# Date 2008-01-16 Time 01:45:10 PST -0800 (1200476710.38 s)
#phil __OFF__

Command line arguments: "../547.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5675
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 547

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99067
Completeness in resolution range: 0.963172
Completeness with d_max=infinity: 0.960151

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9907

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.99067
Completeness in resolution range: 0.963172
Completeness with d_max=infinity: 0.960151

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.2591 [2144/2168]  1926   218  10.2%
  bin  2:  4.2591 -  3.3934 [2046/2065]  1846   200   9.8%
  bin  3:  3.3934 -  2.9683 [2028/2047]  1824   204  10.1%
  bin  4:  2.9683 -  2.6986 [2003/2033]  1798   205  10.2%
  bin  5:  2.6986 -  2.5061 [2004/2023]  1807   197   9.8%
  bin  6:  2.5061 -  2.3590 [1979/2004]  1781   198  10.0%
  bin  7:  2.3590 -  2.2412 [1977/2005]  1781   196   9.9%
  bin  8:  2.2412 -  2.1440 [1973/2009]  1775   198  10.0%
  bin  9:  2.1440 -  2.0616 [1944/1986]  1750   194  10.0%
  bin 10:  2.0616 -  1.9907 [1491/1998]  1342   149  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.77 -     2.39: 15
        2.39 -     3.02: 2026
        3.02 -     3.65: 4579
        3.65 -     4.27: 9053
        4.27 -     4.90: 12463
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.765 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.811 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.978 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.125 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28131 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_547/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 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: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4199   ksol= 0.00   Bsol= 0.00   scale= 0.818    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.232054                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7501 0.99   1394  153 0.3603 0.3308      6.5305      6.4351|
|  2:  4.7501 -  3.7904 0.99   1326  152 0.3260 0.3564        6.63      6.7389|
|  3:  3.7904 -  3.3172 0.99   1311  145 0.3787 0.3502      6.5729      6.5303|
|  4:  3.3172 -  3.0166 0.99   1300  139 0.4194 0.4050      6.4631       6.395|
|  5:  3.0166 -  2.8018 0.99   1292  144 0.4509 0.4570      6.3163      6.3236|
|  6:  2.8018 -  2.6376 0.99   1294  149 0.4533 0.5170      6.2337      6.2041|
|  7:  2.6376 -  2.5061 0.99   1284  142 0.4740 0.4698      6.2007      6.1531|
|  8:  2.5061 -  2.3975 0.98   1280  137 0.4872 0.4349      6.1581       6.112|
|  9:  2.3975 -  2.3055 0.98   1261  146 0.4920 0.4672      6.0956      6.0959|
| 10:  2.3055 -  2.2262 0.99   1280  141 0.5054 0.4133      6.1226      6.0038|
| 11:  2.2262 -  2.1568 0.98   1259  136 0.4931 0.4796        6.02      6.0274|
| 12:  2.1568 -  2.0954 0.97   1251  141 0.5074 0.4594      5.9593      5.9911|
| 13:  2.0954 -  2.0403 1.00   1263  138 0.4863 0.4659      5.8755       5.811|
| 14:  2.0403 -  1.9907 0.65    835   96 0.5094 0.4449      5.8773      5.6993|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7501  1394   153  0.75  30.02   0.81     0.77      55807.28|
|  2:  4.7501 -  3.7904  1326   152  0.77  28.66   0.91     0.82      73942.17|
|  3:  3.7904 -  3.3172  1311   145  0.71  34.67   0.87     0.79      78325.77|
|  4:  3.3172 -  3.0166  1300   139  0.63  40.99   0.82     0.69      71474.74|
|  5:  3.0166 -  2.8018  1292   144  0.54  49.14   0.78     0.61      64732.01|
|  6:  2.8018 -  2.6376  1294   149  0.50  51.91   0.74     0.56      59539.13|
|  7:  2.6376 -  2.5061  1284   142  0.48  53.51   0.76     0.55      54442.56|
|  8:  2.5061 -  2.3975  1280   137  0.50  51.93   0.75     0.57      46347.51|
|  9:  2.3975 -  2.3055  1261   146  0.54  49.12   0.74     0.61      40020.40|
| 10:  2.3055 -  2.2262  1280   141  0.54  48.77   0.76     0.62      35183.29|
| 11:  2.2262 -  2.1568  1259   136  0.52  50.85   0.76     0.61      34382.88|
| 12:  2.1568 -  2.0954  1251   141  0.49  53.28   0.78     0.59      32937.41|
| 13:  2.0954 -  2.0403  1263   138  0.48  53.59   0.76     0.56      28774.09|
| 14:  2.0403 -  1.9907   835    96  0.53  49.90   0.73     0.55      21725.20|
|alpha:            min =        0.55 max =            0.82 mean =         0.64|
|beta:             min =    21725.20 max =        78325.77 mean =     50812.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.91 mean =        45.88|
|phase err.(test): min =        0.00 max =           89.93 mean =        46.08|
|-----------------------------------------------------------------------------|

============================== 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 = 7.457185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.734   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.588049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.687   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1487 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2605 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3915 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5042 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6548 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7688 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.962 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.729 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4447   r_free= 0.4215   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.239084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4272   r_free= 0.4079   ksol= 0.34   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.01,7.75,10.77,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.224647                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.915121              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572889              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.218   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4272      final r-factor (work) = 0.3177          |
| start r-factor (free) = 0.4079      final r-factor (free) = 0.3335          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.5485 = 6.92 * 0.50 * 6.2431 + 1.00 * 53.9625                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0928 = 6.92 * 0.50 * 6.0658 + 1.00 * 0.1200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3177      final r-factor (work) = 0.2540          |
| start r-factor (free) = 0.3335      final r-factor (free) = 0.2877          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4898 = 0.57 * 1.00 * 6.0658 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3812 = 0.57 * 1.00 * 5.8821 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    58.56   10.87    None  None   None       |
|    all(noH): 2823   0      0.00    58.56   10.87    None  None   None       |
|    Sol.    : 438    0      0.00    58.56   27.59    None  None   None       |
|    Mac.    : 2385   0      0.00    53.80   7.79     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 -   5.856: 1194   |   5:    29.281 -  35.137:   95        |
|      1:     5.856 -  11.712:  773   |   6:    35.137 -  40.993:   75        |
|      2:    11.712 -  17.569:  332   |   7:    40.993 -  46.849:   45        |
|      3:    17.569 -  23.425:  145   |   8:    46.849 -  52.706:   25        |
|      4:    23.425 -  29.281:  132   |   9:    52.706 -  58.562:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2540 r_free = 0.2877             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2535 r_free = 0.2881             target_work(ml) = 5.823         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2535   r_free= 0.2881   ksol= 0.34   Bsol= 20.00   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.01,7.75,10.77,0.00,0.00,0.00); trace/3= 8.51                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.822906                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2479   r_free= 0.2834   ksol= 0.33   Bsol= 44.95   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.59,3.98,7.02,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.820759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.355213              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.655   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330288              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2479      final r-factor (work) = 0.1677          |
| start r-factor (free) = 0.2834      final r-factor (free) = 0.2080          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0064 = 3.36 * 0.50 * 5.8934 + 1.00 * 0.1196                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5219 = 3.36 * 0.50 * 5.6381 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1677      final r-factor (work) = 0.1515          |
| start r-factor (free) = 0.2080      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8735 = 0.33 * 1.00 * 5.6381 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7990 = 0.33 * 1.00 * 5.4151 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.15   11.24    None  None   None       |
|    all(noH): 2823   0      0.00    61.15   11.24    None  None   None       |
|    Sol.    : 438    0      0.97    61.15   31.76    None  None   None       |
|    Mac.    : 2385   0      0.00    58.53   7.48     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 -   6.115: 1353   |   5:    30.573 -  36.687:  113        |
|      1:     6.115 -  12.229:  715   |   6:    36.687 -  42.802:   93        |
|      2:    12.229 -  18.344:  235   |   7:    42.802 -  48.916:   73        |
|      3:    18.344 -  24.458:  115   |   8:    48.916 -  55.031:   27        |
|      4:    24.458 -  30.573:   89   |   9:    55.031 -  61.145:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1515 r_free = 0.1938             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1515 r_free = 0.1936             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1515   r_free= 0.1936   ksol= 0.33   Bsol= 44.95   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.59,3.98,7.02,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.383246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1504   r_free= 0.1937   ksol= 0.32   Bsol= 50.88   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.67,3.25,5.06,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.382846                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.215890              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.511  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.759368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.588  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1504      final r-factor (work) = 0.1259          |
| start r-factor (free) = 0.1937      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0723 = 2.22 * 0.50 * 5.4234 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9359 = 2.22 * 0.50 * 5.3021 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1259      final r-factor (work) = 0.1206          |
| start r-factor (free) = 0.1675      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0366 = 0.76 * 1.00 * 5.3021 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9704 = 0.76 * 1.00 * 5.2116 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.07   11.74    None  None   None       |
|    all(noH): 2823   0      0.00    70.07   11.74    None  None   None       |
|    Sol.    : 438    0      0.28    67.50   34.63    None  None   None       |
|    Mac.    : 2385   0      0.00    70.07   7.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.007: 1517   |   5:    35.035 -  42.042:   83        |
|      1:     7.007 -  14.014:  640   |   6:    42.042 -  49.049:   87        |
|      2:    14.014 -  21.021:  189   |   7:    49.049 -  56.056:   78        |
|      3:    21.021 -  28.028:  105   |   8:    56.056 -  63.063:   19        |
|      4:    28.028 -  35.035:   94   |   9:    63.063 -  70.070:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1206 r_free = 0.1648             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1647             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1647   ksol= 0.32   Bsol= 50.88   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.67,3.25,5.06,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.205560                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1644   ksol= 0.33   Bsol= 53.48   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.61,3.12,4.71,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.205251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.987046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.797  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.727102              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.308  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8450 = 2.99 * 0.50 * 5.2115 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8032 = 2.99 * 0.50 * 5.1760 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7763 = 0.73 * 1.00 * 5.1760 + 1.00 * 0.0129                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7991 = 0.73 * 1.00 * 5.1535 + 1.00 * 0.0520                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.95   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    71.95   11.67    None  None   None       |
|    Sol.    : 438    0      0.45    68.58   34.52    None  None   None       |
|    Mac.    : 2385   0      0.00    71.95   7.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.195: 1578   |   5:    35.975 -  43.170:   86        |
|      1:     7.195 -  14.390:  607   |   6:    43.170 -  50.365:   82        |
|      2:    14.390 -  21.585:  177   |   7:    50.365 -  57.560:   71        |
|      3:    21.585 -  28.780:  100   |   8:    57.560 -  64.755:   13        |
|      4:    28.780 -  35.975:   99   |   9:    64.755 -  71.950:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1582             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1582             target_work(ml) = 5.152         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1582   ksol= 0.33   Bsol= 53.48   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.61,3.12,4.71,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.151945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1581   ksol= 0.33   Bsol= 50.78   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.77,3.23,4.78,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.151944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.126608              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.449  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.588770              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.392   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5528 = 2.13 * 0.50 * 5.1538 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5454 = 2.13 * 0.50 * 5.1561 + 1.00 * 0.0628                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1127          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0513 = 0.59 * 1.00 * 5.1561 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0500 = 0.59 * 1.00 * 5.1587 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.23   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    74.23   11.53    None  None   None       |
|    Sol.    : 438    0      0.49    69.50   34.10    None  None   None       |
|    Mac.    : 2385   0      0.00    74.23   7.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.423: 1631   |   5:    37.116 -  44.539:   83        |
|      1:     7.423 -  14.846:  571   |   6:    44.539 -  51.962:   81        |
|      2:    14.846 -  22.270:  173   |   7:    51.962 -  59.385:   51        |
|      3:    22.270 -  29.693:  104   |   8:    59.385 -  66.809:   13        |
|      4:    29.693 -  37.116:  108   |   9:    66.809 -  74.232:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1127 r_free = 0.1588             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1127 r_free = 0.1588             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1588   ksol= 0.33   Bsol= 50.78   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.77,3.23,4.78,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158602                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7501 0.99   1394  153 0.1018 0.1304      5.4085      5.5355|
|  2:  4.7501 -  3.7904 0.99   1326  152 0.0860 0.1106      5.4442      5.6392|
|  3:  3.7904 -  3.3172 0.99   1311  145 0.1050 0.1487      5.4738      5.8454|
|  4:  3.3172 -  3.0166 0.99   1300  139 0.1198 0.1597      5.4454      5.5979|
|  5:  3.0166 -  2.8018 0.99   1292  144 0.1310 0.1677      5.3314      5.5457|
|  6:  2.8018 -  2.6376 0.99   1294  149 0.1216 0.2046      5.2177      5.5296|
|  7:  2.6376 -  2.5061 0.99   1284  142 0.1280 0.1633      5.1917      5.3499|
|  8:  2.5061 -  2.3975 0.98   1280  137 0.1186 0.1699      5.1026      5.3709|
|  9:  2.3975 -  2.3055 0.98   1261  146 0.1202 0.1953      5.0645      5.3587|
| 10:  2.3055 -  2.2262 0.99   1280  141 0.1141 0.1565      4.9736      5.1662|
| 11:  2.2262 -  2.1568 0.98   1259  136 0.1174 0.1813      4.9645      5.2652|
| 12:  2.1568 -  2.0954 0.97   1251  141 0.1154 0.1716      4.8995      5.2587|
| 13:  2.0954 -  2.0403 1.00   1263  138 0.1135 0.1686      4.8021      5.0288|
| 14:  2.0403 -  1.9907 0.65    835   96 0.1024 0.1759      4.6682      4.9386|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7501  1394   153  0.94   9.64   0.97     0.95       7669.56|
|  2:  4.7501 -  3.7904  1326   152  0.95   8.00   1.01     0.99       9174.58|
|  3:  3.7904 -  3.3172  1311   145  0.94  11.07   1.02     1.02      10331.28|
|  4:  3.3172 -  3.0166  1300   139  0.92  13.30   1.01     0.99      10215.47|
|  5:  3.0166 -  2.8018  1292   144  0.90  15.79   1.00     0.97       8386.54|
|  6:  2.8018 -  2.6376  1294   149  0.90  16.38   0.98     0.96       7301.03|
|  7:  2.6376 -  2.5061  1284   142  0.90  16.01   0.98     0.94       6467.84|
|  8:  2.5061 -  2.3975  1280   137  0.91  15.44   0.99     0.97       5674.59|
|  9:  2.3975 -  2.3055  1261   146  0.91  15.81   1.01     0.98       5424.99|
| 10:  2.3055 -  2.2262  1280   141  0.89  16.45   1.00     0.95       4557.69|
| 11:  2.2262 -  2.1568  1259   136  0.90  16.54   0.99     0.96       4642.75|
| 12:  2.1568 -  2.0954  1251   141  0.90  15.98   1.01     0.99       4123.56|
| 13:  2.0954 -  2.0403  1263   138  0.90  16.06   0.99     0.96       3443.94|
| 14:  2.0403 -  1.9907   835    96  0.92  14.32   0.97     0.94       2546.90|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2546.90 max =        10331.28 mean =      6561.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.82|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1588   ksol= 0.33   Bsol= 54.41   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.35,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158640                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1588   ksol= 0.33   Bsol= 54.41   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,-0.35,1.18,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158640                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.7501 0.99   1394  153 0.1018 0.1304      5.4086      5.5356|
|  2:  4.7501 -  3.7904 0.99   1326  152 0.0860 0.1106      5.4442       5.639|
|  3:  3.7904 -  3.3172 0.99   1311  145 0.1050 0.1487      5.4737      5.8453|
|  4:  3.3172 -  3.0166 0.99   1300  139 0.1198 0.1597      5.4454      5.5979|
|  5:  3.0166 -  2.8018 0.99   1292  144 0.1310 0.1677      5.3315      5.5457|
|  6:  2.8018 -  2.6376 0.99   1294  149 0.1216 0.2046      5.2178      5.5297|
|  7:  2.6376 -  2.5061 0.99   1284  142 0.1280 0.1633      5.1917      5.3499|
|  8:  2.5061 -  2.3975 0.98   1280  137 0.1186 0.1699      5.1026      5.3708|
|  9:  2.3975 -  2.3055 0.98   1261  146 0.1202 0.1954      5.0645      5.3587|
| 10:  2.3055 -  2.2262 0.99   1280  141 0.1141 0.1565      4.9737      5.1661|
| 11:  2.2262 -  2.1568 0.98   1259  136 0.1174 0.1813      4.9645      5.2652|
| 12:  2.1568 -  2.0954 0.97   1251  141 0.1154 0.1717      4.8995      5.2587|
| 13:  2.0954 -  2.0403 1.00   1263  138 0.1135 0.1686      4.8022      5.0288|
| 14:  2.0403 -  1.9907 0.65    835   96 0.1024 0.1760      4.6683      4.9388|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9990 -  4.7501  1394   153  0.94   9.64   0.97     0.95       7672.44|
|  2:  4.7501 -  3.7904  1326   152  0.95   8.00   1.01     1.00       9175.35|
|  3:  3.7904 -  3.3172  1311   145  0.94  11.07   1.02     1.02      10329.51|
|  4:  3.3172 -  3.0166  1300   139  0.92  13.30   1.01     0.99      10215.49|
|  5:  3.0166 -  2.8018  1292   144  0.90  15.79   1.00     0.97       8387.58|
|  6:  2.8018 -  2.6376  1294   149  0.90  16.39   0.98     0.96       7301.60|
|  7:  2.6376 -  2.5061  1284   142  0.90  16.01   0.98     0.94       6468.00|
|  8:  2.5061 -  2.3975  1280   137  0.91  15.44   0.99     0.97       5674.71|
|  9:  2.3975 -  2.3055  1261   146  0.91  15.81   1.01     0.98       5424.89|
| 10:  2.3055 -  2.2262  1280   141  0.89  16.45   1.00     0.95       4558.23|
| 11:  2.2262 -  2.1568  1259   136  0.90  16.54   1.00     0.96       4642.80|
| 12:  2.1568 -  2.0954  1251   141  0.90  15.98   1.01     0.99       4123.79|
| 13:  2.0954 -  2.0403  1263   138  0.90  16.06   0.99     0.97       3444.44|
| 14:  2.0403 -  1.9907   835    96  0.92  14.32   0.98     0.94       2548.07|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2548.07 max =        10329.51 mean =      6562.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.28|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.82|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.984)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.63    77.86   15.16    None  None   None       |
|    all(noH): 2823   0      3.63    77.86   15.16    None  None   None       |
|    Sol.    : 438    0      4.12    73.13   37.73    None  None   None       |
|    Mac.    : 2385   0      3.63    77.86   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.632 -  11.055: 1631   |   5:    40.748 -  48.171:   83        |
|      1:    11.055 -  18.479:  571   |   6:    48.171 -  55.594:   81        |
|      2:    18.479 -  25.902:  173   |   7:    55.594 -  63.018:   51        |
|      3:    25.902 -  33.325:  104   |   8:    63.018 -  70.441:   13        |
|      4:    33.325 -  40.748:  108   |   9:    70.441 -  77.864:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.218 - 4.154
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 301
   mapped sites are within: 0.708 - 4.154

peak=   11.294 closest distance to " CB  VAL A 230 " =    1.474
peak=    7.412 closest distance to " CG2 VAL A 296 " =    1.147
peak=    6.566 closest distance to " CG  LEU A   5 " =    1.219
peak=    6.159 closest distance to " NH2 ARG A  56 " =    2.201
peak=    5.700 closest distance to " CG  PRO A  54 " =    1.340
peak=    5.641 closest distance to " CG  LEU A 228 " =    1.182
peak=    5.406 closest distance to " NE2 GLN A  11 " =    1.167
peak=    5.343 closest distance to " O   HOH Z 142 " =    1.830
peak=    5.263 closest distance to " CB  GLN A 223 " =    1.472
peak=    5.229 closest distance to " CD2 LEU A   5 " =    1.156
peak=    5.154 closest distance to " CB  PRO A  54 " =    1.026
peak=    4.960 closest distance to " CB  VAL A 296 " =    1.043
peak=    4.960 closest distance to " CB  ARG A 275 " =    0.936
peak=    4.779 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.726 closest distance to " O   HOH Z 232 " =    2.349
peak=    4.693 closest distance to " O   HOH Z 265 " =    2.222
peak=    4.544 closest distance to " CG  PRO A 243 " =    1.127
peak=    4.543 closest distance to " CG  PRO A 198 " =    1.284
peak=    4.518 closest distance to " CZ  PHE A 218 " =    1.164
peak=    4.498 closest distance to " ND2 ASN A 187 " =    1.568
peak=    4.464 closest distance to " O   SER A  87 " =    2.305
peak=    4.399 closest distance to " O   HOH Z 126 " =    1.893
peak=    4.397 closest distance to " CB  SER A  63 " =    1.185
peak=    4.387 closest distance to " CG  PRO A 213 " =    1.215
peak=    4.361 closest distance to " O   HOH Z 369 " =    2.192
peak=    4.319 closest distance to " CB  ARG A  79 " =    1.436
peak=    4.314 closest distance to " O   HOH Z  43 " =    2.052
peak=    4.313 closest distance to " O   HOH Z 346 " =    1.574
peak=    4.298 closest distance to " O   HOH Z 188 " =    2.968
peak=    4.294 closest distance to " CB  ARG A 190 " =    1.629
peak=    4.272 closest distance to " CB  ASN A 148 " =    1.413
peak=    4.261 closest distance to " O   HOH Z 427 " =    3.092
peak=    4.228 closest distance to " O   HOH Z  61 " =    1.739
peak=    4.227 closest distance to " O   HOH Z 248 " =    1.432
peak=    4.208 closest distance to " C   PRO A 198 " =    1.512
peak=    4.207 closest distance to " CB  VAL A 230 " =    1.195
peak=    4.199 closest distance to " O   HOH Z 303 " =    2.083
peak=    4.179 closest distance to " CB  VAL A 265 " =    1.319
peak=    4.177 closest distance to " O   HOH Z 313 " =    1.887
peak=    4.156 closest distance to " CA  TYR A  30 " =    0.994
peak=    4.092 closest distance to " O   HOH Z 209 " =    2.278
peak=    4.081 closest distance to " CB  GLU A 152 " =    1.183
peak=    4.078 closest distance to " O   HOH Z 236 " =    2.028
peak=    4.048 closest distance to " CB  ASN A 142 " =    1.110
peak=    4.042 closest distance to " O   HOH Z 272 " =    1.838
peak=    4.041 closest distance to " O   HOH Z 423 " =    1.825
peak=    4.037 closest distance to " CB  TRP A 266 " =    1.023
peak=    4.037 closest distance to " O   HOH Z  78 " =    1.648
peak=    4.024 closest distance to " O   HOH Z 402 " =    1.417
peak=    4.016 closest distance to " O   HOH Z 368 " =    2.132
peak=    4.006 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.996 closest distance to " N   ASN A  39 " =    1.163
peak=    3.993 closest distance to " CB  ALA A   9 " =    1.600
peak=    3.987 closest distance to " O   HOH Z 261 " =    1.958
peak=    3.982 closest distance to " CG  MET A 185 " =    1.185
peak=    3.978 closest distance to " CB  GLU A 277 " =    3.644
peak=    3.978 closest distance to " O   HOH Z  92 " =    2.329
peak=    3.974 closest distance to " CD2 LEU A 228 " =    1.189
peak=    3.935 closest distance to " O   HOH Z 214 " =    2.207
peak=    3.928 closest distance to " OG ASER A 258 " =    3.137
peak=    3.917 closest distance to " O   HOH Z 411 " =    3.885
peak=    3.912 closest distance to " O   HOH Z 251 " =    1.559
peak=    3.911 closest distance to " O   HOH Z 158 " =    3.187
peak=    3.902 closest distance to " CB  ASP A 124 " =    0.710
peak=    3.891 closest distance to " CB  ASN A  39 " =    0.904
peak=    3.886 closest distance to " O   HOH Z 298 " =    1.759
peak=    3.871 closest distance to " O   HOH Z 234 " =    3.683
peak=    3.863 closest distance to " O   HOH Z   9 " =    1.230
peak=    3.859 closest distance to " CB  GLU A 128 " =    1.007
peak=    3.828 closest distance to " CB  ASP A 140 " =    1.074
peak=    3.787 closest distance to " OD1 ASN A  69 " =    2.560
peak=    3.780 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.777 closest distance to " ND2 ASN A 249 " =    0.909
peak=    3.772 closest distance to " CB  ARG A  79 " =    0.922
peak=    3.767 closest distance to " O   HOH Z  59 " =    2.025
peak=    3.765 closest distance to " CG2 VAL A 257 " =    0.863
peak=    3.764 closest distance to " CD  LYS A 166 " =    1.301
peak=    3.755 closest distance to " CA  ARG A 195 " =    1.208
peak=    3.742 closest distance to " CG  LEU A 167 " =    1.268
peak=    3.735 closest distance to " O   HOH Z 359 " =    1.470
peak=    3.734 closest distance to " CG1BVAL A  72 " =    1.683
peak=    3.728 closest distance to " CB  ASN A 187 " =    1.297
peak=    3.717 closest distance to " CA  VAL A  41 " =    0.783
peak=    3.715 closest distance to " NH1AARG A 145 " =    1.178
peak=    3.709 closest distance to " O   HOH Z 353 " =    2.616
peak=    3.706 closest distance to " O   HOH Z  63 " =    1.958
peak=    3.704 closest distance to " O   HOH Z 280 " =    2.973
peak=    3.694 closest distance to " CD  ARG A 269 " =    1.014
peak=    3.692 closest distance to " CG1 ILE A  49 " =    1.512
peak=    3.687 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.686 closest distance to " O   HOH Z 389 " =    1.807
peak=    3.684 closest distance to " CG1 VAL A 153 " =    0.968
peak=    3.682 closest distance to " O   HOH Z 371 " =    2.856
peak=    3.681 closest distance to " CB  SER A   3 " =    1.259
peak=    3.679 closest distance to " O   HOH Z  40 " =    1.652
peak=    3.678 closest distance to " CB  GLU A  46 " =    0.971
peak=    3.675 closest distance to " O   HOH Z  68 " =    2.231
peak=    3.673 closest distance to " CA  PHE A 283 " =    1.194
peak=    3.670 closest distance to " CD2 TRP A 179 " =    1.308
peak=    3.664 closest distance to " CB  TRP A 179 " =    1.400
peak=    3.662 closest distance to " O   HOH Z 145 " =    2.272
peak=    3.645 closest distance to " O  BHOH Z 338 " =    2.368
peak=    3.641 closest distance to " O   HOH Z  97 " =    2.412
peak=    3.638 closest distance to " CD  ARG A 159 " =    0.720
peak=    3.638 closest distance to " O   HOH Z 126 " =    1.524
peak=    3.635 closest distance to " CZ3 TRP A 266 " =    1.138
peak=    3.629 closest distance to " CB  SER A  26 " =    1.827
peak=    3.627 closest distance to " O   HOH Z 403 " =    1.522
peak=    3.619 closest distance to " CB  GLN A  89 " =    1.275
peak=    3.615 closest distance to " O   HOH Z 425 " =    1.358
peak=    3.615 closest distance to " CA  SER A  87 " =    1.022
peak=    3.614 closest distance to " CA  ALA A  51 " =    0.913
peak=    3.607 closest distance to " O   HOH Z 422 " =    2.639
peak=    3.600 closest distance to " CB BVAL A  41 " =    1.184
peak=    3.599 closest distance to " O   HOH Z 273 " =    2.836
peak=    3.593 closest distance to " O   HOH Z   9 " =    2.022
peak=    3.589 closest distance to " OG BSER A 164 " =    2.217
peak=    3.564 closest distance to " O   HOH Z  21 " =    1.786
peak=    3.556 closest distance to " O   HOH Z 365 " =    2.895
peak=    3.554 closest distance to " CG  ARG A  66 " =    2.697
peak=    3.548 closest distance to " NZ  LYS A  48 " =    1.212
peak=    3.542 closest distance to " CD1 LEU A  96 " =    0.713
peak=    3.538 closest distance to " CZ  PHE A  38 " =    1.121
peak=    3.535 closest distance to " N   PHE A 130 " =    1.243
peak=    3.535 closest distance to " O   HOH Z 180 " =    2.137
peak=    3.532 closest distance to " CE1 TYR A 186 " =    1.276
peak=    3.527 closest distance to " O   HOH Z 392 " =    3.084
peak=    3.523 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.519 closest distance to " O   HOH Z 128 " =    2.127
peak=    3.517 closest distance to " CB  THR A  31 " =    1.565
peak=    3.514 closest distance to " CB  ASN A 110 " =    1.074
peak=    3.513 closest distance to " O   HOH Z 203 " =    1.685
peak=    3.512 closest distance to " CG1 VAL A 296 " =    1.226
peak=    3.509 closest distance to " O   HOH Z 285 " =    2.515
peak=    3.508 closest distance to " CA  THR A 264 " =    0.799
peak=    3.506 closest distance to " CB  ALA A 104 " =    0.708
peak=    3.503 closest distance to " O   ASP A 124 " =    1.095
peak=    3.502 closest distance to " O   HOH Z 172 " =    3.537
peak=    3.499 closest distance to " NZ  LYS A 117 " =    3.246
peak=    3.498 closest distance to " O   HOH Z 250 " =    1.312
peak=    3.495 closest distance to " O   HOH Z 147 " =    1.796
peak=    3.492 closest distance to " O   HOH Z 166 " =    3.958
peak=    3.486 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.485 closest distance to " O   HOH Z 403 " =    1.610
peak=    3.485 closest distance to " O   HOH Z  80 " =    1.693
peak=    3.484 closest distance to " O   HOH Z  88 " =    3.730
peak=    3.479 closest distance to " CA  ASN A 215 " =    1.091
peak=    3.463 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.458 closest distance to " CA  ALA A  21 " =    1.073
peak=    3.456 closest distance to " CD1 ILE A 199 " =    0.962
peak=    3.455 closest distance to " CA  ALA A 233 " =    1.399
peak=    3.454 closest distance to " NE2 GLN A  77 " =    3.256
peak=    3.453 closest distance to " O   HOH Z 141 " =    1.698
peak=    3.452 closest distance to " O   HOH Z 128 " =    2.148
peak=    3.452 closest distance to " O   HOH Z 337 " =    3.446
peak=    3.448 closest distance to " CA  ALA A 291 " =    0.878
peak=    3.446 closest distance to " O   HOH Z  10 " =    1.725
peak=    3.444 closest distance to " CB  SER A 212 " =    1.293
peak=    3.440 closest distance to " CB  SER A 273 " =    0.894
peak=    3.440 closest distance to " CB  ASN A 215 " =    1.188
peak=    3.440 closest distance to " O   HOH Z 193 " =    1.877
peak=    3.439 closest distance to " CD1 LEU A 300 " =    1.221
peak=    3.433 closest distance to " O   HOH Z 425 " =    2.032
peak=    3.431 closest distance to " O   HOH Z  97 " =    2.035
peak=    3.423 closest distance to " N   SER A 135 " =    1.377
peak=    3.418 closest distance to " CB  PRO A  90 " =    1.155
peak=    3.417 closest distance to " CD BLYS A 290 " =    1.077
peak=    3.416 closest distance to " CB  ALA A 248 " =    1.406
peak=    3.411 closest distance to " CA  VAL A 125 " =    1.216
peak=    3.405 closest distance to " CG  MET A 185 " =    1.001
peak=    3.400 closest distance to " O   HOH Z 329 " =    4.109
peak=    3.394 closest distance to " O   HOH Z 290 " =    1.099
peak=    3.393 closest distance to " N   ASP A 162 " =    1.254
peak=    3.381 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.377 closest distance to " CB  ALA A 291 " =    1.303
peak=    3.377 closest distance to " O   HOH Z 258 " =    2.162
peak=    3.375 closest distance to " O   HOH Z   3 " =    1.881
peak=    3.374 closest distance to " CG2 ILE A 120 " =    1.169
peak=    3.373 closest distance to " CA  TYR A 116 " =    1.469
peak=    3.373 closest distance to " O   TRP A 274 " =    1.861
peak=    3.369 closest distance to " O   HOH Z 294 " =    1.551
peak=    3.367 closest distance to " CA  TYR A  30 " =    1.068
peak=    3.364 closest distance to " CB  THR A  52 " =    0.893
peak=    3.363 closest distance to " CG  GLU A  37 " =    0.875
peak=    3.363 closest distance to " CD1 ILE A  33 " =    1.703
peak=    3.354 closest distance to " O   HOH Z 171 " =    3.921
peak=    3.352 closest distance to " CA  ASN A 217 " =    1.203
peak=    3.352 closest distance to " O   HOH Z 299 " =    4.154
peak=    3.350 closest distance to " CA  MET A 105 " =    0.976
peak=    3.348 closest distance to " CA  ASN A 127 " =    1.050
peak=    3.348 closest distance to " O   HOH Z 435 " =    1.993
peak=    3.348 closest distance to " CD2 LEU A 297 " =    0.953
peak=    3.343 closest distance to " CB  ASN A 173 " =    1.073
peak=    3.335 closest distance to " O   HOH Z  88 " =    2.890
peak=    3.331 closest distance to " O   ASN A  74 " =    1.540
peak=    3.330 closest distance to " O   HOH Z 368 " =    3.510
peak=    3.330 closest distance to " CB  ARG A 139 " =    0.899
peak=    3.328 closest distance to " O   HOH Z 325 " =    2.234
peak=    3.327 closest distance to " O   SER A 164 " =    1.266
peak=    3.325 closest distance to " O   HOH Z 187 " =    2.336
peak=    3.321 closest distance to " CA  ALA A 154 " =    1.022
peak=    3.321 closest distance to " O   HOH Z 148 " =    3.424
peak=    3.317 closest distance to " CA  ALA A 295 " =    1.059
peak=    3.314 closest distance to " CD1 LEU A 261 " =    1.246
peak=    3.312 closest distance to " O   HOH Z 406 " =    1.542
peak=    3.312 closest distance to " OE2 GLU A  53 " =    1.981
peak=    3.308 closest distance to " O   HOH Z 261 " =    1.643
peak=    3.307 closest distance to " CA  ASP A 162 " =    1.013
peak=    3.307 closest distance to " O   HOH Z 407 " =    2.427
peak=    3.307 closest distance to " CG BARG A 102 " =    1.795
peak=    3.305 closest distance to " CG2 ILE A  20 " =    1.516
peak=    3.303 closest distance to " OG  SER A 276 " =    1.230
peak=    3.303 closest distance to " O   MET A 105 " =    1.855
peak=    3.292 closest distance to " O   HOH Z 291 " =    1.528
peak=    3.292 closest distance to " CA  LEU A 282 " =    1.164
peak=    3.291 closest distance to " O   HOH Z  44 " =    1.651
peak=    3.279 closest distance to " CB  GLN A 205 " =    1.125
peak=    3.273 closest distance to " O   HOH Z 345 " =    3.276
peak=    3.272 closest distance to " O   HOH Z 240 " =    2.291
peak=    3.269 closest distance to " CB  ALA A 295 " =    1.272
peak=    3.265 closest distance to " CD1 ILE A 263 " =    1.189
peak=    3.263 closest distance to " CB  VAL A 268 " =    0.816
peak=    3.258 closest distance to " N   ALA A 256 " =    1.080
peak=    3.250 closest distance to " CB  PHE A 204 " =    0.840
peak=    3.231 closest distance to " O   HOH Z 417 " =    3.174
peak=    3.227 closest distance to " CB  GLN A 278 " =    0.888
peak=    3.226 closest distance to " CG2AVAL A 121 " =    2.416
peak=    3.223 closest distance to " NE2 HIS A 207 " =    1.232
peak=    3.221 closest distance to " O   HOH Z 305 " =    3.553
peak=    3.219 closest distance to " OG BSER A 134 " =    3.056
peak=    3.218 closest distance to " O   HOH Z 245 " =    1.363
peak=    3.217 closest distance to " O   HOH Z 344 " =    2.887
peak=    3.215 closest distance to " CB  SER A 216 " =    0.795
peak=    3.214 closest distance to " CB  PRO A 243 " =    1.370
peak=    3.210 closest distance to " N   ASN A 127 " =    1.224
peak=    3.209 closest distance to " O   ALA A   1 " =    1.717
peak=    3.206 closest distance to " CB  THR A 157 " =    1.159
peak=    3.204 closest distance to " CG2 ILE A 239 " =    0.741
peak=    3.202 closest distance to " CB  TRP A 150 " =    1.424
peak=    3.198 closest distance to " CA  GLY A 267 " =    0.742
peak=    3.196 closest distance to " O   HOH Z 302 " =    2.018
peak=    3.195 closest distance to " CB  HIS A 108 " =    0.821
peak=    3.193 closest distance to " O   LYS A 290 " =    2.408
peak=    3.193 closest distance to " CE  LYS A  48 " =    1.155
peak=    3.191 closest distance to " O   HOH Z 171 " =    2.306
peak=    3.187 closest distance to " CD  LYS A 119 " =    1.813
peak=    3.186 closest distance to " CA  LYS A 290 " =    1.158
peak=    3.178 closest distance to " CA  ILE A 234 " =    0.904
peak=    3.177 closest distance to " CB  ALA A 227 " =    1.019
peak=    3.176 closest distance to " O   HOH Z 116 " =    1.775
peak=    3.174 closest distance to " CA  GLY A 211 " =    1.357
peak=    3.173 closest distance to " N   SER A  12 " =    1.600
peak=    3.172 closest distance to " CB  ALA A 242 " =    0.791
peak=    3.170 closest distance to " CB  LEU A 228 " =    1.262
peak=    3.165 closest distance to " CG  GLN A  88 " =    1.046
peak=    3.163 closest distance to " O   HOH Z  48 " =    1.541
peak=    3.163 closest distance to " O   HOH Z 409 " =    3.323
peak=    3.163 closest distance to " O   HOH Z 234 " =    1.827
peak=    3.161 closest distance to " O   HOH Z 361 " =    3.580
peak=    3.155 closest distance to " O   GLN A  88 " =    1.662
peak=    3.153 closest distance to " O   HOH Z 213 " =    1.861
peak=    3.151 closest distance to " CG1 ILE A 151 " =    1.070
peak=    3.150 closest distance to " O   HOH Z  88 " =    2.688
peak=    3.149 closest distance to " CD  ARG A  66 " =    2.626
peak=    3.148 closest distance to " CA  THR A 221 " =    0.963
peak=    3.144 closest distance to " CB  LEU A 300 " =    0.882
peak=    3.143 closest distance to " CD  LYS A  76 " =    1.876
peak=    3.142 closest distance to " CD1 LEU A 228 " =    2.044
peak=    3.138 closest distance to " O   ASN A 284 " =    1.738
peak=    3.134 closest distance to " CA  ALA A 129 " =    1.411
peak=    3.133 closest distance to " CA  ASP A 140 " =    1.288
peak=    3.132 closest distance to " CA  ASP A 191 " =    1.125
peak=    3.128 closest distance to " O   HOH Z 133 " =    2.583
peak=    3.123 closest distance to " O   HOH Z   1 " =    1.949
peak=    3.122 closest distance to " CZ3 TRP A  85 " =    0.955
peak=    3.119 closest distance to " CA  ARG A 139 " =    1.011
peak=    3.118 closest distance to " CG  LEU A 281 " =    1.041
peak=    3.116 closest distance to " CB  TYR A 247 " =    0.961
peak=    3.112 closest distance to " CA  ILE A 106 " =    0.739
peak=    3.110 closest distance to " NH2BARG A 190 " =    1.779
peak=    3.108 closest distance to " CB  ALA A 114 " =    1.152
peak=    3.098 closest distance to " CB  ALA A  43 " =    0.814
peak=    3.097 closest distance to " CA  ALA A 248 " =    1.162
peak=    3.093 closest distance to " C   ALA A 299 " =    0.928
peak=    3.091 closest distance to " O   HOH Z 193 " =    1.620
peak=    3.083 closest distance to " O   THR A 182 " =    1.383
peak=    3.078 closest distance to " O   HOH Z 109 " =    2.611
peak=    3.077 closest distance to " OE2 GLU A   2 " =    1.869
peak=    3.074 closest distance to " O   GLN A 278 " =    1.502
peak=    3.072 closest distance to " O   HOH Z 201 " =    3.003
peak=    3.071 closest distance to " O   HOH Z 421 " =    1.980
peak=    3.071 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.060 closest distance to " O   ALA A 158 " =    1.369
peak=    3.054 closest distance to " CG1 ILE A  33 " =    1.325

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.717 - 5.577
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.717 - 5.577

peak=   -5.144 closest distance to " CG2 VAL A 230 " =    0.717
peak=   -4.738 closest distance to " CD  GLN A  58 " =    1.042
peak=   -4.591 closest distance to " CD  ARG A  14 " =    3.279
peak=   -4.438 closest distance to " CB  PRO A 243 " =    2.726
peak=   -4.425 closest distance to " O   VAL A  67 " =    2.605
peak=   -4.327 closest distance to " OG BSER A 134 " =    1.258
peak=   -4.289 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.265 closest distance to " C   HIS A 108 " =    1.207
peak=   -4.245 closest distance to " CB  PHE A 192 " =    1.940
peak=   -4.211 closest distance to " O   HOH Z 266 " =    5.454
peak=   -4.059 closest distance to " O   HOH Z 231 " =    2.159
peak=   -4.050 closest distance to " CA  VAL A  67 " =    2.919
peak=   -4.004 closest distance to " OE1 GLN A 223 " =    2.163
peak=   -3.988 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.984 closest distance to " CG2 VAL A 296 " =    1.408
peak=   -3.971 closest distance to " O   HOH Z 196 " =    2.181
peak=   -3.962 closest distance to " CZ3 TRP A 179 " =    1.194
peak=   -3.945 closest distance to " CG1 VAL A 112 " =    2.765
peak=   -3.943 closest distance to " O   HOH Z 351 " =    1.529
peak=   -3.925 closest distance to " O   HOH Z 166 " =    1.957
peak=   -3.845 closest distance to " CB  ALA A 248 " =    2.347
peak=   -3.840 closest distance to " O   HOH Z 290 " =    1.212
peak=   -3.810 closest distance to " OG  SER A  97 " =    2.322
peak=   -3.792 closest distance to " CE2 TYR A  30 " =    2.688
peak=   -3.791 closest distance to " O   HOH Z 114 " =    3.062
peak=   -3.791 closest distance to " O   HOH Z 394 " =    1.541
peak=   -3.779 closest distance to " CB  ALA A 161 " =    2.567
peak=   -3.748 closest distance to " O   HOH Z 185 " =    2.429
peak=   -3.747 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.743 closest distance to " CB  ALA A  43 " =    2.479
peak=   -3.735 closest distance to " CG1 VAL A 250 " =    2.757
peak=   -3.719 closest distance to " O   PRO A 163 " =    2.127
peak=   -3.704 closest distance to " OXT GLY A 302 " =    2.868
peak=   -3.694 closest distance to " CZ2 TRP A  92 " =    2.854
peak=   -3.684 closest distance to " CE  MET A 105 " =    2.318
peak=   -3.684 closest distance to " CE BMET A  47 " =    1.426
peak=   -3.680 closest distance to " O   SER A 271 " =    2.139
peak=   -3.659 closest distance to " ND2 ASN A  45 " =    1.163
peak=   -3.659 closest distance to " O   PRO A 198 " =    1.207
peak=   -3.630 closest distance to " C   ILE A 239 " =    2.167
peak=   -3.629 closest distance to " O   HOH Z 435 " =    2.842
peak=   -3.628 closest distance to " O   HOH Z  11 " =    1.891
peak=   -3.625 closest distance to " O   HOH Z  37 " =    1.825
peak=   -3.621 closest distance to " CG1 VAL A 112 " =    2.663
peak=   -3.616 closest distance to " C   MET A 188 " =    1.414
peak=   -3.602 closest distance to " CG  TRP A 266 " =    1.833
peak=   -3.602 closest distance to " CE3 TRP A 150 " =    2.217
peak=   -3.596 closest distance to " O   HOH Z 211 " =    1.474
peak=   -3.592 closest distance to " O   HOH Z  44 " =    2.269
peak=   -3.582 closest distance to " O   VAL A 189 " =    2.660
peak=   -3.577 closest distance to " CA  GLY A 241 " =    3.120
peak=   -3.569 closest distance to " O   HOH Z 407 " =    3.034
peak=   -3.559 closest distance to " N   ALA A 248 " =    1.745
peak=   -3.554 closest distance to " OD1 ASN A 148 " =    1.412
peak=   -3.552 closest distance to " NH2AARG A 275 " =    5.174
peak=   -3.546 closest distance to " O   HOH Z 429 " =    2.080
peak=   -3.542 closest distance to " O   HOH Z 216 " =    1.337
peak=   -3.523 closest distance to " O   HOH Z  73 " =    2.275
peak=   -3.519 closest distance to " O   HOH Z 198 " =    2.155
peak=   -3.502 closest distance to " O   SER A 210 " =    1.950
peak=   -3.498 closest distance to " ND2 ASN A 187 " =    1.514
peak=   -3.495 closest distance to " CG  ASP A 231 " =    0.781
peak=   -3.483 closest distance to " N   THR A 157 " =    1.494
peak=   -3.463 closest distance to " ND2 ASN A 249 " =    2.376
peak=   -3.461 closest distance to " NE2 GLN A  88 " =    1.955
peak=   -3.445 closest distance to " O   HOH Z 193 " =    1.517
peak=   -3.438 closest distance to " CA  GLY A 241 " =    2.383
peak=   -3.437 closest distance to " N   ALA A 226 " =    2.038
peak=   -3.437 closest distance to " O   PHE A 218 " =    1.600
peak=   -3.425 closest distance to " CD1 LEU A 101 " =    2.344
peak=   -3.415 closest distance to " CB  ALA A 291 " =    2.248
peak=   -3.414 closest distance to " ND2 ASN A  45 " =    1.814
peak=   -3.408 closest distance to " CG1 VAL A 265 " =    2.352
peak=   -3.395 closest distance to " CB  PRO A 163 " =    2.508
peak=   -3.392 closest distance to " CB  ASP A 171 " =    2.253
peak=   -3.390 closest distance to " O   HOH Z 389 " =    2.053
peak=   -3.384 closest distance to " CB  GLN A  11 " =    1.850
peak=   -3.383 closest distance to " O   HOH Z  13 " =    1.813
peak=   -3.379 closest distance to " O   HOH Z  10 " =    1.451
peak=   -3.377 closest distance to " CG1 VAL A  67 " =    2.972
peak=   -3.374 closest distance to " OG  SER A  63 " =    1.211
peak=   -3.374 closest distance to " CG1 VAL A 125 " =    1.928
peak=   -3.371 closest distance to " NH2 ARG A  79 " =    1.537
peak=   -3.361 closest distance to " O   HOH Z 243 " =    1.868
peak=   -3.361 closest distance to " C   LEU A 143 " =    1.066
peak=   -3.360 closest distance to " N   ALA A  43 " =    2.571
peak=   -3.358 closest distance to " CG  ASP A 132 " =    2.361
peak=   -3.355 closest distance to " O   HOH Z 421 " =    3.101
peak=   -3.351 closest distance to " O   HOH Z  47 " =    1.658
peak=   -3.350 closest distance to " O   HOH Z 359 " =    3.043
peak=   -3.347 closest distance to " CG  HIS A  86 " =    1.149
peak=   -3.336 closest distance to " N   THR A  52 " =    1.640
peak=   -3.334 closest distance to " O   HOH Z 136 " =    2.423
peak=   -3.330 closest distance to " NE2 GLN A 278 " =    1.868
peak=   -3.330 closest distance to " CB  TRP A  85 " =    2.652
peak=   -3.327 closest distance to " CD  ARG A 139 " =    1.676
peak=   -3.320 closest distance to " CD1 ILE A 199 " =    2.454
peak=   -3.315 closest distance to " O   HOH Z 371 " =    2.127
peak=   -3.314 closest distance to " CB  ALA A  10 " =    2.312
peak=   -3.314 closest distance to " CG  GLU A 277 " =    1.202
peak=   -3.314 closest distance to " C   GLY A  17 " =    1.252
peak=   -3.313 closest distance to " CA  GLY A 203 " =    2.444
peak=   -3.311 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.301 closest distance to " N   ALA A 248 " =    2.290
peak=   -3.298 closest distance to " O   HOH Z 191 " =    5.577
peak=   -3.293 closest distance to " CE2 PHE A  61 " =    2.633
peak=   -3.290 closest distance to " O   ALA A  10 " =    1.779
peak=   -3.289 closest distance to " O   MET A  40 " =    2.782
peak=   -3.287 closest distance to " OH  TYR A 247 " =    2.040
peak=   -3.285 closest distance to " CA  GLY A 133 " =    2.317
peak=   -3.278 closest distance to " CG1 VAL A 230 " =    1.874
peak=   -3.272 closest distance to " O   HOH Z  38 " =    1.703
peak=   -3.267 closest distance to " CG  ARG A 269 " =    2.320
peak=   -3.267 closest distance to " O   HOH Z 174 " =    2.418
peak=   -3.255 closest distance to " O   ASN A 252 " =    1.371
peak=   -3.254 closest distance to " CD  PRO A 213 " =    2.066
peak=   -3.253 closest distance to " OD1 ASN A 249 " =    2.407
peak=   -3.250 closest distance to " O   HOH Z 431 " =    1.913
peak=   -3.250 closest distance to " O   HOH Z 345 " =    2.016
peak=   -3.249 closest distance to " O   HOH Z 262 " =    2.817
peak=   -3.249 closest distance to " O   HOH Z 295 " =    1.531
peak=   -3.247 closest distance to " CG1 VAL A 296 " =    1.364
peak=   -3.244 closest distance to " OE1 GLN A  88 " =    1.049
peak=   -3.243 closest distance to " O   HOH Z 131 " =    4.115
peak=   -3.237 closest distance to " CD2 LEU A 237 " =    2.874
peak=   -3.234 closest distance to " O   GLY A 196 " =    1.261
peak=   -3.231 closest distance to " O   HOH Z   9 " =    1.523
peak=   -3.230 closest distance to " CD1 LEU A 228 " =    2.236
peak=   -3.229 closest distance to " NH2 ARG A 159 " =    2.341
peak=   -3.229 closest distance to " O   HOH Z 166 " =    1.606
peak=   -3.224 closest distance to " OD2 ASP A  50 " =    2.218
peak=   -3.223 closest distance to " CD1 ILE A 239 " =    2.320
peak=   -3.219 closest distance to " CG  LEU A 228 " =    0.969
peak=   -3.216 closest distance to " CG  LEU A   5 " =    1.437
peak=   -3.214 closest distance to " CA  GLY A 133 " =    1.966
peak=   -3.214 closest distance to " O   HOH Z 285 " =    1.873
peak=   -3.211 closest distance to " O   ILE A 106 " =    1.919
peak=   -3.208 closest distance to " CG1 VAL A 197 " =    2.270
peak=   -3.206 closest distance to " NE2 GLN A 194 " =    1.835
peak=   -3.205 closest distance to " O   HOH Z 149 " =    2.222
peak=   -3.204 closest distance to " O   HOH Z 106 " =    1.872
peak=   -3.198 closest distance to " O   SER A  22 " =    2.349
peak=   -3.196 closest distance to " C   ALA A 158 " =    1.347
peak=   -3.196 closest distance to " O   HOH Z 313 " =    1.625
peak=   -3.195 closest distance to " CZ  TYR A 169 " =    1.737
peak=   -3.189 closest distance to " CG  PHE A 283 " =    2.692
peak=   -3.187 closest distance to " O   HOH Z 140 " =    1.511
peak=   -3.186 closest distance to " O   HOH Z 139 " =    5.189
peak=   -3.185 closest distance to " N   MET A 188 " =    1.915
peak=   -3.185 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.182 closest distance to " O   PRO A 198 " =    1.353
peak=   -3.181 closest distance to " O   HOH Z 265 " =    1.748
peak=   -3.180 closest distance to " CB  VAL A 296 " =    1.038
peak=   -3.179 closest distance to " O   HOH Z 380 " =    1.352
peak=   -3.179 closest distance to " O   HOH Z 372 " =    2.339
peak=   -3.175 closest distance to " O   HOH Z 313 " =    1.167
peak=   -3.174 closest distance to " O   HOH Z 232 " =    1.695
peak=   -3.171 closest distance to " N   HIS A 115 " =    2.168
peak=   -3.170 closest distance to " O   HOH Z 353 " =    2.130
peak=   -3.164 closest distance to " O   HOH Z 165 " =    1.924
peak=   -3.164 closest distance to " O   HOH Z 256 " =    1.386
peak=   -3.163 closest distance to " N   ASP A 171 " =    2.244
peak=   -3.161 closest distance to " CD  PRO A 243 " =    2.041
peak=   -3.159 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -3.157 closest distance to " CD2 PHE A 225 " =    1.108
peak=   -3.157 closest distance to " O   HOH Z 389 " =    1.463
peak=   -3.156 closest distance to " O   ALA A   1 " =    1.658
peak=   -3.148 closest distance to " ND2 ASN A 252 " =    1.905
peak=   -3.145 closest distance to " OG  SER A   3 " =    1.744
peak=   -3.145 closest distance to " O   HOH Z 252 " =    3.948
peak=   -3.138 closest distance to " OG  SER A 206 " =    1.702
peak=   -3.132 closest distance to " O   SER A 135 " =    1.448
peak=   -3.127 closest distance to " N   SER A   3 " =    2.069
peak=   -3.126 closest distance to " CA  ASP A  27 " =    2.491
peak=   -3.124 closest distance to " O   ALA A 227 " =    1.491
peak=   -3.121 closest distance to " CD2 PHE A  61 " =    2.014
peak=   -3.119 closest distance to " O   HOH Z 426 " =    1.702
peak=   -3.118 closest distance to " N   SER A 276 " =    1.332
peak=   -3.112 closest distance to " O   HOH Z  52 " =    1.560
peak=   -3.109 closest distance to " CB  ASN A  69 " =    1.275
peak=   -3.104 closest distance to " O   ARG A  24 " =    2.115
peak=   -3.100 closest distance to " O   HOH Z 350 " =    2.080
peak=   -3.099 closest distance to " CG1BVAL A  72 " =    2.316
peak=   -3.098 closest distance to " O   HOH Z 423 " =    2.082
peak=   -3.095 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.091 closest distance to " CA  PRO A 243 " =    2.253
peak=   -3.088 closest distance to " O   HOH Z 128 " =    2.479
peak=   -3.081 closest distance to " O   TRP A  70 " =    1.446
peak=   -3.075 closest distance to " O   ALA A  51 " =    1.327
peak=   -3.075 closest distance to " O   HOH Z 346 " =    1.797
peak=   -3.066 closest distance to " CG  PRO A 163 " =    2.604
peak=   -3.063 closest distance to " OE1 GLN A  77 " =    1.901
peak=   -3.054 closest distance to " CG1 VAL A  78 " =    2.638
peak=   -3.050 closest distance to " O   HOH Z 191 " =    3.292
peak=   -3.032 closest distance to " CG2 VAL A 202 " =    2.700
peak=   -3.028 closest distance to " O   HOH Z 357 " =    2.019

================= 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    :  0.4352 0.4199   6.232054e+00   6.197467e+00
   1_bss:  0.4272 0.4079   6.224647e+00   6.183111e+00
   1_xyz:  0.3177 0.3335   6.013236e+00   6.042255e+00
   1_adp:  0.2540 0.2877   5.824273e+00   5.927694e+00
   1_occ:  0.2535 0.2881   5.822906e+00   5.929678e+00
   2_bss:  0.2479 0.2834   5.820759e+00   5.925856e+00
   2_xyz:  0.1677 0.2080   5.467745e+00   5.638560e+00
   2_adp:  0.1515 0.1938   5.383832e+00   5.571985e+00
   2_occ:  0.1515 0.1936   5.383246e+00   5.571707e+00
   3_bss:  0.1504 0.1937   5.382846e+00   5.570775e+00
   3_xyz:  0.1259 0.1675   5.232274e+00   5.449068e+00
   3_adp:  0.1206 0.1648   5.205421e+00   5.434176e+00
   3_occ:  0.1205 0.1647   5.205560e+00   5.434568e+00
   4_bss:  0.1206 0.1644   5.205251e+00   5.433102e+00
   4_xyz:  0.1128 0.1586   5.156440e+00   5.401039e+00
   4_adp:  0.1121 0.1582   5.152327e+00   5.398467e+00
   4_occ:  0.1120 0.1582   5.151945e+00   5.398277e+00
   5_bss:  0.1120 0.1581   5.151944e+00   5.398301e+00
   5_xyz:  0.1128 0.1589   5.159595e+00   5.404411e+00
   5_adp:  0.1127 0.1588   5.158713e+00   5.402892e+00
   5_occ:  0.1127 0.1588   5.158602e+00   5.402850e+00
   5_bss:  0.1127 0.1588   5.158640e+00   5.402858e+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:  0.336  20.000   7.008   7.747  10.770   0.000   0.000   0.000
   1_xyz:  0.336  20.000   7.008   7.747  10.770   0.000   0.000   0.000
   1_adp:  0.336  20.000   7.008   7.747  10.770   0.000   0.000   0.000
   1_occ:  0.336  20.000   7.008   7.747  10.770   0.000   0.000   0.000
   2_bss:  0.328  44.949   3.590   3.978   7.021   0.000   0.000   0.000
   2_xyz:  0.328  44.949   3.590   3.978   7.021   0.000   0.000   0.000
   2_adp:  0.328  44.949   3.590   3.978   7.021   0.000   0.000   0.000
   2_occ:  0.328  44.949   3.590   3.978   7.021   0.000   0.000   0.000
   3_bss:  0.320  50.879   2.666   3.248   5.059   0.000   0.000   0.000
   3_xyz:  0.320  50.879   2.666   3.248   5.059   0.000   0.000   0.000
   3_adp:  0.320  50.879   2.666   3.248   5.059   0.000   0.000   0.000
   3_occ:  0.320  50.879   2.666   3.248   5.059   0.000   0.000   0.000
   4_bss:  0.329  53.477   2.609   3.123   4.708   0.000   0.000   0.000
   4_xyz:  0.329  53.477   2.609   3.123   4.708   0.000   0.000   0.000
   4_adp:  0.329  53.477   2.609   3.123   4.708   0.000   0.000   0.000
   4_occ:  0.329  53.477   2.609   3.123   4.708   0.000   0.000   0.000
   5_bss:  0.325  50.782   2.769   3.228   4.778   0.000   0.000   0.000
   5_xyz:  0.325  50.782   2.769   3.228   4.778   0.000   0.000   0.000
   5_adp:  0.325  50.782   2.769   3.228   4.778   0.000   0.000   0.000
   5_occ:  0.325  50.782   2.769   3.228   4.778   0.000   0.000   0.000
   5_bss:  0.325  54.415  -0.830  -0.354   1.183   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.897 0.5734  0.6396    50811.696
   1_bss:  45.446 0.5775  0.8345    48362.068
   1_xyz:  35.449 0.6958  0.9665    29905.825
   1_adp:  29.029 0.7691  1.0448    21526.643
   1_occ:  29.082 0.7685  1.0433    21602.940
   2_bss:  28.781 0.7717  0.9192    21259.647
   2_xyz:  19.895 0.8624  0.9990    10736.613
   2_adp:  18.103 0.8797  1.0129     9439.118
   2_occ:  18.089 0.8799  1.0130     9428.298
   3_bss:  18.028 0.8805  0.9699     9431.220
   3_xyz:  15.303 0.9043  0.9782     7246.140
   3_adp:  14.970 0.9073  0.9749     7027.171
   3_occ:  14.979 0.9072  0.9747     7028.401
   4_bss:  14.956 0.9074  0.9686     7003.576
   4_xyz:  14.249 0.9132  0.9733     6537.549
   4_adp:  14.168 0.9139  0.9707     6489.722
   4_occ:  14.162 0.9140  0.9706     6490.128
   5_bss:  14.163 0.9140  0.9745     6489.614
   5_xyz:  14.255 0.9133  0.9733     6578.388
   5_adp:  14.236 0.9135  0.9701     6563.089
   5_occ:  14.235 0.9135  0.9700     6561.435
   5_bss:  14.237 0.9135  0.9714     6561.872
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3962e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3962e+01
   1_xyz:   1.542  0.012  0.103 17.810  0.006  4.124   1.1997e-01
   1_adp:   1.542  0.012  0.103 17.810  0.006  4.124   1.1997e-01
   1_occ:   1.542  0.012  0.103 17.810  0.006  4.124   1.1997e-01
   2_bss:   1.542  0.012  0.103 17.810  0.006  4.124   1.1997e-01
   2_xyz:   1.007  0.007  0.077 16.121  0.004  4.125   6.3445e-02
   2_adp:   1.007  0.007  0.077 16.121  0.004  4.125   6.3445e-02
   2_occ:   1.007  0.007  0.077 16.121  0.004  4.125   6.3445e-02
   3_bss:   1.007  0.007  0.077 16.121  0.004  4.125   6.3445e-02
   3_xyz:   1.003  0.007  0.080 15.682  0.004  4.135   6.1470e-02
   3_adp:   1.003  0.007  0.080 15.682  0.004  4.135   6.1470e-02
   3_occ:   1.003  0.007  0.080 15.682  0.004  4.135   6.1470e-02
   4_bss:   1.003  0.007  0.080 15.682  0.004  4.135   6.1470e-02
   4_xyz:   1.083  0.009  0.089 15.654  0.004  4.113   7.2740e-02
   4_adp:   1.083  0.009  0.089 15.654  0.004  4.113   7.2740e-02
   4_occ:   1.083  0.009  0.089 15.654  0.004  4.113   7.2740e-02
   5_bss:   1.083  0.009  0.089 15.654  0.004  4.113   7.2740e-02
   5_xyz:   1.001  0.008  0.082 15.417  0.004  4.114   6.2844e-02
   5_adp:   1.001  0.008  0.082 15.417  0.004  4.114   6.2844e-02
   5_occ:   1.001  0.008  0.082 15.417  0.004  4.114   6.2844e-02
   5_bss:   1.001  0.008  0.082 15.417  0.004  4.114   6.2844e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9963e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9963e+00
   1_xyz:  13.082  0.139  0.400 88.333  0.035  2.197   8.9862e-02
   1_adp:  13.082  0.139  0.400 88.333  0.035  2.197   8.9862e-02
   1_occ:  13.082  0.139  0.400 88.333  0.035  2.197   8.9862e-02
   2_bss:  13.082  0.139  0.400 88.333  0.035  2.197   8.9862e-02
   2_xyz:   6.543  0.044  0.361 88.228  0.031  2.335   6.3418e-02
   2_adp:   6.543  0.044  0.361 88.228  0.031  2.335   6.3418e-02
   2_occ:   6.543  0.044  0.361 88.228  0.031  2.335   6.3418e-02
   3_bss:   6.543  0.044  0.361 88.228  0.031  2.335   6.3418e-02
   3_xyz:   6.292  0.042  0.517 82.228  0.037  2.322   4.4172e-02
   3_adp:   6.292  0.042  0.517 82.228  0.037  2.322   4.4172e-02
   3_occ:   6.292  0.042  0.517 82.228  0.037  2.322   4.4172e-02
   4_bss:   6.292  0.042  0.517 82.228  0.037  2.322   4.4172e-02
   4_xyz:   7.080  0.055  0.613 82.754  0.039  2.333   5.3795e-02
   4_adp:   7.080  0.055  0.613 82.754  0.039  2.333   5.3795e-02
   4_occ:   7.080  0.055  0.613 82.754  0.039  2.333   5.3795e-02
   5_bss:   7.080  0.055  0.613 82.754  0.039  2.333   5.3795e-02
   5_xyz:   6.473  0.052  0.519 82.609  0.037  2.355   4.1115e-02
   5_adp:   6.473  0.052  0.519 82.609  0.037  2.355   4.1115e-02
   5_occ:   6.473  0.052  0.519 82.609  0.037  2.355   4.1115e-02
   5_bss:   6.473  0.052  0.519 82.609  0.037  2.355   4.1115e-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:  58.56   0.00  10.87  53.80   0.00   7.79  58.56   0.00  27.59
   1_occ:  58.56   0.00  10.87  53.80   0.00   7.79  58.56   0.00  27.59
   2_bss:  58.56   0.00  10.87  53.80   0.00   7.79  58.56   0.00  27.59
   2_xyz:  58.56   0.00  10.87  53.80   0.00   7.79  58.56   0.00  27.59
   2_adp:  61.15   0.00  11.24  58.53   0.00   7.48  61.15   0.97  31.76
   2_occ:  61.15   0.00  11.24  58.53   0.00   7.48  61.15   0.97  31.76
   3_bss:  61.15   0.00  11.24  58.53   0.00   7.48  61.15   0.97  31.76
   3_xyz:  61.15   0.00  11.24  58.53   0.00   7.48  61.15   0.97  31.76
   3_adp:  70.07   0.00  11.74  70.07   0.00   7.54  67.50   0.28  34.63
   3_occ:  70.07   0.00  11.74  70.07   0.00   7.54  67.50   0.28  34.63
   4_bss:  70.07   0.00  11.74  70.07   0.00   7.54  67.50   0.28  34.63
   4_xyz:  70.07   0.00  11.74  70.07   0.00   7.54  67.50   0.28  34.63
   4_adp:  71.95   0.00  11.67  71.95   0.00   7.47  68.58   0.45  34.52
   4_occ:  71.95   0.00  11.67  71.95   0.00   7.47  68.58   0.45  34.52
   5_bss:  71.95   0.00  11.67  71.95   0.00   7.47  68.58   0.45  34.52
   5_xyz:  71.95   0.00  11.67  71.95   0.00   7.47  68.58   0.45  34.52
   5_adp:  74.23   0.00  11.53  74.23   0.00   7.38  69.50   0.49  34.10
   5_occ:  74.23   0.00  11.53  74.23   0.00   7.38  69.50   0.49  34.10
   5_bss:  77.86   3.63  15.16  77.86   3.63  11.01  73.13   4.12  37.73
------------------------------------------------------------------------
 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:    1.229    0.016    0.404
   1_adp:    1.229    0.016    0.404
   1_occ:    1.229    0.016    0.404
   2_bss:    1.229    0.016    0.404
   2_xyz:    1.611    0.029    0.510
   2_adp:    1.611    0.029    0.510
   2_occ:    1.611    0.029    0.510
   3_bss:    1.611    0.029    0.510
   3_xyz:    1.662    0.035    0.541
   3_adp:    1.662    0.035    0.541
   3_occ:    1.662    0.035    0.541
   4_bss:    1.662    0.035    0.541
   4_xyz:    1.735    0.023    0.558
   4_adp:    1.735    0.023    0.558
   4_occ:    1.735    0.023    0.558
   5_bss:    1.735    0.023    0.558
   5_xyz:    1.773    0.021    0.563
   5_adp:    1.773    0.021    0.563
   5_occ:    1.773    0.021    0.563
   5_bss:    1.773    0.021    0.563
------------------------------------------------------------------------

CPU time actual refinement: 330.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/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_547/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_547/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.53 
  Macro-tasks:
    bulk solvent and scale       = 41.43  
    individual site refinement   = 136.05 
    weights calculation          = 32.17  
    collect and process          = 6.63   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.40 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 100.57 
    alpha_beta                      = 8.31   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.62 
    fmodel                         = 7.28   
    r_factors                      = 0.15   
    phase_errors                   = 10.98  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 242.04 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.617 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    657 calls, 100.23 s
gradients_fft:          602 calls,  97.91 s

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

# Date 2008-01-16 Time 01:50:54 PST -0800 (1200477054.03 s)
Start R-work = 0.4352, R-free = 0.4199 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.4272, R-free = 0.4079
Final R-work = 0.1127, R-free = 0.1588