# Date 2008-01-16 Time 06:17:45 PST -0800 (1200493065.37 s)
#phil __OFF__

Command line arguments: "../1088.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3989
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1088

-------------------------------------------------------------------------------
  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: (71.3037, 48.1033, 88.5498, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.0306
Completeness in resolution range: 0.968362
Completeness with d_max=infinity: 0.965308

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2591
                             d_min =   2.0306

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2591 2.0306
Completeness in resolution range: 0.968362
Completeness with d_max=infinity: 0.965308

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2595 -  4.3443 [2129/2156]  1915   214  10.1%
  bin  2:  4.3443 -  3.4614 [2037/2053]  1834   203  10.0%
  bin  3:  3.4614 -  3.0278 [2025/2044]  1823   202  10.0%
  bin  4:  3.0278 -  2.7527 [1988/2018]  1786   202  10.2%
  bin  5:  2.7527 -  2.5564 [1986/2005]  1789   197   9.9%
  bin  6:  2.5564 -  2.4063 [1975/2000]  1780   195   9.9%
  bin  7:  2.4063 -  2.2862 [1968/2001]  1774   194   9.9%
  bin  8:  2.2862 -  2.1870 [1941/1972]  1743   198  10.2%
  bin  9:  2.1870 -  2.1030 [1946/1988]  1751   195  10.0%
  bin 10:  2.1030 -  2.0306 [1594/1992]  1435   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 10
        2.34 -     2.98: 1759
        2.98 -     3.62: 4435
        3.62 -     4.26: 8874
        4.26 -     4.90: 12384
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.701 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.868 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.992 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.040 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27457 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_1088/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/model_refine_001.geo

CPU time processing inputs: 8.83


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 48.10325 88.54975 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: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4992   r_free= 0.4888   ksol= 0.00   Bsol= 0.00   scale= 0.842    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.303311                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8451 0.99   1383  153 0.3997 0.3974      6.6048      6.5639|
|  2:  4.8451 -  3.8663 0.99   1318  150 0.4549 0.4760      6.9143      6.9574|
|  3:  3.8663 -  3.3836 0.99   1313  144 0.4875 0.4267       6.753       6.671|
|  4:  3.3836 -  3.0770 0.99   1294  139 0.4915 0.5014      6.5732      6.5077|
|  5:  3.0770 -  2.8580 0.99   1281  143 0.5298 0.4756      6.3981      6.4234|
|  6:  2.8580 -  2.6905 0.99   1277  145 0.5174 0.5307      6.2964      6.2165|
|  7:  2.6905 -  2.5564 0.99   1281  144 0.5372 0.4988       6.266      6.1948|
|  8:  2.5564 -  2.4456 0.98   1276  138 0.5281 0.4696      6.1963      6.1805|
|  9:  2.4456 -  2.3518 0.98   1250  141 0.5416 0.5592      6.1208      6.1798|
| 10:  2.3518 -  2.2709 0.99   1267  139 0.5356 0.5152      6.1273      6.1175|
| 11:  2.2709 -  2.2001 0.99   1266  143 0.5484 0.5573      6.0468      6.1047|
| 12:  2.2001 -  2.1374 0.97   1242  134 0.5340 0.5475      5.9866      6.0266|
| 13:  2.1374 -  2.0813 0.99   1280  143 0.5346 0.5568      5.9001      5.8665|
| 14:  2.0813 -  2.0306 0.72    902  103 0.5259 0.5239      5.8546      5.7671|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.8451  1383   153  0.68  35.84   0.80     0.72      78750.04|
|  2:  4.8451 -  3.8663  1318   150  0.67  37.43   0.85     0.75     118440.66|
|  3:  3.8663 -  3.3836  1313   144  0.57  46.42   0.84     0.71     125551.77|
|  4:  3.3836 -  3.0770  1294   139  0.46  55.26   0.85     0.59     114798.91|
|  5:  3.0770 -  2.8580  1281   143  0.36  62.89   0.83     0.50      88293.58|
|  6:  2.8580 -  2.6905  1277   145  0.33  65.08   0.84     0.44      77197.30|
|  7:  2.6905 -  2.5564  1281   144  0.30  67.60   0.85     0.40      69967.26|
|  8:  2.5564 -  2.4456  1276   138  0.27  69.88   0.85     0.37      66418.92|
|  9:  2.4456 -  2.3518  1250   141  0.23  73.21   0.86     0.33      63646.94|
| 10:  2.3518 -  2.2709  1267   139  0.26  70.70   0.89     0.36      56024.19|
| 11:  2.2709 -  2.2001  1266   143  0.25  71.63   0.87     0.37      52003.81|
| 12:  2.2001 -  2.1374  1242   134  0.27  70.13   0.87     0.39      46729.41|
| 13:  2.1374 -  2.0813  1280   143  0.24  72.07   0.86     0.35      40859.90|
| 14:  2.0813 -  2.0306   902   103  0.25  71.59   0.89     0.32      32128.92|
|alpha:            min =        0.32 max =            0.75 mean =         0.48|
|beta:             min =    32128.92 max =       125551.77 mean =     74882.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.63|
|phase err.(test): min =        0.00 max =           89.93 mean =        61.81|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.707226             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.999   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.237456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.940   (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 |  1.701 -  2.020:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.020 -  2.340:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.340 -  2.660:       56 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.660 -  2.980:     1703 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.980 -  3.300:     1841 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.300 -  3.620:     2594 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.620 -  3.940:     4596 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.940 -  4.260:     4278 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.260 -  4.580:     5618 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.580 -  4.900:     6766 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.701 |       0.198 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    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: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4992   r_free= 0.4888   ksol= 0.00   Bsol= 0.00   scale= 0.842    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.303311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4935   r_free= 0.4838   ksol= 0.27   Bsol= 50.00   scale= 0.887   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,2.65,2.90,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.300898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.633090             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.877765              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.467   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4935      final r-factor (work) = 0.4111          |
| start r-factor (free) = 0.4838      final r-factor (free) = 0.4472          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.2424 = 14.63 * 0.50 * 6.2973 + 1.00 * 0.1677                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6386 = 14.63 * 0.50 * 6.2172 + 1.00 * 0.1503                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4111      final r-factor (work) = 0.3749          |
| start r-factor (free) = 0.4472      final r-factor (free) = 0.4496          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6804 = 1.88 * 1.00 * 6.2172 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5782 = 1.88 * 1.00 * 6.1517 + 1.00 * 0.0267                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.81  20.19    None  None   None       |
|    all(noH): 2823   0      0.00    123.81  20.19    None  None   None       |
|    Sol.    : 438    0      0.00    123.81  37.29    None  None   None       |
|    Mac.    : 2385   0      0.00    91.95   17.05    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 -  12.381: 1070   |   5:    61.907 -  74.288:   44        |
|      1:    12.381 -  24.763:  889   |   6:    74.288 -  86.670:   21        |
|      2:    24.763 -  37.144:  475   |   7:    86.670 -  99.051:   11        |
|      3:    37.144 -  49.526:  221   |   8:    99.051 - 111.432:    0        |
|      4:    49.526 -  61.907:   91   |   9:   111.432 - 123.814:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3749 r_free = 0.4496             target_work(ml) = 6.156         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3742 r_free = 0.4494             target_work(ml) = 6.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3742   r_free= 0.4494   ksol= 0.27   Bsol= 50.00   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,2.65,2.90,0.00,0.00,0.00); trace/3= 1.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.155492                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3742   r_free= 0.4480   ksol= 0.31   Bsol= 77.15   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,2.35,2.55,0.00,0.00,0.00); trace/3= 1.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.157677                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.415203              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.586   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.128483              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.146  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3742      final r-factor (work) = 0.3350          |
| start r-factor (free) = 0.4480      final r-factor (free) = 0.4083          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1270 = 9.42 * 0.50 * 6.1553 + 1.00 * 0.1503                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8911 = 9.42 * 0.50 * 6.1184 + 1.00 * 0.0882                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3350      final r-factor (work) = 0.3245          |
| start r-factor (free) = 0.4083      final r-factor (free) = 0.3988          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9308 = 1.13 * 1.00 * 6.1184 + 1.00 * 0.0263                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8703 = 1.13 * 1.00 * 6.0674 + 1.00 * 0.0234                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    130.46  19.74    None  None   None       |
|    all(noH): 2823   0      0.00    130.46  19.74    None  None   None       |
|    Sol.    : 438    0      0.00    130.46  37.26    None  None   None       |
|    Mac.    : 2385   0      0.00    93.88   16.52    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 -  13.047: 1163   |   5:    65.232 -  78.279:   39        |
|      1:    13.047 -  26.093:  916   |   6:    78.279 -  91.325:   16        |
|      2:    26.093 -  39.139:  434   |   7:    91.325 - 104.372:    6        |
|      3:    39.139 -  52.186:  177   |   8:   104.372 - 117.418:    0        |
|      4:    52.186 -  65.232:   71   |   9:   117.418 - 130.464:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3245 r_free = 0.3988             target_work(ml) = 6.063         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3243 r_free = 0.3985             target_work(ml) = 6.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3243   r_free= 0.3985   ksol= 0.31   Bsol= 77.15   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,2.35,2.55,0.00,0.00,0.00); trace/3= 1.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.062068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3249   r_free= 0.3989   ksol= 0.33   Bsol= 87.96   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,2.17,2.06,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.063174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.889929             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.176  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.784782              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.771  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3249      final r-factor (work) = 0.2628          |
| start r-factor (free) = 0.3989      final r-factor (free) = 0.3223          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.2610 = 14.89 * 0.50 * 6.0676 + 1.00 * 0.0882                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.6845 = 14.89 * 0.50 * 5.9851 + 1.00 * 0.1255                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2628      final r-factor (work) = 0.2350          |
| start r-factor (free) = 0.3223      final r-factor (free) = 0.2937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7204 = 0.78 * 1.00 * 5.9851 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5840 = 0.78 * 1.00 * 5.8206 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.50  18.37    None  None   None       |
|    all(noH): 2823   0      0.00    127.50  18.37    None  None   None       |
|    Sol.    : 438    0      0.00    127.50  42.73    None  None   None       |
|    Mac.    : 2385   0      0.00    95.73   13.90    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:     0.000 -  12.750: 1414   |   5:    63.749 -  76.499:   60        |
|      1:    12.750 -  25.500:  787   |   6:    76.499 -  89.249:   18        |
|      2:    25.500 -  38.249:  271   |   7:    89.249 - 101.998:    6        |
|      3:    38.249 -  50.999:  174   |   8:   101.998 - 114.748:    1        |
|      4:    50.999 -  63.749:   91   |   9:   114.748 - 127.498:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2350 r_free = 0.2937             target_work(ml) = 5.778         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2347 r_free = 0.2937             target_work(ml) = 5.777         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2347   r_free= 0.2937   ksol= 0.33   Bsol= 87.96   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,2.17,2.06,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.777147                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2344   r_free= 0.2926   ksol= 0.34   Bsol= 91.17   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,0.85,1.02,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.776994                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.328433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.127  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.256368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.381  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2344      final r-factor (work) = 0.1974          |
| start r-factor (free) = 0.2926      final r-factor (free) = 0.2467          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7246 = 4.33 * 0.50 * 5.8216 + 1.00 * 0.1255                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4171 = 4.33 * 0.50 * 5.7034 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1974      final r-factor (work) = 0.1888          |
| start r-factor (free) = 0.2467      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4783 = 0.26 * 1.00 * 5.7034 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4482 = 0.26 * 1.00 * 5.6048 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    119.85  17.11    None  None   None       |
|    all(noH): 2823   0      0.91    119.85  17.11    None  None   None       |
|    Sol.    : 438    0      3.35    119.85  42.02    None  None   None       |
|    Mac.    : 2385   0      0.91    86.36   12.53    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:     0.910 -  12.804: 1597   |   5:    60.382 -  72.276:   60        |
|      1:    12.804 -  24.699:  657   |   6:    72.276 -  84.170:   20        |
|      2:    24.699 -  36.593:  229   |   7:    84.170 -  96.065:    5        |
|      3:    36.593 -  48.487:  148   |   8:    96.065 - 107.959:    1        |
|      4:    48.487 -  60.382:  105   |   9:   107.959 - 119.853:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1888 r_free = 0.2347             target_work(ml) = 5.589         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1887 r_free = 0.2346             target_work(ml) = 5.588         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1887   r_free= 0.2346   ksol= 0.34   Bsol= 91.17   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,0.85,1.02,0.00,0.00,0.00); trace/3= 0.45                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.587792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1888   r_free= 0.2348   ksol= 0.33   Bsol= 80.00   scale= 0.981   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.21,0.59,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.588445                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.964700              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.195  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.291314              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 163.597  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1888      final r-factor (work) = 0.1540          |
| start r-factor (free) = 0.2348      final r-factor (free) = 0.1979          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1850 = 3.96 * 0.50 * 5.6051 + 1.00 * 0.0737                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9936 = 3.96 * 0.50 * 5.5015 + 1.00 * 0.0878                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.1979      final r-factor (free) = 0.1949          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6138 = 0.29 * 1.00 * 5.5015 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6220 = 0.29 * 1.00 * 5.3828 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.86  16.76    None  None   None       |
|    all(noH): 2823   0      0.00    118.86  16.76    None  None   None       |
|    Sol.    : 438    0      2.74    118.86  42.18    None  None   None       |
|    Mac.    : 2385   0      0.00    84.79   12.09    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 -  11.886: 1568   |   5:    59.428 -  71.314:   65        |
|      1:    11.886 -  23.771:  711   |   6:    71.314 -  83.200:   23        |
|      2:    23.771 -  35.657:  182   |   7:    83.200 -  95.085:    6        |
|      3:    35.657 -  47.543:  161   |   8:    95.085 - 106.971:    1        |
|      4:    47.543 -  59.428:  105   |   9:   106.971 - 118.856:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1464 r_free = 0.1949             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1462 r_free = 0.1949             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1949   ksol= 0.33   Bsol= 80.00   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.21,0.59,0.00,0.00,0.00); trace/3= -0.11                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.371725                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8451 0.99   1383  153 0.1114 0.1446       5.497      5.6445|
|  2:  4.8451 -  3.8663 0.99   1318  150 0.1015 0.1191       5.591      5.7742|
|  3:  3.8663 -  3.3836 0.99   1313  144 0.1339 0.1789      5.6897      6.0118|
|  4:  3.3836 -  3.0770 0.99   1294  139 0.1549 0.2100      5.6733      5.8602|
|  5:  3.0770 -  2.8580 0.99   1281  143 0.1835 0.2126      5.6008      5.7496|
|  6:  2.8580 -  2.6905 0.99   1277  145 0.1631 0.2604      5.4636      5.6913|
|  7:  2.6905 -  2.5564 0.99   1281  144 0.1682 0.2092      5.4402      5.6247|
|  8:  2.5564 -  2.4456 0.98   1276  138 0.1692 0.2267      5.3749      5.6219|
|  9:  2.4456 -  2.3518 0.98   1250  141 0.1697 0.2230      5.3099       5.498|
| 10:  2.3518 -  2.2709 0.99   1267  139 0.1576 0.2157      5.2348      5.4148|
| 11:  2.2709 -  2.2001 0.99   1266  143 0.1545 0.2155      5.1757      5.4317|
| 12:  2.2001 -  2.1374 0.97   1242  134 0.1429 0.2130      5.0616      5.4433|
| 13:  2.1374 -  2.0813 0.99   1280  143 0.1468 0.1911      4.9948      5.1336|
| 14:  2.0813 -  2.0306 0.72    902  103 0.1496 0.2238      4.9216      5.2078|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.8451  1383   153  0.92  11.18   0.95     0.93       9614.75|
|  2:  4.8451 -  3.8663  1318   150  0.94  10.14   1.00     0.98      12093.66|
|  3:  3.8663 -  3.3836  1313   144  0.91  14.30   1.01     1.01      15269.89|
|  4:  3.3836 -  3.0770  1294   139  0.89  17.79   1.00     0.96      16016.96|
|  5:  3.0770 -  2.8580  1281   143  0.85  21.42   1.00     0.97      14050.12|
|  6:  2.8580 -  2.6905  1277   145  0.86  20.59   0.97     0.93      11308.90|
|  7:  2.6905 -  2.5564  1281   144  0.85  21.39   0.99     0.96      11105.95|
|  8:  2.5564 -  2.4456  1276   138  0.85  21.33   0.99     0.92       9392.73|
|  9:  2.4456 -  2.3518  1250   141  0.85  21.84   0.99     0.92       8631.94|
| 10:  2.3518 -  2.2709  1267   139  0.86  20.39   0.98     0.93       7061.70|
| 11:  2.2709 -  2.2001  1266   143  0.86  20.95   0.98     0.91       6771.21|
| 12:  2.2001 -  2.1374  1242   134  0.88  19.07   1.00     0.99       5598.16|
| 13:  2.1374 -  2.0813  1280   143  0.88  19.04   0.97     0.94       4731.18|
| 14:  2.0813 -  2.0306   902   103  0.88  19.10   0.94     0.88       3908.36|
|alpha:            min =        0.88 max =            1.01 mean =         0.95|
|beta:             min =     3908.36 max =        16016.96 mean =      9841.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.92 mean =        18.37|
|phase err.(test): min =        0.00 max =           89.75 mean =        17.41|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1949   ksol= 0.33   Bsol= 80.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.16,0.62,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.372639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.03 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1464   r_free= 0.1949   ksol= 0.33   Bsol= 80.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,-0.16,0.62,-0.00,0.00,0.00); trace/3= -0.22                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.372639                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2595 -  4.8451 0.99   1383  153 0.1122 0.1463      5.5062      5.6584|
|  2:  4.8451 -  3.8663 0.99   1318  150 0.1023 0.1179      5.5954      5.7674|
|  3:  3.8663 -  3.3836 0.99   1313  144 0.1346 0.1783      5.6903      6.0112|
|  4:  3.3836 -  3.0770 0.99   1294  139 0.1550 0.2096      5.6743      5.8593|
|  5:  3.0770 -  2.8580 0.99   1281  143 0.1834 0.2131      5.6015      5.7515|
|  6:  2.8580 -  2.6905 0.99   1277  145 0.1629 0.2600      5.4633      5.6891|
|  7:  2.6905 -  2.5564 0.99   1281  144 0.1682 0.2096        5.44      5.6256|
|  8:  2.5564 -  2.4456 0.98   1276  138 0.1691 0.2264      5.3742      5.6222|
|  9:  2.4456 -  2.3518 0.98   1250  141 0.1694 0.2231      5.3092      5.4982|
| 10:  2.3518 -  2.2709 0.99   1267  139 0.1574 0.2164      5.2346      5.4153|
| 11:  2.2709 -  2.2001 0.99   1266  143 0.1542 0.2159      5.1749      5.4326|
| 12:  2.2001 -  2.1374 0.97   1242  134 0.1428 0.2132      5.0613      5.4427|
| 13:  2.1374 -  2.0813 0.99   1280  143 0.1471 0.1908      4.9945      5.1336|
| 14:  2.0813 -  2.0306 0.72    902  103 0.1496 0.2229      4.9207      5.2054|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2595 -  4.8451  1383   153  0.92  11.44   0.95     0.92       9855.36|
|  2:  4.8451 -  3.8663  1318   150  0.94  10.18   1.00     0.98      12107.72|
|  3:  3.8663 -  3.3836  1313   144  0.91  14.17   1.01     1.01      15082.55|
|  4:  3.3836 -  3.0770  1294   139  0.88  17.81   1.00     0.96      16044.20|
|  5:  3.0770 -  2.8580  1281   143  0.85  21.43   0.99     0.97      14059.83|
|  6:  2.8580 -  2.6905  1277   145  0.86  20.59   0.96     0.92      11322.14|
|  7:  2.6905 -  2.5564  1281   144  0.85  21.37   0.99     0.96      11102.20|
|  8:  2.5564 -  2.4456  1276   138  0.85  21.32   0.98     0.92       9387.20|
|  9:  2.4456 -  2.3518  1250   141  0.85  21.83   0.98     0.92       8623.49|
| 10:  2.3518 -  2.2709  1267   139  0.86  20.40   0.98     0.92       7064.98|
| 11:  2.2709 -  2.2001  1266   143  0.86  20.96   0.97     0.91       6780.48|
| 12:  2.2001 -  2.1374  1242   134  0.88  19.07   0.99     0.99       5598.96|
| 13:  2.1374 -  2.0813  1280   143  0.88  19.02   0.96     0.94       4720.78|
| 14:  2.0813 -  2.0306   902   103  0.88  19.07   0.93     0.88       3892.23|
|alpha:            min =        0.88 max =            1.01 mean =         0.94|
|beta:             min =     3892.23 max =        16044.20 mean =      9849.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.96 mean =        18.39|
|phase err.(test): min =        0.00 max =           89.79 mean =        17.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.622)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.86  16.76    None  None   None       |
|    all(noH): 2823   0      0.00    118.86  16.76    None  None   None       |
|    Sol.    : 438    0      2.74    118.86  42.18    None  None   None       |
|    Mac.    : 2385   0      0.00    84.79   12.09    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:     0.003 -  11.889: 1568   |   5:    59.431 -  71.317:   65        |
|      1:    11.889 -  23.774:  711   |   6:    71.317 -  83.203:   23        |
|      2:    23.774 -  35.660:  182   |   7:    83.203 -  95.088:    6        |
|      3:    35.660 -  47.546:  161   |   8:    95.088 - 106.974:    1        |
|      4:    47.546 -  59.431:  105   |   9:   106.974 - 118.859:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.540 - 5.265
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 318 from: 327
   mapped sites are within: 0.721 - 5.265

peak=    9.012 closest distance to " O   HOH Z 400 " =    1.293
peak=    7.454 closest distance to " O   HOH Z  41 " =    1.633
peak=    7.037 closest distance to " O   HOH Z 138 " =    1.232
peak=    6.499 closest distance to " O   SER A   3 " =    0.954
peak=    6.135 closest distance to " O   HOH Z  69 " =    1.051
peak=    5.722 closest distance to " O   HOH Z  54 " =    1.582
peak=    5.414 closest distance to " O   HOH Z 117 " =    1.544
peak=    5.243 closest distance to " O   HOH Z 210 " =    1.659
peak=    5.088 closest distance to " CG  ASN A  69 " =    1.119
peak=    5.084 closest distance to " O   GLN A  11 " =    0.968
peak=    5.059 closest distance to " O   HOH Z  69 " =    1.904
peak=    4.983 closest distance to " O   HOH Z 425 " =    1.866
peak=    4.857 closest distance to " CG AARG A 275 " =    1.125
peak=    4.845 closest distance to " OD1 ASN A 301 " =    0.970
peak=    4.737 closest distance to " O   HOH Z  65 " =    1.178
peak=    4.720 closest distance to " CG  PRO A  54 " =    1.439
peak=    4.696 closest distance to " N   SER A 164 " =    0.949
peak=    4.609 closest distance to " OH  TYR A  68 " =    0.944
peak=    4.571 closest distance to " O   HOH Z  49 " =    1.518
peak=    4.564 closest distance to " CG  GLN A  77 " =    0.807
peak=    4.523 closest distance to " CB  SER A  63 " =    1.301
peak=    4.482 closest distance to " CZ  PHE A 218 " =    1.177
peak=    4.450 closest distance to " NH2AARG A 145 " =    1.181
peak=    4.435 closest distance to " O  BHOH Z  74 " =    1.174
peak=    4.421 closest distance to " O   HOH Z 412 " =    3.512
peak=    4.419 closest distance to " O   HOH Z 113 " =    2.118
peak=    4.409 closest distance to " CB  SER A  62 " =    0.946
peak=    4.408 closest distance to " N   TYR A  15 " =    0.953
peak=    4.391 closest distance to " O   HOH Z 422 " =    1.290
peak=    4.390 closest distance to " CB  GLN A 183 " =    1.104
peak=    4.288 closest distance to " CB  GLU A  37 " =    1.139
peak=    4.272 closest distance to " O   HOH Z 248 " =    1.529
peak=    4.261 closest distance to " CB  VAL A 202 " =    1.327
peak=    4.189 closest distance to " O   HOH Z 139 " =    1.445
peak=    4.168 closest distance to " NH1AARG A 145 " =    1.474
peak=    4.161 closest distance to " O   HOH Z 395 " =    1.645
peak=    4.159 closest distance to " ND2 ASN A 301 " =    0.959
peak=    4.151 closest distance to " O   HOH Z 359 " =    1.715
peak=    4.127 closest distance to " CG1 ILE A 120 " =    1.163
peak=    4.125 closest distance to " NE2 GLN A  11 " =    1.192
peak=    4.081 closest distance to " CB  ASN A  39 " =    0.791
peak=    4.059 closest distance to " ND2 ASN A  69 " =    1.559
peak=    4.015 closest distance to " O   HOH Z 437 " =    2.072
peak=    4.013 closest distance to " O   HOH Z 107 " =    1.048
peak=    4.011 closest distance to " CG  PRO A 280 " =    0.886
peak=    4.011 closest distance to " O   HOH Z 389 " =    2.083
peak=    3.999 closest distance to " CA  TYR A  30 " =    0.966
peak=    3.995 closest distance to " O   HOH Z  67 " =    1.182
peak=    3.995 closest distance to " O   HOH Z 200 " =    1.877
peak=    3.993 closest distance to " CG2 VAL A 197 " =    1.288
peak=    3.986 closest distance to " CD2 TRP A 179 " =    1.219
peak=    3.980 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.978 closest distance to " O   ALA A 165 " =    1.268
peak=    3.965 closest distance to " O   HOH Z 369 " =    1.099
peak=    3.957 closest distance to " O   HOH Z 374 " =    1.030
peak=    3.934 closest distance to " CD  ARG A  66 " =    2.516
peak=    3.932 closest distance to " CA  ILE A 106 " =    0.892
peak=    3.921 closest distance to " CG  PRO A  90 " =    1.379
peak=    3.912 closest distance to " NH1BARG A 102 " =    0.947
peak=    3.909 closest distance to " O   HOH Z 418 " =    2.000
peak=    3.907 closest distance to " O   HOH Z 426 " =    1.169
peak=    3.901 closest distance to " CB  PRO A  54 " =    0.791
peak=    3.899 closest distance to " O   HOH Z 365 " =    2.252
peak=    3.893 closest distance to " O   PRO A 198 " =    1.601
peak=    3.891 closest distance to " CE1 HIS A 115 " =    1.058
peak=    3.886 closest distance to " CD  LYS A 166 " =    1.780
peak=    3.874 closest distance to " O   HOH Z 279 " =    1.089
peak=    3.867 closest distance to " NE2 GLN A  77 " =    3.052
peak=    3.865 closest distance to " CA  GLN A  11 " =    1.152
peak=    3.857 closest distance to " O   HOH Z 404 " =    1.575
peak=    3.856 closest distance to " N   ALA A   1 " =    2.179
peak=    3.849 closest distance to " CB  MET A  40 " =    1.019
peak=    3.842 closest distance to " O   HOH Z 174 " =    1.791
peak=    3.835 closest distance to " CA  GLY A 196 " =    0.916
peak=    3.831 closest distance to " CB  THR A  52 " =    0.950
peak=    3.817 closest distance to " O   HOH Z 394 " =    1.680
peak=    3.816 closest distance to " CB  GLN A 223 " =    1.497
peak=    3.814 closest distance to " CG  GLN A  11 " =    0.883
peak=    3.812 closest distance to " CB  GLU A 128 " =    1.005
peak=    3.810 closest distance to " NH1 ARG A  14 " =    1.201
peak=    3.810 closest distance to " O   HOH Z 223 " =    1.041
peak=    3.790 closest distance to " CB  MET A  47 " =    1.057
peak=    3.786 closest distance to " CD  ARG A  36 " =    0.900
peak=    3.776 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.770 closest distance to " O   HOH Z 377 " =    1.587
peak=    3.764 closest distance to " O   HOH Z 362 " =    3.152
peak=    3.757 closest distance to " CA  ARG A 195 " =    1.179
peak=    3.740 closest distance to " CA  ALA A 100 " =    1.050
peak=    3.734 closest distance to " CG1AVAL A 121 " =    0.897
peak=    3.734 closest distance to " CG2BVAL A  41 " =    0.960
peak=    3.730 closest distance to " O   HOH Z 301 " =    1.706
peak=    3.727 closest distance to " CB  ALA A 104 " =    0.962
peak=    3.721 closest distance to " O   HOH Z 134 " =    2.118
peak=    3.718 closest distance to " CB  ARG A 190 " =    1.873
peak=    3.718 closest distance to " OG BSER A  99 " =    3.031
peak=    3.714 closest distance to " N   SER A 271 " =    1.214
peak=    3.712 closest distance to " O   HOH Z  18 " =    2.323
peak=    3.711 closest distance to " CA  GLY A 267 " =    1.273
peak=    3.699 closest distance to " NH1 ARG A  36 " =    1.396
peak=    3.678 closest distance to " CG  PRO A 213 " =    1.318
peak=    3.677 closest distance to " O   SER A  87 " =    2.363
peak=    3.671 closest distance to " O   HOH Z 147 " =    1.395
peak=    3.669 closest distance to " O   HOH Z 346 " =    1.706
peak=    3.669 closest distance to " CB  ALA A 248 " =    1.475
peak=    3.665 closest distance to " O   HOH Z 417 " =    0.907
peak=    3.663 closest distance to " CB  SER A 141 " =    1.235
peak=    3.656 closest distance to " CB  PRO A  54 " =    1.239
peak=    3.650 closest distance to " CZ3 TRP A 266 " =    1.155
peak=    3.650 closest distance to " O   HOH Z  48 " =    2.236
peak=    3.650 closest distance to " O   THR A 251 " =    1.141
peak=    3.648 closest distance to " O  BHOH Z 338 " =    0.944
peak=    3.642 closest distance to " CB  ASN A 148 " =    1.484
peak=    3.639 closest distance to " CG  PRO A 243 " =    1.133
peak=    3.631 closest distance to " N   ASP A 231 " =    1.744
peak=    3.631 closest distance to " CB  LEU A  83 " =    0.761
peak=    3.627 closest distance to " CB  ASN A 285 " =    0.812
peak=    3.617 closest distance to " O   HOH Z  54 " =    1.819
peak=    3.616 closest distance to " CB  ASP A 140 " =    0.898
peak=    3.610 closest distance to " O   HOH Z  50 " =    1.951
peak=    3.610 closest distance to " O   THR A  29 " =    0.988
peak=    3.609 closest distance to " O   HOH Z  76 " =    1.394
peak=    3.609 closest distance to " CD  ARG A 159 " =    0.860
peak=    3.609 closest distance to " CB  ASP A 124 " =    0.879
peak=    3.608 closest distance to " O   HOH Z 128 " =    1.325
peak=    3.608 closest distance to " O   HOH Z 369 " =    2.372
peak=    3.601 closest distance to " O   HOH Z 431 " =    1.181
peak=    3.596 closest distance to " OE1 GLN A  58 " =    1.087
peak=    3.579 closest distance to " CG1 VAL A 153 " =    1.147
peak=    3.577 closest distance to " O   HOH Z 287 " =    1.855
peak=    3.575 closest distance to " CA  GLN A 223 " =    0.844
peak=    3.561 closest distance to " CZ  PHE A  38 " =    1.160
peak=    3.561 closest distance to " O   HOH Z 222 " =    0.961
peak=    3.558 closest distance to " O   HOH Z 199 " =    1.537
peak=    3.551 closest distance to " CB  ASN A 187 " =    1.207
peak=    3.549 closest distance to " O   HOH Z 102 " =    1.753
peak=    3.546 closest distance to " O   HOH Z 234 " =    3.979
peak=    3.540 closest distance to " O   HOH Z 272 " =    1.280
peak=    3.537 closest distance to " O   HOH Z 403 " =    1.627
peak=    3.536 closest distance to " CE2 TYR A  68 " =    0.871
peak=    3.536 closest distance to " CA  ARG A 139 " =    1.731
peak=    3.535 closest distance to " CA  CYS A 260 " =    0.985
peak=    3.533 closest distance to " O   HOH Z 331 " =    1.223
peak=    3.528 closest distance to " O   ASN A 301 " =    1.416
peak=    3.527 closest distance to " NH2 ARG A  56 " =    1.290
peak=    3.524 closest distance to " O   HOH Z  47 " =    1.474
peak=    3.522 closest distance to " O   HOH Z 343 " =    2.518
peak=    3.522 closest distance to " CB  ALA A 100 " =    1.366
peak=    3.518 closest distance to " CA  ALA A  21 " =    1.461
peak=    3.517 closest distance to " O   HOH Z 421 " =    1.354
peak=    3.513 closest distance to " NH1 ARG A 269 " =    0.756
peak=    3.506 closest distance to " OH  TYR A 293 " =    0.956
peak=    3.497 closest distance to " O   HOH Z 189 " =    2.760
peak=    3.496 closest distance to " O   HOH Z 332 " =    1.704
peak=    3.491 closest distance to " N   THR A  52 " =    1.161
peak=    3.491 closest distance to " CA  SER A  87 " =    0.977
peak=    3.484 closest distance to " O   HOH Z 261 " =    1.962
peak=    3.484 closest distance to " NH2 ARG A 156 " =    1.178
peak=    3.484 closest distance to " O   HOH Z 213 " =    1.791
peak=    3.477 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.475 closest distance to " CG2 THR A 221 " =    1.022
peak=    3.473 closest distance to " CB  ALA A 291 " =    1.265
peak=    3.473 closest distance to " CD  PRO A  54 " =    1.071
peak=    3.472 closest distance to " CA  SER A  32 " =    1.575
peak=    3.471 closest distance to " CA  GLY A   6 " =    0.762
peak=    3.452 closest distance to " CB  SER A  28 " =    1.180
peak=    3.449 closest distance to " O   HOH Z  38 " =    2.343
peak=    3.448 closest distance to " CA  TRP A 274 " =    0.933
peak=    3.447 closest distance to " CB  GLU A 277 " =    3.909
peak=    3.447 closest distance to " CA  ASP A 191 " =    0.936
peak=    3.446 closest distance to " CB  PRO A 198 " =    0.981
peak=    3.444 closest distance to " CD  LYS A  76 " =    1.789
peak=    3.440 closest distance to " CG  TRP A 179 " =    2.591
peak=    3.438 closest distance to " CB  GLU A 152 " =    1.059
peak=    3.434 closest distance to " CE1 PHE A 225 " =    1.182
peak=    3.433 closest distance to " CB  SER A  26 " =    0.854
peak=    3.431 closest distance to " O   HOH Z 291 " =    1.374
peak=    3.425 closest distance to " O   HOH Z  32 " =    1.024
peak=    3.420 closest distance to " CB  ALA A   1 " =    1.039
peak=    3.417 closest distance to " O   HOH Z  21 " =    1.709
peak=    3.415 closest distance to " O   THR A 182 " =    1.509
peak=    3.414 closest distance to " O   HOH Z 232 " =    2.223
peak=    3.413 closest distance to " O   HOH Z 134 " =    2.206
peak=    3.402 closest distance to " O   HOH Z 214 " =    1.964
peak=    3.401 closest distance to " CG  PRO A 198 " =    1.359
peak=    3.399 closest distance to " N   GLY A 111 " =    1.223
peak=    3.393 closest distance to " CB  GLU A 236 " =    1.323
peak=    3.393 closest distance to " CA  ASP A 124 " =    0.963
peak=    3.391 closest distance to " CD  GLN A  88 " =    1.018
peak=    3.390 closest distance to " CB  TRP A 150 " =    1.562
peak=    3.388 closest distance to " O   HOH Z  48 " =    2.081
peak=    3.382 closest distance to " O   HOH Z 177 " =    1.593
peak=    3.380 closest distance to " O   HOH Z 415 " =    1.228
peak=    3.373 closest distance to " CA  ALA A 291 " =    0.860
peak=    3.368 closest distance to " CD ALYS A 290 " =    1.170
peak=    3.367 closest distance to " O   GLU A   2 " =    1.776
peak=    3.366 closest distance to " CA  ARG A 102 " =    1.173
peak=    3.364 closest distance to " CG2AVAL A 121 " =    1.817
peak=    3.357 closest distance to " O   HOH Z  58 " =    1.441
peak=    3.357 closest distance to " N   HIS A 108 " =    1.783
peak=    3.355 closest distance to " O   HOH Z 234 " =    2.064
peak=    3.353 closest distance to " CB  ASN A  45 " =    1.030
peak=    3.349 closest distance to " O   HOH Z 107 " =    1.384
peak=    3.346 closest distance to " O   GLN A  55 " =    1.954
peak=    3.343 closest distance to " O   HOH Z 415 " =    1.596
peak=    3.340 closest distance to " O   HOH Z  15 " =    2.428
peak=    3.336 closest distance to " CB  ARG A 275 " =    0.888
peak=    3.335 closest distance to " O   HOH Z 343 " =    1.584
peak=    3.335 closest distance to " CB  ARG A 269 " =    1.869
peak=    3.331 closest distance to " O   HOH Z 379 " =    3.412
peak=    3.331 closest distance to " O   HOH Z 119 " =    1.680
peak=    3.331 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.330 closest distance to " CB  ALA A 299 " =    0.761
peak=    3.328 closest distance to " O   HOH Z 277 " =    1.381
peak=    3.327 closest distance to " CB  ALA A 256 " =    1.476
peak=    3.324 closest distance to " O   HOH Z 207 " =    1.372
peak=    3.321 closest distance to " CD1 LEU A 300 " =    1.070
peak=    3.318 closest distance to " CG  LYS A  76 " =    1.138
peak=    3.316 closest distance to " NH2AARG A 190 " =    1.945
peak=    3.304 closest distance to " ND2 ASN A 127 " =    1.014
peak=    3.300 closest distance to " O   HOH Z  73 " =    2.498
peak=    3.299 closest distance to " NZ  LYS A 289 " =    1.197
peak=    3.295 closest distance to " CA  SER A  12 " =    1.705
peak=    3.295 closest distance to " CG2 THR A  42 " =    0.905
peak=    3.295 closest distance to " O   HOH Z 392 " =    1.130
peak=    3.295 closest distance to " O   HOH Z 197 " =    5.265
peak=    3.294 closest distance to " CA  ASP A 162 " =    0.937
peak=    3.293 closest distance to " CA  GLU A 152 " =    1.065
peak=    3.288 closest distance to " O   HOH Z   1 " =    2.746
peak=    3.285 closest distance to " O   HOH Z 256 " =    2.119
peak=    3.285 closest distance to " O   HOH Z 371 " =    2.111
peak=    3.276 closest distance to " CA  ALA A 248 " =    1.345
peak=    3.272 closest distance to " N   ASN A  39 " =    1.164
peak=    3.271 closest distance to " CB  PRO A  90 " =    1.167
peak=    3.269 closest distance to " O   HOH Z 159 " =    1.141
peak=    3.267 closest distance to " O   HOH Z 195 " =    1.801
peak=    3.262 closest distance to " CB  VAL A 296 " =    1.574
peak=    3.262 closest distance to " O   HOH Z 133 " =    2.894
peak=    3.261 closest distance to " O   HOH Z   7 " =    1.589
peak=    3.260 closest distance to " N   TYR A 116 " =    1.827
peak=    3.257 closest distance to " NE2 GLN A 278 " =    2.365
peak=    3.251 closest distance to " O   HOH Z 144 " =    1.227
peak=    3.250 closest distance to " O   HOH Z  80 " =    2.236
peak=    3.247 closest distance to " CG  GLU A  37 " =    0.938
peak=    3.243 closest distance to " O   HOH Z 261 " =    1.164
peak=    3.241 closest distance to " CA  ILE A  33 " =    1.674
peak=    3.239 closest distance to " CB  PRO A 243 " =    1.555
peak=    3.237 closest distance to " CG2 THR A  31 " =    1.018
peak=    3.236 closest distance to " CG2 ILE A  20 " =    1.175
peak=    3.233 closest distance to " O   HOH Z 298 " =    2.206
peak=    3.232 closest distance to " N   TYR A 247 " =    1.253
peak=    3.226 closest distance to " O   HOH Z 116 " =    1.521
peak=    3.224 closest distance to " CA  ARG A  66 " =    0.832
peak=    3.223 closest distance to " CB  LYS A 289 " =    1.285
peak=    3.223 closest distance to " OD2 ASP A  27 " =    1.157
peak=    3.221 closest distance to " O   HOH Z  88 " =    3.165
peak=    3.219 closest distance to " O   HOH Z 364 " =    2.173
peak=    3.215 closest distance to " O   HOH Z 158 " =    3.070
peak=    3.212 closest distance to " CB  LEU A 101 " =    1.192
peak=    3.211 closest distance to " C   ALA A 299 " =    1.223
peak=    3.208 closest distance to " N   VAL A 126 " =    1.805
peak=    3.208 closest distance to " O   HOH Z 176 " =    1.984
peak=    3.207 closest distance to " CG2 ILE A 120 " =    0.974
peak=    3.203 closest distance to " O   HOH Z 406 " =    1.836
peak=    3.203 closest distance to " O   HOH Z  59 " =    2.346
peak=    3.200 closest distance to " O   HOH Z 344 " =    1.949
peak=    3.198 closest distance to " O   HOH Z  63 " =    1.317
peak=    3.196 closest distance to " O   HOH Z 411 " =    2.559
peak=    3.190 closest distance to " O   HOH Z 293 " =    2.074
peak=    3.189 closest distance to " CB  ARG A  79 " =    0.922
peak=    3.189 closest distance to " CE3 TRP A  85 " =    1.214
peak=    3.187 closest distance to " O   PHE A  16 " =    1.447
peak=    3.181 closest distance to " CE1 TYR A  30 " =    0.900
peak=    3.180 closest distance to " CA  ILE A 234 " =    0.836
peak=    3.178 closest distance to " O   HOH Z  85 " =    1.973
peak=    3.174 closest distance to " O   HOH Z 132 " =    3.566
peak=    3.171 closest distance to " CG1 VAL A 257 " =    1.367
peak=    3.168 closest distance to " CA  LEU A   5 " =    0.930
peak=    3.166 closest distance to " C   GLN A  88 " =    1.676
peak=    3.164 closest distance to " O   THR A 220 " =    1.103
peak=    3.157 closest distance to " O   HOH Z 271 " =    2.704
peak=    3.155 closest distance to " CG  GLN A  55 " =    0.986
peak=    3.155 closest distance to " O   HOH Z  44 " =    1.929
peak=    3.154 closest distance to " NE2 GLN A  58 " =    3.932
peak=    3.154 closest distance to " O   HOH Z  90 " =    2.497
peak=    3.153 closest distance to " CG2 VAL A 268 " =    1.055
peak=    3.148 closest distance to " O   HOH Z 417 " =    3.014
peak=    3.146 closest distance to " CA  GLN A  94 " =    0.992
peak=    3.136 closest distance to " O   HOH Z 132 " =    1.881
peak=    3.135 closest distance to " O   HOH Z 215 " =    1.431
peak=    3.135 closest distance to " CB  GLU A  46 " =    1.044
peak=    3.135 closest distance to " NH2BARG A 145 " =    1.184
peak=    3.134 closest distance to " CA  ASN A 249 " =    1.180
peak=    3.134 closest distance to " CA  TYR A 116 " =    1.549
peak=    3.132 closest distance to " N   GLU A 152 " =    1.702
peak=    3.129 closest distance to " O   GLN A  58 " =    1.949
peak=    3.128 closest distance to " OD2 ASP A 140 " =    2.062
peak=    3.128 closest distance to " OG  SER A  62 " =    2.936
peak=    3.120 closest distance to " CB  ILE A 120 " =    1.629
peak=    3.115 closest distance to " O   HOH Z 126 " =    2.421
peak=    3.111 closest distance to " CB  GLN A  88 " =    1.247
peak=    3.110 closest distance to " CB  PRO A 280 " =    1.160
peak=    3.102 closest distance to " O   HOH Z  90 " =    3.937
peak=    3.097 closest distance to " O   HOH Z 139 " =    4.212
peak=    3.093 closest distance to " CA  TYR A 293 " =    1.009
peak=    3.090 closest distance to " CB  ALA A  71 " =    1.185
peak=    3.090 closest distance to " O   THR A 294 " =    1.686
peak=    3.083 closest distance to " O   HOH Z  68 " =    1.881
peak=    3.081 closest distance to " O   GLU A 152 " =    1.603
peak=    3.081 closest distance to " N   VAL A 265 " =    0.983
peak=    3.080 closest distance to " CA  ALA A 160 " =    1.078
peak=    3.066 closest distance to " O   HOH Z 313 " =    1.921
peak=    3.062 closest distance to " O   ASN A 209 " =    1.335
peak=    3.058 closest distance to " NE2 GLN A  58 " =    5.198
peak=    3.052 closest distance to " O   HOH Z 435 " =    2.796
peak=    3.050 closest distance to " CZ  PHE A 192 " =    0.954
peak=    3.049 closest distance to " NH2AARG A 275 " =    3.705
peak=    3.039 closest distance to " CA  VAL A 125 " =    1.097
peak=    3.038 closest distance to " CB  ARG A 138 " =    1.039

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 227         
Filter by distance & map next to the model:
   mapped sites are within: 0.292 - 5.993
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 227
   mapped sites are within: 0.733 - 5.993

peak=   -4.784 closest distance to " CD  GLN A 223 " =    1.323
peak=   -4.553 closest distance to " CD1 PHE A  59 " =    2.103
peak=   -4.354 closest distance to " O   HOH Z 166 " =    1.160
peak=   -4.340 closest distance to " N   ALA A  43 " =    2.849
peak=   -4.267 closest distance to " O   HOH Z 418 " =    1.043
peak=   -4.225 closest distance to " CE2 PHE A  61 " =    2.666
peak=   -4.210 closest distance to " O   HOH Z 407 " =    0.876
peak=   -4.138 closest distance to " O   HOH Z 400 " =    0.888
peak=   -4.095 closest distance to " CD2 LEU A 237 " =    2.595
peak=   -4.081 closest distance to " CB  PRO A 243 " =    2.922
peak=   -4.073 closest distance to " CD  ARG A  14 " =    3.179
peak=   -4.069 closest distance to " O   HOH Z 411 " =    5.393
peak=   -4.066 closest distance to " O   HOH Z 114 " =    1.186
peak=   -4.050 closest distance to " O   HOH Z 221 " =    1.043
peak=   -4.022 closest distance to " O   SER A 276 " =    1.852
peak=   -3.987 closest distance to " O   HOH Z 203 " =    0.907
peak=   -3.981 closest distance to " O   HOH Z   7 " =    1.045
peak=   -3.962 closest distance to " NE2 GLN A 194 " =    2.224
peak=   -3.945 closest distance to " CD  GLN A  11 " =    0.933
peak=   -3.937 closest distance to " O   HOH Z   5 " =    1.524
peak=   -3.906 closest distance to " CG2BVAL A 121 " =    1.460
peak=   -3.892 closest distance to " CG  MET A 105 " =    0.929
peak=   -3.882 closest distance to " O   HOH Z 156 " =    3.626
peak=   -3.878 closest distance to " O   VAL A  67 " =    2.921
peak=   -3.844 closest distance to " CG  ARG A 269 " =    2.488
peak=   -3.832 closest distance to " CD1 ILE A 263 " =    2.132
peak=   -3.830 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.810 closest distance to " CG  LEU A  83 " =    1.964
peak=   -3.797 closest distance to " O   HOH Z  37 " =    1.372
peak=   -3.774 closest distance to " CD  GLN A  88 " =    0.935
peak=   -3.753 closest distance to " O   HOH Z 155 " =    1.654
peak=   -3.753 closest distance to " O   HOH Z 203 " =    0.761
peak=   -3.752 closest distance to " O   HOH Z 394 " =    1.653
peak=   -3.751 closest distance to " CD  GLN A 223 " =    0.741
peak=   -3.739 closest distance to " O   HOH Z 424 " =    2.898
peak=   -3.735 closest distance to " OE1 GLN A  88 " =    0.930
peak=   -3.730 closest distance to " CA  SER A  62 " =    2.855
peak=   -3.728 closest distance to " O   HOH Z 183 " =    1.359
peak=   -3.725 closest distance to " O   HOH Z 288 " =    0.879
peak=   -3.711 closest distance to " N   ARG A 275 " =    1.026
peak=   -3.710 closest distance to " O   HOH Z 134 " =    2.158
peak=   -3.710 closest distance to " O   HOH Z 400 " =    1.260
peak=   -3.709 closest distance to " O   HOH Z 132 " =    0.831
peak=   -3.704 closest distance to " O   HOH Z 185 " =    2.808
peak=   -3.703 closest distance to " O   SER A   3 " =    1.293
peak=   -3.688 closest distance to " O   HOH Z 122 " =    0.910
peak=   -3.675 closest distance to " O   HOH Z 186 " =    3.829
peak=   -3.672 closest distance to " O   HOH Z  60 " =    1.555
peak=   -3.670 closest distance to " CG1 VAL A 112 " =    2.725
peak=   -3.667 closest distance to " O   HOH Z  41 " =    2.784
peak=   -3.666 closest distance to " O   HOH Z 216 " =    0.733
peak=   -3.663 closest distance to " CB  ALA A 291 " =    2.492
peak=   -3.660 closest distance to " CG  PRO A 243 " =    1.652
peak=   -3.656 closest distance to " O   HOH Z 119 " =    4.904
peak=   -3.653 closest distance to " O   PRO A 198 " =    1.218
peak=   -3.649 closest distance to " O   HOH Z 340 " =    1.225
peak=   -3.629 closest distance to " CD1 PHE A 130 " =    2.286
peak=   -3.626 closest distance to " CE3 TRP A 274 " =    2.279
peak=   -3.614 closest distance to " O   HOH Z   7 " =    1.456
peak=   -3.611 closest distance to " O   HOH Z 137 " =    1.523
peak=   -3.607 closest distance to " OD1 ASN A 148 " =    1.287
peak=   -3.604 closest distance to " CZ  TYR A  68 " =    1.119
peak=   -3.602 closest distance to " OD1 ASN A 301 " =    1.009
peak=   -3.583 closest distance to " CZ  ARG A 259 " =    0.844
peak=   -3.581 closest distance to " OD2 ASP A 171 " =    2.006
peak=   -3.576 closest distance to " CA  THR A  18 " =    1.272
peak=   -3.564 closest distance to " ND2BASN A 224 " =    1.683
peak=   -3.561 closest distance to " O   HOH Z  55 " =    1.560
peak=   -3.558 closest distance to " O   VAL A 174 " =    2.116
peak=   -3.554 closest distance to " CG2 ILE A  49 " =    2.643
peak=   -3.548 closest distance to " O   HOH Z 166 " =    2.389
peak=   -3.545 closest distance to " N   ILE A 120 " =    1.069
peak=   -3.543 closest distance to " O   HOH Z  19 " =    2.117
peak=   -3.542 closest distance to " CD2 TYR A 293 " =    1.856
peak=   -3.542 closest distance to " O   SER A 210 " =    1.792
peak=   -3.541 closest distance to " O   HOH Z 371 " =    0.799
peak=   -3.536 closest distance to " N   GLN A  58 " =    1.796
peak=   -3.525 closest distance to " CZ  TYR A 169 " =    1.758
peak=   -3.512 closest distance to " O   HOH Z 109 " =    3.828
peak=   -3.499 closest distance to " O   HOH Z 369 " =    2.419
peak=   -3.497 closest distance to " CH2 TRP A 179 " =    1.034
peak=   -3.497 closest distance to " O   HOH Z  53 " =    2.136
peak=   -3.494 closest distance to " CD2 HIS A 115 " =    1.071
peak=   -3.492 closest distance to " O   HOH Z 133 " =    1.636
peak=   -3.490 closest distance to " O   GLN A  11 " =    1.197
peak=   -3.483 closest distance to " NE  ARG A  79 " =    1.162
peak=   -3.479 closest distance to " CA  GLY A 241 " =    3.501
peak=   -3.477 closest distance to " N   SER A 134 " =    1.177
peak=   -3.476 closest distance to " C   ASN A 285 " =    2.305
peak=   -3.474 closest distance to " O   HOH Z 174 " =    1.458
peak=   -3.474 closest distance to " O   HOH Z 198 " =    1.513
peak=   -3.468 closest distance to " OE1 GLN A  88 " =    1.548
peak=   -3.455 closest distance to " O   HOH Z  54 " =    1.387
peak=   -3.447 closest distance to " O   HOH Z 278 " =    0.840
peak=   -3.445 closest distance to " O   HOH Z  90 " =    3.264
peak=   -3.445 closest distance to " CB  SER A 276 " =    1.040
peak=   -3.441 closest distance to " SD  MET A  40 " =    2.062
peak=   -3.437 closest distance to " O   HOH Z   6 " =    1.235
peak=   -3.435 closest distance to " O   HOH Z 184 " =    1.829
peak=   -3.434 closest distance to " ND2 ASN A  60 " =    1.360
peak=   -3.434 closest distance to " O   HOH Z 325 " =    0.734
peak=   -3.432 closest distance to " CG2 VAL A 189 " =    2.244
peak=   -3.426 closest distance to " N   ALA A 184 " =    1.118
peak=   -3.422 closest distance to " O   HOH Z  67 " =    1.583
peak=   -3.421 closest distance to " O   HOH Z 152 " =    1.216
peak=   -3.416 closest distance to " CA  GLU A 277 " =    1.130
peak=   -3.409 closest distance to " O   HOH Z  52 " =    1.862
peak=   -3.408 closest distance to " O   GLY A  17 " =    1.165
peak=   -3.389 closest distance to " C   VAL A 265 " =    0.893
peak=   -3.387 closest distance to " CG2 ILE A  20 " =    2.562
peak=   -3.387 closest distance to " C   ASP A 270 " =    1.346
peak=   -3.386 closest distance to " O   HOH Z 103 " =    2.113
peak=   -3.383 closest distance to " CG2BVAL A  41 " =    1.550
peak=   -3.383 closest distance to " O   HOH Z 150 " =    2.011
peak=   -3.377 closest distance to " CD2 PHE A 225 " =    1.109
peak=   -3.376 closest distance to " O   HOH Z   7 " =    0.834
peak=   -3.372 closest distance to " NH2 ARG A  66 " =    1.855
peak=   -3.371 closest distance to " C   LEU A 101 " =    1.085
peak=   -3.364 closest distance to " CE3 TRP A 150 " =    1.272
peak=   -3.354 closest distance to " O   ASN A 127 " =    2.086
peak=   -3.349 closest distance to " O   VAL A 189 " =    2.520
peak=   -3.339 closest distance to " O   HOH Z 422 " =    0.776
peak=   -3.325 closest distance to " O   HOH Z 250 " =    1.672
peak=   -3.324 closest distance to " O   HOH Z 428 " =    1.389
peak=   -3.315 closest distance to " NH1 ARG A 195 " =    0.961
peak=   -3.313 closest distance to " O   HOH Z 401 " =    1.290
peak=   -3.311 closest distance to " CD  GLN A  77 " =    1.043
peak=   -3.309 closest distance to " O   HOH Z 424 " =    1.260
peak=   -3.307 closest distance to " CZ  ARG A 156 " =    1.848
peak=   -3.307 closest distance to " C   ALA A  10 " =    1.290
peak=   -3.306 closest distance to " CA  PRO A 280 " =    0.999
peak=   -3.305 closest distance to " O   HOH Z 308 " =    0.804
peak=   -3.303 closest distance to " O   HOH Z 109 " =    1.014
peak=   -3.303 closest distance to " O   HOH Z  99 " =    1.181
peak=   -3.291 closest distance to " O   HOH Z  35 " =    1.398
peak=   -3.285 closest distance to " O   PRO A 243 " =    2.117
peak=   -3.271 closest distance to " O   HOH Z 196 " =    1.591
peak=   -3.270 closest distance to " O   HOH Z  11 " =    1.914
peak=   -3.265 closest distance to " O   GLN A  94 " =    2.279
peak=   -3.260 closest distance to " CG  ARG A 259 " =    1.644
peak=   -3.253 closest distance to " O   ALA A  43 " =    1.832
peak=   -3.251 closest distance to " CB  ALA A  43 " =    2.876
peak=   -3.251 closest distance to " CA  VAL A 197 " =    0.932
peak=   -3.247 closest distance to " CB  PRO A  54 " =    2.532
peak=   -3.245 closest distance to " O   HOH Z 155 " =    1.952
peak=   -3.244 closest distance to " OG  SER A  62 " =    4.625
peak=   -3.239 closest distance to " O   HOH Z 287 " =    1.630
peak=   -3.236 closest distance to " C   SER A 206 " =    1.249
peak=   -3.235 closest distance to " CG  GLN A 103 " =    2.270
peak=   -3.234 closest distance to " CZ  ARG A 139 " =    2.000
peak=   -3.234 closest distance to " O   HOH Z  69 " =    1.609
peak=   -3.234 closest distance to " CA  SER A 164 " =    2.064
peak=   -3.233 closest distance to " SD  MET A 105 " =    2.415
peak=   -3.233 closest distance to " O   HOH Z  65 " =    0.811
peak=   -3.232 closest distance to " O   HOH Z 191 " =    5.993
peak=   -3.228 closest distance to " CG  PRO A 163 " =    1.808
peak=   -3.228 closest distance to " O   GLN A 240 " =    3.185
peak=   -3.228 closest distance to " CG  GLU A  53 " =    1.403
peak=   -3.228 closest distance to " OG  SER A  62 " =    0.805
peak=   -3.225 closest distance to " CB  ASP A 286 " =    1.824
peak=   -3.218 closest distance to " O   ALA A   7 " =    1.443
peak=   -3.217 closest distance to " O   HOH Z 272 " =    1.834
peak=   -3.215 closest distance to " CG1BVAL A  72 " =    2.592
peak=   -3.211 closest distance to " O   HOH Z 189 " =    1.773
peak=   -3.209 closest distance to " O   HOH Z 207 " =    1.393
peak=   -3.206 closest distance to " ND2 ASN A 127 " =    1.289
peak=   -3.204 closest distance to " O   HOH Z 438 " =    2.945
peak=   -3.202 closest distance to " CG  ASP A 286 " =    1.515
peak=   -3.202 closest distance to " O   HOH Z 198 " =    1.295
peak=   -3.198 closest distance to " CZ  PHE A  38 " =    1.177
peak=   -3.197 closest distance to " O   HOH Z  49 " =    0.974
peak=   -3.196 closest distance to " OG BSER A 164 " =    1.229
peak=   -3.196 closest distance to " CD1 ILE A 109 " =    2.272
peak=   -3.184 closest distance to " O   HOH Z  64 " =    1.208
peak=   -3.181 closest distance to " O   HOH Z 362 " =    4.272
peak=   -3.174 closest distance to " O   ASN A 187 " =    1.762
peak=   -3.171 closest distance to " CB  ALA A  10 " =    2.104
peak=   -3.170 closest distance to " O   ASP A 171 " =    1.030
peak=   -3.169 closest distance to " O   HOH Z 106 " =    2.219
peak=   -3.167 closest distance to " O   HOH Z  83 " =    1.852
peak=   -3.162 closest distance to " N   ALA A 242 " =    1.660
peak=   -3.160 closest distance to " O   PHE A  59 " =    2.127
peak=   -3.159 closest distance to " CG  ASP A 124 " =    1.015
peak=   -3.159 closest distance to " CB  PHE A 130 " =    1.227
peak=   -3.153 closest distance to " O   HOH Z  73 " =    1.155
peak=   -3.149 closest distance to " O   HOH Z 277 " =    1.578
peak=   -3.147 closest distance to " O   HOH Z 120 " =    4.250
peak=   -3.139 closest distance to " NH2 ARG A  36 " =    1.307
peak=   -3.136 closest distance to " O   HOH Z 252 " =    3.959
peak=   -3.136 closest distance to " O   HOH Z 137 " =    2.051
peak=   -3.135 closest distance to " CD2 TYR A  30 " =    2.755
peak=   -3.131 closest distance to " C   ASN A 187 " =    1.894
peak=   -3.125 closest distance to " CE  MET A  93 " =    2.060
peak=   -3.124 closest distance to " CD2 LEU A 237 " =    2.721
peak=   -3.121 closest distance to " CB  ALA A 131 " =    2.320
peak=   -3.121 closest distance to " CE  MET A  93 " =    2.488
peak=   -3.118 closest distance to " O   HOH Z 179 " =    2.229
peak=   -3.113 closest distance to " O   ALA A   1 " =    2.181
peak=   -3.110 closest distance to " O   HOH Z 323 " =    1.228
peak=   -3.107 closest distance to " O   HOH Z 144 " =    1.158
peak=   -3.105 closest distance to " CG  ARG A 219 " =    2.585
peak=   -3.098 closest distance to " O   HOH Z 392 " =    1.306
peak=   -3.094 closest distance to " O   MET A  47 " =    2.463
peak=   -3.083 closest distance to " OD1AASN A 224 " =    2.353
peak=   -3.076 closest distance to " OG BSER A 210 " =    2.403
peak=   -3.074 closest distance to " O   GLY A 203 " =    2.320
peak=   -3.069 closest distance to " CB  ASN A  45 " =    0.876
peak=   -3.062 closest distance to " O   HOH Z 380 " =    4.386
peak=   -3.049 closest distance to " O   HOH Z  53 " =    1.518
peak=   -3.049 closest distance to " O   ASN A 301 " =    1.304
peak=   -3.041 closest distance to " OD1 ASN A 173 " =    1.490
peak=   -3.040 closest distance to " CB  ASP A 171 " =    2.243
peak=   -3.039 closest distance to " CB  ASP A 286 " =    1.752
peak=   -3.025 closest distance to " O   HOH Z 431 " =    0.890
peak=   -3.015 closest distance to " O   HOH Z 251 " =    1.915

================= 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    :  0.4992 0.4888   6.303311e+00   6.285423e+00
   1_bss:  0.4935 0.4838   6.300898e+00   6.281577e+00
   1_xyz:  0.4111 0.4472   6.193469e+00   6.231084e+00
   1_adp:  0.3749 0.4496   6.155922e+00   6.235935e+00
   1_occ:  0.3742 0.4494   6.155492e+00   6.235700e+00
   2_bss:  0.3742 0.4480   6.157677e+00   6.236444e+00
   2_xyz:  0.3350 0.4083   6.076787e+00   6.186374e+00
   2_adp:  0.3245 0.3988   6.062569e+00   6.177637e+00
   2_occ:  0.3243 0.3985   6.062068e+00   6.177421e+00
   3_bss:  0.3249 0.3989   6.063174e+00   6.177444e+00
   3_xyz:  0.2628 0.3223   5.869927e+00   6.026389e+00
   3_adp:  0.2350 0.2937   5.777722e+00   5.951062e+00
   3_occ:  0.2347 0.2937   5.777147e+00   5.951104e+00
   4_bss:  0.2344 0.2926   5.776994e+00   5.950607e+00
   4_xyz:  0.1974 0.2467   5.622310e+00   5.806887e+00
   4_adp:  0.1888 0.2347   5.588757e+00   5.771769e+00
   4_occ:  0.1887 0.2346   5.587792e+00   5.771161e+00
   5_bss:  0.1888 0.2348   5.588445e+00   5.771665e+00
   5_xyz:  0.1540 0.1979   5.407838e+00   5.609738e+00
   5_adp:  0.1464 0.1949   5.371965e+00   5.587866e+00
   5_occ:  0.1462 0.1949   5.371725e+00   5.588429e+00
   5_bss:  0.1464 0.1949   5.372639e+00   5.588885e+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:  0.272  50.001  -2.342   2.654   2.904   0.000   0.000   0.000
   1_xyz:  0.272  50.001  -2.342   2.654   2.904   0.000   0.000   0.000
   1_adp:  0.272  50.001  -2.342   2.654   2.904   0.000   0.000   0.000
   1_occ:  0.272  50.001  -2.342   2.654   2.904   0.000   0.000   0.000
   2_bss:  0.310  77.145  -0.025   2.347   2.547   0.000   0.000   0.000
   2_xyz:  0.310  77.145  -0.025   2.347   2.547   0.000   0.000   0.000
   2_adp:  0.310  77.145  -0.025   2.347   2.547   0.000   0.000   0.000
   2_occ:  0.310  77.145  -0.025   2.347   2.547   0.000   0.000   0.000
   3_bss:  0.326  87.962   0.027   2.173   2.058   0.000   0.000   0.000
   3_xyz:  0.326  87.962   0.027   2.173   2.058   0.000   0.000   0.000
   3_adp:  0.326  87.962   0.027   2.173   2.058   0.000   0.000   0.000
   3_occ:  0.326  87.962   0.027   2.173   2.058   0.000   0.000   0.000
   4_bss:  0.336  91.172  -0.533   0.853   1.021   0.000   0.000   0.000
   4_xyz:  0.336  91.172  -0.533   0.853   1.021   0.000   0.000   0.000
   4_adp:  0.336  91.172  -0.533   0.853   1.021   0.000   0.000   0.000
   4_occ:  0.336  91.172  -0.533   0.853   1.021   0.000   0.000   0.000
   5_bss:  0.328  80.001  -1.135   0.212   0.589   0.000   0.000   0.000
   5_xyz:  0.328  80.001  -1.135   0.212   0.589   0.000   0.000   0.000
   5_adp:  0.328  80.001  -1.135   0.212   0.589   0.000   0.000   0.000
   5_occ:  0.328  80.001  -1.135   0.212   0.589   0.000   0.000   0.000
   5_bss:  0.331  80.003  -1.128  -0.159   0.622  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.645 0.3720  0.4778    74873.662
   1_bss:  60.717 0.3832  0.5165    73227.534
   1_xyz:  53.021 0.4812  0.6395    58848.810
   1_adp:  53.722 0.4720  0.6280    60318.601
   1_occ:  53.714 0.4722  0.6278    60388.053
   2_bss:  53.628 0.4733  0.6419    60341.056
   2_xyz:  46.735 0.5601  0.7567    48717.471
   2_adp:  45.618 0.5741  0.7634    47219.803
   2_occ:  45.565 0.5748  0.7639    47134.405
   3_bss:  45.555 0.5750  0.7593    47204.303
   3_xyz:  34.664 0.7047  0.9142    28878.335
   3_adp:  30.158 0.7565  0.9373    23159.204
   3_occ:  30.159 0.7565  0.9366    23137.018
   4_bss:  30.084 0.7573  0.9073    23041.801
   4_xyz:  24.913 0.8122  0.9435    15977.593
   4_adp:  23.423 0.8283  0.9388    14697.206
   4_occ:  23.409 0.8284  0.9391    14678.649
   5_bss:  23.406 0.8284  0.9207    14677.960
   5_xyz:  18.931 0.8722  0.9511    10197.606
   5_adp:  18.268 0.8786  0.9470     9828.171
   5_occ:  18.277 0.8785  0.9470     9840.117
   5_bss:  18.287 0.8784  0.9433     9847.867
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6774e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6774e-01
   1_xyz:   1.670  0.013  0.102 16.182  0.006  4.114   1.5030e-01
   1_adp:   1.670  0.013  0.102 16.182  0.006  4.114   1.5030e-01
   1_occ:   1.670  0.013  0.102 16.182  0.006  4.114   1.5030e-01
   2_bss:   1.670  0.013  0.102 16.182  0.006  4.114   1.5030e-01
   2_xyz:   1.246  0.009  0.089 14.875  0.006  4.109   8.8193e-02
   2_adp:   1.246  0.009  0.089 14.875  0.006  4.109   8.8193e-02
   2_occ:   1.246  0.009  0.089 14.875  0.006  4.109   8.8193e-02
   3_bss:   1.246  0.009  0.089 14.875  0.006  4.109   8.8193e-02
   3_xyz:   1.458  0.013  0.097 15.570  0.005  4.108   1.2546e-01
   3_adp:   1.458  0.013  0.097 15.570  0.005  4.108   1.2546e-01
   3_occ:   1.458  0.013  0.097 15.570  0.005  4.108   1.2546e-01
   4_bss:   1.458  0.013  0.097 15.570  0.005  4.108   1.2546e-01
   4_xyz:   1.117  0.009  0.079 14.461  0.004  4.126   7.3670e-02
   4_adp:   1.117  0.009  0.079 14.461  0.004  4.126   7.3670e-02
   4_occ:   1.117  0.009  0.079 14.461  0.004  4.126   7.3670e-02
   5_bss:   1.117  0.009  0.079 14.461  0.004  4.126   7.3670e-02
   5_xyz:   1.218  0.012  0.085 14.686  0.004  4.140   8.7835e-02
   5_adp:   1.218  0.012  0.085 14.686  0.004  4.140   8.7835e-02
   5_occ:   1.218  0.012  0.085 14.686  0.004  4.140   8.7835e-02
   5_bss:   1.218  0.012  0.085 14.686  0.004  4.140   8.7835e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.701   2.4680e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.701   2.4680e-01
   1_xyz:  12.091  0.065  0.342 86.685  0.042  1.962   1.1386e-01
   1_adp:  12.091  0.065  0.342 86.685  0.042  1.962   1.1386e-01
   1_occ:  12.091  0.065  0.342 86.685  0.042  1.962   1.1386e-01
   2_bss:  12.091  0.065  0.342 86.685  0.042  1.962   1.1386e-01
   2_xyz:   8.197  0.041  0.292 87.877  0.045  2.230   7.4436e-02
   2_adp:   8.197  0.041  0.292 87.877  0.045  2.230   7.4436e-02
   2_occ:   8.197  0.041  0.292 87.877  0.045  2.230   7.4436e-02
   3_bss:   8.197  0.041  0.292 87.877  0.045  2.230   7.4436e-02
   3_xyz:  10.878  0.073  0.321 89.106  0.041  1.902   1.4610e-01
   3_adp:  10.878  0.073  0.321 89.106  0.041  1.902   1.4610e-01
   3_occ:  10.878  0.073  0.321 89.106  0.041  1.902   1.4610e-01
   4_bss:  10.878  0.073  0.321 89.106  0.041  1.902   1.4610e-01
   4_xyz:   8.014  0.045  0.267 89.529  0.042  2.133   6.6421e-02
   4_adp:   8.014  0.045  0.267 89.529  0.042  2.133   6.6421e-02
   4_occ:   8.014  0.045  0.267 89.529  0.042  2.133   6.6421e-02
   5_bss:   8.014  0.045  0.267 89.529  0.042  2.133   6.6421e-02
   5_xyz:   8.740  0.060  0.253 87.606  0.028  2.101   7.4208e-02
   5_adp:   8.740  0.060  0.253 87.606  0.028  2.101   7.4208e-02
   5_occ:   8.740  0.060  0.253 87.606  0.028  2.101   7.4208e-02
   5_bss:   8.740  0.060  0.253 87.606  0.028  2.101   7.4208e-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: 123.81   0.00  20.19  91.95   0.00  17.05 123.81   0.00  37.29
   1_occ: 123.81   0.00  20.19  91.95   0.00  17.05 123.81   0.00  37.29
   2_bss: 123.81   0.00  20.19  91.95   0.00  17.05 123.81   0.00  37.29
   2_xyz: 123.81   0.00  20.19  91.95   0.00  17.05 123.81   0.00  37.29
   2_adp: 130.46   0.00  19.74  93.88   0.00  16.52 130.46   0.00  37.26
   2_occ: 130.46   0.00  19.74  93.88   0.00  16.52 130.46   0.00  37.26
   3_bss: 130.46   0.00  19.74  93.88   0.00  16.52 130.46   0.00  37.26
   3_xyz: 130.46   0.00  19.74  93.88   0.00  16.52 130.46   0.00  37.26
   3_adp: 127.50   0.00  18.37  95.73   0.00  13.90 127.50   0.00  42.73
   3_occ: 127.50   0.00  18.37  95.73   0.00  13.90 127.50   0.00  42.73
   4_bss: 127.50   0.00  18.37  95.73   0.00  13.90 127.50   0.00  42.73
   4_xyz: 127.50   0.00  18.37  95.73   0.00  13.90 127.50   0.00  42.73
   4_adp: 119.85   0.91  17.11  86.36   0.91  12.53 119.85   3.35  42.02
   4_occ: 119.85   0.91  17.11  86.36   0.91  12.53 119.85   3.35  42.02
   5_bss: 119.85   0.91  17.11  86.36   0.91  12.53 119.85   3.35  42.02
   5_xyz: 119.85   0.91  17.11  86.36   0.91  12.53 119.85   3.35  42.02
   5_adp: 118.86   0.00  16.76  84.79   0.00  12.09 118.86   2.74  42.18
   5_occ: 118.86   0.00  16.76  84.79   0.00  12.09 118.86   2.74  42.18
   5_bss: 118.86   0.00  16.76  84.79   0.00  12.09 118.86   2.74  42.18
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.654    0.012    0.370
   1_adp:    1.654    0.012    0.370
   1_occ:    1.654    0.012    0.370
   2_bss:    1.654    0.012    0.370
   2_xyz:    1.421    0.030    0.498
   2_adp:    1.421    0.030    0.498
   2_occ:    1.421    0.030    0.498
   3_bss:    1.421    0.030    0.498
   3_xyz:    1.865    0.032    0.777
   3_adp:    1.865    0.032    0.777
   3_occ:    1.865    0.032    0.777
   4_bss:    1.865    0.032    0.777
   4_xyz:    1.857    0.080    0.846
   4_adp:    1.857    0.080    0.846
   4_occ:    1.857    0.080    0.846
   5_bss:    1.857    0.080    0.846
   5_xyz:    1.814    0.081    0.942
   5_adp:    1.814    0.081    0.942
   5_occ:    1.814    0.081    0.942
   5_bss:    1.814    0.081    0.942
------------------------------------------------------------------------

CPU time actual refinement: 358.93


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/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_1088/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1088/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 358.79 
  Macro-tasks:
    bulk solvent and scale       = 61.63  
    individual site refinement   = 141.64 
    weights calculation          = 30.03  
    collect and process          = 6.43   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 239.82 
  Micro-tasks:
    mask                            = 2.71   
    f_calc                          = 109.31 
    alpha_beta                      = 8.60   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 113.44 
    fmodel                         = 10.02  
    r_factors                      = 0.35   
    phase_errors                   = 10.78  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 256.71 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.028 micro seconds
Total CPU time: 6.20 minutes
from_scatterers_fft:    643 calls, 108.74 s
gradients_fft:          588 calls, 102.06 s

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

# Date 2008-01-16 Time 06:23:57 PST -0800 (1200493437.26 s)
Start R-work = 0.4992, R-free = 0.4888 (no bulk solvent and anisotropic scale)
Final R-work = 0.1622, R-free = 0.2084 (no bulk solvent and anisotropic scale)

Start R-work = 0.4935, R-free = 0.4838
Final R-work = 0.1464, R-free = 0.1949