# Date 2008-01-16 Time 02:57:15 PST -0800 (1200481035.57 s)
#phil __OFF__

Command line arguments: "../1041.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4538
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1041

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 87.2539, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.01158
Completeness in resolution range: 0.973657
Completeness with d_max=infinity: 0.970617

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0116

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.01158
Completeness in resolution range: 0.973657
Completeness with d_max=infinity: 0.970617

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.3041 [2108/2132]  1898   210  10.0%
  bin  2:  4.3041 -  3.4292 [2032/2052]  1828   204  10.0%
  bin  3:  3.4292 -  2.9995 [2004/2023]  1802   202  10.1%
  bin  4:  2.9995 -  2.7270 [1986/2016]  1791   195   9.8%
  bin  5:  2.7270 -  2.5325 [1982/2001]  1784   198  10.0%
  bin  6:  2.5325 -  2.3838 [1957/1982]  1756   201  10.3%
  bin  7:  2.3838 -  2.2648 [1948/1976]  1754   194  10.0%
  bin  8:  2.2648 -  2.1665 [1953/1989]  1760   193   9.9%
  bin  9:  2.1665 -  2.0833 [1930/1972]  1738   192   9.9%
  bin 10:  2.0833 -  2.0116 [1689/1976]  1519   170  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 7
        2.42 -     3.04: 2169
        3.04 -     3.66: 4583
        3.66 -     4.28: 8894
        4.28 -     4.90: 12224
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.822 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 27872 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_1041/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/model_refine_001.geo

CPU time processing inputs: 9.40


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4451   r_free= 0.4313   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.242232                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.3693 0.3410      6.5466      6.4261|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.3407 0.3609       6.684      6.7392|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.3902 0.3671      6.5945      6.5908|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.4242 0.3755      6.4793      6.3745|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.4614 0.4435      6.3313      6.3606|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.4752 0.5217      6.2643       6.189|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.4949 0.4811      6.2095      6.2474|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.5021 0.4434       6.176      6.0999|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.4857 0.5048      6.0955      6.1234|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.5008 0.4936      6.1015       6.112|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.4941 0.4655       6.027       6.027|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.5005 0.4972      5.9825      5.9926|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.5157 0.4827      5.9014      5.8551|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.5075 0.4505      5.8521      5.7189|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8004  1378   152  0.75  30.15   0.80     0.77      55741.37|
|  2:  4.8004 -  3.8303  1314   147  0.77  28.71   0.90     0.81      76200.05|
|  3:  3.8303 -  3.3521  1294   143  0.70  35.47   0.85     0.77      81221.47|
|  4:  3.3521 -  3.0483  1277   146  0.62  41.85   0.83     0.69      74573.64|
|  5:  3.0483 -  2.8313  1287   142  0.53  49.29   0.75     0.60      65538.06|
|  6:  2.8313 -  2.6653  1277   139  0.49  52.51   0.75     0.55      60486.16|
|  7:  2.6653 -  2.5325  1276   140  0.45  55.65   0.73     0.51      56644.56|
|  8:  2.5325 -  2.4227  1244   142  0.44  57.12   0.75     0.50      52629.75|
|  9:  2.4227 -  2.3298  1266   139  0.45  56.00   0.73     0.50      47035.98|
| 10:  2.3298 -  2.2496  1253   143  0.46  55.44   0.76     0.51      42109.22|
| 11:  2.2496 -  2.1795  1251   133  0.45  56.08   0.75     0.52      39007.21|
| 12:  2.1795 -  2.1174  1244   141  0.44  56.91   0.76     0.52      36833.60|
| 13:  2.1174 -  2.0618  1266   141  0.45  56.16   0.73     0.53      31120.25|
| 14:  2.0618 -  2.0116  1003   111  0.53  49.86   0.72     0.55      22006.07|
|alpha:            min =        0.50 max =            0.81 mean =         0.60|
|beta:             min =    22006.07 max =        81221.47 mean =     53602.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.97 mean =        48.42|
|phase err.(test): min =        0.00 max =           90.00 mean =        48.42|
|-----------------------------------------------------------------------------|

============================== 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 = 8.899563              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.743   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.755303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.470   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1474 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2580 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3863 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4980 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6485 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7642 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.379 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.610 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4517   r_free= 0.4338   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.245570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4374   r_free= 0.4173   ksol= 0.34   Bsol= 40.20   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.20,7.67,9.06,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.236751                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.247742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.045   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.712509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.553   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4374      final r-factor (work) = 0.3283          |
| start r-factor (free) = 0.4173      final r-factor (free) = 0.3525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.1604 = 8.25 * 0.50 * 6.2516 + 1.00 * 54.3795                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2360 = 8.25 * 0.50 * 6.0886 + 1.00 * 0.1274                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3283      final r-factor (work) = 0.2729          |
| start r-factor (free) = 0.3525      final r-factor (free) = 0.3099          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3526 = 0.71 * 1.00 * 6.0886 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2437 = 0.71 * 1.00 * 5.9388 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.04   10.44    None  None   None       |
|    all(noH): 2823   0      0.00    70.04   10.44    None  None   None       |
|    Sol.    : 438    0      0.00    70.04   26.55    None  None   None       |
|    Mac.    : 2385   0      0.00    55.20   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 -   7.004: 1412   |   5:    35.020 -  42.024:   77        |
|      1:     7.004 -  14.008:  753   |   6:    42.024 -  49.029:   39        |
|      2:    14.008 -  21.012:  250   |   7:    49.029 -  56.033:   17        |
|      3:    21.012 -  28.016:  161   |   8:    56.033 -  63.037:    3        |
|      4:    28.016 -  35.020:  110   |   9:    63.037 -  70.041:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2729 r_free = 0.3099             target_work(ml) = 5.887         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2722 r_free = 0.3105             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2722   r_free= 0.3105   ksol= 0.34   Bsol= 40.20   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.20,7.67,9.06,0.00,0.00,0.00); trace/3= 8.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.885759                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2697   r_free= 0.3071   ksol= 0.32   Bsol= 52.93   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.19,4.76,5.98,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.887070                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.292771              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.574   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.412216              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.455  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.1749          |
| start r-factor (free) = 0.3071      final r-factor (free) = 0.2192          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8460 = 5.29 * 0.50 * 5.9396 + 1.00 * 0.1274                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1909 = 5.29 * 0.50 * 5.7120 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1749      final r-factor (work) = 0.1552          |
| start r-factor (free) = 0.2192      final r-factor (free) = 0.2018          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3778 = 0.41 * 1.00 * 5.7120 + 1.00 * 0.0232                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3223 = 0.41 * 1.00 * 5.4494 + 1.00 * 0.0759                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.69   11.15    None  None   None       |
|    all(noH): 2823   0      0.00    76.69   11.15    None  None   None       |
|    Sol.    : 438    0      0.00    68.37   32.14    None  None   None       |
|    Mac.    : 2385   0      0.00    76.69   7.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.669: 1650   |   5:    38.345 -  46.015:  115        |
|      1:     7.669 -  15.338:  573   |   6:    46.015 -  53.684:   55        |
|      2:    15.338 -  23.007:  176   |   7:    53.684 -  61.353:   15        |
|      3:    23.007 -  30.676:  117   |   8:    61.353 -  69.022:    2        |
|      4:    30.676 -  38.345:  119   |   9:    69.022 -  76.691:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1552 r_free = 0.2018             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1550 r_free = 0.2018             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1550   r_free= 0.2018   ksol= 0.32   Bsol= 52.93   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.19,4.76,5.98,0.00,0.00,0.00); trace/3= 5.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.409653                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1540   r_free= 0.2008   ksol= 0.33   Bsol= 60.95   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.54,4.69,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.409836                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.390836              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.700  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.422130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.163   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0615 = 4.39 * 0.50 * 5.4600 + 1.00 * 0.0746                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7651 = 4.39 * 0.50 * 5.3197 + 1.00 * 0.0862                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5794 = 1.42 * 1.00 * 5.3197 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4170 = 1.42 * 1.00 * 5.2053 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.27   11.84    None  None   None       |
|    all(noH): 2823   0      0.00    74.27   11.84    None  None   None       |
|    Sol.    : 438    0      0.00    73.33   35.63    None  None   None       |
|    Mac.    : 2385   0      0.00    74.27   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 -   7.427: 1609   |   5:    37.137 -  44.564:   75        |
|      1:     7.427 -  14.855:  595   |   6:    44.564 -  51.992:   91        |
|      2:    14.855 -  22.282:  166   |   7:    51.992 -  59.419:   54        |
|      3:    22.282 -  29.710:  101   |   8:    59.419 -  66.847:   21        |
|      4:    29.710 -  37.137:   98   |   9:    66.847 -  74.274:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1650             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1182 r_free = 0.1649             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1649   ksol= 0.33   Bsol= 60.95   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,3.54,4.69,0.00,0.00,0.00); trace/3= 3.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.193461                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1647   ksol= 0.33   Bsol= 60.95   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.36,4.51,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.192699                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.194898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.570  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.328569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.982  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7984 = 2.19 * 0.50 * 5.2050 + 1.00 * 0.0862                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7655 = 2.19 * 0.50 * 5.1914 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1173          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7200 = 0.33 * 1.00 * 5.1914 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7342 = 0.33 * 1.00 * 5.1920 + 1.00 * 0.0282                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.20   11.51    None  None   None       |
|    all(noH): 2823   0      0.00    75.20   11.51    None  None   None       |
|    Sol.    : 438    0      0.67    75.06   34.36    None  None   None       |
|    Mac.    : 2385   0      0.00    75.20   7.31     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 -   7.520: 1667   |   5:    37.598 -  45.118:   69        |
|      1:     7.520 -  15.039:  548   |   6:    45.118 -  52.637:   95        |
|      2:    15.039 -  22.559:  176   |   7:    52.637 -  60.157:   39        |
|      3:    22.559 -  30.078:  100   |   8:    60.157 -  67.676:   18        |
|      4:    30.078 -  37.598:  102   |   9:    67.676 -  75.196:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1173 r_free = 0.1631             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1631             target_work(ml) = 5.187         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1631   ksol= 0.33   Bsol= 60.95   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.36,4.51,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1630   ksol= 0.32   Bsol= 56.89   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.36,4.51,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.186494                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.396481              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.100  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.321720              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.812   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2890 = 2.40 * 0.50 * 5.1916 + 1.00 * 0.0682                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2759 = 2.40 * 0.50 * 5.1756 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0319 = 2.32 * 1.00 * 5.1756 + 1.00 * 0.0156                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0133 = 2.32 * 1.00 * 5.1680 + 1.00 * 0.0146                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.27   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    80.27   11.67    None  None   None       |
|    Sol.    : 438    0      0.40    77.60   35.13    None  None   None       |
|    Mac.    : 2385   0      0.00    80.27   7.36     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.027: 1712   |   5:    40.136 -  48.163:   80        |
|      1:     8.027 -  16.054:  527   |   6:    48.163 -  56.190:   71        |
|      2:    16.054 -  24.082:  153   |   7:    56.190 -  64.218:   33        |
|      3:    24.082 -  32.109:  113   |   8:    64.218 -  72.245:   14        |
|      4:    32.109 -  40.136:  112   |   9:    72.245 -  80.272:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1636             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1637             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1637   ksol= 0.32   Bsol= 56.89   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.36,4.51,0.00,0.00,0.00); trace/3= 3.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174510                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.0992 0.1353      5.3922      5.5339|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.0857 0.1116      5.4468       5.642|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.1051 0.1513      5.4851      5.8554|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.1192 0.1579      5.4612      5.6148|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.1344 0.1836      5.3571      5.5996|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.1229 0.2014       5.251      5.5308|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.1324 0.1641      5.2089      5.3841|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.1203 0.1808      5.1175      5.4059|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.1190 0.1814      5.0767      5.3177|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.1171 0.1790      5.0155      5.2904|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.1191 0.1824      4.9919      5.2794|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.1155 0.1883       4.919      5.2834|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.1183 0.1742      4.8453      5.0911|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.1099 0.1860      4.7306      4.9964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8004  1378   152  0.94   9.32   0.97     0.94       7509.19|
|  2:  4.8004 -  3.8303  1314   147  0.95   8.05   1.00     0.99       9340.00|
|  3:  3.8303 -  3.3521  1294   143  0.93  11.45   1.02     1.01      10743.24|
|  4:  3.3521 -  3.0483  1277   146  0.92  13.49   1.00     0.98      10503.92|
|  5:  3.0483 -  2.8313  1287   142  0.90  16.31   0.99     0.96       8920.54|
|  6:  2.8313 -  2.6653  1277   139  0.89  16.72   0.98     0.95       7894.77|
|  7:  2.6653 -  2.5325  1276   140  0.90  16.64   0.98     0.95       6835.88|
|  8:  2.5325 -  2.4227  1244   142  0.90  15.76   0.98     0.95       5892.66|
|  9:  2.4227 -  2.3298  1266   139  0.90  16.31   0.99     0.95       5614.92|
| 10:  2.3298 -  2.2496  1253   143  0.90  16.25   0.98     0.94       4883.08|
| 11:  2.2496 -  2.1795  1251   133  0.89  17.46   0.98     0.94       4883.83|
| 12:  2.1795 -  2.1174  1244   141  0.91  15.89   1.00     0.98       4310.83|
| 13:  2.1174 -  2.0618  1266   141  0.89  17.00   0.98     0.96       3781.56|
| 14:  2.0618 -  2.0116  1003   111  0.91  15.87   0.96     0.91       2965.28|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2965.28 max =        10743.24 mean =      6807.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.67|
|phase err.(test): min =        0.00 max =           89.36 mean =        14.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1637   ksol= 0.32   Bsol= 60.73   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.38,0.80,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174573                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1637   ksol= 0.32   Bsol= 60.73   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.38,0.80,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.174573                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.0992 0.1354      5.3926      5.5344|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.0857 0.1116      5.4469      5.6417|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.1051 0.1513      5.4849      5.8553|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.1191 0.1579      5.4612      5.6148|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.1344 0.1837      5.3572      5.5997|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.1229 0.2013       5.251      5.5305|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.1324 0.1640      5.2088      5.3839|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.1203 0.1808      5.1174       5.406|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.1190 0.1813      5.0768      5.3175|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.1171 0.1790      5.0157      5.2905|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.1191 0.1825      4.9921      5.2798|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.1155 0.1883      4.9192      5.2837|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.1183 0.1742      4.8453      5.0911|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.1100 0.1859      4.7306      4.9964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8004  1378   152  0.94   9.33   0.97     0.94       7516.14|
|  2:  4.8004 -  3.8303  1314   147  0.95   8.05   1.00     0.99       9342.56|
|  3:  3.8303 -  3.3521  1294   143  0.93  11.45   1.02     1.02      10739.23|
|  4:  3.3521 -  3.0483  1277   146  0.92  13.49   1.00     0.98      10503.88|
|  5:  3.0483 -  2.8313  1287   142  0.90  16.31   0.99     0.96       8919.03|
|  6:  2.8313 -  2.6653  1277   139  0.89  16.72   0.98     0.95       7894.28|
|  7:  2.6653 -  2.5325  1276   140  0.90  16.64   0.98     0.96       6833.61|
|  8:  2.5325 -  2.4227  1244   142  0.90  15.76   0.98     0.96       5891.48|
|  9:  2.4227 -  2.3298  1266   139  0.90  16.31   1.00     0.96       5613.37|
| 10:  2.3298 -  2.2496  1253   143  0.90  16.26   0.99     0.94       4884.85|
| 11:  2.2496 -  2.1795  1251   133  0.89  17.46   0.99     0.94       4886.37|
| 12:  2.1795 -  2.1174  1244   141  0.91  15.90   1.00     0.99       4313.18|
| 13:  2.1174 -  2.0618  1266   141  0.89  17.00   0.99     0.96       3782.28|
| 14:  2.0618 -  2.0116  1003   111  0.91  15.87   0.96     0.92       2965.38|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2965.38 max =        10739.23 mean =      6807.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.68|
|phase err.(test): min =        0.00 max =           89.36 mean =        14.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.85    84.12   15.51    None  None   None       |
|    all(noH): 2823   0      3.85    84.12   15.51    None  None   None       |
|    Sol.    : 438    0      4.24    81.45   38.98    None  None   None       |
|    Mac.    : 2385   0      3.85    84.12   11.20    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:     3.847 -  11.874: 1712   |   5:    43.983 -  52.010:   80        |
|      1:    11.874 -  19.901:  527   |   6:    52.010 -  60.037:   71        |
|      2:    19.901 -  27.928:  153   |   7:    60.037 -  68.064:   33        |
|      3:    27.928 -  35.955:  113   |   8:    68.064 -  76.091:   14        |
|      4:    35.955 -  43.983:  112   |   9:    76.091 -  84.119:    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)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.293 - 4.819
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 325
   mapped sites are within: 0.705 - 4.819

peak=    9.978 closest distance to " CG2 VAL A 230 " =    1.333
peak=    6.849 closest distance to " CG2 VAL A 296 " =    1.101
peak=    6.098 closest distance to " CG  LEU A   5 " =    1.160
peak=    6.079 closest distance to " O   HOH Z 111 " =    2.264
peak=    5.823 closest distance to " CG  LEU A 228 " =    1.155
peak=    5.645 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.310 closest distance to " CD2 LEU A   5 " =    1.139
peak=    5.087 closest distance to " O   HOH Z 232 " =    2.328
peak=    5.057 closest distance to " CB  VAL A 230 " =    1.201
peak=    5.048 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.947 closest distance to " NE2 GLN A  11 " =    1.147
peak=    4.710 closest distance to " CB  VAL A 296 " =    1.056
peak=    4.705 closest distance to " CB  SER A  63 " =    1.289
peak=    4.625 closest distance to " O   HOH Z 369 " =    2.140
peak=    4.541 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.493 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.458 closest distance to " O   HOH Z 265 " =    2.310
peak=    4.442 closest distance to " CG  PRO A 213 " =    1.188
peak=    4.391 closest distance to " C   PRO A 198 " =    1.576
peak=    4.344 closest distance to " O   HOH Z  78 " =    1.780
peak=    4.328 closest distance to " O   HOH Z 298 " =    1.901
peak=    4.315 closest distance to " O   HOH Z 126 " =    2.037
peak=    4.305 closest distance to " O   HOH Z 427 " =    3.141
peak=    4.302 closest distance to " O   HOH Z 368 " =    2.245
peak=    4.277 closest distance to " CB  ARG A 190 " =    1.607
peak=    4.256 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.228 closest distance to " O   HOH Z 303 " =    2.097
peak=    4.221 closest distance to " CB  GLU A 128 " =    1.092
peak=    4.219 closest distance to " CA  TYR A  30 " =    0.976
peak=    4.219 closest distance to " CB  TRP A 266 " =    1.001
peak=    4.215 closest distance to " CB  ASN A 148 " =    1.420
peak=    4.205 closest distance to " O   HOH Z 411 " =    3.800
peak=    4.201 closest distance to " CB  ASP A 124 " =    0.717
peak=    4.118 closest distance to " CB  ASP A 140 " =    1.020
peak=    4.113 closest distance to " CB  ARG A 275 " =    0.904
peak=    4.104 closest distance to " O   SER A  87 " =    2.297
peak=    4.097 closest distance to " CB  GLU A 277 " =    3.708
peak=    4.087 closest distance to " O   HOH Z 261 " =    2.013
peak=    4.059 closest distance to " NH1AARG A 145 " =    1.220
peak=    4.053 closest distance to " O   HOH Z 158 " =    3.142
peak=    4.034 closest distance to " CB  VAL A 202 " =    1.629
peak=    4.016 closest distance to " OD1 ASN A  69 " =    2.656
peak=    4.011 closest distance to " O   HOH Z 403 " =    1.637
peak=    3.999 closest distance to " O   HOH Z 423 " =    1.792
peak=    3.995 closest distance to " CD2 LEU A 228 " =    1.161
peak=    3.986 closest distance to " CB  ARG A  79 " =    1.486
peak=    3.963 closest distance to " O   HOH Z 234 " =    3.740
peak=    3.961 closest distance to " O   HOH Z 142 " =    1.563
peak=    3.954 closest distance to " CD ALYS A 290 " =    1.018
peak=    3.943 closest distance to " O   HOH Z 126 " =    1.615
peak=    3.932 closest distance to " CD  ARG A 159 " =    0.775
peak=    3.929 closest distance to " O   HOH Z 316 " =    3.169
peak=    3.922 closest distance to " O   HOH Z  43 " =    1.993
peak=    3.919 closest distance to " ND2 ASN A 187 " =    1.443
peak=    3.915 closest distance to " O   MET A 105 " =    1.876
peak=    3.909 closest distance to " O   HOH Z  19 " =    2.405
peak=    3.907 closest distance to " O   HOH Z 236 " =    1.957
peak=    3.906 closest distance to " O   HOH Z  61 " =    1.675
peak=    3.879 closest distance to " CB  VAL A 265 " =    1.274
peak=    3.870 closest distance to " CG  MET A 185 " =    1.246
peak=    3.859 closest distance to " CB  PRO A  54 " =    0.776
peak=    3.847 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.843 closest distance to " CA  ALA A  51 " =    0.969
peak=    3.837 closest distance to " OG  SER A  97 " =    3.078
peak=    3.795 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.791 closest distance to " ND2 ASN A 249 " =    1.875
peak=    3.790 closest distance to " O   HOH Z 280 " =    2.952
peak=    3.785 closest distance to " O   HOH Z 214 " =    2.184
peak=    3.784 closest distance to " O   HOH Z 425 " =    1.382
peak=    3.780 closest distance to " O   HOH Z 346 " =    1.622
peak=    3.763 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.752 closest distance to " CG1 VAL A 153 " =    0.976
peak=    3.733 closest distance to " O   HOH Z 180 " =    2.152
peak=    3.731 closest distance to " CE  LYS A  76 " =    0.854
peak=    3.730 closest distance to " O   HOH Z   9 " =    2.161
peak=    3.730 closest distance to " O   HOH Z 203 " =    1.806
peak=    3.715 closest distance to " O   HOH Z  80 " =    1.735
peak=    3.713 closest distance to " CB  ASN A  39 " =    0.929
peak=    3.710 closest distance to " CB  ALA A 104 " =    0.783
peak=    3.707 closest distance to " CB  ASN A 142 " =    1.119
peak=    3.697 closest distance to " CB  LEU A 228 " =    1.215
peak=    3.694 closest distance to " O   HOH Z 227 " =    1.756
peak=    3.689 closest distance to " CB BVAL A  41 " =    1.243
peak=    3.689 closest distance to " CA  ARG A 195 " =    1.223
peak=    3.688 closest distance to " CB  THR A  82 " =    1.392
peak=    3.688 closest distance to " CD  ARG A  66 " =    2.525
peak=    3.680 closest distance to " CB  LEU A 143 " =    1.214
peak=    3.677 closest distance to " CG1 ILE A  33 " =    1.271
peak=    3.677 closest distance to " CD  ARG A 269 " =    0.950
peak=    3.675 closest distance to " O   HOH Z 171 " =    3.841
peak=    3.673 closest distance to " O   HOH Z  21 " =    1.762
peak=    3.663 closest distance to " N   PHE A 130 " =    1.222
peak=    3.662 closest distance to " CG2 THR A 221 " =    1.129
peak=    3.658 closest distance to " CD1 LEU A 300 " =    1.212
peak=    3.653 closest distance to " CB  GLU A  46 " =    0.968
peak=    3.641 closest distance to " CB  SER A 212 " =    1.164
peak=    3.637 closest distance to " O   HOH Z 272 " =    1.912
peak=    3.634 closest distance to " CD1 LEU A  96 " =    0.711
peak=    3.624 closest distance to " N   ASN A  39 " =    1.312
peak=    3.623 closest distance to " O   HOH Z 422 " =    2.688
peak=    3.623 closest distance to " O   HOH Z 359 " =    1.450
peak=    3.622 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.620 closest distance to " O   HOH Z 285 " =    2.659
peak=    3.614 closest distance to " O   HOH Z 290 " =    1.007
peak=    3.612 closest distance to " CG1BVAL A  72 " =    1.783
peak=    3.612 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.612 closest distance to " O   HOH Z 193 " =    2.144
peak=    3.612 closest distance to " CB  SER A   3 " =    1.310
peak=    3.611 closest distance to " CG1 ILE A  49 " =    1.475
peak=    3.611 closest distance to " CZ  PHE A 192 " =    0.950
peak=    3.606 closest distance to " NE2 GLN A  77 " =    3.464
peak=    3.604 closest distance to " O   HOH Z 147 " =    1.749
peak=    3.603 closest distance to " CA  ALA A 291 " =    0.894
peak=    3.602 closest distance to " O   HOH Z 193 " =    1.905
peak=    3.601 closest distance to " O   HOH Z 406 " =    1.540
peak=    3.599 closest distance to " CE1 TYR A 186 " =    1.284
peak=    3.596 closest distance to " O   HOH Z 402 " =    1.462
peak=    3.591 closest distance to " O   HOH Z  63 " =    1.979
peak=    3.587 closest distance to " O   HOH Z 313 " =    1.784
peak=    3.583 closest distance to " OG BSER A 164 " =    2.196
peak=    3.580 closest distance to " O   HOH Z  88 " =    3.252
peak=    3.575 closest distance to " CB  LYS A 117 " =    1.217
peak=    3.568 closest distance to " CG2 VAL A 257 " =    0.835
peak=    3.567 closest distance to " O  BHOH Z 338 " =    2.320
peak=    3.554 closest distance to " CA  ASN A 215 " =    1.239
peak=    3.550 closest distance to " CA  ALA A 158 " =    1.217
peak=    3.550 closest distance to " O   HOH Z  20 " =    1.686
peak=    3.549 closest distance to " CA  THR A 221 " =    0.945
peak=    3.546 closest distance to " CB  TRP A 179 " =    1.445
peak=    3.545 closest distance to " O   HOH Z 133 " =    2.390
peak=    3.536 closest distance to " CA  ARG A  36 " =    1.144
peak=    3.535 closest distance to " O   GLN A 278 " =    1.335
peak=    3.534 closest distance to " CB  ALA A  34 " =    0.985
peak=    3.531 closest distance to " O   HOH Z 213 " =    1.837
peak=    3.526 closest distance to " CA  ALA A 295 " =    1.133
peak=    3.521 closest distance to " CB  THR A  31 " =    1.615
peak=    3.518 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.518 closest distance to " O   HOH Z 112 " =    1.667
peak=    3.517 closest distance to " CA  SER A  87 " =    1.006
peak=    3.516 closest distance to " CB  ALA A 291 " =    1.344
peak=    3.515 closest distance to " CD2 LEU A   5 " =    0.705
peak=    3.514 closest distance to " OG  SER A  22 " =    2.864
peak=    3.506 closest distance to " ND1 HIS A  81 " =    1.689
peak=    3.501 closest distance to " O   HOH Z 273 " =    2.808
peak=    3.496 closest distance to " O   HOH Z 371 " =    3.083
peak=    3.495 closest distance to " O   HOH Z 353 " =    2.640
peak=    3.494 closest distance to " O   HOH Z  68 " =    2.097
peak=    3.493 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.492 closest distance to " CD2 TRP A 179 " =    1.325
peak=    3.488 closest distance to " CA  ALA A 154 " =    0.993
peak=    3.486 closest distance to " O   HOH Z 197 " =    2.923
peak=    3.481 closest distance to " CB  MET A  40 " =    0.805
peak=    3.480 closest distance to " O   HOH Z 193 " =    1.733
peak=    3.480 closest distance to " O   ALA A 165 " =    1.505
peak=    3.479 closest distance to " CB  ASN A 187 " =    1.188
peak=    3.475 closest distance to " CA  TYR A  30 " =    1.065
peak=    3.475 closest distance to " CB  GLN A  89 " =    1.175
peak=    3.475 closest distance to " CA  VAL A 125 " =    1.244
peak=    3.463 closest distance to " CB  ARG A  79 " =    0.919
peak=    3.457 closest distance to " CA  MET A  40 " =    1.171
peak=    3.455 closest distance to " O   HOH Z 128 " =    2.215
peak=    3.451 closest distance to " O   HOH Z  48 " =    1.690
peak=    3.450 closest distance to " N   VAL A 126 " =    1.430
peak=    3.445 closest distance to " CD1 LEU A   5 " =    1.323
peak=    3.442 closest distance to " O   HOH Z 184 " =    1.393
peak=    3.437 closest distance to " O   HOH Z 248 " =    1.643
peak=    3.436 closest distance to " CB  THR A 157 " =    1.114
peak=    3.435 closest distance to " O   HOH Z 368 " =    3.614
peak=    3.434 closest distance to " CA  MET A 105 " =    1.012
peak=    3.432 closest distance to " CG1 VAL A 296 " =    1.234
peak=    3.432 closest distance to " CG BARG A 275 " =    1.513
peak=    3.432 closest distance to " O   HOH Z  97 " =    2.070
peak=    3.428 closest distance to " O   HOH Z 291 " =    1.625
peak=    3.424 closest distance to " O   HOH Z 325 " =    2.322
peak=    3.420 closest distance to " NE2 HIS A 207 " =    1.319
peak=    3.419 closest distance to " CZ  PHE A  38 " =    1.188
peak=    3.419 closest distance to " CB  HIS A 108 " =    0.794
peak=    3.418 closest distance to " N   SER A 135 " =    1.458
peak=    3.416 closest distance to " CD  ARG A  66 " =    2.330
peak=    3.410 closest distance to " NE  ARG A  79 " =    1.218
peak=    3.407 closest distance to " O   HOH Z 437 " =    1.591
peak=    3.395 closest distance to " CG  GLN A  88 " =    1.080
peak=    3.390 closest distance to " CB  ASN A 110 " =    1.197
peak=    3.385 closest distance to " O   HOH Z 245 " =    1.299
peak=    3.385 closest distance to " CG1 ILE A 151 " =    1.066
peak=    3.380 closest distance to " O   HOH Z 108 " =    2.715
peak=    3.379 closest distance to " CB  LEU A  83 " =    0.739
peak=    3.378 closest distance to " CB  TRP A 150 " =    1.355
peak=    3.377 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.376 closest distance to " O   HOH Z 172 " =    3.740
peak=    3.368 closest distance to " O   HOH Z 102 " =    1.332
peak=    3.366 closest distance to " O   TRP A 274 " =    1.864
peak=    3.363 closest distance to " NZ  LYS A  48 " =    1.404
peak=    3.358 closest distance to " CB  SER A 216 " =    0.865
peak=    3.357 closest distance to " O   HOH Z 238 " =    2.359
peak=    3.354 closest distance to " CZ3 TRP A 266 " =    1.125
peak=    3.353 closest distance to " O   HOH Z  10 " =    1.816
peak=    3.353 closest distance to " CG  MET A 185 " =    1.091
peak=    3.353 closest distance to " CG2 THR A 220 " =    0.893
peak=    3.351 closest distance to " O   HOH Z  44 " =    2.156
peak=    3.350 closest distance to " O   HOH Z 171 " =    2.240
peak=    3.345 closest distance to " O   ALA A 158 " =    1.379
peak=    3.336 closest distance to " CA  LYS A 181 " =    1.088
peak=    3.334 closest distance to " O   ASP A 124 " =    1.091
peak=    3.332 closest distance to " C   TYR A 214 " =    1.553
peak=    3.331 closest distance to " O   HOH Z 128 " =    2.222
peak=    3.331 closest distance to " O   HOH Z 403 " =    1.429
peak=    3.329 closest distance to " CB  TYR A 116 " =    0.858
peak=    3.325 closest distance to " O   HOH Z  97 " =    2.494
peak=    3.322 closest distance to " CB  ARG A 138 " =    1.000
peak=    3.320 closest distance to " CA  VAL A  41 " =    0.833
peak=    3.319 closest distance to " CB  SER A 273 " =    0.858
peak=    3.315 closest distance to " CB  ALA A 248 " =    1.135
peak=    3.308 closest distance to " O   HOH Z 133 " =    1.697
peak=    3.307 closest distance to " CG2 ILE A 151 " =    0.746
peak=    3.307 closest distance to " O   HOH Z 166 " =    3.618
peak=    3.306 closest distance to " O   HOH Z 305 " =    3.659
peak=    3.303 closest distance to " CD1 ILE A  33 " =    1.703
peak=    3.301 closest distance to " O   HOH Z 365 " =    2.957
peak=    3.299 closest distance to " O   HOH Z 247 " =    1.357
peak=    3.292 closest distance to " CA  ALA A 160 " =    0.916
peak=    3.291 closest distance to " NZ  LYS A 117 " =    3.263
peak=    3.289 closest distance to " CA  LEU A 282 " =    1.042
peak=    3.287 closest distance to " CB  ALA A 248 " =    1.415
peak=    3.266 closest distance to " CB  ALA A 242 " =    0.814
peak=    3.266 closest distance to " O   HOH Z 329 " =    4.007
peak=    3.262 closest distance to " O   HOH Z 109 " =    2.700
peak=    3.260 closest distance to " O   HOH Z  59 " =    2.328
peak=    3.249 closest distance to " O   HOH Z 313 " =    1.689
peak=    3.248 closest distance to " CG  ARG A 138 " =    1.134
peak=    3.248 closest distance to " CB  MET A  47 " =    1.032
peak=    3.245 closest distance to " CB  ARG A 139 " =    0.858
peak=    3.239 closest distance to " N   ASN A 127 " =    1.205
peak=    3.239 closest distance to " CA  TYR A 116 " =    1.468
peak=    3.236 closest distance to " CA  ASN A  74 " =    1.334
peak=    3.232 closest distance to " O   HOH Z 116 " =    1.907
peak=    3.227 closest distance to " O   HOH Z  62 " =    2.338
peak=    3.227 closest distance to " OH  TYR A 214 " =    1.209
peak=    3.225 closest distance to " CB  THR A  52 " =    0.826
peak=    3.221 closest distance to " CD1 ILE A 106 " =    0.988
peak=    3.221 closest distance to " O   HOH Z 145 " =    1.900
peak=    3.219 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.216 closest distance to " CB  ALA A   1 " =    4.819
peak=    3.215 closest distance to " CD1 ILE A 199 " =    0.788
peak=    3.214 closest distance to " O   GLN A  88 " =    1.664
peak=    3.213 closest distance to " CE  LYS A  48 " =    1.148
peak=    3.210 closest distance to " CA  ASN A 217 " =    1.282
peak=    3.206 closest distance to " CG  GLU A  37 " =    0.817
peak=    3.206 closest distance to " CA  SER A 146 " =    1.740
peak=    3.205 closest distance to " CG BARG A 102 " =    1.855
peak=    3.202 closest distance to " O   HOH Z 134 " =    1.268
peak=    3.199 closest distance to " O   HOH Z 141 " =    1.699
peak=    3.192 closest distance to " CG  ARG A 159 " =    0.992
peak=    3.190 closest distance to " O   HOH Z 435 " =    2.027
peak=    3.190 closest distance to " O   HOH Z 187 " =    2.304
peak=    3.187 closest distance to " CB  ASN A 224 " =    1.003
peak=    3.187 closest distance to " O   HOH Z 299 " =    4.235
peak=    3.186 closest distance to " CB  ILE A 120 " =    1.354
peak=    3.186 closest distance to " CA  GLY A 211 " =    1.361
peak=    3.185 closest distance to " O   HOH Z  88 " =    3.592
peak=    3.185 closest distance to " CA  ASN A 127 " =    1.067
peak=    3.184 closest distance to " O   HOH Z 384 " =    3.106
peak=    3.184 closest distance to " CB  TYR A 247 " =    0.957
peak=    3.182 closest distance to " O   HOH Z 294 " =    1.573
peak=    3.182 closest distance to " CB  GLN A 205 " =    1.044
peak=    3.180 closest distance to " O   HOH Z  49 " =    3.183
peak=    3.178 closest distance to " OG  SER A  62 " =    2.972
peak=    3.176 closest distance to " CB  GLN A 103 " =    1.062
peak=    3.174 closest distance to " CD2 HIS A  81 " =    0.856
peak=    3.173 closest distance to " OG BSER A 134 " =    2.875
peak=    3.168 closest distance to " O   HOH Z 302 " =    1.969
peak=    3.164 closest distance to " CG2 ILE A 234 " =    0.811
peak=    3.163 closest distance to " CB  ALA A 227 " =    1.018
peak=    3.163 closest distance to " O   LYS A 290 " =    2.449
peak=    3.162 closest distance to " O   GLU A   2 " =    1.581
peak=    3.160 closest distance to " OD1 ASN A 217 " =    1.616
peak=    3.159 closest distance to " CA  ASP A 140 " =    1.247
peak=    3.158 closest distance to " CA  ALA A 233 " =    1.571
peak=    3.158 closest distance to " N   ASP A 162 " =    1.249
peak=    3.155 closest distance to " CZ3 TRP A 274 " =    4.670
peak=    3.153 closest distance to " O   HOH Z 425 " =    1.935
peak=    3.150 closest distance to " CD  ARG A 219 " =    1.093
peak=    3.142 closest distance to " CA  ARG A 102 " =    1.184
peak=    3.139 closest distance to " CA  ASP A 191 " =    0.814
peak=    3.136 closest distance to " O   HOH Z 132 " =    3.222
peak=    3.135 closest distance to " O   ASN A  74 " =    1.569
peak=    3.131 closest distance to " CE2 TYR A  30 " =    0.872
peak=    3.130 closest distance to " O   HOH Z 426 " =    1.569
peak=    3.129 closest distance to " CB  ALA A 100 " =    1.250
peak=    3.129 closest distance to " O   THR A 220 " =    1.210
peak=    3.127 closest distance to " N   SER A  12 " =    1.639
peak=    3.125 closest distance to " CB  LEU A  96 " =    1.260
peak=    3.124 closest distance to " ND1 HIS A  86 " =    1.693
peak=    3.121 closest distance to " O   HOH Z 344 " =    3.054
peak=    3.116 closest distance to " CA  LYS A 290 " =    1.230
peak=    3.109 closest distance to " N   GLN A 278 " =    1.133
peak=    3.109 closest distance to " CB  PHE A 204 " =    0.939
peak=    3.108 closest distance to " CA  ILE A 106 " =    0.777
peak=    3.103 closest distance to " O   HOH Z 350 " =    1.669
peak=    3.100 closest distance to " O   HOH Z  89 " =    1.732
peak=    3.099 closest distance to " N   TYR A  15 " =    0.832
peak=    3.093 closest distance to " O   HOH Z 163 " =    1.584
peak=    3.093 closest distance to " C   ALA A 299 " =    0.953
peak=    3.086 closest distance to " O   HOH Z 391 " =    2.957
peak=    3.085 closest distance to " O   HOH Z 295 " =    1.493
peak=    3.080 closest distance to " O   HOH Z 271 " =    2.116
peak=    3.074 closest distance to " CE2 TYR A 186 " =    0.867
peak=    3.074 closest distance to " CB  PRO A 243 " =    1.473
peak=    3.071 closest distance to " CB  LYS A 193 " =    1.050
peak=    3.069 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.059 closest distance to " O   HOH Z 201 " =    3.060
peak=    3.047 closest distance to " CB  ALA A 114 " =    1.221
peak=    3.035 closest distance to " CG  ARG A 269 " =    1.788
peak=    3.033 closest distance to " C   ASN A  39 " =    1.089
peak=    3.021 closest distance to " O   HOH Z 172 " =    4.015
peak=    3.015 closest distance to " O   HOH Z 134 " =    2.613

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.708 - 5.595
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.708 - 5.595

peak=   -5.026 closest distance to " CG2 VAL A 230 " =    0.840
peak=   -4.441 closest distance to " CG1 VAL A 112 " =    2.653
peak=   -4.440 closest distance to " CD  GLN A  58 " =    1.023
peak=   -4.416 closest distance to " CD  ARG A 156 " =    2.069
peak=   -4.362 closest distance to " O   HOH Z 266 " =    5.328
peak=   -4.332 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.293 closest distance to " CD  ARG A  14 " =    3.284
peak=   -4.099 closest distance to " OE1 GLN A 223 " =    2.107
peak=   -4.052 closest distance to " O   HOH Z  73 " =    2.184
peak=   -4.044 closest distance to " O   HOH Z 196 " =    2.231
peak=   -4.005 closest distance to " CA  ASP A 298 " =    1.032
peak=   -4.003 closest distance to " CG1 VAL A 250 " =    2.751
peak=   -4.001 closest distance to " CB  ALA A 161 " =    2.617
peak=   -3.941 closest distance to " CG2 ILE A  49 " =    2.792
peak=   -3.936 closest distance to " O   HOH Z  52 " =    1.590
peak=   -3.891 closest distance to " OG  SER A  97 " =    2.312
peak=   -3.870 closest distance to " CE2 TYR A  30 " =    2.717
peak=   -3.865 closest distance to " OG BSER A 134 " =    1.251
peak=   -3.855 closest distance to " C   HIS A 108 " =    1.162
peak=   -3.847 closest distance to " OD1 ASN A 148 " =    1.440
peak=   -3.842 closest distance to " O   HOH Z 231 " =    2.194
peak=   -3.839 closest distance to " NH2AARG A 275 " =    5.399
peak=   -3.829 closest distance to " O   HOH Z 166 " =    1.931
peak=   -3.817 closest distance to " CA  GLY A 241 " =    3.164
peak=   -3.800 closest distance to " O   VAL A  67 " =    2.742
peak=   -3.796 closest distance to " CG  ARG A 269 " =    2.418
peak=   -3.774 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -3.772 closest distance to " C   ALA A 158 " =    1.293
peak=   -3.768 closest distance to " N   ALA A  43 " =    2.589
peak=   -3.764 closest distance to " CG1 VAL A 112 " =    2.927
peak=   -3.734 closest distance to " O   VAL A  67 " =    2.705
peak=   -3.729 closest distance to " O   VAL A 189 " =    2.639
peak=   -3.719 closest distance to " CG1 VAL A 296 " =    1.410
peak=   -3.718 closest distance to " NE2 GLN A  88 " =    2.085
peak=   -3.714 closest distance to " OXT GLY A 302 " =    3.020
peak=   -3.704 closest distance to " CG2 VAL A 296 " =    1.312
peak=   -3.688 closest distance to " CG  HIS A  86 " =    1.038
peak=   -3.686 closest distance to " O   HOH Z 435 " =    2.736
peak=   -3.681 closest distance to " OG  SER A  87 " =    1.566
peak=   -3.670 closest distance to " O   HOH Z 351 " =    1.551
peak=   -3.658 closest distance to " O   HOH Z 211 " =    1.439
peak=   -3.653 closest distance to " O   HOH Z 114 " =    3.062
peak=   -3.647 closest distance to " O   HOH Z  11 " =    1.893
peak=   -3.645 closest distance to " CA  GLY A 241 " =    2.323
peak=   -3.644 closest distance to " O   HOH Z  38 " =    1.481
peak=   -3.630 closest distance to " CB  PHE A 192 " =    1.989
peak=   -3.625 closest distance to " O   HOH Z 394 " =    1.583
peak=   -3.622 closest distance to " O   HOH Z  10 " =    1.504
peak=   -3.607 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.606 closest distance to " O   HOH Z 426 " =    1.680
peak=   -3.603 closest distance to " O   HOH Z 103 " =    1.862
peak=   -3.592 closest distance to " CG  TRP A 266 " =    1.823
peak=   -3.590 closest distance to " O   HOH Z 185 " =    2.358
peak=   -3.586 closest distance to " CD2 LEU A 300 " =    2.737
peak=   -3.584 closest distance to " O   HOH Z 290 " =    1.314
peak=   -3.579 closest distance to " O   HOH Z 407 " =    3.221
peak=   -3.575 closest distance to " O   HOH Z 389 " =    1.986
peak=   -3.564 closest distance to " C   GLY A  17 " =    1.294
peak=   -3.560 closest distance to " CE3 TRP A 150 " =    2.204
peak=   -3.553 closest distance to " CB  ALA A 248 " =    2.410
peak=   -3.548 closest distance to " O   HOH Z 353 " =    2.126
peak=   -3.546 closest distance to " CD2 LEU A 167 " =    1.787
peak=   -3.542 closest distance to " CD2 TYR A 293 " =    2.059
peak=   -3.540 closest distance to " O   SER A 271 " =    2.138
peak=   -3.538 closest distance to " CD1 LEU A 101 " =    2.485
peak=   -3.534 closest distance to " O   PRO A 163 " =    2.217
peak=   -3.520 closest distance to " NE2 GLN A 194 " =    1.876
peak=   -3.519 closest distance to " O   GLY A 203 " =    2.324
peak=   -3.515 closest distance to " CA  GLY A 203 " =    2.441
peak=   -3.514 closest distance to " CD2 PHE A  61 " =    2.543
peak=   -3.492 closest distance to " N   ALA A 226 " =    2.206
peak=   -3.490 closest distance to " CD1 LEU A 228 " =    2.372
peak=   -3.486 closest distance to " CB  VAL A 230 " =    1.061
peak=   -3.477 closest distance to " O   HOH Z 292 " =    4.695
peak=   -3.461 closest distance to " C   LEU A 143 " =    1.092
peak=   -3.458 closest distance to " O   HOH Z  60 " =    2.111
peak=   -3.453 closest distance to " CB  ALA A  43 " =    2.627
peak=   -3.447 closest distance to " CE  MET A 105 " =    2.284
peak=   -3.443 closest distance to " CG  LEU A 101 " =    2.478
peak=   -3.438 closest distance to " O   HOH Z 350 " =    1.815
peak=   -3.437 closest distance to " CA  GLY A 133 " =    2.328
peak=   -3.437 closest distance to " O   HOH Z 275 " =    1.524
peak=   -3.434 closest distance to " CB  ALA A 248 " =    2.137
peak=   -3.427 closest distance to " O   GLY A  80 " =    2.603
peak=   -3.427 closest distance to " CD  PRO A 213 " =    2.194
peak=   -3.421 closest distance to " O   HOH Z 377 " =    2.077
peak=   -3.420 closest distance to " ND2 ASN A  45 " =    1.149
peak=   -3.417 closest distance to " CG2 ILE A 263 " =    2.443
peak=   -3.409 closest distance to " O   HOH Z  19 " =    2.382
peak=   -3.407 closest distance to " N   ASN A  60 " =    1.282
peak=   -3.407 closest distance to " O   HOH Z 216 " =    1.654
peak=   -3.395 closest distance to " O   HOH Z 393 " =    1.449
peak=   -3.386 closest distance to " C   ASN A 187 " =    1.805
peak=   -3.378 closest distance to " CG  GLU A 277 " =    1.142
peak=   -3.377 closest distance to " NH2 ARG A  79 " =    1.569
peak=   -3.374 closest distance to " O   HOH Z 128 " =    2.622
peak=   -3.371 closest distance to " CE BMET A  47 " =    2.048
peak=   -3.367 closest distance to " O   HOH Z 243 " =    1.963
peak=   -3.366 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.365 closest distance to " O   HOH Z 117 " =    4.572
peak=   -3.363 closest distance to " O   HOH Z 102 " =    1.593
peak=   -3.360 closest distance to " CG1 VAL A 197 " =    2.289
peak=   -3.354 closest distance to " O   HOH Z  44 " =    2.163
peak=   -3.352 closest distance to " O   HOH Z 113 " =    2.367
peak=   -3.347 closest distance to " O   ASP A  27 " =    2.116
peak=   -3.347 closest distance to " O   HOH Z  43 " =    1.726
peak=   -3.344 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.336 closest distance to " N   THR A  52 " =    1.645
peak=   -3.330 closest distance to " N   THR A 157 " =    1.557
peak=   -3.330 closest distance to " NE2 GLN A 103 " =    1.790
peak=   -3.327 closest distance to " O   GLY A 211 " =    1.421
peak=   -3.327 closest distance to " C   LEU A 222 " =    0.870
peak=   -3.326 closest distance to " CB  ASP A 132 " =    2.319
peak=   -3.324 closest distance to " NH2 ARG A  79 " =    2.069
peak=   -3.324 closest distance to " O   PRO A 198 " =    1.248
peak=   -3.324 closest distance to " CD1 ILE A 239 " =    2.122
peak=   -3.323 closest distance to " O   HOH Z 222 " =    1.518
peak=   -3.321 closest distance to " N   SER A 276 " =    1.407
peak=   -3.320 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.318 closest distance to " CD1 TYR A 247 " =    2.887
peak=   -3.313 closest distance to " ND2 ASN A  45 " =    1.440
peak=   -3.313 closest distance to " O   HOH Z  13 " =    1.489
peak=   -3.310 closest distance to " O   HOH Z 139 " =    3.032
peak=   -3.309 closest distance to " O   HOH Z 241 " =    1.309
peak=   -3.306 closest distance to " CG  PRO A 163 " =    2.401
peak=   -3.298 closest distance to " O   HOH Z 123 " =    2.524
peak=   -3.294 closest distance to " CD1 ILE A 151 " =    2.401
peak=   -3.288 closest distance to " O   HOH Z  17 " =    1.586
peak=   -3.285 closest distance to " CD1 TYR A 247 " =    2.299
peak=   -3.284 closest distance to " C   MET A 188 " =    1.406
peak=   -3.282 closest distance to " O   HOH Z 106 " =    1.880
peak=   -3.280 closest distance to " CB  PRO A 163 " =    2.573
peak=   -3.278 closest distance to " CD1 PHE A  59 " =    1.969
peak=   -3.272 closest distance to " ND2 ASN A 187 " =    1.582
peak=   -3.269 closest distance to " O   HOH Z 359 " =    3.036
peak=   -3.260 closest distance to " O   HOH Z   6 " =    1.636
peak=   -3.255 closest distance to " CZ  PHE A 192 " =    2.889
peak=   -3.254 closest distance to " OE1 GLN A  88 " =    1.027
peak=   -3.253 closest distance to " CB  ALA A  10 " =    2.264
peak=   -3.252 closest distance to " O   HOH Z 232 " =    1.765
peak=   -3.251 closest distance to " O   HOH Z 174 " =    2.534
peak=   -3.246 closest distance to " OD2 ASP A  50 " =    2.326
peak=   -3.244 closest distance to " ND2 ASN A  60 " =    1.389
peak=   -3.244 closest distance to " O   LEU A 101 " =    2.872
peak=   -3.243 closest distance to " OH  TYR A 169 " =    0.946
peak=   -3.240 closest distance to " OE1 GLN A 223 " =    2.197
peak=   -3.237 closest distance to " OD1 ASN A 187 " =    1.585
peak=   -3.237 closest distance to " N   ALA A 248 " =    1.812
peak=   -3.234 closest distance to " OG  SER A 206 " =    1.798
peak=   -3.233 closest distance to " CD  ARG A 195 " =    5.080
peak=   -3.233 closest distance to " CG2 VAL A 112 " =    2.543
peak=   -3.231 closest distance to " O   HOH Z 166 " =    1.625
peak=   -3.228 closest distance to " C   ASN A 285 " =    2.457
peak=   -3.227 closest distance to " CD2 PHE A  61 " =    2.027
peak=   -3.226 closest distance to " O   GLY A 196 " =    1.262
peak=   -3.223 closest distance to " CH2 TRP A 177 " =    2.210
peak=   -3.215 closest distance to " O   HOH Z 134 " =    2.712
peak=   -3.211 closest distance to " OH  TYR A 214 " =    1.247
peak=   -3.210 closest distance to " O   HOH Z 313 " =    1.165
peak=   -3.210 closest distance to " ND2 ASN A  69 " =    1.831
peak=   -3.209 closest distance to " O   HOH Z 298 " =    2.796
peak=   -3.209 closest distance to " CA  ASN A 127 " =    1.115
peak=   -3.204 closest distance to " CG2 VAL A 189 " =    2.097
peak=   -3.198 closest distance to " CG1 VAL A 125 " =    1.963
peak=   -3.196 closest distance to " O   HOH Z 252 " =    3.990
peak=   -3.194 closest distance to " OG  SER A  63 " =    1.244
peak=   -3.192 closest distance to " CG  ARG A 269 " =    2.064
peak=   -3.192 closest distance to " O   HOH Z 265 " =    2.387
peak=   -3.192 closest distance to " O   MET A  40 " =    2.812
peak=   -3.191 closest distance to " O   ALA A  10 " =    1.740
peak=   -3.190 closest distance to " CE3 TRP A  70 " =    1.796
peak=   -3.189 closest distance to " O   HOH Z 357 " =    2.249
peak=   -3.188 closest distance to " CB  ALA A 291 " =    2.317
peak=   -3.186 closest distance to " O   HOH Z  90 " =    1.641
peak=   -3.178 closest distance to " CD  GLN A 223 " =    0.708
peak=   -3.175 closest distance to " O   HOH Z 396 " =    1.891
peak=   -3.175 closest distance to " O   HOH Z 234 " =    4.426
peak=   -3.170 closest distance to " O   HOH Z 285 " =    1.732
peak=   -3.170 closest distance to " CA  SER A 135 " =    1.348
peak=   -3.168 closest distance to " O   HOH Z  60 " =    2.012
peak=   -3.166 closest distance to " CB  TRP A  85 " =    2.534
peak=   -3.165 closest distance to " CG1 VAL A  67 " =    2.842
peak=   -3.165 closest distance to " CG2BVAL A  41 " =    1.761
peak=   -3.164 closest distance to " OD2 ASP A 171 " =    1.859
peak=   -3.159 closest distance to " CD  GLN A 223 " =    1.558
peak=   -3.157 closest distance to " NH2 ARG A  66 " =    2.124
peak=   -3.155 closest distance to " O   LEU A 167 " =    1.510
peak=   -3.152 closest distance to " O   HOH Z 311 " =    3.851
peak=   -3.147 closest distance to " OG BSER A 134 " =    1.869
peak=   -3.145 closest distance to " CG  ASN A 252 " =    1.547
peak=   -3.138 closest distance to " O   HOH Z 177 " =    1.776
peak=   -3.137 closest distance to " OG BSER A 210 " =    1.499
peak=   -3.135 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.132 closest distance to " O   HOH Z 191 " =    5.595
peak=   -3.129 closest distance to " O   HOH Z 193 " =    1.749
peak=   -3.121 closest distance to " O   HOH Z 409 " =    4.724
peak=   -3.119 closest distance to " N   SER A   3 " =    2.102
peak=   -3.114 closest distance to " O   HOH Z 174 " =    3.146
peak=   -3.112 closest distance to " O   SER A 276 " =    1.734
peak=   -3.111 closest distance to " O   ASN A 301 " =    1.433
peak=   -3.106 closest distance to " N   ALA A 248 " =    2.533
peak=   -3.106 closest distance to " O   HOH Z  77 " =    1.928
peak=   -3.090 closest distance to " OE1 GLN A  77 " =    1.953
peak=   -3.067 closest distance to " O   VAL A 125 " =    2.316
peak=   -3.063 closest distance to " O   ALA A 180 " =    1.430
peak=   -3.062 closest distance to " CD2 TYR A 247 " =    2.250
peak=   -3.060 closest distance to " O   HOH Z 184 " =    1.559
peak=   -3.048 closest distance to " CG  PRO A 163 " =    2.295
peak=   -3.039 closest distance to " O   PRO A 198 " =    1.413
peak=   -3.029 closest distance to " O   HOH Z 176 " =    0.846

================= 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    :  0.4451 0.4313   6.242232e+00   6.215906e+00
   1_bss:  0.4374 0.4173   6.236751e+00   6.204624e+00
   1_xyz:  0.3283 0.3525   6.040290e+00   6.087088e+00
   1_adp:  0.2729 0.3099   5.886953e+00   5.993498e+00
   1_occ:  0.2722 0.3105   5.885759e+00   5.994556e+00
   2_bss:  0.2697 0.3071   5.887070e+00   5.992615e+00
   2_xyz:  0.1749 0.2192   5.509202e+00   5.685869e+00
   2_adp:  0.1552 0.2018   5.410063e+00   5.607827e+00
   2_occ:  0.1550 0.2018   5.409653e+00   5.607829e+00
   3_bss:  0.1540 0.2008   5.409836e+00   5.607761e+00
   3_xyz:  0.1242 0.1690   5.227188e+00   5.458846e+00
   3_adp:  0.1182 0.1650   5.193446e+00   5.436539e+00
   3_occ:  0.1182 0.1649   5.193461e+00   5.436810e+00
   4_bss:  0.1183 0.1647   5.192699e+00   5.434553e+00
   4_xyz:  0.1172 0.1646   5.190774e+00   5.431667e+00
   4_adp:  0.1173 0.1631   5.186978e+00   5.423302e+00
   4_occ:  0.1173 0.1631   5.186618e+00   5.423219e+00
   5_bss:  0.1172 0.1630   5.186494e+00   5.423161e+00
   5_xyz:  0.1144 0.1622   5.172423e+00   5.417586e+00
   5_adp:  0.1137 0.1636   5.174356e+00   5.424985e+00
   5_occ:  0.1137 0.1637   5.174510e+00   5.425332e+00
   5_bss:  0.1137 0.1637   5.174573e+00   5.425354e+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:  0.337  40.200   8.199   7.667   9.056   0.000   0.000   0.000
   1_xyz:  0.337  40.200   8.199   7.667   9.056   0.000   0.000   0.000
   1_adp:  0.337  40.200   8.199   7.667   9.056   0.000   0.000   0.000
   1_occ:  0.337  40.200   8.199   7.667   9.056   0.000   0.000   0.000
   2_bss:  0.321  52.928   5.187   4.764   5.981   0.000   0.000   0.000
   2_xyz:  0.321  52.928   5.187   4.764   5.981   0.000   0.000   0.000
   2_adp:  0.321  52.928   5.187   4.764   5.981   0.000   0.000   0.000
   2_occ:  0.321  52.928   5.187   4.764   5.981   0.000   0.000   0.000
   3_bss:  0.332  60.952   3.575   3.544   4.689   0.000   0.000   0.000
   3_xyz:  0.332  60.952   3.575   3.544   4.689   0.000   0.000   0.000
   3_adp:  0.332  60.952   3.575   3.544   4.689   0.000   0.000   0.000
   3_occ:  0.332  60.952   3.575   3.544   4.689   0.000   0.000   0.000
   4_bss:  0.332  60.952   3.323   3.358   4.507   0.000   0.000   0.000
   4_xyz:  0.332  60.952   3.323   3.358   4.507   0.000   0.000   0.000
   4_adp:  0.332  60.952   3.323   3.358   4.507   0.000   0.000   0.000
   4_occ:  0.332  60.952   3.323   3.358   4.507   0.000   0.000   0.000
   5_bss:  0.324  56.886   3.323   3.358   4.507   0.000   0.000   0.000
   5_xyz:  0.324  56.886   3.323   3.358   4.507   0.000   0.000   0.000
   5_adp:  0.324  56.886   3.323   3.358   4.507   0.000   0.000   0.000
   5_occ:  0.324  56.886   3.323   3.358   4.507   0.000   0.000   0.000
   5_bss:  0.324  60.733  -0.426  -0.375   0.801   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.418 0.5415  0.5971    53605.259
   1_bss:  47.713 0.5492  0.7788    51512.254
   1_xyz:  38.914 0.6547  0.8995    34846.310
   1_adp:  32.368 0.7317  0.9839    25947.075
   1_occ:  32.415 0.7311  0.9828    25990.738
   2_bss:  32.329 0.7320  0.8841    25889.172
   2_xyz:  21.026 0.8516  0.9936    11979.838
   2_adp:  18.851 0.8730  1.0083    10127.415
   2_occ:  18.854 0.8729  1.0080    10129.012
   3_bss:  18.844 0.8731  0.9588    10134.857
   3_xyz:  15.396 0.9035  0.9746     7325.784
   3_adp:  14.905 0.9078  0.9744     6987.020
   3_occ:  14.910 0.9077  0.9742     6989.186
   4_bss:  14.895 0.9077  0.9662     6940.859
   4_xyz:  14.737 0.9095  0.9654     6873.158
   4_adp:  14.532 0.9112  0.9633     6774.153
   4_occ:  14.531 0.9112  0.9633     6772.472
   5_bss:  14.532 0.9112  0.9632     6768.466
   5_xyz:  14.443 0.9119  0.9640     6721.910
   5_adp:  14.621 0.9105  0.9592     6804.748
   5_occ:  14.626 0.9104  0.9591     6807.527
   5_bss:  14.627 0.9104  0.9631     6807.988
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4379e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4379e+01
   1_xyz:   1.590  0.012  0.105 18.004  0.006  4.113   1.2743e-01
   1_adp:   1.590  0.012  0.105 18.004  0.006  4.113   1.2743e-01
   1_occ:   1.590  0.012  0.105 18.004  0.006  4.113   1.2743e-01
   2_bss:   1.590  0.012  0.105 18.004  0.006  4.113   1.2743e-01
   2_xyz:   1.112  0.009  0.079 16.614  0.004  4.136   7.4598e-02
   2_adp:   1.112  0.009  0.079 16.614  0.004  4.136   7.4598e-02
   2_occ:   1.112  0.009  0.079 16.614  0.004  4.136   7.4598e-02
   3_bss:   1.112  0.009  0.079 16.614  0.004  4.136   7.4598e-02
   3_xyz:   1.182  0.011  0.094 16.227  0.004  4.115   8.6172e-02
   3_adp:   1.182  0.011  0.094 16.227  0.004  4.115   8.6172e-02
   3_occ:   1.182  0.011  0.094 16.227  0.004  4.115   8.6172e-02
   4_bss:   1.182  0.011  0.094 16.227  0.004  4.115   8.6172e-02
   4_xyz:   1.040  0.009  0.083 15.750  0.004  4.116   6.8205e-02
   4_adp:   1.040  0.009  0.083 15.750  0.004  4.116   6.8205e-02
   4_occ:   1.040  0.009  0.083 15.750  0.004  4.116   6.8205e-02
   5_bss:   1.040  0.009  0.083 15.750  0.004  4.116   6.8205e-02
   5_xyz:   1.086  0.010  0.088 15.717  0.004  4.119   7.4316e-02
   5_adp:   1.086  0.010  0.088 15.717  0.004  4.119   7.4316e-02
   5_occ:   1.086  0.010  0.088 15.717  0.004  4.119   7.4316e-02
   5_bss:   1.086  0.010  0.088 15.717  0.004  4.119   7.4316e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0513e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0513e+00
   1_xyz:  12.931  0.150  0.409 85.133  0.037  2.297   9.7519e-02
   1_adp:  12.931  0.150  0.409 85.133  0.037  2.297   9.7519e-02
   1_occ:  12.931  0.150  0.409 85.133  0.037  2.297   9.7519e-02
   2_bss:  12.931  0.150  0.409 85.133  0.037  2.297   9.7519e-02
   2_xyz:   7.416  0.055  0.291 86.869  0.039  2.309   6.3490e-02
   2_adp:   7.416  0.055  0.291 86.869  0.039  2.309   6.3490e-02
   2_occ:   7.416  0.055  0.291 86.869  0.039  2.309   6.3490e-02
   3_bss:   7.416  0.055  0.291 86.869  0.039  2.309   6.3490e-02
   3_xyz:   7.561  0.054  0.654 83.118  0.042  2.300   5.7235e-02
   3_adp:   7.561  0.054  0.654 83.118  0.042  2.300   5.7235e-02
   3_occ:   7.561  0.054  0.654 83.118  0.042  2.300   5.7235e-02
   4_bss:   7.561  0.054  0.654 83.118  0.042  2.300   5.7235e-02
   4_xyz:   7.964  0.043  0.515 82.500  0.039  2.373   4.2231e-02
   4_adp:   7.964  0.043  0.515 82.500  0.039  2.373   4.2231e-02
   4_occ:   7.964  0.043  0.515 82.500  0.039  2.373   4.2231e-02
   5_bss:   7.964  0.043  0.515 82.500  0.039  2.373   4.2231e-02
   5_xyz:   7.662  0.047  0.568 82.528  0.039  2.355   5.2115e-02
   5_adp:   7.662  0.047  0.568 82.528  0.039  2.355   5.2115e-02
   5_occ:   7.662  0.047  0.568 82.528  0.039  2.355   5.2115e-02
   5_bss:   7.662  0.047  0.568 82.528  0.039  2.355   5.2115e-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:  70.04   0.00  10.44  55.20   0.00   7.48  70.04   0.00  26.55
   1_occ:  70.04   0.00  10.44  55.20   0.00   7.48  70.04   0.00  26.55
   2_bss:  70.04   0.00  10.44  55.20   0.00   7.48  70.04   0.00  26.55
   2_xyz:  70.04   0.00  10.44  55.20   0.00   7.48  70.04   0.00  26.55
   2_adp:  76.69   0.00  11.15  76.69   0.00   7.30  68.37   0.00  32.14
   2_occ:  76.69   0.00  11.15  76.69   0.00   7.30  68.37   0.00  32.14
   3_bss:  76.69   0.00  11.15  76.69   0.00   7.30  68.37   0.00  32.14
   3_xyz:  76.69   0.00  11.15  76.69   0.00   7.30  68.37   0.00  32.14
   3_adp:  74.27   0.00  11.84  74.27   0.00   7.47  73.33   0.00  35.63
   3_occ:  74.27   0.00  11.84  74.27   0.00   7.47  73.33   0.00  35.63
   4_bss:  74.27   0.00  11.84  74.27   0.00   7.47  73.33   0.00  35.63
   4_xyz:  74.27   0.00  11.84  74.27   0.00   7.47  73.33   0.00  35.63
   4_adp:  75.20   0.00  11.51  75.20   0.00   7.31  75.06   0.67  34.36
   4_occ:  75.20   0.00  11.51  75.20   0.00   7.31  75.06   0.67  34.36
   5_bss:  75.20   0.00  11.51  75.20   0.00   7.31  75.06   0.67  34.36
   5_xyz:  75.20   0.00  11.51  75.20   0.00   7.31  75.06   0.67  34.36
   5_adp:  80.27   0.00  11.67  80.27   0.00   7.36  77.60   0.40  35.13
   5_occ:  80.27   0.00  11.67  80.27   0.00   7.36  77.60   0.40  35.13
   5_bss:  84.12   3.85  15.51  84.12   3.85  11.20  81.45   4.24  38.98
------------------------------------------------------------------------
 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:    1.226    0.014    0.408
   1_adp:    1.226    0.014    0.408
   1_occ:    1.226    0.014    0.408
   2_bss:    1.226    0.014    0.408
   2_xyz:    1.497    0.036    0.543
   2_adp:    1.497    0.036    0.543
   2_occ:    1.497    0.036    0.543
   3_bss:    1.497    0.036    0.543
   3_xyz:    1.393    0.045    0.580
   3_adp:    1.393    0.045    0.580
   3_occ:    1.393    0.045    0.580
   4_bss:    1.393    0.045    0.580
   4_xyz:    1.520    0.033    0.590
   4_adp:    1.520    0.033    0.590
   4_occ:    1.520    0.033    0.590
   5_bss:    1.520    0.033    0.590
   5_xyz:    1.519    0.039    0.599
   5_adp:    1.519    0.039    0.599
   5_occ:    1.519    0.039    0.599
   5_bss:    1.519    0.039    0.599
------------------------------------------------------------------------

CPU time actual refinement: 328.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/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_1041/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1041/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.87 
  Macro-tasks:
    bulk solvent and scale       = 37.69  
    individual site refinement   = 138.92 
    weights calculation          = 31.39  
    collect and process          = 6.52   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 214.67 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 100.72 
    alpha_beta                      = 8.29   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 112.76 
    fmodel                         = 6.57   
    r_factors                      = 0.20   
    phase_errors                   = 10.63  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 242.43 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.572 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    663 calls, 100.31 s
gradients_fft:          609 calls,  98.67 s

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

# Date 2008-01-16 Time 03:02:57 PST -0800 (1200481377.23 s)
Start R-work = 0.4451, R-free = 0.4313 (no bulk solvent and anisotropic scale)
Final R-work = 0.1303, R-free = 0.1786 (no bulk solvent and anisotropic scale)

Start R-work = 0.4374, R-free = 0.4173
Final R-work = 0.1137, R-free = 0.1637