# Date 2008-01-16 Time 06:35:09 PST -0800 (1200494109.38 s)
#phil __OFF__

Command line arguments: "../1202.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24138
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1202

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 48.1033, 85.5261, 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: 3.26, 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: (71.655, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.98145
Completeness in resolution range: 0.926588
Completeness with d_max=infinity: 0.923835

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1679
                             d_min =   1.9815

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 48.1033, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1679 1.98145
Completeness in resolution range: 0.926588
Completeness with d_max=infinity: 0.923835

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1683 -  4.2407 [2217/2246]  1997   220   9.9%
  bin  2:  4.2407 -  3.3782 [2129/2152]  1917   212  10.0%
  bin  3:  3.3782 -  2.9548 [2098/2123]  1882   216  10.3%
  bin  4:  2.9548 -  2.6863 [2082/2098]  1883   199   9.6%
  bin  5:  2.6863 -  2.4946 [2073/2117]  1859   214  10.3%
  bin  6:  2.4946 -  2.3481 [2051/2079]  1853   198   9.7%
  bin  7:  2.3481 -  2.2309 [2045/2081]  1837   208  10.2%
  bin  8:  2.2309 -  2.1341 [2043/2085]  1838   205  10.0%
  bin  9:  2.1341 -  2.0521 [2027/2072]  1827   200   9.9%
  bin 10:  2.0521 -  1.9815 [ 824/2088]   737    87  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.29 -     2.01: 7
        2.01 -     2.73: 215
        2.73 -     3.46: 4545
        3.46 -     4.18: 9268
        4.18 -     4.90: 13884
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.291 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.395 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.521 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.767 3.120 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 27914 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_1202/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/model_refine_001.geo

CPU time processing inputs: 9.10


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 48.10325 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4657   r_free= 0.4462   ksol= 0.00   Bsol= 0.00   scale= 0.878    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.278489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7303 0.99   1439  163 0.3717 0.4021       6.558      6.5594|
|  2:  4.7303 -  3.7736 0.99   1377  146 0.4084 0.4132      6.8539      6.7986|
|  3:  3.7736 -  3.3022 0.99   1371  156 0.4441 0.3891      6.6716      6.6305|
|  4:  3.3022 -  3.0029 0.99   1339  148 0.4640 0.4568      6.5092      6.5161|
|  5:  3.0029 -  2.7891 0.98   1334  148 0.4819 0.4787      6.3516      6.3574|
|  6:  2.7891 -  2.6255 0.99   1348  152 0.5067 0.4612      6.2704      6.1731|
|  7:  2.6255 -  2.4946 0.98   1330  148 0.5060 0.4268        6.24      6.1562|
|  8:  2.4946 -  2.3865 0.99   1308  143 0.5039 0.4881      6.1454      6.1854|
|  9:  2.3865 -  2.2949 0.99   1328  151 0.5264 0.4886      6.1315      6.0707|
| 10:  2.2949 -  2.2160 0.98   1329  143 0.4955 0.4873      6.0692      6.1167|
| 11:  2.2160 -  2.1469 0.97   1290  142 0.5211 0.4946      6.0338      5.9643|
| 12:  2.1469 -  2.0857 0.99   1329  152 0.5081 0.4921      5.9319      5.9761|
| 13:  2.0857 -  2.0309 0.89   1182  134 0.4855 0.4253      5.8496      5.7906|
| 14:  2.0309 -  1.9815 0.24    326   33 0.5382 0.5070      5.8261      5.7855|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7303  1439   163  0.69  35.17   0.82     0.73      75506.15|
|  2:  4.7303 -  3.7736  1377   146  0.71  34.72   0.90     0.78     100341.35|
|  3:  3.7736 -  3.3022  1371   156  0.60  43.76   0.88     0.76     109267.00|
|  4:  3.3022 -  3.0029  1339   148  0.51  50.92   0.89     0.68      98374.25|
|  5:  3.0029 -  2.7891  1334   148  0.44  56.40   0.86     0.63      79744.67|
|  6:  2.7891 -  2.6255  1348   152  0.45  55.97   0.89     0.62      62500.09|
|  7:  2.6255 -  2.4946  1330   148  0.47  54.11   0.91     0.63      53668.27|
|  8:  2.4946 -  2.3865  1308   143  0.45  56.26   0.87     0.63      50802.98|
|  9:  2.3865 -  2.2949  1328   151  0.43  57.88   0.90     0.63      48062.27|
| 10:  2.2949 -  2.2160  1329   143  0.44  57.23   0.93     0.63      45213.88|
| 11:  2.2160 -  2.1469  1290   142  0.42  58.43   0.91     0.63      41136.77|
| 12:  2.1469 -  2.0857  1329   152  0.41  59.31   0.91     0.63      37889.53|
| 13:  2.0857 -  2.0309  1182   134  0.41  59.14   0.93     0.61      31671.22|
| 14:  2.0309 -  1.9815   326    33  0.42  58.36   0.93     0.62      25307.62|
|alpha:            min =        0.61 max =            0.78 mean =         0.66|
|beta:             min =    25307.62 max =       109267.00 mean =     64085.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.12|
|phase err.(test): min =        0.00 max =           89.98 mean =        51.95|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.952696              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.936   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.175229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.487   (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 |  1.291 -  1.652:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.652 -  2.013:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.013 -  2.374:       16 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.374 -  2.735:      199 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.735 -  3.096:     2300 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.096 -  3.457:     2245 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.457 -  3.817:     4165 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.817 -  4.178:     5103 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.178 -  4.539:     6236 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.539 -  4.900:     7648 |
|-----------------------------------------------------------------------------|
|-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 |        0.180 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.291 |       0.403 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4657   r_free= 0.4462   ksol= 0.00   Bsol= 0.00   scale= 0.878    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.278489                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4577   r_free= 0.4366   ksol= 0.27   Bsol= 20.00   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,4.22,-1.44,0.00,-0.00,-0.00); trace/3= 0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.273272                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.812964              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.680   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.105193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4577      final r-factor (work) = 0.3822          |
| start r-factor (free) = 0.4366      final r-factor (free) = 0.4073          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5379 = 6.81 * 0.50 * 6.2699 + 1.00 * 0.1797                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.1396 = 6.81 * 0.50 * 6.1742 + 1.00 * 0.1073                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3822      final r-factor (work) = 0.3501          |
| start r-factor (free) = 0.4073      final r-factor (free) = 0.4172          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8297 = 1.11 * 1.00 * 6.1742 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7763 = 1.11 * 1.00 * 6.1142 + 1.00 * 0.0189                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.72   19.13    None  None   None       |
|    all(noH): 2823   0      0.00    95.72   19.13    None  None   None       |
|    Sol.    : 438    0      0.00    95.72   36.01    None  None   None       |
|    Mac.    : 2385   0      0.00    81.04   16.02    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 -   9.572:  796   |   5:    47.859 -  57.430:   80        |
|      1:     9.572 -  19.143:  926   |   6:    57.430 -  67.002:   36        |
|      2:    19.143 -  28.715:  533   |   7:    67.002 -  76.574:   24        |
|      3:    28.715 -  38.287:  265   |   8:    76.574 -  86.145:    7        |
|      4:    38.287 -  47.859:  153   |   9:    86.145 -  95.717:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3501 r_free = 0.4172             target_work(ml) = 6.120         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3499 r_free = 0.4181             target_work(ml) = 6.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3499   r_free= 0.4181   ksol= 0.27   Bsol= 20.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.17,4.22,-1.44,0.00,-0.00,-0.00); trace/3= 0.87                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.119144                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3495   r_free= 0.4166   ksol= 0.31   Bsol= 55.07   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,2.21,-0.71,0.00,-0.00,-0.00); trace/3= 0.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.120641                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.335052             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.156   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.870413              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.448  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3495      final r-factor (work) = 0.2922          |
| start r-factor (free) = 0.4166      final r-factor (free) = 0.3565          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.7655 = 11.34 * 0.50 * 6.1151 + 1.00 * 0.1078                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3739 = 11.34 * 0.50 * 6.0462 + 1.00 * 0.1072                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2922      final r-factor (work) = 0.2747          |
| start r-factor (free) = 0.3565      final r-factor (free) = 0.3526          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2814 = 0.87 * 1.00 * 6.0462 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1930 = 0.87 * 1.00 * 5.9471 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.90  19.12    None  None   None       |
|    all(noH): 2823   0      0.00    104.90  19.12    None  None   None       |
|    Sol.    : 438    0      1.79    104.90  38.17    None  None   None       |
|    Mac.    : 2385   0      0.00    91.02   15.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.491:  985   |   5:    52.452 -  62.943:   77        |
|      1:    10.491 -  20.981:  897   |   6:    62.943 -  73.433:   33        |
|      2:    20.981 -  31.471:  441   |   7:    73.433 -  83.924:   13        |
|      3:    31.471 -  41.962:  227   |   8:    83.924 -  94.414:    7        |
|      4:    41.962 -  52.452:  142   |   9:    94.414 - 104.905:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2747 r_free = 0.3526             target_work(ml) = 5.943         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2743 r_free = 0.3521             target_work(ml) = 5.943         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2743   r_free= 0.3521   ksol= 0.31   Bsol= 55.07   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.88,2.21,-0.71,0.00,-0.00,-0.00); trace/3= 0.21                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.942844                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2751   r_free= 0.3510   ksol= 0.32   Bsol= 65.26   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,1.68,-0.50,0.00,-0.00,-0.00); trace/3= 0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.944040                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.387083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.443  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.772806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.196  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2751      final r-factor (work) = 0.2208          |
| start r-factor (free) = 0.3510      final r-factor (free) = 0.2826          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0272 = 9.39 * 0.50 * 5.9486 + 1.00 * 0.1072                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.6023 = 9.39 * 0.50 * 5.8613 + 1.00 * 0.0920                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2208      final r-factor (work) = 0.1951          |
| start r-factor (free) = 0.2826      final r-factor (free) = 0.2556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4076 = 1.77 * 1.00 * 5.8613 + 1.00 * 0.0166                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0832 = 1.77 * 1.00 * 5.6775 + 1.00 * 0.0182                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.45  19.47    None  None   None       |
|    all(noH): 2823   0      0.00    109.45  19.47    None  None   None       |
|    Sol.    : 438    0      2.54    108.41  46.80    None  None   None       |
|    Mac.    : 2385   0      0.00    109.45  14.45    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 -  10.945: 1203   |   5:    54.724 -  65.669:   95        |
|      1:    10.945 -  21.890:  861   |   6:    65.669 -  76.614:   66        |
|      2:    21.890 -  32.835:  277   |   7:    76.614 -  87.559:   27        |
|      3:    32.835 -  43.780:  169   |   8:    87.559 -  98.504:   18        |
|      4:    43.780 -  54.724:   98   |   9:    98.504 - 109.449:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1951 r_free = 0.2556             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1950 r_free = 0.2556             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1950   r_free= 0.2556   ksol= 0.32   Bsol= 65.26   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,1.68,-0.50,0.00,-0.00,-0.00); trace/3= 0.23                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.635026                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1948   r_free= 0.2549   ksol= 0.34   Bsol= 84.09   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.23,-0.97,0.00,-0.00,-0.00); trace/3= -0.62                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.633870                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.545304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.149  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.218738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.597  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1948      final r-factor (work) = 0.1703          |
| start r-factor (free) = 0.2549      final r-factor (free) = 0.2208          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3207 = 2.55 * 0.50 * 5.6801 + 1.00 * 0.0920                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1543 = 2.55 * 0.50 * 5.5777 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1703      final r-factor (work) = 0.1651          |
| start r-factor (free) = 0.2208      final r-factor (free) = 0.2079          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2383 = 0.22 * 1.00 * 5.5777 + 1.00 * 0.0183                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2135 = 0.22 * 1.00 * 5.5010 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    104.71  17.82    None  None   None       |
|    all(noH): 2823   0      1.53    104.71  17.82    None  None   None       |
|    Sol.    : 438    0      4.79    104.71  42.61    None  None   None       |
|    Mac.    : 2385   0      1.53    103.21  13.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.531 -  11.849: 1408   |   5:    53.122 -  63.440:   81        |
|      1:    11.849 -  22.167:  801   |   6:    63.440 -  73.758:   40        |
|      2:    22.167 -  32.486:  211   |   7:    73.758 -  84.077:   17        |
|      3:    32.486 -  42.804:  126   |   8:    84.077 -  94.395:   14        |
|      4:    42.804 -  53.122:  119   |   9:    94.395 - 104.713:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1651 r_free = 0.2079             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1649 r_free = 0.2078             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2078   ksol= 0.34   Bsol= 84.09   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,0.23,-0.97,0.00,-0.00,-0.00); trace/3= -0.62                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.471583                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1649   r_free= 0.2084   ksol= 0.33   Bsol= 76.46   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.69,-1.32,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.472667                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.155625              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.534  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163316              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.562  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1649      final r-factor (work) = 0.1421          |
| start r-factor (free) = 0.2084      final r-factor (free) = 0.1849          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9865 = 2.16 * 0.50 * 5.5025 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8847 = 2.16 * 0.50 * 5.4026 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8925 = 0.16 * 1.00 * 5.4026 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8795 = 0.16 * 1.00 * 5.3292 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    104.81  17.37    None  None   None       |
|    all(noH): 2823   0      1.99    104.81  17.37    None  None   None       |
|    Sol.    : 438    0      4.68    104.81  41.74    None  None   None       |
|    Mac.    : 2385   0      1.99    100.30  12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.985 -  12.267: 1543   |   5:    53.396 -  63.678:   77        |
|      1:    12.267 -  22.549:  725   |   6:    63.678 -  73.960:   38        |
|      2:    22.549 -  32.831:  168   |   7:    73.960 -  84.242:   12        |
|      3:    32.831 -  43.113:  132   |   8:    84.242 -  94.524:    7        |
|      4:    43.113 -  53.396:  115   |   9:    94.524 - 104.806:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1829             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1380 r_free = 0.1830             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1380   r_free= 0.1830   ksol= 0.33   Bsol= 76.46   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.69,-1.32,-0.00,-0.00,-0.00); trace/3= -1.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.321868                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7303 0.99   1439  163 0.1037 0.1357      5.4184      5.6127|
|  2:  4.7303 -  3.7736 0.99   1377  146 0.0953 0.1156      5.5146      5.6882|
|  3:  3.7736 -  3.3022 0.99   1371  156 0.1267 0.1761      5.6141      5.9521|
|  4:  3.3022 -  3.0029 0.99   1339  148 0.1581 0.1833      5.6388      5.7664|
|  5:  3.0029 -  2.7891 0.98   1334  148 0.1731 0.2087      5.5444      5.6858|
|  6:  2.7891 -  2.6255 0.99   1348  152 0.1622 0.2264      5.4141      5.6029|
|  7:  2.6255 -  2.4946 0.98   1330  148 0.1546 0.2105      5.3432       5.561|
|  8:  2.4946 -  2.3865 0.99   1308  143 0.1565 0.1935      5.2581      5.4358|
|  9:  2.3865 -  2.2949 0.99   1328  151 0.1534 0.2164      5.2258      5.4394|
| 10:  2.2949 -  2.2160 0.98   1329  143 0.1442 0.2015      5.1662      5.4085|
| 11:  2.2160 -  2.1469 0.97   1290  142 0.1381 0.2137      5.0927      5.3624|
| 12:  2.1469 -  2.0857 0.99   1329  152 0.1414 0.2004      5.0322        5.25|
| 13:  2.0857 -  2.0309 0.89   1182  134 0.1486 0.2080      4.9672      5.1651|
| 14:  2.0309 -  1.9815 0.24    326   33 0.1375 0.1625      4.8271      5.0298|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7303  1439   163  0.94   9.64   0.96     0.94       7676.91|
|  2:  4.7303 -  3.7736  1377   146  0.95   9.05   1.00     0.99      10306.19|
|  3:  3.7736 -  3.3022  1371   156  0.91  13.84   1.01     1.01      13371.93|
|  4:  3.3022 -  3.0029  1339   148  0.89  17.29   1.00     0.97      14343.30|
|  5:  3.0029 -  2.7891  1334   148  0.86  20.62   0.99     0.97      12643.26|
|  6:  2.7891 -  2.6255  1348   152  0.87  19.65   0.99     0.96      10002.22|
|  7:  2.6255 -  2.4946  1330   148  0.88  18.85   0.98     0.94       8555.92|
|  8:  2.4946 -  2.3865  1308   143  0.87  19.31   1.00     0.96       7605.48|
|  9:  2.3865 -  2.2949  1328   151  0.87  19.60   0.99     0.93       6914.87|
| 10:  2.2949 -  2.2160  1329   143  0.88  19.00   0.99     0.94       6511.27|
| 11:  2.2160 -  2.1469  1290   142  0.87  19.84   0.99     0.94       5960.97|
| 12:  2.1469 -  2.0857  1329   152  0.88  19.27   0.98     0.95       5368.87|
| 13:  2.0857 -  2.0309  1182   134  0.87  19.64   0.98     0.98       4577.11|
| 14:  2.0309 -  1.9815   326    33  0.86  19.91   0.97     0.93       3574.54|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3574.54 max =        14343.30 mean =      8717.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           90.00 mean =        17.30|
|phase err.(test): min =        0.00 max =           89.31 mean =        16.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1382   r_free= 0.1832   ksol= 0.33   Bsol= 68.03   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-0.93,-1.15,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.323449                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.17 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1382   r_free= 0.1832   ksol= 0.33   Bsol= 68.03   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.75,-0.93,-1.15,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.323449                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1683 -  4.7303 0.99   1439  163 0.1049 0.1353      5.4332      5.6134|
|  2:  4.7303 -  3.7736 0.99   1377  146 0.0955 0.1164      5.5163      5.6929|
|  3:  3.7736 -  3.3022 0.99   1371  156 0.1271 0.1750       5.616      5.9476|
|  4:  3.3022 -  3.0029 0.99   1339  148 0.1580 0.1832      5.6385      5.7659|
|  5:  3.0029 -  2.7891 0.98   1334  148 0.1737 0.2094      5.5456      5.6879|
|  6:  2.7891 -  2.6255 0.99   1348  152 0.1622 0.2258      5.4146       5.601|
|  7:  2.6255 -  2.4946 0.98   1330  148 0.1545 0.2109       5.343      5.5604|
|  8:  2.4946 -  2.3865 0.99   1308  143 0.1563 0.1940      5.2585      5.4375|
|  9:  2.3865 -  2.2949 0.99   1328  151 0.1531 0.2167      5.2249      5.4391|
| 10:  2.2949 -  2.2160 0.98   1329  143 0.1442 0.2022      5.1663      5.4107|
| 11:  2.2160 -  2.1469 0.97   1290  142 0.1380 0.2135      5.0923      5.3618|
| 12:  2.1469 -  2.0857 0.99   1329  152 0.1415 0.2011      5.0336       5.253|
| 13:  2.0857 -  2.0309 0.89   1182  134 0.1486 0.2075      4.9672      5.1628|
| 14:  2.0309 -  1.9815 0.24    326   33 0.1378 0.1611      4.8258      5.0214|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1683 -  4.7303  1439   163  0.93   9.78   0.96     0.93       7787.98|
|  2:  4.7303 -  3.7736  1377   146  0.95   9.09   1.00     0.99      10373.42|
|  3:  3.7736 -  3.3022  1371   156  0.92  13.80   1.01     1.01      13327.37|
|  4:  3.3022 -  3.0029  1339   148  0.89  17.22   1.00     0.97      14273.60|
|  5:  3.0029 -  2.7891  1334   148  0.86  20.60   0.99     0.97      12613.15|
|  6:  2.7891 -  2.6255  1348   152  0.87  19.65   0.98     0.95      10005.33|
|  7:  2.6255 -  2.4946  1330   148  0.88  18.85   0.98     0.94       8557.65|
|  8:  2.4946 -  2.3865  1308   143  0.87  19.33   0.99     0.95       7623.80|
|  9:  2.3865 -  2.2949  1328   151  0.87  19.61   0.99     0.93       6923.52|
| 10:  2.2949 -  2.2160  1329   143  0.88  19.01   0.99     0.94       6523.31|
| 11:  2.2160 -  2.1469  1290   142  0.87  19.84   0.98     0.93       5962.68|
| 12:  2.1469 -  2.0857  1329   152  0.88  19.31   0.98     0.95       5389.64|
| 13:  2.0857 -  2.0309  1182   134  0.87  19.61   0.98     0.98       4567.30|
| 14:  2.0309 -  1.9815   326    33  0.86  19.85   0.97     0.93       3540.65|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     3540.65 max =        14273.60 mean =      8724.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.85 mean =        17.31|
|phase err.(test): min =        0.00 max =           89.38 mean =        16.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.279)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.91    104.73  17.30    None  None   None       |
|    all(noH): 2823   0      1.91    104.73  17.30    None  None   None       |
|    Sol.    : 438    0      4.61    104.73  41.67    None  None   None       |
|    Mac.    : 2385   0      1.91    100.23  12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.914 -  12.196: 1543   |   5:    53.324 -  63.606:   77        |
|      1:    12.196 -  22.478:  725   |   6:    63.606 -  73.888:   38        |
|      2:    22.478 -  32.760:  168   |   7:    73.888 -  84.170:   12        |
|      3:    32.760 -  43.042:  132   |   8:    84.170 -  94.452:    7        |
|      4:    43.042 -  53.324:  115   |   9:    94.452 - 104.734:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.641 - 5.762
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 338 from: 343
   mapped sites are within: 0.700 - 5.762

peak=    8.328 closest distance to " O   HOH Z  41 " =    1.477
peak=    6.625 closest distance to " O   HOH Z 400 " =    1.044
peak=    6.346 closest distance to " O   ARG A 275 " =    0.858
peak=    5.652 closest distance to " O   HOH Z 120 " =    1.156
peak=    5.214 closest distance to " CB  SER A  63 " =    1.325
peak=    4.987 closest distance to " O   HOH Z 210 " =    1.593
peak=    4.909 closest distance to " OG  SER A 276 " =    0.827
peak=    4.887 closest distance to " CB  GLN A 223 " =    1.459
peak=    4.771 closest distance to " O   HOH Z  15 " =    2.016
peak=    4.672 closest distance to " CG  PRO A 280 " =    0.956
peak=    4.658 closest distance to " O   PRO A 198 " =    1.585
peak=    4.622 closest distance to " O   HOH Z  61 " =    1.631
peak=    4.622 closest distance to " N   GLU A 277 " =    0.993
peak=    4.614 closest distance to " CA  TYR A  30 " =    1.034
peak=    4.606 closest distance to " O   HOH Z 111 " =    1.922
peak=    4.601 closest distance to " O   HOH Z 411 " =    2.762
peak=    4.587 closest distance to " O   HOH Z 433 " =    1.987
peak=    4.575 closest distance to " CG  PRO A  90 " =    1.274
peak=    4.561 closest distance to " NE2 HIS A 115 " =    1.131
peak=    4.557 closest distance to " NH2BARG A 102 " =    1.115
peak=    4.551 closest distance to " CG  GLN A  77 " =    0.828
peak=    4.542 closest distance to " O  BHOH Z 338 " =    1.127
peak=    4.541 closest distance to " CB  ARG A 275 " =    0.913
peak=    4.538 closest distance to " O   HOH Z 133 " =    2.065
peak=    4.495 closest distance to " O   HOH Z 134 " =    1.896
peak=    4.463 closest distance to " O   HOH Z  47 " =    1.831
peak=    4.462 closest distance to " CG  PRO A 198 " =    1.338
peak=    4.456 closest distance to " O   HOH Z 404 " =    1.466
peak=    4.442 closest distance to " CG  PRO A  54 " =    1.277
peak=    4.439 closest distance to " CG  PRO A 213 " =    1.351
peak=    4.394 closest distance to " N   ARG A 275 " =    0.863
peak=    4.373 closest distance to " O   HOH Z 209 " =    2.339
peak=    4.333 closest distance to " O   HOH Z 426 " =    1.316
peak=    4.319 closest distance to " O   HOH Z 389 " =    1.960
peak=    4.289 closest distance to " O   HOH Z  67 " =    2.089
peak=    4.282 closest distance to " CB  PRO A  54 " =    0.819
peak=    4.278 closest distance to " O   HOH Z 234 " =    3.800
peak=    4.274 closest distance to " CB  PRO A 198 " =    1.025
peak=    4.270 closest distance to " O   HOH Z 411 " =    1.517
peak=    4.265 closest distance to " CG2BVAL A  41 " =    0.910
peak=    4.257 closest distance to " O   HOH Z 350 " =    1.236
peak=    4.198 closest distance to " CE  LYS A 119 " =    1.215
peak=    4.197 closest distance to " CG AARG A 275 " =    1.115
peak=    4.195 closest distance to " O   HOH Z 418 " =    1.722
peak=    4.186 closest distance to " O   HOH Z 250 " =    2.258
peak=    4.186 closest distance to " CZ  PHE A 218 " =    1.044
peak=    4.181 closest distance to " CA  GLY A 196 " =    0.957
peak=    4.179 closest distance to " O   HOH Z 126 " =    1.814
peak=    4.156 closest distance to " OE1 GLN A  11 " =    2.111
peak=    4.152 closest distance to " CB  SER A  62 " =    0.863
peak=    4.141 closest distance to " O   HOH Z  83 " =    1.124
peak=    4.138 closest distance to " O   HOH Z  11 " =    1.126
peak=    4.131 closest distance to " CB  GLU A 277 " =    0.866
peak=    4.105 closest distance to " O   HOH Z 247 " =    1.565
peak=    4.087 closest distance to " OE1 GLN A  77 " =    0.927
peak=    4.079 closest distance to " CB  LEU A 228 " =    1.136
peak=    4.069 closest distance to " CB  TRP A 179 " =    1.546
peak=    4.051 closest distance to " CB  SER A  26 " =    0.875
peak=    4.050 closest distance to " OE1 GLN A  88 " =    0.894
peak=    4.042 closest distance to " CB  ASN A 148 " =    1.300
peak=    4.037 closest distance to " O   HOH Z 265 " =    2.022
peak=    4.036 closest distance to " CB  ALA A   1 " =    1.258
peak=    4.033 closest distance to " O   HOH Z 214 " =    1.538
peak=    4.014 closest distance to " O   HOH Z  78 " =    2.184
peak=    4.010 closest distance to " CG1 ILE A  33 " =    1.387
peak=    4.008 closest distance to " CB  GLN A  73 " =    1.006
peak=    3.994 closest distance to " O   HOH Z  78 " =    1.270
peak=    3.992 closest distance to " O   HOH Z 324 " =    1.693
peak=    3.985 closest distance to " O   HOH Z 215 " =    1.504
peak=    3.977 closest distance to " O   HOH Z  97 " =    1.976
peak=    3.976 closest distance to " CB  ASN A 285 " =    0.856
peak=    3.965 closest distance to " O   HOH Z   4 " =    1.255
peak=    3.964 closest distance to " O   SER A 276 " =    1.150
peak=    3.962 closest distance to " CB  TRP A 266 " =    0.941
peak=    3.947 closest distance to " O   HOH Z 271 " =    2.402
peak=    3.943 closest distance to " CB  MET A  47 " =    1.008
peak=    3.935 closest distance to " O   HOH Z 394 " =    1.700
peak=    3.924 closest distance to " CA  ASP A 191 " =    0.871
peak=    3.924 closest distance to " O   HOH Z  80 " =    2.274
peak=    3.916 closest distance to " OG  SER A 276 " =    1.241
peak=    3.896 closest distance to " O   HOH Z 128 " =    2.355
peak=    3.883 closest distance to " CB  GLN A  58 " =    1.007
peak=    3.879 closest distance to " O   HOH Z 432 " =    1.891
peak=    3.871 closest distance to " CB  ASN A 187 " =    1.190
peak=    3.839 closest distance to " O   HOH Z   7 " =    1.251
peak=    3.830 closest distance to " CB  ALA A 256 " =    1.486
peak=    3.830 closest distance to " N   SER A 164 " =    1.044
peak=    3.808 closest distance to " O   HOH Z  54 " =    1.244
peak=    3.803 closest distance to " O   HOH Z 422 " =    1.105
peak=    3.802 closest distance to " O   HOH Z  48 " =    1.936
peak=    3.799 closest distance to " N   ASN A  39 " =    1.117
peak=    3.795 closest distance to " O   HOH Z 369 " =    2.107
peak=    3.792 closest distance to " O   HOH Z 227 " =    1.862
peak=    3.791 closest distance to " CG2 VAL A 197 " =    1.322
peak=    3.789 closest distance to " CB  ARG A 190 " =    1.815
peak=    3.787 closest distance to " CB  SER A 141 " =    1.022
peak=    3.785 closest distance to " CA  GLU A 152 " =    0.965
peak=    3.780 closest distance to " NH1 ARG A 269 " =    0.816
peak=    3.778 closest distance to " CG1 VAL A 153 " =    1.122
peak=    3.778 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.765 closest distance to " CA  VAL A  41 " =    0.760
peak=    3.753 closest distance to " N   ILE A  33 " =    1.132
peak=    3.750 closest distance to " O   HOH Z 184 " =    1.436
peak=    3.750 closest distance to " O   HOH Z 124 " =    1.230
peak=    3.745 closest distance to " CB  VAL A 202 " =    1.447
peak=    3.736 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.733 closest distance to " OG  SER A  97 " =    3.468
peak=    3.726 closest distance to " CG1 ILE A 120 " =    1.103
peak=    3.722 closest distance to " O   HOH Z 200 " =    1.327
peak=    3.721 closest distance to " CB  GLN A 194 " =    0.898
peak=    3.717 closest distance to " CG2 THR A 220 " =    0.746
peak=    3.713 closest distance to " O   HOH Z 193 " =    2.149
peak=    3.709 closest distance to " O   HOH Z 132 " =    1.222
peak=    3.707 closest distance to " CB  GLU A 128 " =    1.117
peak=    3.705 closest distance to " CG2 VAL A  78 " =    1.066
peak=    3.705 closest distance to " CE BMET A  47 " =    1.354
peak=    3.705 closest distance to " O   HOH Z  40 " =    2.188
peak=    3.685 closest distance to " O   THR A 251 " =    1.331
peak=    3.683 closest distance to " O   HOH Z 301 " =    1.707
peak=    3.680 closest distance to " O   HOH Z 387 " =    2.525
peak=    3.677 closest distance to " CA  SER A  87 " =    0.831
peak=    3.671 closest distance to " O   HOH Z 174 " =    1.492
peak=    3.664 closest distance to " O   HOH Z 431 " =    1.439
peak=    3.662 closest distance to " O   HOH Z 272 " =    2.015
peak=    3.657 closest distance to " CB  GLN A 183 " =    1.174
peak=    3.655 closest distance to " CA  ILE A 106 " =    0.794
peak=    3.654 closest distance to " O   HOH Z 425 " =    1.678
peak=    3.641 closest distance to " CE3 TRP A 274 " =    3.611
peak=    3.637 closest distance to " N   LYS A 166 " =    0.847
peak=    3.628 closest distance to " O   HOH Z   1 " =    3.258
peak=    3.627 closest distance to " OD1 ASN A 301 " =    1.052
peak=    3.626 closest distance to " CA  ALA A  21 " =    1.476
peak=    3.623 closest distance to " O   HOH Z 406 " =    1.500
peak=    3.623 closest distance to " CA  GLN A 223 " =    0.908
peak=    3.621 closest distance to " CB  GLU A 152 " =    1.245
peak=    3.618 closest distance to " O   HOH Z 374 " =    2.697
peak=    3.611 closest distance to " CD  ARG A  66 " =    2.776
peak=    3.607 closest distance to " CD1 LEU A 222 " =    0.950
peak=    3.600 closest distance to " O   HOH Z 420 " =    2.267
peak=    3.598 closest distance to " CB  ARG A  79 " =    1.325
peak=    3.597 closest distance to " O   HOH Z 174 " =    1.751
peak=    3.592 closest distance to " O   HOH Z 189 " =    2.380
peak=    3.586 closest distance to " CA  THR A 294 " =    1.804
peak=    3.583 closest distance to " O   HOH Z  22 " =    2.616
peak=    3.576 closest distance to " O   HOH Z 196 " =    2.158
peak=    3.573 closest distance to " CG1 ILE A  49 " =    1.597
peak=    3.571 closest distance to " O   ALA A 165 " =    1.289
peak=    3.571 closest distance to " O   GLY A  91 " =    1.170
peak=    3.566 closest distance to " O   HOH Z 298 " =    1.979
peak=    3.565 closest distance to " CG  PRO A 243 " =    1.173
peak=    3.563 closest distance to " O   HOH Z  88 " =    3.467
peak=    3.563 closest distance to " ND2 ASN A 301 " =    1.025
peak=    3.548 closest distance to " O   HOH Z 327 " =    2.561
peak=    3.547 closest distance to " CA  LYS A  48 " =    1.443
peak=    3.547 closest distance to " O   HOH Z 104 " =    2.939
peak=    3.547 closest distance to " CB  PRO A  54 " =    1.272
peak=    3.543 closest distance to " O   HOH Z 133 " =    1.535
peak=    3.532 closest distance to " CD BLYS A 290 " =    1.037
peak=    3.528 closest distance to " O   HOH Z 327 " =    1.780
peak=    3.526 closest distance to " NZ  LYS A 193 " =    1.478
peak=    3.524 closest distance to " CA  ARG A 195 " =    1.143
peak=    3.515 closest distance to " O   HOH Z  49 " =    2.035
peak=    3.513 closest distance to " CD  ARG A 269 " =    0.808
peak=    3.510 closest distance to " CD1 TRP A 274 " =    1.036
peak=    3.510 closest distance to " O   HOH Z 234 " =    1.824
peak=    3.509 closest distance to " CB  GLN A  88 " =    1.097
peak=    3.505 closest distance to " O   HOH Z 402 " =    1.612
peak=    3.503 closest distance to " O   HOH Z 352 " =    1.948
peak=    3.499 closest distance to " O   HOH Z 134 " =    2.540
peak=    3.498 closest distance to " O   HOH Z 357 " =    2.167
peak=    3.498 closest distance to " O   HOH Z 207 " =    2.647
peak=    3.496 closest distance to " O   HOH Z 243 " =    1.070
peak=    3.496 closest distance to " CD1 TRP A 266 " =    1.158
peak=    3.492 closest distance to " CB  ASP A 140 " =    0.767
peak=    3.491 closest distance to " O   HOH Z 126 " =    1.934
peak=    3.490 closest distance to " CB  PHE A  61 " =    0.757
peak=    3.485 closest distance to " N   TYR A 116 " =    1.890
peak=    3.473 closest distance to " O   HOH Z 373 " =    1.751
peak=    3.469 closest distance to " CB  ALA A 100 " =    1.596
peak=    3.468 closest distance to " CB  LEU A  83 " =    0.851
peak=    3.445 closest distance to " O   HOH Z 163 " =    1.867
peak=    3.441 closest distance to " O   HOH Z  37 " =    0.967
peak=    3.439 closest distance to " CA  ILE A  33 " =    1.515
peak=    3.439 closest distance to " CA  GLU A  46 " =    1.005
peak=    3.438 closest distance to " O   HOH Z 139 " =    4.606
peak=    3.435 closest distance to " O   HOH Z 403 " =    1.871
peak=    3.435 closest distance to " CE1 TYR A 186 " =    1.428
peak=    3.427 closest distance to " O   HOH Z 362 " =    3.106
peak=    3.426 closest distance to " CD2 LEU A 297 " =    1.006
peak=    3.414 closest distance to " O   HOH Z 303 " =    2.437
peak=    3.412 closest distance to " O   HOH Z 162 " =    1.872
peak=    3.411 closest distance to " O   HOH Z 372 " =    1.195
peak=    3.410 closest distance to " CA  GLY A 229 " =    0.888
peak=    3.409 closest distance to " CB  PHE A  16 " =    1.398
peak=    3.407 closest distance to " N   PHE A 130 " =    1.232
peak=    3.406 closest distance to " CB  GLU A 236 " =    1.126
peak=    3.404 closest distance to " O   HOH Z 250 " =    1.515
peak=    3.398 closest distance to " O   HOH Z  21 " =    1.800
peak=    3.397 closest distance to " CB  SER A 276 " =    1.190
peak=    3.397 closest distance to " O   HOH Z  63 " =    1.574
peak=    3.393 closest distance to " CD2 TRP A 179 " =    1.311
peak=    3.388 closest distance to " CG2 ILE A 151 " =    0.794
peak=    3.387 closest distance to " C   VAL A 265 " =    1.152
peak=    3.384 closest distance to " O   HOH Z 139 " =    3.455
peak=    3.378 closest distance to " ND1 HIS A  81 " =    1.496
peak=    3.373 closest distance to " CB  GLU A 175 " =    1.324
peak=    3.369 closest distance to " CD1 LEU A   5 " =    1.293
peak=    3.365 closest distance to " O   VAL A  72 " =    1.167
peak=    3.358 closest distance to " CB  ILE A 199 " =    1.079
peak=    3.358 closest distance to " CB  ALA A 129 " =    0.867
peak=    3.356 closest distance to " O   SER A  87 " =    2.429
peak=    3.354 closest distance to " O   HOH Z 118 " =    1.915
peak=    3.353 closest distance to " O   HOH Z 423 " =    3.275
peak=    3.351 closest distance to " O   HOH Z 418 " =    5.762
peak=    3.350 closest distance to " O   HOH Z 155 " =    3.172
peak=    3.349 closest distance to " NH2 ARG A 156 " =    1.280
peak=    3.348 closest distance to " OE1 GLN A  58 " =    0.862
peak=    3.347 closest distance to " O   HOH Z 343 " =    2.467
peak=    3.347 closest distance to " O   HOH Z 437 " =    1.714
peak=    3.343 closest distance to " CG2 THR A  42 " =    0.912
peak=    3.332 closest distance to " O   HOH Z 176 " =    2.475
peak=    3.329 closest distance to " O   HOH Z 182 " =    0.967
peak=    3.326 closest distance to " O   HOH Z 395 " =    1.482
peak=    3.325 closest distance to " O   HOH Z  20 " =    2.001
peak=    3.322 closest distance to " O   HOH Z 240 " =    1.884
peak=    3.322 closest distance to " CB  TRP A 150 " =    1.044
peak=    3.317 closest distance to " N   TYR A  15 " =    0.841
peak=    3.314 closest distance to " CB  MET A 105 " =    1.120
peak=    3.308 closest distance to " O   HOH Z 171 " =    4.013
peak=    3.308 closest distance to " O   HOH Z 223 " =    1.311
peak=    3.307 closest distance to " O   HOH Z 132 " =    2.459
peak=    3.305 closest distance to " O   GLN A  11 " =    1.069
peak=    3.304 closest distance to " CA  HIS A 115 " =    1.012
peak=    3.303 closest distance to " CA  GLY A 241 " =    0.817
peak=    3.300 closest distance to " NZ  LYS A 166 " =    3.224
peak=    3.300 closest distance to " CG  LYS A 181 " =    0.700
peak=    3.297 closest distance to " O   HOH Z 287 " =    1.886
peak=    3.297 closest distance to " CD1 LEU A 300 " =    1.260
peak=    3.293 closest distance to " CA  ALA A   9 " =    1.172
peak=    3.291 closest distance to " O   HOH Z 416 " =    1.223
peak=    3.290 closest distance to " O   HOH Z 142 " =    1.565
peak=    3.290 closest distance to " CA  ARG A 139 " =    1.533
peak=    3.290 closest distance to " CB  ASP A 253 " =    1.061
peak=    3.288 closest distance to " CZ  PHE A 192 " =    0.950
peak=    3.288 closest distance to " O   HOH Z 151 " =    1.661
peak=    3.286 closest distance to " O   HOH Z  66 " =    2.094
peak=    3.286 closest distance to " O   HOH Z 325 " =    3.813
peak=    3.283 closest distance to " O   HOH Z 344 " =    3.389
peak=    3.282 closest distance to " CG2AVAL A 121 " =    1.997
peak=    3.281 closest distance to " O   HOH Z  54 " =    1.646
peak=    3.281 closest distance to " CE3 TRP A  85 " =    1.258
peak=    3.280 closest distance to " CD  PRO A  54 " =    1.004
peak=    3.279 closest distance to " CG ALYS A 290 " =    1.145
peak=    3.277 closest distance to " CA  ARG A  66 " =    1.076
peak=    3.277 closest distance to " CB  ALA A 137 " =    1.211
peak=    3.270 closest distance to " O   HOH Z 433 " =    3.819
peak=    3.263 closest distance to " CA  ALA A 100 " =    1.182
peak=    3.261 closest distance to " NE2 GLN A  89 " =    1.168
peak=    3.260 closest distance to " CE1 PHE A 208 " =    1.195
peak=    3.255 closest distance to " O   HOH Z 368 " =    1.984
peak=    3.251 closest distance to " O   HOH Z  50 " =    3.591
peak=    3.248 closest distance to " O   HOH Z 272 " =    1.410
peak=    3.247 closest distance to " CD  LYS A 166 " =    1.450
peak=    3.246 closest distance to " O   HOH Z 192 " =    1.842
peak=    3.236 closest distance to " CA  THR A 246 " =    1.209
peak=    3.235 closest distance to " O   HOH Z 150 " =    1.864
peak=    3.231 closest distance to " NE2 HIS A  86 " =    1.328
peak=    3.228 closest distance to " O   HOH Z 428 " =    1.127
peak=    3.228 closest distance to " C   ILE A 106 " =    1.816
peak=    3.226 closest distance to " CD  ARG A  56 " =    1.224
peak=    3.222 closest distance to " O   HOH Z 316 " =    3.058
peak=    3.221 closest distance to " NZ  LYS A 117 " =    3.096
peak=    3.220 closest distance to " CA  ASP A 124 " =    0.912
peak=    3.216 closest distance to " NZ  LYS A 181 " =    0.722
peak=    3.216 closest distance to " O   HOH Z  32 " =    1.957
peak=    3.209 closest distance to " NH1BARG A 145 " =    1.976
peak=    3.207 closest distance to " CB  TYR A 169 " =    1.225
peak=    3.201 closest distance to " O   ASN A 217 " =    1.229
peak=    3.200 closest distance to " CB  SER A 276 " =    0.986
peak=    3.198 closest distance to " N   THR A  52 " =    1.086
peak=    3.196 closest distance to " CA  LYS A 117 " =    1.209
peak=    3.195 closest distance to " CA  TRP A 274 " =    1.012
peak=    3.194 closest distance to " O   HOH Z  43 " =    1.878
peak=    3.193 closest distance to " CB  ARG A 275 " =    1.506
peak=    3.192 closest distance to " CD  GLU A 236 " =    1.205
peak=    3.189 closest distance to " N   ALA A 233 " =    0.984
peak=    3.188 closest distance to " OD1 ASN A  69 " =    2.476
peak=    3.187 closest distance to " O   HOH Z 281 " =    4.196
peak=    3.185 closest distance to " CZ3 TRP A  85 " =    0.958
peak=    3.185 closest distance to " O   HOH Z 215 " =    2.229
peak=    3.181 closest distance to " O   HOH Z 294 " =    1.667
peak=    3.181 closest distance to " CE  MET A 188 " =    1.549
peak=    3.180 closest distance to " CB  ALA A 104 " =    0.852
peak=    3.177 closest distance to " CA  LEU A 282 " =    0.963
peak=    3.172 closest distance to " O   HOH Z 427 " =    1.167
peak=    3.170 closest distance to " O   HOH Z 245 " =    1.476
peak=    3.170 closest distance to " O   HOH Z 180 " =    2.185
peak=    3.170 closest distance to " CD  LYS A 119 " =    1.421
peak=    3.169 closest distance to " O   SER A  26 " =    2.014
peak=    3.169 closest distance to " CB  PHE A 283 " =    1.044
peak=    3.168 closest distance to " O   HOH Z 435 " =    2.038
peak=    3.167 closest distance to " CG2 ILE A 120 " =    0.971
peak=    3.166 closest distance to " O   HOH Z 409 " =    3.121
peak=    3.165 closest distance to " CB  ASN A  45 " =    0.964
peak=    3.161 closest distance to " O   HOH Z  49 " =    0.857
peak=    3.160 closest distance to " O   HOH Z  44 " =    1.660
peak=    3.159 closest distance to " O   HOH Z  64 " =    2.162
peak=    3.157 closest distance to " NH1 ARG A  14 " =    1.242
peak=    3.152 closest distance to " CB  ASN A 148 " =    1.741
peak=    3.151 closest distance to " CA  GLY A  75 " =    1.008
peak=    3.151 closest distance to " CA  ALA A 248 " =    1.191
peak=    3.149 closest distance to " CA  LEU A  83 " =    1.501
peak=    3.142 closest distance to " NH1 ARG A  56 " =    1.569
peak=    3.139 closest distance to " O   ALA A  84 " =    1.135
peak=    3.137 closest distance to " O   HOH Z 380 " =    1.860
peak=    3.135 closest distance to " NH1BARG A 145 " =    1.120
peak=    3.134 closest distance to " CE3 TRP A 150 " =    1.191
peak=    3.130 closest distance to " O   HOH Z 298 " =    4.195
peak=    3.130 closest distance to " O   HOH Z  88 " =    1.607
peak=    3.129 closest distance to " CB  ALA A  51 " =    0.785
peak=    3.129 closest distance to " CA  ALA A 160 " =    1.082
peak=    3.127 closest distance to " CD  ARG A 195 " =    0.954
peak=    3.125 closest distance to " CB  ALA A  71 " =    1.190
peak=    3.125 closest distance to " O   HOH Z 377 " =    1.631
peak=    3.118 closest distance to " CA  VAL A 112 " =    1.216
peak=    3.117 closest distance to " CA  ALA A 299 " =    1.191
peak=    3.115 closest distance to " O   HOH Z 336 " =    1.594
peak=    3.115 closest distance to " CB  PRO A  90 " =    1.323
peak=    3.106 closest distance to " CG  GLN A 205 " =    1.273
peak=    3.106 closest distance to " OD1 ASP A 238 " =    0.914
peak=    3.090 closest distance to " CG2 ILE A  20 " =    1.179
peak=    3.089 closest distance to " O   HOH Z 358 " =    1.564
peak=    3.087 closest distance to " NE2 GLN A 278 " =    2.469
peak=    3.080 closest distance to " OD2 ASP A 286 " =    3.107
peak=    3.077 closest distance to " N   ARG A 156 " =    1.447
peak=    3.074 closest distance to " CG  LYS A  76 " =    1.115
peak=    3.062 closest distance to " CB  ALA A 291 " =    1.182
peak=    3.042 closest distance to " CD  ARG A  66 " =    2.652

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.342 - 5.693
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 225
   mapped sites are within: 0.745 - 5.693

peak=   -5.554 closest distance to " N   ARG A 275 " =    0.798
peak=   -4.608 closest distance to " O   HOH Z 166 " =    1.513
peak=   -4.602 closest distance to " CA  GLU A 277 " =    1.194
peak=   -4.481 closest distance to " CB  SER A 276 " =    1.006
peak=   -4.255 closest distance to " O   HOH Z 184 " =    0.970
peak=   -4.239 closest distance to " CD1 PHE A  59 " =    1.872
peak=   -4.202 closest distance to " O   HOH Z 290 " =    0.896
peak=   -4.183 closest distance to " O   HOH Z 407 " =    0.745
peak=   -4.161 closest distance to " C   ASN A 285 " =    2.609
peak=   -4.145 closest distance to " CD  GLN A 223 " =    0.872
peak=   -4.140 closest distance to " O   ARG A 275 " =    0.820
peak=   -4.118 closest distance to " O   HOH Z  37 " =    1.367
peak=   -4.098 closest distance to " CB  LEU A 167 " =    2.113
peak=   -4.065 closest distance to " NH2 ARG A  66 " =    1.003
peak=   -4.027 closest distance to " O   HOH Z 411 " =    4.435
peak=   -4.006 closest distance to " O   HOH Z 151 " =    1.254
peak=   -3.958 closest distance to " CD  GLN A  88 " =    0.882
peak=   -3.932 closest distance to " CA  GLY A 203 " =    2.231
peak=   -3.909 closest distance to " CA  ASN A 127 " =    1.127
peak=   -3.879 closest distance to " CB  SER A 146 " =    2.077
peak=   -3.867 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.866 closest distance to " O   HOH Z  13 " =    1.706
peak=   -3.822 closest distance to " O   HOH Z 418 " =    1.403
peak=   -3.815 closest distance to " CG2 ILE A  49 " =    2.618
peak=   -3.813 closest distance to " N   ALA A  43 " =    2.771
peak=   -3.808 closest distance to " O   GLN A  11 " =    1.023
peak=   -3.807 closest distance to " O   ALA A   1 " =    2.050
peak=   -3.788 closest distance to " C   THR A 279 " =    1.155
peak=   -3.765 closest distance to " CD  GLN A 223 " =    1.652
peak=   -3.765 closest distance to " O   HOH Z  38 " =    0.870
peak=   -3.756 closest distance to " CB  ALA A  43 " =    2.647
peak=   -3.726 closest distance to " C   SER A 271 " =    1.295
peak=   -3.705 closest distance to " O   HOH Z 423 " =    1.169
peak=   -3.703 closest distance to " O   HOH Z   5 " =    1.494
peak=   -3.702 closest distance to " O   HOH Z  11 " =    1.080
peak=   -3.699 closest distance to " O   HOH Z 210 " =    0.930
peak=   -3.696 closest distance to " CA  GLY A  23 " =    2.288
peak=   -3.692 closest distance to " NH2 ARG A  66 " =    1.032
peak=   -3.692 closest distance to " O   HOH Z 422 " =    1.041
peak=   -3.691 closest distance to " O   HOH Z 325 " =    1.547
peak=   -3.691 closest distance to " O   HOH Z  19 " =    2.026
peak=   -3.685 closest distance to " OH  TYR A 169 " =    0.921
peak=   -3.676 closest distance to " O   HOH Z 348 " =    2.363
peak=   -3.668 closest distance to " O   HOH Z 281 " =    4.858
peak=   -3.667 closest distance to " O   PRO A 198 " =    1.361
peak=   -3.664 closest distance to " CG  PRO A 243 " =    1.499
peak=   -3.657 closest distance to " O   HOH Z 128 " =    4.340
peak=   -3.657 closest distance to " N   SER A 134 " =    1.136
peak=   -3.656 closest distance to " CG2 ILE A  20 " =    2.966
peak=   -3.652 closest distance to " O   HOH Z  71 " =    1.470
peak=   -3.636 closest distance to " O   HOH Z  91 " =    2.256
peak=   -3.636 closest distance to " O   HOH Z   7 " =    1.007
peak=   -3.634 closest distance to " OG  SER A  97 " =    2.191
peak=   -3.621 closest distance to " O   ALA A   7 " =    1.651
peak=   -3.604 closest distance to " O   HOH Z 198 " =    1.495
peak=   -3.578 closest distance to " O   HOH Z 109 " =    3.404
peak=   -3.572 closest distance to " CG  ARG A 269 " =    2.402
peak=   -3.571 closest distance to " O   HOH Z  52 " =    1.761
peak=   -3.568 closest distance to " O   HOH Z 308 " =    1.236
peak=   -3.563 closest distance to " O   HOH Z 103 " =    2.447
peak=   -3.562 closest distance to " O   TYR A  15 " =    1.509
peak=   -3.557 closest distance to " O   PHE A 218 " =    1.326
peak=   -3.556 closest distance to " O   VAL A 174 " =    2.004
peak=   -3.546 closest distance to " O   ARG A 275 " =    1.035
peak=   -3.539 closest distance to " CD  ARG A  14 " =    3.303
peak=   -3.537 closest distance to " O   HOH Z 222 " =    1.266
peak=   -3.534 closest distance to " OD1 ASN A 148 " =    1.424
peak=   -3.533 closest distance to " N   GLN A  58 " =    1.599
peak=   -3.519 closest distance to " O   HOH Z   7 " =    1.569
peak=   -3.510 closest distance to " O   VAL A  67 " =    2.785
peak=   -3.508 closest distance to " CA  SER A 276 " =    1.324
peak=   -3.508 closest distance to " ND2 ASN A  60 " =    1.325
peak=   -3.506 closest distance to " CB  ALA A 291 " =    2.459
peak=   -3.505 closest distance to " OG1 THR A  82 " =    1.875
peak=   -3.504 closest distance to " CA  SER A 164 " =    2.152
peak=   -3.494 closest distance to " O   HOH Z 186 " =    1.507
peak=   -3.482 closest distance to " O   HOH Z 124 " =    1.266
peak=   -3.481 closest distance to " O   HOH Z 313 " =    1.269
peak=   -3.480 closest distance to " O   HOH Z 414 " =    1.761
peak=   -3.477 closest distance to " CA  VAL A 197 " =    1.077
peak=   -3.473 closest distance to " CA  ALA A 137 " =    2.584
peak=   -3.470 closest distance to " OD2 ASP A 171 " =    2.287
peak=   -3.463 closest distance to " O   HOH Z 120 " =    0.942
peak=   -3.452 closest distance to " O   VAL A 121 " =    0.896
peak=   -3.451 closest distance to " CD2 LEU A 237 " =    2.389
peak=   -3.446 closest distance to " O   THR A  18 " =    1.581
peak=   -3.440 closest distance to " O   HOH Z 414 " =    1.593
peak=   -3.436 closest distance to " OE2 GLU A   2 " =    1.345
peak=   -3.431 closest distance to " OD1 ASP A 298 " =    1.996
peak=   -3.430 closest distance to " OXT GLY A 302 " =    3.103
peak=   -3.423 closest distance to " CB  ALA A 291 " =    2.486
peak=   -3.421 closest distance to " O   HOH Z  60 " =    1.970
peak=   -3.410 closest distance to " OD1 ASP A 191 " =    1.784
peak=   -3.408 closest distance to " CE  MET A  93 " =    1.272
peak=   -3.405 closest distance to " O   ALA A 256 " =    1.665
peak=   -3.398 closest distance to " O   HOH Z 185 " =    2.497
peak=   -3.393 closest distance to " O   HOH Z 400 " =    0.975
peak=   -3.391 closest distance to " CD  GLU A 236 " =    1.014
peak=   -3.390 closest distance to " CG  GLN A  58 " =    1.131
peak=   -3.388 closest distance to " CB  ALA A 131 " =    2.395
peak=   -3.387 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.387 closest distance to " CD2 TRP A 274 " =    2.340
peak=   -3.380 closest distance to " CD2 PHE A  59 " =    2.224
peak=   -3.379 closest distance to " O   HOH Z 207 " =    1.259
peak=   -3.379 closest distance to " NZ  LYS A 119 " =    1.723
peak=   -3.377 closest distance to " CB  CYS A 254 " =    2.240
peak=   -3.376 closest distance to " O   HOH Z 186 " =    3.694
peak=   -3.375 closest distance to " CG  MET A 105 " =    0.847
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.348
peak=   -3.366 closest distance to " CB  ALA A  10 " =    1.959
peak=   -3.364 closest distance to " O   HOH Z  17 " =    1.244
peak=   -3.359 closest distance to " O   GLY A 118 " =    2.333
peak=   -3.355 closest distance to " O   HOH Z 200 " =    1.322
peak=   -3.350 closest distance to " O   HOH Z 400 " =    1.132
peak=   -3.344 closest distance to " CD  GLN A  77 " =    1.105
peak=   -3.341 closest distance to " OE1 GLN A  88 " =    1.006
peak=   -3.338 closest distance to " O   HOH Z  90 " =    3.428
peak=   -3.336 closest distance to " OD1 ASN A 301 " =    0.804
peak=   -3.332 closest distance to " O   HOH Z 275 " =    1.869
peak=   -3.327 closest distance to " CB  ASN A 215 " =    1.872
peak=   -3.326 closest distance to " O   HOH Z 118 " =    5.693
peak=   -3.326 closest distance to " OD2 ASP A 171 " =    1.938
peak=   -3.323 closest distance to " O   HOH Z 322 " =    1.613
peak=   -3.323 closest distance to " O   HOH Z 275 " =    1.592
peak=   -3.320 closest distance to " CB  PRO A 243 " =    2.773
peak=   -3.319 closest distance to " ND2 ASN A  45 " =    1.484
peak=   -3.318 closest distance to " CG  LEU A  83 " =    1.899
peak=   -3.316 closest distance to " CB  ALA A 161 " =    2.691
peak=   -3.313 closest distance to " CD1 LEU A  25 " =    2.547
peak=   -3.309 closest distance to " C   HIS A 108 " =    1.087
peak=   -3.302 closest distance to " O   HOH Z 426 " =    0.943
peak=   -3.301 closest distance to " C   SER A 206 " =    1.541
peak=   -3.299 closest distance to " O   HOH Z 221 " =    1.374
peak=   -3.290 closest distance to " CG  ARG A 219 " =    2.391
peak=   -3.284 closest distance to " CE  MET A 105 " =    2.144
peak=   -3.284 closest distance to " CA  PRO A 198 " =    1.196
peak=   -3.282 closest distance to " O   HOH Z  23 " =    1.653
peak=   -3.280 closest distance to " CG1 VAL A 125 " =    2.140
peak=   -3.280 closest distance to " O   HOH Z  30 " =    0.917
peak=   -3.280 closest distance to " OG  SER A  26 " =    1.306
peak=   -3.278 closest distance to " O   HOH Z 241 " =    0.946
peak=   -3.275 closest distance to " CZ  ARG A 259 " =    0.837
peak=   -3.274 closest distance to " CB  GLN A  55 " =    1.553
peak=   -3.268 closest distance to " O   HOH Z 251 " =    1.815
peak=   -3.268 closest distance to " O   HOH Z 407 " =    1.684
peak=   -3.267 closest distance to " O   HOH Z 388 " =    1.984
peak=   -3.265 closest distance to " O   HOH Z  93 " =    2.020
peak=   -3.263 closest distance to " N   THR A 157 " =    1.734
peak=   -3.258 closest distance to " O   HOH Z 290 " =    1.220
peak=   -3.247 closest distance to " O   HOH Z 298 " =    2.991
peak=   -3.246 closest distance to " O   HOH Z 111 " =    1.160
peak=   -3.242 closest distance to " N   THR A 235 " =    1.107
peak=   -3.237 closest distance to " O   HOH Z 221 " =    1.411
peak=   -3.236 closest distance to " O   HOH Z 207 " =    2.279
peak=   -3.230 closest distance to " O   HOH Z 177 " =    1.645
peak=   -3.224 closest distance to " O   GLY A 196 " =    1.168
peak=   -3.223 closest distance to " O   HOH Z  43 " =    1.593
peak=   -3.222 closest distance to " N   GLU A 277 " =    0.886
peak=   -3.221 closest distance to " CD  GLN A 223 " =    1.011
peak=   -3.218 closest distance to " O   HOH Z 157 " =    3.717
peak=   -3.218 closest distance to " O   HOH Z 198 " =    2.391
peak=   -3.216 closest distance to " SD  MET A  93 " =    1.435
peak=   -3.214 closest distance to " CH2 TRP A 179 " =    1.063
peak=   -3.211 closest distance to " CG  ASP A  50 " =    2.342
peak=   -3.209 closest distance to " O   HOH Z 256 " =    2.270
peak=   -3.207 closest distance to " OG  SER A  87 " =    1.861
peak=   -3.205 closest distance to " CA  GLY A 241 " =    3.256
peak=   -3.205 closest distance to " OE1 GLN A  88 " =    2.828
peak=   -3.204 closest distance to " O   HOH Z 370 " =    2.391
peak=   -3.202 closest distance to " SG  CYS A 254 " =    3.268
peak=   -3.202 closest distance to " O   HOH Z 396 " =    1.327
peak=   -3.199 closest distance to " CE2 PHE A  38 " =    1.876
peak=   -3.197 closest distance to " NH2 ARG A 269 " =    2.404
peak=   -3.196 closest distance to " CG2 VAL A 189 " =    2.124
peak=   -3.196 closest distance to " CD2 TRP A  85 " =    1.170
peak=   -3.195 closest distance to " O   HOH Z 401 " =    1.292
peak=   -3.192 closest distance to " O   HOH Z 219 " =    2.491
peak=   -3.189 closest distance to " C   ALA A 158 " =    1.314
peak=   -3.187 closest distance to " O   HOH Z 113 " =    2.273
peak=   -3.185 closest distance to " O   HOH Z 234 " =    4.355
peak=   -3.177 closest distance to " O  BHOH Z 338 " =    0.842
peak=   -3.165 closest distance to " CD2 PHE A  61 " =    1.815
peak=   -3.163 closest distance to " OG ASER A 134 " =    1.260
peak=   -3.163 closest distance to " CD  ARG A 156 " =    2.014
peak=   -3.162 closest distance to " O   VAL A 125 " =    2.132
peak=   -3.157 closest distance to " O   HOH Z 166 " =    2.205
peak=   -3.154 closest distance to " CH2 TRP A 177 " =    2.109
peak=   -3.152 closest distance to " O   HOH Z 402 " =    1.098
peak=   -3.148 closest distance to " CA  GLY A 241 " =    2.284
peak=   -3.147 closest distance to " O   HOH Z 436 " =    1.310
peak=   -3.137 closest distance to " CE2 PHE A  61 " =    2.482
peak=   -3.137 closest distance to " NH2 ARG A 156 " =    1.104
peak=   -3.136 closest distance to " O   HOH Z 174 " =    2.004
peak=   -3.135 closest distance to " O   HOH Z 250 " =    1.134
peak=   -3.135 closest distance to " N   ILE A 120 " =    1.121
peak=   -3.130 closest distance to " CA  VAL A 232 " =    2.382
peak=   -3.128 closest distance to " OG  SER A  32 " =    1.150
peak=   -3.128 closest distance to " CE3 TRP A 150 " =    1.161
peak=   -3.126 closest distance to " CB  ALA A   9 " =    2.741
peak=   -3.120 closest distance to " O   HOH Z  83 " =    1.376
peak=   -3.118 closest distance to " O   HOH Z 136 " =    1.819
peak=   -3.118 closest distance to " N   GLY A  17 " =    1.718
peak=   -3.114 closest distance to " CD  PRO A 198 " =    1.086
peak=   -3.113 closest distance to " CG  LYS A 166 " =    1.878
peak=   -3.109 closest distance to " O   HOH Z 422 " =    1.417
peak=   -3.108 closest distance to " O   HOH Z 428 " =    1.145
peak=   -3.107 closest distance to " OD1 ASN A 173 " =    1.433
peak=   -3.105 closest distance to " O   HOH Z 231 " =    1.455
peak=   -3.088 closest distance to " CE3 TRP A 150 " =    2.197
peak=   -3.080 closest distance to " O   HOH Z 295 " =    1.455
peak=   -3.056 closest distance to " C   ASP A 270 " =    0.810
peak=   -3.048 closest distance to " CD2 LEU A 237 " =    2.598
peak=   -3.045 closest distance to " O   ALA A 158 " =    1.126
peak=   -3.003 closest distance to " O   HOH Z 423 " =    1.042

================= 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    :  0.4657 0.4462   6.278489e+00   6.252608e+00
   1_bss:  0.4577 0.4366   6.273272e+00   6.242422e+00
   1_xyz:  0.3822 0.4073   6.161828e+00   6.199869e+00
   1_adp:  0.3501 0.4172   6.119597e+00   6.208141e+00
   1_occ:  0.3499 0.4181   6.119144e+00   6.208875e+00
   2_bss:  0.3495 0.4166   6.120641e+00   6.208718e+00
   2_xyz:  0.2922 0.3565   5.969913e+00   6.111247e+00
   2_adp:  0.2747 0.3526   5.943346e+00   6.100840e+00
   2_occ:  0.2743 0.3521   5.942844e+00   6.100810e+00
   3_bss:  0.2751 0.3510   5.944040e+00   6.101213e+00
   3_xyz:  0.2208 0.2826   5.733466e+00   5.911016e+00
   3_adp:  0.1951 0.2556   5.635462e+00   5.834263e+00
   3_occ:  0.1950 0.2556   5.635026e+00   5.833761e+00
   4_bss:  0.1948 0.2549   5.633870e+00   5.832370e+00
   4_xyz:  0.1703 0.2208   5.506528e+00   5.712323e+00
   4_adp:  0.1651 0.2079   5.472257e+00   5.657252e+00
   4_occ:  0.1649 0.2078   5.471583e+00   5.656508e+00
   5_bss:  0.1649 0.2084   5.472667e+00   5.657070e+00
   5_xyz:  0.1421 0.1849   5.341419e+00   5.543851e+00
   5_adp:  0.1381 0.1829   5.321968e+00   5.529544e+00
   5_occ:  0.1380 0.1830   5.321868e+00   5.529917e+00
   5_bss:  0.1382 0.1832   5.323449e+00   5.530060e+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:  0.274  20.000  -0.169   4.221  -1.435   0.000  -0.000  -0.000
   1_xyz:  0.274  20.000  -0.169   4.221  -1.435   0.000  -0.000  -0.000
   1_adp:  0.274  20.000  -0.169   4.221  -1.435   0.000  -0.000  -0.000
   1_occ:  0.274  20.000  -0.169   4.221  -1.435   0.000  -0.000  -0.000
   2_bss:  0.311  55.066  -0.877   2.210  -0.710   0.000  -0.000  -0.000
   2_xyz:  0.311  55.066  -0.877   2.210  -0.710   0.000  -0.000  -0.000
   2_adp:  0.311  55.066  -0.877   2.210  -0.710   0.000  -0.000  -0.000
   2_occ:  0.311  55.066  -0.877   2.210  -0.710   0.000  -0.000  -0.000
   3_bss:  0.323  65.260  -0.492   1.684  -0.497   0.000  -0.000  -0.000
   3_xyz:  0.323  65.260  -0.492   1.684  -0.497   0.000  -0.000  -0.000
   3_adp:  0.323  65.260  -0.492   1.684  -0.497   0.000  -0.000  -0.000
   3_occ:  0.323  65.260  -0.492   1.684  -0.497   0.000  -0.000  -0.000
   4_bss:  0.336  84.089  -1.123   0.228  -0.965   0.000  -0.000  -0.000
   4_xyz:  0.336  84.089  -1.123   0.228  -0.965   0.000  -0.000  -0.000
   4_adp:  0.336  84.089  -1.123   0.228  -0.965   0.000  -0.000  -0.000
   4_occ:  0.336  84.089  -1.123   0.228  -0.965   0.000  -0.000  -0.000
   5_bss:  0.331  76.459  -1.796  -0.690  -1.316  -0.000  -0.000  -0.000
   5_xyz:  0.331  76.459  -1.796  -0.690  -1.316  -0.000  -0.000  -0.000
   5_adp:  0.331  76.459  -1.796  -0.690  -1.316  -0.000  -0.000  -0.000
   5_occ:  0.331  76.459  -1.796  -0.690  -1.316  -0.000  -0.000  -0.000
   5_bss:  0.325  68.030  -1.746  -0.933  -1.152  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.102 0.4961  0.6615    64082.314
   1_bss:  51.399 0.5034  0.6906    61013.606
   1_xyz:  46.910 0.5588  0.7531    50897.061
   1_adp:  48.362 0.5400  0.7358    52601.789
   1_occ:  48.429 0.5391  0.7337    52715.318
   2_bss:  48.260 0.5412  0.7241    52487.155
   2_xyz:  40.044 0.6403  0.8458    36526.363
   2_adp:  39.100 0.6520  0.8417    35482.249
   2_occ:  39.083 0.6522  0.8413    35465.960
   3_bss:  39.032 0.6528  0.8432    35373.870
   3_xyz:  29.316 0.7638  0.9552    20963.239
   3_adp:  26.084 0.7994  0.9659    17540.186
   3_occ:  26.071 0.7995  0.9659    17524.791
   4_bss:  25.977 0.8004  0.9392    17423.400
   4_xyz:  22.185 0.8390  0.9623    12852.267
   4_adp:  20.275 0.8590  0.9686    11377.136
   4_occ:  20.263 0.8592  0.9688    11373.857
   5_bss:  20.264 0.8592  0.9477    11394.262
   5_xyz:  17.629 0.8837  0.9623     8915.025
   5_adp:  17.218 0.8877  0.9591     8706.946
   5_occ:  17.223 0.8877  0.9591     8717.639
   5_bss:  17.230 0.8876  0.9564     8724.604
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.7970e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.7970e-01
   1_xyz:   1.424  0.010  0.087 15.473  0.005  4.115   1.0734e-01
   1_adp:   1.424  0.010  0.087 15.473  0.005  4.115   1.0734e-01
   1_occ:   1.424  0.010  0.087 15.473  0.005  4.115   1.0734e-01
   2_bss:   1.424  0.010  0.087 15.473  0.005  4.115   1.0734e-01
   2_xyz:   1.392  0.010  0.090 15.342  0.006  4.108   1.0722e-01
   2_adp:   1.392  0.010  0.090 15.342  0.006  4.108   1.0722e-01
   2_occ:   1.392  0.010  0.090 15.342  0.006  4.108   1.0722e-01
   3_bss:   1.392  0.010  0.090 15.342  0.006  4.108   1.0722e-01
   3_xyz:   1.285  0.011  0.082 14.976  0.005  4.114   9.1969e-02
   3_adp:   1.285  0.011  0.082 14.976  0.005  4.114   9.1969e-02
   3_occ:   1.285  0.011  0.082 14.976  0.005  4.114   9.1969e-02
   4_bss:   1.285  0.011  0.082 14.976  0.005  4.114   9.1969e-02
   4_xyz:   0.972  0.006  0.071 14.279  0.003  4.124   5.5804e-02
   4_adp:   0.972  0.006  0.071 14.279  0.003  4.124   5.5804e-02
   4_occ:   0.972  0.006  0.071 14.279  0.003  4.124   5.5804e-02
   5_bss:   0.972  0.006  0.071 14.279  0.003  4.124   5.5804e-02
   5_xyz:   1.038  0.008  0.073 14.362  0.003  4.115   6.1752e-02
   5_adp:   1.038  0.008  0.073 14.362  0.003  4.115   6.1752e-02
   5_occ:   1.038  0.008  0.073 14.362  0.003  4.115   6.1752e-02
   5_bss:   1.038  0.008  0.073 14.362  0.003  4.115   6.1752e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.291   2.4468e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.291   2.4468e-01
   1_xyz:   9.609  0.065  0.312 86.598  0.014  2.042   1.0183e-01
   1_adp:   9.609  0.065  0.312 86.598  0.014  2.042   1.0183e-01
   1_occ:   9.609  0.065  0.312 86.598  0.014  2.042   1.0183e-01
   2_bss:   9.609  0.065  0.312 86.598  0.014  2.042   1.0183e-01
   2_xyz:   7.988  0.046  0.309 83.870  0.037  2.109   8.5739e-02
   2_adp:   7.988  0.046  0.309 83.870  0.037  2.109   8.5739e-02
   2_occ:   7.988  0.046  0.309 83.870  0.037  2.109   8.5739e-02
   3_bss:   7.988  0.046  0.309 83.870  0.037  2.109   8.5739e-02
   3_xyz:   7.660  0.058  0.270 83.326  0.029  2.133   8.6306e-02
   3_adp:   7.660  0.058  0.270 83.326  0.029  2.133   8.6306e-02
   3_occ:   7.660  0.058  0.270 83.326  0.029  2.133   8.6306e-02
   4_bss:   7.660  0.058  0.270 83.326  0.029  2.133   8.6306e-02
   4_xyz:   7.228  0.045  0.246 87.333  0.037  2.338   4.1036e-02
   4_adp:   7.228  0.045  0.246 87.333  0.037  2.338   4.1036e-02
   4_occ:   7.228  0.045  0.246 87.333  0.037  2.338   4.1036e-02
   5_bss:   7.228  0.045  0.246 87.333  0.037  2.338   4.1036e-02
   5_xyz:   7.421  0.050  0.216 83.430  0.030  2.291   3.8825e-02
   5_adp:   7.421  0.050  0.216 83.430  0.030  2.291   3.8825e-02
   5_occ:   7.421  0.050  0.216 83.430  0.030  2.291   3.8825e-02
   5_bss:   7.421  0.050  0.216 83.430  0.030  2.291   3.8825e-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:  95.72   0.00  19.13  81.04   0.00  16.02  95.72   0.00  36.01
   1_occ:  95.72   0.00  19.13  81.04   0.00  16.02  95.72   0.00  36.01
   2_bss:  95.72   0.00  19.13  81.04   0.00  16.02  95.72   0.00  36.01
   2_xyz:  95.72   0.00  19.13  81.04   0.00  16.02  95.72   0.00  36.01
   2_adp: 104.90   0.00  19.12  91.02   0.00  15.62 104.90   1.79  38.17
   2_occ: 104.90   0.00  19.12  91.02   0.00  15.62 104.90   1.79  38.17
   3_bss: 104.90   0.00  19.12  91.02   0.00  15.62 104.90   1.79  38.17
   3_xyz: 104.90   0.00  19.12  91.02   0.00  15.62 104.90   1.79  38.17
   3_adp: 109.45   0.00  19.47 109.45   0.00  14.45 108.41   2.54  46.80
   3_occ: 109.45   0.00  19.47 109.45   0.00  14.45 108.41   2.54  46.80
   4_bss: 109.45   0.00  19.47 109.45   0.00  14.45 108.41   2.54  46.80
   4_xyz: 109.45   0.00  19.47 109.45   0.00  14.45 108.41   2.54  46.80
   4_adp: 104.71   1.53  17.82 103.21   1.53  13.26 104.71   4.79  42.61
   4_occ: 104.71   1.53  17.82 103.21   1.53  13.26 104.71   4.79  42.61
   5_bss: 104.71   1.53  17.82 103.21   1.53  13.26 104.71   4.79  42.61
   5_xyz: 104.71   1.53  17.82 103.21   1.53  13.26 104.71   4.79  42.61
   5_adp: 104.81   1.99  17.37 100.30   1.99  12.90 104.81   4.68  41.74
   5_occ: 104.81   1.99  17.37 100.30   1.99  12.90 104.81   4.68  41.74
   5_bss: 104.73   1.91  17.30 100.23   1.91  12.83 104.73   4.61  41.67
------------------------------------------------------------------------
 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:    1.866    0.019    0.283
   1_adp:    1.866    0.019    0.283
   1_occ:    1.866    0.019    0.283
   2_bss:    1.866    0.019    0.283
   2_xyz:    1.618    0.048    0.523
   2_adp:    1.618    0.048    0.523
   2_occ:    1.618    0.048    0.523
   3_bss:    1.618    0.048    0.523
   3_xyz:    1.984    0.081    0.736
   3_adp:    1.984    0.081    0.736
   3_occ:    1.984    0.081    0.736
   4_bss:    1.984    0.081    0.736
   4_xyz:    1.792    0.101    0.778
   4_adp:    1.792    0.101    0.778
   4_occ:    1.792    0.101    0.778
   5_bss:    1.792    0.101    0.778
   5_xyz:    1.768    0.095    0.843
   5_adp:    1.768    0.095    0.843
   5_occ:    1.768    0.095    0.843
   5_bss:    1.768    0.095    0.843
------------------------------------------------------------------------

CPU time actual refinement: 375.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/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_1202/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1202/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 375.08 
  Macro-tasks:
    bulk solvent and scale       = 54.45  
    individual site refinement   = 153.03 
    weights calculation          = 30.18  
    collect and process          = 6.39   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 244.16 
  Micro-tasks:
    mask                            = 3.12   
    f_calc                          = 119.30 
    alpha_beta                      = 8.24   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 127.84 
    fmodel                         = 8.59   
    r_factors                      = 0.37   
    phase_errors                   = 10.26  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 279.21 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.247 micro seconds
Total CPU time: 6.48 minutes
from_scatterers_fft:    650 calls, 119.02 s
gradients_fft:          595 calls, 114.49 s

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

# Date 2008-01-16 Time 06:41:37 PST -0800 (1200494497.20 s)
Start R-work = 0.4657, R-free = 0.4462 (no bulk solvent and anisotropic scale)
Final R-work = 0.1565, R-free = 0.2001 (no bulk solvent and anisotropic scale)

Start R-work = 0.4577, R-free = 0.4366
Final R-work = 0.1382, R-free = 0.1832