.802
peak=    3.987 closest distance to " CA  GLU A 152 " =    0.908
peak=    3.986 closest distance to " CG2 THR A 221 " =    1.003
peak=    3.986 closest distance to " O   HOH Z  68 " =    1.912
peak=    3.978 closest distance to " OG ASER A 134 " =    1.322
peak=    3.968 closest distance to " CB  TRP A 179 " =    1.314
peak=    3.968 closest distance to " CG1BVAL A 121 " =    1.370
peak=    3.964 closest distance to " CG  PRO A 243 " =    1.212
peak=    3.953 closest distance to " O   HOH Z 301 " =    1.589
peak=    3.948 closest distance to " CA  LEU A 282 " =    1.119
peak=    3.927 closest distance to " O   HOH Z 369 " =    2.020
peak=    3.923 closest distance to " O   GLY A  91 " =    1.252
peak=    3.918 closest distance to " O   HOH Z 163 " =    2.048
peak=    3.914 closest distance to " O   HOH Z 102 " =    1.467
peak=    3.897 closest distance to " CD BLYS A 290 " =    1.083
peak=    3.884 closest distance to " CD  LYS A 166 " =    1.670
peak=    3.882 closest distance to " O   HOH Z 374 " =    1.161
peak=    3.867 closest distance to " CB  ALA A 256 " =    1.076
peak=    3.860 closest distance to " O   HOH Z  39 " =    1.897
peak=    3.851 closest distance to " O   HOH Z 136 " =    1.577
peak=    3.838 closest distance to " O   HOH Z 215 " =    1.517
peak=    3.838 closest distance to " O   HOH Z  47 " =    1.748
peak=    3.829 closest distance to " O   HOH Z 108 " =    1.377
peak=    3.829 closest distance to " CB  ASN A 187 " =    1.204
peak=    3.828 closest distance to " OE1 GLN A  58 " =    5.826
peak=    3.826 closest distance to " O   HOH Z  54 " =    1.255
peak=    3.823 closest distance to " CB  GLN A 183 " =    1.270
peak=    3.811 closest distance to " CB  TYR A 169 " =    1.003
peak=    3.801 closest distance to " O   HOH Z 133 " =    1.819
peak=    3.793 closest distance to " CG1 VAL A 153 " =    1.117
peak=    3.787 closest distance to " O   HOH Z 232 " =    2.116
peak=    3.763 closest distance to " CG  GLN A  77 " =    1.077
peak=    3.758 closest distance to " O   HOH Z  30 " =    1.671
peak=    3.758 closest distance to " N   LYS A 166 " =    0.898
peak=    3.753 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.751 closest distance to " O   HOH Z 186 " =    1.227
peak=    3.750 closest distance to " O   HOH Z  44 " =    1.817
peak=    3.747 closest distance to " O   HOH Z  15 " =    2.230
peak=    3.747 closest distance to " CB  LEU A 228 " =    1.350
peak=    3.734 closest distance to " NH1 ARG A  14 " =    1.181
peak=    3.724 closest distance to " O   HOH Z 427 " =    3.505
peak=    3.721 closest distance to " O   HOH Z 240 " =    2.100
peak=    3.720 closest distance to " O   HOH Z 404 " =    1.461
peak=    3.708 closest distance to " NZ  LYS A 117 " =    3.153
peak=    3.707 closest distance to " CB  ALA A   1 " =    1.261
peak=    3.704 closest distance to " CB BVAL A  41 " =    1.267
peak=    3.699 closest distance to " O   HOH Z 174 " =    1.531
peak=    3.696 closest distance to " CA  ALA A 295 " =    1.040
peak=    3.691 closest distance to " O   HOH Z 144 " =    1.595
peak=    3.688 closest distance to " C   SER A  32 " =    1.110
peak=    3.683 closest distance to " O   HOH Z  89 " =    3.622
peak=    3.682 closest distance to " N   HIS A 108 " =    1.849
peak=    3.682 closest distance to " O   HOH Z 272 " =    2.047
peak=    3.668 closest distance to " O   HOH Z 263 " =    1.469
peak=    3.664 closest distance to " CD2 LEU A 255 " =    1.236
peak=    3.656 closest distance to " CA  SER A  87 " =    0.845
peak=    3.651 closest distance to " O   HOH Z 217 " =    1.576
peak=    3.645 closest distance to " CA  GLY A 196 " =    0.925
peak=    3.644 closest distance to " O   HOH Z 112 " =    1.570
peak=    3.641 closest distance to " O   HOH Z 202 " =    1.253
peak=    3.635 closest distance to " CB  GLN A 194 " =    0.839
peak=    3.633 closest distance to " OD1 ASP A 238 " =    0.976
peak=    3.619 closest distance to " CD  PRO A 280 " =    1.004
peak=    3.616 closest distance to " CG1 ILE A  33 " =    1.420
peak=    3.616 closest distance to " O   HOH Z  94 " =    2.146
peak=    3.613 closest distance to " CB  ILE A 199 " =    1.147
peak=    3.606 closest distance to " CB  MET A  47 " =    1.051
peak=    3.600 closest distance to " O   HOH Z 316 " =    2.896
peak=    3.595 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.595 closest distance to " CG AARG A 275 " =    1.030
peak=    3.593 closest distance to " O   HOH Z 196 " =    2.164
peak=    3.591 closest distance to " O   HOH Z 368 " =    1.116
peak=    3.590 closest distance to " CB  LYS A  76 " =    1.015
peak=    3.590 closest distance to " O   HOH Z 192 " =    1.514
peak=    3.585 closest distance to " CZ3 TRP A  92 " =    1.085
peak=    3.582 closest distance to " O   HOH Z 261 " =    1.989
peak=    3.580 closest distance to " CA  THR A 246 " =    1.165
peak=    3.576 closest distance to " CA  VAL A  41 " =    0.864
peak=    3.575 closest distance to " O   ASN A 301 " =    2.590
peak=    3.574 closest distance to " CA  LYS A 117 " =    1.307
peak=    3.571 closest distance to " O   HOH Z 368 " =    2.857
peak=    3.566 closest distance to " CA  VAL A 296 " =    1.157
peak=    3.564 closest distance to " O   HOH Z 118 " =    1.842
peak=    3.558 closest distance to " O   ASP A 124 " =    1.430
peak=    3.556 closest distance to " CD  LYS A 119 " =    1.232
peak=    3.550 closest distance to " O   HOH Z   1 " =    2.793
peak=    3.550 closest distance to " O   GLY A 211 " =    1.217
peak=    3.548 closest distance to " CB  TRP A 266 " =    0.980
peak=    3.545 closest distance to " N   ASN A  39 " =    1.275
peak=    3.543 closest distance to " O   HOH Z 132 " =    2.474
peak=    3.539 closest distance to " OD2 ASP A 286 " =    2.961
peak=    3.537 closest distance to " O   HOH Z 373 " =    1.632
peak=    3.530 closest distance to " O   HOH Z 425 " =    1.547
peak=    3.520 closest distance to " O   HOH Z  92 " =    1.229
peak=    3.515 closest distance to " O   HOH Z 272 " =    1.233
peak=    3.509 closest distance to " NH2 ARG A 156 " =    1.198
peak=    3.506 closest distance to " O   HOH Z  99 " =    2.759
peak=    3.504 closest distance to " CB  GLN A  88 " =    1.292
peak=    3.493 closest distance to " O   HOH Z 214 " =    1.053
peak=    3.489 closest distance to " CG  PRO A 213 " =    1.340
peak=    3.483 closest distance to " O   HOH Z 217 " =    2.697
peak=    3.481 closest distance to " O   HOH Z 133 " =    1.607
peak=    3.480 closest distance to " NE2 GLN A  89 " =    1.275
peak=    3.472 closest distance to " O   HOH Z 280 " =    2.925
peak=    3.470 closest distance to " O   HOH Z 281 " =    3.944
peak=    3.462 closest distance to " CB  SER A  28 " =    1.086
peak=    3.462 closest distance to " O   HOH Z 386 " =    2.312
peak=    3.462 closest distance to " CA  SER A  12 " =    1.478
peak=    3.461 closest distance to " CB  GLN A  73 " =    1.014
peak=    3.453 closest distance to " O   HOH Z 387 " =    2.567
peak=    3.452 closest distance to " O   HOH Z  19 " =    1.749
peak=    3.450 closest distance to " CB  ASN A 148 " =    1.171
peak=    3.446 closest distance to " CA  ILE A 263 " =    0.952
peak=    3.446 closest distance to " O   HOH Z 236 " =    1.847
peak=    3.446 closest distance to " O   HOH Z  78 " =    2.359
peak=    3.446 closest distance to " O   HOH Z 189 " =    2.735
peak=    3.445 closest distance to " CE3 TRP A  85 " =    1.031
peak=    3.443 closest distance to " N   TYR A  15 " =    0.927
peak=    3.441 closest distance to " CB  MET A  40 " =    0.755
peak=    3.438 closest distance to " CG  LEU A 228 " =    1.499
peak=    3.437 closest distance to " CG1 ILE A  49 " =    1.795
peak=    3.437 closest distance to " OE1 GLU A   2 " =    1.948
peak=    3.432 closest distance to " CG2 ILE A 234 " =    0.961
peak=    3.430 closest distance to " O   HOH Z  93 " =    2.585
peak=    3.426 closest distance to " O   HOH Z 359 " =    2.129
peak=    3.426 closest distance to " O   HOH Z 130 " =    2.887
peak=    3.423 closest distance to " CD1 TRP A 266 " =    1.179
peak=    3.420 closest distance to " O   ALA A 165 " =    1.240
peak=    3.412 closest distance to " CZ  PHE A 218 " =    1.186
peak=    3.411 closest distance to " O   HOH Z  13 " =    1.606
peak=    3.403 closest distance to " CD1 LEU A 300 " =    1.162
peak=    3.399 closest distance to " C   GLY A  80 " =    1.250
peak=    3.397 closest distance to " CG2 THR A  42 " =    0.899
peak=    3.395 closest distance to " CD  LYS A 289 " =    1.252
peak=    3.390 closest distance to " O   HOH Z 104 " =    3.442
peak=    3.388 closest distance to " CG  LEU A 167 " =    1.074
peak=    3.388 closest distance to " O   SER A  87 " =    2.334
peak=    3.385 closest distance to " CG2 THR A 220 " =    0.817
peak=    3.382 closest distance to " O   HOH Z 185 " =    1.826
peak=    3.381 closest distance to " O   HOH Z  99 " =    1.792
peak=    3.376 closest distance to " NE2 GLN A  11 " =    1.099
peak=    3.375 closest distance to " O   HOH Z 154 " =    1.239
peak=    3.373 closest distance to " CB  ASP A 107 " =    1.058
peak=    3.372 closest distance to " CB  ALA A 137 " =    1.213
peak=    3.372 closest distance to " CE1 TYR A 186 " =    1.364
peak=    3.370 closest distance to " CB  VAL A 202 " =    1.455
peak=    3.366 closest distance to " O   HOH Z 418 " =    1.494
peak=    3.358 closest distance to " O   HOH Z 150 " =    3.274
peak=    3.357 closest distance to " O   HOH Z 315 " =    2.004
peak=    3.355 closest distance to " CB  PHE A  61 " =    0.853
peak=    3.355 closest distance to " N   ASN A 110 " =    1.270
peak=    3.354 closest distance to " CB  VAL A 265 " =    1.306
peak=    3.353 closest distance to " CD1 TRP A 274 " =    1.089
peak=    3.351 closest distance to " N   ALA A 233 " =    0.952
peak=    3.349 closest distance to " O   HOH Z 368 " =    2.418
peak=    3.346 closest distance to " N   GLN A  55 " =    0.836
peak=    3.338 closest distance to " CB  ASP A 124 " =    0.907
peak=    3.333 closest distance to " O   HOH Z 331 " =    1.350
peak=    3.330 closest distance to " O   HOH Z 374 " =    2.594
peak=    3.329 closest distance to " N   TYR A 247 " =    1.363
peak=    3.328 closest distance to " CB  SER A 141 " =    1.057
peak=    3.327 closest distance to " CG2AVAL A  72 " =    1.831
peak=    3.326 closest distance to " CA  ASP A 191 " =    0.840
peak=    3.320 closest distance to " O   HOH Z 200 " =    1.454
peak=    3.319 closest distance to " CA  LEU A 101 " =    1.447
peak=    3.316 closest distance to " CD1 LEU A 222 " =    0.920
peak=    3.314 closest distance to " CA  MET A  40 " =    1.087
peak=    3.314 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.311 closest distance to " CA  ILE A  33 " =    1.631
peak=    3.310 closest distance to " CA  ALA A 100 " =    1.227
peak=    3.306 closest distance to " O   HOH Z 174 " =    1.980
peak=    3.306 closest distance to " OG1 THR A 294 " =    1.688
peak=    3.303 closest distance to " NE AARG A 275 " =    1.408
peak=    3.302 closest distance to " CB  GLU A 152 " =    1.095
peak=    3.301 closest distance to " O   HOH Z 363 " =    1.018
peak=    3.300 closest distance to " O   HOH Z 183 " =    1.432
peak=    3.298 closest distance to " CB  GLU A 277 " =    0.794
peak=    3.294 closest distance to " O   HOH Z 234 " =    1.981
peak=    3.289 closest distance to " CB  ALA A 291 " =    1.217
peak=    3.287 closest distance to " O   HOH Z  85 " =    2.154
peak=    3.285 closest distance to " CB  ARG A 275 " =    1.210
peak=    3.285 closest distance to " CB  ASN A 285 " =    0.852
peak=    3.283 closest distance to " CG1 ILE A 120 " =    1.127
peak=    3.282 closest distance to " OG  SER A  62 " =    3.715
peak=    3.280 closest distance to " NZ  LYS A 166 " =    3.279
peak=    3.279 closest distance to " NH1 ARG A 269 " =    0.941
peak=    3.279 closest distance to " CB  ALA A  34 " =    0.850
peak=    3.278 closest distance to " O   THR A  31 " =    1.461
peak=    3.277 closest distance to " O   SER A 164 " =    1.211
peak=    3.277 closest distance to " CA  ASP A 140 " =    1.383
peak=    3.271 closest distance to " O   HOH Z 172 " =    2.093
peak=    3.271 closest distance to " O   SER A  62 " =    1.026
peak=    3.270 closest distance to " O   HOH Z 420 " =    5.582
peak=    3.269 closest distance to " CB  GLU A 128 " =    1.205
peak=    3.258 closest distance to " CZ  PHE A 192 " =    0.984
peak=    3.256 closest distance to " O   HOH Z 339 " =    1.118
peak=    3.256 closest distance to " O   HOH Z 279 " =    2.315
peak=    3.254 closest distance to " CB  ALA A  71 " =    1.327
peak=    3.254 closest distance to " CG2 THR A 251 " =    1.161
peak=    3.254 closest distance to " C   VAL A 265 " =    1.128
peak=    3.253 closest distance to " O   HOH Z  66 " =    2.293
peak=    3.252 closest distance to " O   HOH Z 361 " =    2.804
peak=    3.246 closest distance to " CG  GLN A  88 " =    1.016
peak=    3.244 closest distance to " CD ALYS A 290 " =    1.240
peak=    3.240 closest distance to " CA  ASP A 162 " =    1.153
peak=    3.239 closest distance to " OG  SER A  22 " =    2.893
peak=    3.239 closest distance to " CG2 VAL A  78 " =    1.045
peak=    3.237 closest distance to " CB  PHE A  16 " =    1.471
peak=    3.237 closest distance to " CB  ASN A 217 " =    1.063
peak=    3.236 closest distance to " CD  ARG A 159 " =    0.825
peak=    3.233 closest distance to " CB  LYS A 193 " =    1.097
peak=    3.232 closest distance to " O   HOH Z 197 " =    2.007
peak=    3.228 closest distance to " ND1 HIS A  81 " =    1.457
peak=    3.227 closest distance to " CB  ASN A 215 " =    1.218
peak=    3.225 closest distance to " O   HOH Z 336 " =    1.814
peak=    3.222 closest distance to " O   HOH Z 290 " =    1.227
peak=    3.220 closest distance to " CB  TRP A 123 " =    1.057
peak=    3.220 closest distance to " CG2 VAL A 265 " =    1.222
peak=    3.218 closest distance to " NH2BARG A 145 " =    2.063
peak=    3.205 closest distance to " O   HOH Z 252 " =    1.589
peak=    3.203 closest distance to " O   HOH Z 277 " =    1.829
peak=    3.202 closest distance to " OG BSER A 258 " =    2.978
peak=    3.201 closest distance to " CE BMET A  47 " =    1.364
peak=    3.198 closest distance to " O   HOH Z 148 " =    1.974
peak=    3.196 closest distance to " O   HOH Z 344 " =    2.942
peak=    3.191 closest distance to " CA  MET A 105 " =    1.474
peak=    3.190 closest distance to " O   HOH Z 410 " =    1.293
peak=    3.190 closest distance to " O   HOH Z   5 " =    1.496
peak=    3.190 closest distance to " CB  MET A 105 " =    1.366
peak=    3.189 closest distance to " N   SER A 164 " =    0.980
peak=    3.184 closest distance to " O   HOH Z 298 " =    5.274
peak=    3.183 closest distance to " O   HOH Z 258 " =    2.373
peak=    3.181 closest distance to " CG2 ILE A 106 " =    1.071
peak=    3.180 closest distance to " O   HOH Z 424 " =    3.469
peak=    3.177 closest distance to " CB  LEU A 143 " =    1.140
peak=    3.176 closest distance to " CB  ARG A  56 " =    0.981
peak=    3.175 closest distance to " O   HOH Z 260 " =    1.284
peak=    3.174 closest distance to " CB  THR A  31 " =    1.441
peak=    3.174 closest distance to " O   HOH Z 417 " =    1.129
peak=    3.174 closest distance to " O   HOH Z 422 " =    2.575
peak=    3.173 closest distance to " CE  MET A  93 " =    1.515
peak=    3.172 closest distance to " O   HOH Z 411 " =    1.426
peak=    3.172 closest distance to " O   HOH Z 426 " =    3.132
peak=    3.167 closest distance to " OG  SER A  97 " =    3.374
peak=    3.166 closest distance to " O   HOH Z  39 " =    1.851
peak=    3.158 closest distance to " O   HOH Z 205 " =    1.208
peak=    3.155 closest distance to " CB  ALA A 114 " =    1.502
peak=    3.150 closest distance to " O   HOH Z 206 " =    1.077
peak=    3.150 closest distance to " O   HOH Z 415 " =    3.556
peak=    3.148 closest distance to " O   HOH Z 209 " =    1.112
peak=    3.148 closest distance to " ND2 ASN A  45 " =    1.350
peak=    3.148 closest distance to " O   HOH Z 434 " =    2.823
peak=    3.146 closest distance to " OE1 GLN A  58 " =    1.245
peak=    3.143 closest distance to " CA  ARG A 195 " =    1.201
peak=    3.141 closest distance to " CB  LEU A 261 " =    1.263
peak=    3.140 closest distance to " O   HOH Z 189 " =    3.379
peak=    3.131 closest distance to " CD1 LEU A  96 " =    0.740
peak=    3.130 closest distance to " O   HOH Z 365 " =    2.984
peak=    3.125 closest distance to " N   THR A  52 " =    1.124
peak=    3.124 closest distance to " NE2 GLN A  58 " =    2.414
peak=    3.123 closest distance to " O   HOH Z 303 " =    2.365
peak=    3.123 closest distance to " CB  SER A   3 " =    1.588
peak=    3.119 closest distance to " CG AARG A 190 " =    1.224
peak=    3.115 closest distance to " O   HOH Z 108 " =    2.335
peak=    3.111 closest distance to " O   HOH Z   1 " =    2.918
peak=    3.095 closest distance to " O   HOH Z 271 " =    1.987
peak=    3.094 closest distance to " CD  GLU A 236 " =    1.184
peak=    3.094 closest distance to " O   HOH Z 139 " =    4.461
peak=    3.090 closest distance to " CA  ASN A 127 " =    1.176
peak=    3.090 closest distance to " O   HOH Z 329 " =    3.448
peak=    3.080 closest distance to " O   HOH Z 327 " =    2.830
peak=    3.080 closest distance to " CB  GLN A 240 " =    1.522
peak=    3.078 closest distance to " CA  ALA A 248 " =    1.186
peak=    3.077 closest distance to " OD2 ASP A  50 " =    1.125
peak=    3.073 closest distance to " CD2 TRP A 179 " =    1.229
peak=    3.073 closest distance to " CA  VAL A 126 " =    1.052
peak=    3.070 closest distance to " CA  ARG A 102 " =    1.438
peak=    3.065 closest distance to " NZ  LYS A 181 " =    1.021
peak=    3.063 closest distance to " O   HOH Z  22 " =    2.417
peak=    3.059 closest distance to " ND1 HIS A 207 " =    1.438
peak=    3.057 closest distance to " CA  LEU A   5 " =    1.002
peak=    3.010 closest distance to " N   GLY A 111 " =    1.251

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.293 - 5.307
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 215
   mapped sites are within: 0.706 - 5.307

peak=   -4.888 closest distance to " CG2 VAL A 230 " =    0.871
peak=   -4.684 closest distance to " O   HOH Z 166 " =    1.688
peak=   -4.618 closest distance to " O   HOH Z  52 " =    2.322
peak=   -4.513 closest distance to " O   HOH Z  13 " =    1.292
peak=   -4.323 closest distance to " CG  ARG A 138 " =    0.863
peak=   -4.283 closest distance to " CD  ARG A 138 " =    1.327
peak=   -4.272 closest distance to " O   HOH Z 221 " =    1.142
peak=   -4.255 closest distance to " OG ASER A 134 " =    1.144
peak=   -4.217 closest distance to " O   HOH Z 151 " =    1.226
peak=   -4.208 closest distance to " CD1 PHE A  59 " =    1.929
peak=   -4.207 closest distance to " NH2 ARG A  66 " =    1.251
peak=   -4.132 closest distance to " O   HOH Z 400 " =    0.987
peak=   -4.086 closest distance to " O   HOH Z 380 " =    4.300
peak=   -4.042 closest distance to " CG  ASP A 231 " =    0.790
peak=   -4.029 closest distance to " O   HOH Z 430 " =    1.275
peak=   -4.022 closest distance to " O   HOH Z 274 " =    2.713
peak=   -4.015 closest distance to " O   HOH Z 407 " =    3.532
peak=   -3.992 closest distance to " N   ALA A 226 " =    2.092
peak=   -3.985 closest distance to " CD2 PHE A  59 " =    2.503
peak=   -3.979 closest distance to " N   GLN A  58 " =    1.600
peak=   -3.978 closest distance to " NE2 GLN A  55 " =    2.431
peak=   -3.968 closest distance to " O   HOH Z 423 " =    0.993
peak=   -3.963 closest distance to " C   ASN A 187 " =    1.871
peak=   -3.958 closest distance to " O   HOH Z 231 " =    1.261
peak=   -3.926 closest distance to " CG  GLU A   2 " =    1.654
peak=   -3.919 closest distance to " O   HOH Z 124 " =    1.475
peak=   -3.890 closest distance to " O   HOH Z 120 " =    0.866
peak=   -3.865 closest distance to " O   HOH Z 184 " =    0.938
peak=   -3.854 closest distance to " O   HOH Z 103 " =    2.357
peak=   -3.847 closest distance to " O   HOH Z 210 " =    0.884
peak=   -3.844 closest distance to " OG1 THR A  82 " =    1.931
peak=   -3.830 closest distance to " O   HOH Z 198 " =    1.349
peak=   -3.827 closest distance to " C   GLY A  91 " =    1.646
peak=   -3.818 closest distance to " O   HOH Z  38 " =    1.164
peak=   -3.789 closest distance to " CB  ALA A 291 " =    2.458
peak=   -3.782 closest distance to " O   HOH Z 290 " =    0.967
peak=   -3.777 closest distance to " CD  LYS A 289 " =    2.499
peak=   -3.776 closest distance to " O   HOH Z 266 " =    4.414
peak=   -3.773 closest distance to " O   HOH Z 208 " =    1.372
peak=   -3.771 closest distance to " C   GLY A 133 " =    1.267
peak=   -3.759 closest distance to " N   ARG A 275 " =    1.112
peak=   -3.758 closest distance to " O   HOH Z 166 " =    2.141
peak=   -3.757 closest distance to " OG1 THR A   4 " =    1.689
peak=   -3.753 closest distance to " CA  SER A 164 " =    1.765
peak=   -3.750 closest distance to " OG ASER A 164 " =    0.767
peak=   -3.750 closest distance to " CB  ALA A 161 " =    2.634
peak=   -3.749 closest distance to " O   HOH Z 186 " =    1.188
peak=   -3.735 closest distance to " O   VAL A 121 " =    0.917
peak=   -3.732 closest distance to " O   HOH Z  71 " =    0.744
peak=   -3.706 closest distance to " NE2 GLN A  88 " =    0.892
peak=   -3.705 closest distance to " CA  GLY A  23 " =    2.284
peak=   -3.703 closest distance to " O   GLY A 118 " =    2.244
peak=   -3.698 closest distance to " O   HOH Z 246 " =    1.081
peak=   -3.696 closest distance to " OH  TYR A 169 " =    0.998
peak=   -3.690 closest distance to " O   HOH Z 131 " =    0.842
peak=   -3.688 closest distance to " O   HOH Z  91 " =    1.964
peak=   -3.668 closest distance to " OG  SER A  97 " =    2.322
peak=   -3.660 closest distance to " C   THR A 279 " =    1.194
peak=   -3.659 closest distance to " NH1BARG A 190 " =    2.180
peak=   -3.645 closest distance to " O   ALA A  34 " =    2.101
peak=   -3.642 closest distance to " O   MET A  47 " =    2.498
peak=   -3.642 closest distance to " O   HOH Z  93 " =    1.555
peak=   -3.621 closest distance to " O   HOH Z  19 " =    2.137
peak=   -3.613 closest distance to " NH2AARG A 275 " =    5.232
peak=   -3.604 closest distance to " O   HOH Z 351 " =    1.557
peak=   -3.598 closest distance to " O   HOH Z  92 " =    1.116
peak=   -3.596 closest distance to " CB  GLN A  55 " =    1.487
peak=   -3.578 closest distance to " O   HOH Z  49 " =    0.840
peak=   -3.576 closest distance to " OG  SER A  32 " =    1.278
peak=   -3.575 closest distance to " O   HOH Z 222 " =    1.142
peak=   -3.574 closest distance to " CA  VAL A 197 " =    1.037
peak=   -3.570 closest distance to " O   HOH Z 385 " =    3.982
peak=   -3.563 closest distance to " CG  GLU A   2 " =    1.332
peak=   -3.559 closest distance to " CD  GLU A 236 " =    1.012
peak=   -3.557 closest distance to " CB  ALA A 227 " =    2.392
peak=   -3.550 closest distance to " CA  GLY A 203 " =    2.289
peak=   -3.534 closest distance to " C   VAL A 265 " =    0.884
peak=   -3.532 closest distance to " O   HOH Z  60 " =    1.706
peak=   -3.528 closest distance to " CG  ARG A 269 " =    2.360
peak=   -3.526 closest distance to " O   HOH Z 272 " =    0.706
peak=   -3.519 closest distance to " CG2BVAL A  41 " =    2.401
peak=   -3.518 closest distance to " CA  TYR A  68 " =    2.698
peak=   -3.511 closest distance to " N   GLY A  17 " =    1.533
peak=   -3.503 closest distance to " CE3 TRP A 150 " =    2.092
peak=   -3.501 closest distance to " CB  SER A 146 " =    2.166
peak=   -3.499 closest distance to " O   HOH Z 132 " =    1.042
peak=   -3.499 closest distance to " O   HOH Z  37 " =    1.486
peak=   -3.490 closest distance to " OD2 ASP A 298 " =    1.015
peak=   -3.490 closest distance to " O   HOH Z  17 " =    1.293
peak=   -3.484 closest distance to " CE2 TRP A  85 " =    1.091
peak=   -3.477 closest distance to " OD2 ASP A 171 " =    1.918
peak=   -3.475 closest distance to " O   HOH Z 189 " =    1.981
peak=   -3.474 closest distance to " O   HOH Z 117 " =    1.282
peak=   -3.473 closest distance to " CA  ALA A 137 " =    2.698
peak=   -3.467 closest distance to " O   PRO A 198 " =    1.276
peak=   -3.460 closest distance to " O   HOH Z 325 " =    1.487
peak=   -3.454 closest distance to " O   HOH Z 243 " =    1.630
peak=   -3.452 closest distance to " O   HOH Z 179 " =    2.282
peak=   -3.452 closest distance to " CD2 LEU A 167 " =    1.708
peak=   -3.437 closest distance to " N   THR A 235 " =    1.177
peak=   -3.436 closest distance to " OG  SER A  26 " =    1.522
peak=   -3.436 closest distance to " O   HOH Z  30 " =    0.907
peak=   -3.428 closest distance to " CB  LEU A 167 " =    2.086
peak=   -3.425 closest distance to " CD  LYS A 119 " =    0.904
peak=   -3.421 closest distance to " CB  GLU A 277 " =    1.391
peak=   -3.415 closest distance to " O   HOH Z 171 " =    2.425
peak=   -3.413 closest distance to " O   HOH Z  55 " =    2.561
peak=   -3.413 closest distance to " N   ARG A 275 " =    1.364
peak=   -3.390 closest distance to " ND2 ASN A  60 " =    1.437
peak=   -3.389 closest distance to " O   HOH Z 402 " =    1.207
peak=   -3.389 closest distance to " O   HOH Z 193 " =    1.108
peak=   -3.381 closest distance to " SG  CYS A 168 " =    1.122
peak=   -3.381 closest distance to " CA  SER A 276 " =    1.411
peak=   -3.380 closest distance to " CG2 ILE A  49 " =    2.646
peak=   -3.372 closest distance to " CG  GLU A  53 " =    1.442
peak=   -3.371 closest distance to " N   ALA A 114 " =    1.111
peak=   -3.368 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.364 closest distance to " CB  ALA A  43 " =    2.596
peak=   -3.362 closest distance to " CZ  ARG A 259 " =    0.874
peak=   -3.355 closest distance to " O   HOH Z 396 " =    1.695
peak=   -3.354 closest distance to " O   HOH Z 297 " =    3.661
peak=   -3.351 closest distance to " CE2 TYR A 293 " =    2.601
peak=   -3.348 closest distance to " O   HOH Z 275 " =    1.503
peak=   -3.344 closest distance to " O   HOH Z 416 " =    0.835
peak=   -3.344 closest distance to " N   ASP A 272 " =    1.176
peak=   -3.341 closest distance to " CE  MET A  93 " =    1.239
peak=   -3.338 closest distance to " O   ALA A 161 " =    1.472
peak=   -3.335 closest distance to " O   VAL A  67 " =    2.748
peak=   -3.327 closest distance to " CD2 LEU A 237 " =    2.553
peak=   -3.323 closest distance to " CD2 PHE A  61 " =    1.981
peak=   -3.314 closest distance to " NH2 ARG A 156 " =    1.153
peak=   -3.312 closest distance to " OD1 ASP A 298 " =    2.136
peak=   -3.307 closest distance to " CG2 THR A 221 " =    2.395
peak=   -3.297 closest distance to " O   TYR A  15 " =    1.511
peak=   -3.297 closest distance to " O   HOH Z 423 " =    2.311
peak=   -3.294 closest distance to " O   HOH Z 221 " =    1.664
peak=   -3.294 closest distance to " CG  ARG A 219 " =    2.404
peak=   -3.293 closest distance to " O   HOH Z 435 " =    1.878
peak=   -3.285 closest distance to " O   HOH Z 113 " =    2.111
peak=   -3.281 closest distance to " O   HOH Z  94 " =    2.199
peak=   -3.277 closest distance to " O   HOH Z 231 " =    1.461
peak=   -3.274 closest distance to " O   HOH Z 427 " =    1.356
peak=   -3.270 closest distance to " CD2 LEU A 237 " =    2.872
peak=   -3.265 closest distance to " CG  PRO A 243 " =    1.495
peak=   -3.263 closest distance to " O   HOH Z 210 " =    2.635
peak=   -3.262 closest distance to " CD  ARG A 259 " =    1.883
peak=   -3.262 closest distance to " CD2 HIS A 115 " =    0.942
peak=   -3.258 closest distance to " CB  TYR A  15 " =    2.281
peak=   -3.258 closest distance to " O   HOH Z 352 " =    1.002
peak=   -3.258 closest distance to " O   ASP A 253 " =    1.749
peak=   -3.256 closest distance to " O   LEU A 143 " =    1.287
peak=   -3.251 closest distance to " CG  MET A 105 " =    0.826
peak=   -3.250 closest distance to " O   HOH Z 377 " =    0.840
peak=   -3.249 closest distance to " C   LEU A 101 " =    0.950
peak=   -3.246 closest distance to " O   HOH Z 185 " =    2.111
peak=   -3.245 closest distance to " O   HOH Z 243 " =    2.131
peak=   -3.244 closest distance to " O   HOH Z  43 " =    1.934
peak=   -3.238 closest distance to " O   HOH Z 100 " =    0.992
peak=   -3.233 closest distance to " OG  SER A  28 " =    2.190
peak=   -3.233 closest distance to " CB  ALA A 114 " =    2.348
peak=   -3.232 closest distance to " O   HOH Z 234 " =    4.338
peak=   -3.231 closest distance to " O   LEU A 300 " =    2.606
peak=   -3.231 closest distance to " CG1 VAL A 296 " =    1.305
peak=   -3.227 closest distance to " O   HOH Z 407 " =    1.570
peak=   -3.227 closest distance to " CD2 LEU A 143 " =    2.470
peak=   -3.225 closest distance to " CD1 TRP A 179 " =    1.004
peak=   -3.218 closest distance to " O   HOH Z 111 " =    1.276
peak=   -3.210 closest distance to " O   HOH Z  11 " =    1.524
peak=   -3.209 closest distance to " O   ASN A 170 " =    1.006
peak=   -3.208 closest distance to " O   HOH Z 410 " =    2.267
peak=   -3.207 closest distance to " C   MET A 113 " =    1.053
peak=   -3.206 closest distance to " O   ALA A   1 " =    2.002
peak=   -3.205 closest distance to " O   VAL A 197 " =    1.355
peak=   -3.202 closest distance to " OD2 ASP A 286 " =    2.641
peak=   -3.200 closest distance to " CG  TRP A 266 " =    1.998
peak=   -3.196 closest distance to " O   HOH Z 283 " =    2.009
peak=   -3.191 closest distance to " O   HOH Z  15 " =    1.643
peak=   -3.187 closest distance to " CE2 TYR A  30 " =    2.734
peak=   -3.187 closest distance to " CB  GLN A  58 " =    1.222
peak=   -3.181 closest distance to " O   HOH Z 252 " =    0.929
peak=   -3.179 closest distance to " O   GLY A 211 " =    1.498
peak=   -3.173 closest distance to " NE2 HIS A  86 " =    0.904
peak=   -3.171 closest distance to " N   LEU A 282 " =    2.370
peak=   -3.170 closest distance to " O   HOH Z 292 " =    4.340
peak=   -3.170 closest distance to " O   HOH Z  39 " =    1.951
peak=   -3.167 closest distance to " N   LEU A 261 " =    1.390
peak=   -3.160 closest distance to " O   HOH Z 384 " =    1.928
peak=   -3.155 closest distance to " O   HOH Z   5 " =    1.647
peak=   -3.154 closest distance to " ND2 ASN A  39 " =    1.407
peak=   -3.154 closest distance to " O   HOH Z 378 " =    1.360
peak=   -3.147 closest distance to " CB  SER A  63 " =    3.222
peak=   -3.147 closest distance to " CB  CYS A 254 " =    2.319
peak=   -3.147 closest distance to " O   HOH Z 306 " =    2.883
peak=   -3.142 closest distance to " O   SER A 135 " =    1.874
peak=   -3.140 closest distance to " OH  TYR A 172 " =    1.674
peak=   -3.139 closest distance to " CD  ARG A 219 " =    2.563
peak=   -3.134 closest distance to " NE  ARG A 156 " =    1.828
peak=   -3.131 closest distance to " ND2 ASN A  60 " =    1.573
peak=   -3.123 closest distance to " CD1 LEU A 228 " =    2.595
peak=   -3.115 closest distance to " O  BHOH Z  74 " =    1.518
peak=   -3.112 closest distance to " OD2 ASP A 162 " =    1.665
peak=   -3.112 closest distance to " O   HOH Z 308 " =    1.309
peak=   -3.106 closest distance to " OE2 GLU A  53 " =    1.109
peak=   -3.103 closest distance to " O   HOH Z 298 " =    2.994
peak=   -3.096 closest distance to " O   HOH Z 191 " =    5.307
peak=   -3.094 closest distance to " CD1 ILE A  33 " =    1.939
peak=   -3.065 closest distance to " CG  GLN A 223 " =    2.406
peak=   -3.054 closest distance to " CG  TYR A 169 " =    2.200
peak=   -3.054 closest distance to " CB  TRP A  85 " =    2.380
peak=   -3.042 closest distance to " O   LEU A 101 " =    2.501
peak=   -3.025 closest distance to " N   ALA A  43 " =    2.557
peak=   -3.000 closest distance to " CD2 LEU A 255 " =    1.587

================= 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    :  0.5022 0.4957   6.303796e+00   6.292360e+00
   1_bss:  0.4950 0.4852   6.209483e+00   6.204149e+00
   1_xyz:  0.4400 0.4638   6.235512e+00   6.258987e+00
   1_adp:  0.4038 0.4549   6.191459e+00   6.250650e+00
   1_occ:  0.4036 0.4558   6.190911e+00   6.251115e+00
   2_bss:  0.4025 0.4505   6.192040e+00   6.250928e+00
   2_xyz:  0.3372 0.4076   6.077673e+00   6.195376e+00
   2_adp:  0.3211 0.3995   6.049582e+00   6.178696e+00
   2_occ:  0.3210 0.3995   6.049179e+00   6.178461e+00
   3_bss:  0.3196 0.3976   6.049458e+00   6.177773e+00
   3_xyz:  0.2494 0.3117   5.833782e+00   6.001375e+00
   3_adp:  0.2270 0.2913   5.761399e+00   5.941664e+00
   3_occ:  0.2268 0.2907   5.760346e+00   5.940393e+00
   4_bss:  0.2257 0.2893   5.758776e+00   5.938409e+00
   4_xyz:  0.1756 0.2278   5.532810e+00   5.737795e+00
   4_adp:  0.1592 0.2138   5.456876e+00   5.674056e+00
   4_occ:  0.1591 0.2136   5.456210e+00   5.673162e+00
   5_bss:  0.1594 0.2144   5.458881e+00   5.675341e+00
   5_xyz:  0.1399 0.1898   5.344222e+00   5.569575e+00
   5_adp:  0.1363 0.1833   5.319779e+00   5.541232e+00
   5_occ:  0.1361 0.1831   5.319213e+00   5.540819e+00
   5_bss:  0.1365 0.1834   5.321458e+00   5.541827e+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:  0.300  20.000   6.820  10.102   7.298   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.820  10.102   7.298   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.820  10.102   7.298   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.820  10.102   7.298   0.000   0.000   0.000
   2_bss:  0.316  38.030   3.720   6.426   4.717   0.000   0.000   0.000
   2_xyz:  0.316  38.030   3.720   6.426   4.717   0.000   0.000   0.000
   2_adp:  0.316  38.030   3.720   6.426   4.717   0.000   0.000   0.000
   2_occ:  0.316  38.030   3.720   6.426   4.717   0.000   0.000   0.000
   3_bss:  0.307  57.903   1.870   3.642   2.388   0.000   0.000   0.000
   3_xyz:  0.307  57.903   1.870   3.642   2.388   0.000   0.000   0.000
   3_adp:  0.307  57.903   1.870   3.642   2.388   0.000   0.000   0.000
   3_occ:  0.307  57.903   1.870   3.642   2.388   0.000   0.000   0.000
   4_bss:  0.316  57.903   0.676   1.934   0.893   0.000   0.000   0.000
   4_xyz:  0.316  57.903   0.676   1.934   0.893   0.000   0.000   0.000
   4_adp:  0.316  57.903   0.676   1.934   0.893   0.000   0.000   0.000
   4_occ:  0.316  57.903   0.676   1.934   0.893   0.000   0.000   0.000
   5_bss:  0.324  63.503   0.291   1.217   0.697   0.000   0.000   0.000
   5_xyz:  0.324  63.503   0.291   1.217   0.697   0.000   0.000   0.000
   5_adp:  0.324  63.503   0.291   1.217   0.697   0.000   0.000   0.000
   5_occ:  0.324  63.503   0.291   1.217   0.697   0.000   0.000   0.000
   5_bss:  0.321  57.041  -0.378   0.366   0.012   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.297 0.3371  0.3985    79638.375
   1_bss:  64.072 0.3382  0.4933    76964.823
   1_xyz:  59.011 0.4027  0.5789    66558.397
   1_adp:  57.057 0.4278  0.6832    63566.438
   1_occ:  57.057 0.4278  0.6833    63691.835
   2_bss:  56.787 0.4311  0.6259    63204.639
   2_xyz:  47.814 0.5455  0.8049    50564.649
   2_adp:  45.610 0.5731  0.8461    47080.644
   2_occ:  45.593 0.5733  0.8465    47042.869
   3_bss:  45.379 0.5759  0.7856    46808.466
   3_xyz:  33.129 0.7217  0.9407    26621.998
   3_adp:  30.168 0.7555  0.9583    22908.981
   3_occ:  30.129 0.7559  0.9582    22825.155
   4_bss:  29.981 0.7574  0.9116    22621.778
   4_xyz:  22.679 0.8342  0.9697    13570.972
   4_adp:  20.834 0.8530  0.9693    11880.895
   4_occ:  20.816 0.8532  0.9693    11859.699
   5_bss:  20.853 0.8530  0.9549    11949.047
   5_xyz:  18.344 0.8768  0.9689     9466.138
   5_adp:  17.555 0.8845  0.9696     8948.646
   5_occ:  17.542 0.8846  0.9695     8951.140
   5_bss:  17.566 0.8845  0.9628     8983.094
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3920e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3920e+01
   1_xyz:   1.784  0.014  0.110 18.311  0.007  4.123   1.5646e-01
   1_adp:   1.784  0.014  0.110 18.311  0.007  4.123   1.5646e-01
   1_occ:   1.784  0.014  0.110 18.311  0.007  4.123   1.5646e-01
   2_bss:   1.784  0.014  0.110 18.311  0.007  4.123   1.5646e-01
   2_xyz:   1.293  0.009  0.087 17.052  0.005  4.109   1.0442e-01
   2_adp:   1.293  0.009  0.087 17.052  0.005  4.109   1.0442e-01
   2_occ:   1.293  0.009  0.087 17.052  0.005  4.109   1.0442e-01
   3_bss:   1.293  0.009  0.087 17.052  0.005  4.109   1.0442e-01
   3_xyz:   1.237  0.009  0.089 16.122  0.004  4.111   8.9523e-02
   3_adp:   1.237  0.009  0.089 16.122  0.004  4.111   8.9523e-02
   3_occ:   1.237  0.009  0.089 16.122  0.004  4.111   8.9523e-02
   4_bss:   1.237  0.009  0.089 16.122  0.004  4.111   8.9523e-02
   4_xyz:   1.081  0.008  0.075 15.605  0.004  4.126   7.1379e-02
   4_adp:   1.081  0.008  0.075 15.605  0.004  4.126   7.1379e-02
   4_occ:   1.081  0.008  0.075 15.605  0.004  4.126   7.1379e-02
   5_bss:   1.081  0.008  0.075 15.605  0.004  4.126   7.1379e-02
   5_xyz:   1.031  0.007  0.079 15.403  0.003  4.123   6.4997e-02
   5_adp:   1.031  0.007  0.079 15.403  0.003  4.123   6.4997e-02
   5_occ:   1.031  0.007  0.079 15.403  0.003  4.123   6.4997e-02
   5_bss:   1.031  0.007  0.079 15.403  0.003  4.123   6.4997e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.123   6.9875e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.123   6.9875e+00
   1_xyz:  15.609  0.177  0.504 87.649  0.050  2.143   1.0553e-01
   1_adp:  15.609  0.177  0.504 87.649  0.050  2.143   1.0553e-01
   1_occ:  15.609  0.177  0.504 87.649  0.050  2.143   1.0553e-01
   2_bss:  15.609  0.177  0.504 87.649  0.050  2.143   1.0553e-01
   2_xyz:   8.850  0.094  0.283 85.029  0.035  2.084   6.5881e-02
   2_adp:   8.850  0.094  0.283 85.029  0.035  2.084   6.5881e-02
   2_occ:   8.850  0.094  0.283 85.029  0.035  2.084   6.5881e-02
   3_bss:   8.850  0.094  0.283 85.029  0.035  2.084   6.5881e-02
   3_xyz:   7.428  0.058  0.255 76.425  0.032  2.270   1.0833e-01
   3_adp:   7.428  0.058  0.255 76.425  0.032  2.270   1.0833e-01
   3_occ:   7.428  0.058  0.255 76.425  0.032  2.270   1.0833e-01
   4_bss:   7.428  0.058  0.255 76.425  0.032  2.270   1.0833e-01
   4_xyz:   7.836  0.055  0.303 81.233  0.035  2.290   1.0199e-01
   4_adp:   7.836  0.055  0.303 81.233  0.035  2.290   1.0199e-01
   4_occ:   7.836  0.055  0.303 81.233  0.035  2.290   1.0199e-01
   5_bss:   7.836  0.055  0.303 81.233  0.035  2.290   1.0199e-01
   5_xyz:   7.323  0.048  0.479 82.426  0.025  2.383   7.8101e-02
   5_adp:   7.323  0.048  0.479 82.426  0.025  2.383   7.8101e-02
   5_occ:   7.323  0.048  0.479 82.426  0.025  2.383   7.8101e-02
   5_bss:   7.323  0.048  0.479 82.426  0.025  2.383   7.8101e-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: 135.93   0.00  15.97  86.07   0.00  13.92 135.93   0.00  27.12
   1_occ: 135.93   0.00  15.97  86.07   0.00  13.92 135.93   0.00  27.12
   2_bss: 135.93   0.00  15.97  86.07   0.00  13.92 135.93   0.00  27.12
   2_xyz: 135.93   0.00  15.97  86.07   0.00  13.92 135.93   0.00  27.12
   2_adp: 126.74   0.00  15.39  84.30   0.00  12.72 126.74   0.00  29.96
   2_occ: 126.74   0.00  15.39  84.30   0.00  12.72 126.74   0.00  29.96
   3_bss: 126.74   0.00  15.39  84.30   0.00  12.72 126.74   0.00  29.96
   3_xyz: 126.74   0.00  15.39  84.30   0.00  12.72 126.74   0.00  29.96
   3_adp: 121.13   0.00  15.58  77.04   0.00  11.69 121.13   3.13  36.79
   3_occ: 121.13   0.00  15.58  77.04   0.00  11.69 121.13   3.13  36.79
   4_bss: 121.13   0.00  15.58  77.04   0.00  11.69 121.13   3.13  36.79
   4_xyz: 121.13   0.00  15.58  77.04   0.00  11.69 121.13   3.13  36.79
   4_adp: 111.20   0.00  16.64 111.20   0.00  11.34 107.85   2.88  45.50
   4_occ: 111.20   0.00  16.64 111.20   0.00  11.34 107.85   2.88  45.50
   5_bss: 111.20   0.00  16.64 111.20   0.00  11.34 107.85   2.88  45.50
   5_xyz: 111.20   0.00  16.64 111.20   0.00  11.34 107.85   2.88  45.50
   5_adp: 110.10   0.00  15.76 110.10   0.00  10.78  98.41   3.16  42.84
   5_occ: 110.10   0.00  15.76 110.10   0.00  10.78  98.41   3.16  42.84
   5_bss: 110.64   0.54  16.30 110.64   0.54  11.32  98.95   3.70  43.38
------------------------------------------------------------------------
 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:    1.144    0.020    0.414
   1_adp:    1.144    0.020    0.414
   1_occ:    1.144    0.020    0.414
   2_bss:    1.144    0.020    0.414
   2_xyz:    1.755    0.033    0.591
   2_adp:    1.755    0.033    0.591
   2_occ:    1.755    0.033    0.591
   3_bss:    1.755    0.033    0.591
   3_xyz:    1.841    0.029    0.742
   3_adp:    1.841    0.029    0.742
   3_occ:    1.841    0.029    0.742
   4_bss:    1.841    0.029    0.742
   4_xyz:    1.840    0.031    0.840
   4_adp:    1.840    0.031    0.840
   4_occ:    1.840    0.031    0.840
   5_bss:    1.840    0.031    0.840
   5_xyz:    1.879    0.031    0.882
   5_adp:    1.879    0.031    0.882
   5_occ:    1.879    0.031    0.882
   5_bss:    1.879    0.031    0.882
------------------------------------------------------------------------

CPU time actual refinement: 370.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/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_1068/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1068/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 370.22 
  Macro-tasks:
    bulk solvent and scale       = 42.91  
    individual site refinement   = 157.40 
    weights calculation          = 33.71  
    collect and process          = 6.38   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 240.55 
  Micro-tasks:
    mask                            = 3.12   
    f_calc                          = 119.79 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 129.53 
    fmodel                         = 7.49   
    r_factors                      = 0.26   
    phase_errors                   = 9.87   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 279.82 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.208 micro seconds
Total CPU time: 6.40 minutes
from_scatterers_fft:    643 calls, 119.35 s
gradients_fft:          589 calls, 116.39 s

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

# Date 2008-01-16 Time 03:08:00 PST -0800 (1200481680.53 s)
Start R-work = 0.5022, R-free = 0.4957 (no bulk solvent and anisotropic scale)
Final R-work = 0.1512, R-free = 0.2005 (no bulk solvent and anisotropic scale)

Start R-work = 0.4950, R-free = 0.4852
Final R-work = 0.1365, R-free = 0.1834