# Date 2008-01-16 Time 02:45:33 PST -0800 (1200480333.28 s)
#phil __OFF__

Command line arguments: "../965.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10236
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 965

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 48.1033, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02057
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1641
                             d_min =   2.0206

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 48.1033, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1641 2.02057
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1645 -  4.3227 [2125/2152]  1912   213  10.0%
  bin  2:  4.3227 -  3.4443 [2035/2051]  1832   203  10.0%
  bin  3:  3.4443 -  3.0128 [2025/2044]  1823   202  10.0%
  bin  4:  3.0128 -  2.7391 [1996/2026]  1798   198   9.9%
  bin  5:  2.7391 -  2.5438 [1982/2001]  1783   199  10.0%
  bin  6:  2.5438 -  2.3944 [1972/2008]  1775   197  10.0%
  bin  7:  2.3944 -  2.2749 [1961/1994]  1764   197  10.0%
  bin  8:  2.2749 -  2.1762 [1952/1986]  1756   196  10.0%
  bin  9:  2.1762 -  2.0926 [1937/1965]  1742   195  10.1%
  bin 10:  2.0926 -  2.0206 [1604/2020]  1445   159   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.30: 9
        2.30 -     2.95: 1584
        2.95 -     3.60: 4393
        3.60 -     4.25: 8970
        4.25 -     4.90: 12681
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.645 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.771 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.100 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.114 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27632 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_965/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 48.10325 87.68585 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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5120   r_free= 0.4983   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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: 6.306559                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.4191 0.4139      6.6382      6.6224|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.4513 0.4885      6.8797      6.9541|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.4910 0.4416      6.7516      6.6881|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.5056 0.4638      6.5821      6.5019|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.5447 0.5079      6.4059      6.4383|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.5405 0.5158      6.3094      6.1994|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.5267 0.4828      6.2567      6.1759|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.5380 0.4806      6.2041      6.1861|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.5454 0.6516      6.1204      6.1711|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.5659 0.5411      6.1347        6.13|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.5439 0.5419      6.0484      6.1066|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.5512 0.5171      5.9877      6.0366|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.5543 0.5057      5.9026      5.8596|
| 14:  2.0710 -  2.0206 0.72    912  103 0.5544 0.5431      5.8628      5.7537|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8209  1379   153  0.63  40.08   0.77     0.66      92100.83|
|  2:  4.8209 -  3.8471  1325   149  0.64  40.03   0.84     0.69     128884.99|
|  3:  3.8471 -  3.3669  1309   146  0.54  48.42   0.77     0.64     133276.80|
|  4:  3.3669 -  3.0618  1291   136  0.45  55.68   0.77     0.53     114050.19|
|  5:  3.0618 -  2.8439  1285   145  0.39  60.86   0.70     0.45      87789.43|
|  6:  2.8439 -  2.6772  1278   145  0.38  61.61   0.68     0.43      73271.06|
|  7:  2.6772 -  2.5438  1281   141  0.36  62.80   0.72     0.40      65567.18|
|  8:  2.5438 -  2.4335  1268   142  0.30  67.69   0.72     0.34      64122.54|
|  9:  2.4335 -  2.3402  1270   143  0.21  74.13   0.67     0.25      62935.28|
| 10:  2.3402 -  2.2597  1250   135  0.18  76.65   0.69     0.21      59374.34|
| 11:  2.2597 -  2.1892  1262   146  0.20  75.37   0.72     0.24      54348.19|
| 12:  2.1892 -  2.1268  1260   133  0.23  73.26   0.72     0.28      48891.51|
| 13:  2.1268 -  2.0710  1260   142  0.21  74.45   0.69     0.25      41601.10|
| 14:  2.0710 -  2.0206   912   103  0.14  79.92   0.70     0.14      34178.15|
|alpha:            min =        0.14 max =            0.69 mean =         0.40|
|beta:             min =    34178.15 max =       133276.80 mean =     77093.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.01|
|phase err.(test): min =        0.00 max =           89.82 mean =        63.29|
|-----------------------------------------------------------------------------|

============================== 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 = 20.299140             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.590   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.054160              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.906   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      668 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1467 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2557 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3824 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4963 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6405 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7605 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.702 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.762 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    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 = 12.461)------------------------------------------|
|    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: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5163   r_free= 0.5017   ksol= 0.00   Bsol= 0.00   scale= 0.727    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.307627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5060   r_free= 0.4919   ksol= 0.29   Bsol= 20.00   scale= 0.941   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.90,11.22,8.91,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.302712                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.244248             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.771866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.255   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5060      final r-factor (work) = 0.4434          |
| start r-factor (free) = 0.4919      final r-factor (free) = 0.4547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 112.2249 = 18.24 * 0.50 * 6.3059 + 1.00 * 54.7017                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.1752 = 18.24 * 0.50 * 6.2511 + 1.00 * 0.1518                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4434      final r-factor (work) = 0.4021          |
| start r-factor (free) = 0.4547      final r-factor (free) = 0.4473          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0909 = 1.77 * 1.00 * 6.2511 + 1.00 * 0.0148                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0090 = 1.77 * 1.00 * 6.1986 + 1.00 * 0.0258                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.39  16.82    None  None   None       |
|    all(noH): 2823   0      0.00    123.39  16.82    None  None   None       |
|    Sol.    : 438    0      0.00    123.39  27.87    None  None   None       |
|    Mac.    : 2385   0      0.00    89.10   14.79    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 -  12.339: 1365   |   5:    61.696 -  74.035:   29        |
|      1:    12.339 -  24.678:  783   |   6:    74.035 -  86.374:    8        |
|      2:    24.678 -  37.018:  417   |   7:    86.374 -  98.713:    4        |
|      3:    37.018 -  49.357:  150   |   8:    98.713 - 111.052:    1        |
|      4:    49.357 -  61.696:   64   |   9:   111.052 - 123.392:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4021 r_free = 0.4473             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4011 r_free = 0.4469             target_work(ml) = 6.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4011   r_free= 0.4469   ksol= 0.29   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.90,11.22,8.91,0.00,0.00,0.00); trace/3= 8.68                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.187754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3993   r_free= 0.4409   ksol= 0.31   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,6.97,5.39,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.188758                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.033413             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.029  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608170              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.347  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3993      final r-factor (work) = 0.3374          |
| start r-factor (free) = 0.4409      final r-factor (free) = 0.4134          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.5058 = 13.03 * 0.50 * 6.1925 + 1.00 * 0.1514                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.9684 = 13.03 * 0.50 * 6.1165 + 1.00 * 0.1090                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3374      final r-factor (work) = 0.3284          |
| start r-factor (free) = 0.4134      final r-factor (free) = 0.3959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7453 = 0.61 * 1.00 * 6.1165 + 1.00 * 0.0254                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7056 = 0.61 * 1.00 * 6.0751 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.00  14.65    None  None   None       |
|    all(noH): 2823   0      0.00    122.00  14.65    None  None   None       |
|    Sol.    : 438    0      0.00    122.00  27.83    None  None   None       |
|    Mac.    : 2385   0      0.00    70.62   12.23    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 -  12.200: 1528   |   5:    60.999 -  73.199:   14        |
|      1:    12.200 -  24.400:  820   |   6:    73.199 -  85.399:    7        |
|      2:    24.400 -  36.600:  313   |   7:    85.399 -  97.599:    3        |
|      3:    36.600 -  48.799:  103   |   8:    97.599 - 109.798:    1        |
|      4:    48.799 -  60.999:   33   |   9:   109.798 - 121.998:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3284 r_free = 0.3959             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3284 r_free = 0.3959             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3284   r_free= 0.3959   ksol= 0.31   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,6.97,5.39,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.061635                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3282   r_free= 0.3951   ksol= 0.33   Bsol= 73.92   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,5.31,3.72,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.062965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.067061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.796  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.463783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3282      final r-factor (work) = 0.2696          |
| start r-factor (free) = 0.3951      final r-factor (free) = 0.3209          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6477 = 9.07 * 0.50 * 6.0744 + 1.00 * 0.1090                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2473 = 9.07 * 0.50 * 5.9884 + 1.00 * 0.0986                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2696      final r-factor (work) = 0.2502          |
| start r-factor (free) = 0.3209      final r-factor (free) = 0.3019          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7887 = 0.46 * 1.00 * 5.9884 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8144 = 0.46 * 1.00 * 5.8581 + 1.00 * 0.0975                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.04  14.50    None  None   None       |
|    all(noH): 2823   0      0.00    109.04  14.50    None  None   None       |
|    Sol.    : 438    0      0.00    109.04  33.26    None  None   None       |
|    Mac.    : 2385   0      0.00    77.03   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.904: 1549   |   5:    54.518 -  65.422:   49        |
|      1:    10.904 -  21.807:  694   |   6:    65.422 -  76.325:   11        |
|      2:    21.807 -  32.711:  280   |   7:    76.325 -  87.229:    5        |
|      3:    32.711 -  43.614:  158   |   8:    87.229 -  98.132:    1        |
|      4:    43.614 -  54.518:   75   |   9:    98.132 - 109.036:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2502 r_free = 0.3019             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2497 r_free = 0.3025             target_work(ml) = 5.838         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2497   r_free= 0.3025   ksol= 0.33   Bsol= 73.92   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,5.31,3.72,0.00,0.00,0.00); trace/3= 3.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.838371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2492   r_free= 0.3030   ksol= 0.32   Bsol= 71.14   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.35,3.64,2.71,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.837992                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.886640              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.976393              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.350   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2492      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.3030      final r-factor (free) = 0.2438          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4813 = 3.89 * 0.50 * 5.8573 + 1.00 * 0.0986                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2484 = 3.89 * 0.50 * 5.7444 + 1.00 * 0.0852                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2005      final r-factor (work) = 0.1842          |
| start r-factor (free) = 0.2438      final r-factor (free) = 0.2353          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3833 = 1.98 * 1.00 * 5.7444 + 1.00 * 0.0301                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0709 = 1.98 * 1.00 * 5.5892 + 1.00 * 0.0244                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.17  15.90    None  None   None       |
|    all(noH): 2823   0      0.00    109.17  15.90    None  None   None       |
|    Sol.    : 438    0      0.00    109.17  43.46    None  None   None       |
|    Mac.    : 2385   0      0.00    94.53   10.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.917: 1622   |   5:    54.583 -  65.500:   78        |
|      1:    10.917 -  21.833:  592   |   6:    65.500 -  76.416:   53        |
|      2:    21.833 -  32.750:  210   |   7:    76.416 -  87.333:   32        |
|      3:    32.750 -  43.666:  125   |   8:    87.333 -  98.249:   13        |
|      4:    43.666 -  54.583:   94   |   9:    98.249 - 109.166:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1842 r_free = 0.2353             target_work(ml) = 5.578         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1841 r_free = 0.2354             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1841   r_free= 0.2354   ksol= 0.32   Bsol= 71.14   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.35,3.64,2.71,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.577490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1841   r_free= 0.2360   ksol= 0.34   Bsol= 84.41   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,2.79,2.74,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.578874                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.663290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.611   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.775116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.812  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1841      final r-factor (work) = 0.1478          |
| start r-factor (free) = 0.2360      final r-factor (free) = 0.2006          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9116 = 5.66 * 0.50 * 5.5891 + 1.00 * 0.0853                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6409 = 5.66 * 0.50 * 5.4884 + 1.00 * 0.0997                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1478      final r-factor (work) = 0.1383          |
| start r-factor (free) = 0.2006      final r-factor (free) = 0.1907          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2816 = 0.78 * 1.00 * 5.4884 + 1.00 * 0.0275                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1747 = 0.78 * 1.00 * 5.3640 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.54  15.17    None  None   None       |
|    all(noH): 2823   0      0.00    108.54  15.17    None  None   None       |
|    Sol.    : 438    0      1.17    108.54  43.82    None  None   None       |
|    Mac.    : 2385   0      0.00    95.93   9.91     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.854: 1719   |   5:    54.271 -  65.125:   75        |
|      1:    10.854 -  21.708:  572   |   6:    65.125 -  75.979:   52        |
|      2:    21.708 -  32.562:  153   |   7:    75.979 -  86.833:   33        |
|      3:    32.562 -  43.417:  105   |   8:    86.833 -  97.687:   14        |
|      4:    43.417 -  54.271:   96   |   9:    97.687 - 108.541:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1383 r_free = 0.1907             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1382 r_free = 0.1906             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1382   r_free= 0.1906   ksol= 0.34   Bsol= 84.41   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.29,2.79,2.74,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.330284                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.1082 0.1424      5.4705      5.6188|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.0955 0.1237       5.547      5.7608|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.1241 0.1783      5.6421      6.0208|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.1442 0.1936       5.622       5.797|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.1655 0.1983      5.5338       5.685|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.1496 0.2397      5.4008      5.6488|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.1538 0.2108      5.3527      5.5563|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.1534 0.2083      5.3003      5.5586|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.1606 0.2118      5.2459        5.44|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.1515 0.2220      5.1978       5.431|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.1495 0.2245      5.1512      5.4709|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.1421 0.1957      5.0721       5.345|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.1522 0.2135      5.0179      5.2135|
| 14:  2.0710 -  2.0206 0.72    912  103 0.1447 0.2184      4.9025      5.1785|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8209  1379   153  0.93  11.02   0.96     0.93       9138.07|
|  2:  4.8209 -  3.8471  1325   149  0.94  10.03   1.00     0.98      11701.67|
|  3:  3.8471 -  3.3669  1309   146  0.91  14.11   1.02     1.02      14777.62|
|  4:  3.3669 -  3.0618  1291   136  0.89  16.80   1.01     0.98      14557.15|
|  5:  3.0618 -  2.8439  1285   145  0.86  20.28   1.01     1.00      12851.03|
|  6:  2.8439 -  2.6772  1278   145  0.87  19.98   0.98     0.93      10316.38|
|  7:  2.6772 -  2.5438  1281   141  0.87  19.72   0.99     0.97       9204.20|
|  8:  2.5438 -  2.4335  1268   142  0.87  19.37   0.98     0.93       8078.44|
|  9:  2.4335 -  2.3402  1270   143  0.86  20.45   0.99     0.95       7526.64|
| 10:  2.3402 -  2.2597  1250   135  0.86  20.47   0.99     0.94       6984.80|
| 11:  2.2597 -  2.1892  1262   146  0.86  20.63   0.98     0.93       6652.24|
| 12:  2.1892 -  2.1268  1260   133  0.87  19.71   0.99     0.97       5930.81|
| 13:  2.1268 -  2.0710  1260   142  0.87  20.18   0.97     0.94       5055.86|
| 14:  2.0710 -  2.0206   912   103  0.87  19.52   0.94     0.91       4002.71|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     4002.71 max =        14777.62 mean =      9197.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.91|
|phase err.(test): min =        0.00 max =           87.79 mean =        16.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1910   ksol= 0.33   Bsol= 79.21   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.23,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.331291                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1910   ksol= 0.33   Bsol= 79.21   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.23,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.331291                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1645 -  4.8209 0.99   1379  153 0.1087 0.1427      5.4779      5.6224|
|  2:  4.8209 -  3.8471 0.99   1325  149 0.0958 0.1235      5.5506      5.7587|
|  3:  3.8471 -  3.3669 0.99   1309  146 0.1247 0.1783      5.6446      6.0225|
|  4:  3.3669 -  3.0618 0.99   1291  136 0.1443 0.1941      5.6236      5.8007|
|  5:  3.0618 -  2.8439 0.99   1285  145 0.1658 0.1987       5.536      5.6855|
|  6:  2.8439 -  2.6772 0.99   1278  145 0.1495 0.2393      5.4012      5.6474|
|  7:  2.6772 -  2.5438 0.99   1281  141 0.1538 0.2113      5.3528      5.5577|
|  8:  2.5438 -  2.4335 0.98   1268  142 0.1533 0.2084      5.2999      5.5572|
|  9:  2.4335 -  2.3402 0.98   1270  143 0.1604 0.2121      5.2449      5.4403|
| 10:  2.3402 -  2.2597 0.98   1250  135 0.1513 0.2230      5.1974      5.4317|
| 11:  2.2597 -  2.1892 1.00   1262  146 0.1493 0.2242      5.1505      5.4691|
| 12:  2.1892 -  2.1268 0.97   1260  133 0.1420 0.1959      5.0719       5.346|
| 13:  2.1268 -  2.0710 0.98   1260  142 0.1522 0.2137       5.017      5.2131|
| 14:  2.0710 -  2.0206 0.72    912  103 0.1446 0.2177      4.9012       5.175|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1645 -  4.8209  1379   153  0.93  11.03   0.95     0.93       9132.20|
|  2:  4.8209 -  3.8471  1325   149  0.94  10.04   1.01     0.98      11755.37|
|  3:  3.8471 -  3.3669  1309   146  0.91  14.14   1.03     1.02      14868.20|
|  4:  3.3669 -  3.0618  1291   136  0.89  16.85   1.02     0.98      14598.61|
|  5:  3.0618 -  2.8439  1285   145  0.86  20.33   1.01     1.00      12908.09|
|  6:  2.8439 -  2.6772  1278   145  0.87  20.00   0.98     0.93      10340.61|
|  7:  2.6772 -  2.5438  1281   141  0.87  19.71   1.00     0.98       9206.55|
|  8:  2.5438 -  2.4335  1268   142  0.87  19.36   0.99     0.93       8068.57|
|  9:  2.4335 -  2.3402  1270   143  0.86  20.43   1.00     0.95       7515.95|
| 10:  2.3402 -  2.2597  1250   135  0.86  20.46   1.00     0.95       6978.68|
| 11:  2.2597 -  2.1892  1262   146  0.86  20.62   0.99     0.94       6650.96|
| 12:  2.1892 -  2.1268  1260   133  0.87  19.70   0.99     0.97       5929.24|
| 13:  2.1268 -  2.0710  1260   142  0.87  20.15   0.97     0.94       5039.21|
| 14:  2.0710 -  2.0206   912   103  0.87  19.46   0.95     0.91       3975.78|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3975.78 max =        14868.20 mean =      9212.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.94 mean =        17.91|
|phase err.(test): min =        0.00 max =           89.79 mean =        16.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.461)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.39    110.93  17.56    None  None   None       |
|    all(noH): 2823   0      2.39    110.93  17.56    None  None   None       |
|    Sol.    : 438    0      3.56    110.93  46.21    None  None   None       |
|    Mac.    : 2385   0      2.39    98.32   12.30    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:     2.393 -  13.247: 1719   |   5:    56.663 -  67.517:   75        |
|      1:    13.247 -  24.101:  572   |   6:    67.517 -  78.372:   52        |
|      2:    24.101 -  34.955:  153   |   7:    78.372 -  89.226:   33        |
|      3:    34.955 -  45.809:  105   |   8:    89.226 - 100.080:   14        |
|      4:    45.809 -  56.663:   96   |   9:   100.080 - 110.934:    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)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.580 - 4.339
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 340
   mapped sites are within: 0.775 - 4.339

peak=    6.877 closest distance to " O   GLN A  11 " =    1.107
peak=    6.831 closest distance to " O   HOH Z 120 " =    1.643
peak=    6.589 closest distance to " CG1 ILE A 234 " =    1.408
peak=    6.102 closest distance to " CG2 VAL A 230 " =    1.195
peak=    5.850 closest distance to " CG  LEU A   5 " =    1.189
peak=    5.849 closest distance to " O   HOH Z 210 " =    1.727
peak=    5.377 closest distance to " O   HOH Z 117 " =    1.644
peak=    5.363 closest distance to " O   HOH Z  82 " =    1.108
peak=    5.317 closest distance to " CB  VAL A 230 " =    1.310
peak=    5.296 closest distance to " O   HOH Z 425 " =    1.947
peak=    5.243 closest distance to " O   HOH Z  54 " =    1.289
peak=    5.239 closest distance to " OD1 ASN A  69 " =    0.814
peak=    5.236 closest distance to " OD1 ASN A 301 " =    1.092
peak=    5.130 closest distance to " O   HOH Z 422 " =    1.254
peak=    5.067 closest distance to " O   HOH Z 102 " =    1.520
peak=    4.981 closest distance to " CB  SER A  63 " =    1.242
peak=    4.946 closest distance to " CB  VAL A 296 " =    1.181
peak=    4.871 closest distance to " O   HOH Z 431 " =    1.680
peak=    4.725 closest distance to " O   HOH Z 111 " =    2.261
peak=    4.722 closest distance to " O   HOH Z 426 " =    1.212
peak=    4.681 closest distance to " O   HOH Z 128 " =    1.837
peak=    4.661 closest distance to " O   HOH Z 412 " =    3.482
peak=    4.638 closest distance to " O   HOH Z 248 " =    1.750
peak=    4.626 closest distance to " O   HOH Z 124 " =    1.227
peak=    4.568 closest distance to " CB  GLN A 183 " =    1.179
peak=    4.534 closest distance to " O   HOH Z 394 " =    1.848
peak=    4.511 closest distance to " OE1 GLN A  88 " =    0.987
peak=    4.499 closest distance to " CG BARG A 275 " =    1.191
peak=    4.498 closest distance to " CG  LEU A 228 " =    1.348
peak=    4.498 closest distance to " CB  TRP A 179 " =    1.302
peak=    4.455 closest distance to " CA  ARG A 195 " =    1.223
peak=    4.429 closest distance to " O   HOH Z  57 " =    0.957
peak=    4.387 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.377 closest distance to " O   HOH Z 404 " =    1.374
peak=    4.376 closest distance to " CG1 ILE A 120 " =    1.111
peak=    4.373 closest distance to " O   HOH Z 139 " =    1.485
peak=    4.329 closest distance to " OD2 ASP A 298 " =    0.845
peak=    4.327 closest distance to " O   HOH Z 403 " =    2.028
peak=    4.315 closest distance to " N   SER A 164 " =    0.950
peak=    4.307 closest distance to " NE2 HIS A 115 " =    1.185
peak=    4.283 closest distance to " CD2 LEU A 228 " =    1.267
peak=    4.259 closest distance to " O   HOH Z  54 " =    1.107
peak=    4.248 closest distance to " O  BHOH Z 338 " =    0.956
peak=    4.245 closest distance to " O   HOH Z 377 " =    1.645
peak=    4.230 closest distance to " NE2 GLN A  11 " =    1.152
peak=    4.209 closest distance to " O   ALA A 165 " =    1.257
peak=    4.204 closest distance to " CB  ARG A 275 " =    0.815
peak=    4.165 closest distance to " OE1 GLN A  11 " =    2.308
peak=    4.145 closest distance to " CD  LYS A 166 " =    1.666
peak=    4.126 closest distance to " O   HOH Z 261 " =    2.258
peak=    4.091 closest distance to " O   HOH Z 395 " =    1.534
peak=    4.078 closest distance to " CB  ASN A 285 " =    0.932
peak=    4.074 closest distance to " CA  ARG A  66 " =    0.934
peak=    4.072 closest distance to " O   HOH Z 234 " =    3.485
peak=    4.070 closest distance to " NZ  LYS A  48 " =    1.312
peak=    4.060 closest distance to " O   HOH Z  80 " =    2.105
peak=    4.045 closest distance to " CB  TRP A 266 " =    1.015
peak=    4.031 closest distance to " O   HOH Z  49 " =    1.510
peak=    4.013 closest distance to " CB  GLN A 223 " =    1.468
peak=    4.012 closest distance to " ND2 ASN A 249 " =    2.185
peak=    4.012 closest distance to " O   ASP A 124 " =    1.461
peak=    3.989 closest distance to " O   HOH Z 417 " =    3.201
peak=    3.984 closest distance to " O   HOH Z 174 " =    1.312
peak=    3.976 closest distance to " O   HOH Z 388 " =    1.092
peak=    3.976 closest distance to " O   HOH Z 350 " =    1.321
peak=    3.972 closest distance to " O   HOH Z  40 " =    2.067
peak=    3.956 closest distance to " O   HOH Z 369 " =    1.881
peak=    3.944 closest distance to " O   PRO A  90 " =    1.454
peak=    3.941 closest distance to " O   HOH Z 433 " =    2.090
peak=    3.937 closest distance to " NH1 ARG A 138 " =    1.040
peak=    3.916 closest distance to " NH2 ARG A 156 " =    1.170
peak=    3.908 closest distance to " O   HOH Z   4 " =    1.683
peak=    3.888 closest distance to " CD2 LEU A 297 " =    1.078
peak=    3.872 closest distance to " O   HOH Z 359 " =    1.655
peak=    3.862 closest distance to " CD2 TRP A 179 " =    1.176
peak=    3.859 closest distance to " O   HOH Z 149 " =    2.136
peak=    3.854 closest distance to " CE  LYS A 119 " =    1.513
peak=    3.848 closest distance to " O   HOH Z 193 " =    1.529
peak=    3.827 closest distance to " O   HOH Z  63 " =    2.124
peak=    3.823 closest distance to " CA  ALA A  21 " =    1.345
peak=    3.823 closest distance to " CZ  PHE A 218 " =    1.127
peak=    3.823 closest distance to " N   TYR A 247 " =    1.251
peak=    3.812 closest distance to " O   HOH Z 199 " =    1.524
peak=    3.801 closest distance to " O   SER A  87 " =    2.341
peak=    3.797 closest distance to " O   HOH Z 134 " =    2.367
peak=    3.793 closest distance to " CG  PRO A 280 " =    1.052
peak=    3.788 closest distance to " CB  ALA A 100 " =    1.558
peak=    3.787 closest distance to " CG  PRO A  54 " =    1.209
peak=    3.787 closest distance to " CG2 THR A 221 " =    1.109
peak=    3.786 closest distance to " CB  PRO A  54 " =    0.882
peak=    3.774 closest distance to " CB  SER A  62 " =    1.016
peak=    3.764 closest distance to " O   HOH Z 126 " =    1.619
peak=    3.759 closest distance to " O   HOH Z  85 " =    2.079
peak=    3.757 closest distance to " O   HOH Z 337 " =    1.602
peak=    3.739 closest distance to " O   HOH Z 146 " =    1.890
peak=    3.734 closest distance to " O   ASP A 200 " =    1.682
peak=    3.733 closest distance to " O   HOH Z 154 " =    1.625
peak=    3.726 closest distance to " CD  ARG A  36 " =    0.927
peak=    3.724 closest distance to " CD  GLN A  73 " =    1.178
peak=    3.705 closest distance to " ND2 ASN A 301 " =    0.938
peak=    3.705 closest distance to " NE  ARG A  36 " =    1.069
peak=    3.691 closest distance to " CD ALYS A 290 " =    1.264
peak=    3.679 closest distance to " CD  PRO A  54 " =    1.116
peak=    3.659 closest distance to " O   HOH Z 130 " =    2.822
peak=    3.652 closest distance to " O   HOH Z  68 " =    1.979
peak=    3.644 closest distance to " O   HOH Z  43 " =    2.219
peak=    3.637 closest distance to " O   HOH Z  99 " =    2.791
peak=    3.631 closest distance to " CB  TRP A 179 " =    1.406
peak=    3.630 closest distance to " O   HOH Z 418 " =    1.755
peak=    3.629 closest distance to " OE1 GLU A   2 " =    1.383
peak=    3.626 closest distance to " N   GLN A 278 " =    1.367
peak=    3.626 closest distance to " O   HOH Z  37 " =    1.265
peak=    3.618 closest distance to " O   GLU A   2 " =    1.823
peak=    3.616 closest distance to " O   ALA A 180 " =    1.292
peak=    3.607 closest distance to " O   HOH Z 393 " =    3.534
peak=    3.602 closest distance to " CA  ALA A 295 " =    1.049
peak=    3.595 closest distance to " CB  SER A  26 " =    0.938
peak=    3.595 closest distance to " NH1AARG A 145 " =    1.289
peak=    3.592 closest distance to " OG  SER A 245 " =    1.564
peak=    3.590 closest distance to " CE1 HIS A 108 " =    1.115
peak=    3.588 closest distance to " O   HOH Z 403 " =    1.340
peak=    3.581 closest distance to " O   HOH Z 227 " =    1.674
peak=    3.579 closest distance to " CB  GLN A  88 " =    1.251
peak=    3.577 closest distance to " CB  MET A  40 " =    0.862
peak=    3.573 closest distance to " CA  ASN A 217 " =    1.222
peak=    3.572 closest distance to " CA  THR A 246 " =    1.035
peak=    3.556 closest distance to " CZ3 TRP A  92 " =    1.306
peak=    3.547 closest distance to " O   HOH Z 301 " =    2.216
peak=    3.544 closest distance to " CB  LEU A 281 " =    0.851
peak=    3.542 closest distance to " NE2 GLN A 278 " =    2.462
peak=    3.535 closest distance to " OE1 GLN A  73 " =    1.109
peak=    3.532 closest distance to " O   HOH Z  27 " =    1.104
peak=    3.529 closest distance to " O   HOH Z 144 " =    2.048
peak=    3.528 closest distance to " N   ASN A  39 " =    1.180
peak=    3.524 closest distance to " N   GLU A   2 " =    0.897
peak=    3.521 closest distance to " CD2 TRP A 179 " =    2.543
peak=    3.520 closest distance to " O   HOH Z 214 " =    1.417
peak=    3.515 closest distance to " O   HOH Z 294 " =    1.823
peak=    3.513 closest distance to " CB  THR A 235 " =    1.381
peak=    3.512 closest distance to " CB  VAL A 202 " =    1.404
peak=    3.508 closest distance to " CB  SER A 288 " =    1.712
peak=    3.503 closest distance to " CA  ALA A 248 " =    1.287
peak=    3.499 closest distance to " O   HOH Z 343 " =    2.532
peak=    3.498 closest distance to " O   THR A 294 " =    1.864
peak=    3.498 closest distance to " CB  GLU A 128 " =    1.120
peak=    3.494 closest distance to " O   HOH Z 368 " =    4.071
peak=    3.492 closest distance to " O   HOH Z  59 " =    2.063
peak=    3.484 closest distance to " O   HOH Z  30 " =    1.331
peak=    3.481 closest distance to " CB  ALA A 299 " =    1.027
peak=    3.476 closest distance to " CA  ARG A 156 " =    1.090
peak=    3.476 closest distance to " CB  TYR A  30 " =    0.993
peak=    3.474 closest distance to " O   HOH Z   9 " =    2.309
peak=    3.474 closest distance to " O   HOH Z 437 " =    2.182
peak=    3.465 closest distance to " CA  GLN A  11 " =    0.950
peak=    3.464 closest distance to " CA  ALA A 100 " =    1.060
peak=    3.454 closest distance to " CG  GLN A  77 " =    0.847
peak=    3.453 closest distance to " O   HOH Z 130 " =    1.078
peak=    3.453 closest distance to " CG2 ILE A 234 " =    1.287
peak=    3.447 closest distance to " O   HOH Z 215 " =    1.388
peak=    3.446 closest distance to " CB  MET A 105 " =    1.431
peak=    3.444 closest distance to " CB  ALA A 248 " =    1.349
peak=    3.443 closest distance to " CG1 VAL A 153 " =    1.069
peak=    3.443 closest distance to " CB  ARG A 259 " =    1.880
peak=    3.433 closest distance to " O   HOH Z  58 " =    1.598
peak=    3.431 closest distance to " O   HOH Z  88 " =    3.152
peak=    3.430 closest distance to " CA  GLY A 267 " =    0.795
peak=    3.426 closest distance to " OE2 GLU A   2 " =    2.148
peak=    3.425 closest distance to " O   HOH Z 415 " =    1.245
peak=    3.417 closest distance to " CB  VAL A 265 " =    1.464
peak=    3.416 closest distance to " O   HOH Z   7 " =    0.777
peak=    3.415 closest distance to " CA  LEU A   5 " =    0.983
peak=    3.414 closest distance to " CB  ALA A  34 " =    0.885
peak=    3.412 closest distance to " O   HOH Z  33 " =    2.078
peak=    3.404 closest distance to " CB  PHE A 283 " =    0.848
peak=    3.404 closest distance to " O   HOH Z  57 " =    2.878
peak=    3.402 closest distance to " CB AVAL A  41 " =    1.341
peak=    3.402 closest distance to " CA  ALA A 154 " =    1.073
peak=    3.400 closest distance to " O   HOH Z 435 " =    1.787
peak=    3.396 closest distance to " CA  ARG A 139 " =    1.442
peak=    3.393 closest distance to " O   HOH Z 232 " =    2.074
peak=    3.393 closest distance to " CZ3 TRP A 266 " =    1.124
peak=    3.382 closest distance to " O   HOH Z 368 " =    3.234
peak=    3.381 closest distance to " CA  TRP A 274 " =    0.911
peak=    3.380 closest distance to " CD  LYS A 289 " =    1.142
peak=    3.380 closest distance to " O   HOH Z 126 " =    2.827
peak=    3.373 closest distance to " O   HOH Z 402 " =    1.645
peak=    3.370 closest distance to " O   HOH Z 155 " =    2.904
peak=    3.369 closest distance to " O   HOH Z  90 " =    3.609
peak=    3.369 closest distance to " O   HOH Z 183 " =    1.634
peak=    3.367 closest distance to " O   HOH Z  38 " =    2.527
peak=    3.365 closest distance to " CD1 LEU A 222 " =    0.863
peak=    3.365 closest distance to " O   HOH Z 153 " =    2.265
peak=    3.364 closest distance to " O   GLY A 229 " =    1.016
peak=    3.363 closest distance to " CG2 VAL A 296 " =    0.986
peak=    3.363 closest distance to " O   HOH Z 171 " =    3.662
peak=    3.361 closest distance to " CB  TRP A 150 " =    1.532
peak=    3.353 closest distance to " O   HOH Z 247 " =    1.408
peak=    3.353 closest distance to " O   HOH Z 141 " =    1.637
peak=    3.352 closest distance to " O   HOH Z 280 " =    2.959
peak=    3.349 closest distance to " CB  ASP A 124 " =    0.878
peak=    3.349 closest distance to " O   HOH Z 289 " =    1.626
peak=    3.349 closest distance to " CA  ALA A 291 " =    0.921
peak=    3.349 closest distance to " O   HOH Z  14 " =    1.590
peak=    3.347 closest distance to " O   HOH Z 146 " =    1.741
peak=    3.345 closest distance to " O   HOH Z  56 " =    1.968
peak=    3.340 closest distance to " O   HOH Z 261 " =    1.223
peak=    3.339 closest distance to " CA  TYR A 214 " =    1.368
peak=    3.337 closest distance to " CA  ASP A 140 " =    1.313
peak=    3.333 closest distance to " CZ3 TRP A  85 " =    0.882
peak=    3.332 closest distance to " O   HOH Z 150 " =    1.864
peak=    3.325 closest distance to " O   HOH Z 273 " =    3.001
peak=    3.323 closest distance to " CG  PRO A 198 " =    1.248
peak=    3.320 closest distance to " N   ALA A 292 " =    1.041
peak=    3.319 closest distance to " O   PRO A 198 " =    1.555
peak=    3.315 closest distance to " CG  MET A 188 " =    0.953
peak=    3.314 closest distance to " O   HOH Z 265 " =    2.005
peak=    3.312 closest distance to " N   MET A  47 " =    1.512
peak=    3.311 closest distance to " O   HOH Z  95 " =    1.737
peak=    3.308 closest distance to " NE1 TRP A  92 " =    1.610
peak=    3.307 closest distance to " O   HOH Z 326 " =    1.683
peak=    3.307 closest distance to " CA  ALA A  51 " =    1.102
peak=    3.300 closest distance to " CB  ARG A  79 " =    1.257
peak=    3.300 closest distance to " CB  ARG A 190 " =    1.818
peak=    3.300 closest distance to " O   HOH Z 281 " =    2.685
peak=    3.298 closest distance to " O   HOH Z 417 " =    1.369
peak=    3.295 closest distance to " CG  ARG A 138 " =    1.093
peak=    3.293 closest distance to " CB  PHE A  16 " =    1.546
peak=    3.292 closest distance to " O   HOH Z 200 " =    2.282
peak=    3.290 closest distance to " O   HOH Z 134 " =    2.023
peak=    3.290 closest distance to " CA  GLY A 196 " =    0.915
peak=    3.290 closest distance to " CB  ASN A 148 " =    1.414
peak=    3.288 closest distance to " CA  ASP A 191 " =    0.869
peak=    3.287 closest distance to " CG  GLN A  11 " =    0.915
peak=    3.283 closest distance to " OD1 ASN A 217 " =    1.609
peak=    3.279 closest distance to " CG2AVAL A 121 " =    1.857
peak=    3.277 closest distance to " CG2 ILE A  33 " =    1.312
peak=    3.274 closest distance to " CG1 ILE A  49 " =    1.908
peak=    3.273 closest distance to " O   HOH Z 196 " =    1.749
peak=    3.273 closest distance to " O   HOH Z 406 " =    1.603
peak=    3.272 closest distance to " O   HOH Z 158 " =    1.202
peak=    3.271 closest distance to " ND2 ASN A  69 " =    1.219
peak=    3.270 closest distance to " CB  THR A  52 " =    0.854
peak=    3.259 closest distance to " CE  LYS A 166 " =    4.258
peak=    3.257 closest distance to " CB  SER A   3 " =    1.108
peak=    3.256 closest distance to " CD ALYS A 290 " =    1.339
peak=    3.254 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.253 closest distance to " O   HOH Z 135 " =    2.338
peak=    3.249 closest distance to " ND1 HIS A  81 " =    1.275
peak=    3.249 closest distance to " O   ARG A  14 " =    1.595
peak=    3.244 closest distance to " O   HOH Z 272 " =    2.027
peak=    3.242 closest distance to " O   HOH Z 367 " =    1.800
peak=    3.240 closest distance to " CB  GLN A  89 " =    1.178
peak=    3.234 closest distance to " CA  TYR A 116 " =    1.518
peak=    3.233 closest distance to " CB  ALA A  34 " =    0.929
peak=    3.226 closest distance to " CB  THR A  31 " =    1.451
peak=    3.223 closest distance to " OE1 GLN A  58 " =    3.238
peak=    3.222 closest distance to " CA  GLU A 152 " =    1.005
peak=    3.218 closest distance to " NZ  LYS A  76 " =    1.343
peak=    3.218 closest distance to " O   ASP A 298 " =    0.898
peak=    3.218 closest distance to " CB  ALA A   1 " =    1.548
peak=    3.212 closest distance to " O   HOH Z 217 " =    3.043
peak=    3.211 closest distance to " O   HOH Z 379 " =    1.607
peak=    3.211 closest distance to " NH1 ARG A  14 " =    1.166
peak=    3.211 closest distance to " O   HOH Z  44 " =    1.685
peak=    3.208 closest distance to " O   HOH Z 256 " =    2.075
peak=    3.208 closest distance to " CD  ARG A 269 " =    0.852
peak=    3.208 closest distance to " O   HOH Z 365 " =    2.247
peak=    3.207 closest distance to " CG  PRO A 213 " =    1.282
peak=    3.205 closest distance to " O   HOH Z 133 " =    1.418
peak=    3.202 closest distance to " O   HOH Z 316 " =    3.292
peak=    3.200 closest distance to " OG  SER A  62 " =    3.019
peak=    3.200 closest distance to " O   HOH Z 251 " =    2.026
peak=    3.192 closest distance to " CB  SER A  62 " =    1.088
peak=    3.191 closest distance to " OD2 ASP A 171 " =    1.278
peak=    3.189 closest distance to " CD  ARG A 138 " =    1.280
peak=    3.187 closest distance to " CB  GLU A 152 " =    0.990
peak=    3.186 closest distance to " O   HOH Z  44 " =    2.040
peak=    3.186 closest distance to " O   HOH Z 387 " =    3.053
peak=    3.186 closest distance to " N   ALA A 256 " =    1.220
peak=    3.179 closest distance to " CG2 THR A  42 " =    0.874
peak=    3.178 closest distance to " CG2 THR A  29 " =    1.780
peak=    3.177 closest distance to " O   HOH Z   5 " =    2.021
peak=    3.175 closest distance to " O   HOH Z 344 " =    3.042
peak=    3.173 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.171 closest distance to " O   HOH Z  38 " =    1.384
peak=    3.169 closest distance to " OG1 THR A 279 " =    1.792
peak=    3.169 closest distance to " CG  GLN A 278 " =    1.016
peak=    3.168 closest distance to " CG1 ILE A 106 " =    1.162
peak=    3.165 closest distance to " O   ASN A 284 " =    1.891
peak=    3.164 closest distance to " CA  LEU A 101 " =    1.416
peak=    3.157 closest distance to " O   GLU A 277 " =    1.615
peak=    3.155 closest distance to " CB  ASP A 140 " =    0.979
peak=    3.154 closest distance to " O   HOH Z 427 " =    3.276
peak=    3.154 closest distance to " OD1 ASP A 191 " =    1.699
peak=    3.151 closest distance to " CB  SER A  97 " =    1.062
peak=    3.147 closest distance to " O   HOH Z 258 " =    2.412
peak=    3.146 closest distance to " CG1BVAL A 121 " =    1.255
peak=    3.143 closest distance to " O   HOH Z 409 " =    3.113
peak=    3.141 closest distance to " O   HOH Z 394 " =    4.116
peak=    3.140 closest distance to " O   HOH Z  47 " =    1.357
peak=    3.140 closest distance to " NH2 ARG A  79 " =    1.465
peak=    3.139 closest distance to " O   HOH Z 133 " =    2.305
peak=    3.137 closest distance to " CG  ASN A 252 " =    1.239
peak=    3.136 closest distance to " CZ3 TRP A 274 " =    4.339
peak=    3.136 closest distance to " O   HOH Z 132 " =    2.871
peak=    3.134 closest distance to " O   HOH Z 408 " =    2.959
peak=    3.133 closest distance to " CA  ASP A 132 " =    1.228
peak=    3.131 closest distance to " CG  PRO A 243 " =    1.263
peak=    3.128 closest distance to " CG2 THR A 220 " =    1.021
peak=    3.128 closest distance to " CA  ILE A 106 " =    0.783
peak=    3.126 closest distance to " O   HOH Z 155 " =    1.467
peak=    3.121 closest distance to " C   ALA A 299 " =    0.965
peak=    3.120 closest distance to " OD2 ASP A 298 " =    3.255
peak=    3.117 closest distance to " CB  ALA A 292 " =    0.775
peak=    3.116 closest distance to " CG  GLN A  11 " =    1.081
peak=    3.115 closest distance to " ND2 ASN A 110 " =    1.236
peak=    3.112 closest distance to " O   HOH Z 285 " =    2.522
peak=    3.111 closest distance to " O   HOH Z 116 " =    3.150
peak=    3.110 closest distance to " CA  ALA A 160 " =    1.014
peak=    3.107 closest distance to " O   HOH Z 435 " =    2.852
peak=    3.104 closest distance to " NH1BARG A 102 " =    1.172
peak=    3.099 closest distance to " O   HOH Z  26 " =    1.030
peak=    3.094 closest distance to " CA  LEU A 282 " =    1.030
peak=    3.090 closest distance to " N   GLU A  53 " =    1.792
peak=    3.086 closest distance to " CB  ASN A 187 " =    1.171
peak=    3.077 closest distance to " CA  ASP A 149 " =    1.288
peak=    3.063 closest distance to " O   HOH Z 142 " =    1.831
peak=    3.060 closest distance to " OE1 GLN A  58 " =    1.800
peak=    3.059 closest distance to " CA  VAL A 125 " =    1.123
peak=    3.045 closest distance to " CB  VAL A 257 " =    0.819
peak=    3.031 closest distance to " O   HOH Z  76 " =    1.338
peak=    3.020 closest distance to " O   HOH Z  20 " =    2.802
peak=    2.984 closest distance to " O   HOH Z 130 " =    2.382

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 240         
Filter by distance & map next to the model:
   mapped sites are within: 0.857 - 5.939
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 240 from: 240
   mapped sites are within: 0.857 - 5.939

peak=   -4.660 closest distance to " O   HOH Z 411 " =    5.280
peak=   -4.636 closest distance to " CD  GLN A 223 " =    1.352
peak=   -4.632 closest distance to " CG2 VAL A 230 " =    0.965
peak=   -4.597 closest distance to " O   HOH Z 166 " =    1.447
peak=   -4.475 closest distance to " CB  ALA A 291 " =    2.466
peak=   -4.376 closest distance to " CG2 ILE A  49 " =    2.802
peak=   -4.329 closest distance to " O   HOH Z 400 " =    1.014
peak=   -4.269 closest distance to " CA  TYR A  68 " =    2.937
peak=   -4.243 closest distance to " O   GLN A  11 " =    0.990
peak=   -4.231 closest distance to " OD1 ASN A 301 " =    0.857
peak=   -4.200 closest distance to " CA  ASP A 298 " =    1.121
peak=   -4.182 closest distance to " CG  PRO A 243 " =    1.754
peak=   -4.133 closest distance to " CD  GLN A  58 " =    0.963
peak=   -4.116 closest distance to " O   HOH Z 216 " =    1.012
peak=   -4.055 closest distance to " CD1 PHE A  59 " =    1.950
peak=   -4.053 closest distance to " N   ALA A 226 " =    2.277
peak=   -4.030 closest distance to " O   HOH Z 407 " =    1.560
peak=   -4.029 closest distance to " O   HOH Z 103 " =    2.329
peak=   -3.995 closest distance to " CD  ARG A  14 " =    3.122
peak=   -3.960 closest distance to " CG1 VAL A 112 " =    2.593
peak=   -3.943 closest distance to " O   SER A 135 " =    2.014
peak=   -3.932 closest distance to " O   HOH Z  52 " =    2.137
peak=   -3.919 closest distance to " O   HOH Z 119 " =    2.085
peak=   -3.890 closest distance to " O   SER A 276 " =    1.565
peak=   -3.857 closest distance to " CG1 VAL A 250 " =    2.587
peak=   -3.853 closest distance to " O   HOH Z 184 " =    1.251
peak=   -3.852 closest distance to " N   SER A 134 " =    1.232
peak=   -3.845 closest distance to " O   HOH Z 361 " =    4.413
peak=   -3.833 closest distance to " CG  GLN A  58 " =    1.193
peak=   -3.831 closest distance to " OD1 ASN A 148 " =    1.454
peak=   -3.823 closest distance to " CB  ALA A 161 " =    2.678
peak=   -3.822 closest distance to " CE  MET A 105 " =    2.308
peak=   -3.820 closest distance to " O   HOH Z 196 " =    1.925
peak=   -3.808 closest distance to " O   HOH Z  54 " =    1.100
peak=   -3.804 closest distance to " CG2BVAL A  41 " =    2.895
peak=   -3.794 closest distance to " CG  ARG A 259 " =    2.451
peak=   -3.792 closest distance to " CD  LYS A 289 " =    2.275
peak=   -3.772 closest distance to " O   HOH Z   7 " =    1.407
peak=   -3.758 closest distance to " O   HOH Z 388 " =    1.810
peak=   -3.754 closest distance to " CA  VAL A 197 " =    0.960
peak=   -3.749 closest distance to " O   HOH Z  13 " =    1.685
peak=   -3.736 closest distance to " CD1 TYR A 247 " =    2.392
peak=   -3.735 closest distance to " NH2 ARG A  66 " =    1.355
peak=   -3.718 closest distance to " O   HOH Z 250 " =    1.825
peak=   -3.715 closest distance to " CB  ALA A  10 " =    1.989
peak=   -3.713 closest distance to " O   HOH Z  10 " =    1.735
peak=   -3.710 closest distance to " CG  ARG A 269 " =    2.508
peak=   -3.709 closest distance to " OE1 GLN A  88 " =    1.072
peak=   -3.706 closest distance to " CE3 TRP A 150 " =    2.351
peak=   -3.686 closest distance to " ND2 ASN A  60 " =    1.461
peak=   -3.683 closest distance to " C   ASN A 285 " =    2.525
peak=   -3.677 closest distance to " O   SER A 271 " =    2.151
peak=   -3.664 closest distance to " NH1 ARG A 195 " =    1.059
peak=   -3.662 closest distance to " OG  SER A  63 " =    1.109
peak=   -3.653 closest distance to " O   HOH Z 137 " =    1.584
peak=   -3.630 closest distance to " OXT GLY A 302 " =    2.982
peak=   -3.622 closest distance to " O   HOH Z 156 " =    3.471
peak=   -3.621 closest distance to " O   HOH Z 418 " =    1.474
peak=   -3.612 closest distance to " CG1 VAL A 197 " =    2.504
peak=   -3.597 closest distance to " O   HOH Z  37 " =    1.412
peak=   -3.594 closest distance to " C   THR A 264 " =    1.444
peak=   -3.590 closest distance to " CA  GLY A  98 " =    2.184
peak=   -3.575 closest distance to " O   HOH Z 127 " =    1.528
peak=   -3.569 closest distance to " O   HOH Z 107 " =    0.898
peak=   -3.565 closest distance to " O   HOH Z  43 " =    1.478
peak=   -3.552 closest distance to " O   ASP A 298 " =    1.751
peak=   -3.545 closest distance to " O   ILE A  49 " =    1.807
peak=   -3.544 closest distance to " O   HOH Z 414 " =    2.176
peak=   -3.541 closest distance to " O   HOH Z 108 " =    1.972
peak=   -3.534 closest distance to " CD1 ILE A 151 " =    2.380
peak=   -3.530 closest distance to " CG  GLN A 103 " =    2.297
peak=   -3.512 closest distance to " O   HOH Z 109 " =    3.545
peak=   -3.507 closest distance to " CA  SER A 276 " =    1.469
peak=   -3.503 closest distance to " O   PRO A 198 " =    1.253
peak=   -3.501 closest distance to " NE2 HIS A 115 " =    1.065
peak=   -3.500 closest distance to " ND2 ASN A  39 " =    1.519
peak=   -3.497 closest distance to " O   HOH Z 151 " =    1.176
peak=   -3.495 closest distance to " O   HOH Z 265 " =    1.390
peak=   -3.489 closest distance to " O   SER A 206 " =    1.192
peak=   -3.487 closest distance to " O   HOH Z 150 " =    1.667
peak=   -3.481 closest distance to " O   HOH Z 423 " =    1.077
peak=   -3.479 closest distance to " O   HOH Z 259 " =    1.772
peak=   -3.475 closest distance to " CG1 VAL A 296 " =    1.039
peak=   -3.474 closest distance to " O   HOH Z 407 " =    3.620
peak=   -3.470 closest distance to " CG2 VAL A 189 " =    2.198
peak=   -3.465 closest distance to " O   HOH Z  64 " =    1.574
peak=   -3.465 closest distance to " O   HOH Z 351 " =    1.772
peak=   -3.460 closest distance to " O   HOH Z 174 " =    1.689
peak=   -3.458 closest distance to " CG  PRO A 163 " =    1.724
peak=   -3.458 closest distance to " C   GLY A  91 " =    1.566
peak=   -3.454 closest distance to " O   HOH Z 120 " =    4.910
peak=   -3.452 closest distance to " O   HOH Z 133 " =    1.486
peak=   -3.445 closest distance to " CG  ASP A  50 " =    2.107
peak=   -3.441 closest distance to " O   HOH Z 384 " =    1.673
peak=   -3.437 closest distance to " O   HOH Z  82 " =    1.292
peak=   -3.434 closest distance to " NH2 ARG A  36 " =    1.196
peak=   -3.429 closest distance to " O   HOH Z 200 " =    1.487
peak=   -3.425 closest distance to " O   HOH Z 136 " =    1.250
peak=   -3.419 closest distance to " N   ARG A 275 " =    1.079
peak=   -3.413 closest distance to " CD  GLN A  11 " =    1.397
peak=   -3.412 closest distance to " CD  PRO A 213 " =    2.304
peak=   -3.410 closest distance to " OD2 ASP A 171 " =    2.082
peak=   -3.410 closest distance to " O   HOH Z  33 " =    2.019
peak=   -3.409 closest distance to " CB  PHE A 130 " =    1.236
peak=   -3.408 closest distance to " O   HOH Z 183 " =    1.390
peak=   -3.408 closest distance to " O   HOH Z 124 " =    1.551
peak=   -3.408 closest distance to " O   HOH Z 150 " =    1.119
peak=   -3.405 closest distance to " CA  GLY A 203 " =    2.386
peak=   -3.403 closest distance to " O   HOH Z 394 " =    1.793
peak=   -3.398 closest distance to " O   HOH Z 369 " =    2.458
peak=   -3.392 closest distance to " O   HOH Z 221 " =    1.154
peak=   -3.380 closest distance to " SG  CYS A 254 " =    2.844
peak=   -3.379 closest distance to " O   HOH Z 368 " =    2.088
peak=   -3.378 closest distance to " O   HOH Z 426 " =    1.002
peak=   -3.377 closest distance to " O   HOH Z 211 " =    1.341
peak=   -3.374 closest distance to " OD1 ASP A 231 " =    1.018
peak=   -3.374 closest distance to " CE2 PHE A 218 " =    2.258
peak=   -3.373 closest distance to " O   HOH Z 111 " =    1.347
peak=   -3.370 closest distance to " O   VAL A 125 " =    2.019
peak=   -3.370 closest distance to " N   ILE A 120 " =    1.124
peak=   -3.367 closest distance to " O   HOH Z 114 " =    1.480
peak=   -3.351 closest distance to " O   HOH Z 295 " =    1.593
peak=   -3.349 closest distance to " CD2 LEU A 228 " =    2.635
peak=   -3.348 closest distance to " O   HOH Z 331 " =    1.332
peak=   -3.346 closest distance to " O   HOH Z 120 " =    1.904
peak=   -3.344 closest distance to " CA  TRP A 274 " =    1.055
peak=   -3.343 closest distance to " CG  LYS A 119 " =    2.957
peak=   -3.343 closest distance to " NZ  LYS A 119 " =    2.033
peak=   -3.342 closest distance to " CB  PRO A  54 " =    2.586
peak=   -3.324 closest distance to " N   ALA A   1 " =    2.785
peak=   -3.311 closest distance to " O   HOH Z  91 " =    1.905
peak=   -3.311 closest distance to " N   SER A   3 " =    2.556
peak=   -3.308 closest distance to " O   HOH Z 402 " =    1.255
peak=   -3.295 closest distance to " O   HOH Z 259 " =    1.138
peak=   -3.294 closest distance to " O   HOH Z  19 " =    2.139
peak=   -3.293 closest distance to " O   ASN A 187 " =    1.672
peak=   -3.292 closest distance to " CA  SER A 164 " =    2.034
peak=   -3.290 closest distance to " SD  MET A 105 " =    2.380
peak=   -3.284 closest distance to " O   HOH Z  30 " =    1.559
peak=   -3.284 closest distance to " OG  SER A  87 " =    1.842
peak=   -3.281 closest distance to " O   HOH Z  73 " =    2.643
peak=   -3.280 closest distance to " CA  ASN A 127 " =    0.997
peak=   -3.269 closest distance to " O   HOH Z 269 " =    4.705
peak=   -3.268 closest distance to " O   HOH Z 109 " =    1.305
peak=   -3.265 closest distance to " O   HOH Z 185 " =    2.628
peak=   -3.263 closest distance to " O   HOH Z  56 " =    2.225
peak=   -3.263 closest distance to " CB  ALA A 100 " =    1.801
peak=   -3.263 closest distance to " CE2 PHE A 283 " =    2.533
peak=   -3.260 closest distance to " OG  SER A 141 " =    2.455
peak=   -3.260 closest distance to " O   ALA A   7 " =    1.606
peak=   -3.259 closest distance to " O   ALA A  34 " =    2.541
peak=   -3.256 closest distance to " O   HOH Z 275 " =    1.653
peak=   -3.255 closest distance to " O   HOH Z 198 " =    1.322
peak=   -3.252 closest distance to " O   HOH Z  60 " =    1.387
peak=   -3.249 closest distance to " O   HOH Z  78 " =    1.624
peak=   -3.248 closest distance to " CD2 TYR A  15 " =    2.347
peak=   -3.246 closest distance to " OG  SER A  97 " =    2.353
peak=   -3.245 closest distance to " CG1BVAL A  72 " =    2.661
peak=   -3.242 closest distance to " CG2 VAL A 230 " =    2.636
peak=   -3.240 closest distance to " N   GLU A   2 " =    1.399
peak=   -3.239 closest distance to " O   HOH Z 171 " =    2.490
peak=   -3.237 closest distance to " CG1AVAL A 121 " =    1.371
peak=   -3.236 closest distance to " OG1 THR A   4 " =    1.712
peak=   -3.235 closest distance to " C   ALA A 158 " =    1.310
peak=   -3.234 closest distance to " OG BSER A 210 " =    1.272
peak=   -3.233 closest distance to " CD  GLU A 128 " =    1.830
peak=   -3.227 closest distance to " CD  GLN A 223 " =    0.964
peak=   -3.226 closest distance to " O   THR A 251 " =    1.712
peak=   -3.226 closest distance to " O   GLY A  80 " =    2.259
peak=   -3.222 closest distance to " O   HOH Z 396 " =    1.938
peak=   -3.220 closest distance to " CA  PRO A 198 " =    1.086
peak=   -3.220 closest distance to " CZ  TYR A 169 " =    1.691
peak=   -3.219 closest distance to " O   HOH Z 252 " =    3.701
peak=   -3.218 closest distance to " O   HOH Z  81 " =    1.444
peak=   -3.217 closest distance to " CE2 PHE A  61 " =    2.562
peak=   -3.215 closest distance to " CA  GLY A 241 " =    3.295
peak=   -3.213 closest distance to " CZ  PHE A  38 " =    2.625
peak=   -3.212 closest distance to " O   HOH Z 208 " =    1.984
peak=   -3.206 closest distance to " O   HOH Z 120 " =    1.313
peak=   -3.205 closest distance to " N   VAL A 230 " =    0.994
peak=   -3.204 closest distance to " CD1 LEU A 167 " =    2.043
peak=   -3.202 closest distance to " C   VAL A 265 " =    0.982
peak=   -3.202 closest distance to " OG BSER A 134 " =    1.618
peak=   -3.199 closest distance to " N   ALA A 184 " =    1.000
peak=   -3.197 closest distance to " NE1 TRP A 266 " =    1.927
peak=   -3.196 closest distance to " CD2 TRP A 274 " =    2.277
peak=   -3.191 closest distance to " CB  SER A 271 " =    2.270
peak=   -3.191 closest distance to " O   HOH Z  17 " =    1.273
peak=   -3.190 closest distance to " OD1 ASP A 298 " =    2.319
peak=   -3.189 closest distance to " O   HOH Z 378 " =    1.283
peak=   -3.188 closest distance to " CD1 LEU A 101 " =    2.481
peak=   -3.186 closest distance to " O   HOH Z 144 " =    1.418
peak=   -3.181 closest distance to " CE2 PHE A  59 " =    2.413
peak=   -3.180 closest distance to " O   SER A   3 " =    1.093
peak=   -3.180 closest distance to " NE  ARG A  66 " =    4.565
peak=   -3.178 closest distance to " O   HOH Z 380 " =    4.374
peak=   -3.178 closest distance to " O   ASP A 171 " =    1.039
peak=   -3.178 closest distance to " CG1 VAL A 189 " =    2.615
peak=   -3.177 closest distance to " CB  ALA A   9 " =    2.521
peak=   -3.175 closest distance to " O   MET A  47 " =    2.471
peak=   -3.173 closest distance to " O   HOH Z 244 " =    1.879
peak=   -3.172 closest distance to " CZ  ARG A 156 " =    1.696
peak=   -3.172 closest distance to " CD2 TYR A 293 " =    1.834
peak=   -3.171 closest distance to " CB  SER A  62 " =    5.939
peak=   -3.169 closest distance to " ND2 ASN A  60 " =    2.342
peak=   -3.164 closest distance to " CA  VAL A 232 " =    2.175
peak=   -3.163 closest distance to " O   HOH Z 132 " =    2.034
peak=   -3.163 closest distance to " CD  GLN A  88 " =    0.997
peak=   -3.163 closest distance to " O   ASP A 298 " =    0.879
peak=   -3.158 closest distance to " O   HOH Z 389 " =    1.931
peak=   -3.146 closest distance to " O   HOH Z  90 " =    1.952
peak=   -3.140 closest distance to " CD1 ILE A 109 " =    2.184
peak=   -3.139 closest distance to " CB  PRO A 243 " =    2.817
peak=   -3.139 closest distance to " OE2 GLU A 277 " =    2.905
peak=   -3.137 closest distance to " CB  MET A 188 " =    1.754
peak=   -3.133 closest distance to " OG  SER A  62 " =    0.991
peak=   -3.131 closest distance to " NE2 GLN A 194 " =    1.973
peak=   -3.130 closest distance to " O   HOH Z 234 " =    4.291
peak=   -3.123 closest distance to " O   HOH Z 292 " =    1.722
peak=   -3.123 closest distance to " O   HOH Z  57 " =    1.007
peak=   -3.123 closest distance to " O   HOH Z 165 " =    1.634
peak=   -3.123 closest distance to " O   HOH Z  38 " =    3.482
peak=   -3.116 closest distance to " CZ  ARG A  79 " =    1.819
peak=   -3.115 closest distance to " CB  ALA A 291 " =    2.484
peak=   -3.112 closest distance to " CG  ARG A 259 " =    1.493
peak=   -3.109 closest distance to " O   ALA A  43 " =    2.095
peak=   -3.103 closest distance to " O   HOH Z 301 " =    2.609
peak=   -3.100 closest distance to " O   HOH Z 174 " =    1.569
peak=   -3.100 closest distance to " CE  MET A 105 " =    2.355
peak=   -3.094 closest distance to " O   HOH Z 289 " =    1.899
peak=   -3.088 closest distance to " NH2AARG A 275 " =    1.584
peak=   -3.087 closest distance to " O   HOH Z 422 " =    1.277
peak=   -3.084 closest distance to " O   TYR A  15 " =    1.767
peak=   -3.082 closest distance to " O   HOH Z 290 " =    1.184
peak=   -3.081 closest distance to " O   VAL A 121 " =    0.937
peak=   -3.073 closest distance to " CG  LEU A  83 " =    1.939
peak=   -3.066 closest distance to " CG2 VAL A 189 " =    1.971
peak=   -3.053 closest distance to " O   HOH Z 385 " =    3.925
peak=   -3.050 closest distance to " O   HOH Z 340 " =    1.500
peak=   -3.047 closest distance to " ND2 ASN A  60 " =    1.902

================= 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    :  0.5120 0.4983   6.306559e+00   6.289410e+00
   1_bss:  0.5060 0.4919   6.302712e+00   6.284224e+00
   1_xyz:  0.4434 0.4547   6.242526e+00   6.246887e+00
   1_adp:  0.4021 0.4473   6.188469e+00   6.239764e+00
   1_occ:  0.4011 0.4469   6.187754e+00   6.240060e+00
   2_bss:  0.3993 0.4409   6.188758e+00   6.239344e+00
   2_xyz:  0.3374 0.4134   6.080740e+00   6.190870e+00
   2_adp:  0.3284 0.3959   6.061713e+00   6.168004e+00
   2_occ:  0.3284 0.3959   6.061635e+00   6.168458e+00
   3_bss:  0.3282 0.3951   6.062965e+00   6.168496e+00
   3_xyz:  0.2696 0.3209   5.893675e+00   6.028210e+00
   3_adp:  0.2502 0.3019   5.839088e+00   5.983247e+00
   3_occ:  0.2497 0.3025   5.838371e+00   5.984257e+00
   4_bss:  0.2492 0.3030   5.837992e+00   5.983937e+00
   4_xyz:  0.2005 0.2438   5.635277e+00   5.802341e+00
   4_adp:  0.1842 0.2353   5.577582e+00   5.770836e+00
   4_occ:  0.1841 0.2354   5.577490e+00   5.771041e+00
   5_bss:  0.1841 0.2360   5.578874e+00   5.772181e+00
   5_xyz:  0.1478 0.2006   5.393089e+00   5.619595e+00
   5_adp:  0.1383 0.1907   5.330579e+00   5.562115e+00
   5_occ:  0.1382 0.1906   5.330284e+00   5.562050e+00
   5_bss:  0.1385 0.1910   5.331291e+00   5.562278e+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:  0.293  20.000   5.905  11.220   8.907   0.000   0.000   0.000
   1_xyz:  0.293  20.000   5.905  11.220   8.907   0.000   0.000   0.000
   1_adp:  0.293  20.000   5.905  11.220   8.907   0.000   0.000   0.000
   1_occ:  0.293  20.000   5.905  11.220   8.907   0.000   0.000   0.000
   2_bss:  0.306  50.001   2.796   6.970   5.395   0.000   0.000   0.000
   2_xyz:  0.306  50.001   2.796   6.970   5.395   0.000   0.000   0.000
   2_adp:  0.306  50.001   2.796   6.970   5.395   0.000   0.000   0.000
   2_occ:  0.306  50.001   2.796   6.970   5.395   0.000   0.000   0.000
   3_bss:  0.328  73.925   2.341   5.314   3.724   0.000   0.000   0.000
   3_xyz:  0.328  73.925   2.341   5.314   3.724   0.000   0.000   0.000
   3_adp:  0.328  73.925   2.341   5.314   3.724   0.000   0.000   0.000
   3_occ:  0.328  73.925   2.341   5.314   3.724   0.000   0.000   0.000
   4_bss:  0.324  71.140   1.351   3.638   2.709   0.000   0.000   0.000
   4_xyz:  0.324  71.140   1.351   3.638   2.709   0.000   0.000   0.000
   4_adp:  0.324  71.140   1.351   3.638   2.709   0.000   0.000   0.000
   4_occ:  0.324  71.140   1.351   3.638   2.709   0.000   0.000   0.000
   5_bss:  0.337  84.408   1.288   2.786   2.741   0.000   0.000   0.000
   5_xyz:  0.337  84.408   1.288   2.786   2.741   0.000   0.000   0.000
   5_adp:  0.337  84.408   1.288   2.786   2.741   0.000   0.000   0.000
   5_occ:  0.337  84.408   1.288   2.786   2.741   0.000   0.000   0.000
   5_bss:  0.333  79.212  -0.860   0.232   0.628   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.037 0.3543  0.4024    77084.074
   1_bss:  61.880 0.3688  0.5374    75842.460
   1_xyz:  54.155 0.4675  0.6666    61512.577
   1_adp:  52.590 0.4874  0.7640    59700.240
   1_occ:  52.565 0.4878  0.7634    59790.342
   2_bss:  52.267 0.4915  0.6835    59233.598
   2_xyz:  47.331 0.5524  0.7712    49298.793
   2_adp:  44.605 0.5867  0.8011    45371.185
   2_occ:  44.613 0.5866  0.8009    45425.562
   3_bss:  44.543 0.5875  0.7690    45373.592
   3_xyz:  34.384 0.7087  0.9057    29004.352
   3_adp:  31.884 0.7375  0.9205    25576.378
   3_occ:  31.897 0.7374  0.9197    25610.880
   4_bss:  31.819 0.7382  0.8822    25498.732
   4_xyz:  24.421 0.8180  0.9445    15718.275
   4_adp:  23.417 0.8283  0.9360    14587.890
   4_occ:  23.422 0.8283  0.9358    14596.371
   5_bss:  23.446 0.8282  0.9269    14664.412
   5_xyz:  19.413 0.8671  0.9565    10309.643
   5_adp:  17.822 0.8822  0.9560     9194.510
   5_occ:  17.816 0.8823  0.9560     9196.313
   5_bss:  17.817 0.8823  0.9599     9211.033
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4702e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4702e+01
   1_xyz:   1.750  0.014  0.110 18.238  0.007  4.126   1.5175e-01
   1_adp:   1.750  0.014  0.110 18.238  0.007  4.126   1.5175e-01
   1_occ:   1.750  0.014  0.110 18.238  0.007  4.126   1.5175e-01
   2_bss:   1.750  0.014  0.110 18.238  0.007  4.126   1.5175e-01
   2_xyz:   1.369  0.010  0.093 17.197  0.005  4.109   1.0898e-01
   2_adp:   1.369  0.010  0.093 17.197  0.005  4.109   1.0898e-01
   2_occ:   1.369  0.010  0.093 17.197  0.005  4.109   1.0898e-01
   3_bss:   1.369  0.010  0.093 17.197  0.005  4.109   1.0898e-01
   3_xyz:   1.338  0.010  0.096 16.168  0.005  4.110   9.8606e-02
   3_adp:   1.338  0.010  0.096 16.168  0.005  4.110   9.8606e-02
   3_occ:   1.338  0.010  0.096 16.168  0.005  4.110   9.8606e-02
   4_bss:   1.338  0.010  0.096 16.168  0.005  4.110   9.8606e-02
   4_xyz:   1.095  0.010  0.078 15.454  0.005  4.128   8.5192e-02
   4_adp:   1.095  0.010  0.078 15.454  0.005  4.128   8.5192e-02
   4_occ:   1.095  0.010  0.078 15.454  0.005  4.128   8.5192e-02
   5_bss:   1.095  0.010  0.078 15.454  0.005  4.128   8.5192e-02
   5_xyz:   1.296  0.012  0.098 15.757  0.004  4.139   9.9671e-02
   5_adp:   1.296  0.012  0.098 15.757  0.004  4.139   9.9671e-02
   5_occ:   1.296  0.012  0.098 15.757  0.004  4.139   9.9671e-02
   5_bss:   1.296  0.012  0.098 15.757  0.004  4.139   9.9671e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0918e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0918e+00
   1_xyz:  14.591  0.125  0.468 88.222  0.053  2.148   1.0749e-01
   1_adp:  14.591  0.125  0.468 88.222  0.053  2.148   1.0749e-01
   1_occ:  14.591  0.125  0.468 88.222  0.053  2.148   1.0749e-01
   2_bss:  14.591  0.125  0.468 88.222  0.053  2.148   1.0749e-01
   2_xyz:   8.511  0.071  0.292 89.309  0.027  2.121   7.0851e-02
   2_adp:   8.511  0.071  0.292 89.309  0.027  2.121   7.0851e-02
   2_occ:   8.511  0.071  0.292 89.309  0.027  2.121   7.0851e-02
   3_bss:   8.511  0.071  0.292 89.309  0.027  2.121   7.0851e-02
   3_xyz:   9.288  0.072  0.326 89.166  0.039  2.199   8.4234e-02
   3_adp:   9.288  0.072  0.326 89.166  0.039  2.199   8.4234e-02
   3_occ:   9.288  0.072  0.326 89.166  0.039  2.199   8.4234e-02
   4_bss:   9.288  0.072  0.326 89.166  0.039  2.199   8.4234e-02
   4_xyz:   7.775  0.069  0.239 82.942  0.051  2.273   2.0271e-01
   4_adp:   7.775  0.069  0.239 82.942  0.051  2.273   2.0271e-01
   4_occ:   7.775  0.069  0.239 82.942  0.051  2.273   2.0271e-01
   5_bss:   7.775  0.069  0.239 82.942  0.051  2.273   2.0271e-01
   5_xyz:   8.373  0.071  0.589 85.957  0.033  2.089   6.3827e-02
   5_adp:   8.373  0.071  0.589 85.957  0.033  2.089   6.3827e-02
   5_occ:   8.373  0.071  0.589 85.957  0.033  2.089   6.3827e-02
   5_bss:   8.373  0.071  0.589 85.957  0.033  2.089   6.3827e-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: 123.39   0.00  16.82  89.10   0.00  14.79 123.39   0.00  27.87
   1_occ: 123.39   0.00  16.82  89.10   0.00  14.79 123.39   0.00  27.87
   2_bss: 123.39   0.00  16.82  89.10   0.00  14.79 123.39   0.00  27.87
   2_xyz: 123.39   0.00  16.82  89.10   0.00  14.79 123.39   0.00  27.87
   2_adp: 122.00   0.00  14.65  70.62   0.00  12.23 122.00   0.00  27.83
   2_occ: 122.00   0.00  14.65  70.62   0.00  12.23 122.00   0.00  27.83
   3_bss: 122.00   0.00  14.65  70.62   0.00  12.23 122.00   0.00  27.83
   3_xyz: 122.00   0.00  14.65  70.62   0.00  12.23 122.00   0.00  27.83
   3_adp: 109.04   0.00  14.50  77.03   0.00  11.06 109.04   0.00  33.26
   3_occ: 109.04   0.00  14.50  77.03   0.00  11.06 109.04   0.00  33.26
   4_bss: 109.04   0.00  14.50  77.03   0.00  11.06 109.04   0.00  33.26
   4_xyz: 109.04   0.00  14.50  77.03   0.00  11.06 109.04   0.00  33.26
   4_adp: 109.17   0.00  15.90  94.53   0.00  10.84 109.17   0.00  43.46
   4_occ: 109.17   0.00  15.90  94.53   0.00  10.84 109.17   0.00  43.46
   5_bss: 109.17   0.00  15.90  94.53   0.00  10.84 109.17   0.00  43.46
   5_xyz: 109.17   0.00  15.90  94.53   0.00  10.84 109.17   0.00  43.46
   5_adp: 108.54   0.00  15.17  95.93   0.00   9.91 108.54   1.17  43.82
   5_occ: 108.54   0.00  15.17  95.93   0.00   9.91 108.54   1.17  43.82
   5_bss: 110.93   2.39  17.56  98.32   2.39  12.30 110.93   3.56  46.21
------------------------------------------------------------------------
 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:    1.157    0.026    0.411
   1_adp:    1.157    0.026    0.411
   1_occ:    1.157    0.026    0.411
   2_bss:    1.157    0.026    0.411
   2_xyz:    1.588    0.050    0.593
   2_adp:    1.588    0.050    0.593
   2_occ:    1.588    0.050    0.593
   3_bss:    1.588    0.050    0.593
   3_xyz:    1.658    0.039    0.726
   3_adp:    1.658    0.039    0.726
   3_occ:    1.658    0.039    0.726
   4_bss:    1.658    0.039    0.726
   4_xyz:    1.818    0.068    0.838
   4_adp:    1.818    0.068    0.838
   4_occ:    1.818    0.068    0.838
   5_bss:    1.818    0.068    0.838
   5_xyz:    2.090    0.056    0.915
   5_adp:    2.090    0.056    0.915
   5_occ:    2.090    0.056    0.915
   5_bss:    2.090    0.056    0.915
------------------------------------------------------------------------

CPU time actual refinement: 337.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/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_965/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_965/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.17 
  Macro-tasks:
    bulk solvent and scale       = 46.86  
    individual site refinement   = 134.73 
    weights calculation          = 32.22  
    collect and process          = 6.28   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 220.22 
  Micro-tasks:
    mask                            = 2.96   
    f_calc                          = 102.38 
    alpha_beta                      = 8.35   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.79 
    fmodel                         = 8.03   
    r_factors                      = 0.23   
    phase_errors                   = 10.02  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 245.18 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.792 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    633 calls, 102.11 s
gradients_fft:          578 calls,  99.33 s

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

# Date 2008-01-16 Time 02:51:23 PST -0800 (1200480683.28 s)
Start R-work = 0.5120, R-free = 0.4983 (no bulk solvent and anisotropic scale)
Final R-work = 0.1539, R-free = 0.2058 (no bulk solvent and anisotropic scale)

Start R-work = 0.5060, R-free = 0.4919
Final R-work = 0.1385, R-free = 0.1910