# Date 2008-01-16 Time 04:59:22 PST -0800 (1200488362.12 s)
#phil __OFF__

Command line arguments: "../543.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6575
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 543

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.93, 85.9581, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9904

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.99044
Completeness in resolution range: 0.981659
Completeness with d_max=infinity: 0.97852

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2581 [2093/2118]  1884   209  10.0%
  bin  2:  4.2581 -  3.3929 [2024/2042]  1822   202  10.0%
  bin  3:  3.3929 -  2.9678 [1983/2002]  1784   199  10.0%
  bin  4:  2.9678 -  2.6982 [1956/1986]  1761   195  10.0%
  bin  5:  2.6982 -  2.5058 [1960/1979]  1764   196  10.0%
  bin  6:  2.5058 -  2.3587 [1949/1974]  1751   198  10.2%
  bin  7:  2.3587 -  2.2410 [1944/1972]  1755   189   9.7%
  bin  8:  2.2410 -  2.1437 [1941/1977]  1744   197  10.1%
  bin  9:  2.1437 -  2.0614 [1902/1944]  1711   191  10.0%
  bin 10:  2.0614 -  1.9904 [1837/1961]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 10
        2.42 -     3.04: 2220
        3.04 -     3.66: 4689
        3.66 -     4.28: 9087
        4.28 -     4.90: 12414
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.171 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.337 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.341 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28415 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 =====================


==================== 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/noshake/run_543/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.93 85.95805 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.1986   ksol= 0.00   Bsol= 0.00   scale= 1.018    |
|                                                                             |
| 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:   0.11 A                  |
| x-ray target function (ml) for work reflections: 5.539732                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.2426 0.2401       6.231      6.1995|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.1562 0.1518      5.9719        5.96|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.1570 0.1526      5.8064       5.849|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.1627 0.1778      5.6628      5.6861|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.1781 0.1685      5.5496      5.5266|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.1834 0.1787      5.4979       5.461|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.1993 0.1791      5.5173      5.3976|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.1933 0.1947      5.4454      5.4707|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.1991 0.2013      5.4066      5.3868|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.1919 0.2382      5.3578       5.476|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.1957 0.2040      5.3102      5.3601|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.1985 0.1949      5.2902      5.3113|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.2081 0.2135      5.2323      5.2267|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.2040 0.2223      5.1469      5.1327|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7489  1370   153  0.82  23.42   0.88     0.82      34704.17|
|  2:  4.7489 -  3.7897  1303   145  0.90  14.88   1.01     0.96      22008.61|
|  3:  3.7897 -  3.3166  1280   142  0.92  13.15   1.03     1.03      14021.53|
|  4:  3.3166 -  3.0161  1281   140  0.92  13.62   1.04     1.04      10925.71|
|  5:  3.0161 -  2.8015  1257   142  0.91  15.39   1.05     1.03       8740.03|
|  6:  2.8015 -  2.6372  1274   140  0.91  15.62   1.06     1.04       7393.06|
|  7:  2.6372 -  2.5058  1250   139  0.90  15.89   1.06     1.06       6687.97|
|  8:  2.5058 -  2.3972  1254   140  0.90  16.65   1.08     1.07       6665.24|
|  9:  2.3972 -  2.3053  1241   140  0.89  17.62   1.10     1.07       6506.76|
| 10:  2.3053 -  2.2260  1236   137  0.88  18.50   1.13     1.08       6375.49|
| 11:  2.2260 -  2.1566  1253   137  0.88  18.40   1.12     1.10       5847.42|
| 12:  2.1566 -  2.0951  1236   138  0.89  17.74   1.14     1.12       5348.53|
| 13:  2.0951 -  2.0401  1229   134  0.88  18.77   1.13     1.11       4797.04|
| 14:  2.0401 -  1.9904  1166   132  0.87  19.68   1.13     1.08       4340.41|
|alpha:            min =        0.82 max =            1.12 mean =         1.04|
|beta:             min =     4340.41 max =        34704.17 mean =     10558.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        17.10|
|phase err.(test): min =        0.00 max =           89.19 mean =        17.04|
|-----------------------------------------------------------------------------|

============================== 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 = 2.563566              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.271   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.289459              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.791   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      198 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2022 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1840 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2849 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4681 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4406 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5636 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6778 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.160 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.146 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.1986   ksol= 0.00   Bsol= 0.00   scale= 1.018    |
|                                                                             |
| 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:   0.11 A                  |
| x-ray target function (ml) for work reflections: 5.539732                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1742   r_free= 0.1749   ksol= 0.32   Bsol= 38.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.71,-1.33,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.489240                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.356768              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.380   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.151586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.694   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1742      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1442          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7724 = 2.36 * 0.50 * 5.6117 + 1.00 * 0.1597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2456 = 2.36 * 0.50 * 5.2468 + 1.00 * 0.0628                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1239      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1442      final r-factor (free) = 0.1441          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8018 = 0.15 * 1.00 * 5.2468 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8383 = 0.15 * 1.00 * 5.1198 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 4      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.39   16.19    None  None   None       |
|    all(noH): 2823   0      0.00    74.39   16.19    None  None   None       |
|    Sol.    : 438    0      5.20    62.37   36.82    None  None   None       |
|    Mac.    : 2385   0      0.00    74.39   12.40    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 -   7.439:  255   |   5:    37.196 -  44.635:  115        |
|      1:     7.439 -  14.878: 1655   |   6:    44.635 -  52.074:   83        |
|      2:    14.878 -  22.317:  411   |   7:    52.074 -  59.513:   49        |
|      3:    22.317 -  29.757:  135   |   8:    59.513 -  66.952:    6        |
|      4:    29.757 -  37.196:  113   |   9:    66.952 -  74.391:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1441             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1437             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1437   ksol= 0.32   Bsol= 38.62   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.87,-2.71,-1.33,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.116929                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1167   r_free= 0.1431   ksol= 0.32   Bsol= 42.70   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.68,-1.60,-0.00,-0.00,-0.00); trace/3= -2.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.118528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.390271              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.371  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332109              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.764   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1431      final r-factor (free) = 0.1452          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6221 = 1.39 * 0.50 * 5.1204 + 1.00 * 0.0628                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6059 = 1.39 * 0.50 * 5.1061 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1145      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1452      final r-factor (free) = 0.1470          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9407 = 0.33 * 1.00 * 5.1061 + 1.00 * 0.2449                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6966 = 0.33 * 1.00 * 5.0865 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    68.65   16.63    None  None   None       |
|    all(noH): 2823   0      1.52    68.65   16.63    None  None   None       |
|    Sol.    : 438    0      4.93    67.08   37.66    None  None   None       |
|    Mac.    : 2385   0      1.52    68.65   12.77    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:     1.525 -   8.237:  539   |   5:    35.086 -  41.798:  112        |
|      1:     8.237 -  14.949: 1338   |   6:    41.798 -  48.511:   90        |
|      2:    14.949 -  21.662:  387   |   7:    48.511 -  55.223:   88        |
|      3:    21.662 -  28.374:  127   |   8:    55.223 -  61.935:   37        |
|      4:    28.374 -  35.086:   99   |   9:    61.935 -  68.647:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1470             target_work(ml) = 5.098         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1093 r_free = 0.1471             target_work(ml) = 5.097         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1471   ksol= 0.32   Bsol= 42.70   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.68,-1.60,-0.00,-0.00,-0.00); trace/3= -2.46                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1471   ksol= 0.32   Bsol= 42.70   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.38,-1.41,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.097543                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.330061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.553  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.601653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.883  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1471      final r-factor (free) = 0.1482          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9844 = 2.33 * 0.50 * 5.0882 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9858 = 2.33 * 0.50 * 5.0824 + 1.00 * 0.0646                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1058      final r-factor (work) = 0.1049          |
| start r-factor (free) = 0.1482      final r-factor (free) = 0.1505          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1476 = 1.60 * 1.00 * 5.0824 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1433 = 1.60 * 1.00 * 5.0788 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.62    79.85   16.84    None  None   None       |
|    all(noH): 2823   0      0.62    79.85   16.84    None  None   None       |
|    Sol.    : 438    0      6.06    71.46   38.91    None  None   None       |
|    Mac.    : 2385   0      0.62    79.85   12.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.616 -   8.540:  677   |   5:    40.234 -  48.158:  115        |
|      1:     8.540 -  16.464: 1311   |   6:    48.158 -  56.082:   87        |
|      2:    16.464 -  24.387:  329   |   7:    56.082 -  64.005:   47        |
|      3:    24.387 -  32.311:  127   |   8:    64.005 -  71.929:   19        |
|      4:    32.311 -  40.234:  106   |   9:    71.929 -  79.852:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1049 r_free = 0.1505             target_work(ml) = 5.087         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1048 r_free = 0.1505             target_work(ml) = 5.087         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1048   r_free= 0.1505   ksol= 0.32   Bsol= 42.70   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.81,-2.38,-1.41,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.087282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1047   r_free= 0.1505   ksol= 0.32   Bsol= 43.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.09,-1.15,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.087248                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.212948              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.848  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.097366              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.515  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1047      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1505      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6862 = 2.21 * 0.50 * 5.0806 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6905 = 2.21 * 0.50 * 5.0883 + 1.00 * 0.0605                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1050      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1520      final r-factor (free) = 0.1506          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5043 = 0.10 * 1.00 * 5.0883 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5033 = 0.10 * 1.00 * 5.1069 + 1.00 * 0.0061                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.17    73.70   15.92    None  None   None       |
|    all(noH): 2823   0      2.17    73.70   15.92    None  None   None       |
|    Sol.    : 438    0      5.89    67.46   35.00    None  None   None       |
|    Mac.    : 2385   0      2.17    73.70   12.42    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:     2.167 -   9.321:  869   |   5:    37.936 -  45.089:  112        |
|      1:     9.321 -  16.474: 1164   |   6:    45.089 -  52.243:   79        |
|      2:    16.474 -  23.628:  297   |   7:    52.243 -  59.397:   23        |
|      3:    23.628 -  30.782:  127   |   8:    59.397 -  66.551:    8        |
|      4:    30.782 -  37.936:  140   |   9:    66.551 -  73.704:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1506             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1077 r_free = 0.1507             target_work(ml) = 5.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1507   ksol= 0.32   Bsol= 43.68   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.52,-2.09,-1.15,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102063                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1508   ksol= 0.33   Bsol= 43.68   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.02,-1.06,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.102315                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.349870              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.463  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207124              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.170  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1515          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5075 = 1.35 * 0.50 * 5.1072 + 1.00 * 0.0605                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5012 = 1.35 * 0.50 * 5.1110 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1515      final r-factor (free) = 0.1517          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0647 = 0.21 * 1.00 * 5.1110 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0650 = 0.21 * 1.00 * 5.1084 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.40    74.13   16.01    None  None   None       |
|    all(noH): 2823   0      1.40    74.13   16.01    None  None   None       |
|    Sol.    : 438    0      5.89    66.80   35.98    None  None   None       |
|    Mac.    : 2385   0      1.40    74.13   12.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.403 -   8.676:  734   |   5:    37.765 -  45.037:  120        |
|      1:     8.676 -  15.948: 1254   |   6:    45.037 -  52.309:   89        |
|      2:    15.948 -  23.220:  334   |   7:    52.309 -  59.581:   36        |
|      3:    23.220 -  30.492:  119   |   8:    59.581 -  66.854:    8        |
|      4:    30.492 -  37.765:  125   |   9:    66.854 -  74.126:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1517             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1517             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1517   ksol= 0.33   Bsol= 43.68   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.02,-1.06,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110567                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.1018 0.1246      5.3941      5.4999|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.0876 0.1126      5.4491      5.6362|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.1037 0.1479      5.4654      5.8551|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.1179 0.1455      5.4315      5.5568|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.1259 0.1691      5.2952      5.5106|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.1153 0.1679      5.1762      5.3903|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.1205 0.1598      5.1213      5.3544|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.1108 0.1706       5.034      5.3345|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.1116 0.1597      4.9894      5.1999|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.1081 0.1768      4.9385       5.229|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.1102 0.1611      4.9018       5.182|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.1077 0.1625      4.8485      5.1897|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.1039 0.1593       4.758      5.0292|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.1022 0.1724       4.642      4.9303|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7489  1370   153  0.94   9.12   0.98     0.95       7003.48|
|  2:  4.7489 -  3.7897  1303   145  0.95   7.87   1.01     1.00       8917.16|
|  3:  3.7897 -  3.3166  1280   142  0.94  10.67   1.02     1.01       9994.80|
|  4:  3.3166 -  3.0161  1281   140  0.93  12.85   1.00     0.99       9704.09|
|  5:  3.0161 -  2.8015  1257   142  0.91  14.84   0.99     0.96       7632.25|
|  6:  2.8015 -  2.6372  1274   140  0.91  14.88   0.98     0.96       6477.89|
|  7:  2.6372 -  2.5058  1250   139  0.91  14.71   0.98     0.96       5573.95|
|  8:  2.5058 -  2.3972  1254   140  0.92  13.63   0.99     0.97       4793.66|
|  9:  2.3972 -  2.3053  1241   140  0.92  14.40   1.00     0.97       4529.06|
| 10:  2.3053 -  2.2260  1236   137  0.91  14.55   1.00     0.96       4060.12|
| 11:  2.2260 -  2.1566  1253   137  0.91  15.19   0.99     0.96       4005.21|
| 12:  2.1566 -  2.0951  1236   138  0.92  14.21   1.00     0.99       3633.31|
| 13:  2.0951 -  2.0401  1229   134  0.92  14.52   1.00     1.00       3126.49|
| 14:  2.0401 -  1.9904  1166   132  0.92  13.98   0.98     0.94       2385.98|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2385.98 max =         9994.80 mean =      5901.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.19|
|phase err.(test): min =        0.00 max =           89.85 mean =        12.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1517   ksol= 0.33   Bsol= 43.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.86,-0.90,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1517   ksol= 0.33   Bsol= 43.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.30,-1.86,-0.90,-0.00,-0.00,-0.00); trace/3= -1.69                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.110615                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7489 0.99   1370  153 0.1018 0.1247      5.3946      5.5006|
|  2:  4.7489 -  3.7897 0.99   1303  145 0.0876 0.1126      5.4493       5.636|
|  3:  3.7897 -  3.3166 0.99   1280  142 0.1037 0.1479      5.4654      5.8552|
|  4:  3.3166 -  3.0161 0.99   1281  140 0.1179 0.1455      5.4315      5.5568|
|  5:  3.0161 -  2.8015 0.99   1257  142 0.1259 0.1690      5.2952      5.5105|
|  6:  2.8015 -  2.6372 0.99   1274  140 0.1153 0.1679      5.1762      5.3903|
|  7:  2.6372 -  2.5058 0.99   1250  139 0.1205 0.1598      5.1213      5.3544|
|  8:  2.5058 -  2.3972 0.98   1254  140 0.1108 0.1706       5.034      5.3344|
|  9:  2.3972 -  2.3053 0.98   1241  140 0.1116 0.1597      4.9895      5.1999|
| 10:  2.3053 -  2.2260 0.99   1236  137 0.1081 0.1768      4.9385       5.229|
| 11:  2.2260 -  2.1566 0.98   1253  137 0.1102 0.1611      4.9018      5.1819|
| 12:  2.1566 -  2.0951 0.97   1236  138 0.1077 0.1625      4.8485      5.1897|
| 13:  2.0951 -  2.0401 1.00   1229  134 0.1039 0.1593       4.758      5.0291|
| 14:  2.0401 -  1.9904 0.91   1166  132 0.1022 0.1724       4.642      4.9304|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7489  1370   153  0.94   9.12   0.98     0.95       7012.53|
|  2:  4.7489 -  3.7897  1303   145  0.95   7.87   1.02     1.00       8922.92|
|  3:  3.7897 -  3.3166  1280   142  0.94  10.67   1.02     1.01       9994.74|
|  4:  3.3166 -  3.0161  1281   140  0.93  12.85   1.01     0.99       9703.27|
|  5:  3.0161 -  2.8015  1257   142  0.91  14.84   0.99     0.96       7631.29|
|  6:  2.8015 -  2.6372  1274   140  0.91  14.88   0.99     0.96       6477.20|
|  7:  2.6372 -  2.5058  1250   139  0.91  14.71   0.99     0.96       5573.88|
|  8:  2.5058 -  2.3972  1254   140  0.92  13.63   0.99     0.98       4793.44|
|  9:  2.3972 -  2.3053  1241   140  0.92  14.40   1.01     0.98       4529.19|
| 10:  2.3053 -  2.2260  1236   137  0.91  14.55   1.00     0.96       4059.97|
| 11:  2.2260 -  2.1566  1253   137  0.91  15.19   1.00     0.97       4004.95|
| 12:  2.1566 -  2.0951  1236   138  0.92  14.21   1.01     1.00       3632.88|
| 13:  2.0951 -  2.0401  1229   134  0.92  14.52   1.01     1.00       3126.13|
| 14:  2.0401 -  1.9904  1166   132  0.92  13.98   0.98     0.95       2385.92|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2385.92 max =         9994.74 mean =      5901.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.19|
|phase err.(test): min =        0.00 max =           89.85 mean =        12.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.794)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    74.08   15.96    None  None   None       |
|    all(noH): 2823   0      1.35    74.08   15.96    None  None   None       |
|    Sol.    : 438    0      5.84    66.75   35.93    None  None   None       |
|    Mac.    : 2385   0      1.35    74.08   12.29    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:     1.354 -   8.626:  734   |   5:    37.715 -  44.987:  120        |
|      1:     8.626 -  15.898: 1254   |   6:    44.987 -  52.259:   89        |
|      2:    15.898 -  23.170:  334   |   7:    52.259 -  59.532:   36        |
|      3:    23.170 -  30.443:  119   |   8:    59.532 -  66.804:    8        |
|      4:    30.443 -  37.715:  125   |   9:    66.804 -  74.076:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 278         
Filter by distance & map next to the model:
   mapped sites are within: 0.519 - 5.449
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 278
   mapped sites are within: 0.701 - 5.449

peak=    5.752 closest distance to " CB  ARG A 275 " =    0.945
peak=    5.680 closest distance to " NH2 ARG A  56 " =    2.217
peak=    5.444 closest distance to " O   HOH Z 126 " =    1.881
peak=    5.283 closest distance to " CB  GLN A 223 " =    1.389
peak=    4.929 closest distance to " CB  SER A  63 " =    1.166
peak=    4.929 closest distance to " O   HOH Z 232 " =    2.354
peak=    4.886 closest distance to " O   HOH Z 142 " =    1.699
peak=    4.795 closest distance to " CB  GLU A 152 " =    1.150
peak=    4.794 closest distance to " CG  PRO A  90 " =    1.150
peak=    4.778 closest distance to " CB  GLN A 183 " =    1.174
peak=    4.705 closest distance to " O   HOH Z 236 " =    1.878
peak=    4.658 closest distance to " O   HOH Z  78 " =    1.757
peak=    4.655 closest distance to " C   PRO A 198 " =    1.466
peak=    4.531 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.490 closest distance to " CB  ASN A 148 " =    1.523
peak=    4.461 closest distance to " CG  PRO A 243 " =    1.046
peak=    4.459 closest distance to " CG  PRO A 280 " =    0.789
peak=    4.415 closest distance to " NE2 GLN A  11 " =    1.061
peak=    4.367 closest distance to " CG  PRO A 198 " =    1.298
peak=    4.350 closest distance to " O   HOH Z 234 " =    3.664
peak=    4.341 closest distance to " O   HOH Z 298 " =    1.872
peak=    4.336 closest distance to " O   HOH Z  15 " =    2.253
peak=    4.317 closest distance to " ND2 ASN A 187 " =    1.511
peak=    4.279 closest distance to " O   HOH Z 427 " =    2.891
peak=    4.257 closest distance to " CG2 VAL A 257 " =    0.937
peak=    4.242 closest distance to " O   HOH Z 303 " =    2.033
peak=    4.241 closest distance to " O   HOH Z 369 " =    2.116
peak=    4.183 closest distance to " O   HOH Z  66 " =    2.124
peak=    4.168 closest distance to " O   HOH Z 402 " =    1.440
peak=    4.166 closest distance to " OD1 ASN A  69 " =    2.564
peak=    4.162 closest distance to " CB  LEU A 228 " =    1.068
peak=    4.161 closest distance to " O   HOH Z  40 " =    1.744
peak=    4.153 closest distance to " CB  GLU A 128 " =    1.015
peak=    4.151 closest distance to " O   HOH Z 250 " =    1.474
peak=    4.139 closest distance to " O   HOH Z 189 " =    2.156
peak=    4.126 closest distance to " CB  ARG A 190 " =    1.707
peak=    4.120 closest distance to " O   HOH Z 193 " =    1.861
peak=    4.109 closest distance to " CB  ARG A  79 " =    1.336
peak=    4.107 closest distance to " CZ  PHE A 218 " =    1.039
peak=    4.058 closest distance to " O   HOH Z 158 " =    3.084
peak=    4.048 closest distance to " CA  ASN A 215 " =    1.093
peak=    4.030 closest distance to " O   HOH Z 316 " =    3.099
peak=    4.019 closest distance to " O   HOH Z 389 " =    1.849
peak=    4.013 closest distance to " O   HOH Z  43 " =    1.944
peak=    4.012 closest distance to " CB  VAL A 265 " =    1.230
peak=    4.003 closest distance to " O   HOH Z  44 " =    1.855
peak=    3.991 closest distance to " CB  SER A   3 " =    1.299
peak=    3.976 closest distance to " O   HOH Z  61 " =    1.597
peak=    3.962 closest distance to " O   HOH Z 403 " =    1.673
peak=    3.952 closest distance to " O   HOH Z 144 " =    2.176
peak=    3.952 closest distance to " O   HOH Z 346 " =    1.691
peak=    3.936 closest distance to " CB  TRP A 266 " =    0.960
peak=    3.929 closest distance to " CB  ALA A 291 " =    1.301
peak=    3.923 closest distance to " O   HOH Z  54 " =    1.724
peak=    3.922 closest distance to " CE  LYS A  76 " =    0.905
peak=    3.915 closest distance to " O   HOH Z 203 " =    1.719
peak=    3.914 closest distance to " O   SER A  87 " =    2.225
peak=    3.900 closest distance to " O   HOH Z 344 " =    3.155
peak=    3.854 closest distance to " O   HOH Z 392 " =    3.108
peak=    3.841 closest distance to " CD2 TRP A 179 " =    1.388
peak=    3.837 closest distance to " O   HOH Z  10 " =    1.790
peak=    3.830 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.828 closest distance to " CD  ARG A 159 " =    0.701
peak=    3.804 closest distance to " CG2 ILE A 120 " =    1.175
peak=    3.797 closest distance to " CB  TRP A 179 " =    1.290
peak=    3.782 closest distance to " O   HOH Z 245 " =    1.320
peak=    3.779 closest distance to " O   HOH Z 128 " =    2.029
peak=    3.774 closest distance to " OD2 ASP A 286 " =    2.815
peak=    3.772 closest distance to " NH1AARG A 145 " =    1.185
peak=    3.771 closest distance to " CB  ILE A 120 " =    1.201
peak=    3.762 closest distance to " CB  ASP A 140 " =    0.822
peak=    3.759 closest distance to " O   HOH Z 368 " =    1.898
peak=    3.746 closest distance to " O   HOH Z 423 " =    1.883
peak=    3.730 closest distance to " O   HOH Z 209 " =    2.310
peak=    3.723 closest distance to " NZ  LYS A 117 " =    3.284
peak=    3.719 closest distance to " N   ARG A 156 " =    1.317
peak=    3.719 closest distance to " CA  ARG A  36 " =    0.994
peak=    3.715 closest distance to " O   HOH Z 132 " =    2.551
peak=    3.713 closest distance to " CB  VAL A 202 " =    1.519
peak=    3.711 closest distance to " O   HOH Z  19 " =    2.393
peak=    3.697 closest distance to " O   HOH Z  21 " =    1.799
peak=    3.690 closest distance to " CB  ARG A  79 " =    0.880
peak=    3.689 closest distance to " O   HOH Z  97 " =    2.545
peak=    3.675 closest distance to " O   TRP A 274 " =    1.882
peak=    3.675 closest distance to " CB  GLU A 277 " =    3.517
peak=    3.672 closest distance to " O   HOH Z   9 " =    2.108
peak=    3.671 closest distance to " O   HOH Z 147 " =    1.764
peak=    3.666 closest distance to " N   ASN A  39 " =    1.187
peak=    3.663 closest distance to " O   HOH Z 173 " =    1.942
peak=    3.652 closest distance to " CG1BVAL A  72 " =    1.576
peak=    3.651 closest distance to " CA  ALA A  21 " =    1.137
peak=    3.643 closest distance to " NH2BARG A 145 " =    2.003
peak=    3.642 closest distance to " CB  SER A  26 " =    1.612
peak=    3.629 closest distance to " O   HOH Z 148 " =    3.306
peak=    3.616 closest distance to " CG1 ILE A  33 " =    1.276
peak=    3.614 closest distance to " O   HOH Z 248 " =    1.659
peak=    3.612 closest distance to " O   HOH Z 291 " =    1.541
peak=    3.601 closest distance to " CA  THR A 264 " =    0.896
peak=    3.594 closest distance to " CD1 ILE A 106 " =    0.882
peak=    3.590 closest distance to " O   HOH Z  97 " =    1.949
peak=    3.585 closest distance to " O   HOH Z 172 " =    3.462
peak=    3.584 closest distance to " ND2 ASN A 110 " =    1.757
peak=    3.573 closest distance to " CB  SER A 216 " =    0.775
peak=    3.572 closest distance to " O   HOH Z 371 " =    3.133
peak=    3.569 closest distance to " O   HOH Z   1 " =    2.064
peak=    3.557 closest distance to " O   HOH Z 407 " =    2.401
peak=    3.557 closest distance to " CD1 LEU A 300 " =    1.274
peak=    3.552 closest distance to " CG  ARG A  66 " =    2.643
peak=    3.547 closest distance to " CB  ARG A 139 " =    0.936
peak=    3.545 closest distance to " CA  GLY A  80 " =    0.757
peak=    3.534 closest distance to " O   HOH Z 425 " =    1.884
peak=    3.525 closest distance to " O   HOH Z  59 " =    1.996
peak=    3.523 closest distance to " CD BLYS A 290 " =    1.071
peak=    3.518 closest distance to " O   HOH Z 426 " =    1.551
peak=    3.517 closest distance to " CB  GLU A  46 " =    0.994
peak=    3.515 closest distance to " CA  THR A 221 " =    0.962
peak=    3.515 closest distance to " O   HOH Z  61 " =    1.488
peak=    3.511 closest distance to " CG  GLN A  77 " =    2.015
peak=    3.501 closest distance to " O   HOH Z 305 " =    3.614
peak=    3.500 closest distance to " CG1 VAL A 153 " =    0.977
peak=    3.499 closest distance to " O   HOH Z 272 " =    1.790
peak=    3.496 closest distance to " OE1 GLU A   2 " =    2.264
peak=    3.496 closest distance to " NE2 GLN A  77 " =    3.223
peak=    3.484 closest distance to " CA  ASP A 162 " =    1.078
peak=    3.470 closest distance to " O   HOH Z 214 " =    2.059
peak=    3.468 closest distance to " O   HOH Z 421 " =    1.722
peak=    3.467 closest distance to " O   HOH Z 280 " =    2.975
peak=    3.465 closest distance to " O   HOH Z 419 " =    1.966
peak=    3.464 closest distance to " O   HOH Z 368 " =    3.570
peak=    3.464 closest distance to " CD2 LEU A 297 " =    0.893
peak=    3.463 closest distance to " CB  MET A  40 " =    0.874
peak=    3.461 closest distance to " O   HOH Z 417 " =    3.103
peak=    3.459 closest distance to " CA  ALA A  84 " =    1.194
peak=    3.457 closest distance to " O   HOH Z 383 " =    1.675
peak=    3.453 closest distance to " CA  SER A  87 " =    0.994
peak=    3.450 closest distance to " O   HOH Z 187 " =    2.285
peak=    3.445 closest distance to " CB  HIS A 108 " =    0.841
peak=    3.444 closest distance to " O   HOH Z 193 " =    1.623
peak=    3.439 closest distance to " CA  ILE A  33 " =    1.428
peak=    3.438 closest distance to " O   HOH Z 433 " =    1.833
peak=    3.425 closest distance to " CA  ILE A 234 " =    0.893
peak=    3.423 closest distance to " O   MET A 105 " =    1.825
peak=    3.404 closest distance to " O   HOH Z 175 " =    2.166
peak=    3.403 closest distance to " CG2 ILE A  20 " =    1.425
peak=    3.402 closest distance to " NH2 ARG A 156 " =    1.103
peak=    3.399 closest distance to " O   HOH Z 234 " =    1.898
peak=    3.392 closest distance to " CA  ARG A 195 " =    1.155
peak=    3.388 closest distance to " CA  ALA A  51 " =    0.846
peak=    3.387 closest distance to " CZ2 TRP A 179 " =    1.787
peak=    3.379 closest distance to " CG  GLN A  11 " =    1.579
peak=    3.375 closest distance to " O   HOH Z 313 " =    1.806
peak=    3.374 closest distance to " CG2 THR A 221 " =    1.135
peak=    3.372 closest distance to " CB  THR A  31 " =    1.584
peak=    3.370 closest distance to " O   HOH Z 193 " =    2.002
peak=    3.370 closest distance to " O   ALA A   1 " =    1.661
peak=    3.368 closest distance to " O   HOH Z 327 " =    1.678
peak=    3.366 closest distance to " O   HOH Z 128 " =    2.124
peak=    3.365 closest distance to " CG  LYS A  76 " =    0.973
peak=    3.364 closest distance to " CB  PRO A 198 " =    1.057
peak=    3.358 closest distance to " CB  SER A 212 " =    1.121
peak=    3.358 closest distance to " O   HOH Z 185 " =    1.723
peak=    3.353 closest distance to " O   HOH Z 435 " =    1.939
peak=    3.352 closest distance to " O   HOH Z 219 " =    2.056
peak=    3.349 closest distance to " CB  ALA A 248 " =    1.336
peak=    3.347 closest distance to " CD  ARG A 269 " =    0.959
peak=    3.347 closest distance to " CB  ASN A 110 " =    1.049
peak=    3.346 closest distance to " CB  ALA A 114 " =    1.162
peak=    3.333 closest distance to " NH1BARG A 145 " =    1.260
peak=    3.332 closest distance to " O   HOH Z 365 " =    3.071
peak=    3.329 closest distance to " CB  SER A 141 " =    1.032
peak=    3.328 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.328 closest distance to " O   HOH Z 286 " =    2.266
peak=    3.327 closest distance to " CG1 ILE A 120 " =    1.095
peak=    3.323 closest distance to " O   HOH Z  66 " =    2.132
peak=    3.322 closest distance to " CA  ASP A 140 " =    1.120
peak=    3.322 closest distance to " CD  LYS A 166 " =    1.192
peak=    3.321 closest distance to " O   HOH Z 163 " =    1.763
peak=    3.317 closest distance to " O   HOH Z 227 " =    1.539
peak=    3.308 closest distance to " CB  GLN A 278 " =    0.854
peak=    3.308 closest distance to " O   HOH Z 359 " =    1.513
peak=    3.307 closest distance to " O   HOH Z 329 " =    3.807
peak=    3.304 closest distance to " CD  ARG A  36 " =    1.004
peak=    3.301 closest distance to " CA  ALA A 233 " =    1.354
peak=    3.299 closest distance to " CA  ALA A  43 " =    1.189
peak=    3.298 closest distance to " CB  ALA A 242 " =    0.902
peak=    3.297 closest distance to " O   HOH Z 265 " =    2.399
peak=    3.297 closest distance to " CB  SER A  62 " =    1.286
peak=    3.295 closest distance to " CB  ALA A  34 " =    0.935
peak=    3.294 closest distance to " OG BSER A 164 " =    2.337
peak=    3.290 closest distance to " O   HOH Z 227 " =    2.132
peak=    3.286 closest distance to " O   HOH Z 273 " =    2.683
peak=    3.286 closest distance to " CD  LYS A 119 " =    1.385
peak=    3.282 closest distance to " O   HOH Z 213 " =    1.809
peak=    3.274 closest distance to " CA  ALA A 248 " =    1.259
peak=    3.268 closest distance to " CE1 TYR A 186 " =    1.365
peak=    3.266 closest distance to " NE2 GLN A  73 " =    3.851
peak=    3.265 closest distance to " N   PHE A 130 " =    1.280
peak=    3.265 closest distance to " CA  MET A  40 " =    1.067
peak=    3.263 closest distance to " O   ALA A 165 " =    1.493
peak=    3.258 closest distance to " O   HOH Z 406 " =    1.559
peak=    3.247 closest distance to " CB  ASN A 142 " =    1.061
peak=    3.245 closest distance to " CD1 LEU A  96 " =    0.756
peak=    3.245 closest distance to " CB  LYS A 290 " =    1.025
peak=    3.241 closest distance to " O   HOH Z  49 " =    2.197
peak=    3.237 closest distance to " CA  MET A 105 " =    0.975
peak=    3.229 closest distance to " OG  SER A 206 " =    1.307
peak=    3.228 closest distance to " O   HOH Z  88 " =    2.684
peak=    3.224 closest distance to " O   HOH Z 123 " =    2.239
peak=    3.221 closest distance to " CB  ASN A 224 " =    1.088
peak=    3.219 closest distance to " O   HOH Z  85 " =    2.244
peak=    3.217 closest distance to " OG1 THR A 294 " =    1.651
peak=    3.217 closest distance to " CD1AILE A 234 " =    0.970
peak=    3.217 closest distance to " CB  ASN A 215 " =    1.159
peak=    3.214 closest distance to " O   HOH Z 261 " =    2.172
peak=    3.212 closest distance to " CG  GLU A 277 " =    2.229
peak=    3.212 closest distance to " CB  VAL A 126 " =    1.021
peak=    3.210 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.205 closest distance to " O   HOH Z 261 " =    1.545
peak=    3.199 closest distance to " O   HOH Z 345 " =    3.296
peak=    3.197 closest distance to " CG  MET A 113 " =    1.066
peak=    3.191 closest distance to " CB  TYR A 116 " =    0.788
peak=    3.189 closest distance to " O   HOH Z 295 " =    1.504
peak=    3.188 closest distance to " CB  THR A 157 " =    1.070
peak=    3.188 closest distance to " CB  GLN A  88 " =    1.152
peak=    3.187 closest distance to " CD2 LEU A 255 " =    1.336
peak=    3.187 closest distance to " CG1 ILE A 151 " =    0.956
peak=    3.184 closest distance to " O   HOH Z 410 " =    1.934
peak=    3.182 closest distance to " O   HOH Z 430 " =    5.449
peak=    3.180 closest distance to " O   THR A 220 " =    1.262
peak=    3.178 closest distance to " CE BLYS A 290 " =    1.122
peak=    3.178 closest distance to " N   SER A 135 " =    1.262
peak=    3.177 closest distance to " CB  SER A 273 " =    0.850
peak=    3.174 closest distance to " O   HOH Z  88 " =    1.867
peak=    3.172 closest distance to " CB  MET A  47 " =    1.203
peak=    3.171 closest distance to " CB  GLN A 103 " =    0.787
peak=    3.171 closest distance to " CD2 HIS A  81 " =    1.200
peak=    3.168 closest distance to " O   HOH Z 163 " =    1.845
peak=    3.163 closest distance to " CD  ARG A 219 " =    1.124
peak=    3.162 closest distance to " O   HOH Z 371 " =    1.723
peak=    3.157 closest distance to " O   HOH Z 336 " =    1.762
peak=    3.151 closest distance to " CD1 ILE A 263 " =    1.294
peak=    3.149 closest distance to " O   HOH Z 411 " =    3.839
peak=    3.147 closest distance to " O   HOH Z 337 " =    3.590
peak=    3.139 closest distance to " C   TYR A 214 " =    1.420
peak=    3.136 closest distance to " CG2 VAL A 197 " =    1.055
peak=    3.134 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.134 closest distance to " O   HOH Z 298 " =    2.555
peak=    3.133 closest distance to " CD  ARG A 156 " =    1.544
peak=    3.125 closest distance to " O   HOH Z 133 " =    2.699
peak=    3.124 closest distance to " NH1 ARG A 138 " =    1.137
peak=    3.123 closest distance to " O   HOH Z  44 " =    3.246
peak=    3.118 closest distance to " NH2AARG A 190 " =    1.128
peak=    3.117 closest distance to " O   HOH Z 267 " =    2.025
peak=    3.116 closest distance to " O   HOH Z 357 " =    1.841
peak=    3.115 closest distance to " ND1 HIS A  86 " =    1.735
peak=    3.112 closest distance to " O   HOH Z 257 " =    2.154
peak=    3.111 closest distance to " O   THR A 251 " =    1.124
peak=    3.105 closest distance to " CG BARG A 275 " =    1.456
peak=    3.103 closest distance to " NZ  LYS A  76 " =    1.393
peak=    3.094 closest distance to " ND1 HIS A  81 " =    1.663
peak=    3.077 closest distance to " O   HOH Z 391 " =    2.974
peak=    3.077 closest distance to " O   HOH Z 423 " =    2.992
peak=    3.072 closest distance to " CB  ALA A 291 " =    0.788
peak=    3.072 closest distance to " OE1 GLN A  55 " =    1.362
peak=    3.053 closest distance to " O   HOH Z 417 " =    2.448
peak=    3.051 closest distance to " O   HOH Z 374 " =    2.576
peak=    3.048 closest distance to " CA  THR A 221 " =    1.436
peak=    3.042 closest distance to " O   HOH Z 325 " =    3.788
peak=    3.036 closest distance to " O   HOH Z 285 " =    2.944
peak=    3.027 closest distance to " NH1AARG A 145 " =    0.859
peak=    3.019 closest distance to " O   GLN A 278 " =    1.491

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.525 - 5.211
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 200
   mapped sites are within: 0.792 - 5.211

peak=   -4.634 closest distance to " O   HOH Z 266 " =    4.878
peak=   -4.610 closest distance to " O   HOH Z 290 " =    1.050
peak=   -4.483 closest distance to " CD  GLN A  58 " =    0.979
peak=   -4.438 closest distance to " CB  PRO A 243 " =    2.658
peak=   -4.409 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.333 closest distance to " O   VAL A  67 " =    2.695
peak=   -4.320 closest distance to " C   HIS A 108 " =    1.096
peak=   -4.245 closest distance to " SG  CYS A 254 " =    3.527
peak=   -4.191 closest distance to " CG  GLN A 223 " =    1.767
peak=   -4.188 closest distance to " CA  VAL A  67 " =    2.855
peak=   -4.176 closest distance to " CZ3 TRP A 179 " =    1.207
peak=   -4.128 closest distance to " ND2 ASN A  45 " =    1.498
peak=   -4.126 closest distance to " CG  ASP A 231 " =    0.796
peak=   -4.032 closest distance to " OG BSER A 134 " =    1.187
peak=   -3.977 closest distance to " O   PRO A 198 " =    1.234
peak=   -3.970 closest distance to " O   HOH Z 372 " =    2.329
peak=   -3.963 closest distance to " CB  ALA A 161 " =    2.530
peak=   -3.899 closest distance to " O   HOH Z 198 " =    1.993
peak=   -3.894 closest distance to " CG1 VAL A 112 " =    2.803
peak=   -3.888 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.881 closest distance to " CD2 PHE A 192 " =    2.075
peak=   -3.878 closest distance to " O   HOH Z 389 " =    1.849
peak=   -3.850 closest distance to " O   HOH Z 351 " =    1.430
peak=   -3.848 closest distance to " O   HOH Z 114 " =    3.142
peak=   -3.842 closest distance to " O   HOH Z 435 " =    2.819
peak=   -3.836 closest distance to " CB  ALA A 291 " =    2.240
peak=   -3.830 closest distance to " O   HOH Z 377 " =    2.041
peak=   -3.824 closest distance to " O   HOH Z 231 " =    2.239
peak=   -3.815 closest distance to " O   HOH Z 407 " =    2.999
peak=   -3.797 closest distance to " O   HOH Z 211 " =    1.743
peak=   -3.796 closest distance to " CG2 ILE A 263 " =    2.275
peak=   -3.791 closest distance to " CB  ASN A  39 " =    2.266
peak=   -3.775 closest distance to " O   HOH Z 185 " =    2.347
peak=   -3.770 closest distance to " CD  ARG A 139 " =    1.502
peak=   -3.766 closest distance to " ND2 ASN A  45 " =    1.070
peak=   -3.757 closest distance to " C   ASP A 231 " =    2.634
peak=   -3.731 closest distance to " N   ALA A  43 " =    2.470
peak=   -3.699 closest distance to " O   PRO A 163 " =    2.016
peak=   -3.692 closest distance to " CZ  TYR A 169 " =    1.721
peak=   -3.692 closest distance to " O   HOH Z 126 " =    1.928
peak=   -3.678 closest distance to " CD1 PHE A  59 " =    1.837
peak=   -3.675 closest distance to " OG  SER A  97 " =    2.226
peak=   -3.667 closest distance to " O   HOH Z 196 " =    1.997
peak=   -3.664 closest distance to " OXT GLY A 302 " =    2.769
peak=   -3.659 closest distance to " CG  PHE A 283 " =    2.729
peak=   -3.655 closest distance to " O   HOH Z 353 " =    2.134
peak=   -3.630 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.625 closest distance to " O   HOH Z 313 " =    1.897
peak=   -3.613 closest distance to " CD1 LEU A 101 " =    2.312
peak=   -3.603 closest distance to " N   SER A 212 " =    1.908
peak=   -3.601 closest distance to " OD1 ASP A 171 " =    1.608
peak=   -3.586 closest distance to " O   HOH Z 311 " =    3.594
peak=   -3.561 closest distance to " O   ALA A 161 " =    1.586
peak=   -3.558 closest distance to " CG  ARG A 269 " =    2.326
peak=   -3.556 closest distance to " OD2 ASP A 171 " =    2.337
peak=   -3.554 closest distance to " O   HOH Z  43 " =    1.629
peak=   -3.546 closest distance to " CD  ARG A 195 " =    5.169
peak=   -3.544 closest distance to " N   GLN A  58 " =    1.805
peak=   -3.544 closest distance to " CG  GLU A 277 " =    1.173
peak=   -3.539 closest distance to " CG  ASP A 132 " =    2.287
peak=   -3.538 closest distance to " C   ALA A 158 " =    1.289
peak=   -3.533 closest distance to " CE  MET A 105 " =    2.270
peak=   -3.531 closest distance to " NH2AARG A 275 " =    5.211
peak=   -3.530 closest distance to " CZ  PHE A  59 " =    1.506
peak=   -3.527 closest distance to " NH2 ARG A  79 " =    1.596
peak=   -3.526 closest distance to " CD2 LEU A 300 " =    2.871
peak=   -3.523 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -3.523 closest distance to " CG1 VAL A 230 " =    2.121
peak=   -3.519 closest distance to " CZ3 TRP A 274 " =    1.133
peak=   -3.513 closest distance to " CA  GLY A 203 " =    2.285
peak=   -3.500 closest distance to " CD1 LEU A 228 " =    2.204
peak=   -3.472 closest distance to " C   MET A 188 " =    1.390
peak=   -3.457 closest distance to " OD1 ASN A 187 " =    1.608
peak=   -3.455 closest distance to " CG  ARG A  66 " =    2.469
peak=   -3.453 closest distance to " CB  ALA A 248 " =    2.173
peak=   -3.448 closest distance to " CG1 VAL A  78 " =    3.151
peak=   -3.447 closest distance to " O   ARG A 145 " =    1.568
peak=   -3.447 closest distance to " CB  PRO A 163 " =    2.520
peak=   -3.440 closest distance to " CA  GLY A 241 " =    3.023
peak=   -3.439 closest distance to " N   ASP A 286 " =    2.396
peak=   -3.433 closest distance to " O   HOH Z 298 " =    1.231
peak=   -3.429 closest distance to " C   LEU A 143 " =    1.015
peak=   -3.427 closest distance to " O   HOH Z 385 " =    2.128
peak=   -3.421 closest distance to " CB  ALA A 291 " =    2.313
peak=   -3.417 closest distance to " NH1 ARG A 195 " =    2.524
peak=   -3.398 closest distance to " O   SER A  95 " =    1.561
peak=   -3.393 closest distance to " O   HOH Z 244 " =    2.081
peak=   -3.392 closest distance to " CD1 ILE A 239 " =    2.136
peak=   -3.390 closest distance to " NE2 GLN A 278 " =    1.798
peak=   -3.387 closest distance to " OD2 ASP A 191 " =    1.441
peak=   -3.386 closest distance to " CB  ALA A 248 " =    2.317
peak=   -3.376 closest distance to " CG  GLU A 152 " =    0.792
peak=   -3.375 closest distance to " O   GLY A 211 " =    1.350
peak=   -3.373 closest distance to " O   HOH Z  52 " =    1.258
peak=   -3.372 closest distance to " O   HOH Z 322 " =    1.600
peak=   -3.370 closest distance to " CD1 LEU A 297 " =    2.367
peak=   -3.368 closest distance to " CE2 PHE A 218 " =    2.443
peak=   -3.367 closest distance to " SG ACYS A 201 " =    2.018
peak=   -3.357 closest distance to " OD1 ASN A 148 " =    1.527
peak=   -3.355 closest distance to " N   ALA A 248 " =    1.728
peak=   -3.341 closest distance to " O   HOH Z 102 " =    1.585
peak=   -3.340 closest distance to " N   ALA A 226 " =    2.008
peak=   -3.335 closest distance to " OG BSER A 134 " =    1.791
peak=   -3.330 closest distance to " O   HOH Z  44 " =    2.289
peak=   -3.322 closest distance to " CB  ASP A 286 " =    2.101
peak=   -3.321 closest distance to " N   THR A 157 " =    1.574
peak=   -3.320 closest distance to " OD2 ASP A  50 " =    2.338
peak=   -3.318 closest distance to " CB  GLN A  11 " =    1.712
peak=   -3.316 closest distance to " N   MET A 105 " =    2.917
peak=   -3.315 closest distance to " O   HOH Z  13 " =    1.468
peak=   -3.311 closest distance to " O   HOH Z 377 " =    1.652
peak=   -3.310 closest distance to " O   HOH Z 166 " =    1.996
peak=   -3.309 closest distance to " O   SER A 135 " =    1.476
peak=   -3.308 closest distance to " ND2 ASN A 187 " =    1.491
peak=   -3.303 closest distance to " CD2 PHE A  61 " =    2.489
peak=   -3.301 closest distance to " OE1 GLN A  88 " =    1.153
peak=   -3.301 closest distance to " O   HOH Z  11 " =    1.725
peak=   -3.300 closest distance to " O   HOH Z 292 " =    4.512
peak=   -3.291 closest distance to " CZ  PHE A 155 " =    1.203
peak=   -3.289 closest distance to " OG  SER A  62 " =    1.590
peak=   -3.286 closest distance to " N   PHE A  59 " =    2.162
peak=   -3.275 closest distance to " O   HOH Z  60 " =    2.306
peak=   -3.274 closest distance to " CB  ALA A  43 " =    2.492
peak=   -3.270 closest distance to " O   HOH Z 165 " =    1.963
peak=   -3.269 closest distance to " OG  SER A 206 " =    1.691
peak=   -3.255 closest distance to " O   HOH Z 193 " =    2.058
peak=   -3.254 closest distance to " NH2 ARG A  79 " =    2.013
peak=   -3.253 closest distance to " O   HOH Z  76 " =    1.911
peak=   -3.251 closest distance to " CA  GLY A 133 " =    1.977
peak=   -3.250 closest distance to " CZ  PHE A 130 " =    0.945
peak=   -3.250 closest distance to " CA  GLY A  98 " =    1.900
peak=   -3.250 closest distance to " O   GLN A 240 " =    2.016
peak=   -3.247 closest distance to " O   HOH Z 174 " =    4.351
peak=   -3.244 closest distance to " CB  TYR A  15 " =    2.181
peak=   -3.243 closest distance to " O   VAL A 189 " =    2.569
peak=   -3.236 closest distance to " OG BSER A 210 " =    2.397
peak=   -3.233 closest distance to " O   HOH Z  91 " =    1.572
peak=   -3.233 closest distance to " NE2 GLN A 194 " =    1.738
peak=   -3.229 closest distance to " CE1 TYR A 247 " =    2.799
peak=   -3.228 closest distance to " NE2 GLN A  88 " =    0.953
peak=   -3.227 closest distance to " O   LEU A 167 " =    1.378
peak=   -3.227 closest distance to " O   ALA A  51 " =    1.450
peak=   -3.225 closest distance to " O   HOH Z 417 " =    2.482
peak=   -3.223 closest distance to " O   HOH Z 394 " =    1.498
peak=   -3.218 closest distance to " N   GLY A  23 " =    2.253
peak=   -3.214 closest distance to " O   HOH Z 123 " =    2.304
peak=   -3.213 closest distance to " O   HOH Z 351 " =    1.380
peak=   -3.210 closest distance to " O   HOH Z  38 " =    1.602
peak=   -3.206 closest distance to " CG1 VAL A 197 " =    2.295
peak=   -3.204 closest distance to " C   PRO A  90 " =    1.490
peak=   -3.201 closest distance to " OE2 GLU A   2 " =    1.784
peak=   -3.199 closest distance to " CG1 VAL A 125 " =    1.981
peak=   -3.196 closest distance to " O   HOH Z 134 " =    2.929
peak=   -3.191 closest distance to " CB  ASP A 132 " =    2.376
peak=   -3.190 closest distance to " O   HOH Z  73 " =    2.333
peak=   -3.184 closest distance to " CB  LEU A  83 " =    2.360
peak=   -3.183 closest distance to " O   HOH Z 317 " =    1.579
peak=   -3.183 closest distance to " O   HOH Z  63 " =    1.584
peak=   -3.182 closest distance to " O   HOH Z 200 " =    4.717
peak=   -3.179 closest distance to " CG  LEU A  83 " =    1.830
peak=   -3.178 closest distance to " O   ALA A  10 " =    1.696
peak=   -3.163 closest distance to " CG  TRP A 266 " =    1.972
peak=   -3.160 closest distance to " O   LYS A 117 " =    1.658
peak=   -3.160 closest distance to " OG1 THR A 246 " =    1.427
peak=   -3.155 closest distance to " O   VAL A 174 " =    2.028
peak=   -3.153 closest distance to " O   HOH Z 250 " =    1.409
peak=   -3.151 closest distance to " CB  PHE A 208 " =    2.232
peak=   -3.149 closest distance to " CZ  ARG A 259 " =    0.847
peak=   -3.147 closest distance to " CD2 LEU A 237 " =    2.736
peak=   -3.144 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.143 closest distance to " CG  MET A 105 " =    0.958
peak=   -3.141 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.140 closest distance to " C   GLN A 205 " =    1.958
peak=   -3.139 closest distance to " OXT GLY A 302 " =    3.323
peak=   -3.131 closest distance to " O   ALA A  34 " =    2.516
peak=   -3.127 closest distance to " O   PHE A 218 " =    1.572
peak=   -3.126 closest distance to " O   HOH Z 148 " =    3.412
peak=   -3.122 closest distance to " O   PRO A 198 " =    1.234
peak=   -3.118 closest distance to " O   HOH Z  41 " =    2.472
peak=   -3.109 closest distance to " CB  SER A 273 " =    1.942
peak=   -3.107 closest distance to " O   HOH Z   6 " =    1.427
peak=   -3.107 closest distance to " O   HOH Z 198 " =    1.013
peak=   -3.105 closest distance to " O   HOH Z 210 " =    1.033
peak=   -3.105 closest distance to " O   TRP A  70 " =    1.481
peak=   -3.099 closest distance to " O   HOH Z 262 " =    2.862
peak=   -3.097 closest distance to " CA  GLY A 241 " =    2.768
peak=   -3.097 closest distance to " NE2 GLN A  88 " =    1.791
peak=   -3.081 closest distance to " O   HOH Z 111 " =    2.404
peak=   -3.078 closest distance to " O   HOH Z 385 " =    1.876
peak=   -3.071 closest distance to " O   HOH Z 298 " =    2.444
peak=   -3.066 closest distance to " O   HOH Z 137 " =    1.543
peak=   -3.061 closest distance to " CD2 TYR A 293 " =    2.070
peak=   -3.057 closest distance to " O   ALA A 292 " =    1.961
peak=   -3.057 closest distance to " CG1AVAL A  41 " =    2.850
peak=   -3.028 closest distance to " O   LYS A 289 " =    2.840
peak=   -3.016 closest distance to " O   GLU A 152 " =    1.415

================= 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    :  0.1958 0.1986   5.539732e+00   5.540774e+00
   1_bss:  0.1742 0.1749   5.489240e+00   5.476402e+00
   1_xyz:  0.1239 0.1442   5.167651e+00   5.291967e+00
   1_adp:  0.1169 0.1441   5.119986e+00   5.292680e+00
   1_occ:  0.1163 0.1437   5.116929e+00   5.290844e+00
   2_bss:  0.1167 0.1431   5.118528e+00   5.288759e+00
   2_xyz:  0.1145 0.1452   5.113166e+00   5.305256e+00
   2_adp:  0.1094 0.1470   5.097520e+00   5.322369e+00
   2_occ:  0.1093 0.1471   5.097491e+00   5.322794e+00
   3_bss:  0.1092 0.1471   5.097543e+00   5.322787e+00
   3_xyz:  0.1058 0.1482   5.084454e+00   5.329177e+00
   3_adp:  0.1049 0.1505   5.086999e+00   5.340442e+00
   3_occ:  0.1048 0.1505   5.087282e+00   5.341103e+00
   4_bss:  0.1047 0.1505   5.087248e+00   5.340942e+00
   4_xyz:  0.1050 0.1520   5.094374e+00   5.352350e+00
   4_adp:  0.1078 0.1506   5.101688e+00   5.345941e+00
   4_occ:  0.1077 0.1507   5.102063e+00   5.346725e+00
   5_bss:  0.1077 0.1508   5.102315e+00   5.347036e+00
   5_xyz:  0.1096 0.1515   5.114939e+00   5.353593e+00
   5_adp:  0.1085 0.1517   5.110502e+00   5.355462e+00
   5_occ:  0.1085 0.1517   5.110567e+00   5.355558e+00
   5_bss:  0.1085 0.1517   5.110615e+00   5.355584e+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:  0.322  38.619  -2.875  -2.714  -1.330  -0.000  -0.000  -0.000
   1_xyz:  0.322  38.619  -2.875  -2.714  -1.330  -0.000  -0.000  -0.000
   1_adp:  0.322  38.619  -2.875  -2.714  -1.330  -0.000  -0.000  -0.000
   1_occ:  0.322  38.619  -2.875  -2.714  -1.330  -0.000  -0.000  -0.000
   2_bss:  0.322  42.703  -3.087  -2.681  -1.601  -0.000  -0.000  -0.000
   2_xyz:  0.322  42.703  -3.087  -2.681  -1.601  -0.000  -0.000  -0.000
   2_adp:  0.322  42.703  -3.087  -2.681  -1.601  -0.000  -0.000  -0.000
   2_occ:  0.322  42.703  -3.087  -2.681  -1.601  -0.000  -0.000  -0.000
   3_bss:  0.322  42.702  -2.814  -2.376  -1.409  -0.000  -0.000  -0.000
   3_xyz:  0.322  42.702  -2.814  -2.376  -1.409  -0.000  -0.000  -0.000
   3_adp:  0.322  42.702  -2.814  -2.376  -1.409  -0.000  -0.000  -0.000
   3_occ:  0.322  42.702  -2.814  -2.376  -1.409  -0.000  -0.000  -0.000
   4_bss:  0.321  43.679  -2.521  -2.088  -1.149  -0.000  -0.000  -0.000
   4_xyz:  0.321  43.679  -2.521  -2.088  -1.149  -0.000  -0.000  -0.000
   4_adp:  0.321  43.679  -2.521  -2.088  -1.149  -0.000  -0.000  -0.000
   4_occ:  0.321  43.679  -2.521  -2.088  -1.149  -0.000  -0.000  -0.000
   5_bss:  0.326  43.679  -2.466  -2.020  -1.060  -0.000  -0.000  -0.000
   5_xyz:  0.326  43.679  -2.466  -2.020  -1.060  -0.000  -0.000  -0.000
   5_adp:  0.326  43.679  -2.466  -2.020  -1.060  -0.000  -0.000  -0.000
   5_occ:  0.326  43.679  -2.466  -2.020  -1.060  -0.000  -0.000  -0.000
   5_bss:  0.326  43.630  -2.304  -1.863  -0.903  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  17.093 0.8915  1.0415    10558.853
   1_bss:  15.381 0.9055  0.9719     7412.753
   1_xyz:  11.985 0.9310  0.9834     5318.991
   1_adp:  12.065 0.9300  0.9807     5306.854
   1_occ:  12.029 0.9303  0.9805     5265.072
   2_bss:  11.988 0.9306  0.9754     5217.665
   2_xyz:  12.218 0.9293  0.9737     5405.013
   2_adp:  12.598 0.9262  0.9688     5500.803
   2_occ:  12.602 0.9261  0.9686     5505.240
   3_bss:  12.605 0.9261  0.9778     5506.662
   3_xyz:  12.709 0.9253  0.9777     5607.389
   3_adp:  12.935 0.9235  0.9705     5699.518
   3_occ:  12.947 0.9235  0.9703     5706.827
   4_bss:  12.946 0.9235  0.9804     5706.055
   4_xyz:  13.126 0.9222  0.9795     5842.397
   4_adp:  12.957 0.9235  0.9758     5800.016
   4_occ:  12.973 0.9233  0.9757     5807.035
   5_bss:  12.979 0.9233  0.9782     5814.193
   5_xyz:  13.095 0.9225  0.9779     5886.878
   5_adp:  13.145 0.9221  0.9731     5898.995
   5_occ:  13.150 0.9221  0.9730     5900.724
   5_bss:  13.150 0.9221  0.9769     5901.572
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.5968e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.5968e-01
   1_xyz:   1.013  0.007  0.076 15.301  0.004  4.108   6.2773e-02
   1_adp:   1.013  0.007  0.076 15.301  0.004  4.108   6.2773e-02
   1_occ:   1.013  0.007  0.076 15.301  0.004  4.108   6.2773e-02
   2_bss:   1.013  0.007  0.076 15.301  0.004  4.108   6.2773e-02
   2_xyz:   0.948  0.006  0.074 15.061  0.004  4.108   5.6490e-02
   2_adp:   0.948  0.006  0.074 15.061  0.004  4.108   5.6490e-02
   2_occ:   0.948  0.006  0.074 15.061  0.004  4.108   5.6490e-02
   3_bss:   0.948  0.006  0.074 15.061  0.004  4.108   5.6490e-02
   3_xyz:   1.019  0.008  0.079 15.250  0.004  4.109   6.4625e-02
   3_adp:   1.019  0.008  0.079 15.250  0.004  4.109   6.4625e-02
   3_occ:   1.019  0.008  0.079 15.250  0.004  4.109   6.4625e-02
   4_bss:   1.019  0.008  0.079 15.250  0.004  4.109   6.4625e-02
   4_xyz:   0.982  0.007  0.076 15.093  0.004  4.110   6.0455e-02
   4_adp:   0.982  0.007  0.076 15.093  0.004  4.110   6.0455e-02
   4_occ:   0.982  0.007  0.076 15.093  0.004  4.110   6.0455e-02
   5_bss:   0.982  0.007  0.076 15.093  0.004  4.110   6.0455e-02
   5_xyz:   0.891  0.005  0.070 14.867  0.004  4.109   5.1658e-02
   5_adp:   0.891  0.005  0.070 14.867  0.004  4.109   5.1658e-02
   5_occ:   0.891  0.005  0.070 14.867  0.004  4.109   5.1658e-02
   5_bss:   0.891  0.005  0.070 14.867  0.004  4.109   5.1658e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4005e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4005e-01
   1_xyz:   7.010  0.047  0.245 84.858  0.028  2.285   5.4548e-02
   1_adp:   7.010  0.047  0.245 84.858  0.028  2.285   5.4548e-02
   1_occ:   7.010  0.047  0.245 84.858  0.028  2.285   5.4548e-02
   2_bss:   7.010  0.047  0.245 84.858  0.028  2.285   5.4548e-02
   2_xyz:   6.442  0.038  0.234 83.900  0.043  2.350   4.0230e-02
   2_adp:   6.442  0.038  0.234 83.900  0.043  2.350   4.0230e-02
   2_occ:   6.442  0.038  0.234 83.900  0.043  2.350   4.0230e-02
   3_bss:   6.442  0.038  0.234 83.900  0.043  2.350   4.0230e-02
   3_xyz:   6.878  0.039  0.261 83.563  0.038  2.311   4.9805e-02
   3_adp:   6.878  0.039  0.261 83.563  0.038  2.311   4.9805e-02
   3_occ:   6.878  0.039  0.261 83.563  0.038  2.311   4.9805e-02
   4_bss:   6.878  0.039  0.261 83.563  0.038  2.311   4.9805e-02
   4_xyz:   6.579  0.036  0.246 82.963  0.040  2.339   4.3911e-02
   4_adp:   6.579  0.036  0.246 82.963  0.040  2.339   4.3911e-02
   4_occ:   6.579  0.036  0.246 82.963  0.040  2.339   4.3911e-02
   5_bss:   6.579  0.036  0.246 82.963  0.040  2.339   4.3911e-02
   5_xyz:   6.179  0.039  0.217 83.386  0.038  2.358   3.0360e-02
   5_adp:   6.179  0.039  0.217 83.386  0.038  2.358   3.0360e-02
   5_occ:   6.179  0.039  0.217 83.386  0.038  2.358   3.0360e-02
   5_bss:   6.179  0.039  0.217 83.386  0.038  2.358   3.0360e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  74.39   0.00  16.19  74.39   0.00  12.40  62.37   5.20  36.82
   1_occ:  74.39   0.00  16.19  74.39   0.00  12.40  62.37   5.20  36.82
   2_bss:  74.39   0.00  16.19  74.39   0.00  12.40  62.37   5.20  36.82
   2_xyz:  74.39   0.00  16.19  74.39   0.00  12.40  62.37   5.20  36.82
   2_adp:  68.65   1.52  16.63  68.65   1.52  12.77  67.08   4.93  37.66
   2_occ:  68.65   1.52  16.63  68.65   1.52  12.77  67.08   4.93  37.66
   3_bss:  68.65   1.52  16.63  68.65   1.52  12.77  67.08   4.93  37.66
   3_xyz:  68.65   1.52  16.63  68.65   1.52  12.77  67.08   4.93  37.66
   3_adp:  79.85   0.62  16.84  79.85   0.62  12.79  71.46   6.06  38.91
   3_occ:  79.85   0.62  16.84  79.85   0.62  12.79  71.46   6.06  38.91
   4_bss:  79.85   0.62  16.84  79.85   0.62  12.79  71.46   6.06  38.91
   4_xyz:  79.85   0.62  16.84  79.85   0.62  12.79  71.46   6.06  38.91
   4_adp:  73.70   2.17  15.92  73.70   2.17  12.42  67.46   5.89  35.00
   4_occ:  73.70   2.17  15.92  73.70   2.17  12.42  67.46   5.89  35.00
   5_bss:  73.70   2.17  15.92  73.70   2.17  12.42  67.46   5.89  35.00
   5_xyz:  73.70   2.17  15.92  73.70   2.17  12.42  67.46   5.89  35.00
   5_adp:  74.13   1.40  16.01  74.13   1.40  12.34  66.80   5.89  35.98
   5_occ:  74.13   1.40  16.01  74.13   1.40  12.34  66.80   5.89  35.98
   5_bss:  74.08   1.35  15.96  74.08   1.35  12.29  66.75   5.84  35.93
------------------------------------------------------------------------
 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:    0.477    0.006    0.136
   1_adp:    0.477    0.006    0.136
   1_occ:    0.477    0.006    0.136
   2_bss:    0.477    0.006    0.136
   2_xyz:    0.627    0.009    0.149
   2_adp:    0.627    0.009    0.149
   2_occ:    0.627    0.009    0.149
   3_bss:    0.627    0.009    0.149
   3_xyz:    0.758    0.008    0.160
   3_adp:    0.758    0.008    0.160
   3_occ:    0.758    0.008    0.160
   4_bss:    0.758    0.008    0.160
   4_xyz:    0.857    0.007    0.165
   4_adp:    0.857    0.007    0.165
   4_occ:    0.857    0.007    0.165
   5_bss:    0.857    0.007    0.165
   5_xyz:    0.924    0.003    0.166
   5_adp:    0.924    0.003    0.166
   5_occ:    0.924    0.003    0.166
   5_bss:    0.924    0.003    0.166
------------------------------------------------------------------------

CPU time actual refinement: 315.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/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/noshake/run_543/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_543/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.57 
  Macro-tasks:
    bulk solvent and scale       = 35.22  
    individual site refinement   = 132.62 
    weights calculation          = 28.36  
    collect and process          = 6.49   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 202.78 
  Micro-tasks:
    mask                            = 0.57   
    f_calc                          = 101.02 
    alpha_beta                      = 8.08   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.87 
    fmodel                         = 6.32   
    r_factors                      = 0.13   
    phase_errors                   = 11.03  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 239.49 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.449 micro seconds
Total CPU time: 5.48 minutes
from_scatterers_fft:    654 calls, 100.80 s
gradients_fft:          599 calls,  96.85 s

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

# Date 2008-01-16 Time 05:04:49 PST -0800 (1200488689.72 s)
Start R-work = 0.1958, R-free = 0.1986 (no bulk solvent and anisotropic scale)
Final R-work = 0.1331, R-free = 0.1717 (no bulk solvent and anisotropic scale)

Start R-work = 0.1742, R-free = 0.1749
Final R-work = 0.1085, R-free = 0.1517