# Date 2008-01-16 Time 05:40:01 PST -0800 (1200490801.15 s)
#phil __OFF__

Command line arguments: "../827.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26374
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 827

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.8686, 85.0941, 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: 3.22, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97143
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933476

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9858
                             d_min =   1.9714

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9858 1.97143
Completeness in resolution range: 0.936332
Completeness with d_max=infinity: 0.933476

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9863 -  4.2187 [2202/2230]  1983   219   9.9%
  bin  2:  4.2187 -  3.3609 [2098/2121]  1889   209  10.0%
  bin  3:  3.3609 -  2.9397 [2084/2109]  1871   213  10.2%
  bin  4:  2.9397 -  2.6726 [2065/2081]  1864   201   9.7%
  bin  5:  2.6726 -  2.4820 [2042/2086]  1834   208  10.2%
  bin  6:  2.4820 -  2.3362 [2056/2084]  1854   202   9.8%
  bin  7:  2.3362 -  2.2196 [2007/2043]  1806   201  10.0%
  bin  8:  2.2196 -  2.1233 [2014/2056]  1813   201  10.0%
  bin  9:  2.1233 -  2.0417 [2017/2062]  1814   203  10.1%
  bin 10:  2.0417 -  1.9714 [1004/2049]   902   102  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/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:
        1.66 -     2.31: 19
        2.31 -     2.96: 1680
        2.96 -     3.60: 4504
        3.60 -     4.25: 9134
        4.25 -     4.90: 12880
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.662 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.669 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.775 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.881 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28212 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_827/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/model_refine_001.geo

CPU time processing inputs: 8.62


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.8686 85.09415 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: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4234   r_free= 0.4121   ksol= 0.00   Bsol= 0.00   scale= 0.915    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.232158                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.3367 0.3560      6.4844      6.4953|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.3541 0.3648      6.7379      6.7041|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.3855 0.3528      6.5838      6.5739|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.4003 0.3971      6.4415      6.4129|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.4303 0.4049      6.3081      6.2784|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.4612 0.4119      6.2391      6.1057|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.4546 0.3831      6.2001      6.1115|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.4767 0.4873      6.1238      6.1901|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.5040 0.4739       6.111      6.0938|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.4635 0.5060      6.0656      6.1145|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.4866 0.4586        6.01      5.9692|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.4733 0.5030      5.9183      5.9889|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.4791 0.4151      5.8451      5.7967|
| 14:  2.0206 -  1.9714 0.33    434   46 0.5079 0.4716       5.818      5.7251|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7055  1425   161  0.72  32.07   0.84     0.75      63712.07|
|  2:  4.7055 -  3.7542  1371   148  0.75  30.42   0.93     0.83      80029.31|
|  3:  3.7542 -  3.2853  1345   153  0.68  36.91   0.93     0.84      82797.99|
|  4:  3.2853 -  2.9876  1336   147  0.63  41.48   0.94     0.82      72536.14|
|  5:  2.9876 -  2.7749  1331   148  0.58  45.64   0.91     0.77      59150.79|
|  6:  2.7749 -  2.6122  1325   146  0.55  48.03   0.93     0.75      50384.83|
|  7:  2.6122 -  2.4820  1308   147  0.55  48.38   0.93     0.72      46515.82|
|  8:  2.4820 -  2.3744  1309   145  0.48  53.81   0.91     0.68      47312.98|
|  9:  2.3744 -  2.2833  1315   146  0.45  55.71   0.92     0.65      45138.62|
| 10:  2.2833 -  2.2048  1303   144  0.44  56.78   0.98     0.63      44532.72|
| 11:  2.2048 -  2.1360  1282   138  0.43  57.60   0.95     0.64      40429.30|
| 12:  2.1360 -  2.0751  1290   153  0.42  58.54   0.96     0.65      37781.70|
| 13:  2.0751 -  2.0206  1256   137  0.45  56.45   0.96     0.66      29921.50|
| 14:  2.0206 -  1.9714   434    46  0.50  52.49   0.94     0.71      22685.85|
|alpha:            min =        0.63 max =            0.84 mean =         0.72|
|beta:             min =    22685.85 max =        82797.99 mean =     53455.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.69|
|phase err.(test): min =        0.00 max =           89.74 mean =        47.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.552709              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.530   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.729213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.178   (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 |  1.662 -  1.986:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.986 -  2.310:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.310 -  2.634:       50 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.634 -  2.957:     1630 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.957 -  3.281:     1914 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.281 -  3.605:     2590 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.605 -  3.929:     4712 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.929 -  4.252:     4422 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.252 -  4.576:     5871 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.576 -  4.900:     7009 |
|-----------------------------------------------------------------------------|
|-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 |        0.173 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.662 |       0.323 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    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: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4234   r_free= 0.4121   ksol= 0.00   Bsol= 0.00   scale= 0.915    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.232158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4118   r_free= 0.3982   ksol= 0.30   Bsol= 30.70   scale= 0.951   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,4.53,0.25,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.220000                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.651050              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.814774              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.969   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4118      final r-factor (work) = 0.3045          |
| start r-factor (free) = 0.3982      final r-factor (free) = 0.3328          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.8548 = 6.65 * 0.50 * 6.2192 + 1.00 * 0.1727                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2433 = 6.65 * 0.50 * 6.0540 + 1.00 * 0.1107                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3045      final r-factor (work) = 0.2779          |
| start r-factor (free) = 0.3328      final r-factor (free) = 0.3445          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9387 = 0.81 * 1.00 * 6.0540 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8489 = 0.81 * 1.00 * 5.9333 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.64   17.89    None  None   None       |
|    all(noH): 2823   0      0.00    92.64   17.89    None  None   None       |
|    Sol.    : 438    0      2.06    92.64   37.64    None  None   None       |
|    Mac.    : 2385   0      0.00    90.90   14.27    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 -   9.264:  888   |   5:    46.322 -  55.586:   74        |
|      1:     9.264 -  18.529:  994   |   6:    55.586 -  64.850:   50        |
|      2:    18.529 -  27.793:  414   |   7:    64.850 -  74.114:   23        |
|      3:    27.793 -  37.057:  229   |   8:    74.114 -  83.379:   13        |
|      4:    37.057 -  46.322:  133   |   9:    83.379 -  92.643:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2779 r_free = 0.3445             target_work(ml) = 5.941         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2775 r_free = 0.3445             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2775   r_free= 0.3445   ksol= 0.30   Bsol= 30.70   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.03,4.53,0.25,0.00,0.00,0.00); trace/3= 0.58                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.939593                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2760   r_free= 0.3410   ksol= 0.32   Bsol= 54.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,1.84,-0.70,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.937704                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.980683              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.579   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.406152              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.327  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2760      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.3410      final r-factor (free) = 0.2456          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7861 = 7.98 * 0.50 * 5.9332 + 1.00 * 0.1107                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2864 = 7.98 * 0.50 * 5.8132 + 1.00 * 0.0896                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1981      final r-factor (work) = 0.1752          |
| start r-factor (free) = 0.2456      final r-factor (free) = 0.2231          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3756 = 0.41 * 1.00 * 5.8132 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2716 = 0.41 * 1.00 * 5.5679 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.66   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    87.66   17.37    None  None   None       |
|    Sol.    : 438    0      4.25    87.66   40.23    None  None   None       |
|    Mac.    : 2385   0      0.00    83.24   13.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.766:  861   |   5:    43.831 -  52.598:  109        |
|      1:     8.766 -  17.533: 1141   |   6:    52.598 -  61.364:   74        |
|      2:    17.533 -  26.299:  302   |   7:    61.364 -  70.130:   33        |
|      3:    26.299 -  35.065:  152   |   8:    70.130 -  78.896:   15        |
|      4:    35.065 -  43.831:  128   |   9:    78.896 -  87.663:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1752 r_free = 0.2231             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1750 r_free = 0.2231             target_work(ml) = 5.525         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1750   r_free= 0.2231   ksol= 0.32   Bsol= 54.76   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,1.84,-0.70,0.00,-0.00,-0.00); trace/3= -0.31                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.524691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1743   r_free= 0.2218   ksol= 0.32   Bsol= 54.76   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.03,-1.13,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.521181                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.284135              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.997   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.470865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.224  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1743      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2218      final r-factor (free) = 0.1806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2347 = 3.28 * 0.50 * 5.5693 + 1.00 * 0.0896                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9667 = 3.28 * 0.50 * 5.4226 + 1.00 * 0.0624                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1806      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5635 = 0.47 * 1.00 * 5.4226 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4986 = 0.47 * 1.00 * 5.2845 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.20    92.84   17.27    None  None   None       |
|    all(noH): 2823   0      1.20    92.84   17.27    None  None   None       |
|    Sol.    : 438    0      4.06    90.80   41.72    None  None   None       |
|    Mac.    : 2385   0      1.20    92.84   12.78    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:     1.199 -  10.363: 1195   |   5:    47.018 -  56.182:   99        |
|      1:    10.363 -  19.527:  958   |   6:    56.182 -  65.346:   66        |
|      2:    19.527 -  28.691:  222   |   7:    65.346 -  74.509:   34        |
|      3:    28.691 -  37.854:  123   |   8:    74.509 -  83.673:   12        |
|      4:    37.854 -  47.018:  106   |   9:    83.673 -  92.837:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1298 r_free = 0.1724             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1298 r_free = 0.1722             target_work(ml) = 5.263         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1722   ksol= 0.32   Bsol= 54.76   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.03,-1.13,-0.00,-0.00,-0.00); trace/3= -1.07                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.262524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1723   ksol= 0.32   Bsol= 54.76   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-0.86,-1.30,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264088                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.134605              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.541  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.286948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.010  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1302      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7054 = 2.13 * 0.50 * 5.2871 + 1.00 * 0.0624                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6410 = 2.13 * 0.50 * 5.2290 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1649      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5106 = 0.29 * 1.00 * 5.2290 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5008 = 0.29 * 1.00 * 5.1978 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.45    93.36   16.87    None  None   None       |
|    all(noH): 2823   0      1.45    93.36   16.87    None  None   None       |
|    Sol.    : 438    0      4.82    88.51   40.61    None  None   None       |
|    Mac.    : 2385   0      1.45    93.36   12.51    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:     1.445 -  10.637: 1270   |   5:    47.405 -  56.596:   94        |
|      1:    10.637 -  19.829:  936   |   6:    56.596 -  65.788:   59        |
|      2:    19.829 -  29.021:  193   |   7:    65.788 -  74.980:   25        |
|      3:    29.021 -  38.213:  124   |   8:    74.980 -  84.172:    9        |
|      4:    38.213 -  47.405:  106   |   9:    84.172 -  93.364:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1633             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1633             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1633   ksol= 0.32   Bsol= 54.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-0.86,-1.30,-0.00,-0.00,-0.00); trace/3= -1.43                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.190809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1633   ksol= 0.32   Bsol= 55.95   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.06,-1.22,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.190765                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.668257              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.268  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.617269              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.421  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1183      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3955 = 1.67 * 0.50 * 5.1975 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3801 = 1.67 * 0.50 * 5.1866 + 1.00 * 0.0539                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3973 = 1.62 * 1.00 * 5.1866 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3803 = 1.62 * 1.00 * 5.1750 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.32    106.29  17.01    None  None   None       |
|    all(noH): 2823   0      0.32    106.29  17.01    None  None   None       |
|    Sol.    : 438    0      4.89    93.38   41.72    None  None   None       |
|    Mac.    : 2385   0      0.32    106.29  12.47    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:     0.324 -  10.920: 1365   |   5:    53.307 -  63.903:   87        |
|      1:    10.920 -  21.517:  888   |   6:    63.903 -  74.500:   34        |
|      2:    21.517 -  32.114:  185   |   7:    74.500 -  85.097:   16        |
|      3:    32.114 -  42.710:  114   |   8:    85.097 -  95.693:    8        |
|      4:    42.710 -  53.307:  123   |   9:    95.693 - 106.290:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1158 r_free = 0.1625             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1626             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1626   ksol= 0.32   Bsol= 55.95   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.03,-1.06,-1.22,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.180182                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.0975 0.1244      5.3646      5.5139|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.0847 0.1047      5.4146      5.5999|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.1064 0.1542      5.4654      5.8448|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.1303 0.1622      5.4953      5.6638|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.1413 0.1926      5.3831       5.563|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.1313 0.2019      5.2689      5.4949|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.1308 0.1789      5.1988      5.4151|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.1234 0.1696      5.1043      5.3001|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.1239 0.1938      5.0685      5.3478|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.1158 0.1769      5.0003       5.274|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.1173 0.1857      4.9502      5.2581|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.1149 0.1714      4.8918      5.1161|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.1175 0.1896      4.8208      5.1107|
| 14:  2.0206 -  1.9714 0.33    434   46 0.1171 0.1729      4.7151       4.955|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7055  1425   161  0.94   8.67   0.97     0.95       6738.57|
|  2:  4.7055 -  3.7542  1371   148  0.95   7.70   1.01     0.99       8368.79|
|  3:  3.7542 -  3.2853  1345   153  0.94  11.17   1.02     1.02      10069.24|
|  4:  3.2853 -  2.9876  1336   147  0.91  14.85   1.00     0.98      11142.10|
|  5:  2.9876 -  2.7749  1331   148  0.89  17.26   0.99     0.97       9330.76|
|  6:  2.7749 -  2.6122  1325   146  0.89  17.01   0.98     0.96       7904.05|
|  7:  2.6122 -  2.4820  1308   147  0.90  16.06   0.98     0.95       6601.91|
|  8:  2.4820 -  2.3744  1309   145  0.90  16.31   0.99     0.96       5856.64|
|  9:  2.3744 -  2.2833  1315   146  0.89  17.01   0.98     0.94       5346.54|
| 10:  2.2833 -  2.2048  1303   144  0.90  15.75   0.98     0.95       4797.42|
| 11:  2.2048 -  2.1360  1282   138  0.89  16.89   0.98     0.94       4499.05|
| 12:  2.1360 -  2.0751  1290   153  0.91  15.72   0.98     0.97       4083.83|
| 13:  2.0751 -  2.0206  1256   137  0.89  17.29   0.98     0.97       3661.29|
| 14:  2.0206 -  1.9714   434    46  0.89  17.30   0.96     0.92       2935.96|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2935.96 max =        11142.10 mean =      6743.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.73|
|phase err.(test): min =        0.00 max =           88.55 mean =        14.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1626   ksol= 0.32   Bsol= 58.36   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.94,-1.02,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.180307                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1626   ksol= 0.32   Bsol= 58.36   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-0.94,-1.02,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.180307                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9863 -  4.7055 0.99   1425  161 0.0976 0.1247      5.3656      5.5169|
|  2:  4.7055 -  3.7542 0.99   1371  148 0.0849 0.1049       5.417      5.6023|
|  3:  3.7542 -  3.2853 0.99   1345  153 0.1064 0.1543      5.4667      5.8453|
|  4:  3.2853 -  2.9876 0.99   1336  147 0.1302 0.1624       5.495      5.6641|
|  5:  2.9876 -  2.7749 0.98   1331  148 0.1411 0.1923      5.3821      5.5619|
|  6:  2.7749 -  2.6122 0.99   1325  146 0.1312 0.2018      5.2681       5.494|
|  7:  2.6122 -  2.4820 0.98   1308  147 0.1308 0.1790      5.1984      5.4152|
|  8:  2.4820 -  2.3744 0.99   1309  145 0.1233 0.1694      5.1042       5.299|
|  9:  2.3744 -  2.2833 0.99   1315  146 0.1238 0.1940      5.0684      5.3485|
| 10:  2.2833 -  2.2048 0.98   1303  144 0.1157 0.1767      5.0001      5.2735|
| 11:  2.2048 -  2.1360 0.97   1282  138 0.1172 0.1855        4.95      5.2577|
| 12:  2.1360 -  2.0751 0.99   1290  153 0.1149 0.1716      4.8917      5.1168|
| 13:  2.0751 -  2.0206 0.93   1256  137 0.1176 0.1896      4.8207      5.1095|
| 14:  2.0206 -  1.9714 0.33    434   46 0.1171 0.1728       4.715      4.9548|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9863 -  4.7055  1425   161  0.94   8.69   0.97     0.95       6761.25|
|  2:  4.7055 -  3.7542  1371   148  0.95   7.72   1.01     1.00       8410.57|
|  3:  3.7542 -  3.2853  1345   153  0.93  11.21   1.02     1.02      10117.46|
|  4:  3.2853 -  2.9876  1336   147  0.91  14.85   1.01     0.98      11142.70|
|  5:  2.9876 -  2.7749  1331   148  0.89  17.25   1.00     0.97       9316.99|
|  6:  2.7749 -  2.6122  1325   146  0.89  16.99   0.99     0.97       7887.81|
|  7:  2.6122 -  2.4820  1308   147  0.90  16.05   0.99     0.96       6594.08|
|  8:  2.4820 -  2.3744  1309   145  0.90  16.30   1.00     0.97       5854.29|
|  9:  2.3744 -  2.2833  1315   146  0.89  17.01   0.99     0.95       5348.34|
| 10:  2.2833 -  2.2048  1303   144  0.90  15.74   0.99     0.95       4795.53|
| 11:  2.2048 -  2.1360  1282   138  0.89  16.88   0.99     0.95       4496.20|
| 12:  2.1360 -  2.0751  1290   153  0.91  15.72   0.99     0.98       4082.73|
| 13:  2.0751 -  2.0206  1256   137  0.89  17.29   0.99     0.98       3659.32|
| 14:  2.0206 -  1.9714   434    46  0.89  17.30   0.97     0.93       2932.63|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2932.63 max =        11142.70 mean =      6748.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.73|
|phase err.(test): min =        0.00 max =           88.52 mean =        14.18|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.31    106.28  17.00    None  None   None       |
|    all(noH): 2823   0      0.31    106.28  17.00    None  None   None       |
|    Sol.    : 438    0      4.88    93.37   41.71    None  None   None       |
|    Mac.    : 2385   0      0.31    106.28  12.46    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:     0.315 -  10.911: 1365   |   5:    53.298 -  63.894:   87        |
|      1:    10.911 -  21.508:  888   |   6:    63.894 -  74.491:   34        |
|      2:    21.508 -  32.104:  185   |   7:    74.491 -  85.087:   16        |
|      3:    32.104 -  42.701:  114   |   8:    85.087 -  95.684:    8        |
|      4:    42.701 -  53.298:  123   |   9:    95.684 - 106.281:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.724 - 4.539
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 323
   mapped sites are within: 0.724 - 4.539

peak=    5.820 closest distance to " NH2 ARG A  56 " =    2.371
peak=    5.804 closest distance to " CB  GLN A 223 " =    1.398
peak=    5.589 closest distance to " CG  PRO A  54 " =    1.252
peak=    5.437 closest distance to " CB  SER A  63 " =    1.228
peak=    5.149 closest distance to " CG  PRO A 198 " =    1.223
peak=    5.019 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.960 closest distance to " CA  TYR A  30 " =    0.959
peak=    4.859 closest distance to " C   PRO A 198 " =    1.530
peak=    4.721 closest distance to " CG  PRO A  90 " =    1.150
peak=    4.703 closest distance to " CB  GLU A 128 " =    1.151
peak=    4.663 closest distance to " O   HOH Z  15 " =    2.132
peak=    4.650 closest distance to " O   HOH Z 134 " =    1.772
peak=    4.633 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.613 closest distance to " O   HOH Z 232 " =    2.367
peak=    4.605 closest distance to " CG  PRO A 280 " =    0.737
peak=    4.568 closest distance to " O   HOH Z 234 " =    3.822
peak=    4.528 closest distance to " O   HOH Z 210 " =    1.056
peak=    4.504 closest distance to " CB  PRO A  54 " =    0.834
peak=    4.493 closest distance to " CB  GLN A 183 " =    1.323
peak=    4.365 closest distance to " O   HOH Z 247 " =    1.407
peak=    4.362 closest distance to " O   HOH Z  80 " =    1.783
peak=    4.357 closest distance to " O   HOH Z 402 " =    1.549
peak=    4.330 closest distance to " CB  ARG A 190 " =    1.677
peak=    4.326 closest distance to " O   HOH Z  97 " =    1.953
peak=    4.315 closest distance to " O   HOH Z 209 " =    2.361
peak=    4.309 closest distance to " O   HOH Z 193 " =    1.780
peak=    4.277 closest distance to " O   HOH Z 124 " =    1.423
peak=    4.275 closest distance to " O   HOH Z  20 " =    1.716
peak=    4.270 closest distance to " CB  TYR A 169 " =    0.870
peak=    4.242 closest distance to " O   HOH Z 433 " =    1.528
peak=    4.238 closest distance to " CB  LEU A 228 " =    1.168
peak=    4.226 closest distance to " O   HOH Z 298 " =    1.927
peak=    4.217 closest distance to " CA  ALA A  21 " =    1.374
peak=    4.212 closest distance to " O   HOH Z  78 " =    1.922
peak=    4.187 closest distance to " CD  ARG A 269 " =    1.021
peak=    4.185 closest distance to " CG1 ILE A  33 " =    1.220
peak=    4.181 closest distance to " NH2 ARG A 156 " =    1.218
peak=    4.163 closest distance to " CB  SER A   3 " =    1.288
peak=    4.160 closest distance to " O   HOH Z 132 " =    2.207
peak=    4.146 closest distance to " CB  GLU A 152 " =    1.122
peak=    4.140 closest distance to " CB  ARG A  79 " =    1.381
peak=    4.134 closest distance to " O   HOH Z 352 " =    1.868
peak=    4.120 closest distance to " O   HOH Z 369 " =    2.443
peak=    4.081 closest distance to " O   HOH Z 189 " =    2.083
peak=    4.080 closest distance to " O   GLY A  23 " =    2.346
peak=    4.067 closest distance to " CG  ARG A  66 " =    2.692
peak=    4.067 closest distance to " O   HOH Z  67 " =    2.022
peak=    4.062 closest distance to " CB  GLU A 277 " =    3.663
peak=    4.060 closest distance to " O   HOH Z 403 " =    1.759
peak=    4.055 closest distance to " O   HOH Z  40 " =    1.868
peak=    4.053 closest distance to " O   HOH Z 108 " =    2.632
peak=    4.046 closest distance to " CB  ASN A 148 " =    1.272
peak=    4.046 closest distance to " CG2BVAL A  41 " =    0.841
peak=    4.044 closest distance to " NZ  LYS A 117 " =    3.084
peak=    4.042 closest distance to " CG  PRO A 243 " =    1.154
peak=    4.037 closest distance to " O   HOH Z 316 " =    2.954
peak=    4.036 closest distance to " O   HOH Z 411 " =    3.455
peak=    4.005 closest distance to " CB  SER A 141 " =    1.054
peak=    3.997 closest distance to " O   HOH Z 423 " =    1.903
peak=    3.994 closest distance to " O   HOH Z 374 " =    2.687
peak=    3.992 closest distance to " O   HOH Z 279 " =    2.144
peak=    3.987 closest distance to " O   SER A  87 " =    2.254
peak=    3.984 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.982 closest distance to " O   HOH Z  59 " =    2.568
peak=    3.978 closest distance to " CA  ARG A 195 " =    1.149
peak=    3.978 closest distance to " OD1 ASN A  69 " =    2.551
peak=    3.969 closest distance to " O   HOH Z 163 " =    1.569
peak=    3.963 closest distance to " O   HOH Z 389 " =    1.966
peak=    3.946 closest distance to " O   HOH Z 426 " =    1.480
peak=    3.946 closest distance to " CA  ARG A  36 " =    1.129
peak=    3.942 closest distance to " NH2BARG A 145 " =    2.089
peak=    3.942 closest distance to " CD1 LEU A 300 " =    1.182
peak=    3.928 closest distance to " CA  ASP A 191 " =    0.799
peak=    3.926 closest distance to " O   HOH Z 368 " =    2.064
peak=    3.920 closest distance to " O   HOH Z 142 " =    1.502
peak=    3.916 closest distance to " O   HOH Z 126 " =    1.622
peak=    3.905 closest distance to " CB  TRP A 179 " =    1.320
peak=    3.896 closest distance to " N   ASN A  39 " =    1.270
peak=    3.893 closest distance to " O   HOH Z 132 " =    2.646
peak=    3.886 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.878 closest distance to " O   HOH Z 357 " =    2.095
peak=    3.872 closest distance to " C   ILE A 106 " =    1.887
peak=    3.870 closest distance to " O   HOH Z  44 " =    1.893
peak=    3.853 closest distance to " O   HOH Z 284 " =    2.881
peak=    3.850 closest distance to " CB  PRO A  54 " =    1.332
peak=    3.811 closest distance to " NE2 GLN A  11 " =    1.001
peak=    3.806 closest distance to " O   HOH Z 245 " =    1.349
peak=    3.805 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.802 closest distance to " O   HOH Z  61 " =    1.500
peak=    3.795 closest distance to " O   HOH Z  21 " =    1.761
peak=    3.778 closest distance to " CD  LYS A 166 " =    1.382
peak=    3.770 closest distance to " NZ  LYS A  76 " =    1.412
peak=    3.758 closest distance to " CG2 VAL A 197 " =    1.162
peak=    3.756 closest distance to " CA  GLU A 152 " =    0.867
peak=    3.754 closest distance to " OG BSER A 164 " =    2.381
peak=    3.753 closest distance to " CB  VAL A 202 " =    1.546
peak=    3.751 closest distance to " O   HOH Z 344 " =    3.132
peak=    3.739 closest distance to " O   HOH Z  47 " =    1.242
peak=    3.716 closest distance to " CG2 VAL A  78 " =    0.921
peak=    3.716 closest distance to " CD  ARG A 159 " =    0.857
peak=    3.714 closest distance to " O   HOH Z 368 " =    3.603
peak=    3.705 closest distance to " O   HOH Z 154 " =    1.251
peak=    3.695 closest distance to " O   HOH Z 418 " =    1.519
peak=    3.695 closest distance to " O   HOH Z 406 " =    1.611
peak=    3.692 closest distance to " CA  THR A 221 " =    0.957
peak=    3.689 closest distance to " O   HOH Z 180 " =    2.283
peak=    3.686 closest distance to " O   HOH Z 272 " =    1.888
peak=    3.685 closest distance to " O   HOH Z 196 " =    1.202
peak=    3.685 closest distance to " CA  ASN A 176 " =    1.357
peak=    3.682 closest distance to " O   HOH Z 145 " =    2.201
peak=    3.678 closest distance to " O   HOH Z 102 " =    1.242
peak=    3.673 closest distance to " O   HOH Z  48 " =    1.475
peak=    3.669 closest distance to " CZ  PHE A 218 " =    1.103
peak=    3.665 closest distance to " CB  TRP A 266 " =    0.959
peak=    3.663 closest distance to " O   HOH Z 133 " =    1.560
peak=    3.649 closest distance to " CB  PRO A 198 " =    1.071
peak=    3.629 closest distance to " CZ  PHE A  38 " =    1.376
peak=    3.628 closest distance to " O   HOH Z 345 " =    1.646
peak=    3.622 closest distance to " OG  SER A  62 " =    2.974
peak=    3.618 closest distance to " CA  ALA A 160 " =    0.850
peak=    3.618 closest distance to " O   HOH Z 126 " =    2.025
peak=    3.611 closest distance to " O   HOH Z 250 " =    1.480
peak=    3.609 closest distance to " O   HOH Z  63 " =    1.917
peak=    3.608 closest distance to " CD2 LEU A 297 " =    0.932
peak=    3.605 closest distance to " O   HOH Z  54 " =    2.263
peak=    3.603 closest distance to " CA  ASP A 140 " =    1.135
peak=    3.596 closest distance to " O   HOH Z  49 " =    1.850
peak=    3.590 closest distance to " O   HOH Z 128 " =    2.173
peak=    3.589 closest distance to " O   HOH Z 383 " =    2.080
peak=    3.580 closest distance to " CD2 TRP A 179 " =    1.367
peak=    3.580 closest distance to " O   HOH Z 345 " =    3.003
peak=    3.579 closest distance to " O   HOH Z 358 " =    2.022
peak=    3.578 closest distance to " CG  GLN A  58 " =    2.507
peak=    3.575 closest distance to " CB  ARG A 139 " =    0.746
peak=    3.574 closest distance to " O   HOH Z 391 " =    3.017
peak=    3.572 closest distance to " O   HOH Z  88 " =    3.453
peak=    3.571 closest distance to " O   TRP A 274 " =    1.806
peak=    3.566 closest distance to " O   THR A 251 " =    1.225
peak=    3.558 closest distance to " O   HOH Z 227 " =    1.695
peak=    3.557 closest distance to " O   HOH Z  54 " =    1.717
peak=    3.556 closest distance to " O   HOH Z 327 " =    2.322
peak=    3.554 closest distance to " O   HOH Z 130 " =    2.200
peak=    3.553 closest distance to " OE1 GLN A  11 " =    1.998
peak=    3.550 closest distance to " O   HOH Z 336 " =    1.604
peak=    3.547 closest distance to " O   HOH Z 421 " =    1.728
peak=    3.544 closest distance to " O   HOH Z 287 " =    1.890
peak=    3.544 closest distance to " CE  LYS A  76 " =    0.835
peak=    3.538 closest distance to " O   HOH Z 394 " =    1.661
peak=    3.533 closest distance to " O   HOH Z 214 " =    2.390
peak=    3.532 closest distance to " CB  ALA A 291 " =    1.264
peak=    3.532 closest distance to " OG1 THR A 294 " =    2.423
peak=    3.531 closest distance to " C   SER A  32 " =    1.059
peak=    3.524 closest distance to " O   HOH Z 128 " =    2.141
peak=    3.523 closest distance to " CB  SER A  62 " =    0.793
peak=    3.512 closest distance to " O   HOH Z 371 " =    3.429
peak=    3.511 closest distance to " CB  ASN A 148 " =    1.559
peak=    3.510 closest distance to " CG2 ILE A 120 " =    1.075
peak=    3.509 closest distance to " CG2 VAL A 257 " =    0.831
peak=    3.505 closest distance to " O   HOH Z 425 " =    1.329
peak=    3.499 closest distance to " C   GLY A  80 " =    1.107
peak=    3.488 closest distance to " O   HOH Z 118 " =    1.404
peak=    3.486 closest distance to " CB  ARG A 269 " =    0.778
peak=    3.485 closest distance to " CD BLYS A 290 " =    1.026
peak=    3.481 closest distance to " CA  ASP A 124 " =    0.749
peak=    3.475 closest distance to " OD1 ASP A 238 " =    0.837
peak=    3.469 closest distance to " O   HOH Z 427 " =    2.852
peak=    3.456 closest distance to " O   HOH Z  19 " =    1.572
peak=    3.452 closest distance to " CD1 LEU A  96 " =    0.750
peak=    3.448 closest distance to " CB  ALA A  71 " =    1.266
peak=    3.448 closest distance to " O   HOH Z  35 " =    2.454
peak=    3.447 closest distance to " O   HOH Z 437 " =    1.527
peak=    3.446 closest distance to " O   HOH Z 158 " =    2.842
peak=    3.446 closest distance to " O   ALA A 165 " =    1.364
peak=    3.445 closest distance to " O   HOH Z 173 " =    2.161
peak=    3.436 closest distance to " CG1 VAL A 153 " =    1.060
peak=    3.435 closest distance to " CA  ASP A 162 " =    1.216
peak=    3.434 closest distance to " CA  VAL A  41 " =    0.914
peak=    3.433 closest distance to " O   HOH Z 261 " =    1.626
peak=    3.430 closest distance to " CG2AVAL A 121 " =    2.180
peak=    3.430 closest distance to " O   HOH Z 197 " =    1.995
peak=    3.426 closest distance to " O   ALA A 158 " =    1.205
peak=    3.422 closest distance to " CB  ASN A  39 " =    0.886
peak=    3.418 closest distance to " CB  MET A  47 " =    1.020
peak=    3.417 closest distance to " O   HOH Z   6 " =    2.133
peak=    3.415 closest distance to " O   HOH Z 386 " =    2.287
peak=    3.414 closest distance to " O   HOH Z 402 " =    2.975
peak=    3.406 closest distance to " CA  ILE A  33 " =    1.481
peak=    3.405 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.405 closest distance to " CD2 HIS A  81 " =    1.230
peak=    3.399 closest distance to " CG AARG A 275 " =    1.170
peak=    3.396 closest distance to " CA  ALA A 248 " =    1.175
peak=    3.393 closest distance to " O   HOH Z 365 " =    2.919
peak=    3.392 closest distance to " O   HOH Z 250 " =    1.752
peak=    3.389 closest distance to " CB  PHE A  16 " =    0.980
peak=    3.387 closest distance to " O   HOH Z 258 " =    2.250
peak=    3.384 closest distance to " CB  ASN A 187 " =    1.180
peak=    3.382 closest distance to " O   HOH Z 291 " =    1.529
peak=    3.381 closest distance to " O   HOH Z 404 " =    1.461
peak=    3.377 closest distance to " ND2 ASN A 187 " =    1.482
peak=    3.371 closest distance to " O   HOH Z 132 " =    0.980
peak=    3.369 closest distance to " CA  THR A 221 " =    1.344
peak=    3.362 closest distance to " CZ  PHE A 192 " =    0.918
peak=    3.361 closest distance to " CA  GLN A 223 " =    0.914
peak=    3.361 closest distance to " O   HOH Z 295 " =    1.471
peak=    3.357 closest distance to " O   HOH Z  39 " =    0.973
peak=    3.350 closest distance to " O   HOH Z 419 " =    1.615
peak=    3.347 closest distance to " CD1 TRP A 266 " =    1.219
peak=    3.340 closest distance to " O   HOH Z 263 " =    2.196
peak=    3.338 closest distance to " O   HOH Z 261 " =    1.861
peak=    3.338 closest distance to " OG  SER A 245 " =    1.582
peak=    3.334 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.333 closest distance to " CB  MET A  40 " =    0.815
peak=    3.330 closest distance to " O   SER A  26 " =    1.701
peak=    3.321 closest distance to " CB  ASP A 140 " =    0.834
peak=    3.312 closest distance to " CB  VAL A 265 " =    1.174
peak=    3.311 closest distance to " O   HOH Z 417 " =    3.188
peak=    3.311 closest distance to " OD2 ASP A 298 " =    4.016
peak=    3.310 closest distance to " CG1BVAL A  72 " =    1.723
peak=    3.309 closest distance to " O   HOH Z 387 " =    2.450
peak=    3.308 closest distance to " O   HOH Z 346 " =    1.573
peak=    3.305 closest distance to " O   HOH Z 303 " =    2.133
peak=    3.292 closest distance to " CA  LYS A 117 " =    1.219
peak=    3.289 closest distance to " CB  SER A 273 " =    0.821
peak=    3.287 closest distance to " CB  ALA A 100 " =    1.309
peak=    3.287 closest distance to " CE1 TYR A 186 " =    1.313
peak=    3.287 closest distance to " O   HOH Z 207 " =    2.365
peak=    3.281 closest distance to " CD1 ILE A 106 " =    0.869
peak=    3.276 closest distance to " O   HOH Z 313 " =    2.018
peak=    3.273 closest distance to " OH  TYR A 116 " =    1.153
peak=    3.271 closest distance to " CA  ALA A 295 " =    1.147
peak=    3.271 closest distance to " O   HOH Z 214 " =    1.261
peak=    3.270 closest distance to " O   ASP A 124 " =    1.459
peak=    3.270 closest distance to " CB  ASN A 285 " =    0.863
peak=    3.268 closest distance to " O   HOH Z 109 " =    2.365
peak=    3.267 closest distance to " CE  LYS A 119 " =    1.061
peak=    3.267 closest distance to " O   HOH Z 438 " =    2.141
peak=    3.264 closest distance to " CG2 THR A 220 " =    0.827
peak=    3.264 closest distance to " CB  SER A  28 " =    1.015
peak=    3.260 closest distance to " N   CYS A 260 " =    0.789
peak=    3.259 closest distance to " CA  GLU A  46 " =    0.724
peak=    3.258 closest distance to " O   HOH Z 255 " =    1.754
peak=    3.258 closest distance to " CG2 ILE A 106 " =    1.004
peak=    3.253 closest distance to " O   HOH Z 192 " =    1.722
peak=    3.253 closest distance to " CB  THR A 157 " =    1.054
peak=    3.249 closest distance to " O   HOH Z 144 " =    1.932
peak=    3.249 closest distance to " O   PHE A 155 " =    1.303
peak=    3.243 closest distance to " O   HOH Z 419 " =    2.908
peak=    3.242 closest distance to " CA  MET A  40 " =    1.059
peak=    3.241 closest distance to " O   HOH Z  11 " =    1.266
peak=    3.240 closest distance to " O   GLY A  57 " =    2.604
peak=    3.239 closest distance to " CA  GLY A 196 " =    1.061
peak=    3.238 closest distance to " O   HOH Z 189 " =    2.949
peak=    3.237 closest distance to " CG2 ILE A  20 " =    1.314
peak=    3.236 closest distance to " CD  LYS A 119 " =    1.345
peak=    3.236 closest distance to " O   HOH Z 423 " =    3.376
peak=    3.235 closest distance to " O   HOH Z  43 " =    1.489
peak=    3.232 closest distance to " O   HOH Z 337 " =    3.823
peak=    3.232 closest distance to " CD2 LEU A 255 " =    1.298
peak=    3.229 closest distance to " O   HOH Z   1 " =    2.722
peak=    3.227 closest distance to " O   HOH Z  97 " =    2.617
peak=    3.226 closest distance to " OG  SER A  97 " =    3.567
peak=    3.225 closest distance to " CA  ARG A  66 " =    1.009
peak=    3.222 closest distance to " NE2 HIS A 115 " =    0.988
peak=    3.220 closest distance to " O   HOH Z 409 " =    3.056
peak=    3.220 closest distance to " ND1 HIS A  81 " =    1.642
peak=    3.213 closest distance to " CG  GLN A  11 " =    1.204
peak=    3.212 closest distance to " O   VAL A  72 " =    3.176
peak=    3.210 closest distance to " CB  ALA A 256 " =    1.104
peak=    3.210 closest distance to " N   ASP A 132 " =    1.211
peak=    3.207 closest distance to " CA  LEU A  83 " =    1.391
peak=    3.205 closest distance to " O   HOH Z 427 " =    3.037
peak=    3.201 closest distance to " CA  SER A  87 " =    1.012
peak=    3.200 closest distance to " CD1 LEU A 222 " =    0.767
peak=    3.197 closest distance to " NZ  LYS A 119 " =    1.584
peak=    3.196 closest distance to " O   HOH Z 162 " =    1.657
peak=    3.193 closest distance to " O   HOH Z 227 " =    1.590
peak=    3.190 closest distance to " CB  ALA A 248 " =    1.366
peak=    3.186 closest distance to " ND2 ASN A 110 " =    1.588
peak=    3.185 closest distance to " CG  ARG A  66 " =    0.902
peak=    3.184 closest distance to " O   HOH Z 334 " =    1.317
peak=    3.184 closest distance to " O   HOH Z 217 " =    2.155
peak=    3.183 closest distance to " O   HOH Z 432 " =    1.764
peak=    3.176 closest distance to " O   HOH Z 299 " =    2.279
peak=    3.170 closest distance to " CA  VAL A 125 " =    1.279
peak=    3.167 closest distance to " CG  MET A 185 " =    1.194
peak=    3.162 closest distance to " OG BSER A 134 " =    2.898
peak=    3.161 closest distance to " CB  TYR A 116 " =    1.037
peak=    3.156 closest distance to " N   ARG A 190 " =    1.042
peak=    3.155 closest distance to " O   HOH Z 156 " =    2.608
peak=    3.150 closest distance to " CB  TYR A  30 " =    1.477
peak=    3.147 closest distance to " NH1 ARG A 269 " =    0.742
peak=    3.146 closest distance to " O   HOH Z  30 " =    1.305
peak=    3.144 closest distance to " O   HOH Z 368 " =    4.539
peak=    3.144 closest distance to " OG BSER A 134 " =    2.728
peak=    3.139 closest distance to " CB  GLU A 175 " =    1.435
peak=    3.135 closest distance to " O   HOH Z 281 " =    4.370
peak=    3.132 closest distance to " CB  ALA A 242 " =    1.013
peak=    3.132 closest distance to " O   GLY A  91 " =    1.262
peak=    3.131 closest distance to " CB  PRO A 243 " =    1.184
peak=    3.131 closest distance to " O   HOH Z 123 " =    2.166
peak=    3.125 closest distance to " CB  ILE A 120 " =    1.277
peak=    3.124 closest distance to " O   HOH Z  89 " =    2.188
peak=    3.119 closest distance to " O   HOH Z 353 " =    2.821
peak=    3.116 closest distance to " CB  TRP A 123 " =    1.127
peak=    3.114 closest distance to " CD  ARG A  14 " =    1.170
peak=    3.111 closest distance to " CB  ARG A 259 " =    1.867
peak=    3.109 closest distance to " N   TYR A 116 " =    1.644
peak=    3.085 closest distance to " O   HOH Z 280 " =    3.014
peak=    3.085 closest distance to " N   ARG A 156 " =    1.424
peak=    3.081 closest distance to " O   GLN A 278 " =    1.342
peak=    3.077 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.073 closest distance to " O   HOH Z 104 " =    2.823
peak=    3.066 closest distance to " CA  PRO A  90 " =    0.860
peak=    3.065 closest distance to " CB  SER A 216 " =    0.794
peak=    3.063 closest distance to " OH  TYR A  30 " =    1.316
peak=    3.052 closest distance to " O   HOH Z  47 " =    2.364
peak=    3.041 closest distance to " O   HOH Z 197 " =    2.281
peak=    3.036 closest distance to " CA  LYS A 290 " =    1.149
peak=    3.033 closest distance to " CD  ARG A  66 " =    2.513
peak=    3.020 closest distance to " CG1 ILE A 120 " =    1.001
peak=    2.874 closest distance to " O   HOH Z 271 " =    1.959

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.810 - 5.776
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 218 from: 218
   mapped sites are within: 0.810 - 5.776

peak=   -4.716 closest distance to " O   HOH Z 266 " =    4.569
peak=   -4.500 closest distance to " CD  ARG A 156 " =    2.048
peak=   -4.395 closest distance to " OXT GLY A 302 " =    2.781
peak=   -4.215 closest distance to " O   PRO A 163 " =    2.115
peak=   -4.128 closest distance to " O   VAL A  67 " =    2.794
peak=   -4.113 closest distance to " CE2 TYR A  30 " =    2.632
peak=   -4.094 closest distance to " C   HIS A 108 " =    1.071
peak=   -4.089 closest distance to " O   HOH Z  10 " =    1.631
peak=   -4.074 closest distance to " O   HOH Z  13 " =    1.664
peak=   -4.066 closest distance to " N   ALA A  43 " =    2.634
peak=   -4.057 closest distance to " O   PRO A 198 " =    1.334
peak=   -4.027 closest distance to " CD1 LEU A 101 " =    2.574
peak=   -4.015 closest distance to " O   HOH Z 165 " =    2.021
peak=   -3.942 closest distance to " O   ALA A 256 " =    1.536
peak=   -3.939 closest distance to " OG  SER A  97 " =    2.165
peak=   -3.934 closest distance to " SG  CYS A 254 " =    3.443
peak=   -3.931 closest distance to " O   HOH Z 292 " =    4.513
peak=   -3.875 closest distance to " O   HOH Z 166 " =    1.872
peak=   -3.865 closest distance to " O   HOH Z 407 " =    3.577
peak=   -3.852 closest distance to " CD2 LEU A 237 " =    2.519
peak=   -3.850 closest distance to " CD1 LEU A  25 " =    2.461
peak=   -3.844 closest distance to " CA  TYR A  68 " =    2.682
peak=   -3.841 closest distance to " NH2 ARG A  66 " =    1.558
peak=   -3.800 closest distance to " O   HOH Z 372 " =    2.502
peak=   -3.791 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.779 closest distance to " CB  ALA A 291 " =    2.454
peak=   -3.769 closest distance to " O   HOH Z 377 " =    1.166
peak=   -3.768 closest distance to " ND2 ASN A  45 " =    1.014
peak=   -3.760 closest distance to " CH2 TRP A 179 " =    1.200
peak=   -3.757 closest distance to " CA  SER A 276 " =    1.480
peak=   -3.748 closest distance to " C   ASN A 285 " =    2.369
peak=   -3.744 closest distance to " C   SER A 206 " =    1.581
peak=   -3.728 closest distance to " CD1 PHE A  59 " =    1.848
peak=   -3.700 closest distance to " ND2 ASN A 187 " =    1.610
peak=   -3.696 closest distance to " O   HOH Z 234 " =    4.312
peak=   -3.677 closest distance to " CB  PHE A 208 " =    2.288
peak=   -3.676 closest distance to " O   HOH Z 196 " =    2.299
peak=   -3.671 closest distance to " CA  VAL A 197 " =    1.009
peak=   -3.664 closest distance to " O   HOH Z  52 " =    1.689
peak=   -3.657 closest distance to " O   HOH Z 283 " =    1.933
peak=   -3.654 closest distance to " O   HOH Z  43 " =    1.587
peak=   -3.652 closest distance to " CB  ALA A  43 " =    2.527
peak=   -3.642 closest distance to " CD1 LEU A 228 " =    2.373
peak=   -3.625 closest distance to " O   TRP A  92 " =    1.857
peak=   -3.624 closest distance to " CB  PRO A 243 " =    2.652
peak=   -3.616 closest distance to " CD2 LEU A 167 " =    1.749
peak=   -3.614 closest distance to " O   HOH Z 377 " =    2.156
peak=   -3.608 closest distance to " ND2 ASN A  45 " =    1.450
peak=   -3.600 closest distance to " O   SER A 210 " =    1.865
peak=   -3.595 closest distance to " OD1 ASN A 187 " =    1.769
peak=   -3.593 closest distance to " CG  GLU A  53 " =    1.349
peak=   -3.585 closest distance to " CB  LEU A 167 " =    2.156
peak=   -3.582 closest distance to " OD1 ASN A 148 " =    1.577
peak=   -3.579 closest distance to " CG  ASP A 231 " =    0.894
peak=   -3.578 closest distance to " OD2 ASP A 171 " =    1.815
peak=   -3.570 closest distance to " ND2 ASN A  60 " =    1.536
peak=   -3.568 closest distance to " O   HOH Z  15 " =    1.526
peak=   -3.562 closest distance to " O   ALA A   1 " =    2.047
peak=   -3.556 closest distance to " O   HOH Z 353 " =    2.222
peak=   -3.555 closest distance to " CD  GLN A 223 " =    1.363
peak=   -3.555 closest distance to " N   GLN A  58 " =    1.626
peak=   -3.554 closest distance to " O   HOH Z 210 " =    0.810
peak=   -3.549 closest distance to " O   HOH Z  19 " =    2.160
peak=   -3.546 closest distance to " OD1 ASP A 191 " =    1.732
peak=   -3.535 closest distance to " CA  GLY A  98 " =    2.203
peak=   -3.530 closest distance to " O   HOH Z 145 " =    1.768
peak=   -3.527 closest distance to " CB  ASN A  39 " =    2.275
peak=   -3.525 closest distance to " CA  GLY A 203 " =    2.210
peak=   -3.525 closest distance to " OD2 ASP A 171 " =    2.467
peak=   -3.524 closest distance to " OG  SER A  62 " =    1.499
peak=   -3.521 closest distance to " OH  TYR A 169 " =    1.024
peak=   -3.517 closest distance to " O   HOH Z 418 " =    1.395
peak=   -3.513 closest distance to " CG  PRO A 243 " =    1.679
peak=   -3.510 closest distance to " O   HOH Z 426 " =    1.753
peak=   -3.508 closest distance to " ND2 ASN A 249 " =    2.156
peak=   -3.505 closest distance to " CD2 LEU A 300 " =    2.845
peak=   -3.504 closest distance to " OG1 THR A   4 " =    1.869
peak=   -3.495 closest distance to " CD  ARG A 139 " =    1.613
peak=   -3.495 closest distance to " O   HOH Z 417 " =    2.814
peak=   -3.492 closest distance to " O   HOH Z 118 " =    3.275
peak=   -3.490 closest distance to " O   HOH Z  17 " =    1.314
peak=   -3.488 closest distance to " CG2 ILE A 263 " =    2.362
peak=   -3.487 closest distance to " CB  TYR A  15 " =    2.299
peak=   -3.483 closest distance to " CD  LYS A 289 " =    2.445
peak=   -3.478 closest distance to " CA  VAL A  67 " =    2.954
peak=   -3.474 closest distance to " O   HOH Z  93 " =    1.545
peak=   -3.472 closest distance to " N   ALA A 226 " =    2.108
peak=   -3.468 closest distance to " CB  ALA A 161 " =    2.639
peak=   -3.457 closest distance to " O   HOH Z  71 " =    1.603
peak=   -3.451 closest distance to " O   HOH Z 422 " =    1.401
peak=   -3.447 closest distance to " O   HOH Z 185 " =    2.248
peak=   -3.447 closest distance to " N   MET A 188 " =    1.955
peak=   -3.446 closest distance to " NE2 GLN A  88 " =    1.879
peak=   -3.442 closest distance to " CG  ASP A  50 " =    2.411
peak=   -3.439 closest distance to " OG ASER A 134 " =    1.204
peak=   -3.437 closest distance to " O   GLY A 196 " =    1.034
peak=   -3.433 closest distance to " OE1 GLN A 223 " =    2.127
peak=   -3.431 closest distance to " NH1 ARG A 195 " =    2.646
peak=   -3.429 closest distance to " O   HOH Z  91 " =    2.090
peak=   -3.424 closest distance to " O   HOH Z  90 " =    3.231
peak=   -3.422 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -3.420 closest distance to " O   HOH Z 414 " =    1.603
peak=   -3.414 closest distance to " OG BSER A 210 " =    2.140
peak=   -3.411 closest distance to " CB  ALA A 248 " =    2.013
peak=   -3.404 closest distance to " O   HOH Z 290 " =    1.114
peak=   -3.401 closest distance to " C   THR A 279 " =    1.156
peak=   -3.399 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.394 closest distance to " O   HOH Z 198 " =    2.175
peak=   -3.394 closest distance to " CD  PRO A 198 " =    1.257
peak=   -3.388 closest distance to " OE2 GLU A   2 " =    1.473
peak=   -3.388 closest distance to " O   HOH Z  11 " =    1.708
peak=   -3.385 closest distance to " O   HOH Z 166 " =    1.831
peak=   -3.378 closest distance to " O   ALA A 160 " =    1.486
peak=   -3.373 closest distance to " O   HOH Z 231 " =    2.295
peak=   -3.370 closest distance to " O   ALA A  34 " =    2.359
peak=   -3.368 closest distance to " O   HOH Z 150 " =    1.721
peak=   -3.358 closest distance to " NH2 ARG A  66 " =    5.501
peak=   -3.357 closest distance to " CB  ASP A 132 " =    2.393
peak=   -3.354 closest distance to " O   HOH Z 111 " =    1.421
peak=   -3.343 closest distance to " CB  CYS A 254 " =    2.485
peak=   -3.339 closest distance to " CB  ALA A 291 " =    2.357
peak=   -3.338 closest distance to " C   ALA A 158 " =    1.218
peak=   -3.328 closest distance to " OE1 GLN A  58 " =    1.200
peak=   -3.327 closest distance to " O   HOH Z 350 " =    2.056
peak=   -3.327 closest distance to " CA  GLY A 133 " =    2.381
peak=   -3.325 closest distance to " CG  MET A 105 " =    0.847
peak=   -3.320 closest distance to " CE  MET A  93 " =    1.270
peak=   -3.317 closest distance to " O   HOH Z 311 " =    3.572
peak=   -3.315 closest distance to " CD  ARG A 195 " =    5.041
peak=   -3.314 closest distance to " O   HOH Z 275 " =    1.520
peak=   -3.313 closest distance to " NE1 TRP A 266 " =    2.264
peak=   -3.299 closest distance to " CG  GLN A  58 " =    1.250
peak=   -3.294 closest distance to " NE2 GLN A 103 " =    1.672
peak=   -3.290 closest distance to " CB  TRP A  85 " =    2.364
peak=   -3.286 closest distance to " O   HOH Z  37 " =    1.804
peak=   -3.286 closest distance to " CD2 PHE A  59 " =    2.460
peak=   -3.286 closest distance to " O   ALA A  10 " =    1.656
peak=   -3.282 closest distance to " NH2 ARG A  79 " =    1.926
peak=   -3.278 closest distance to " O   HOH Z 393 " =    1.661
peak=   -3.275 closest distance to " CG  LYS A 119 " =    2.948
peak=   -3.274 closest distance to " O   HOH Z 313 " =    1.182
peak=   -3.265 closest distance to " O   HOH Z 384 " =    2.211
peak=   -3.264 closest distance to " O   HOH Z 396 " =    1.701
peak=   -3.262 closest distance to " O   HOH Z 423 " =    2.404
peak=   -3.261 closest distance to " O   HOH Z 388 " =    2.116
peak=   -3.256 closest distance to " CE3 TRP A 150 " =    2.084
peak=   -3.253 closest distance to " O   HOH Z 351 " =    1.462
peak=   -3.251 closest distance to " O   LEU A 167 " =    1.623
peak=   -3.250 closest distance to " N   LEU A 281 " =    1.780
peak=   -3.248 closest distance to " O   HOH Z 399 " =    2.228
peak=   -3.247 closest distance to " CB  ALA A  10 " =    2.070
peak=   -3.246 closest distance to " O   HOH Z 265 " =    2.080
peak=   -3.244 closest distance to " OG BSER A 134 " =    1.221
peak=   -3.242 closest distance to " O   HOH Z 213 " =    1.386
peak=   -3.239 closest distance to " O   VAL A 125 " =    2.191
peak=   -3.238 closest distance to " CG2 VAL A 189 " =    2.233
peak=   -3.232 closest distance to " ND2BASN A 224 " =    1.921
peak=   -3.226 closest distance to " CB  ASP A 162 " =    2.760
peak=   -3.225 closest distance to " O   HOH Z 366 " =    1.795
peak=   -3.224 closest distance to " O   HOH Z 128 " =    2.435
peak=   -3.223 closest distance to " O   HOH Z   6 " =    1.652
peak=   -3.222 closest distance to " O   HOH Z  40 " =    2.993
peak=   -3.221 closest distance to " O   HOH Z  63 " =    1.178
peak=   -3.221 closest distance to " O   SER A  26 " =    1.299
peak=   -3.220 closest distance to " N   VAL A 189 " =    1.871
peak=   -3.218 closest distance to " N   ALA A 248 " =    1.797
peak=   -3.212 closest distance to " O   ASN A 187 " =    1.547
peak=   -3.209 closest distance to " OG  SER A  26 " =    1.429
peak=   -3.208 closest distance to " CB  ASP A 286 " =    2.253
peak=   -3.208 closest distance to " O   HOH Z 392 " =    1.418
peak=   -3.207 closest distance to " CD1 TYR A 247 " =    2.241
peak=   -3.203 closest distance to " CD  GLN A 223 " =    1.726
peak=   -3.201 closest distance to " CB  PHE A 192 " =    1.944
peak=   -3.198 closest distance to " O   HOH Z  37 " =    2.577
peak=   -3.198 closest distance to " O   VAL A 189 " =    2.605
peak=   -3.196 closest distance to " C   LEU A 143 " =    1.163
peak=   -3.192 closest distance to " CA  GLY A 133 " =    1.891
peak=   -3.189 closest distance to " O   HOH Z  25 " =    2.168
peak=   -3.185 closest distance to " CE2 PHE A  38 " =    1.968
peak=   -3.182 closest distance to " O  BHOH Z 338 " =    1.460
peak=   -3.182 closest distance to " ND2 ASN A  69 " =    1.503
peak=   -3.181 closest distance to " CA  GLY A 241 " =    3.130
peak=   -3.180 closest distance to " CE3 TRP A 274 " =    2.436
peak=   -3.179 closest distance to " O   HOH Z 151 " =    1.626
peak=   -3.178 closest distance to " NH2 ARG A 159 " =    2.292
peak=   -3.178 closest distance to " O   HOH Z 171 " =    2.177
peak=   -3.175 closest distance to " O   HOH Z 298 " =    2.773
peak=   -3.167 closest distance to " CZ  PHE A 130 " =    2.335
peak=   -3.158 closest distance to " NE2 GLN A  58 " =    1.122
peak=   -3.149 closest distance to " O   HOH Z 252 " =    3.468
peak=   -3.145 closest distance to " O   HOH Z  90 " =    2.040
peak=   -3.139 closest distance to " C   ALA A   8 " =    1.610
peak=   -3.137 closest distance to " O   HOH Z 430 " =    5.694
peak=   -3.135 closest distance to " O   HOH Z 380 " =    4.641
peak=   -3.128 closest distance to " O   HOH Z 280 " =    2.267
peak=   -3.125 closest distance to " O   HOH Z 191 " =    5.776
peak=   -3.121 closest distance to " O   HOH Z  39 " =    1.860
peak=   -3.116 closest distance to " O   HOH Z  61 " =    1.539
peak=   -3.113 closest distance to " O   HOH Z 361 " =    3.387
peak=   -3.113 closest distance to " O   HOH Z 119 " =    1.696
peak=   -3.113 closest distance to " O   ALA A  34 " =    2.081
peak=   -3.109 closest distance to " CB  PRO A 163 " =    2.784
peak=   -3.105 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.101 closest distance to " OD1 ASP A 200 " =    1.407
peak=   -3.100 closest distance to " O   HOH Z 407 " =    1.166
peak=   -3.095 closest distance to " N   GLY A  17 " =    1.676
peak=   -3.094 closest distance to " O   HOH Z 427 " =    1.332
peak=   -3.089 closest distance to " C   ALA A 242 " =    1.999
peak=   -3.074 closest distance to " O   HOH Z 193 " =    1.887
peak=   -3.072 closest distance to " CD2 PHE A  61 " =    2.029
peak=   -3.065 closest distance to " ND2 ASN A  60 " =    1.727
peak=   -3.055 closest distance to " O   HOH Z 385 " =    3.827
peak=   -3.055 closest distance to " O   GLY A  23 " =    1.759
peak=   -3.051 closest distance to " OG BSER A 134 " =    1.837
peak=   -3.049 closest distance to " CG  GLN A  88 " =    0.946
peak=   -3.043 closest distance to " CG1 VAL A 112 " =    2.828
peak=   -3.016 closest distance to " CD1 ILE A 263 " =    2.371
peak=   -3.009 closest distance to " O   HOH Z 111 " =    3.706

================= 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    :  0.4234 0.4121   6.232158e+00   6.212755e+00
   1_bss:  0.4118 0.3982   6.220000e+00   6.194703e+00
   1_xyz:  0.3045 0.3328   5.990047e+00   6.060449e+00
   1_adp:  0.2779 0.3445   5.940569e+00   6.077495e+00
   1_occ:  0.2775 0.3445   5.939593e+00   6.077319e+00
   2_bss:  0.2760 0.3410   5.937704e+00   6.074505e+00
   2_xyz:  0.1981 0.2456   5.624707e+00   5.797693e+00
   2_adp:  0.1752 0.2231   5.525107e+00   5.712842e+00
   2_occ:  0.1750 0.2231   5.524691e+00   5.712618e+00
   3_bss:  0.1743 0.2218   5.521181e+00   5.708083e+00
   3_xyz:  0.1387 0.1806   5.314908e+00   5.524720e+00
   3_adp:  0.1298 0.1724   5.262717e+00   5.482369e+00
   3_occ:  0.1298 0.1722   5.262524e+00   5.482264e+00
   4_bss:  0.1302 0.1723   5.264088e+00   5.481690e+00
   4_xyz:  0.1201 0.1649   5.202999e+00   5.432945e+00
   4_adp:  0.1184 0.1633   5.190767e+00   5.419701e+00
   4_occ:  0.1183 0.1633   5.190809e+00   5.420160e+00
   5_bss:  0.1183 0.1633   5.190765e+00   5.420169e+00
   5_xyz:  0.1167 0.1611   5.179905e+00   5.408745e+00
   5_adp:  0.1158 0.1625   5.180205e+00   5.416005e+00
   5_occ:  0.1157 0.1626   5.180182e+00   5.416126e+00
   5_bss:  0.1157 0.1626   5.180307e+00   5.416353e+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:  0.297  30.699  -3.031   4.531   0.245   0.000   0.000   0.000
   1_xyz:  0.297  30.699  -3.031   4.531   0.245   0.000   0.000   0.000
   1_adp:  0.297  30.699  -3.031   4.531   0.245   0.000   0.000   0.000
   1_occ:  0.297  30.699  -3.031   4.531   0.245   0.000   0.000   0.000
   2_bss:  0.317  54.758  -2.071   1.844  -0.702   0.000  -0.000  -0.000
   2_xyz:  0.317  54.758  -2.071   1.844  -0.702   0.000  -0.000  -0.000
   2_adp:  0.317  54.758  -2.071   1.844  -0.702   0.000  -0.000  -0.000
   2_occ:  0.317  54.758  -2.071   1.844  -0.702   0.000  -0.000  -0.000
   3_bss:  0.317  54.758  -2.042  -0.032  -1.133  -0.000  -0.000  -0.000
   3_xyz:  0.317  54.758  -2.042  -0.032  -1.133  -0.000  -0.000  -0.000
   3_adp:  0.317  54.758  -2.042  -0.032  -1.133  -0.000  -0.000  -0.000
   3_occ:  0.317  54.758  -2.042  -0.032  -1.133  -0.000  -0.000  -0.000
   4_bss:  0.317  54.758  -2.123  -0.863  -1.303  -0.000  -0.000  -0.000
   4_xyz:  0.317  54.758  -2.123  -0.863  -1.303  -0.000  -0.000  -0.000
   4_adp:  0.317  54.758  -2.123  -0.863  -1.303  -0.000  -0.000  -0.000
   4_occ:  0.317  54.758  -2.123  -0.863  -1.303  -0.000  -0.000  -0.000
   5_bss:  0.319  55.952  -2.034  -1.059  -1.222  -0.000  -0.000  -0.000
   5_xyz:  0.319  55.952  -2.034  -1.059  -1.222  -0.000  -0.000  -0.000
   5_adp:  0.319  55.952  -2.034  -1.059  -1.222  -0.000  -0.000  -0.000
   5_occ:  0.319  55.952  -2.034  -1.059  -1.222  -0.000  -0.000  -0.000
   5_bss:  0.320  58.363  -1.801  -0.941  -1.024  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.707 0.5506  0.7243    53457.188
   1_bss:  46.474 0.5640  0.7541    49451.091
   1_xyz:  36.273 0.6869  0.8881    31812.972
   1_adp:  37.340 0.6737  0.8676    33278.514
   1_occ:  37.333 0.6737  0.8671    33250.511
   2_bss:  36.899 0.6789  0.8511    32773.104
   2_xyz:  25.051 0.8094  0.9708    15619.163
   2_adp:  22.007 0.8416  0.9813    12879.178
   2_occ:  22.003 0.8417  0.9812    12870.271
   3_bss:  21.800 0.8436  0.9580    12669.092
   3_xyz:  17.128 0.8879  0.9834     8383.193
   3_adp:  16.078 0.8977  0.9822     7739.359
   3_occ:  16.073 0.8977  0.9821     7737.338
   4_bss:  16.063 0.8978  0.9702     7734.175
   4_xyz:  15.088 0.9059  0.9738     6986.953
   4_adp:  14.780 0.9087  0.9698     6844.540
   4_occ:  14.784 0.9087  0.9697     6851.570
   5_bss:  14.783 0.9087  0.9697     6853.162
   5_xyz:  14.522 0.9108  0.9707     6652.419
   5_adp:  14.673 0.9096  0.9640     6740.550
   5_occ:  14.674 0.9096  0.9639     6743.561
   5_bss:  14.676 0.9096  0.9700     6748.840
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7274e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7274e-01
   1_xyz:   1.469  0.011  0.089 15.664  0.006  4.115   1.1069e-01
   1_adp:   1.469  0.011  0.089 15.664  0.006  4.115   1.1069e-01
   1_occ:   1.469  0.011  0.089 15.664  0.006  4.115   1.1069e-01
   2_bss:   1.469  0.011  0.089 15.664  0.006  4.115   1.1069e-01
   2_xyz:   1.318  0.010  0.085 14.646  0.005  4.113   8.9586e-02
   2_adp:   1.318  0.010  0.085 14.646  0.005  4.113   8.9586e-02
   2_occ:   1.318  0.010  0.085 14.646  0.005  4.113   8.9586e-02
   3_bss:   1.318  0.010  0.085 14.646  0.005  4.113   8.9586e-02
   3_xyz:   1.031  0.008  0.071 14.520  0.004  4.123   6.2427e-02
   3_adp:   1.031  0.008  0.071 14.520  0.004  4.123   6.2427e-02
   3_occ:   1.031  0.008  0.071 14.520  0.004  4.123   6.2427e-02
   4_bss:   1.031  0.008  0.071 14.520  0.004  4.123   6.2427e-02
   4_xyz:   1.029  0.007  0.074 14.499  0.004  4.130   6.0046e-02
   4_adp:   1.029  0.007  0.074 14.499  0.004  4.130   6.0046e-02
   4_occ:   1.029  0.007  0.074 14.499  0.004  4.130   6.0046e-02
   5_bss:   1.029  0.007  0.074 14.499  0.004  4.130   6.0046e-02
   5_xyz:   0.958  0.007  0.070 14.319  0.004  4.131   5.3892e-02
   5_adp:   0.958  0.007  0.070 14.319  0.004  4.131   5.3892e-02
   5_occ:   0.958  0.007  0.070 14.319  0.004  4.131   5.3892e-02
   5_bss:   0.958  0.007  0.070 14.319  0.004  4.131   5.3892e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.662   2.4201e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.662   2.4201e-01
   1_xyz:   9.618  0.073  0.449 86.939  0.020  2.187   1.0594e-01
   1_adp:   9.618  0.073  0.449 86.939  0.020  2.187   1.0594e-01
   1_occ:   9.618  0.073  0.449 86.939  0.020  2.187   1.0594e-01
   2_bss:   9.618  0.073  0.449 86.939  0.020  2.187   1.0594e-01
   2_xyz:   7.960  0.062  0.267 87.451  0.045  2.192   1.2764e-01
   2_adp:   7.960  0.062  0.267 87.451  0.045  2.192   1.2764e-01
   2_occ:   7.960  0.062  0.267 87.451  0.045  2.192   1.2764e-01
   3_bss:   7.960  0.062  0.267 87.451  0.045  2.192   1.2764e-01
   3_xyz:   7.072  0.056  0.237 81.698  0.035  2.333   4.2309e-02
   3_adp:   7.072  0.056  0.237 81.698  0.035  2.333   4.2309e-02
   3_occ:   7.072  0.056  0.237 81.698  0.035  2.333   4.2309e-02
   4_bss:   7.072  0.056  0.237 81.698  0.035  2.333   4.2309e-02
   4_xyz:   7.311  0.042  0.256 83.725  0.031  2.342   4.1111e-02
   4_adp:   7.311  0.042  0.256 83.725  0.031  2.342   4.1111e-02
   4_occ:   7.311  0.042  0.256 83.725  0.031  2.342   4.1111e-02
   5_bss:   7.311  0.042  0.256 83.725  0.031  2.342   4.1111e-02
   5_xyz:   7.214  0.042  0.244 81.224  0.029  2.381   3.3708e-02
   5_adp:   7.214  0.042  0.244 81.224  0.029  2.381   3.3708e-02
   5_occ:   7.214  0.042  0.244 81.224  0.029  2.381   3.3708e-02
   5_bss:   7.214  0.042  0.244 81.224  0.029  2.381   3.3708e-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:  92.64   0.00  17.89  90.90   0.00  14.27  92.64   2.06  37.64
   1_occ:  92.64   0.00  17.89  90.90   0.00  14.27  92.64   2.06  37.64
   2_bss:  92.64   0.00  17.89  90.90   0.00  14.27  92.64   2.06  37.64
   2_xyz:  92.64   0.00  17.89  90.90   0.00  14.27  92.64   2.06  37.64
   2_adp:  87.66   0.00  17.37  83.24   0.00  13.18  87.66   4.25  40.23
   2_occ:  87.66   0.00  17.37  83.24   0.00  13.18  87.66   4.25  40.23
   3_bss:  87.66   0.00  17.37  83.24   0.00  13.18  87.66   4.25  40.23
   3_xyz:  87.66   0.00  17.37  83.24   0.00  13.18  87.66   4.25  40.23
   3_adp:  92.84   1.20  17.27  92.84   1.20  12.78  90.80   4.06  41.72
   3_occ:  92.84   1.20  17.27  92.84   1.20  12.78  90.80   4.06  41.72
   4_bss:  92.84   1.20  17.27  92.84   1.20  12.78  90.80   4.06  41.72
   4_xyz:  92.84   1.20  17.27  92.84   1.20  12.78  90.80   4.06  41.72
   4_adp:  93.36   1.45  16.87  93.36   1.45  12.51  88.51   4.82  40.61
   4_occ:  93.36   1.45  16.87  93.36   1.45  12.51  88.51   4.82  40.61
   5_bss:  93.36   1.45  16.87  93.36   1.45  12.51  88.51   4.82  40.61
   5_xyz:  93.36   1.45  16.87  93.36   1.45  12.51  88.51   4.82  40.61
   5_adp: 106.29   0.32  17.01 106.29   0.32  12.47  93.38   4.89  41.72
   5_occ: 106.29   0.32  17.01 106.29   0.32  12.47  93.38   4.89  41.72
   5_bss: 106.28   0.31  17.00 106.28   0.31  12.46  93.37   4.88  41.71
------------------------------------------------------------------------
 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:    1.880    0.016    0.351
   1_adp:    1.880    0.016    0.351
   1_occ:    1.880    0.016    0.351
   2_bss:    1.880    0.016    0.351
   2_xyz:    1.275    0.062    0.572
   2_adp:    1.275    0.062    0.572
   2_occ:    1.275    0.062    0.572
   3_bss:    1.275    0.062    0.572
   3_xyz:    1.315    0.072    0.647
   3_adp:    1.315    0.072    0.647
   3_occ:    1.315    0.072    0.647
   4_bss:    1.315    0.072    0.647
   4_xyz:    1.343    0.052    0.683
   4_adp:    1.343    0.052    0.683
   4_occ:    1.343    0.052    0.683
   5_bss:    1.343    0.052    0.683
   5_xyz:    1.330    0.069    0.693
   5_adp:    1.330    0.069    0.693
   5_occ:    1.330    0.069    0.693
   5_bss:    1.330    0.069    0.693
------------------------------------------------------------------------

CPU time actual refinement: 334.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/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_827/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_827/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.30 
  Macro-tasks:
    bulk solvent and scale       = 41.62  
    individual site refinement   = 136.10 
    weights calculation          = 29.71  
    collect and process          = 6.75   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 214.27 
  Micro-tasks:
    mask                            = 1.70   
    f_calc                          = 107.46 
    alpha_beta                      = 8.63   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 111.23 
    fmodel                         = 6.82   
    r_factors                      = 0.18   
    phase_errors                   = 11.76  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 249.30 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.747 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    638 calls, 106.97 s
gradients_fft:          583 calls,  99.83 s

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

# Date 2008-01-16 Time 05:45:48 PST -0800 (1200491148.59 s)
Start R-work = 0.4234, R-free = 0.4121 (no bulk solvent and anisotropic scale)
Final R-work = 0.1352, R-free = 0.1800 (no bulk solvent and anisotropic scale)

Start R-work = 0.4118, R-free = 0.3982
Final R-work = 0.1157, R-free = 0.1626