# Date 2008-01-16 Time 01:09:30 PST -0800 (1200474570.29 s)
#phil __OFF__

Command line arguments: "../299.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30975
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 299

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.93, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97047
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.968602

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7691
                             d_min =   1.9705

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7691 1.97047
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.968602

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7695 -  4.2154 [2114/2141]  1903   211  10.0%
  bin  2:  4.2154 -  3.3589 [2031/2047]  1827   204  10.0%
  bin  3:  3.3589 -  2.9381 [2014/2033]  1811   203  10.1%
  bin  4:  2.9381 -  2.6712 [1983/2013]  1791   192   9.7%
  bin  5:  2.6712 -  2.4807 [1969/1988]  1768   201  10.2%
  bin  6:  2.4807 -  2.3350 [1964/2000]  1769   195   9.9%
  bin  7:  2.3350 -  2.2185 [1957/1990]  1763   194   9.9%
  bin  8:  2.2185 -  2.1222 [1943/1978]  1745   198  10.2%
  bin  9:  2.1222 -  2.0407 [1939/1966]  1745   194  10.0%
  bin 10:  2.0407 -  1.9705 [1675/2004]  1508   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 14
        2.14 -     2.83: 975
        2.83 -     3.52: 4484
        3.52 -     4.21: 9470
        4.21 -     4.90: 13769
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.449 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.708 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.721 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.731 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28707 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_299/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.93 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4528   r_free= 0.4472   ksol= 0.00   Bsol= 0.00   scale= 0.821    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.249424                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1374  153 0.3747 0.3621      6.5391      6.5494|
|  2:  4.7012 -  3.7516 0.99   1322  146 0.3655 0.3595      6.7042      6.7135|
|  3:  3.7516 -  3.2833 0.99   1299  146 0.3939 0.3765      6.6083      6.6632|
|  4:  3.2833 -  2.9859 0.99   1284  138 0.4227 0.4322      6.4735        6.44|
|  5:  2.9859 -  2.7733 0.99   1276  143 0.4632 0.4986      6.3484      6.3602|
|  6:  2.7733 -  2.6108 0.99   1278  146 0.4814 0.5077      6.2678      6.2449|
|  7:  2.6108 -  2.4807 0.99   1267  139 0.4927 0.4845      6.2341      6.1452|
|  8:  2.4807 -  2.3731 0.98   1270  142 0.4963 0.4752      6.1761       6.159|
|  9:  2.3731 -  2.2821 0.98   1259  139 0.5100 0.5077      6.1056      6.1219|
| 10:  2.2821 -  2.2036 0.98   1247  136 0.5055 0.5010      6.1131      6.0675|
| 11:  2.2036 -  2.1349 1.00   1266  147 0.5170 0.4939      6.0424      6.0664|
| 12:  2.1349 -  2.0741 0.97   1254  128 0.5042 0.4812      5.9755      5.9978|
| 13:  2.0741 -  2.0196 0.98   1239  138 0.5311 0.5471      5.9036      5.8916|
| 14:  2.0196 -  1.9705 0.79    995  118 0.5127 0.4706      5.8423      5.7446|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.7012  1374   153  0.69  35.06   0.81     0.71      71016.09|
|  2:  4.7012 -  3.7516  1322   146  0.73  33.01   0.91     0.79      93266.53|
|  3:  3.7516 -  3.2833  1299   146  0.65  39.58   0.88     0.77      97292.55|
|  4:  3.2833 -  2.9859  1284   138  0.59  45.03   0.84     0.68      85047.93|
|  5:  2.9859 -  2.7733  1276   143  0.49  52.36   0.76     0.59      73530.38|
|  6:  2.7733 -  2.6108  1278   146  0.47  54.47   0.75     0.54      63338.90|
|  7:  2.6108 -  2.4807  1267   139  0.45  55.92   0.75     0.52      58889.59|
|  8:  2.4807 -  2.3731  1270   142  0.46  55.38   0.76     0.52      51076.00|
|  9:  2.3731 -  2.2821  1259   139  0.44  56.62   0.75     0.53      47055.56|
| 10:  2.2821 -  2.2036  1247   136  0.47  54.72   0.78     0.54      41330.19|
| 11:  2.2036 -  2.1349  1266   147  0.43  57.40   0.77     0.53      40502.32|
| 12:  2.1349 -  2.0741  1254   128  0.41  59.57   0.76     0.50      39462.65|
| 13:  2.0741 -  2.0196  1239   138  0.35  63.87   0.76     0.43      36041.30|
| 14:  2.0196 -  1.9705   995   118  0.35  64.02   0.75     0.38      29041.91|
|alpha:            min =        0.38 max =            0.79 mean =         0.58|
|beta:             min =    29041.91 max =        97292.55 mean =     59886.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.96 mean =        51.52|
|phase err.(test): min =        0.00 max =           89.99 mean =        51.78|
|-----------------------------------------------------------------------------|

============================== 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 = 9.880417              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.779   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.836890              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.385   (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 |  0.978 -  1.371:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.371 -  1.763:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.763 -  2.155:       81 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.155 -  2.547:      499 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.547 -  2.939:     1311 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.939 -  3.331:     2454 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.331 -  3.723:     4003 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.723 -  4.116:     5286 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.116 -  4.508:     6890 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.508 -  4.900:     8217 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.110 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.978 |       2.178 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4605   r_free= 0.4530   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.253406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4445   r_free= 0.4361   ksol= 0.36   Bsol= 14.09   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.84,7.89,8.90,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.241872                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.931102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.236   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.839619              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.481   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4445      final r-factor (work) = 0.3489          |
| start r-factor (free) = 0.4361      final r-factor (free) = 0.3702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.0529 = 8.93 * 0.50 * 6.2573 + 1.00 * 53.1105                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4914 = 8.93 * 0.50 * 6.1270 + 1.00 * 0.1308                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3489      final r-factor (work) = 0.2916          |
| start r-factor (free) = 0.3702      final r-factor (free) = 0.3330          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1587 = 0.84 * 1.00 * 6.1270 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0419 = 0.84 * 1.00 * 5.9878 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.01   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    78.01   11.68    None  None   None       |
|    Sol.    : 438    0      0.00    78.01   27.80    None  None   None       |
|    Mac.    : 2385   0      0.00    74.44   8.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.801: 1417   |   5:    39.003 -  46.803:   58        |
|      1:     7.801 -  15.601:  710   |   6:    46.803 -  54.604:   42        |
|      2:    15.601 -  23.402:  280   |   7:    54.604 -  62.404:   12        |
|      3:    23.402 -  31.202:  180   |   8:    62.404 -  70.205:    4        |
|      4:    31.202 -  39.003:  118   |   9:    70.205 -  78.005:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2916 r_free = 0.3330             target_work(ml) = 5.944         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2911 r_free = 0.3329             target_work(ml) = 5.943         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2911   r_free= 0.3329   ksol= 0.36   Bsol= 14.09   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.84,7.89,8.90,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.942939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2867   r_free= 0.3280   ksol= 0.34   Bsol= 27.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.35,4.26,5.85,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.941279                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.359555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.364187              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.524  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2867      final r-factor (work) = 0.2001          |
| start r-factor (free) = 0.3280      final r-factor (free) = 0.2428          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1872 = 3.36 * 0.50 * 5.9867 + 1.00 * 0.1308                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7794 = 3.36 * 0.50 * 5.7846 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2001      final r-factor (work) = 0.1791          |
| start r-factor (free) = 0.2428      final r-factor (free) = 0.2202          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1229 = 0.36 * 1.00 * 5.7846 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0396 = 0.36 * 1.00 * 5.5707 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.96   11.92    None  None   None       |
|    all(noH): 2823   0      0.00    78.96   11.92    None  None   None       |
|    Sol.    : 438    0      1.14    78.96   32.29    None  None   None       |
|    Mac.    : 2385   0      0.00    78.36   8.18     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 -   7.896: 1573   |   5:    39.479 -  47.375:   93        |
|      1:     7.896 -  15.792:  611   |   6:    47.375 -  55.271:   57        |
|      2:    15.792 -  23.687:  202   |   7:    55.271 -  63.166:   14        |
|      3:    23.687 -  31.583:  127   |   8:    63.166 -  71.062:    6        |
|      4:    31.583 -  39.479:  137   |   9:    71.062 -  78.958:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1791 r_free = 0.2202             target_work(ml) = 5.527         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1786 r_free = 0.2197             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1786   r_free= 0.2197   ksol= 0.34   Bsol= 27.00   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.35,4.26,5.85,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.525177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1770   r_free= 0.2184   ksol= 0.32   Bsol= 32.73   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,3.18,4.11,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.522115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.733074              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.925   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.229687              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.359  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1770      final r-factor (work) = 0.1335          |
| start r-factor (free) = 0.2184      final r-factor (free) = 0.1742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6862 = 2.73 * 0.50 * 5.5789 + 1.00 * 0.0625                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4342 = 2.73 * 0.50 * 5.3961 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1335      final r-factor (work) = 0.1271          |
| start r-factor (free) = 0.1742      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2500 = 0.23 * 1.00 * 5.3961 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2170 = 0.23 * 1.00 * 5.2521 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.47   11.91    None  None   None       |
|    all(noH): 2823   0      0.00    82.47   11.91    None  None   None       |
|    Sol.    : 438    0      1.99    69.62   33.50    None  None   None       |
|    Mac.    : 2385   0      0.00    82.47   7.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.247: 1688   |   5:    41.237 -  49.484:   90        |
|      1:     8.247 -  16.495:  571   |   6:    49.484 -  57.732:   54        |
|      2:    16.495 -  24.742:  145   |   7:    57.732 -  65.979:   16        |
|      3:    24.742 -  32.990:  121   |   8:    65.979 -  74.226:    3        |
|      4:    32.990 -  41.237:  133   |   9:    74.226 -  82.474:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1271 r_free = 0.1657             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1269 r_free = 0.1656             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1269   r_free= 0.1656   ksol= 0.32   Bsol= 32.73   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,3.18,4.11,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.225177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1654   ksol= 0.32   Bsol= 32.73   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.80,3.48,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.226183                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.404097              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.421  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.222971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.360  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7492 = 1.40 * 0.50 * 5.2546 + 1.00 * 0.0602                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7011 = 1.40 * 0.50 * 5.1983 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1705 = 0.22 * 1.00 * 5.1983 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1620 = 0.22 * 1.00 * 5.1692 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.28   11.86    None  None   None       |
|    all(noH): 2823   0      0.00    83.28   11.86    None  None   None       |
|    Sol.    : 438    0      1.34    67.50   33.31    None  None   None       |
|    Mac.    : 2385   0      0.00    83.28   7.92     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.328: 1684   |   5:    41.640 -  49.968:   87        |
|      1:     8.328 -  16.656:  591   |   6:    49.968 -  58.296:   50        |
|      2:    16.656 -  24.984:  136   |   7:    58.296 -  66.624:   13        |
|      3:    24.984 -  33.312:  130   |   8:    66.624 -  74.952:    5        |
|      4:    33.312 -  41.640:  125   |   9:    74.952 -  83.280:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1576             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1170 r_free = 0.1576             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1576   ksol= 0.32   Bsol= 32.73   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.80,3.48,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168001                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1170   r_free= 0.1576   ksol= 0.32   Bsol= 33.42   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.03,2.74,3.36,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167906                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.495836              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.308  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.269960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.614  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1555          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9175 = 1.50 * 0.50 * 5.1688 + 1.00 * 0.0517                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9078 = 1.50 * 0.50 * 5.1526 + 1.00 * 0.0541                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4004 = 0.27 * 1.00 * 5.1526 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3976 = 0.27 * 1.00 * 5.1415 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.46   11.82    None  None   None       |
|    all(noH): 2823   0      0.00    83.46   11.82    None  None   None       |
|    Sol.    : 438    0      1.42    67.72   33.31    None  None   None       |
|    Mac.    : 2385   0      0.00    83.46   7.88     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 -   8.347: 1698   |   5:    41.732 -  50.079:   86        |
|      1:     8.347 -  16.693:  577   |   6:    50.079 -  58.425:   48        |
|      2:    16.693 -  25.039:  138   |   7:    58.425 -  66.772:   13        |
|      3:    25.039 -  33.386:  129   |   8:    66.772 -  75.118:    5        |
|      4:    33.386 -  41.732:  127   |   9:    75.118 -  83.465:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1557             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1557             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1557   ksol= 0.32   Bsol= 33.42   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.03,2.74,3.36,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1374  153 0.1028 0.1275      5.4083      5.5303|
|  2:  4.7012 -  3.7516 0.99   1322  146 0.0875 0.1104       5.446      5.6161|
|  3:  3.7516 -  3.2833 0.99   1299  146 0.1059 0.1497       5.466      5.8395|
|  4:  3.2833 -  2.9859 0.99   1284  138 0.1209 0.1521      5.4468      5.5928|
|  5:  2.9859 -  2.7733 0.99   1276  143 0.1283 0.1643      5.3091      5.4814|
|  6:  2.7733 -  2.6108 0.99   1278  146 0.1243 0.1826      5.2177      5.4535|
|  7:  2.6108 -  2.4807 0.99   1267  139 0.1226 0.1624      5.1541      5.3569|
|  8:  2.4807 -  2.3731 0.98   1270  142 0.1195 0.1751      5.0919      5.3647|
|  9:  2.3731 -  2.2821 0.98   1259  139 0.1193 0.1776      5.0253      5.2489|
| 10:  2.2821 -  2.2036 0.98   1247  136 0.1136 0.1677      4.9699       5.204|
| 11:  2.2036 -  2.1349 1.00   1266  147 0.1143 0.1689      4.9169      5.2657|
| 12:  2.1349 -  2.0741 0.97   1254  128 0.1109 0.1676      4.8624      5.1431|
| 13:  2.0741 -  2.0196 0.98   1239  138 0.1179 0.1649       4.805      5.0338|
| 14:  2.0196 -  1.9705 0.79    995  118 0.1122 0.1827      4.7163      4.9794|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.7012  1374   153  0.94   9.19   0.99     0.96       7279.11|
|  2:  4.7012 -  3.7516  1322   146  0.96   7.69   1.02     1.01       8764.45|
|  3:  3.7516 -  3.2833  1299   146  0.94  10.99   1.03     1.02       9944.88|
|  4:  3.2833 -  2.9859  1284   138  0.93  12.76   1.01     1.00       9733.04|
|  5:  2.9859 -  2.7733  1276   143  0.91  15.15   0.99     0.96       7777.29|
|  6:  2.7733 -  2.6108  1278   146  0.90  15.55   0.98     0.95       6795.19|
|  7:  2.6108 -  2.4807  1267   139  0.91  15.36   0.99     0.96       6035.02|
|  8:  2.4807 -  2.3731  1270   142  0.91  15.05   1.00     0.98       5403.52|
|  9:  2.3731 -  2.2821  1259   139  0.91  15.29   1.01     0.99       4863.59|
| 10:  2.2821 -  2.2036  1247   136  0.91  15.14   1.01     0.98       4348.38|
| 11:  2.2036 -  2.1349  1266   147  0.91  15.29   1.00     0.97       4057.34|
| 12:  2.1349 -  2.0741  1254   128  0.92  14.61   1.02     1.00       3733.09|
| 13:  2.0741 -  2.0196  1239   138  0.91  15.56   1.01     1.00       3318.66|
| 14:  2.0196 -  1.9705   995   118  0.91  15.45   1.00     0.96       2766.17|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2766.17 max =         9944.88 mean =      6145.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.71|
|phase err.(test): min =        0.00 max =           87.19 mean =        13.23|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1557   ksol= 0.32   Bsol= 36.19   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,0.03,0.65,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142229                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.77 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1557   ksol= 0.32   Bsol= 36.19   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,0.03,0.65,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142229                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7695 -  4.7012 0.99   1374  153 0.1029 0.1275      5.4086      5.5308|
|  2:  4.7012 -  3.7516 0.99   1322  146 0.0875 0.1104      5.4461      5.6159|
|  3:  3.7516 -  3.2833 0.99   1299  146 0.1059 0.1497       5.466      5.8394|
|  4:  3.2833 -  2.9859 0.99   1284  138 0.1209 0.1521      5.4467      5.5928|
|  5:  2.9859 -  2.7733 0.99   1276  143 0.1283 0.1643      5.3091      5.4814|
|  6:  2.7733 -  2.6108 0.99   1278  146 0.1243 0.1826      5.2177      5.4535|
|  7:  2.6108 -  2.4807 0.99   1267  139 0.1226 0.1624      5.1541      5.3569|
|  8:  2.4807 -  2.3731 0.98   1270  142 0.1195 0.1751      5.0918      5.3647|
|  9:  2.3731 -  2.2821 0.98   1259  139 0.1193 0.1776      5.0253      5.2489|
| 10:  2.2821 -  2.2036 0.98   1247  136 0.1136 0.1677      4.9699       5.204|
| 11:  2.2036 -  2.1349 1.00   1266  147 0.1143 0.1689       4.917      5.2658|
| 12:  2.1349 -  2.0741 0.97   1254  128 0.1109 0.1676      4.8625      5.1432|
| 13:  2.0741 -  2.0196 0.98   1239  138 0.1179 0.1649       4.805      5.0339|
| 14:  2.0196 -  1.9705 0.79    995  118 0.1122 0.1827      4.7163      4.9794|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7695 -  4.7012  1374   153  0.94   9.19   0.99     0.96       7285.15|
|  2:  4.7012 -  3.7516  1322   146  0.95   7.69   1.03     1.01       8767.11|
|  3:  3.7516 -  3.2833  1299   146  0.94  10.99   1.03     1.03       9943.88|
|  4:  3.2833 -  2.9859  1284   138  0.93  12.76   1.01     1.01       9732.44|
|  5:  2.9859 -  2.7733  1276   143  0.91  15.15   1.00     0.96       7776.26|
|  6:  2.7733 -  2.6108  1278   146  0.90  15.55   0.98     0.95       6794.76|
|  7:  2.6108 -  2.4807  1267   139  0.91  15.36   0.99     0.96       6034.54|
|  8:  2.4807 -  2.3731  1270   142  0.91  15.05   1.00     0.98       5403.32|
|  9:  2.3731 -  2.2821  1259   139  0.91  15.29   1.01     1.00       4863.47|
| 10:  2.2821 -  2.2036  1247   136  0.91  15.14   1.02     0.99       4348.62|
| 11:  2.2036 -  2.1349  1266   147  0.91  15.29   1.01     0.98       4057.64|
| 12:  2.1349 -  2.0741  1254   128  0.92  14.61   1.02     1.01       3733.39|
| 13:  2.0741 -  2.0196  1239   138  0.91  15.56   1.02     1.00       3318.72|
| 14:  2.0196 -  1.9705   995   118  0.91  15.45   1.00     0.97       2766.04|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2766.04 max =         9943.88 mean =      6146.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.71|
|phase err.(test): min =        0.00 max =           87.19 mean =        13.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.541)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.77    86.24   14.59    None  None   None       |
|    all(noH): 2823   0      2.77    86.24   14.59    None  None   None       |
|    Sol.    : 438    0      4.19    70.50   36.08    None  None   None       |
|    Mac.    : 2385   0      2.77    86.24   10.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.773 -  11.119: 1698   |   5:    44.505 -  52.852:   86        |
|      1:    11.119 -  19.466:  577   |   6:    52.852 -  61.198:   48        |
|      2:    19.466 -  27.812:  138   |   7:    61.198 -  69.545:   13        |
|      3:    27.812 -  36.159:  129   |   8:    69.545 -  77.891:    5        |
|      4:    36.159 -  44.505:  127   |   9:    77.891 -  86.238:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 5.823
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 317
   mapped sites are within: 0.713 - 5.823

peak=   11.229 closest distance to " CB  VAL A 230 " =    1.459
peak=    8.874 closest distance to " CG2 VAL A 296 " =    1.283
peak=    6.049 closest distance to " CG  LEU A   5 " =    1.245
peak=    5.962 closest distance to " CD2 LEU A   5 " =    1.233
peak=    5.557 closest distance to " O   HOH Z 193 " =    1.759
peak=    5.267 closest distance to " O   HOH Z 142 " =    1.837
peak=    5.196 closest distance to " O   HOH Z 126 " =    1.972
peak=    5.158 closest distance to " NE2 GLN A  11 " =    1.097
peak=    5.107 closest distance to " CB  ARG A 275 " =    0.966
peak=    5.061 closest distance to " CG  PRO A  54 " =    1.301
peak=    5.026 closest distance to " CB  GLN A 223 " =    1.426
peak=    4.983 closest distance to " O   HOH Z 124 " =    1.534
peak=    4.906 closest distance to " NH2 ARG A  56 " =    2.043
peak=    4.904 closest distance to " CG  LEU A 228 " =    1.210
peak=    4.855 closest distance to " O   HOH Z 402 " =    1.441
peak=    4.851 closest distance to " CB  GLN A 183 " =    1.274
peak=    4.823 closest distance to " CB  VAL A 296 " =    1.020
peak=    4.786 closest distance to " CG  PRO A 213 " =    1.304
peak=    4.778 closest distance to " O   HOH Z 272 " =    1.891
peak=    4.759 closest distance to " CB  SER A  63 " =    1.203
peak=    4.714 closest distance to " O   HOH Z 232 " =    2.320
peak=    4.649 closest distance to " CB  SER A   3 " =    1.301
peak=    4.621 closest distance to " O   HOH Z 209 " =    2.316
peak=    4.595 closest distance to " CB  PRO A  54 " =    0.989
peak=    4.540 closest distance to " CD1AILE A 234 " =    0.961
peak=    4.521 closest distance to " C   PRO A 198 " =    1.512
peak=    4.488 closest distance to " O   HOH Z 278 " =    1.026
peak=    4.449 closest distance to " CB  VAL A 230 " =    1.128
peak=    4.447 closest distance to " O   SER A  87 " =    2.250
peak=    4.421 closest distance to " CB  GLU A 152 " =    1.125
peak=    4.407 closest distance to " CD2 LEU A 228 " =    1.175
peak=    4.389 closest distance to " O   HOH Z  59 " =    2.067
peak=    4.370 closest distance to " O   HOH Z  97 " =    2.392
peak=    4.364 closest distance to " O   HOH Z 427 " =    2.707
peak=    4.362 closest distance to " CG  PRO A 198 " =    1.176
peak=    4.348 closest distance to " CB  TYR A 169 " =    0.787
peak=    4.322 closest distance to " O   HOH Z 234 " =    3.606
peak=    4.260 closest distance to " O   HOH Z  85 " =    1.438
peak=    4.258 closest distance to " O   HOH Z 346 " =    1.537
peak=    4.230 closest distance to " O   HOH Z 303 " =    2.058
peak=    4.230 closest distance to " O   HOH Z 368 " =    2.091
peak=    4.224 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.220 closest distance to " O   HOH Z 403 " =    1.813
peak=    4.220 closest distance to " O   HOH Z 298 " =    1.794
peak=    4.207 closest distance to " CG1BVAL A  72 " =    1.603
peak=    4.203 closest distance to " O   HOH Z 128 " =    2.047
peak=    4.180 closest distance to " O   HOH Z 263 " =    1.525
peak=    4.177 closest distance to " O   HOH Z 236 " =    1.824
peak=    4.140 closest distance to " CA  ALA A  21 " =    1.110
peak=    4.128 closest distance to " O   HOH Z  54 " =    1.535
peak=    4.107 closest distance to " O   HOH Z  97 " =    1.930
peak=    4.106 closest distance to " O   HOH Z  61 " =    1.634
peak=    4.100 closest distance to " O   HOH Z 411 " =    3.648
peak=    4.096 closest distance to " O   HOH Z  44 " =    1.860
peak=    4.091 closest distance to " O   HOH Z  78 " =    1.675
peak=    4.087 closest distance to " CG  PRO A 243 " =    1.159
peak=    4.074 closest distance to " ND2 ASN A 187 " =    1.561
peak=    4.045 closest distance to " O   HOH Z 316 " =    2.827
peak=    4.038 closest distance to " O   HOH Z 371 " =    3.103
peak=    4.023 closest distance to " CA  VAL A  41 " =    0.828
peak=    4.018 closest distance to " CD2 TRP A 179 " =    1.395
peak=    4.017 closest distance to " O   HOH Z 203 " =    1.589
peak=    4.004 closest distance to " CB  VAL A 265 " =    1.208
peak=    3.994 closest distance to " O   TRP A 274 " =    1.924
peak=    3.990 closest distance to " CB  SER A  26 " =    1.640
peak=    3.983 closest distance to " O   HOH Z 322 " =    2.109
peak=    3.980 closest distance to " CB  GLU A 128 " =    1.044
peak=    3.975 closest distance to " O   HOH Z  48 " =    1.574
peak=    3.968 closest distance to " N   ASN A  39 " =    1.132
peak=    3.966 closest distance to " CB  TRP A 179 " =    1.234
peak=    3.961 closest distance to " O   HOH Z 423 " =    1.857
peak=    3.958 closest distance to " O   HOH Z 369 " =    2.109
peak=    3.952 closest distance to " O   HOH Z 392 " =    3.012
peak=    3.942 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.901 closest distance to " O   HOH Z 344 " =    2.638
peak=    3.861 closest distance to " CA  TYR A  30 " =    1.013
peak=    3.857 closest distance to " CB  ARG A  79 " =    1.369
peak=    3.854 closest distance to " O   HOH Z  15 " =    2.304
peak=    3.834 closest distance to " O   HOH Z 128 " =    1.923
peak=    3.829 closest distance to " OD1 ASN A  69 " =    2.654
peak=    3.825 closest distance to " O   HOH Z 407 " =    2.479
peak=    3.810 closest distance to " CB  ARG A 139 " =    0.954
peak=    3.808 closest distance to " O   HOH Z 248 " =    1.734
peak=    3.801 closest distance to " O   HOH Z 189 " =    2.527
peak=    3.800 closest distance to " O   HOH Z 126 " =    2.174
peak=    3.798 closest distance to " CD  ARG A 269 " =    1.076
peak=    3.795 closest distance to " CB  ASN A  39 " =    0.833
peak=    3.792 closest distance to " CB  TRP A 266 " =    1.041
peak=    3.780 closest distance to " CA  ALA A  51 " =    0.971
peak=    3.753 closest distance to " O   HOH Z  68 " =    2.166
peak=    3.753 closest distance to " CG2 ILE A 120 " =    1.290
peak=    3.735 closest distance to " O   HOH Z 366 " =    2.921
peak=    3.734 closest distance to " O   HOH Z 425 " =    1.394
peak=    3.734 closest distance to " CG AARG A 275 " =    1.138
peak=    3.731 closest distance to " O   HOH Z 273 " =    2.756
peak=    3.709 closest distance to " CB  THR A  31 " =    1.628
peak=    3.708 closest distance to " CB  VAL A 202 " =    1.586
peak=    3.706 closest distance to " O   HOH Z 327 " =    1.606
peak=    3.701 closest distance to " CB  ALA A 248 " =    1.349
peak=    3.699 closest distance to " O   HOH Z 130 " =    2.371
peak=    3.691 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.690 closest distance to " O   HOH Z 118 " =    1.441
peak=    3.689 closest distance to " CB  GLN A  88 " =    1.195
peak=    3.687 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.687 closest distance to " CB  ALA A 295 " =    1.203
peak=    3.682 closest distance to " O   HOH Z 118 " =    1.312
peak=    3.679 closest distance to " O   ASP A 124 " =    1.202
peak=    3.675 closest distance to " O   HOH Z 345 " =    2.993
peak=    3.668 closest distance to " O   HOH Z 329 " =    3.663
peak=    3.665 closest distance to " OD2 ASP A 286 " =    2.651
peak=    3.653 closest distance to " NZ  LYS A 117 " =    2.994
peak=    3.647 closest distance to " O   HOH Z 299 " =    4.252
peak=    3.643 closest distance to " O   HOH Z  43 " =    2.225
peak=    3.641 closest distance to " O   HOH Z 148 " =    3.295
peak=    3.633 closest distance to " O   HOH Z 144 " =    2.192
peak=    3.624 closest distance to " CG2AVAL A 121 " =    2.243
peak=    3.616 closest distance to " O   HOH Z 244 " =    1.555
peak=    3.616 closest distance to " CA  ASP A 140 " =    1.156
peak=    3.605 closest distance to " CB  PRO A 198 " =    1.004
peak=    3.604 closest distance to " O   HOH Z 227 " =    2.168
peak=    3.603 closest distance to " CD BLYS A 290 " =    1.166
peak=    3.602 closest distance to " CB  GLN A 278 " =    0.861
peak=    3.602 closest distance to " O   HOH Z 247 " =    1.304
peak=    3.602 closest distance to " N   ARG A 156 " =    1.324
peak=    3.601 closest distance to " O   HOH Z 389 " =    1.725
peak=    3.598 closest distance to " O   HOH Z  54 " =    2.439
peak=    3.596 closest distance to " OE1 GLU A   2 " =    2.140
peak=    3.593 closest distance to " O   HOH Z 130 " =    2.849
peak=    3.593 closest distance to " O   HOH Z 426 " =    1.438
peak=    3.590 closest distance to " O   HOH Z 102 " =    1.221
peak=    3.586 closest distance to " O   HOH Z  48 " =    1.610
peak=    3.585 closest distance to " CG2 ILE A  20 " =    1.524
peak=    3.582 closest distance to " O   HOH Z 227 " =    1.481
peak=    3.578 closest distance to " CZ AARG A 102 " =    1.757
peak=    3.573 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.571 closest distance to " CA  LYS A 117 " =    1.245
peak=    3.566 closest distance to " CD  GLN A 194 " =    1.456
peak=    3.564 closest distance to " O   HOH Z 236 " =    1.392
peak=    3.563 closest distance to " O   HOH Z   9 " =    2.040
peak=    3.562 closest distance to " O   HOH Z 108 " =    2.175
peak=    3.557 closest distance to " O   HOH Z 145 " =    2.098
peak=    3.556 closest distance to " O   HOH Z  78 " =    2.131
peak=    3.555 closest distance to " O   HOH Z 134 " =    1.424
peak=    3.546 closest distance to " O   HOH Z 425 " =    2.021
peak=    3.546 closest distance to " CA  PHE A 283 " =    1.156
peak=    3.532 closest distance to " O   HOH Z 222 " =    2.348
peak=    3.525 closest distance to " OG BSER A 164 " =    2.122
peak=    3.524 closest distance to " CD1 ILE A 106 " =    1.211
peak=    3.521 closest distance to " CG  MET A 185 " =    1.186
peak=    3.518 closest distance to " CG  GLN A  77 " =    2.215
peak=    3.515 closest distance to " CG1 ILE A  33 " =    1.383
peak=    3.514 closest distance to " OG1 THR A 294 " =    2.321
peak=    3.512 closest distance to " CB  ALA A   1 " =    1.208
peak=    3.512 closest distance to " O   HOH Z 245 " =    1.386
peak=    3.511 closest distance to " CB  GLU A 277 " =    3.519
peak=    3.510 closest distance to " O   HOH Z 417 " =    3.214
peak=    3.504 closest distance to " O   HOH Z 435 " =    1.991
peak=    3.501 closest distance to " O   HOH Z 374 " =    2.452
peak=    3.501 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.498 closest distance to " O   HOH Z 334 " =    1.494
peak=    3.497 closest distance to " CB BVAL A  41 " =    1.109
peak=    3.492 closest distance to " CA  ASN A 215 " =    1.080
peak=    3.490 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.466 closest distance to " O   HOH Z 303 " =    1.627
peak=    3.466 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.463 closest distance to " CE1 HIS A 108 " =    1.168
peak=    3.450 closest distance to " O   HOH Z 172 " =    3.874
peak=    3.444 closest distance to " O   HOH Z  10 " =    1.707
peak=    3.441 closest distance to " O   HOH Z 404 " =    2.227
peak=    3.441 closest distance to " O   HOH Z  40 " =    1.434
peak=    3.437 closest distance to " O   HOH Z 213 " =    1.650
peak=    3.429 closest distance to " O   HOH Z  88 " =    2.787
peak=    3.428 closest distance to " O   HOH Z   3 " =    1.737
peak=    3.423 closest distance to " CA  ASN A 176 " =    1.021
peak=    3.422 closest distance to " O   GLY A  91 " =    1.543
peak=    3.421 closest distance to " O   HOH Z  80 " =    1.588
peak=    3.419 closest distance to " O   HOH Z 313 " =    1.876
peak=    3.417 closest distance to " ND2 ASN A 110 " =    1.662
peak=    3.416 closest distance to " O   HOH Z 123 " =    1.075
peak=    3.411 closest distance to " CA  GLY A  80 " =    0.724
peak=    3.407 closest distance to " CG  ARG A  66 " =    0.996
peak=    3.407 closest distance to " O   HOH Z 261 " =    1.716
peak=    3.405 closest distance to " CG2 THR A 294 " =    1.609
peak=    3.400 closest distance to " O   HOH Z 164 " =    2.062
peak=    3.400 closest distance to " N   SER A 135 " =    1.253
peak=    3.396 closest distance to " CG AARG A 275 " =    1.123
peak=    3.396 closest distance to " CD2 TYR A  30 " =    0.896
peak=    3.390 closest distance to " O   HOH Z 209 " =    2.279
peak=    3.387 closest distance to " OD1 ASP A 286 " =    1.707
peak=    3.386 closest distance to " O   HOH Z 145 " =    3.504
peak=    3.386 closest distance to " N   ARG A 190 " =    1.015
peak=    3.382 closest distance to " CA  GLN A 194 " =    1.161
peak=    3.381 closest distance to " O   ALA A   1 " =    1.809
peak=    3.379 closest distance to " O   HOH Z 383 " =    1.754
peak=    3.376 closest distance to " NZ  LYS A  76 " =    1.363
peak=    3.374 closest distance to " CZ2 TRP A 179 " =    1.839
peak=    3.370 closest distance to " O   HOH Z 422 " =    2.572
peak=    3.369 closest distance to " CZ  PHE A 218 " =    1.107
peak=    3.366 closest distance to " O   HOH Z 192 " =    1.719
peak=    3.366 closest distance to " O   HOH Z  59 " =    2.089
peak=    3.365 closest distance to " O   HOH Z 214 " =    2.486
peak=    3.364 closest distance to " CZ2 TRP A 274 " =    1.521
peak=    3.360 closest distance to " CG1 ILE A 120 " =    1.226
peak=    3.360 closest distance to " O   HOH Z  43 " =    2.756
peak=    3.357 closest distance to " O   HOH Z  63 " =    2.219
peak=    3.355 closest distance to " O   HOH Z 433 " =    1.799
peak=    3.354 closest distance to " CB  LEU A 255 " =    0.846
peak=    3.353 closest distance to " O   HOH Z 158 " =    2.954
peak=    3.343 closest distance to " CA  ARG A  36 " =    1.021
peak=    3.342 closest distance to " CG2 THR A 221 " =    1.257
peak=    3.339 closest distance to " C   ALA A 299 " =    0.941
peak=    3.336 closest distance to " NH2 ARG A 156 " =    1.062
peak=    3.336 closest distance to " O   PHE A  38 " =    1.910
peak=    3.335 closest distance to " CD1 LEU A  96 " =    0.735
peak=    3.334 closest distance to " O   HOH Z 173 " =    2.257
peak=    3.334 closest distance to " NH1BARG A 190 " =    1.983
peak=    3.333 closest distance to " CA  THR A 221 " =    0.896
peak=    3.332 closest distance to " O   HOH Z  61 " =    1.540
peak=    3.320 closest distance to " CA  LYS A 290 " =    1.238
peak=    3.318 closest distance to " O   HOH Z 249 " =    0.995
peak=    3.315 closest distance to " CB  HIS A 108 " =    0.879
peak=    3.314 closest distance to " CE  MET A  93 " =    1.480
peak=    3.311 closest distance to " CB  ALA A 291 " =    1.253
peak=    3.307 closest distance to " CD2 HIS A  81 " =    1.143
peak=    3.307 closest distance to " O   HOH Z 227 " =    1.654
peak=    3.306 closest distance to " CA  VAL A 126 " =    0.963
peak=    3.306 closest distance to " N   PHE A 130 " =    1.356
peak=    3.305 closest distance to " O   HOH Z 344 " =    1.399
peak=    3.297 closest distance to " CG  MET A 188 " =    1.169
peak=    3.297 closest distance to " O   HOH Z 251 " =    1.683
peak=    3.289 closest distance to " O   HOH Z 392 " =    1.600
peak=    3.289 closest distance to " O   SER A 164 " =    1.228
peak=    3.288 closest distance to " O   HOH Z 406 " =    1.469
peak=    3.285 closest distance to " O   HOH Z 357 " =    1.782
peak=    3.284 closest distance to " CB  ARG A 190 " =    1.810
peak=    3.279 closest distance to " O   HOH Z 367 " =    3.479
peak=    3.277 closest distance to " CE BLYS A 290 " =    0.995
peak=    3.270 closest distance to " O   HOH Z 419 " =    1.652
peak=    3.269 closest distance to " O   HOH Z 334 " =    1.279
peak=    3.266 closest distance to " O   HOH Z 250 " =    1.467
peak=    3.263 closest distance to " O   HOH Z 112 " =    1.606
peak=    3.263 closest distance to " O   HOH Z 352 " =    1.322
peak=    3.262 closest distance to " O   HOH Z 132 " =    2.539
peak=    3.262 closest distance to " O   HOH Z 193 " =    1.879
peak=    3.258 closest distance to " CD2 LEU A 297 " =    0.993
peak=    3.249 closest distance to " O   HOH Z  47 " =    1.647
peak=    3.246 closest distance to " O   HOH Z 128 " =    1.885
peak=    3.241 closest distance to " CG  LYS A 119 " =    1.179
peak=    3.240 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.239 closest distance to " CA  LEU A 237 " =    1.157
peak=    3.239 closest distance to " NH2BARG A 145 " =    2.110
peak=    3.228 closest distance to " CD  LYS A 166 " =    1.331
peak=    3.228 closest distance to " CG  GLU A 277 " =    2.170
peak=    3.228 closest distance to " CA  ILE A  20 " =    0.722
peak=    3.227 closest distance to " O   HOH Z 411 " =    1.739
peak=    3.225 closest distance to " O   HOH Z 189 " =    2.543
peak=    3.219 closest distance to " CB  GLN A 205 " =    1.220
peak=    3.216 closest distance to " O   HOH Z 280 " =    1.618
peak=    3.213 closest distance to " NE2 GLN A  58 " =    5.823
peak=    3.211 closest distance to " O   HOH Z 151 " =    1.791
peak=    3.209 closest distance to " O   HOH Z 421 " =    1.548
peak=    3.209 closest distance to " CA  ALA A 158 " =    1.244
peak=    3.204 closest distance to " CB  GLU A  46 " =    1.106
peak=    3.202 closest distance to " OD1 ASP A 231 " =    1.888
peak=    3.201 closest distance to " CB  SER A 216 " =    0.725
peak=    3.194 closest distance to " O   HOH Z  40 " =    1.796
peak=    3.193 closest distance to " O   HOH Z  49 " =    2.271
peak=    3.191 closest distance to " OE1 GLN A  11 " =    1.708
peak=    3.190 closest distance to " O   HOH Z 392 " =    2.231
peak=    3.188 closest distance to " CA  ASP A 191 " =    0.947
peak=    3.187 closest distance to " NH1 ARG A  14 " =    0.998
peak=    3.181 closest distance to " CA  LEU A 282 " =    1.115
peak=    3.181 closest distance to " CB  LEU A 228 " =    1.385
peak=    3.180 closest distance to " CA  ILE A 106 " =    0.761
peak=    3.180 closest distance to " CD1 ILE A  33 " =    1.610
peak=    3.177 closest distance to " CA  ASP A 162 " =    1.043
peak=    3.177 closest distance to " CG  LEU A 167 " =    1.130
peak=    3.175 closest distance to " O   HOH Z 368 " =    3.627
peak=    3.174 closest distance to " CA  ALA A 291 " =    0.927
peak=    3.168 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.167 closest distance to " CB  ASP A 140 " =    0.843
peak=    3.167 closest distance to " O   HOH Z 109 " =    2.444
peak=    3.158 closest distance to " CD  LYS A 119 " =    1.979
peak=    3.154 closest distance to " O   HOH Z 438 " =    2.042
peak=    3.153 closest distance to " O   HOH Z 291 " =    1.644
peak=    3.151 closest distance to " CB  SER A  62 " =    1.238
peak=    3.148 closest distance to " O   HOH Z  68 " =    2.760
peak=    3.147 closest distance to " O   HOH Z  19 " =    2.007
peak=    3.139 closest distance to " ND1 HIS A  81 " =    1.475
peak=    3.136 closest distance to " OG  SER A  97 " =    2.615
peak=    3.136 closest distance to " OD1 ASN A 148 " =    1.688
peak=    3.133 closest distance to " CB  TYR A  30 " =    1.563
peak=    3.131 closest distance to " O   HOH Z  80 " =    2.136
peak=    3.131 closest distance to " O   HOH Z 180 " =    2.151
peak=    3.123 closest distance to " CD2 TYR A 186 " =    1.010
peak=    3.120 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.120 closest distance to " O   HOH Z 406 " =    1.102
peak=    3.118 closest distance to " OH  TYR A 116 " =    1.062
peak=    3.111 closest distance to " O   ASP A 124 " =    1.745
peak=    3.106 closest distance to " O   HOH Z 175 " =    2.135
peak=    3.106 closest distance to " O   HOH Z  88 " =    2.511
peak=    3.105 closest distance to " OE2 GLU A  53 " =    2.034
peak=    3.103 closest distance to " CB  TYR A 169 " =    1.188
peak=    3.100 closest distance to " CB  ILE A  20 " =    1.364
peak=    3.097 closest distance to " O   HOH Z 380 " =    2.042
peak=    3.093 closest distance to " O   HOH Z 250 " =    1.815
peak=    3.091 closest distance to " O   HOH Z  89 " =    1.580
peak=    3.089 closest distance to " O   HOH Z 423 " =    2.960
peak=    3.083 closest distance to " CA  THR A 264 " =    0.774
peak=    3.082 closest distance to " O   HOH Z 276 " =    1.204
peak=    3.077 closest distance to " CA  LEU A 101 " =    1.491
peak=    3.073 closest distance to " CD2 LEU A 255 " =    1.385
peak=    3.053 closest distance to " CG  LEU A 281 " =    0.974
peak=    3.050 closest distance to " O   HOH Z 424 " =    1.464
peak=    3.011 closest distance to " N   ASP A 162 " =    1.327

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.548 - 5.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 193
   mapped sites are within: 0.730 - 5.878

peak=   -4.698 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.692 closest distance to " O   HOH Z 290 " =    0.926
peak=   -4.563 closest distance to " SG  CYS A 254 " =    3.176
peak=   -4.470 closest distance to " CG2BVAL A  41 " =    2.631
peak=   -4.319 closest distance to " OXT GLY A 302 " =    2.704
peak=   -4.247 closest distance to " O   HOH Z 266 " =    4.695
peak=   -4.245 closest distance to " CB  ALA A 161 " =    2.474
peak=   -4.227 closest distance to " CD1 LEU A 101 " =    2.437
peak=   -4.197 closest distance to " C   HIS A 108 " =    1.201
peak=   -4.169 closest distance to " CA  VAL A  67 " =    2.723
peak=   -4.153 closest distance to " CE2 TYR A  30 " =    2.855
peak=   -4.076 closest distance to " N   GLN A  58 " =    1.965
peak=   -4.044 closest distance to " CB  ALA A 248 " =    2.073
peak=   -3.986 closest distance to " CG2 VAL A 296 " =    1.360
peak=   -3.964 closest distance to " OG BSER A 134 " =    1.191
peak=   -3.944 closest distance to " CG  ASP A 231 " =    0.816
peak=   -3.935 closest distance to " ND2 ASN A  45 " =    0.986
peak=   -3.923 closest distance to " C   ASP A 231 " =    2.529
peak=   -3.920 closest distance to " O   PRO A 163 " =    2.029
peak=   -3.881 closest distance to " O   HOH Z 423 " =    2.173
peak=   -3.852 closest distance to " CD1 LEU A 255 " =    2.772
peak=   -3.842 closest distance to " O   ALA A 161 " =    1.611
peak=   -3.822 closest distance to " CZ  TYR A 169 " =    1.759
peak=   -3.802 closest distance to " O   PRO A 198 " =    1.198
peak=   -3.771 closest distance to " O   HOH Z 166 " =    1.999
peak=   -3.768 closest distance to " O   HOH Z 351 " =    1.453
peak=   -3.764 closest distance to " CB  GLN A  11 " =    1.875
peak=   -3.753 closest distance to " O   HOH Z 362 " =    5.878
peak=   -3.737 closest distance to " CG  PHE A 283 " =    2.731
peak=   -3.729 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.729 closest distance to " CD  GLN A  58 " =    1.230
peak=   -3.725 closest distance to " OG  SER A   3 " =    1.342
peak=   -3.719 closest distance to " CG  GLN A 223 " =    1.961
peak=   -3.718 closest distance to " OG ASER A 134 " =    1.273
peak=   -3.712 closest distance to " N   ALA A 226 " =    1.968
peak=   -3.707 closest distance to " CG  ASP A  50 " =    2.398
peak=   -3.693 closest distance to " OG  SER A  97 " =    2.210
peak=   -3.689 closest distance to " ND2 ASN A 187 " =    1.568
peak=   -3.687 closest distance to " O   HOH Z 103 " =    1.828
peak=   -3.686 closest distance to " O   ALA A  51 " =    1.314
peak=   -3.683 closest distance to " O   HOH Z 166 " =    1.547
peak=   -3.678 closest distance to " O   HOH Z 102 " =    1.709
peak=   -3.677 closest distance to " NH2 ARG A  79 " =    1.928
peak=   -3.674 closest distance to " CA  GLY A  23 " =    1.951
peak=   -3.673 closest distance to " O   HOH Z 407 " =    2.972
peak=   -3.660 closest distance to " N   PHE A  59 " =    2.291
peak=   -3.658 closest distance to " N   ALA A 248 " =    1.643
peak=   -3.656 closest distance to " O   HOH Z 191 " =    5.158
peak=   -3.655 closest distance to " O   HOH Z 231 " =    2.033
peak=   -3.652 closest distance to " O   HOH Z  11 " =    1.835
peak=   -3.639 closest distance to " OD1 ASN A  39 " =    2.165
peak=   -3.623 closest distance to " CE  MET A 105 " =    2.009
peak=   -3.623 closest distance to " O   HOH Z 389 " =    1.801
peak=   -3.617 closest distance to " O   HOH Z 118 " =    2.978
peak=   -3.606 closest distance to " O   MET A  40 " =    2.668
peak=   -3.594 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.589 closest distance to " C   MET A 188 " =    1.496
peak=   -3.582 closest distance to " CD  ARG A 139 " =    1.566
peak=   -3.580 closest distance to " NE2 GLN A  88 " =    1.112
peak=   -3.578 closest distance to " CG1 VAL A 112 " =    2.720
peak=   -3.570 closest distance to " CG  LYS A 193 " =    2.114
peak=   -3.565 closest distance to " CB  PHE A 192 " =    1.884
peak=   -3.556 closest distance to " CD  LYS A 289 " =    2.537
peak=   -3.555 closest distance to " CB  ALA A  51 " =    1.893
peak=   -3.553 closest distance to " CA  GLY A  98 " =    1.894
peak=   -3.547 closest distance to " O   HOH Z 165 " =    1.965
peak=   -3.545 closest distance to " OG BSER A 134 " =    1.679
peak=   -3.544 closest distance to " N   HIS A 115 " =    2.006
peak=   -3.541 closest distance to " N   SER A 206 " =    1.871
peak=   -3.539 closest distance to " CB  PRO A 243 " =    2.610
peak=   -3.538 closest distance to " O   HOH Z  13 " =    1.335
peak=   -3.519 closest distance to " CD2 LEU A 300 " =    2.895
peak=   -3.514 closest distance to " NZ  LYS A 119 " =    3.343
peak=   -3.508 closest distance to " OG  SER A 206 " =    1.469
peak=   -3.503 closest distance to " O   HOH Z 174 " =    4.350
peak=   -3.502 closest distance to " O   HOH Z 185 " =    2.331
peak=   -3.491 closest distance to " O   HOH Z 250 " =    1.411
peak=   -3.466 closest distance to " CB  ASN A  39 " =    2.147
peak=   -3.465 closest distance to " CH2 TRP A 179 " =    1.363
peak=   -3.457 closest distance to " CB  ALA A  43 " =    2.242
peak=   -3.453 closest distance to " N   SER A 276 " =    1.191
peak=   -3.448 closest distance to " OXT GLY A 302 " =    3.515
peak=   -3.437 closest distance to " O   HOH Z 394 " =    1.592
peak=   -3.436 closest distance to " CB  PRO A 163 " =    2.602
peak=   -3.435 closest distance to " O   ALA A 100 " =    2.522
peak=   -3.432 closest distance to " NE2 GLN A  88 " =    2.104
peak=   -3.428 closest distance to " O   HOH Z 211 " =    1.542
peak=   -3.428 closest distance to " O   HOH Z  11 " =    1.874
peak=   -3.423 closest distance to " O   HOH Z 353 " =    2.136
peak=   -3.422 closest distance to " O   HOH Z 111 " =    4.691
peak=   -3.417 closest distance to " O   HOH Z 301 " =    2.362
peak=   -3.416 closest distance to " O   SER A 210 " =    1.883
peak=   -3.409 closest distance to " OD1 ASN A 249 " =    1.436
peak=   -3.405 closest distance to " CG  LEU A 228 " =    1.094
peak=   -3.405 closest distance to " CE2 PHE A 218 " =    2.659
peak=   -3.401 closest distance to " O   HOH Z 384 " =    3.367
peak=   -3.399 closest distance to " O   HOH Z 295 " =    1.467
peak=   -3.398 closest distance to " O   HOH Z  71 " =    1.053
peak=   -3.396 closest distance to " O   GLY A  80 " =    2.299
peak=   -3.393 closest distance to " N   THR A 157 " =    1.450
peak=   -3.390 closest distance to " CB  ALA A 291 " =    2.394
peak=   -3.381 closest distance to " CB  ALA A 291 " =    2.141
peak=   -3.376 closest distance to " O   HOH Z  44 " =    2.163
peak=   -3.375 closest distance to " CB  ASP A 132 " =    2.181
peak=   -3.369 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.368 closest distance to " O   HOH Z 385 " =    2.142
peak=   -3.368 closest distance to " O   HOH Z 427 " =    1.491
peak=   -3.368 closest distance to " CD1 TYR A 247 " =    2.559
peak=   -3.350 closest distance to " O   HOH Z 311 " =    3.586
peak=   -3.350 closest distance to " O   HOH Z  19 " =    2.310
peak=   -3.348 closest distance to " O   GLY A 196 " =    1.093
peak=   -3.340 closest distance to " O   HOH Z 193 " =    1.666
peak=   -3.339 closest distance to " NH2AARG A 275 " =    4.847
peak=   -3.334 closest distance to " CA  GLY A 133 " =    1.868
peak=   -3.333 closest distance to " O   HOH Z 198 " =    2.085
peak=   -3.330 closest distance to " O   HOH Z 431 " =    1.987
peak=   -3.325 closest distance to " O   HOH Z  47 " =    1.525
peak=   -3.324 closest distance to " O   HOH Z 344 " =    2.490
peak=   -3.323 closest distance to " CB  ASP A 162 " =    2.590
peak=   -3.320 closest distance to " CD2 TYR A 293 " =    2.110
peak=   -3.315 closest distance to " C   THR A 279 " =    1.228
peak=   -3.314 closest distance to " O   HOH Z 196 " =    2.176
peak=   -3.312 closest distance to " N   VAL A 230 " =    1.239
peak=   -3.311 closest distance to " O   HOH Z 407 " =    3.372
peak=   -3.310 closest distance to " CG  GLU A   2 " =    1.908
peak=   -3.306 closest distance to " O   HOH Z 313 " =    1.761
peak=   -3.304 closest distance to " O   HOH Z 312 " =    1.505
peak=   -3.302 closest distance to " ND2 ASN A  39 " =    1.204
peak=   -3.298 closest distance to " O   HOH Z  17 " =    1.519
peak=   -3.289 closest distance to " N   MET A 188 " =    1.909
peak=   -3.285 closest distance to " O   VAL A 197 " =    1.240
peak=   -3.284 closest distance to " CG  TRP A 266 " =    2.044
peak=   -3.270 closest distance to " CG1 VAL A 230 " =    1.798
peak=   -3.269 closest distance to " OD1 ASP A 200 " =    1.305
peak=   -3.258 closest distance to " O   HOH Z 148 " =    1.814
peak=   -3.251 closest distance to " OD2 ASP A 191 " =    1.457
peak=   -3.245 closest distance to " CD  GLU A 152 " =    2.544
peak=   -3.241 closest distance to " O   PHE A 218 " =    1.718
peak=   -3.238 closest distance to " C   ARG A 269 " =    1.504
peak=   -3.235 closest distance to " O   HOH Z 134 " =    2.725
peak=   -3.229 closest distance to " C   ASN A 285 " =    2.268
peak=   -3.224 closest distance to " O   VAL A 174 " =    1.938
peak=   -3.223 closest distance to " OD1 ASN A 301 " =    1.971
peak=   -3.223 closest distance to " CD1 LEU A 228 " =    2.071
peak=   -3.215 closest distance to " CB  ASN A  69 " =    1.078
peak=   -3.213 closest distance to " O   HOH Z  60 " =    2.098
peak=   -3.206 closest distance to " O   HOH Z 426 " =    1.603
peak=   -3.205 closest distance to " O   HOH Z 202 " =    2.151
peak=   -3.201 closest distance to " CD2 LEU A 237 " =    2.858
peak=   -3.195 closest distance to " OG1 THR A  82 " =    1.326
peak=   -3.190 closest distance to " O   HOH Z 210 " =    0.991
peak=   -3.190 closest distance to " O   HOH Z 193 " =    1.687
peak=   -3.186 closest distance to " O   HOH Z 388 " =    2.133
peak=   -3.186 closest distance to " OD2 ASP A 171 " =    2.326
peak=   -3.183 closest distance to " CG2 VAL A 296 " =    1.833
peak=   -3.183 closest distance to " CG  MET A 105 " =    0.842
peak=   -3.180 closest distance to " O   HOH Z 234 " =    4.065
peak=   -3.180 closest distance to " O   SER A  22 " =    2.239
peak=   -3.178 closest distance to " O   HOH Z  97 " =    1.307
peak=   -3.178 closest distance to " OD1 ASP A 191 " =    1.479
peak=   -3.170 closest distance to " O   HOH Z 417 " =    2.584
peak=   -3.161 closest distance to " O   GLY A  75 " =    1.688
peak=   -3.160 closest distance to " N   GLN A  77 " =    1.425
peak=   -3.157 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.157 closest distance to " CD  GLN A  11 " =    0.730
peak=   -3.156 closest distance to " CB  PRO A 280 " =    2.026
peak=   -3.154 closest distance to " CZ  ARG A 259 " =    0.853
peak=   -3.151 closest distance to " CG  GLU A  53 " =    1.631
peak=   -3.143 closest distance to " O   HOH Z 407 " =    3.061
peak=   -3.141 closest distance to " NE2 GLN A 194 " =    1.748
peak=   -3.141 closest distance to " OG1 THR A 178 " =    1.208
peak=   -3.138 closest distance to " O   HOH Z 377 " =    0.762
peak=   -3.137 closest distance to " CE  LYS A 166 " =    3.006
peak=   -3.131 closest distance to " O   PRO A 198 " =    1.176
peak=   -3.131 closest distance to " CD2 LEU A 237 " =    2.719
peak=   -3.130 closest distance to " CB  SER A 210 " =    1.249
peak=   -3.125 closest distance to " O   HOH Z 281 " =    2.907
peak=   -3.121 closest distance to " CD  GLN A  88 " =    0.777
peak=   -3.108 closest distance to " CD  PRO A 243 " =    2.067
peak=   -3.106 closest distance to " OE1 GLN A  88 " =    1.121
peak=   -3.100 closest distance to " CB  ALA A 256 " =    2.886
peak=   -3.098 closest distance to " O   HOH Z 421 " =    3.126
peak=   -3.094 closest distance to " CG1 VAL A 296 " =    1.280
peak=   -3.086 closest distance to " CD2 LEU A   5 " =    1.154
peak=   -3.074 closest distance to " NH2 ARG A  66 " =    1.801
peak=   -3.060 closest distance to " O   HOH Z 210 " =    1.139
peak=   -3.059 closest distance to " CG  ARG A 269 " =    2.166
peak=   -3.055 closest distance to " NE2 GLN A 278 " =    1.942
peak=   -3.043 closest distance to " O   TRP A  92 " =    1.771
peak=   -3.026 closest distance to " CA  GLY A 133 " =    2.208

================= 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    :  0.4528 0.4472   6.249424e+00   6.238031e+00
   1_bss:  0.4445 0.4361   6.241872e+00   6.223231e+00
   1_xyz:  0.3489 0.3702   6.082335e+00   6.119570e+00
   1_adp:  0.2916 0.3330   5.943635e+00   6.045291e+00
   1_occ:  0.2911 0.3329   5.942939e+00   6.046057e+00
   2_bss:  0.2867 0.3280   5.941279e+00   6.042345e+00
   2_xyz:  0.2001 0.2428   5.626223e+00   5.790102e+00
   2_adp:  0.1791 0.2202   5.526502e+00   5.701800e+00
   2_occ:  0.1786 0.2197   5.525177e+00   5.700341e+00
   3_bss:  0.1770 0.2184   5.522115e+00   5.695011e+00
   3_xyz:  0.1335 0.1742   5.274836e+00   5.484885e+00
   3_adp:  0.1271 0.1657   5.226274e+00   5.433717e+00
   3_occ:  0.1269 0.1656   5.225177e+00   5.432746e+00
   4_bss:  0.1272 0.1654   5.226183e+00   5.432602e+00
   4_xyz:  0.1187 0.1576   5.176032e+00   5.390227e+00
   4_adp:  0.1170 0.1576   5.168146e+00   5.387870e+00
   4_occ:  0.1170 0.1576   5.168001e+00   5.387936e+00
   5_bss:  0.1170 0.1576   5.167906e+00   5.387844e+00
   5_xyz:  0.1134 0.1555   5.143598e+00   5.373225e+00
   5_adp:  0.1130 0.1557   5.142101e+00   5.374357e+00
   5_occ:  0.1130 0.1557   5.142194e+00   5.374607e+00
   5_bss:  0.1130 0.1557   5.142229e+00   5.374633e+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:  0.363  14.089   7.841   7.890   8.899   0.000   0.000   0.000
   1_xyz:  0.363  14.089   7.841   7.890   8.899   0.000   0.000   0.000
   1_adp:  0.363  14.089   7.841   7.890   8.899   0.000   0.000   0.000
   1_occ:  0.363  14.089   7.841   7.890   8.899   0.000   0.000   0.000
   2_bss:  0.338  26.996   4.349   4.257   5.850   0.000   0.000   0.000
   2_xyz:  0.338  26.996   4.349   4.257   5.850   0.000   0.000   0.000
   2_adp:  0.338  26.996   4.349   4.257   5.850   0.000   0.000   0.000
   2_occ:  0.338  26.996   4.349   4.257   5.850   0.000   0.000   0.000
   3_bss:  0.320  32.729   2.603   3.175   4.108   0.000   0.000   0.000
   3_xyz:  0.320  32.729   2.603   3.175   4.108   0.000   0.000   0.000
   3_adp:  0.320  32.729   2.603   3.175   4.108   0.000   0.000   0.000
   3_occ:  0.320  32.729   2.603   3.175   4.108   0.000   0.000   0.000
   4_bss:  0.322  32.729   2.153   2.802   3.481   0.000   0.000   0.000
   4_xyz:  0.322  32.729   2.153   2.802   3.481   0.000   0.000   0.000
   4_adp:  0.322  32.729   2.153   2.802   3.481   0.000   0.000   0.000
   4_occ:  0.322  32.729   2.153   2.802   3.481   0.000   0.000   0.000
   5_bss:  0.324  33.421   2.032   2.742   3.359   0.000   0.000   0.000
   5_xyz:  0.324  33.421   2.032   2.742   3.359   0.000   0.000   0.000
   5_adp:  0.324  33.421   2.032   2.742   3.359   0.000   0.000   0.000
   5_occ:  0.324  33.421   2.032   2.742   3.359   0.000   0.000   0.000
   5_bss:  0.324  36.194  -0.683   0.030   0.653   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.550 0.5027  0.5782    59880.444
   1_bss:  51.970 0.4946  0.7226    56879.065
   1_xyz:  41.310 0.6257  0.8986    38570.564
   1_adp:  34.963 0.7019  1.0089    29878.180
   1_occ:  34.983 0.7016  1.0079    29878.788
   2_bss:  34.688 0.7048  0.8952    29436.458
   2_xyz:  24.181 0.8193  1.0050    15030.548
   2_adp:  21.113 0.8514  1.0328    12363.588
   2_occ:  21.072 0.8518  1.0328    12312.099
   3_bss:  20.918 0.8532  0.9759    12133.102
   3_xyz:  16.144 0.8966  0.9992     7678.067
   3_adp:  14.957 0.9072  1.0038     6982.088
   3_occ:  14.935 0.9074  1.0037     6970.796
   4_bss:  14.931 0.9074  0.9858     6971.547
   4_xyz:  13.979 0.9155  0.9889     6343.075
   4_adp:  13.902 0.9163  0.9894     6323.372
   4_occ:  13.899 0.9163  0.9892     6321.636
   5_bss:  13.897 0.9163  0.9855     6321.399
   5_xyz:  13.650 0.9180  0.9855     6130.562
   5_adp:  13.659 0.9180  0.9838     6141.881
   5_occ:  13.662 0.9180  0.9836     6144.943
   5_bss:  13.663 0.9180  0.9859     6145.387
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3110e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3110e+01
   1_xyz:   1.623  0.013  0.105 17.975  0.006  4.108   1.3083e-01
   1_adp:   1.623  0.013  0.105 17.975  0.006  4.108   1.3083e-01
   1_occ:   1.623  0.013  0.105 17.975  0.006  4.108   1.3083e-01
   2_bss:   1.623  0.013  0.105 17.975  0.006  4.108   1.3083e-01
   2_xyz:   0.971  0.006  0.072 15.707  0.004  4.118   6.2453e-02
   2_adp:   0.971  0.006  0.072 15.707  0.004  4.118   6.2453e-02
   2_occ:   0.971  0.006  0.072 15.707  0.004  4.118   6.2453e-02
   3_bss:   0.971  0.006  0.072 15.707  0.004  4.118   6.2453e-02
   3_xyz:   1.009  0.006  0.076 15.683  0.003  4.108   6.0208e-02
   3_adp:   1.009  0.006  0.076 15.683  0.003  4.108   6.0208e-02
   3_occ:   1.009  0.006  0.076 15.683  0.003  4.108   6.0208e-02
   4_bss:   1.009  0.006  0.076 15.683  0.003  4.108   6.0208e-02
   4_xyz:   0.895  0.005  0.070 15.378  0.003  4.107   5.1676e-02
   4_adp:   0.895  0.005  0.070 15.378  0.003  4.107   5.1676e-02
   4_occ:   0.895  0.005  0.070 15.378  0.003  4.107   5.1676e-02
   5_bss:   0.895  0.005  0.070 15.378  0.003  4.107   5.1676e-02
   5_xyz:   0.934  0.005  0.073 15.324  0.003  4.107   5.4093e-02
   5_adp:   0.934  0.005  0.073 15.324  0.003  4.107   5.4093e-02
   5_occ:   0.934  0.005  0.073 15.324  0.003  4.107   5.4093e-02
   5_bss:   0.934  0.005  0.073 15.324  0.003  4.107   5.4093e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.978   6.8825e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.978   6.8825e+00
   1_xyz:  14.384  0.157  0.485 88.067  0.046  2.236   9.4960e-02
   1_adp:  14.384  0.157  0.485 88.067  0.046  2.236   9.4960e-02
   1_occ:  14.384  0.157  0.485 88.067  0.046  2.236   9.4960e-02
   2_bss:  14.384  0.157  0.485 88.067  0.046  2.236   9.4960e-02
   2_xyz:   6.554  0.053  0.282 82.956  0.029  2.345   8.7701e-02
   2_adp:   6.554  0.053  0.282 82.956  0.029  2.345   8.7701e-02
   2_occ:   6.554  0.053  0.282 82.956  0.029  2.345   8.7701e-02
   3_bss:   6.554  0.053  0.282 82.956  0.029  2.345   8.7701e-02
   3_xyz:   7.083  0.045  0.511 83.224  0.029  2.327   4.1232e-02
   3_adp:   7.083  0.045  0.511 83.224  0.029  2.327   4.1232e-02
   3_occ:   7.083  0.045  0.511 83.224  0.029  2.327   4.1232e-02
   4_bss:   7.083  0.045  0.511 83.224  0.029  2.327   4.1232e-02
   4_xyz:   5.987  0.032  0.392 81.683  0.029  2.377   3.4167e-02
   4_adp:   5.987  0.032  0.392 81.683  0.029  2.377   3.4167e-02
   4_occ:   5.987  0.032  0.392 81.683  0.029  2.377   3.4167e-02
   5_bss:   5.987  0.032  0.392 81.683  0.029  2.377   3.4167e-02
   5_xyz:   6.189  0.038  0.462 82.926  0.027  2.367   3.0409e-02
   5_adp:   6.189  0.038  0.462 82.926  0.027  2.367   3.0409e-02
   5_occ:   6.189  0.038  0.462 82.926  0.027  2.367   3.0409e-02
   5_bss:   6.189  0.038  0.462 82.926  0.027  2.367   3.0409e-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:  78.01   0.00  11.68  74.44   0.00   8.72  78.01   0.00  27.80
   1_occ:  78.01   0.00  11.68  74.44   0.00   8.72  78.01   0.00  27.80
   2_bss:  78.01   0.00  11.68  74.44   0.00   8.72  78.01   0.00  27.80
   2_xyz:  78.01   0.00  11.68  74.44   0.00   8.72  78.01   0.00  27.80
   2_adp:  78.96   0.00  11.92  78.36   0.00   8.18  78.96   1.14  32.29
   2_occ:  78.96   0.00  11.92  78.36   0.00   8.18  78.96   1.14  32.29
   3_bss:  78.96   0.00  11.92  78.36   0.00   8.18  78.96   1.14  32.29
   3_xyz:  78.96   0.00  11.92  78.36   0.00   8.18  78.96   1.14  32.29
   3_adp:  82.47   0.00  11.91  82.47   0.00   7.95  69.62   1.99  33.50
   3_occ:  82.47   0.00  11.91  82.47   0.00   7.95  69.62   1.99  33.50
   4_bss:  82.47   0.00  11.91  82.47   0.00   7.95  69.62   1.99  33.50
   4_xyz:  82.47   0.00  11.91  82.47   0.00   7.95  69.62   1.99  33.50
   4_adp:  83.28   0.00  11.86  83.28   0.00   7.92  67.50   1.34  33.31
   4_occ:  83.28   0.00  11.86  83.28   0.00   7.92  67.50   1.34  33.31
   5_bss:  83.28   0.00  11.86  83.28   0.00   7.92  67.50   1.34  33.31
   5_xyz:  83.28   0.00  11.86  83.28   0.00   7.92  67.50   1.34  33.31
   5_adp:  83.46   0.00  11.82  83.46   0.00   7.88  67.72   1.42  33.31
   5_occ:  83.46   0.00  11.82  83.46   0.00   7.88  67.72   1.42  33.31
   5_bss:  86.24   2.77  14.59  86.24   2.77  10.65  70.50   4.19  36.08
------------------------------------------------------------------------
 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:    1.214    0.024    0.409
   1_adp:    1.214    0.024    0.409
   1_occ:    1.214    0.024    0.409
   2_bss:    1.214    0.024    0.409
   2_xyz:    1.527    0.024    0.536
   2_adp:    1.527    0.024    0.536
   2_occ:    1.527    0.024    0.536
   3_bss:    1.527    0.024    0.536
   3_xyz:    1.482    0.060    0.580
   3_adp:    1.482    0.060    0.580
   3_occ:    1.482    0.060    0.580
   4_bss:    1.482    0.060    0.580
   4_xyz:    1.647    0.025    0.607
   4_adp:    1.647    0.025    0.607
   4_occ:    1.647    0.025    0.607
   5_bss:    1.647    0.025    0.607
   5_xyz:    1.585    0.029    0.613
   5_adp:    1.585    0.029    0.613
   5_occ:    1.585    0.029    0.613
   5_bss:    1.585    0.029    0.613
------------------------------------------------------------------------

CPU time actual refinement: 327.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/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_299/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_299/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.65 
  Macro-tasks:
    bulk solvent and scale       = 41.38  
    individual site refinement   = 134.10 
    weights calculation          = 32.67  
    collect and process          = 6.76   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 215.03 
  Micro-tasks:
    mask                            = 1.80   
    f_calc                          = 98.25  
    alpha_beta                      = 8.28   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.01 
    fmodel                         = 7.81   
    r_factors                      = 0.29   
    phase_errors                   = 10.74  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 237.60 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.638 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    635 calls, 97.77 s
gradients_fft:          580 calls, 95.76 s

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

# Date 2008-01-16 Time 01:15:11 PST -0800 (1200474911.25 s)
Start R-work = 0.4528, R-free = 0.4472 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1722 (no bulk solvent and anisotropic scale)

Start R-work = 0.4445, R-free = 0.4361
Final R-work = 0.1130, R-free = 0.1557