# Date 2008-01-16 Time 05:18:06 PST -0800 (1200489486.22 s)
#phil __OFF__

Command line arguments: "../675.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17109
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 675

-------------------------------------------------------------------------------
  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: (70.25, 47.1647, 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: 3.36, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.99108
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9735
                             d_min =   1.9911

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9735 1.99108
Completeness in resolution range: 0.972835
Completeness with d_max=infinity: 0.969752

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9740 -  4.2598 [2113/2140]  1902   211  10.0%
  bin  2:  4.2598 -  3.3941 [2029/2045]  1826   203  10.0%
  bin  3:  3.3941 -  2.9689 [2005/2024]  1802   203  10.1%
  bin  4:  2.9689 -  2.6991 [1991/2021]  1796   195   9.8%
  bin  5:  2.6991 -  2.5066 [1960/1979]  1761   199  10.2%
  bin  6:  2.5066 -  2.3595 [1962/1987]  1768   194   9.9%
  bin  7:  2.3595 -  2.2417 [1966/1999]  1770   196  10.0%
  bin  8:  2.2417 -  2.1444 [1935/1966]  1740   195  10.1%
  bin  9:  2.1444 -  2.0621 [1943/1985]  1748   195  10.0%
  bin 10:  2.0621 -  1.9911 [1685/1990]  1517   168  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 9
        2.42 -     3.04: 2209
        3.04 -     3.66: 4656
        3.66 -     4.28: 9034
        4.28 -     4.90: 12377
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.226 3.040 -x+1/2,-y+1,z+1/2
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.342 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28280 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_675/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/model_refine_001.geo

CPU time processing inputs: 9.29


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.16465 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 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2080   ksol= 0.00   Bsol= 0.00   scale= 1.010    |
|                                                                             |
| 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:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.652414                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7509 0.99   1375  153 0.2461 0.2451      6.2403      6.1976|
|  2:  4.7509 -  3.7911 0.99   1319  145 0.1621 0.1563      6.0238       5.994|
|  3:  3.7911 -  3.3178 0.99   1300  145 0.1696 0.1607      5.8825      5.9355|
|  4:  3.3178 -  3.0171 0.99   1286  144 0.1865 0.1822      5.8049      5.7477|
|  5:  3.0171 -  2.8024 0.99   1272  140 0.1967 0.1577      5.6478      5.5298|
|  6:  2.8024 -  2.6381 0.99   1278  143 0.2079 0.2066      5.6088      5.6019|
|  7:  2.6381 -  2.5066 0.99   1257  141 0.2189 0.1832      5.6287      5.4465|
|  8:  2.5066 -  2.3980 0.98   1268  140 0.2220 0.2341      5.5738      5.6114|
|  9:  2.3980 -  2.3060 0.98   1270  138 0.2233 0.2288      5.5098      5.5362|
| 10:  2.3060 -  2.2267 0.98   1232  137 0.2346 0.2487       5.553      5.5516|
| 11:  2.2267 -  2.1573 0.99   1270  147 0.2236 0.2265       5.426      5.5196|
| 12:  2.1573 -  2.0958 0.97   1249  129 0.2340 0.2054      5.4373      5.3858|
| 13:  2.0958 -  2.0408 0.99   1234  142 0.2362 0.2457      5.3463      5.3485|
| 14:  2.0408 -  1.9911 0.80   1020  115 0.2339 0.2212      5.2948      5.2197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7509  1375   153  0.82  23.52   0.88     0.82      34908.15|
|  2:  4.7509 -  3.7911  1319   145  0.90  15.60   1.00     0.95      23532.98|
|  3:  3.7911 -  3.3178  1300   145  0.92  14.24   1.02     1.01      15893.59|
|  4:  3.3178 -  3.0171  1286   144  0.91  15.04   1.03     1.02      12593.33|
|  5:  3.0171 -  2.8024  1272   140  0.89  17.25   1.04     1.02      10046.61|
|  6:  2.8024 -  2.6381  1278   143  0.88  17.98   1.05     1.02       8838.86|
|  7:  2.6381 -  2.5066  1257   141  0.89  17.79   1.05     1.04       8116.74|
|  8:  2.5066 -  2.3980  1268   140  0.88  19.07   1.06     1.04       8431.34|
|  9:  2.3980 -  2.3060  1270   138  0.86  20.70   1.09     1.04       8234.43|
| 10:  2.3060 -  2.2267  1232   137  0.86  21.22   1.10     1.04       8149.29|
| 11:  2.2267 -  2.1573  1270   147  0.86  21.24   1.11     1.08       7540.85|
| 12:  2.1573 -  2.0958  1249   129  0.87  20.74   1.11     1.10       6985.95|
| 13:  2.0958 -  2.0408  1234   142  0.86  21.08   1.11     1.11       6003.30|
| 14:  2.0408 -  1.9911  1020   115  0.87  20.30   1.11     1.10       4827.65|
|alpha:            min =        0.82 max =            1.11 mean =         1.02|
|beta:             min =     4827.65 max =        34908.15 mean =     12024.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        18.96|
|phase err.(test): min =        0.00 max =           89.42 mean =        18.67|
|-----------------------------------------------------------------------------|

============================== 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 = 2.467553              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.077   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.329138              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.405   (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:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      193 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2016 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1822 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2834 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4640 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4394 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5608 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6769 |
|-----------------------------------------------------------------------------|
|-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 |   4.114    4.900  1.806 |       0.137 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    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 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2080   ksol= 0.00   Bsol= 0.00   scale= 1.010    |
|                                                                             |
| 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:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.652414                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1947   r_free= 0.1874   ksol= 0.32   Bsol= 50.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-1.56,-1.36,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.610133                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.304467              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.217   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1947      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1874      final r-factor (free) = 0.1485          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7170 = 2.30 * 0.50 * 5.6909 + 1.00 * 0.1597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1926 = 2.30 * 0.50 * 5.3212 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1485      final r-factor (free) = 0.1494          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9199 = 0.17 * 1.00 * 5.3212 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9234 = 0.17 * 1.00 * 5.1540 + 1.00 * 0.0384                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.18   16.41    None  None   None       |
|    all(noH): 2823   0      0.00    72.18   16.41    None  None   None       |
|    Sol.    : 438    0      5.58    62.58   36.97    None  None   None       |
|    Mac.    : 2385   0      0.00    72.18   12.63    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 -   7.219:  269   |   5:    36.092 -  43.311:  116        |
|      1:     7.219 -  14.437: 1526   |   6:    43.311 -  50.529:   89        |
|      2:    14.437 -  21.655:  491   |   7:    50.529 -  57.747:   58        |
|      3:    21.655 -  28.874:  137   |   8:    57.747 -  64.966:   13        |
|      4:    28.874 -  36.092:  123   |   9:    64.966 -  72.184:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1203 r_free = 0.1494             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1489             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1489   ksol= 0.32   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-1.56,-1.36,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.156767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1488   ksol= 0.33   Bsol= 50.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.25,-1.68,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157254                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.227173              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.837  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223045              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.058   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1488      final r-factor (free) = 0.1487          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2245 = 1.23 * 0.50 * 5.1552 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.2046 = 1.23 * 0.50 * 5.1354 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1487      final r-factor (free) = 0.1490          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4910 = 0.22 * 1.00 * 5.1354 + 1.00 * 0.3456                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1489 = 0.22 * 1.00 * 5.1186 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.61    65.62   16.65    None  None   None       |
|    all(noH): 2823   0      1.61    65.62   16.65    None  None   None       |
|    Sol.    : 438    0      5.92    64.71   37.36    None  None   None       |
|    Mac.    : 2385   0      1.61    65.62   12.85    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:     1.613 -   8.014:  471   |   5:    33.616 -  40.017:  104        |
|      1:     8.014 -  14.414: 1329   |   6:    40.017 -  46.417:   91        |
|      2:    14.414 -  20.815:  423   |   7:    46.417 -  52.818:   92        |
|      3:    20.815 -  27.215:  148   |   8:    52.818 -  59.218:   52        |
|      4:    27.215 -  33.616:  105   |   9:    59.218 -  65.619:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1490             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1491             target_work(ml) = 5.123         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1491   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.25,-1.68,-0.00,-0.00,-0.00); trace/3= -2.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122942                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1491   ksol= 0.33   Bsol= 50.00   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,-1.50,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.122724                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.873488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.317  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.384263              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.385  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1491      final r-factor (free) = 0.1508          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4089 = 2.87 * 0.50 * 5.1194 + 1.00 * 0.0536                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3949 = 2.87 * 0.50 * 5.0971 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1508      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1601 = 2.38 * 1.00 * 5.0971 + 1.00 * 0.0072                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1432 = 2.38 * 1.00 * 5.0892 + 1.00 * 0.0092                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.58    83.34   17.01    None  None   None       |
|    all(noH): 2823   0      0.58    83.34   17.01    None  None   None       |
|    Sol.    : 438    0      6.22    73.07   39.42    None  None   None       |
|    Mac.    : 2385   0      0.58    83.34   12.90    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:     0.582 -   8.858:  743   |   5:    41.963 -  50.239:  106        |
|      1:     8.858 -  17.134: 1288   |   6:    50.239 -  58.515:   81        |
|      2:    17.134 -  25.411:  304   |   7:    58.515 -  66.791:   51        |
|      3:    25.411 -  33.687:  127   |   8:    66.791 -  75.068:   13        |
|      4:    33.687 -  41.963:  105   |   9:    75.068 -  83.344:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1050 r_free = 0.1525             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1050 r_free = 0.1526             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1526   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-2.18,-1.50,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1048   r_free= 0.1526   ksol= 0.33   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.97,-1.24,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096034                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.386327              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.202  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.095907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.609  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1048      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6004 = 1.39 * 0.50 * 5.0909 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.5965 = 1.39 * 0.50 * 5.1118 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4994 = 0.10 * 1.00 * 5.1118 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.4987 = 0.10 * 1.00 * 5.1328 + 1.00 * 0.0064                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.19    79.50   16.25    None  None   None       |
|    all(noH): 2823   0      2.19    79.50   16.25    None  None   None       |
|    Sol.    : 438    0      5.81    67.14   36.01    None  None   None       |
|    Mac.    : 2385   0      2.19    79.50   12.62    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:     2.189 -   9.920: 1018   |   5:    40.844 -  48.575:   87        |
|      1:     9.920 -  17.651: 1094   |   6:    48.575 -  56.306:   73        |
|      2:    17.651 -  25.382:  251   |   7:    56.306 -  64.037:   25        |
|      3:    25.382 -  33.113:  128   |   8:    64.037 -  71.768:    9        |
|      4:    33.113 -  40.844:  134   |   9:    71.768 -  79.498:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1526             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1527             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1527   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.97,-1.24,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1527   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.97,-1.24,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126711                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.405906              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.593  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.303343              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.676  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1527      final r-factor (free) = 0.1525          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2277 = 2.41 * 0.50 * 5.1327 + 1.00 * 0.0533                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2141 = 2.41 * 0.50 * 5.1116 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1525      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8917 = 3.30 * 1.00 * 5.1116 + 1.00 * 0.0064                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.8515 = 3.30 * 1.00 * 5.0987 + 1.00 * 0.0088                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.18    84.16   16.61    None  None   None       |
|    all(noH): 2823   0      0.18    84.16   16.61    None  None   None       |
|    Sol.    : 438    0      5.85    70.42   38.52    None  None   None       |
|    Mac.    : 2385   0      0.18    84.16   12.58    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:     0.180 -   8.577:  725   |   5:    42.169 -  50.566:  114        |
|      1:     8.577 -  16.975: 1327   |   6:    50.566 -  58.964:   81        |
|      2:    16.975 -  25.373:  292   |   7:    58.964 -  67.362:   28        |
|      3:    25.373 -  33.771:  127   |   8:    67.362 -  75.760:    9        |
|      4:    33.771 -  42.169:  115   |   9:    75.760 -  84.158:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1539             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1058 r_free = 0.1539             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1058   r_free= 0.1539   ksol= 0.33   Bsol= 50.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-1.97,-1.24,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105292                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7509 0.99   1375  153 0.0980 0.1250      5.3715      5.4941|
|  2:  4.7509 -  3.7911 0.99   1319  145 0.0842 0.1106      5.4218       5.606|
|  3:  3.7911 -  3.3178 0.99   1300  145 0.1006 0.1482      5.4422      5.8515|
|  4:  3.3178 -  3.0171 0.99   1286  144 0.1155 0.1492      5.4223      5.5635|
|  5:  3.0171 -  2.8024 0.99   1272  140 0.1233 0.1705      5.2846      5.5132|
|  6:  2.8024 -  2.6381 0.99   1278  143 0.1137 0.1742      5.1747      5.3977|
|  7:  2.6381 -  2.5066 0.99   1257  141 0.1174 0.1653      5.1129      5.3725|
|  8:  2.5066 -  2.3980 0.98   1268  140 0.1094 0.1716      5.0309      5.3273|
|  9:  2.3980 -  2.3060 0.98   1270  138 0.1109 0.1653      4.9885      5.2427|
| 10:  2.3060 -  2.2267 0.98   1232  137 0.1026 0.1741      4.9374      5.2107|
| 11:  2.2267 -  2.1573 0.99   1270  147 0.1085 0.1700      4.9095      5.2315|
| 12:  2.1573 -  2.0958 0.97   1249  129 0.1036 0.1635      4.8442      5.1891|
| 13:  2.0958 -  2.0408 0.99   1234  142 0.1021 0.1613      4.7505      5.0098|
| 14:  2.0408 -  1.9911 0.80   1020  115 0.0971 0.1790      4.6215      4.9484|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7509  1375   153  0.94   9.07   0.98     0.95       6946.44|
|  2:  4.7509 -  3.7911  1319   145  0.95   7.77   1.01     1.00       8688.53|
|  3:  3.7911 -  3.3178  1300   145  0.94  10.71   1.02     1.01       9774.33|
|  4:  3.3178 -  3.0171  1286   144  0.92  13.04   1.00     0.99       9844.48|
|  5:  3.0171 -  2.8024  1272   140  0.91  15.07   0.99     0.96       7716.33|
|  6:  2.8024 -  2.6381  1278   143  0.91  15.13   0.98     0.95       6631.87|
|  7:  2.6381 -  2.5066  1257   141  0.91  14.79   0.98     0.96       5674.32|
|  8:  2.5066 -  2.3980  1268   140  0.92  14.13   0.99     0.97       4970.48|
|  9:  2.3980 -  2.3060  1270   138  0.91  14.75   0.99     0.96       4615.01|
| 10:  2.3060 -  2.2267  1232   137  0.91  14.78   0.99     0.95       4246.41|
| 11:  2.2267 -  2.1573  1270   147  0.90  15.80   0.99     0.95       4196.37|
| 12:  2.1573 -  2.0958  1249   129  0.92  14.55   0.99     0.98       3753.51|
| 13:  2.0958 -  2.0408  1234   142  0.91  14.94   1.00     0.99       3177.22|
| 14:  2.0408 -  1.9911  1020   115  0.92  13.98   0.97     0.93       2363.63|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2363.63 max =         9844.48 mean =      5986.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.40|
|phase err.(test): min =        0.00 max =           89.39 mean =        13.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1540   ksol= 0.33   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.76,-1.01,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105359                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.97 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1540   ksol= 0.33   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.23,-1.76,-1.01,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105359                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9740 -  4.7509 0.99   1375  153 0.0980 0.1253      5.3725      5.4954|
|  2:  4.7509 -  3.7911 0.99   1319  145 0.0843 0.1105      5.4223      5.6058|
|  3:  3.7911 -  3.3178 0.99   1300  145 0.1006 0.1483      5.4423      5.8519|
|  4:  3.3178 -  3.0171 0.99   1286  144 0.1155 0.1492      5.4222      5.5636|
|  5:  3.0171 -  2.8024 0.99   1272  140 0.1233 0.1705      5.2844      5.5128|
|  6:  2.8024 -  2.6381 0.99   1278  143 0.1137 0.1741      5.1746      5.3974|
|  7:  2.6381 -  2.5066 0.99   1257  141 0.1174 0.1653      5.1129      5.3728|
|  8:  2.5066 -  2.3980 0.98   1268  140 0.1094 0.1716       5.031      5.3272|
|  9:  2.3980 -  2.3060 0.98   1270  138 0.1109 0.1652      4.9886      5.2427|
| 10:  2.3060 -  2.2267 0.98   1232  137 0.1026 0.1742      4.9375      5.2109|
| 11:  2.2267 -  2.1573 0.99   1270  147 0.1085 0.1699      4.9094      5.2313|
| 12:  2.1573 -  2.0958 0.97   1249  129 0.1036 0.1634       4.844      5.1888|
| 13:  2.0958 -  2.0408 0.99   1234  142 0.1021 0.1613      4.7503      5.0096|
| 14:  2.0408 -  1.9911 0.80   1020  115 0.0971 0.1789      4.6213      4.9482|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9740 -  4.7509  1375   153  0.94   9.08   0.98     0.95       6964.39|
|  2:  4.7509 -  3.7911  1319   145  0.95   7.78   1.01     1.00       8700.66|
|  3:  3.7911 -  3.3178  1300   145  0.94  10.72   1.02     1.02       9777.47|
|  4:  3.3178 -  3.0171  1286   144  0.92  13.04   1.01     1.00       9842.04|
|  5:  3.0171 -  2.8024  1272   140  0.91  15.06   1.00     0.97       7712.33|
|  6:  2.8024 -  2.6381  1278   143  0.91  15.13   0.99     0.96       6628.09|
|  7:  2.6381 -  2.5066  1257   141  0.91  14.79   0.99     0.97       5673.64|
|  8:  2.5066 -  2.3980  1268   140  0.92  14.13   1.00     0.98       4970.04|
|  9:  2.3980 -  2.3060  1270   138  0.91  14.76   1.00     0.97       4617.15|
| 10:  2.3060 -  2.2267  1232   137  0.91  14.78   1.00     0.96       4246.35|
| 11:  2.2267 -  2.1573  1270   147  0.90  15.80   1.00     0.96       4195.81|
| 12:  2.1573 -  2.0958  1249   129  0.92  14.55   1.00     0.99       3751.83|
| 13:  2.0958 -  2.0408  1234   142  0.91  14.93   1.01     1.00       3175.08|
| 14:  2.0408 -  1.9911  1020   115  0.92  13.97   0.98     0.94       2361.85|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2361.85 max =         9842.04 mean =      5988.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.40|
|phase err.(test): min =        0.00 max =           89.39 mean =        13.04|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.18    84.15   16.60    None  None   None       |
|    all(noH): 2823   0      0.18    84.15   16.60    None  None   None       |
|    Sol.    : 438    0      5.85    70.41   38.52    None  None   None       |
|    Mac.    : 2385   0      0.18    84.15   12.58    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:     0.176 -   8.574:  725   |   5:    42.165 -  50.563:  114        |
|      1:     8.574 -  16.971: 1327   |   6:    50.563 -  58.961:   81        |
|      2:    16.971 -  25.369:  292   |   7:    58.961 -  67.358:   28        |
|      3:    25.369 -  33.767:  127   |   8:    67.358 -  75.756:    9        |
|      4:    33.767 -  42.165:  115   |   9:    75.756 -  84.154:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.556 - 5.447
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 288
   mapped sites are within: 0.741 - 5.447

peak=    6.058 closest distance to " NH2 ARG A  56 " =    2.296
peak=    5.699 closest distance to " CB  GLN A 223 " =    1.427
peak=    5.375 closest distance to " O   HOH Z 126 " =    1.865
peak=    5.252 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.984 closest distance to " CB  SER A  63 " =    1.164
peak=    4.900 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.718 closest distance to " O   HOH Z 232 " =    2.376
peak=    4.698 closest distance to " CB  GLU A 152 " =    1.175
peak=    4.644 closest distance to " CA  TYR A  30 " =    0.953
peak=    4.634 closest distance to " C   PRO A 198 " =    1.484
peak=    4.634 closest distance to " O   HOH Z 298 " =    1.964
peak=    4.630 closest distance to " O   HOH Z 142 " =    1.604
peak=    4.550 closest distance to " CB  TYR A 169 " =    0.761
peak=    4.535 closest distance to " O   HOH Z 369 " =    2.197
peak=    4.499 closest distance to " O   HOH Z 236 " =    1.989
peak=    4.480 closest distance to " CB  ASN A 148 " =    1.438
peak=    4.463 closest distance to " O   HOH Z  78 " =    1.704
peak=    4.455 closest distance to " NE2 GLN A  11 " =    1.029
peak=    4.372 closest distance to " O   HOH Z  40 " =    1.772
peak=    4.320 closest distance to " CB  LEU A 228 " =    1.070
peak=    4.312 closest distance to " O   HOH Z 234 " =    3.684
peak=    4.293 closest distance to " O   HOH Z 250 " =    1.474
peak=    4.237 closest distance to " CB  ARG A  79 " =    1.368
peak=    4.232 closest distance to " CB  ARG A 190 " =    1.678
peak=    4.228 closest distance to " O   HOH Z 427 " =    2.963
peak=    4.211 closest distance to " O   HOH Z 193 " =    1.748
peak=    4.204 closest distance to " O   HOH Z 403 " =    1.696
peak=    4.192 closest distance to " O   HOH Z 203 " =    1.732
peak=    4.175 closest distance to " O   HOH Z 158 " =    3.053
peak=    4.173 closest distance to " O   HOH Z  15 " =    2.165
peak=    4.162 closest distance to " O   HOH Z 144 " =    2.293
peak=    4.161 closest distance to " O   HOH Z 303 " =    2.046
peak=    4.137 closest distance to " O   HOH Z  61 " =    1.591
peak=    4.131 closest distance to " OD1 ASN A  69 " =    2.574
peak=    4.086 closest distance to " O   HOH Z 197 " =    3.041
peak=    4.053 closest distance to " CB  VAL A 265 " =    1.273
peak=    4.016 closest distance to " O   HOH Z 346 " =    1.722
peak=    4.011 closest distance to " CE  LYS A  76 " =    0.872
peak=    4.003 closest distance to " CA  ASN A 215 " =    1.171
peak=    3.991 closest distance to " O   HOH Z 344 " =    3.189
peak=    3.976 closest distance to " ND2 ASN A 187 " =    1.420
peak=    3.968 closest distance to " CB  GLU A 128 " =    1.081
peak=    3.967 closest distance to " CA  TYR A  30 " =    1.031
peak=    3.950 closest distance to " O   HOH Z  43 " =    1.932
peak=    3.945 closest distance to " O   HOH Z  19 " =    2.368
peak=    3.920 closest distance to " O   HOH Z 316 " =    3.062
peak=    3.914 closest distance to " CZ  PHE A 218 " =    1.071
peak=    3.913 closest distance to " CB  TRP A 266 " =    0.969
peak=    3.905 closest distance to " CB  GLU A 277 " =    3.581
peak=    3.881 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.879 closest distance to " O   HOH Z 147 " =    1.802
peak=    3.873 closest distance to " O   HOH Z 402 " =    1.455
peak=    3.872 closest distance to " O   HOH Z  66 " =    2.059
peak=    3.872 closest distance to " CG2 VAL A 257 " =    0.882
peak=    3.869 closest distance to " O   HOH Z 189 " =    2.218
peak=    3.863 closest distance to " CA  ALA A  21 " =    1.200
peak=    3.840 closest distance to " CB  ASP A 140 " =    0.919
peak=    3.839 closest distance to " CD2 TRP A 179 " =    1.404
peak=    3.835 closest distance to " CB  SER A   3 " =    1.256
peak=    3.834 closest distance to " CG  PRO A 198 " =    1.236
peak=    3.825 closest distance to " CB  TYR A 169 " =    0.836
peak=    3.822 closest distance to " O   HOH Z  97 " =    2.539
peak=    3.812 closest distance to " O   HOH Z 245 " =    1.282
peak=    3.808 closest distance to " O   HOH Z 389 " =    1.884
peak=    3.801 closest distance to " O   SER A  87 " =    2.270
peak=    3.797 closest distance to " O   HOH Z 368 " =    2.082
peak=    3.783 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.780 closest distance to " CG  PRO A 243 " =    1.048
peak=    3.779 closest distance to " O   HOH Z 280 " =    2.938
peak=    3.779 closest distance to " O   HOH Z  54 " =    1.679
peak=    3.763 closest distance to " O   HOH Z 209 " =    2.334
peak=    3.759 closest distance to " O   HOH Z  10 " =    1.772
peak=    3.756 closest distance to " O   MET A 105 " =    1.883
peak=    3.752 closest distance to " CG  PRO A  90 " =    1.093
peak=    3.752 closest distance to " O   HOH Z  44 " =    1.895
peak=    3.742 closest distance to " O   HOH Z  97 " =    1.916
peak=    3.742 closest distance to " CG1 ILE A  33 " =    1.207
peak=    3.736 closest distance to " CB  ALA A 291 " =    1.349
peak=    3.733 closest distance to " O   HOH Z 425 " =    1.996
peak=    3.725 closest distance to " CG2 ILE A 120 " =    1.077
peak=    3.720 closest distance to " CG  ARG A  66 " =    2.524
peak=    3.711 closest distance to " O   HOH Z 214 " =    2.141
peak=    3.708 closest distance to " O   HOH Z 172 " =    3.793
peak=    3.702 closest distance to " O   HOH Z 423 " =    1.932
peak=    3.690 closest distance to " CB  ARG A 139 " =    0.948
peak=    3.675 closest distance to " CD1 ILE A 106 " =    0.815
peak=    3.669 closest distance to " CB  TRP A 179 " =    1.374
peak=    3.668 closest distance to " O   HOH Z 371 " =    3.333
peak=    3.663 closest distance to " OD2 ASP A 286 " =    2.859
peak=    3.650 closest distance to " CZ2 TRP A 179 " =    1.700
peak=    3.646 closest distance to " CG1BVAL A  72 " =    1.659
peak=    3.642 closest distance to " CA  ALA A 291 " =    0.837
peak=    3.642 closest distance to " CB  VAL A 202 " =    1.498
peak=    3.640 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.634 closest distance to " CA  THR A 221 " =    0.978
peak=    3.628 closest distance to " OE1 GLU A   2 " =    2.213
peak=    3.621 closest distance to " CA  ARG A 195 " =    1.224
peak=    3.618 closest distance to " N   ARG A 156 " =    1.344
peak=    3.610 closest distance to " NH2BARG A 145 " =    2.055
peak=    3.609 closest distance to " CB  ILE A 120 " =    1.289
peak=    3.609 closest distance to " CD2 LEU A 297 " =    0.835
peak=    3.604 closest distance to " O   HOH Z   1 " =    1.983
peak=    3.599 closest distance to " CD  ARG A 159 " =    0.741
peak=    3.597 closest distance to " OG BSER A 164 " =    2.268
peak=    3.588 closest distance to " CA  ASN A 176 " =    1.212
peak=    3.574 closest distance to " O   HOH Z 180 " =    2.160
peak=    3.573 closest distance to " CG2 THR A 221 " =    1.184
peak=    3.568 closest distance to " O   HOH Z 128 " =    2.025
peak=    3.561 closest distance to " NH2 ARG A 156 " =    1.159
peak=    3.558 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.558 closest distance to " O   TRP A 274 " =    1.914
peak=    3.554 closest distance to " CD1 LEU A 300 " =    1.236
peak=    3.549 closest distance to " CA  ALA A  51 " =    0.917
peak=    3.543 closest distance to " CD BLYS A 290 " =    0.989
peak=    3.539 closest distance to " O   HOH Z  21 " =    1.751
peak=    3.538 closest distance to " OG1 THR A 294 " =    2.376
peak=    3.521 closest distance to " O   HOH Z 272 " =    1.791
peak=    3.519 closest distance to " NH1AARG A 145 " =    1.189
peak=    3.511 closest distance to " CB  SER A 212 " =    1.088
peak=    3.508 closest distance to " CG2 ILE A  20 " =    1.350
peak=    3.507 closest distance to " O   HOH Z 193 " =    2.117
peak=    3.506 closest distance to " O   HOH Z 327 " =    1.592
peak=    3.505 closest distance to " O   HOH Z 407 " =    2.598
peak=    3.503 closest distance to " O   HOH Z 132 " =    2.588
peak=    3.484 closest distance to " O   HOH Z 175 " =    2.142
peak=    3.477 closest distance to " O   HOH Z 248 " =    1.679
peak=    3.475 closest distance to " O   HOH Z 133 " =    2.545
peak=    3.463 closest distance to " O   HOH Z 108 " =    2.602
peak=    3.460 closest distance to " CA  ASP A 140 " =    1.121
peak=    3.458 closest distance to " CB  SER A  26 " =    1.643
peak=    3.454 closest distance to " CE1 TYR A 186 " =    1.347
peak=    3.452 closest distance to " O   HOH Z 305 " =    3.585
peak=    3.449 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.447 closest distance to " CB  SER A 141 " =    0.976
peak=    3.444 closest distance to " O   HOH Z 417 " =    3.171
peak=    3.443 closest distance to " O   HOH Z 185 " =    1.746
peak=    3.441 closest distance to " O   HOH Z 193 " =    1.661
peak=    3.437 closest distance to " O   HOH Z  61 " =    1.483
peak=    3.435 closest distance to " O   HOH Z 148 " =    3.309
peak=    3.433 closest distance to " O   HOH Z 426 " =    1.578
peak=    3.431 closest distance to " O   ALA A 165 " =    1.494
peak=    3.425 closest distance to " CG2 VAL A 197 " =    1.078
peak=    3.421 closest distance to " O   HOH Z 368 " =    3.625
peak=    3.413 closest distance to " O   HOH Z 173 " =    1.937
peak=    3.412 closest distance to " O   HOH Z 337 " =    3.659
peak=    3.411 closest distance to " O   THR A 220 " =    1.274
peak=    3.410 closest distance to " O   HOH Z 383 " =    1.842
peak=    3.410 closest distance to " O   HOH Z  59 " =    2.281
peak=    3.408 closest distance to " CG  GLN A  58 " =    2.688
peak=    3.403 closest distance to " CB  THR A 157 " =    1.124
peak=    3.399 closest distance to " ND1 HIS A  81 " =    1.679
peak=    3.392 closest distance to " O   HOH Z 391 " =    2.963
peak=    3.391 closest distance to " CA  THR A 264 " =    0.913
peak=    3.390 closest distance to " CA  MET A  40 " =    1.100
peak=    3.389 closest distance to " O   HOH Z 421 " =    1.738
peak=    3.384 closest distance to " CD  LYS A 166 " =    1.260
peak=    3.382 closest distance to " CB  MET A  47 " =    1.036
peak=    3.381 closest distance to " NE2 GLN A  77 " =    3.226
peak=    3.371 closest distance to " N   VAL A 126 " =    1.293
peak=    3.364 closest distance to " O   HOH Z 298 " =    2.540
peak=    3.357 closest distance to " O   HOH Z 403 " =    1.339
peak=    3.356 closest distance to " O   HOH Z 279 " =    2.129
peak=    3.356 closest distance to " CB  GLU A  46 " =    1.030
peak=    3.346 closest distance to " O   HOH Z 209 " =    2.449
peak=    3.345 closest distance to " O   HOH Z  66 " =    2.122
peak=    3.342 closest distance to " O   HOH Z 265 " =    2.380
peak=    3.342 closest distance to " CG1 VAL A 153 " =    0.948
peak=    3.340 closest distance to " OG  SER A  22 " =    2.603
peak=    3.335 closest distance to " O   HOH Z 365 " =    2.971
peak=    3.334 closest distance to " O   HOH Z 187 " =    2.277
peak=    3.333 closest distance to " CA  ASN A 217 " =    1.201
peak=    3.332 closest distance to " CD  ARG A 269 " =    0.958
peak=    3.332 closest distance to " CB  MET A  40 " =    0.854
peak=    3.329 closest distance to " CA  MET A 105 " =    1.019
peak=    3.325 closest distance to " ND1 HIS A  86 " =    1.826
peak=    3.323 closest distance to " O   HOH Z 411 " =    3.846
peak=    3.322 closest distance to " CB  ASN A 142 " =    1.101
peak=    3.321 closest distance to " CB  THR A  31 " =    1.697
peak=    3.320 closest distance to " CA  ALA A 158 " =    1.257
peak=    3.319 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.311 closest distance to " CG  GLN A  77 " =    2.037
peak=    3.309 closest distance to " O   HOH Z 163 " =    1.690
peak=    3.304 closest distance to " ND2 ASN A 110 " =    1.634
peak=    3.302 closest distance to " CD1AILE A 234 " =    0.928
peak=    3.301 closest distance to " CG2AVAL A 121 " =    2.230
peak=    3.299 closest distance to " O   HOH Z 258 " =    1.675
peak=    3.293 closest distance to " CD  LYS A 119 " =    1.323
peak=    3.291 closest distance to " O   HOH Z 171 " =    2.103
peak=    3.289 closest distance to " N   ASN A 127 " =    1.254
peak=    3.288 closest distance to " O   HOH Z  85 " =    2.264
peak=    3.285 closest distance to " O   HOH Z 299 " =    4.515
peak=    3.284 closest distance to " CB  HIS A 108 " =    0.840
peak=    3.284 closest distance to " O   HOH Z 213 " =    1.648
peak=    3.284 closest distance to " CG2 THR A 220 " =    0.919
peak=    3.283 closest distance to " O   HOH Z 411 " =    1.738
peak=    3.282 closest distance to " CE  LYS A  48 " =    1.010
peak=    3.282 closest distance to " O   THR A 251 " =    1.169
peak=    3.279 closest distance to " CG  LYS A  76 " =    0.992
peak=    3.276 closest distance to " O   HOH Z 144 " =    1.836
peak=    3.275 closest distance to " N   ASN A  39 " =    1.310
peak=    3.274 closest distance to " NH2AARG A 190 " =    1.919
peak=    3.273 closest distance to " O   HOH Z  88 " =    3.195
peak=    3.272 closest distance to " O   HOH Z 163 " =    1.826
peak=    3.272 closest distance to " CB  ALA A 114 " =    1.148
peak=    3.264 closest distance to " CA  ALA A  84 " =    1.302
peak=    3.263 closest distance to " O   HOH Z 410 " =    1.909
peak=    3.261 closest distance to " O   HOH Z 345 " =    3.242
peak=    3.260 closest distance to " CB  GLN A 278 " =    0.873
peak=    3.258 closest distance to " CA  ALA A 233 " =    1.359
peak=    3.251 closest distance to " O   HOH Z 261 " =    1.571
peak=    3.250 closest distance to " O   HOH Z 199 " =    1.529
peak=    3.247 closest distance to " O  BHOH Z 338 " =    2.292
peak=    3.242 closest distance to " CA  ASP A 162 " =    1.076
peak=    3.242 closest distance to " CD  ARG A  66 " =    2.511
peak=    3.239 closest distance to " CG  MET A 185 " =    1.097
peak=    3.238 closest distance to " CB  SER A 216 " =    0.834
peak=    3.235 closest distance to " O   HOH Z 374 " =    2.667
peak=    3.235 closest distance to " O   HOH Z 281 " =    4.770
peak=    3.228 closest distance to " CD2 LEU A 255 " =    1.442
peak=    3.227 closest distance to " CG  GLU A 277 " =    2.139
peak=    3.226 closest distance to " CB  ALA A  34 " =    1.045
peak=    3.223 closest distance to " O   HOH Z 419 " =    1.911
peak=    3.223 closest distance to " O   ALA A   1 " =    1.646
peak=    3.223 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.217 closest distance to " O   HOH Z 116 " =    1.737
peak=    3.214 closest distance to " O   HOH Z  35 " =    2.550
peak=    3.207 closest distance to " O   HOH Z 433 " =    1.713
peak=    3.206 closest distance to " O   HOH Z 365 " =    3.154
peak=    3.203 closest distance to " CA  TYR A 116 " =    1.377
peak=    3.202 closest distance to " CB  GLN A 103 " =    0.848
peak=    3.200 closest distance to " O   HOH Z  49 " =    2.883
peak=    3.198 closest distance to " O   HOH Z 234 " =    1.884
peak=    3.198 closest distance to " CB  ALA A 248 " =    1.325
peak=    3.194 closest distance to " CB  ASN A 110 " =    1.150
peak=    3.193 closest distance to " CB  ASN A 215 " =    1.180
peak=    3.192 closest distance to " O   HOH Z 128 " =    2.271
peak=    3.192 closest distance to " O   HOH Z  49 " =    2.209
peak=    3.185 closest distance to " CA  THR A 221 " =    1.446
peak=    3.179 closest distance to " CA  LEU A 101 " =    1.528
peak=    3.178 closest distance to " C   TYR A 214 " =    1.420
peak=    3.178 closest distance to " CA  SER A  87 " =    1.086
peak=    3.175 closest distance to " CA  ILE A  33 " =    1.445
peak=    3.171 closest distance to " CB  ALA A 248 " =    0.857
peak=    3.162 closest distance to " O   HOH Z 435 " =    1.931
peak=    3.162 closest distance to " O   HOH Z 359 " =    1.406
peak=    3.162 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.162 closest distance to " O   HOH Z 329 " =    3.849
peak=    3.161 closest distance to " CA  ASN A  74 " =    1.269
peak=    3.160 closest distance to " CA  ALA A 248 " =    1.217
peak=    3.156 closest distance to " CB  TYR A 116 " =    0.756
peak=    3.152 closest distance to " O   HOH Z 406 " =    1.527
peak=    3.151 closest distance to " O   HOH Z 189 " =    2.802
peak=    3.146 closest distance to " O   HOH Z  71 " =    2.319
peak=    3.145 closest distance to " CG  MET A 185 " =    1.039
peak=    3.137 closest distance to " N   SER A 135 " =    1.293
peak=    3.137 closest distance to " CB  GLN A  88 " =    1.201
peak=    3.134 closest distance to " O   HOH Z 336 " =    1.695
peak=    3.133 closest distance to " O   HOH Z  44 " =    3.348
peak=    3.133 closest distance to " N   TYR A 116 " =    1.571
peak=    3.132 closest distance to " CB  ARG A 259 " =    1.916
peak=    3.130 closest distance to " CG1 ILE A 151 " =    0.934
peak=    3.128 closest distance to " CA  ASP A 191 " =    0.804
peak=    3.123 closest distance to " CB  ALA A 100 " =    1.143
peak=    3.122 closest distance to " O   HOH Z 124 " =    2.232
peak=    3.122 closest distance to " NZ  LYS A 166 " =    2.986
peak=    3.118 closest distance to " O   HOH Z 357 " =    1.846
peak=    3.114 closest distance to " O   HOH Z 273 " =    2.729
peak=    3.110 closest distance to " O   HOH Z 358 " =    3.612
peak=    3.109 closest distance to " O   HOH Z 430 " =    5.447
peak=    3.087 closest distance to " CB  ASN A 224 " =    1.018
peak=    3.082 closest distance to " CG2BVAL A  41 " =    0.828
peak=    3.081 closest distance to " CB  GLN A 205 " =    1.113
peak=    3.077 closest distance to " CA  GLY A  80 " =    0.863
peak=    3.074 closest distance to " O   HOH Z 156 " =    2.937
peak=    3.073 closest distance to " O   HOH Z 392 " =    1.962
peak=    3.068 closest distance to " CG  GLN A  11 " =    1.535
peak=    3.061 closest distance to " N   ALA A 154 " =    0.911
peak=    3.056 closest distance to " CG BARG A 275 " =    1.395
peak=    3.053 closest distance to " O   ALA A 158 " =    1.262
peak=    3.041 closest distance to " OE2 GLU A  53 " =    2.044
peak=    3.038 closest distance to " CB  VAL A 126 " =    1.103
peak=    3.033 closest distance to " CB  LEU A 255 " =    0.780
peak=    3.029 closest distance to " O   HOH Z  88 " =    1.923
peak=    3.009 closest distance to " NH2AARG A 190 " =    1.057
peak=    3.006 closest distance to " O   HOH Z   9 " =    2.203

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.810 - 5.645
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 190
   mapped sites are within: 0.810 - 5.645

peak=   -4.834 closest distance to " O   HOH Z 266 " =    4.878
peak=   -4.465 closest distance to " O   VAL A  67 " =    2.784
peak=   -4.415 closest distance to " CD  ARG A 156 " =    2.010
peak=   -4.403 closest distance to " CB  PRO A 243 " =    2.640
peak=   -4.370 closest distance to " C   HIS A 108 " =    1.072
peak=   -4.337 closest distance to " CG  GLN A 223 " =    1.947
peak=   -4.256 closest distance to " SG  CYS A 254 " =    3.459
peak=   -4.190 closest distance to " O   HOH Z 372 " =    2.344
peak=   -4.153 closest distance to " CD  GLN A  58 " =    1.035
peak=   -4.120 closest distance to " O   ILE A 109 " =    2.596
peak=   -4.120 closest distance to " OG BSER A 134 " =    1.219
peak=   -4.092 closest distance to " O   HOH Z 198 " =    1.999
peak=   -4.088 closest distance to " O   HOH Z 389 " =    1.784
peak=   -4.070 closest distance to " O   HOH Z 126 " =    1.895
peak=   -4.064 closest distance to " O   HOH Z 377 " =    2.161
peak=   -4.018 closest distance to " CG  ASP A 231 " =    0.810
peak=   -4.005 closest distance to " N   ALA A  43 " =    2.598
peak=   -3.990 closest distance to " CE2 TYR A  30 " =    2.746
peak=   -3.965 closest distance to " O   HOH Z 290 " =    1.226
peak=   -3.960 closest distance to " OG  SER A  97 " =    2.187
peak=   -3.938 closest distance to " CA  VAL A  67 " =    2.789
peak=   -3.924 closest distance to " CG1 VAL A 112 " =    2.814
peak=   -3.904 closest distance to " O   HOH Z  10 " =    1.528
peak=   -3.874 closest distance to " O   HOH Z 231 " =    2.274
peak=   -3.872 closest distance to " O   PRO A 198 " =    1.281
peak=   -3.860 closest distance to " O   HOH Z 196 " =    1.970
peak=   -3.855 closest distance to " O   HOH Z 114 " =    3.192
peak=   -3.850 closest distance to " ND2 ASN A  45 " =    1.665
peak=   -3.819 closest distance to " CD  ARG A 139 " =    1.538
peak=   -3.811 closest distance to " CB  ASN A  39 " =    2.337
peak=   -3.807 closest distance to " CZ3 TRP A 179 " =    1.202
peak=   -3.801 closest distance to " OXT GLY A 302 " =    2.859
peak=   -3.791 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.784 closest distance to " O   HOH Z 311 " =    3.630
peak=   -3.755 closest distance to " CG2 ILE A 263 " =    2.305
peak=   -3.743 closest distance to " O   HOH Z 353 " =    2.104
peak=   -3.738 closest distance to " CB  PHE A 192 " =    2.012
peak=   -3.722 closest distance to " O   HOH Z 185 " =    2.297
peak=   -3.702 closest distance to " CG1 VAL A 112 " =    2.888
peak=   -3.687 closest distance to " O   HOH Z  13 " =    1.575
peak=   -3.680 closest distance to " O   HOH Z 407 " =    3.043
peak=   -3.666 closest distance to " O   HOH Z 435 " =    2.771
peak=   -3.653 closest distance to " O   PRO A 163 " =    2.092
peak=   -3.637 closest distance to " CB  ALA A  43 " =    2.523
peak=   -3.622 closest distance to " CB  ALA A 291 " =    2.374
peak=   -3.621 closest distance to " CD1 LEU A 101 " =    2.405
peak=   -3.618 closest distance to " CG  ASP A 132 " =    2.322
peak=   -3.608 closest distance to " CZ  PHE A  59 " =    1.582
peak=   -3.604 closest distance to " O   HOH Z  43 " =    1.640
peak=   -3.585 closest distance to " NH2AARG A 275 " =    5.258
peak=   -3.583 closest distance to " O   HOH Z 165 " =    1.946
peak=   -3.582 closest distance to " N   GLN A  58 " =    1.622
peak=   -3.575 closest distance to " O   SER A 210 " =    2.023
peak=   -3.567 closest distance to " OD2 ASP A 191 " =    1.473
peak=   -3.566 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.556 closest distance to " OG  SER A  62 " =    1.742
peak=   -3.549 closest distance to " CG  ARG A  66 " =    2.447
peak=   -3.548 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.544 closest distance to " CD1 LEU A 297 " =    2.276
peak=   -3.544 closest distance to " O   HOH Z  52 " =    1.422
peak=   -3.540 closest distance to " CG  PHE A 283 " =    2.565
peak=   -3.530 closest distance to " C   LEU A 143 " =    1.055
peak=   -3.523 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.521 closest distance to " O   HOH Z 292 " =    4.471
peak=   -3.504 closest distance to " CD1 LEU A 228 " =    2.232
peak=   -3.503 closest distance to " NH1 ARG A 195 " =    2.572
peak=   -3.500 closest distance to " OD1 ASN A 187 " =    1.639
peak=   -3.491 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.489 closest distance to " CE2 PHE A 218 " =    2.441
peak=   -3.483 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.483 closest distance to " CB  TYR A  15 " =    2.185
peak=   -3.474 closest distance to " ND2 ASN A  45 " =    1.030
peak=   -3.472 closest distance to " O   HOH Z 394 " =    1.514
peak=   -3.469 closest distance to " OE2 GLU A   2 " =    1.761
peak=   -3.468 closest distance to " CA  GLY A 203 " =    2.278
peak=   -3.465 closest distance to " OD1 ASP A 171 " =    1.609
peak=   -3.464 closest distance to " CD  ARG A 195 " =    5.197
peak=   -3.456 closest distance to " O   HOH Z 298 " =    1.301
peak=   -3.454 closest distance to " CD2 LEU A 300 " =    2.994
peak=   -3.446 closest distance to " OD1 ASN A 148 " =    1.533
peak=   -3.445 closest distance to " O   HOH Z 211 " =    1.705
peak=   -3.445 closest distance to " SG ACYS A 201 " =    2.038
peak=   -3.439 closest distance to " OD2 ASP A 171 " =    2.400
peak=   -3.436 closest distance to " O   HOH Z   6 " =    1.498
peak=   -3.436 closest distance to " CB  ASP A 286 " =    2.168
peak=   -3.434 closest distance to " CG1 VAL A 250 " =    2.637
peak=   -3.424 closest distance to " O   HOH Z 166 " =    1.526
peak=   -3.423 closest distance to " O   HOH Z  11 " =    1.745
peak=   -3.421 closest distance to " N   ALA A 226 " =    1.998
peak=   -3.420 closest distance to " OG BSER A 134 " =    1.769
peak=   -3.418 closest distance to " N   ASP A 286 " =    2.389
peak=   -3.415 closest distance to " O   LEU A 167 " =    1.494
peak=   -3.413 closest distance to " O   HOH Z 252 " =    3.898
peak=   -3.412 closest distance to " O   HOH Z  73 " =    2.314
peak=   -3.407 closest distance to " NE2 GLN A  88 " =    1.854
peak=   -3.395 closest distance to " O   HOH Z 198 " =    1.383
peak=   -3.389 closest distance to " O   PHE A 218 " =    1.670
peak=   -3.383 closest distance to " C   ALA A 158 " =    1.248
peak=   -3.383 closest distance to " C   ASP A 231 " =    2.692
peak=   -3.381 closest distance to " CE  MET A 105 " =    2.280
peak=   -3.376 closest distance to " CD1 ILE A 239 " =    2.130
peak=   -3.376 closest distance to " O   HOH Z 243 " =    2.071
peak=   -3.376 closest distance to " CB  TRP A  85 " =    2.552
peak=   -3.370 closest distance to " O   HOH Z 414 " =    1.614
peak=   -3.367 closest distance to " CD2 PHE A  61 " =    2.488
peak=   -3.353 closest distance to " N   TYR A  68 " =    3.130
peak=   -3.351 closest distance to " O   VAL A 189 " =    2.608
peak=   -3.350 closest distance to " CB  PRO A 163 " =    2.456
peak=   -3.350 closest distance to " O   HOH Z 166 " =    1.875
peak=   -3.349 closest distance to " O   HOH Z 313 " =    1.960
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    1.993
peak=   -3.348 closest distance to " O   HOH Z 102 " =    1.610
peak=   -3.344 closest distance to " C   MET A 188 " =    1.446
peak=   -3.333 closest distance to " NH2 ARG A  79 " =    1.597
peak=   -3.329 closest distance to " O   HOH Z 377 " =    1.757
peak=   -3.328 closest distance to " O   HOH Z 134 " =    2.851
peak=   -3.327 closest distance to " O   HOH Z  38 " =    1.543
peak=   -3.321 closest distance to " O   HOH Z  37 " =    1.825
peak=   -3.320 closest distance to " O   HOH Z 361 " =    3.436
peak=   -3.315 closest distance to " CD  LYS A 289 " =    2.441
peak=   -3.310 closest distance to " O   MET A  40 " =    2.715
peak=   -3.309 closest distance to " CB  ALA A 248 " =    2.307
peak=   -3.309 closest distance to " O   HOH Z  44 " =    2.167
peak=   -3.307 closest distance to " OD2 ASP A  50 " =    2.249
peak=   -3.301 closest distance to " CB  ALA A 248 " =    2.123
peak=   -3.300 closest distance to " NH2BARG A 275 " =    2.086
peak=   -3.298 closest distance to " N   ALA A 248 " =    1.652
peak=   -3.293 closest distance to " O   GLY A 211 " =    1.423
peak=   -3.293 closest distance to " O   HOH Z 417 " =    2.532
peak=   -3.288 closest distance to " OD1 ASP A 191 " =    1.593
peak=   -3.286 closest distance to " O   HOH Z  93 " =    2.092
peak=   -3.280 closest distance to " OG  SER A  26 " =    1.264
peak=   -3.271 closest distance to " CB  PHE A 208 " =    2.245
peak=   -3.271 closest distance to " O   HOH Z 244 " =    2.042
peak=   -3.260 closest distance to " OG  SER A 206 " =    1.775
peak=   -3.258 closest distance to " CG  PRO A 163 " =    2.580
peak=   -3.248 closest distance to " O   HOH Z 322 " =    1.636
peak=   -3.247 closest distance to " CG  GLN A  11 " =    1.725
peak=   -3.240 closest distance to " CA  GLY A 241 " =    3.059
peak=   -3.236 closest distance to " O   ARG A 145 " =    1.597
peak=   -3.234 closest distance to " CZ  PHE A 155 " =    1.242
peak=   -3.231 closest distance to " ND2 ASN A 249 " =    2.114
peak=   -3.230 closest distance to " O   ALA A 161 " =    1.654
peak=   -3.226 closest distance to " O   HOH Z 426 " =    1.542
peak=   -3.224 closest distance to " CD1 PHE A  16 " =    2.659
peak=   -3.221 closest distance to " CG1 VAL A 125 " =    2.387
peak=   -3.221 closest distance to " CG  GLU A 277 " =    1.166
peak=   -3.221 closest distance to " O   PRO A 198 " =    1.639
peak=   -3.212 closest distance to " CE3 TRP A 150 " =    2.120
peak=   -3.209 closest distance to " O   HOH Z 191 " =    5.645
peak=   -3.208 closest distance to " O   SER A  95 " =    1.598
peak=   -3.205 closest distance to " O   HOH Z 200 " =    3.533
peak=   -3.200 closest distance to " O   HOH Z 234 " =    4.076
peak=   -3.196 closest distance to " O   SER A 135 " =    1.521
peak=   -3.195 closest distance to " O   HOH Z 385 " =    1.939
peak=   -3.194 closest distance to " CG  ARG A 269 " =    2.257
peak=   -3.190 closest distance to " O   ALA A  10 " =    1.731
peak=   -3.185 closest distance to " CD2 TYR A 247 " =    2.419
peak=   -3.183 closest distance to " O   HOH Z   6 " =    2.118
peak=   -3.183 closest distance to " O   HOH Z 150 " =    1.881
peak=   -3.182 closest distance to " O   ALA A  34 " =    2.444
peak=   -3.177 closest distance to " O   HOH Z 385 " =    2.108
peak=   -3.175 closest distance to " O   VAL A 174 " =    2.030
peak=   -3.169 closest distance to " CE BMET A  47 " =    2.043
peak=   -3.167 closest distance to " O   GLY A  80 " =    2.564
peak=   -3.167 closest distance to " CA  GLY A  98 " =    1.970
peak=   -3.157 closest distance to " O   TRP A  70 " =    1.486
peak=   -3.153 closest distance to " O   TRP A  92 " =    1.694
peak=   -3.152 closest distance to " O   HOH Z 123 " =    2.246
peak=   -3.148 closest distance to " O   HOH Z  76 " =    1.946
peak=   -3.148 closest distance to " CG1 VAL A  67 " =    2.909
peak=   -3.145 closest distance to " OG BSER A 210 " =    2.147
peak=   -3.133 closest distance to " O   HOH Z 295 " =    1.596
peak=   -3.126 closest distance to " O   ASN A 301 " =    1.433
peak=   -3.123 closest distance to " OD2 ASP A 171 " =    1.876
peak=   -3.122 closest distance to " CD2 TYR A 293 " =    2.042
peak=   -3.112 closest distance to " O   HOH Z  60 " =    2.305
peak=   -3.104 closest distance to " OXT GLY A 302 " =    3.253
peak=   -3.099 closest distance to " CG2 VAL A 189 " =    2.151
peak=   -3.098 closest distance to " CG2 THR A 221 " =    2.235
peak=   -3.092 closest distance to " CD1 TYR A 247 " =    2.734
peak=   -3.090 closest distance to " CD2 LEU A 237 " =    2.576
peak=   -3.088 closest distance to " O   ALA A  51 " =    1.348
peak=   -3.080 closest distance to " O   PRO A 198 " =    1.309
peak=   -3.077 closest distance to " OG1 THR A 157 " =    2.907
peak=   -3.064 closest distance to " C   PRO A  90 " =    1.490
peak=   -3.059 closest distance to " O   HOH Z 351 " =    1.347
peak=   -3.046 closest distance to " O   HOH Z 317 " =    2.313
peak=   -3.014 closest distance to " CA  GLY A 241 " =    2.778

================= 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    :  0.2140 0.2080   5.652414e+00   5.627831e+00
   1_bss:  0.1947 0.1874   5.610133e+00   5.571788e+00
   1_xyz:  0.1303 0.1485   5.214379e+00   5.330432e+00
   1_adp:  0.1203 0.1494   5.159274e+00   5.341935e+00
   1_occ:  0.1197 0.1489   5.156767e+00   5.340060e+00
   2_bss:  0.1199 0.1488   5.157254e+00   5.338826e+00
   2_xyz:  0.1150 0.1487   5.133265e+00   5.335847e+00
   2_adp:  0.1123 0.1490   5.123009e+00   5.341890e+00
   2_occ:  0.1122 0.1491   5.122942e+00   5.342137e+00
   3_bss:  0.1121 0.1491   5.122724e+00   5.342069e+00
   3_xyz:  0.1064 0.1508   5.096642e+00   5.344479e+00
   3_adp:  0.1050 0.1525   5.095833e+00   5.352182e+00
   3_occ:  0.1050 0.1526   5.096015e+00   5.352673e+00
   4_bss:  0.1048 0.1526   5.096034e+00   5.352727e+00
   4_xyz:  0.1085 0.1545   5.120858e+00   5.367688e+00
   4_adp:  0.1111 0.1526   5.126392e+00   5.358268e+00
   4_occ:  0.1111 0.1527   5.126666e+00   5.358933e+00
   5_bss:  0.1111 0.1527   5.126711e+00   5.358990e+00
   5_xyz:  0.1075 0.1525   5.108584e+00   5.354789e+00
   5_adp:  0.1058 0.1539   5.105264e+00   5.362974e+00
   5_occ:  0.1058 0.1539   5.105292e+00   5.363135e+00
   5_bss:  0.1056 0.1540   5.105359e+00   5.363183e+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:  0.325  50.000  -3.155  -1.561  -1.358  -0.000  -0.000  -0.000
   1_xyz:  0.325  50.000  -3.155  -1.561  -1.358  -0.000  -0.000  -0.000
   1_adp:  0.325  50.000  -3.155  -1.561  -1.358  -0.000  -0.000  -0.000
   1_occ:  0.325  50.000  -3.155  -1.561  -1.358  -0.000  -0.000  -0.000
   2_bss:  0.327  50.000  -3.152  -2.255  -1.679  -0.000  -0.000  -0.000
   2_xyz:  0.327  50.000  -3.152  -2.255  -1.679  -0.000  -0.000  -0.000
   2_adp:  0.327  50.000  -3.152  -2.255  -1.679  -0.000  -0.000  -0.000
   2_occ:  0.327  50.000  -3.152  -2.255  -1.679  -0.000  -0.000  -0.000
   3_bss:  0.327  50.000  -2.828  -2.178  -1.504  -0.000  -0.000  -0.000
   3_xyz:  0.327  50.000  -2.828  -2.178  -1.504  -0.000  -0.000  -0.000
   3_adp:  0.327  50.000  -2.828  -2.178  -1.504  -0.000  -0.000  -0.000
   3_occ:  0.327  50.000  -2.828  -2.178  -1.504  -0.000  -0.000  -0.000
   4_bss:  0.327  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   4_xyz:  0.327  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   4_adp:  0.327  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   4_occ:  0.327  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   5_bss:  0.328  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   5_xyz:  0.328  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   5_adp:  0.328  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   5_occ:  0.328  50.000  -2.492  -1.966  -1.237  -0.000  -0.000  -0.000
   5_bss:  0.328  49.996  -2.235  -1.756  -1.007  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  18.930 0.8753  1.0240    12023.758
   1_bss:  17.406 0.8880  0.9650     9009.141
   1_xyz:  12.709 0.9258  0.9870     5688.453
   1_adp:  13.025 0.9230  0.9850     5761.872
   1_occ:  12.997 0.9232  0.9848     5722.605
   2_bss:  12.969 0.9234  0.9734     5709.238
   2_xyz:  12.842 0.9245  0.9725     5705.096
   2_adp:  12.968 0.9235  0.9685     5727.313
   2_occ:  12.972 0.9234  0.9684     5728.668
   3_bss:  12.968 0.9235  0.9754     5729.481
   3_xyz:  13.005 0.9230  0.9756     5785.843
   3_adp:  13.178 0.9217  0.9690     5847.925
   3_occ:  13.187 0.9216  0.9690     5854.223
   4_bss:  13.185 0.9216  0.9787     5856.131
   4_xyz:  13.442 0.9199  0.9771     6029.511
   4_adp:  13.241 0.9214  0.9744     5963.848
   4_occ:  13.255 0.9213  0.9742     5968.398
   5_bss:  13.256 0.9212  0.9743     5969.414
   5_xyz:  13.176 0.9218  0.9751     5933.111
   5_adp:  13.362 0.9204  0.9685     5983.800
   5_occ:  13.366 0.9203  0.9684     5986.552
   5_bss:  13.367 0.9203  0.9765     5988.009
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.5973e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.5973e-01
   1_xyz:   1.003  0.008  0.074 15.302  0.004  4.114   6.1322e-02
   1_adp:   1.003  0.008  0.074 15.302  0.004  4.114   6.1322e-02
   1_occ:   1.003  0.008  0.074 15.302  0.004  4.114   6.1322e-02
   2_bss:   1.003  0.008  0.074 15.302  0.004  4.114   6.1322e-02
   2_xyz:   0.915  0.006  0.071 15.046  0.004  4.115   5.3608e-02
   2_adp:   0.915  0.006  0.071 15.046  0.004  4.115   5.3608e-02
   2_occ:   0.915  0.006  0.071 15.046  0.004  4.115   5.3608e-02
   3_bss:   0.915  0.006  0.071 15.046  0.004  4.115   5.3608e-02
   3_xyz:   1.076  0.009  0.083 15.414  0.005  4.117   7.1573e-02
   3_adp:   1.076  0.009  0.083 15.414  0.005  4.117   7.1573e-02
   3_occ:   1.076  0.009  0.083 15.414  0.005  4.117   7.1573e-02
   4_bss:   1.076  0.009  0.083 15.414  0.005  4.117   7.1573e-02
   4_xyz:   0.913  0.006  0.071 15.082  0.004  4.116   5.3252e-02
   4_adp:   0.913  0.006  0.071 15.082  0.004  4.116   5.3252e-02
   4_occ:   0.913  0.006  0.071 15.082  0.004  4.116   5.3252e-02
   5_bss:   0.913  0.006  0.071 15.082  0.004  4.116   5.3252e-02
   5_xyz:   1.022  0.008  0.080 15.227  0.004  4.117   6.5128e-02
   5_adp:   1.022  0.008  0.080 15.227  0.004  4.117   6.5128e-02
   5_occ:   1.022  0.008  0.080 15.227  0.004  4.117   6.5128e-02
   5_bss:   1.022  0.008  0.080 15.227  0.004  4.117   6.5128e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4095e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4095e-01
   1_xyz:   7.424  0.047  0.230 83.792  0.032  2.341   4.7856e-02
   1_adp:   7.424  0.047  0.230 83.792  0.032  2.341   4.7856e-02
   1_occ:   7.424  0.047  0.230 83.792  0.032  2.341   4.7856e-02
   2_bss:   7.424  0.047  0.230 83.792  0.032  2.341   4.7856e-02
   2_xyz:   6.809  0.035  0.219 84.333  0.037  2.402   4.2156e-02
   2_adp:   6.809  0.035  0.219 84.333  0.037  2.402   4.2156e-02
   2_occ:   6.809  0.035  0.219 84.333  0.037  2.402   4.2156e-02
   3_bss:   6.809  0.035  0.219 84.333  0.037  2.402   4.2156e-02
   3_xyz:   7.370  0.048  0.264 83.236  0.036  2.283   5.5785e-02
   3_adp:   7.370  0.048  0.264 83.236  0.036  2.283   5.5785e-02
   3_occ:   7.370  0.048  0.264 83.236  0.036  2.283   5.5785e-02
   4_bss:   7.370  0.048  0.264 83.236  0.036  2.283   5.5785e-02
   4_xyz:   6.596  0.041  0.227 83.133  0.036  2.380   3.0325e-02
   4_adp:   6.596  0.041  0.227 83.133  0.036  2.380   3.0325e-02
   4_occ:   6.596  0.041  0.227 83.133  0.036  2.380   3.0325e-02
   5_bss:   6.596  0.041  0.227 83.133  0.036  2.380   3.0325e-02
   5_xyz:   7.214  0.046  0.252 83.428  0.036  2.278   4.6966e-02
   5_adp:   7.214  0.046  0.252 83.428  0.036  2.278   4.6966e-02
   5_occ:   7.214  0.046  0.252 83.428  0.036  2.278   4.6966e-02
   5_bss:   7.214  0.046  0.252 83.428  0.036  2.278   4.6966e-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:  72.18   0.00  16.41  72.18   0.00  12.63  62.58   5.58  36.97
   1_occ:  72.18   0.00  16.41  72.18   0.00  12.63  62.58   5.58  36.97
   2_bss:  72.18   0.00  16.41  72.18   0.00  12.63  62.58   5.58  36.97
   2_xyz:  72.18   0.00  16.41  72.18   0.00  12.63  62.58   5.58  36.97
   2_adp:  65.62   1.61  16.65  65.62   1.61  12.85  64.71   5.92  37.36
   2_occ:  65.62   1.61  16.65  65.62   1.61  12.85  64.71   5.92  37.36
   3_bss:  65.62   1.61  16.65  65.62   1.61  12.85  64.71   5.92  37.36
   3_xyz:  65.62   1.61  16.65  65.62   1.61  12.85  64.71   5.92  37.36
   3_adp:  83.34   0.58  17.01  83.34   0.58  12.90  73.07   6.22  39.42
   3_occ:  83.34   0.58  17.01  83.34   0.58  12.90  73.07   6.22  39.42
   4_bss:  83.34   0.58  17.01  83.34   0.58  12.90  73.07   6.22  39.42
   4_xyz:  83.34   0.58  17.01  83.34   0.58  12.90  73.07   6.22  39.42
   4_adp:  79.50   2.19  16.25  79.50   2.19  12.62  67.14   5.81  36.01
   4_occ:  79.50   2.19  16.25  79.50   2.19  12.62  67.14   5.81  36.01
   5_bss:  79.50   2.19  16.25  79.50   2.19  12.62  67.14   5.81  36.01
   5_xyz:  79.50   2.19  16.25  79.50   2.19  12.62  67.14   5.81  36.01
   5_adp:  84.16   0.18  16.61  84.16   0.18  12.58  70.42   5.85  38.52
   5_occ:  84.16   0.18  16.61  84.16   0.18  12.58  70.42   5.85  38.52
   5_bss:  84.15   0.18  16.60  84.15   0.18  12.58  70.41   5.85  38.52
------------------------------------------------------------------------
 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:    0.623    0.007    0.173
   1_adp:    0.623    0.007    0.173
   1_occ:    0.623    0.007    0.173
   2_bss:    0.623    0.007    0.173
   2_xyz:    0.705    0.009    0.190
   2_adp:    0.705    0.009    0.190
   2_occ:    0.705    0.009    0.190
   3_bss:    0.705    0.009    0.190
   3_xyz:    0.653    0.022    0.205
   3_adp:    0.653    0.022    0.205
   3_occ:    0.653    0.022    0.205
   4_bss:    0.653    0.022    0.205
   4_xyz:    0.728    0.016    0.208
   4_adp:    0.728    0.016    0.208
   4_occ:    0.728    0.016    0.208
   5_bss:    0.728    0.016    0.208
   5_xyz:    0.788    0.021    0.211
   5_adp:    0.788    0.021    0.211
   5_occ:    0.788    0.021    0.211
   5_bss:    0.788    0.021    0.211
------------------------------------------------------------------------

CPU time actual refinement: 306.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/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_675/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_675/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 306.84 
  Macro-tasks:
    bulk solvent and scale       = 37.65  
    individual site refinement   = 121.07 
    weights calculation          = 28.82  
    collect and process          = 6.55   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 194.20 
  Micro-tasks:
    mask                            = 0.60   
    f_calc                          = 96.08  
    alpha_beta                      = 7.63   
    target                          = 1.09   
    gradients_wrt_atomic_parameters = 104.11 
    fmodel                         = 6.51   
    r_factors                      = 0.16   
    phase_errors                   = 11.35  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 227.83 
NUMBER OF MASK CALCS=  2
Time per interpreted Python bytecode instruction: 4.444 micro seconds
Total CPU time: 5.34 minutes
from_scatterers_fft:    625 calls, 95.78 s
gradients_fft:          570 calls, 91.44 s

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

# Date 2008-01-16 Time 05:23:25 PST -0800 (1200489805.38 s)
Start R-work = 0.2140, R-free = 0.2080 (no bulk solvent and anisotropic scale)
Final R-work = 0.1296, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.1947, R-free = 0.1874
Final R-work = 0.1056, R-free = 0.1540