# Date 2008-01-16 Time 05:41:52 PST -0800 (1200490912.18 s)
#phil __OFF__

Command line arguments: "../843.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29921
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 843

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01059
Completeness in resolution range: 0.963551
Completeness with d_max=infinity: 0.960528

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   2.0106

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 2.01059
Completeness in resolution range: 0.963551
Completeness with d_max=infinity: 0.960528

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.3014 [2135/2163]  1921   214  10.0%
  bin  2:  4.3014 -  3.4273 [2043/2062]  1840   203   9.9%
  bin  3:  3.4273 -  2.9979 [2033/2053]  1829   204  10.0%
  bin  4:  2.9979 -  2.7256 [2002/2027]  1805   197   9.8%
  bin  5:  2.7256 -  2.5312 [2002/2021]  1799   203  10.1%
  bin  6:  2.5312 -  2.3826 [1971/2017]  1776   195   9.9%
  bin  7:  2.3826 -  2.2637 [1970/2003]  1773   197  10.0%
  bin  8:  2.2637 -  2.1654 [1964/2000]  1763   201  10.2%
  bin  9:  2.1654 -  2.0823 [1940/1969]  1745   195  10.1%
  bin 10:  2.0823 -  2.0106 [1529/2015]  1379   150   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 9
        2.38 -     3.01: 1947
        3.01 -     3.64: 4516
        3.64 -     4.27: 8920
        4.27 -     4.90: 12393
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.750 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.800 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 206 " - " O   HOH Z 342 "  1.985 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.149 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27780 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_843/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4346   r_free= 0.4166   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.252252                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1388  154 0.3524 0.3672      6.5212      6.5098|
|  2:  4.7971 -  3.8281 0.99   1330  150 0.3820 0.3812      6.8118      6.8091|
|  3:  3.8281 -  3.3502 0.99   1311  148 0.4131 0.3729      6.6652      6.5628|
|  4:  3.3502 -  3.0467 0.99   1305  134 0.4259 0.4039      6.4987      6.4261|
|  5:  3.0467 -  2.8298 0.99   1285  148 0.4568 0.3957      6.3609      6.3392|
|  6:  2.8298 -  2.6639 0.98   1284  143 0.4647 0.4512      6.2463      6.1424|
|  7:  2.6639 -  2.5312 0.99   1291  144 0.4638 0.3982       6.223      6.0982|
|  8:  2.5312 -  2.4215 0.98   1273  139 0.4613 0.4425      6.1465      6.1462|
|  9:  2.4215 -  2.3286 0.98   1271  146 0.4661 0.4624      6.0801      6.1341|
| 10:  2.3286 -  2.2485 0.97   1240  136 0.4783 0.4312      6.0935      5.9877|
| 11:  2.2485 -  2.1784 0.99   1277  144 0.4760 0.4248      6.0225      6.0173|
| 12:  2.1784 -  2.1163 0.98   1276  141 0.4803 0.5323      5.9535      6.0375|
| 13:  2.1163 -  2.0607 0.97   1254  134 0.4803 0.4337      5.8674      5.8315|
| 14:  2.0607 -  2.0106 0.67    845   98 0.4511 0.5210      5.8173       5.744|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1388   154  0.71  33.75   0.83     0.74      69687.62|
|  2:  4.7971 -  3.8281  1330   150  0.74  31.84   0.90     0.81      88769.58|
|  3:  3.8281 -  3.3502  1311   148  0.67  37.96   0.90     0.82      90621.76|
|  4:  3.3502 -  3.0467  1305   134  0.61  43.00   0.90     0.76      78832.43|
|  5:  3.0467 -  2.8298  1285   148  0.55  48.00   0.89     0.71      62516.05|
|  6:  2.8298 -  2.6639  1284   143  0.53  49.50   0.89     0.69      52017.70|
|  7:  2.6639 -  2.5312  1291   144  0.53  49.37   0.92     0.68      45990.58|
|  8:  2.5312 -  2.4215  1273   139  0.52  50.18   0.92     0.69      43884.02|
|  9:  2.4215 -  2.3286  1271   146  0.51  51.18   0.92     0.70      40821.21|
| 10:  2.3286 -  2.2485  1240   136  0.53  50.11   0.94     0.72      37443.47|
| 11:  2.2485 -  2.1784  1277   144  0.51  51.85   0.94     0.71      36265.06|
| 12:  2.1784 -  2.1163  1276   141  0.45  56.44   0.94     0.65      36797.41|
| 13:  2.1163 -  2.0607  1254   134  0.39  60.47   0.92     0.56      34057.81|
| 14:  2.0607 -  2.0106   845    98  0.38  61.91   0.97     0.48      27155.48|
|alpha:            min =        0.48 max =            0.82 mean =         0.70|
|beta:             min =    27155.48 max =        90621.76 mean =     54229.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.98 mean =        47.73|
|phase err.(test): min =        0.00 max =           89.80 mean =        47.89|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.705218             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.096   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.558775              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.149   (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 |  1.750 -  2.065:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.065 -  2.380:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.380 -  2.695:      105 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.695 -  3.010:     1842 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.010 -  3.325:     1847 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.325 -  3.640:     2669 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.640 -  3.955:     4615 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.955 -  4.270:     4305 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.270 -  4.585:     5613 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.585 -  4.900:     6780 |
|-----------------------------------------------------------------------------|
|-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 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.750 |       0.187 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    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: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4346   r_free= 0.4166   ksol= 0.00   Bsol= 0.00   scale= 0.893    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.252252                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4232   r_free= 0.4052   ksol= 0.29   Bsol= 38.28   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.64,5.37,-0.40,0.00,-0.00,-0.00); trace/3= 0.44                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.241007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.531728             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.708   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783845              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.008   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4232      final r-factor (work) = 0.3195          |
| start r-factor (free) = 0.4052      final r-factor (free) = 0.3468          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.1410 = 11.53 * 0.50 * 6.2394 + 1.00 * 0.1654                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.1900 = 11.53 * 0.50 * 6.0794 + 1.00 * 0.1371                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3195      final r-factor (work) = 0.2931          |
| start r-factor (free) = 0.3468      final r-factor (free) = 0.3548          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7714 = 0.78 * 1.00 * 6.0794 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7028 = 0.78 * 1.00 * 5.9779 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.07   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    86.07   17.61    None  None   None       |
|    Sol.    : 438    0      2.27    86.07   36.84    None  None   None       |
|    Mac.    : 2385   0      0.00    78.18   14.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.607:  791   |   5:    43.033 -  51.639:   92        |
|      1:     8.607 -  17.213:  980   |   6:    51.639 -  60.246:   58        |
|      2:    17.213 -  25.820:  477   |   7:    60.246 -  68.852:   37        |
|      3:    25.820 -  34.426:  225   |   8:    68.852 -  77.459:   13        |
|      4:    34.426 -  43.033:  145   |   9:    77.459 -  86.065:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2931 r_free = 0.3548             target_work(ml) = 5.982         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2930 r_free = 0.3547             target_work(ml) = 5.981         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2930   r_free= 0.3547   ksol= 0.29   Bsol= 38.28   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.64,5.37,-0.40,0.00,-0.00,-0.00); trace/3= 0.44                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.981425                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2912   r_free= 0.3520   ksol= 0.32   Bsol= 66.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,2.83,0.30,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 5.981469                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.659649              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.197  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.477186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.915  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2912      final r-factor (work) = 0.2329          |
| start r-factor (free) = 0.3520      final r-factor (free) = 0.2777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0490 = 6.66 * 0.50 * 5.9799 + 1.00 * 0.1371                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6921 = 6.66 * 0.50 * 5.8896 + 1.00 * 0.0808                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2329      final r-factor (work) = 0.2149          |
| start r-factor (free) = 0.2777      final r-factor (free) = 0.2642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8258 = 0.48 * 1.00 * 5.8896 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7478 = 0.48 * 1.00 * 5.7327 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.28   17.32    None  None   None       |
|    all(noH): 2823   0      0.00    87.28   17.32    None  None   None       |
|    Sol.    : 438    0      1.38    87.28   39.49    None  None   None       |
|    Mac.    : 2385   0      0.00    82.46   13.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.728:  922   |   5:    43.638 -  52.366:  101        |
|      1:     8.728 -  17.455:  987   |   6:    52.366 -  61.094:   70        |
|      2:    17.455 -  26.183:  368   |   7:    61.094 -  69.821:   37        |
|      3:    26.183 -  34.911:  190   |   8:    69.821 -  78.549:   22        |
|      4:    34.911 -  43.638:  120   |   9:    78.549 -  87.277:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2149 r_free = 0.2642             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2146 r_free = 0.2642             target_work(ml) = 5.714         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2146   r_free= 0.2642   ksol= 0.32   Bsol= 66.54   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,2.83,0.30,0.00,0.00,0.00); trace/3= 0.55                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.713885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2144   r_free= 0.2638   ksol= 0.32   Bsol= 71.61   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,1.25,0.20,0.00,0.00,0.00); trace/3= 0.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.713231                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.108332              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.624  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.690  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2144      final r-factor (work) = 0.1582          |
| start r-factor (free) = 0.2638      final r-factor (free) = 0.2017          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5888 = 6.11 * 0.50 * 5.7325 + 1.00 * 0.0808                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1579 = 6.11 * 0.50 * 5.5878 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1582      final r-factor (work) = 0.1447          |
| start r-factor (free) = 0.2017      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5502 = 0.28 * 1.00 * 5.5878 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4945 = 0.28 * 1.00 * 5.3931 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.45   16.65    None  None   None       |
|    all(noH): 2823   0      0.00    86.45   16.65    None  None   None       |
|    Sol.    : 438    0      4.52    86.45   40.32    None  None   None       |
|    Mac.    : 2385   0      0.00    84.04   12.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.645:  969   |   5:    43.225 -  51.870:  100        |
|      1:     8.645 -  17.290: 1080   |   6:    51.870 -  60.515:   86        |
|      2:    17.290 -  25.935:  278   |   7:    60.515 -  69.160:   35        |
|      3:    25.935 -  34.580:  139   |   8:    69.160 -  77.805:   17        |
|      4:    34.580 -  43.225:  110   |   9:    77.805 -  86.449:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1447 r_free = 0.1880             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1446 r_free = 0.1878             target_work(ml) = 5.353         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1446   r_free= 0.1878   ksol= 0.32   Bsol= 71.61   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.36,1.25,0.20,0.00,0.00,0.00); trace/3= 0.03                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.353124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1448   r_free= 0.1874   ksol= 0.33   Bsol= 69.44   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.03,0.03,0.00,0.00,0.00); trace/3= -0.50                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.352975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.187068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.765  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.659703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.346  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1448      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1874      final r-factor (free) = 0.1762          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9916 = 2.19 * 0.50 * 5.3950 + 1.00 * 0.0919                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8748 = 2.19 * 0.50 * 5.3134 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1762      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5153 = 0.66 * 1.00 * 5.3134 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4853 = 0.66 * 1.00 * 5.2653 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.45   16.60    None  None   None       |
|    all(noH): 2823   0      0.00    94.45   16.60    None  None   None       |
|    Sol.    : 438    0      0.00    94.45   41.79    None  None   None       |
|    Mac.    : 2385   0      0.00    92.35   11.98    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 -   9.445: 1167   |   5:    47.225 -  56.670:  101        |
|      1:     9.445 -  18.890:  992   |   6:    56.670 -  66.115:   75        |
|      2:    18.890 -  28.335:  222   |   7:    66.115 -  75.560:   35        |
|      3:    28.335 -  37.780:  118   |   8:    75.560 -  85.005:    9        |
|      4:    37.780 -  47.225:   98   |   9:    85.005 -  94.450:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1748             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1282 r_free = 0.1747             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1282   r_free= 0.1747   ksol= 0.33   Bsol= 69.44   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,0.03,0.03,0.00,0.00,0.00); trace/3= -0.50                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.259538                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1747   ksol= 0.32   Bsol= 70.23   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,-0.20,0.14,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.259274                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.478492              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.924  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.351678              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.014  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1281      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2214 = 3.48 * 0.50 * 5.2649 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1698 = 3.48 * 0.50 * 5.2258 + 1.00 * 0.0809                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0752 = 1.35 * 1.00 * 5.2258 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0349 = 1.35 * 1.00 * 5.1954 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.28  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    101.28  16.42    None  None   None       |
|    Sol.    : 438    0      0.44    101.28  42.07    None  None   None       |
|    Mac.    : 2385   0      0.00    99.10   11.71    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 -  10.128: 1338   |   5:    50.641 -  60.769:   95        |
|      1:    10.128 -  20.256:  887   |   6:    60.769 -  70.897:   60        |
|      2:    20.256 -  30.385:  188   |   7:    70.897 -  81.026:   24        |
|      3:    30.385 -  40.513:  124   |   8:    81.026 -  91.154:    7        |
|      4:    40.513 -  50.641:   95   |   9:    91.154 - 101.282:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1679             target_work(ml) = 5.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1175 r_free = 0.1679             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1679   ksol= 0.32   Bsol= 70.23   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.43,-0.20,0.14,-0.00,0.00,0.00); trace/3= -0.49                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.196473                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1388  154 0.0997 0.1308      5.3988      5.5487|
|  2:  4.7971 -  3.8281 0.99   1330  150 0.0843 0.1063        5.43      5.6193|
|  3:  3.8281 -  3.3502 0.99   1311  148 0.1060 0.1568      5.4846      5.8871|
|  4:  3.3502 -  3.0467 0.99   1305  134 0.1278 0.1693      5.4987      5.6471|
|  5:  3.0467 -  2.8298 0.99   1285  148 0.1413 0.1844      5.4052      5.5919|
|  6:  2.8298 -  2.6639 0.98   1284  143 0.1382 0.2189       5.311      5.5575|
|  7:  2.6639 -  2.5312 0.99   1291  144 0.1339 0.1821      5.2374      5.4221|
|  8:  2.5312 -  2.4215 0.98   1273  139 0.1253 0.1885      5.1519      5.4453|
|  9:  2.4215 -  2.3286 0.98   1271  146 0.1255 0.1872      5.0944      5.3664|
| 10:  2.3286 -  2.2485 0.97   1240  136 0.1239 0.1825      5.0491      5.2392|
| 11:  2.2485 -  2.1784 0.99   1277  144 0.1219 0.1938       4.992      5.3439|
| 12:  2.1784 -  2.1163 0.98   1276  141 0.1146 0.1763      4.9131      5.1945|
| 13:  2.1163 -  2.0607 0.97   1254  134 0.1168 0.1716      4.8316      5.0568|
| 14:  2.0607 -  2.0106 0.67    845   98 0.1131 0.1980      4.7443       5.051|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1388   154  0.94   9.40   0.96     0.94       7669.49|
|  2:  4.7971 -  3.8281  1330   150  0.95   8.24   1.00     0.98       9169.09|
|  3:  3.8281 -  3.3502  1311   148  0.94  11.17   1.02     1.01      10568.79|
|  4:  3.3502 -  3.0467  1305   134  0.91  14.61   1.00     0.97      11228.26|
|  5:  3.0467 -  2.8298  1285   148  0.89  17.35   0.99     0.97       9836.87|
|  6:  2.8298 -  2.6639  1284   143  0.88  17.97   0.97     0.94       8549.57|
|  7:  2.6639 -  2.5312  1291   144  0.89  17.06   0.98     0.95       7320.21|
|  8:  2.5312 -  2.4215  1273   139  0.90  16.58   0.97     0.94       6358.72|
|  9:  2.4215 -  2.3286  1271   146  0.89  17.32   0.98     0.93       5730.61|
| 10:  2.3286 -  2.2485  1240   136  0.89  17.33   0.98     0.93       5264.12|
| 11:  2.2485 -  2.1784  1277   144  0.89  16.93   0.97     0.92       4806.65|
| 12:  2.1784 -  2.1163  1276   141  0.90  16.50   0.98     0.97       4364.09|
| 13:  2.1163 -  2.0607  1254   134  0.90  16.89   0.96     0.94       3701.84|
| 14:  2.0607 -  2.0106   845    98  0.90  16.32   0.94     0.89       3027.46|
|alpha:            min =        0.89 max =            1.01 mean =         0.95|
|beta:             min =     3027.46 max =        11228.26 mean =      7103.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.16|
|phase err.(test): min =        0.00 max =           89.91 mean =        14.62|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1676   ksol= 0.32   Bsol= 71.13   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.08,0.42,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.196361                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1676   ksol= 0.32   Bsol= 71.13   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.08,0.42,-0.00,0.00,0.00); trace/3= -0.26                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.196361                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.7971 0.99   1388  154 0.1008 0.1288      5.3964      5.5438|
|  2:  4.7971 -  3.8281 0.99   1330  150 0.0852 0.1049      5.4337       5.617|
|  3:  3.8281 -  3.3502 0.99   1311  148 0.1061 0.1570      5.4857      5.8871|
|  4:  3.3502 -  3.0467 0.99   1305  134 0.1281 0.1699      5.4989      5.6482|
|  5:  3.0467 -  2.8298 0.99   1285  148 0.1412 0.1836      5.4045      5.5877|
|  6:  2.8298 -  2.6639 0.98   1284  143 0.1381 0.2187      5.3096      5.5563|
|  7:  2.6639 -  2.5312 0.99   1291  144 0.1339 0.1826       5.237      5.4238|
|  8:  2.5312 -  2.4215 0.98   1273  139 0.1253 0.1885      5.1523      5.4456|
|  9:  2.4215 -  2.3286 0.98   1271  146 0.1254 0.1870      5.0941      5.3655|
| 10:  2.3286 -  2.2485 0.97   1240  136 0.1237 0.1828      5.0487      5.2402|
| 11:  2.2485 -  2.1784 0.99   1277  144 0.1218 0.1934      4.9915      5.3421|
| 12:  2.1784 -  2.1163 0.98   1276  141 0.1146 0.1763      4.9128      5.1951|
| 13:  2.1163 -  2.0607 0.97   1254  134 0.1168 0.1718      4.8314      5.0568|
| 14:  2.0607 -  2.0106 0.67    845   98 0.1130 0.1978      4.7437      5.0498|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0896 -  4.7971  1388   154  0.94   9.39   0.96     0.94       7461.09|
|  2:  4.7971 -  3.8281  1330   150  0.95   8.24   1.00     0.98       9096.17|
|  3:  3.8281 -  3.3502  1311   148  0.93  11.19   1.02     1.02      10605.54|
|  4:  3.3502 -  3.0467  1305   134  0.91  14.60   1.00     0.98      11196.74|
|  5:  3.0467 -  2.8298  1285   148  0.89  17.31   1.00     0.97       9792.70|
|  6:  2.8298 -  2.6639  1284   143  0.88  17.93   0.98     0.95       8517.75|
|  7:  2.6639 -  2.5312  1291   144  0.89  17.05   0.99     0.96       7317.49|
|  8:  2.5312 -  2.4215  1273   139  0.90  16.60   0.98     0.94       6366.48|
|  9:  2.4215 -  2.3286  1271   146  0.89  17.32   0.99     0.94       5732.20|
| 10:  2.3286 -  2.2485  1240   136  0.89  17.33   0.99     0.94       5258.45|
| 11:  2.2485 -  2.1784  1277   144  0.89  16.92   0.98     0.93       4802.88|
| 12:  2.1784 -  2.1163  1276   141  0.90  16.50   1.00     0.98       4363.21|
| 13:  2.1163 -  2.0607  1254   134  0.90  16.88   0.97     0.95       3698.55|
| 14:  2.0607 -  2.0106   845    98  0.90  16.30   0.95     0.91       3019.54|
|alpha:            min =        0.91 max =            1.02 mean =         0.96|
|beta:             min =     3019.54 max =        11196.74 mean =      7075.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.16|
|phase err.(test): min =        0.00 max =           89.94 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.339)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.28  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    101.28  16.42    None  None   None       |
|    Sol.    : 438    0      0.44    101.28  42.07    None  None   None       |
|    Mac.    : 2385   0      0.00    99.10   11.71    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 -  10.131: 1338   |   5:    50.644 -  60.772:   95        |
|      1:    10.131 -  20.259:  887   |   6:    60.772 -  70.900:   60        |
|      2:    20.259 -  30.388:  188   |   7:    70.900 -  81.028:   24        |
|      3:    30.388 -  40.516:  124   |   8:    81.028 -  91.157:    7        |
|      4:    40.516 -  50.644:   95   |   9:    91.157 - 101.285:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.419 - 5.388
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 333
   mapped sites are within: 0.731 - 5.388

peak=    6.073 closest distance to " O   HOH Z 210 " =    1.299
peak=    5.591 closest distance to " O   HOH Z 113 " =    2.410
peak=    5.199 closest distance to " CB  SER A  63 " =    1.204
peak=    4.991 closest distance to " CB  GLN A 223 " =    1.385
peak=    4.936 closest distance to " O   HOH Z 433 " =    1.749
peak=    4.917 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.721 closest distance to " CB  ARG A 190 " =    1.774
peak=    4.670 closest distance to " O   HOH Z  43 " =    2.109
peak=    4.649 closest distance to " O   PRO A 198 " =    1.554
peak=    4.629 closest distance to " O   HOH Z 134 " =    1.966
peak=    4.554 closest distance to " O   HOH Z 176 " =    2.009
peak=    4.487 closest distance to " O   HOH Z 369 " =    2.056
peak=    4.457 closest distance to " CG  PRO A  54 " =    1.321
peak=    4.408 closest distance to " O   HOH Z 403 " =    1.795
peak=    4.397 closest distance to " O   HOH Z 418 " =    2.039
peak=    4.379 closest distance to " O   HOH Z  49 " =    0.956
peak=    4.317 closest distance to " O   HOH Z 425 " =    1.585
peak=    4.311 closest distance to " CB  ARG A 275 " =    0.863
peak=    4.309 closest distance to " O   HOH Z 133 " =    2.543
peak=    4.303 closest distance to " O   HOH Z  44 " =    2.313
peak=    4.293 closest distance to " CA  ALA A  51 " =    0.982
peak=    4.292 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.286 closest distance to " O   HOH Z 423 " =    1.874
peak=    4.284 closest distance to " CG  PRO A 213 " =    1.196
peak=    4.271 closest distance to " O   HOH Z 234 " =    3.833
peak=    4.255 closest distance to " CB  GLU A 128 " =    1.131
peak=    4.219 closest distance to " O   HOH Z  40 " =    1.858
peak=    4.212 closest distance to " O   HOH Z 154 " =    2.446
peak=    4.192 closest distance to " CG1 ILE A  33 " =    1.177
peak=    4.160 closest distance to " O   HOH Z 214 " =    1.418
peak=    4.148 closest distance to " CB  VAL A 202 " =    1.524
peak=    4.146 closest distance to " O   SER A  87 " =    2.306
peak=    4.138 closest distance to " O   HOH Z 422 " =    0.823
peak=    4.130 closest distance to " CB  GLU A 277 " =    3.800
peak=    4.123 closest distance to " O   HOH Z  63 " =    1.867
peak=    4.099 closest distance to " CD  LYS A 166 " =    1.408
peak=    4.096 closest distance to " CG  ARG A  66 " =    2.616
peak=    4.090 closest distance to " CB  ARG A  79 " =    1.339
peak=    4.080 closest distance to " O   ALA A 165 " =    1.369
peak=    4.077 closest distance to " O   HOH Z  15 " =    2.150
peak=    4.069 closest distance to " O   HOH Z 298 " =    2.042
peak=    4.067 closest distance to " CZ  PHE A 218 " =    1.238
peak=    4.056 closest distance to " O   HOH Z 232 " =    2.427
peak=    4.055 closest distance to " CG  PRO A 280 " =    0.767
peak=    4.024 closest distance to " CB  TRP A 179 " =    1.332
peak=    4.022 closest distance to " O   HOH Z 189 " =    2.579
peak=    4.017 closest distance to " O   HOH Z 196 " =    1.723
peak=    4.010 closest distance to " CB  TRP A 266 " =    1.058
peak=    4.007 closest distance to " O   HOH Z  44 " =    1.882
peak=    3.991 closest distance to " O   HOH Z 412 " =    3.380
peak=    3.989 closest distance to " CB  PRO A  54 " =    0.843
peak=    3.986 closest distance to " NH2 ARG A 156 " =    1.183
peak=    3.966 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.963 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.956 closest distance to " CA  ARG A 195 " =    1.162
peak=    3.937 closest distance to " O   HOH Z 406 " =    1.658
peak=    3.906 closest distance to " CG2BVAL A  41 " =    0.927
peak=    3.902 closest distance to " CB  SER A 141 " =    1.076
peak=    3.902 closest distance to " OD1 ASN A 217 " =    1.763
peak=    3.878 closest distance to " O   HOH Z 258 " =    2.133
peak=    3.870 closest distance to " NE2 GLN A  11 " =    1.055
peak=    3.868 closest distance to " O   HOH Z  97 " =    2.036
peak=    3.854 closest distance to " CB  TYR A 169 " =    0.855
peak=    3.852 closest distance to " O   HOH Z 261 " =    2.038
peak=    3.846 closest distance to " O   HOH Z 362 " =    3.390
peak=    3.843 closest distance to " O   HOH Z 128 " =    2.181
peak=    3.833 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.833 closest distance to " O   HOH Z 154 " =    1.453
peak=    3.830 closest distance to " O   HOH Z 265 " =    2.025
peak=    3.826 closest distance to " O   HOH Z  80 " =    1.974
peak=    3.821 closest distance to " O   HOH Z  20 " =    1.810
peak=    3.811 closest distance to " OE1 GLN A  11 " =    2.094
peak=    3.811 closest distance to " O   HOH Z 357 " =    2.189
peak=    3.808 closest distance to " O   HOH Z 284 " =    2.940
peak=    3.804 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.802 closest distance to " CB  GLU A 152 " =    1.108
peak=    3.790 closest distance to " OG BSER A 164 " =    2.308
peak=    3.783 closest distance to " O   HOH Z 203 " =    1.877
peak=    3.773 closest distance to " CG  PRO A 198 " =    1.134
peak=    3.766 closest distance to " CB  ASN A 148 " =    1.434
peak=    3.759 closest distance to " O   HOH Z  30 " =    1.507
peak=    3.750 closest distance to " NE2 GLN A  77 " =    3.282
peak=    3.740 closest distance to " O   HOH Z 303 " =    2.362
peak=    3.739 closest distance to " O   HOH Z 368 " =    2.213
peak=    3.739 closest distance to " CD  ARG A 195 " =    1.033
peak=    3.726 closest distance to " O   HOH Z 417 " =    3.137
peak=    3.726 closest distance to " O   ASN A  74 " =    1.690
peak=    3.717 closest distance to " OD1 ASN A  69 " =    2.522
peak=    3.710 closest distance to " O   HOH Z 271 " =    2.689
peak=    3.705 closest distance to " O   HOH Z 132 " =    2.875
peak=    3.702 closest distance to " O   HOH Z 415 " =    1.658
peak=    3.698 closest distance to " O   HOH Z   7 " =    1.125
peak=    3.689 closest distance to " O   HOH Z 374 " =    2.769
peak=    3.685 closest distance to " O   HOH Z 128 " =    2.062
peak=    3.685 closest distance to " O   HOH Z 435 " =    2.835
peak=    3.681 closest distance to " O   HOH Z 336 " =    1.795
peak=    3.677 closest distance to " CA  ARG A  36 " =    1.086
peak=    3.659 closest distance to " O   HOH Z  61 " =    1.548
peak=    3.652 closest distance to " N   ASN A  39 " =    1.308
peak=    3.648 closest distance to " O   HOH Z 180 " =    2.338
peak=    3.644 closest distance to " CE1 TYR A 186 " =    1.157
peak=    3.643 closest distance to " O   HOH Z 248 " =    1.534
peak=    3.634 closest distance to " O   HOH Z 394 " =    1.525
peak=    3.632 closest distance to " CA  ALA A 295 " =    1.108
peak=    3.631 closest distance to " O   HOH Z 214 " =    2.384
peak=    3.629 closest distance to " CB  ASP A 140 " =    0.939
peak=    3.625 closest distance to " CG1 VAL A 153 " =    1.128
peak=    3.625 closest distance to " CG2 VAL A 197 " =    1.177
peak=    3.621 closest distance to " O   HOH Z 415 " =    1.178
peak=    3.619 closest distance to " O   HOH Z 146 " =    1.549
peak=    3.617 closest distance to " O   HOH Z 346 " =    1.547
peak=    3.615 closest distance to " O   HOH Z 345 " =    1.648
peak=    3.608 closest distance to " CB  ASN A 142 " =    1.175
peak=    3.604 closest distance to " O   HOH Z  21 " =    1.819
peak=    3.603 closest distance to " CG AARG A 275 " =    1.188
peak=    3.601 closest distance to " O   HOH Z 437 " =    1.771
peak=    3.596 closest distance to " CZ3 TRP A  85 " =    0.930
peak=    3.595 closest distance to " O   HOH Z 285 " =    2.964
peak=    3.593 closest distance to " CZ3 TRP A 266 " =    1.109
peak=    3.591 closest distance to " CG2 THR A 221 " =    1.102
peak=    3.590 closest distance to " O   HOH Z  35 " =    2.239
peak=    3.588 closest distance to " CD1 LEU A 300 " =    1.119
peak=    3.583 closest distance to " CA  ALA A 160 " =    0.927
peak=    3.579 closest distance to " C   ILE A 106 " =    1.871
peak=    3.578 closest distance to " O   HOH Z  48 " =    1.886
peak=    3.565 closest distance to " O  BHOH Z  74 " =    1.328
peak=    3.560 closest distance to " CG  PRO A 243 " =    1.190
peak=    3.555 closest distance to " CA  TYR A 116 " =    1.341
peak=    3.552 closest distance to " O   HOH Z 279 " =    2.163
peak=    3.544 closest distance to " CA  ASP A 191 " =    0.974
peak=    3.540 closest distance to " CB  GLN A  88 " =    1.170
peak=    3.538 closest distance to " O   HOH Z 316 " =    3.145
peak=    3.536 closest distance to " O   HOH Z 163 " =    1.654
peak=    3.536 closest distance to " O   HOH Z 147 " =    1.677
peak=    3.533 closest distance to " O   ASP A 124 " =    1.402
peak=    3.530 closest distance to " CB  SER A  62 " =    0.851
peak=    3.524 closest distance to " CB  ASN A 285 " =    0.855
peak=    3.518 closest distance to " O   HOH Z 245 " =    1.325
peak=    3.516 closest distance to " CB  THR A  52 " =    0.825
peak=    3.515 closest distance to " OE1 GLN A  58 " =    3.339
peak=    3.512 closest distance to " O   HOH Z 126 " =    1.625
peak=    3.510 closest distance to " CA  THR A 221 " =    1.679
peak=    3.509 closest distance to " NE2 HIS A 115 " =    1.058
peak=    3.506 closest distance to " O   HOH Z  68 " =    1.999
peak=    3.502 closest distance to " O   HOH Z 386 " =    2.366
peak=    3.493 closest distance to " CA  GLY A 196 " =    1.121
peak=    3.488 closest distance to " O   HOH Z 371 " =    2.974
peak=    3.486 closest distance to " O   ALA A 158 " =    1.212
peak=    3.484 closest distance to " ND2 ASN A 249 " =    2.063
peak=    3.483 closest distance to " CB  MET A 105 " =    1.192
peak=    3.478 closest distance to " O   HOH Z 403 " =    1.567
peak=    3.478 closest distance to " O   HOH Z 156 " =    2.598
peak=    3.474 closest distance to " CA  ALA A  21 " =    1.363
peak=    3.472 closest distance to " CA  SER A  12 " =    1.549
peak=    3.466 closest distance to " CD2 LEU A 297 " =    0.962
peak=    3.465 closest distance to " O   HOH Z 380 " =    1.868
peak=    3.460 closest distance to " O   HOH Z  66 " =    2.113
peak=    3.457 closest distance to " O   HOH Z 368 " =    4.583
peak=    3.454 closest distance to " ND2 ASN A 187 " =    1.488
peak=    3.451 closest distance to " CG2 VAL A  78 " =    0.903
peak=    3.451 closest distance to " O   HOH Z 150 " =    1.934
peak=    3.446 closest distance to " CA  LEU A  83 " =    1.378
peak=    3.443 closest distance to " O   HOH Z 109 " =    2.266
peak=    3.443 closest distance to " CA  PRO A  54 " =    1.373
peak=    3.443 closest distance to " N   CYS A 260 " =    0.786
peak=    3.442 closest distance to " O   HOH Z 192 " =    2.010
peak=    3.435 closest distance to " O   HOH Z 327 " =    1.594
peak=    3.432 closest distance to " CB  PHE A 283 " =    0.754
peak=    3.428 closest distance to " CA  ILE A 106 " =    0.820
peak=    3.421 closest distance to " CB  GLU A  37 " =    0.805
peak=    3.420 closest distance to " CZ  PHE A  38 " =    1.214
peak=    3.416 closest distance to " O   HOH Z 124 " =    2.151
peak=    3.409 closest distance to " CD1 LEU A  96 " =    0.731
peak=    3.404 closest distance to " CE  LYS A  76 " =    0.772
peak=    3.404 closest distance to " O   HOH Z 294 " =    1.519
peak=    3.402 closest distance to " NH2BARG A 145 " =    2.093
peak=    3.401 closest distance to " O   HOH Z  48 " =    1.596
peak=    3.400 closest distance to " CG2 ILE A  20 " =    1.391
peak=    3.395 closest distance to " CA  VAL A 125 " =    1.196
peak=    3.392 closest distance to " O   HOH Z 281 " =    4.909
peak=    3.389 closest distance to " CD  ARG A 159 " =    0.891
peak=    3.388 closest distance to " OD2 ASP A 298 " =    3.795
peak=    3.387 closest distance to " O   HOH Z  78 " =    1.707
peak=    3.385 closest distance to " OE1 GLU A   2 " =    1.712
peak=    3.385 closest distance to " O   HOH Z 185 " =    1.747
peak=    3.381 closest distance to " CA  LYS A 166 " =    1.397
peak=    3.380 closest distance to " CA  LYS A 117 " =    1.286
peak=    3.379 closest distance to " O   HOH Z 227 " =    1.761
peak=    3.368 closest distance to " O   HOH Z 199 " =    1.646
peak=    3.368 closest distance to " O   THR A 251 " =    1.267
peak=    3.368 closest distance to " O   HOH Z 416 " =    2.939
peak=    3.367 closest distance to " CB  GLU A  46 " =    1.094
peak=    3.366 closest distance to " O   HOH Z  90 " =    3.459
peak=    3.365 closest distance to " CG  GLN A  11 " =    1.303
peak=    3.361 closest distance to " O   HOH Z  78 " =    2.195
peak=    3.357 closest distance to " O   HOH Z 189 " =    2.954
peak=    3.357 closest distance to " C   TYR A 214 " =    1.534
peak=    3.357 closest distance to " O   HOH Z 247 " =    1.486
peak=    3.354 closest distance to " CD  PRO A  54 " =    1.089
peak=    3.353 closest distance to " O   HOH Z 291 " =    1.433
peak=    3.351 closest distance to " CB  ALA A  71 " =    1.318
peak=    3.350 closest distance to " CB  MET A  40 " =    0.878
peak=    3.349 closest distance to " N   ILE A  33 " =    0.969
peak=    3.344 closest distance to " CB  SER A   3 " =    1.388
peak=    3.342 closest distance to " O   HOH Z 365 " =    2.755
peak=    3.340 closest distance to " NZ  LYS A 117 " =    3.093
peak=    3.337 closest distance to " O   HOH Z 250 " =    1.358
peak=    3.336 closest distance to " CB  LEU A   5 " =    1.105
peak=    3.331 closest distance to " CG2 ILE A 234 " =    0.915
peak=    3.329 closest distance to " O   HOH Z 393 " =    3.281
peak=    3.327 closest distance to " O   HOH Z 200 " =    1.525
peak=    3.326 closest distance to " CB  ALA A  43 " =    0.894
peak=    3.326 closest distance to " O   HOH Z 135 " =    2.031
peak=    3.323 closest distance to " CA  ASP A 162 " =    1.167
peak=    3.322 closest distance to " OG BSER A 134 " =    2.904
peak=    3.319 closest distance to " CG  MET A 185 " =    1.059
peak=    3.314 closest distance to " O   HOH Z 353 " =    2.837
peak=    3.313 closest distance to " NH1 ARG A  14 " =    1.176
peak=    3.313 closest distance to " O  BHOH Z 338 " =    2.181
peak=    3.309 closest distance to " O   HOH Z 394 " =    3.934
peak=    3.307 closest distance to " O   HOH Z 125 " =    3.857
peak=    3.306 closest distance to " O   TYR A 116 " =    1.401
peak=    3.305 closest distance to " CG2 THR A  29 " =    1.426
peak=    3.304 closest distance to " CA  ALA A 100 " =    1.098
peak=    3.303 closest distance to " O   HOH Z 126 " =    2.254
peak=    3.302 closest distance to " OG  SER A 276 " =    1.556
peak=    3.298 closest distance to " N   THR A  52 " =    1.112
peak=    3.293 closest distance to " O   HOH Z 413 " =    3.427
peak=    3.291 closest distance to " CB  LEU A  83 " =    0.872
peak=    3.288 closest distance to " CA  GLU A  46 " =    0.911
peak=    3.286 closest distance to " O   HOH Z 193 " =    1.752
peak=    3.279 closest distance to " O   GLY A  57 " =    2.783
peak=    3.278 closest distance to " NH1AARG A 145 " =    1.263
peak=    3.274 closest distance to " NZ  LYS A  48 " =    1.353
peak=    3.270 closest distance to " OG  SER A 245 " =    1.632
peak=    3.259 closest distance to " O   HOH Z 383 " =    2.320
peak=    3.257 closest distance to " O   HOH Z 377 " =    1.149
peak=    3.255 closest distance to " O   HOH Z 420 " =    2.195
peak=    3.254 closest distance to " O   HOH Z  88 " =    1.732
peak=    3.254 closest distance to " O   HOH Z 325 " =    2.118
peak=    3.254 closest distance to " CD  ARG A  66 " =    2.477
peak=    3.249 closest distance to " O   HOH Z 130 " =    2.259
peak=    3.247 closest distance to " CB  TYR A 116 " =    1.141
peak=    3.245 closest distance to " CB  ALA A 100 " =    1.339
peak=    3.236 closest distance to " O   HOH Z  54 " =    1.233
peak=    3.234 closest distance to " CA  SER A  87 " =    1.088
peak=    3.234 closest distance to " O   HOH Z 118 " =    0.849
peak=    3.233 closest distance to " CB  GLN A 103 " =    0.937
peak=    3.231 closest distance to " O   HOH Z 434 " =    3.042
peak=    3.227 closest distance to " O   HOH Z 244 " =    1.709
peak=    3.225 closest distance to " CD  LYS A 119 " =    1.763
peak=    3.224 closest distance to " O   HOH Z 139 " =    4.863
peak=    3.222 closest distance to " OG1 THR A 294 " =    2.460
peak=    3.222 closest distance to " O   HOH Z 427 " =    3.141
peak=    3.220 closest distance to " N   ASP A 132 " =    1.241
peak=    3.213 closest distance to " CD2 TYR A 186 " =    1.052
peak=    3.210 closest distance to " CA  ASN A 217 " =    1.282
peak=    3.209 closest distance to " CB  ALA A 291 " =    1.281
peak=    3.207 closest distance to " O   HOH Z 432 " =    1.837
peak=    3.201 closest distance to " N   ASN A 127 " =    1.237
peak=    3.201 closest distance to " CG  GLU A  37 " =    0.946
peak=    3.198 closest distance to " CB  PHE A 204 " =    0.945
peak=    3.198 closest distance to " O   HOH Z 421 " =    1.819
peak=    3.197 closest distance to " CA  VAL A  41 " =    0.911
peak=    3.197 closest distance to " CB  PRO A 243 " =    1.183
peak=    3.195 closest distance to " CG  GLN A  58 " =    2.665
peak=    3.194 closest distance to " O   HOH Z 139 " =    1.181
peak=    3.193 closest distance to " NZ  LYS A 117 " =    1.830
peak=    3.192 closest distance to " O   PHE A  61 " =    1.393
peak=    3.191 closest distance to " O   HOH Z 422 " =    2.446
peak=    3.187 closest distance to " O   HOH Z 173 " =    2.238
peak=    3.187 closest distance to " O   HOH Z 423 " =    3.338
peak=    3.184 closest distance to " CD  PRO A 213 " =    1.280
peak=    3.183 closest distance to " O   HOH Z 367 " =    2.000
peak=    3.177 closest distance to " CB  GLN A  89 " =    1.211
peak=    3.173 closest distance to " CG1BVAL A  72 " =    1.821
peak=    3.172 closest distance to " CG  ARG A 219 " =    1.242
peak=    3.172 closest distance to " O   HOH Z 255 " =    1.911
peak=    3.171 closest distance to " O   HOH Z  47 " =    1.154
peak=    3.170 closest distance to " CG2 THR A 220 " =    0.746
peak=    3.165 closest distance to " O   HOH Z  88 " =    3.474
peak=    3.161 closest distance to " N   ILE A  20 " =    2.320
peak=    3.161 closest distance to " O   HOH Z 282 " =    2.021
peak=    3.158 closest distance to " CA  GLN A  88 " =    1.422
peak=    3.155 closest distance to " CB  PRO A  90 " =    1.269
peak=    3.151 closest distance to " ND2 ASN A 301 " =    1.287
peak=    3.142 closest distance to " O   HOH Z 261 " =    2.040
peak=    3.137 closest distance to " CB  ARG A  79 " =    0.866
peak=    3.136 closest distance to " O   HOH Z 431 " =    0.978
peak=    3.135 closest distance to " OG  SER A  62 " =    2.987
peak=    3.135 closest distance to " O   HOH Z 344 " =    3.155
peak=    3.133 closest distance to " CE1 HIS A 108 " =    1.117
peak=    3.131 closest distance to " O   HOH Z 357 " =    2.608
peak=    3.130 closest distance to " O   HOH Z 251 " =    1.558
peak=    3.126 closest distance to " O   HOH Z 426 " =    1.448
peak=    3.124 closest distance to " CG  ARG A 139 " =    1.085
peak=    3.124 closest distance to " CB  ASN A 187 " =    1.132
peak=    3.123 closest distance to " OH  TYR A 116 " =    1.223
peak=    3.119 closest distance to " O   HOH Z 387 " =    2.748
peak=    3.117 closest distance to " CA  MET A 188 " =    1.030
peak=    3.116 closest distance to " OD1 ASP A 231 " =    1.898
peak=    3.112 closest distance to " O   HOH Z 219 " =    5.388
peak=    3.109 closest distance to " O   GLY A  91 " =    1.187
peak=    3.108 closest distance to " O   HOH Z 301 " =    1.965
peak=    3.105 closest distance to " CB  SER A  97 " =    0.803
peak=    3.103 closest distance to " CG  GLN A  89 " =    1.517
peak=    3.098 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.097 closest distance to " CB  ALA A 248 " =    0.929
peak=    3.095 closest distance to " O   HOH Z 417 " =    2.496
peak=    3.094 closest distance to " OH  TYR A  30 " =    1.450
peak=    3.092 closest distance to " CB  TYR A 247 " =    0.913
peak=    3.090 closest distance to " CD BLYS A 290 " =    0.978
peak=    3.089 closest distance to " O   HOH Z 301 " =    1.467
peak=    3.087 closest distance to " N   SER A 164 " =    1.075
peak=    3.086 closest distance to " O   HOH Z  83 " =    1.607
peak=    3.084 closest distance to " CG ALYS A 290 " =    1.091
peak=    3.081 closest distance to " O   HOH Z 148 " =    3.379
peak=    3.057 closest distance to " CA  ARG A 156 " =    1.101
peak=    3.051 closest distance to " ND2 ASN A 249 " =    0.874
peak=    3.042 closest distance to " O   HOH Z 126 " =    1.783
peak=    3.034 closest distance to " O   HOH Z  48 " =    1.848
peak=    3.034 closest distance to " O   HOH Z 428 " =    1.022
peak=    3.033 closest distance to " CB  ASN A 148 " =    1.992
peak=    3.027 closest distance to " O   HOH Z 313 " =    1.894
peak=    3.020 closest distance to " CA  ARG A  66 " =    0.955
peak=    3.001 closest distance to " O   HOH Z   6 " =    2.336
peak=    2.999 closest distance to " O   THR A 251 " =    1.790

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 232         
Filter by distance & map next to the model:
   mapped sites are within: 0.809 - 5.882
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 230 from: 232
   mapped sites are within: 0.809 - 5.882

peak=   -4.698 closest distance to " O   HOH Z 266 " =    5.303
peak=   -4.567 closest distance to " CD  GLN A  58 " =    0.959
peak=   -4.280 closest distance to " O   HOH Z 150 " =    0.878
peak=   -4.268 closest distance to " CD  GLN A 223 " =    1.438
peak=   -4.240 closest distance to " O   HOH Z   5 " =    1.653
peak=   -4.213 closest distance to " CB  PRO A 243 " =    2.741
peak=   -4.181 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -4.158 closest distance to " O   HOH Z 166 " =    1.743
peak=   -4.139 closest distance to " CD  ARG A 156 " =    2.115
peak=   -4.139 closest distance to " OXT GLY A 302 " =    3.013
peak=   -4.122 closest distance to " CD1 PHE A  59 " =    2.039
peak=   -4.102 closest distance to " O   HOH Z 231 " =    2.380
peak=   -4.097 closest distance to " CG1 VAL A 250 " =    2.720
peak=   -4.085 closest distance to " ND2 ASN A  45 " =    1.975
peak=   -4.051 closest distance to " CD  GLN A  58 " =    0.856
peak=   -3.993 closest distance to " O   HOH Z 283 " =    2.184
peak=   -3.977 closest distance to " CA  VAL A  67 " =    3.046
peak=   -3.974 closest distance to " CB  ALA A  10 " =    2.102
peak=   -3.973 closest distance to " OG  SER A  97 " =    2.218
peak=   -3.967 closest distance to " O   PRO A 198 " =    1.373
peak=   -3.963 closest distance to " O   HOH Z 166 " =    2.486
peak=   -3.956 closest distance to " O   HOH Z  13 " =    1.840
peak=   -3.952 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.939 closest distance to " CD  ARG A  14 " =    3.427
peak=   -3.934 closest distance to " OG BSER A 210 " =    1.283
peak=   -3.921 closest distance to " O   HOH Z 348 " =    2.337
peak=   -3.904 closest distance to " NE2 GLN A 223 " =    1.058
peak=   -3.866 closest distance to " CD1 LEU A 101 " =    2.515
peak=   -3.859 closest distance to " OE1 GLN A 223 " =    2.406
peak=   -3.857 closest distance to " O   HOH Z 234 " =    4.419
peak=   -3.847 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.839 closest distance to " C   SER A 206 " =    1.443
peak=   -3.838 closest distance to " C   ASN A 285 " =    2.417
peak=   -3.835 closest distance to " O   HOH Z 377 " =    2.052
peak=   -3.829 closest distance to " CD  GLN A  88 " =    0.931
peak=   -3.826 closest distance to " O   PRO A 163 " =    2.222
peak=   -3.797 closest distance to " CD2 TYR A 293 " =    1.861
peak=   -3.794 closest distance to " CG  ARG A 269 " =    2.356
peak=   -3.777 closest distance to " O   HOH Z   6 " =    1.405
peak=   -3.767 closest distance to " CB  ALA A 161 " =    2.670
peak=   -3.763 closest distance to " OD1 ASN A 148 " =    1.478
peak=   -3.762 closest distance to " O   HOH Z 407 " =    0.885
peak=   -3.760 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.758 closest distance to " CG2 ILE A  49 " =    2.729
peak=   -3.751 closest distance to " CE2 TYR A  30 " =    2.697
peak=   -3.686 closest distance to " CE2 PHE A  61 " =    2.586
peak=   -3.684 closest distance to " CB  ALA A 291 " =    2.426
peak=   -3.683 closest distance to " OE1 GLN A  88 " =    1.142
peak=   -3.673 closest distance to " CD2 PHE A 225 " =    1.315
peak=   -3.654 closest distance to " CA  GLY A 203 " =    2.434
peak=   -3.653 closest distance to " O   HOH Z 252 " =    3.954
peak=   -3.652 closest distance to " C   HIS A 108 " =    1.105
peak=   -3.636 closest distance to " O   HOH Z 185 " =    2.374
peak=   -3.635 closest distance to " NE2 GLN A 194 " =    1.995
peak=   -3.605 closest distance to " O   HOH Z 351 " =    1.492
peak=   -3.603 closest distance to " OD1 ASP A 191 " =    1.654
peak=   -3.602 closest distance to " O   ALA A  34 " =    2.400
peak=   -3.591 closest distance to " CE3 TRP A 150 " =    2.229
peak=   -3.567 closest distance to " N   ALA A  43 " =    2.766
peak=   -3.553 closest distance to " CG2 ILE A 263 " =    2.279
peak=   -3.551 closest distance to " O   PHE A 218 " =    1.444
peak=   -3.550 closest distance to " O   SER A 271 " =    2.139
peak=   -3.549 closest distance to " O   HOH Z 308 " =    1.648
peak=   -3.533 closest distance to " CD2 PHE A  61 " =    2.075
peak=   -3.528 closest distance to " O   HOH Z 418 " =    1.340
peak=   -3.524 closest distance to " CB  ASP A 132 " =    2.432
peak=   -3.518 closest distance to " CB  PHE A 192 " =    1.853
peak=   -3.516 closest distance to " O   HOH Z 392 " =    1.316
peak=   -3.506 closest distance to " NH2 ARG A  66 " =    1.745
peak=   -3.498 closest distance to " O   HOH Z   7 " =    1.334
peak=   -3.497 closest distance to " O   ALA A  10 " =    1.849
peak=   -3.496 closest distance to " CB  TRP A  85 " =    2.491
peak=   -3.493 closest distance to " O   SER A 276 " =    1.686
peak=   -3.487 closest distance to " CG  GLU A  53 " =    1.544
peak=   -3.472 closest distance to " O   HOH Z 109 " =    3.286
peak=   -3.469 closest distance to " O   HOH Z 275 " =    1.535
peak=   -3.469 closest distance to " O   HOH Z 128 " =    2.610
peak=   -3.466 closest distance to " O   HOH Z 109 " =    3.679
peak=   -3.460 closest distance to " O   HOH Z 377 " =    1.119
peak=   -3.455 closest distance to " NE2 GLN A 103 " =    1.789
peak=   -3.450 closest distance to " CD1 ILE A 109 " =    2.934
peak=   -3.446 closest distance to " ND2 ASN A  45 " =    1.168
peak=   -3.443 closest distance to " CZ  TYR A 169 " =    1.862
peak=   -3.442 closest distance to " O   HOH Z 264 " =    1.845
peak=   -3.442 closest distance to " CA  VAL A 197 " =    1.019
peak=   -3.440 closest distance to " O   HOH Z 290 " =    1.182
peak=   -3.439 closest distance to " N   SER A 276 " =    1.526
peak=   -3.430 closest distance to " O   HOH Z  19 " =    2.275
peak=   -3.428 closest distance to " O   HOH Z  49 " =    1.197
peak=   -3.426 closest distance to " OG BSER A 210 " =    2.322
peak=   -3.423 closest distance to " O   HOH Z 117 " =    4.609
peak=   -3.422 closest distance to " O   HOH Z  71 " =    1.952
peak=   -3.422 closest distance to " CA  GLY A 133 " =    2.349
peak=   -3.419 closest distance to " O   HOH Z 292 " =    4.719
peak=   -3.411 closest distance to " O   HOH Z 150 " =    1.266
peak=   -3.402 closest distance to " ND2 ASN A  69 " =    1.560
peak=   -3.401 closest distance to " C   ALA A 158 " =    1.330
peak=   -3.400 closest distance to " O   GLY A  75 " =    2.090
peak=   -3.395 closest distance to " CE BMET A  47 " =    1.805
peak=   -3.394 closest distance to " CG1 VAL A 189 " =    2.594
peak=   -3.393 closest distance to " O   HOH Z 165 " =    1.986
peak=   -3.393 closest distance to " CG2 VAL A 189 " =    2.245
peak=   -3.392 closest distance to " CD  ARG A 139 " =    1.536
peak=   -3.388 closest distance to " O   HOH Z  40 " =    3.008
peak=   -3.384 closest distance to " O   HOH Z 236 " =    1.693
peak=   -3.379 closest distance to " CG  GLN A  11 " =    1.508
peak=   -3.378 closest distance to " O   HOH Z  90 " =    3.779
peak=   -3.376 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.374 closest distance to " O   HOH Z 394 " =    1.629
peak=   -3.363 closest distance to " O   HOH Z 136 " =    2.193
peak=   -3.362 closest distance to " ND2 ASN A 249 " =    2.376
peak=   -3.362 closest distance to " O   HOH Z 123 " =    2.480
peak=   -3.361 closest distance to " O   HOH Z 134 " =    2.137
peak=   -3.359 closest distance to " O   HOH Z  78 " =    1.822
peak=   -3.355 closest distance to " CB  SER A 210 " =    1.097
peak=   -3.353 closest distance to " O   HOH Z 233 " =    2.440
peak=   -3.353 closest distance to " O   SER A 210 " =    1.721
peak=   -3.350 closest distance to " CG  PRO A 243 " =    1.686
peak=   -3.346 closest distance to " O   HOH Z 193 " =    2.429
peak=   -3.343 closest distance to " NE  ARG A  66 " =    4.417
peak=   -3.337 closest distance to " O   HOH Z  11 " =    1.912
peak=   -3.336 closest distance to " CA  GLY A  98 " =    2.214
peak=   -3.335 closest distance to " O   HOH Z 171 " =    2.340
peak=   -3.334 closest distance to " O   HOH Z   7 " =    1.692
peak=   -3.332 closest distance to " O   HOH Z 102 " =    1.644
peak=   -3.330 closest distance to " O   HOH Z 200 " =    1.315
peak=   -3.326 closest distance to " CG1 VAL A  78 " =    2.639
peak=   -3.321 closest distance to " O   HOH Z 111 " =    1.571
peak=   -3.319 closest distance to " ND2BASN A 224 " =    1.880
peak=   -3.319 closest distance to " CD1 LEU A  25 " =    2.512
peak=   -3.316 closest distance to " CA  GLY A 241 " =    3.182
peak=   -3.313 closest distance to " C   LEU A 143 " =    1.154
peak=   -3.312 closest distance to " OG  SER A  26 " =    1.357
peak=   -3.310 closest distance to " O   HOH Z 251 " =    5.142
peak=   -3.310 closest distance to " O   HOH Z 106 " =    2.072
peak=   -3.309 closest distance to " O   HOH Z 133 " =    1.485
peak=   -3.303 closest distance to " NH2 ARG A  66 " =    3.882
peak=   -3.302 closest distance to " C   ARG A  79 " =    2.695
peak=   -3.299 closest distance to " O   HOH Z  37 " =    1.882
peak=   -3.294 closest distance to " O   HOH Z 197 " =    2.087
peak=   -3.293 closest distance to " CG  LEU A  83 " =    2.100
peak=   -3.291 closest distance to " O   HOH Z 311 " =    3.768
peak=   -3.290 closest distance to " O   HOH Z  52 " =    1.692
peak=   -3.289 closest distance to " O   HOH Z 150 " =    2.041
peak=   -3.288 closest distance to " CB  ALA A  43 " =    2.630
peak=   -3.282 closest distance to " CD2 PHE A  59 " =    2.435
peak=   -3.281 closest distance to " CB  PHE A  16 " =    2.505
peak=   -3.281 closest distance to " C   THR A 279 " =    1.084
peak=   -3.281 closest distance to " NE2 GLN A  58 " =    2.664
peak=   -3.280 closest distance to " O   HOH Z 298 " =    2.684
peak=   -3.278 closest distance to " NE2 GLN A  88 " =    1.986
peak=   -3.276 closest distance to " O   HOH Z 198 " =    2.241
peak=   -3.270 closest distance to " O   HOH Z 388 " =    1.974
peak=   -3.268 closest distance to " O   ALA A   1 " =    2.003
peak=   -3.257 closest distance to " O   HOH Z 139 " =    3.341
peak=   -3.255 closest distance to " CG  MET A 105 " =    0.889
peak=   -3.252 closest distance to " OE1 GLN A  89 " =    1.975
peak=   -3.250 closest distance to " O   HOH Z 118 " =    1.278
peak=   -3.248 closest distance to " CD  ARG A 195 " =    5.111
peak=   -3.246 closest distance to " NE2 GLN A  94 " =    1.831
peak=   -3.246 closest distance to " O   ALA A  34 " =    2.053
peak=   -3.244 closest distance to " OD1 ASN A 187 " =    1.576
peak=   -3.239 closest distance to " O   HOH Z 422 " =    1.560
peak=   -3.239 closest distance to " NH2 ARG A  66 " =    5.882
peak=   -3.232 closest distance to " CD1 TRP A 179 " =    1.092
peak=   -3.231 closest distance to " CD1 ILE A 106 " =    2.165
peak=   -3.229 closest distance to " CB  ALA A 100 " =    1.834
peak=   -3.229 closest distance to " O   PRO A 198 " =    1.680
peak=   -3.228 closest distance to " OD2 ASP A 171 " =    1.843
peak=   -3.216 closest distance to " CB  ARG A 219 " =    2.297
peak=   -3.214 closest distance to " O   HOH Z 409 " =    4.870
peak=   -3.212 closest distance to " CZ  PHE A 155 " =    1.402
peak=   -3.212 closest distance to " O   HOH Z   2 " =    2.472
peak=   -3.212 closest distance to " O   HOH Z 114 " =    3.833
peak=   -3.211 closest distance to " N   SER A 134 " =    1.296
peak=   -3.205 closest distance to " O   TRP A  92 " =    1.975
peak=   -3.205 closest distance to " NH2 ARG A  79 " =    2.134
peak=   -3.200 closest distance to " CB  ASP A 162 " =    2.532
peak=   -3.197 closest distance to " O   HOH Z 137 " =    2.252
peak=   -3.196 closest distance to " O   HOH Z 196 " =    1.965
peak=   -3.196 closest distance to " O   HOH Z 285 " =    1.317
peak=   -3.195 closest distance to " O   SER A 135 " =    1.629
peak=   -3.193 closest distance to " O   HOH Z 372 " =    2.519
peak=   -3.191 closest distance to " O   HOH Z 371 " =    1.594
peak=   -3.189 closest distance to " CD2 LEU A 300 " =    2.747
peak=   -3.187 closest distance to " O   ALA A 160 " =    1.461
peak=   -3.183 closest distance to " O   HOH Z  41 " =    2.209
peak=   -3.181 closest distance to " O   HOH Z 281 " =    2.191
peak=   -3.180 closest distance to " O   HOH Z 396 " =    1.800
peak=   -3.166 closest distance to " O   HOH Z 211 " =    1.644
peak=   -3.165 closest distance to " O   HOH Z 111 " =    1.783
peak=   -3.165 closest distance to " OG BSER A 134 " =    1.943
peak=   -3.161 closest distance to " O   HOH Z 385 " =    3.780
peak=   -3.159 closest distance to " O   HOH Z  94 " =    2.425
peak=   -3.158 closest distance to " CD  PRO A 213 " =    2.216
peak=   -3.151 closest distance to " O   HOH Z  58 " =    1.375
peak=   -3.150 closest distance to " O   HOH Z 350 " =    1.998
peak=   -3.140 closest distance to " O   HOH Z 156 " =    3.665
peak=   -3.138 closest distance to " N   TYR A  68 " =    3.017
peak=   -3.138 closest distance to " O   HOH Z 210 " =    0.809
peak=   -3.135 closest distance to " CH2 TRP A 150 " =    1.172
peak=   -3.135 closest distance to " O   HOH Z  60 " =    1.763
peak=   -3.134 closest distance to " O   HOH Z 149 " =    2.002
peak=   -3.133 closest distance to " O   HOH Z 422 " =    1.379
peak=   -3.128 closest distance to " O   HOH Z 120 " =    4.363
peak=   -3.125 closest distance to " SG  CYS A 254 " =    2.792
peak=   -3.125 closest distance to " CD  ARG A 139 " =    1.133
peak=   -3.120 closest distance to " O   HOH Z 191 " =    5.766
peak=   -3.116 closest distance to " ND2 ASN A  60 " =    1.539
peak=   -3.115 closest distance to " OD2 ASP A  50 " =    2.185
peak=   -3.106 closest distance to " O   HOH Z  91 " =    2.202
peak=   -3.101 closest distance to " O   ASN A 127 " =    2.128
peak=   -3.094 closest distance to " O   VAL A 174 " =    2.163
peak=   -3.092 closest distance to " CG  ASP A 286 " =    1.514
peak=   -3.088 closest distance to " O   HOH Z 259 " =    1.988
peak=   -3.087 closest distance to " OE1 GLN A  88 " =    1.244
peak=   -3.086 closest distance to " CD  LYS A 289 " =    2.350
peak=   -3.076 closest distance to " CG  PHE A 283 " =    2.779
peak=   -3.075 closest distance to " O   HOH Z 219 " =    4.419
peak=   -3.071 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.067 closest distance to " CG  ASN A 301 " =    1.963
peak=   -3.065 closest distance to " O   GLN A 240 " =    2.640
peak=   -3.063 closest distance to " O   HOH Z 174 " =    2.073
peak=   -3.062 closest distance to " CB  ASP A 132 " =    2.496
peak=   -3.062 closest distance to " C   GLU A  46 " =    1.038
peak=   -3.058 closest distance to " O   ASP A 171 " =    1.084
peak=   -3.051 closest distance to " O   HOH Z  88 " =    2.351
peak=   -3.044 closest distance to " OE1 GLN A  88 " =    1.020
peak=   -3.016 closest distance to " CG1 VAL A 112 " =    2.876
peak=   -3.013 closest distance to " SD  MET A  40 " =    2.019

================= 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    :  0.4346 0.4166   6.252252e+00   6.216081e+00
   1_bss:  0.4232 0.4052   6.241007e+00   6.200778e+00
   1_xyz:  0.3195 0.3468   6.031835e+00   6.091243e+00
   1_adp:  0.2931 0.3548   5.981780e+00   6.102887e+00
   1_occ:  0.2930 0.3547   5.981425e+00   6.102706e+00
   2_bss:  0.2912 0.3520   5.981469e+00   6.103215e+00
   2_xyz:  0.2329 0.2777   5.769078e+00   5.916063e+00
   2_adp:  0.2149 0.2642   5.714261e+00   5.874173e+00
   2_occ:  0.2146 0.2642   5.713885e+00   5.874698e+00
   3_bss:  0.2144 0.2638   5.713231e+00   5.873445e+00
   3_xyz:  0.1582 0.2017   5.434724e+00   5.630145e+00
   3_adp:  0.1447 0.1880   5.354275e+00   5.557660e+00
   3_occ:  0.1446 0.1878   5.353124e+00   5.556341e+00
   4_bss:  0.1448 0.1874   5.352975e+00   5.553699e+00
   4_xyz:  0.1329 0.1762   5.283896e+00   5.494281e+00
   4_adp:  0.1283 0.1748   5.259823e+00   5.481333e+00
   4_occ:  0.1282 0.1747   5.259538e+00   5.481201e+00
   5_bss:  0.1281 0.1747   5.259274e+00   5.481223e+00
   5_xyz:  0.1188 0.1674   5.201404e+00   5.440499e+00
   5_adp:  0.1176 0.1679   5.196620e+00   5.439510e+00
   5_occ:  0.1175 0.1679   5.196473e+00   5.439501e+00
   5_bss:  0.1176 0.1676   5.196361e+00   5.438621e+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:  0.286  38.277  -3.638   5.367  -0.397   0.000  -0.000  -0.000
   1_xyz:  0.286  38.277  -3.638   5.367  -0.397   0.000  -0.000  -0.000
   1_adp:  0.286  38.277  -3.638   5.367  -0.397   0.000  -0.000  -0.000
   1_occ:  0.286  38.277  -3.638   5.367  -0.397   0.000  -0.000  -0.000
   2_bss:  0.320  66.536  -1.484   2.835   0.303   0.000   0.000   0.000
   2_xyz:  0.320  66.536  -1.484   2.835   0.303   0.000   0.000   0.000
   2_adp:  0.320  66.536  -1.484   2.835   0.303   0.000   0.000   0.000
   2_occ:  0.320  66.536  -1.484   2.835   0.303   0.000   0.000   0.000
   3_bss:  0.323  71.609  -1.358   1.246   0.205   0.000   0.000   0.000
   3_xyz:  0.323  71.609  -1.358   1.246   0.205   0.000   0.000   0.000
   3_adp:  0.323  71.609  -1.358   1.246   0.205   0.000   0.000   0.000
   3_occ:  0.323  71.609  -1.358   1.246   0.205   0.000   0.000   0.000
   4_bss:  0.328  69.444  -1.552   0.029   0.025   0.000   0.000   0.000
   4_xyz:  0.328  69.444  -1.552   0.029   0.025   0.000   0.000   0.000
   4_adp:  0.328  69.444  -1.552   0.029   0.025   0.000   0.000   0.000
   4_occ:  0.328  69.444  -1.552   0.029   0.025   0.000   0.000   0.000
   5_bss:  0.323  70.230  -1.429  -0.196   0.144  -0.000   0.000   0.000
   5_xyz:  0.323  70.230  -1.429  -0.196   0.144  -0.000   0.000   0.000
   5_adp:  0.323  70.230  -1.429  -0.196   0.144  -0.000   0.000   0.000
   5_occ:  0.323  70.230  -1.429  -0.196   0.144  -0.000   0.000   0.000
   5_bss:  0.324  71.128  -1.117  -0.082   0.419  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.746 0.5507  0.7015    54223.803
   1_bss:  46.985 0.5587  0.7223    51295.911
   1_xyz:  39.020 0.6540  0.8276    35342.104
   1_adp:  39.483 0.6483  0.8102    36326.762
   1_occ:  39.545 0.6475  0.8086    36320.553
   2_bss:  39.174 0.6521  0.8222    36028.456
   2_xyz:  29.337 0.7644  0.9324    20882.386
   2_adp:  27.263 0.7878  0.9323    18795.963
   2_occ:  27.284 0.7875  0.9319    18821.861
   3_bss:  27.176 0.7888  0.9179    18751.070
   3_xyz:  19.907 0.8618  0.9717    10486.352
   3_adp:  17.857 0.8816  0.9736     9086.518
   3_occ:  17.821 0.8820  0.9738     9071.362
   4_bss:  17.744 0.8826  0.9570     8985.498
   4_xyz:  16.298 0.8959  0.9627     7919.852
   4_adp:  15.963 0.8990  0.9546     7741.398
   4_occ:  15.957 0.8990  0.9544     7738.536
   5_bss:  15.952 0.8991  0.9549     7738.633
   5_xyz:  15.141 0.9058  0.9595     7119.605
   5_adp:  15.114 0.9061  0.9500     7101.609
   5_occ:  15.110 0.9061  0.9500     7102.167
   5_bss:  15.098 0.9062  0.9578     7074.250
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6541e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6541e-01
   1_xyz:   1.602  0.014  0.100 16.222  0.006  4.115   1.3715e-01
   1_adp:   1.602  0.014  0.100 16.222  0.006  4.115   1.3715e-01
   1_occ:   1.602  0.014  0.100 16.222  0.006  4.115   1.3715e-01
   2_bss:   1.602  0.014  0.100 16.222  0.006  4.115   1.3715e-01
   2_xyz:   1.232  0.009  0.083 14.859  0.005  4.113   8.0841e-02
   2_adp:   1.232  0.009  0.083 14.859  0.005  4.113   8.0841e-02
   2_occ:   1.232  0.009  0.083 14.859  0.005  4.113   8.0841e-02
   3_bss:   1.232  0.009  0.083 14.859  0.005  4.113   8.0841e-02
   3_xyz:   1.217  0.012  0.085 15.070  0.004  4.132   9.1946e-02
   3_adp:   1.217  0.012  0.085 15.070  0.004  4.132   9.1946e-02
   3_occ:   1.217  0.012  0.085 15.070  0.004  4.132   9.1946e-02
   4_bss:   1.217  0.012  0.085 15.070  0.004  4.132   9.1946e-02
   4_xyz:   1.038  0.008  0.076 14.716  0.004  4.116   6.4484e-02
   4_adp:   1.038  0.008  0.076 14.716  0.004  4.116   6.4484e-02
   4_occ:   1.038  0.008  0.076 14.716  0.004  4.116   6.4484e-02
   5_bss:   1.038  0.008  0.076 14.716  0.004  4.116   6.4484e-02
   5_xyz:   1.145  0.012  0.084 14.990  0.004  4.122   8.0858e-02
   5_adp:   1.145  0.012  0.084 14.990  0.004  4.122   8.0858e-02
   5_occ:   1.145  0.012  0.084 14.990  0.004  4.122   8.0858e-02
   5_bss:   1.145  0.012  0.084 14.990  0.004  4.122   8.0858e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.750   2.4451e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.750   2.4451e-01
   1_xyz:  10.002  0.092  0.363 85.994  0.041  2.081   1.1148e-01
   1_adp:  10.002  0.092  0.363 85.994  0.041  2.081   1.1148e-01
   1_occ:  10.002  0.092  0.363 85.994  0.041  2.081   1.1148e-01
   2_bss:  10.002  0.092  0.363 85.994  0.041  2.081   1.1148e-01
   2_xyz:   7.763  0.046  0.260 88.929  0.033  2.260   7.8135e-02
   2_adp:   7.763  0.046  0.260 88.929  0.033  2.260   7.8135e-02
   2_occ:   7.763  0.046  0.260 88.929  0.033  2.260   7.8135e-02
   3_bss:   7.763  0.046  0.260 88.929  0.033  2.260   7.8135e-02
   3_xyz:   7.683  0.060  0.239 85.932  0.034  2.123   1.3521e-01
   3_adp:   7.683  0.060  0.239 85.932  0.034  2.123   1.3521e-01
   3_occ:   7.683  0.060  0.239 85.932  0.034  2.123   1.3521e-01
   4_bss:   7.683  0.060  0.239 85.932  0.034  2.123   1.3521e-01
   4_xyz:   7.167  0.041  0.252 80.722  0.037  2.303   4.6838e-02
   4_adp:   7.167  0.041  0.252 80.722  0.037  2.303   4.6838e-02
   4_occ:   7.167  0.041  0.252 80.722  0.037  2.303   4.6838e-02
   5_bss:   7.167  0.041  0.252 80.722  0.037  2.303   4.6838e-02
   5_xyz:   8.536  0.052  0.290 82.140  0.036  2.296   6.1647e-02
   5_adp:   8.536  0.052  0.290 82.140  0.036  2.296   6.1647e-02
   5_occ:   8.536  0.052  0.290 82.140  0.036  2.296   6.1647e-02
   5_bss:   8.536  0.052  0.290 82.140  0.036  2.296   6.1647e-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:  86.07   0.00  17.61  78.18   0.00  14.07  86.07   2.27  36.84
   1_occ:  86.07   0.00  17.61  78.18   0.00  14.07  86.07   2.27  36.84
   2_bss:  86.07   0.00  17.61  78.18   0.00  14.07  86.07   2.27  36.84
   2_xyz:  86.07   0.00  17.61  78.18   0.00  14.07  86.07   2.27  36.84
   2_adp:  87.28   0.00  17.32  82.46   0.00  13.25  87.28   1.38  39.49
   2_occ:  87.28   0.00  17.32  82.46   0.00  13.25  87.28   1.38  39.49
   3_bss:  87.28   0.00  17.32  82.46   0.00  13.25  87.28   1.38  39.49
   3_xyz:  87.28   0.00  17.32  82.46   0.00  13.25  87.28   1.38  39.49
   3_adp:  86.45   0.00  16.65  84.04   0.00  12.30  86.45   4.52  40.32
   3_occ:  86.45   0.00  16.65  84.04   0.00  12.30  86.45   4.52  40.32
   4_bss:  86.45   0.00  16.65  84.04   0.00  12.30  86.45   4.52  40.32
   4_xyz:  86.45   0.00  16.65  84.04   0.00  12.30  86.45   4.52  40.32
   4_adp:  94.45   0.00  16.60  92.35   0.00  11.98  94.45   0.00  41.79
   4_occ:  94.45   0.00  16.60  92.35   0.00  11.98  94.45   0.00  41.79
   5_bss:  94.45   0.00  16.60  92.35   0.00  11.98  94.45   0.00  41.79
   5_xyz:  94.45   0.00  16.60  92.35   0.00  11.98  94.45   0.00  41.79
   5_adp: 101.28   0.00  16.42  99.10   0.00  11.71 101.28   0.44  42.07
   5_occ: 101.28   0.00  16.42  99.10   0.00  11.71 101.28   0.44  42.07
   5_bss: 101.28   0.00  16.42  99.10   0.00  11.71 101.28   0.44  42.07
------------------------------------------------------------------------
 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:    1.341    0.035    0.437
   1_adp:    1.341    0.035    0.437
   1_occ:    1.341    0.035    0.437
   2_bss:    1.341    0.035    0.437
   2_xyz:    1.480    0.072    0.571
   2_adp:    1.480    0.072    0.571
   2_occ:    1.480    0.072    0.571
   3_bss:    1.480    0.072    0.571
   3_xyz:    1.597    0.077    0.730
   3_adp:    1.597    0.077    0.730
   3_occ:    1.597    0.077    0.730
   4_bss:    1.597    0.077    0.730
   4_xyz:    1.553    0.071    0.759
   4_adp:    1.553    0.071    0.759
   4_occ:    1.553    0.071    0.759
   5_bss:    1.553    0.071    0.759
   5_xyz:    1.559    0.066    0.784
   5_adp:    1.559    0.066    0.784
   5_occ:    1.559    0.066    0.784
   5_bss:    1.559    0.066    0.784
------------------------------------------------------------------------

CPU time actual refinement: 315.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/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_843/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_843/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 315.64 
  Macro-tasks:
    bulk solvent and scale       = 35.29  
    individual site refinement   = 132.47 
    weights calculation          = 28.35  
    collect and process          = 6.40   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 202.62 
  Micro-tasks:
    mask                            = 2.31   
    f_calc                          = 100.14 
    alpha_beta                      = 7.95   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 109.54 
    fmodel                         = 6.18   
    r_factors                      = 0.13   
    phase_errors                   = 10.81  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 238.42 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.495 micro seconds
Total CPU time: 5.48 minutes
from_scatterers_fft:    633 calls, 99.88 s
gradients_fft:          578 calls, 96.27 s

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

# Date 2008-01-16 Time 05:47:19 PST -0800 (1200491239.95 s)
Start R-work = 0.4346, R-free = 0.4166 (no bulk solvent and anisotropic scale)
Final R-work = 0.1340, R-free = 0.1812 (no bulk solvent and anisotropic scale)

Start R-work = 0.4232, R-free = 0.4052
Final R-work = 0.1176, R-free = 0.1676