# Date 2008-01-16 Time 06:13:29 PST -0800 (1200492809.37 s)
#phil __OFF__

Command line arguments: "../1061.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31178
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1061

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.6339, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00117
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955468

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   2.0012

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 2.00117
Completeness in resolution range: 0.958413
Completeness with d_max=infinity: 0.955468

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2820 [2140/2168]  1928   212   9.9%
  bin  2:  4.2820 -  3.4115 [2054/2070]  1846   208  10.1%
  bin  3:  3.4115 -  2.9840 [2033/2052]  1829   204  10.0%
  bin  4:  2.9840 -  2.7129 [2027/2057]  1830   197   9.7%
  bin  5:  2.7129 -  2.5194 [2006/2025]  1804   202  10.1%
  bin  6:  2.5194 -  2.3714 [1977/2013]  1780   197  10.0%
  bin  7:  2.3714 -  2.2531 [1973/2006]  1773   200  10.1%
  bin  8:  2.2531 -  2.1553 [1989/2022]  1790   199  10.0%
  bin  9:  2.1553 -  2.0725 [1979/2008]  1785   194   9.8%
  bin 10:  2.0725 -  2.0012 [1411/2018]  1265   146  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.19: 6
        2.19 -     2.87: 1177
        2.87 -     3.55: 4377
        3.55 -     4.22: 9068
        4.22 -     4.90: 13254
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.519 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.017 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.147 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.168 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27877 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_1061/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.63395 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3726   r_free= 0.3635   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.152873                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7759 0.99   1386  154 0.3049 0.3156      6.3989      6.3408|
|  2:  4.7759 -  3.8106 0.99   1353  147 0.2952 0.3065      6.5923      6.6048|
|  3:  3.8106 -  3.3348 0.99   1306  149 0.3246 0.3018      6.4623      6.4285|
|  4:  3.3348 -  3.0326 0.99   1309  146 0.3580 0.3213      6.3778      6.2641|
|  5:  3.0326 -  2.8167 0.99   1305  142 0.3829 0.3968      6.2228      6.2834|
|  6:  2.8167 -  2.6515 0.99   1284  146 0.4000 0.3700      6.1608      6.0865|
|  7:  2.6515 -  2.5194 0.99   1294  139 0.4019 0.3701      6.1168      6.0617|
|  8:  2.5194 -  2.4102 0.98   1269  149 0.4184 0.4079        6.08      6.0778|
|  9:  2.4102 -  2.3177 0.98   1282  142 0.4223 0.4199       6.027      6.0848|
| 10:  2.3177 -  2.2380 0.98   1264  133 0.4280 0.4057      6.0186      5.9894|
| 11:  2.2380 -  2.1682 1.00   1273  146 0.4334 0.4139      5.9776      5.9944|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.4309 0.4289      5.9116      5.9339|
| 13:  2.1064 -  2.0511 0.98   1267  144 0.4392 0.4162      5.8244      5.7594|
| 14:  2.0511 -  2.0012 0.60    777   86 0.4123 0.4548      5.7389       5.756|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7759  1386   154  0.77  28.01   0.85     0.79      48634.19|
|  2:  4.7759 -  3.8106  1353   147  0.82  24.72   0.95     0.87      56902.63|
|  3:  3.8106 -  3.3348  1306   149  0.76  30.09   0.95     0.89      58403.39|
|  4:  3.3348 -  3.0326  1309   146  0.72  33.65   0.94     0.86      52217.69|
|  5:  3.0326 -  2.8167  1305   142  0.64  40.36   0.95     0.81      45694.14|
|  6:  2.8167 -  2.6515  1284   146  0.63  41.23   0.95     0.80      39964.37|
|  7:  2.6515 -  2.5194  1294   139  0.62  42.43   0.96     0.79      37746.46|
|  8:  2.5194 -  2.4102  1269   149  0.59  45.30   0.96     0.78      36541.73|
|  9:  2.4102 -  2.3177  1282   142  0.57  46.69   0.96     0.76      35831.05|
| 10:  2.3177 -  2.2380  1264   133  0.56  47.70   0.97     0.76      33845.96|
| 11:  2.2380 -  2.1682  1273   146  0.56  47.45   0.98     0.78      31129.40|
| 12:  2.1682 -  2.1064  1261   136  0.57  46.72   0.98     0.81      28376.43|
| 13:  2.1064 -  2.0511  1267   144  0.55  48.57   0.95     0.78      24815.92|
| 14:  2.0511 -  2.0012   777    86  0.54  49.01   0.98     0.71      21180.50|
|alpha:            min =        0.71 max =            0.89 mean =         0.80|
|beta:             min =    21180.50 max =        58403.39 mean =     40114.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.64|
|phase err.(work): min =        0.00 max =           90.00 mean =        40.43|
|phase err.(test): min =        0.00 max =           89.94 mean =        40.50|
|-----------------------------------------------------------------------------|

============================== 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 = 3.870806              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.155   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.043925              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.259   (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 |  1.519 -  1.857:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.857 -  2.195:        4 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.195 -  2.533:       18 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.533 -  2.871:     1159 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.871 -  3.209:     1888 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.209 -  3.547:     2489 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.547 -  3.886:     4590 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.886 -  4.224:     4478 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.224 -  4.562:     6025 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.562 -  4.900:     7229 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.165 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.519 |       0.181 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3726   r_free= 0.3635   ksol= 0.00   Bsol= 0.00   scale= 0.935    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.152873                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3613   r_free= 0.3531   ksol= 0.30   Bsol= 50.00   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,2.95,-1.97,0.00,-0.00,-0.00); trace/3= 0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.136483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.489624              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.205   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559866              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.996   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3613      final r-factor (work) = 0.2520          |
| start r-factor (free) = 0.3531      final r-factor (free) = 0.2769          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8771 = 3.49 * 0.50 * 6.1396 + 1.00 * 0.1645                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4382 = 3.49 * 0.50 * 5.9292 + 1.00 * 0.0928                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2520      final r-factor (work) = 0.2305          |
| start r-factor (free) = 0.2769      final r-factor (free) = 0.2805          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3256 = 0.56 * 1.00 * 5.9292 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2404 = 0.56 * 1.00 * 5.7665 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.10   17.41    None  None   None       |
|    all(noH): 2823   0      0.00    89.10   17.41    None  None   None       |
|    Sol.    : 438    0      2.94    89.10   39.34    None  None   None       |
|    Mac.    : 2385   0      0.00    79.38   13.38    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 -   8.910:  843   |   5:    44.552 -  53.462:   94        |
|      1:     8.910 -  17.821: 1100   |   6:    53.462 -  62.372:   65        |
|      2:    17.821 -  26.731:  384   |   7:    62.372 -  71.282:   38        |
|      3:    26.731 -  35.641:  170   |   8:    71.282 -  80.193:    9        |
|      4:    35.641 -  44.552:  118   |   9:    80.193 -  89.103:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2305 r_free = 0.2805             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2301 r_free = 0.2803             target_work(ml) = 5.770         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2301   r_free= 0.2803   ksol= 0.30   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,2.95,-1.97,0.00,-0.00,-0.00); trace/3= 0.11                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.769734                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2287   r_free= 0.2783   ksol= 0.33   Bsol= 71.38   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.33,-1.49,0.00,-0.00,-0.00); trace/3= -0.90                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.766603                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.413664              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.554   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284068              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.003  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2287      final r-factor (work) = 0.1680          |
| start r-factor (free) = 0.2783      final r-factor (free) = 0.2095          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9364 = 3.41 * 0.50 * 5.7672 + 1.00 * 0.0928                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6874 = 3.41 * 0.50 * 5.6369 + 1.00 * 0.0661                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1565          |
| start r-factor (free) = 0.2095      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6131 = 0.28 * 1.00 * 5.6369 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5572 = 0.28 * 1.00 * 5.4492 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    88.58   17.13    None  None   None       |
|    all(noH): 2823   0      0.91    88.58   17.13    None  None   None       |
|    Sol.    : 438    0      4.54    88.58   40.01    None  None   None       |
|    Mac.    : 2385   0      0.91    82.03   12.93    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:     0.906 -   9.674: 1008   |   5:    44.745 -  53.513:   98        |
|      1:     9.674 -  18.442: 1065   |   6:    53.513 -  62.281:   67        |
|      2:    18.442 -  27.210:  278   |   7:    62.281 -  71.049:   35        |
|      3:    27.210 -  35.978:  139   |   8:    71.049 -  79.817:    8        |
|      4:    35.978 -  44.745:  121   |   9:    79.817 -  88.585:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1565 r_free = 0.1946             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1564 r_free = 0.1947             target_work(ml) = 5.419         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1564   r_free= 0.1947   ksol= 0.33   Bsol= 71.38   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.53,0.33,-1.49,0.00,-0.00,-0.00); trace/3= -0.90                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.418940                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1562   r_free= 0.1948   ksol= 0.33   Bsol= 71.38   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.87,-1.21,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.418109                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.610118              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.295  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.809610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.287  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1562      final r-factor (work) = 0.1287          |
| start r-factor (free) = 0.1948      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1778 = 2.61 * 0.50 * 5.4493 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0159 = 2.61 * 0.50 * 5.3280 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1287      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3228 = 0.81 * 1.00 * 5.3280 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2472 = 0.81 * 1.00 * 5.2329 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.87   17.19    None  None   None       |
|    all(noH): 2823   0      0.00    91.87   17.19    None  None   None       |
|    Sol.    : 438    0      5.15    89.68   41.65    None  None   None       |
|    Mac.    : 2385   0      0.00    91.87   12.70    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 -   9.187:  936   |   5:    45.933 -  55.119:   95        |
|      1:     9.187 -  18.373: 1176   |   6:    55.119 -  64.306:   82        |
|      2:    18.373 -  27.560:  242   |   7:    64.306 -  73.492:   35        |
|      3:    27.560 -  36.746:  134   |   8:    73.492 -  82.679:   10        |
|      4:    36.746 -  45.933:  108   |   9:    82.679 -  91.865:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1669             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1669             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1669   ksol= 0.33   Bsol= 71.38   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-0.87,-1.21,-0.00,-0.00,-0.00); trace/3= -1.32                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.221443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1668   ksol= 0.33   Bsol= 69.10   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.26,-1.04,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222021                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.386069              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.538  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822637              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.113  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1668      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6904 = 1.39 * 0.50 * 5.2338 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6659 = 1.39 * 0.50 * 5.2168 + 1.00 * 0.0505                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3022 = 0.82 * 1.00 * 5.2168 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2966 = 0.82 * 1.00 * 5.2095 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    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   17.01    None  None   None       |
|    all(noH): 2823   0      0.00    92.64   17.01    None  None   None       |
|    Sol.    : 438    0      4.90    89.94   41.55    None  None   None       |
|    Mac.    : 2385   0      0.00    92.64   12.50    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:  995   |   5:    46.318 -  55.582:   98        |
|      1:     9.264 -  18.527: 1130   |   6:    55.582 -  64.845:   81        |
|      2:    18.527 -  27.791:  235   |   7:    64.845 -  74.109:   31        |
|      3:    27.791 -  37.054:  132   |   8:    74.109 -  83.372:    9        |
|      4:    37.054 -  46.318:  106   |   9:    83.372 -  92.636:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1208 r_free = 0.1665             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1665             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1665   ksol= 0.33   Bsol= 69.10   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.89,-1.26,-1.04,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.210697                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1664   ksol= 0.32   Bsol= 66.82   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.25,-0.80,-0.00,-0.00,-0.00); trace/3= -1.26                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.210660                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.174564              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 150.832  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.327123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.047  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1640          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7148 = 2.17 * 0.50 * 5.2096 + 1.00 * 0.0505                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7046 = 2.17 * 0.50 * 5.1882 + 1.00 * 0.0636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1143          |
| start r-factor (free) = 0.1640      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2727 = 3.33 * 1.00 * 5.1882 + 1.00 * 0.0110                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2289 = 3.33 * 1.00 * 5.1747 + 1.00 * 0.0119                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.96  16.92    None  None   None       |
|    all(noH): 2823   0      0.00    103.96  16.92    None  None   None       |
|    Sol.    : 438    0      4.73    92.53   41.75    None  None   None       |
|    Mac.    : 2385   0      0.00    103.96  12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.397: 1289   |   5:    51.982 -  62.379:   88        |
|      1:    10.397 -  20.793:  926   |   6:    62.379 -  72.775:   49        |
|      2:    20.793 -  31.190:  205   |   7:    72.775 -  83.172:   19        |
|      3:    31.190 -  41.586:  130   |   8:    83.172 -  93.568:    5        |
|      4:    41.586 -  51.982:  109   |   9:    93.568 - 103.965:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1143 r_free = 0.1642             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1642             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1642   ksol= 0.32   Bsol= 66.82   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.25,-0.80,-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: 5.176635                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7759 0.99   1386  154 0.0982 0.1325      5.3802      5.5358|
|  2:  4.7759 -  3.8106 0.99   1353  147 0.0828 0.1033       5.408      5.5868|
|  3:  3.8106 -  3.3348 0.99   1306  149 0.1039 0.1504      5.4597      5.8536|
|  4:  3.3348 -  3.0326 0.99   1309  146 0.1226 0.1609      5.4788      5.6259|
|  5:  3.0326 -  2.8167 0.99   1305  142 0.1389 0.1887      5.3739      5.5991|
|  6:  2.8167 -  2.6515 0.99   1284  146 0.1281 0.1898      5.2629      5.4922|
|  7:  2.6515 -  2.5194 0.99   1294  139 0.1276 0.1722      5.1952      5.4144|
|  8:  2.5194 -  2.4102 0.98   1269  149 0.1208 0.1750      5.1052       5.349|
|  9:  2.4102 -  2.3177 0.98   1282  142 0.1228 0.1960      5.0777      5.3865|
| 10:  2.3177 -  2.2380 0.98   1264  133 0.1174 0.1921      5.0156       5.287|
| 11:  2.2380 -  2.1682 1.00   1273  146 0.1194 0.1799      4.9887      5.2939|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.1147 0.1760      4.9254      5.1902|
| 13:  2.1064 -  2.0511 0.98   1267  144 0.1203 0.1876      4.8491      5.1482|
| 14:  2.0511 -  2.0012 0.60    777   86 0.1121 0.1813      4.7128       4.995|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7759  1386   154  0.94   9.34   0.96     0.94       7322.18|
|  2:  4.7759 -  3.8106  1353   147  0.95   7.72   1.00     0.98       8589.81|
|  3:  3.8106 -  3.3348  1306   149  0.93  11.14   1.02     1.01      10111.44|
|  4:  3.3348 -  3.0326  1309   146  0.91  14.41   1.00     0.98      11121.32|
|  5:  3.0326 -  2.8167  1305   142  0.89  16.92   0.99     0.96       9188.84|
|  6:  2.8167 -  2.6515  1284   146  0.89  16.93   0.98     0.96       7943.92|
|  7:  2.6515 -  2.5194  1294   139  0.90  16.00   0.98     0.95       6644.34|
|  8:  2.5194 -  2.4102  1269   149  0.90  16.25   0.97     0.95       5869.97|
|  9:  2.4102 -  2.3177  1282   142  0.90  16.35   0.98     0.94       5506.35|
| 10:  2.3177 -  2.2380  1264   133  0.89  16.71   0.97     0.93       4939.06|
| 11:  2.2380 -  2.1682  1273   146  0.89  17.50   0.97     0.93       4868.57|
| 12:  2.1682 -  2.1064  1261   136  0.91  15.74   0.97     0.95       4403.59|
| 13:  2.1064 -  2.0511  1267   144  0.89  17.55   0.97     0.97       3880.69|
| 14:  2.0511 -  2.0012   777    86  0.90  15.88   0.94     0.90       2825.78|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     2825.78 max =        11121.32 mean =      6803.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.79|
|phase err.(test): min =        0.00 max =           89.76 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1641   ksol= 0.32   Bsol= 65.39   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-1.03,-0.51,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1641   ksol= 0.32   Bsol= 65.39   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.42,-1.03,-0.51,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176720                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7759 0.99   1386  154 0.0981 0.1327      5.3806      5.5371|
|  2:  4.7759 -  3.8106 0.99   1353  147 0.0828 0.1032      5.4082      5.5859|
|  3:  3.8106 -  3.3348 0.99   1306  149 0.1040 0.1505      5.4596      5.8542|
|  4:  3.3348 -  3.0326 0.99   1309  146 0.1227 0.1611       5.479      5.6263|
|  5:  3.0326 -  2.8167 0.99   1305  142 0.1389 0.1888      5.3741       5.599|
|  6:  2.8167 -  2.6515 0.99   1284  146 0.1281 0.1896      5.2628      5.4918|
|  7:  2.6515 -  2.5194 0.99   1294  139 0.1277 0.1724      5.1953      5.4151|
|  8:  2.5194 -  2.4102 0.98   1269  149 0.1209 0.1750      5.1052      5.3486|
|  9:  2.4102 -  2.3177 0.98   1282  142 0.1227 0.1959      5.0779      5.3866|
| 10:  2.3177 -  2.2380 0.98   1264  133 0.1174 0.1922       5.016      5.2875|
| 11:  2.2380 -  2.1682 1.00   1273  146 0.1194 0.1798      4.9887      5.2938|
| 12:  2.1682 -  2.1064 0.97   1261  136 0.1147 0.1761      4.9253       5.191|
| 13:  2.1064 -  2.0511 0.98   1267  144 0.1203 0.1876      4.8487      5.1476|
| 14:  2.0511 -  2.0012 0.60    777   86 0.1122 0.1812      4.7127      4.9942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7759  1386   154  0.94   9.35   0.96     0.94       7338.43|
|  2:  4.7759 -  3.8106  1353   147  0.95   7.72   1.00     0.98       8594.70|
|  3:  3.8106 -  3.3348  1306   149  0.93  11.14   1.02     1.02      10110.55|
|  4:  3.3348 -  3.0326  1309   146  0.91  14.42   1.01     0.99      11125.83|
|  5:  3.0326 -  2.8167  1305   142  0.89  16.92   1.00     0.97       9186.42|
|  6:  2.8167 -  2.6515  1284   146  0.89  16.93   0.99     0.97       7940.69|
|  7:  2.6515 -  2.5194  1294   139  0.90  16.00   0.99     0.96       6642.49|
|  8:  2.5194 -  2.4102  1269   149  0.90  16.26   0.99     0.96       5869.46|
|  9:  2.4102 -  2.3177  1282   142  0.90  16.35   0.99     0.95       5509.13|
| 10:  2.3177 -  2.2380  1264   133  0.89  16.72   0.99     0.94       4941.19|
| 11:  2.2380 -  2.1682  1273   146  0.89  17.51   0.98     0.94       4870.04|
| 12:  2.1682 -  2.1064  1261   136  0.91  15.74   0.99     0.96       4403.31|
| 13:  2.1064 -  2.0511  1267   144  0.89  17.54   0.99     0.98       3877.39|
| 14:  2.0511 -  2.0012   777    86  0.90  15.88   0.96     0.92       2822.09|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2822.09 max =        11125.83 mean =      6804.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.79|
|phase err.(test): min =        0.00 max =           89.78 mean =        14.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.266)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.97  16.92    None  None   None       |
|    all(noH): 2823   0      0.00    103.97  16.92    None  None   None       |
|    Sol.    : 438    0      4.73    92.54   41.75    None  None   None       |
|    Mac.    : 2385   0      0.00    103.97  12.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.400: 1289   |   5:    51.985 -  62.382:   88        |
|      1:    10.400 -  20.796:  926   |   6:    62.382 -  72.778:   49        |
|      2:    20.796 -  31.192:  205   |   7:    72.778 -  83.175:   19        |
|      3:    31.192 -  41.589:  130   |   8:    83.175 -  93.571:    5        |
|      4:    41.589 -  51.985:  109   |   9:    93.571 - 103.968:    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)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.483 - 4.712
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 317
   mapped sites are within: 0.708 - 4.712

peak=    6.039 closest distance to " O   HOH Z 111 " =    2.134
peak=    5.773 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.291 closest distance to " CG  PRO A  54 " =    1.250
peak=    5.161 closest distance to " CB  SER A  63 " =    1.278
peak=    4.990 closest distance to " O   HOH Z 232 " =    2.320
peak=    4.629 closest distance to " CB  GLU A 128 " =    1.146
peak=    4.618 closest distance to " CB  PRO A  54 " =    0.897
peak=    4.605 closest distance to " CB  GLN A 183 " =    1.287
peak=    4.595 closest distance to " O   HOH Z 298 " =    2.007
peak=    4.579 closest distance to " CB  ARG A 275 " =    0.885
peak=    4.575 closest distance to " CG  PRO A 213 " =    1.190
peak=    4.557 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.484 closest distance to " O   HOH Z 369 " =    2.131
peak=    4.483 closest distance to " C   PRO A 198 " =    1.552
peak=    4.476 closest distance to " CB  ARG A 190 " =    1.708
peak=    4.413 closest distance to " CG  PRO A 198 " =    1.225
peak=    4.345 closest distance to " CB  LEU A 228 " =    1.104
peak=    4.341 closest distance to " CG  PRO A  90 " =    1.120
peak=    4.280 closest distance to " O   HOH Z  15 " =    2.153
peak=    4.241 closest distance to " CZ  PHE A 218 " =    1.108
peak=    4.209 closest distance to " OD1 ASN A  69 " =    2.557
peak=    4.194 closest distance to " CB  TRP A 266 " =    0.994
peak=    4.191 closest distance to " O   HOH Z  68 " =    1.822
peak=    4.174 closest distance to " CD  ARG A 269 " =    0.962
peak=    4.168 closest distance to " O   HOH Z  40 " =    1.856
peak=    4.166 closest distance to " O   HOH Z 403 " =    1.770
peak=    4.165 closest distance to " O   HOH Z 234 " =    3.880
peak=    4.162 closest distance to " CB  TYR A 169 " =    0.812
peak=    4.159 closest distance to " NH2 ARG A 156 " =    1.176
peak=    4.158 closest distance to " O   HOH Z 134 " =    1.438
peak=    4.154 closest distance to " O   HOH Z  44 " =    2.291
peak=    4.111 closest distance to " CG1 ILE A  33 " =    1.221
peak=    4.098 closest distance to " CG  PRO A 243 " =    1.136
peak=    4.069 closest distance to " O   HOH Z 133 " =    2.428
peak=    4.054 closest distance to " O   HOH Z 271 " =    2.929
peak=    4.047 closest distance to " O   HOH Z  20 " =    1.772
peak=    4.038 closest distance to " CB  VAL A 202 " =    1.600
peak=    4.025 closest distance to " C   ILE A 106 " =    1.846
peak=    4.004 closest distance to " CG2 THR A 221 " =    1.081
peak=    3.969 closest distance to " CB  ARG A  79 " =    1.362
peak=    3.953 closest distance to " O   HOH Z  19 " =    2.171
peak=    3.951 closest distance to " CD1 LEU A 300 " =    1.206
peak=    3.949 closest distance to " O   HOH Z 425 " =    1.318
peak=    3.948 closest distance to " O   HOH Z 126 " =    2.089
peak=    3.948 closest distance to " CD BLYS A 290 " =    0.991
peak=    3.947 closest distance to " CB  GLU A 152 " =    1.116
peak=    3.946 closest distance to " O   HOH Z 411 " =    3.724
peak=    3.946 closest distance to " CB  GLU A 277 " =    3.768
peak=    3.943 closest distance to " CB  ASN A 148 " =    1.401
peak=    3.927 closest distance to " O   HOH Z 368 " =    2.173
peak=    3.926 closest distance to " NE2 GLN A  11 " =    0.994
peak=    3.921 closest distance to " O   HOH Z 265 " =    2.220
peak=    3.909 closest distance to " O   HOH Z 214 " =    2.203
peak=    3.905 closest distance to " O   HOH Z 287 " =    2.069
peak=    3.895 closest distance to " O   HOH Z  21 " =    1.794
peak=    3.880 closest distance to " O   HOH Z 402 " =    1.489
peak=    3.880 closest distance to " O   HOH Z 261 " =    1.925
peak=    3.878 closest distance to " CA  ARG A 195 " =    1.209
peak=    3.870 closest distance to " CB  ASP A 140 " =    0.949
peak=    3.867 closest distance to " O   HOH Z 189 " =    2.574
peak=    3.860 closest distance to " O   THR A 251 " =    1.276
peak=    3.860 closest distance to " O   HOH Z  78 " =    1.662
peak=    3.860 closest distance to " CA  ALA A  21 " =    1.323
peak=    3.837 closest distance to " CA  PRO A  54 " =    1.368
peak=    3.826 closest distance to " CA  THR A 221 " =    0.943
peak=    3.824 closest distance to " CA  ALA A  51 " =    0.997
peak=    3.824 closest distance to " O   HOH Z 158 " =    2.966
peak=    3.821 closest distance to " O   HOH Z 280 " =    3.008
peak=    3.817 closest distance to " O   ALA A 165 " =    1.395
peak=    3.814 closest distance to " CB  TRP A 179 " =    1.507
peak=    3.805 closest distance to " O   HOH Z  43 " =    1.871
peak=    3.804 closest distance to " CD  ARG A 159 " =    0.836
peak=    3.800 closest distance to " CD2 LEU A 297 " =    0.936
peak=    3.800 closest distance to " O   HOH Z 361 " =    3.597
peak=    3.793 closest distance to " O   HOH Z 193 " =    1.894
peak=    3.793 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.791 closest distance to " CA  ARG A  36 " =    1.191
peak=    3.789 closest distance to " O   HOH Z 203 " =    1.921
peak=    3.781 closest distance to " CA  ASP A 191 " =    0.832
peak=    3.759 closest distance to " O   HOH Z 180 " =    2.170
peak=    3.757 closest distance to " O   HOH Z 128 " =    2.159
peak=    3.723 closest distance to " CG  ARG A  66 " =    2.530
peak=    3.722 closest distance to " CA  MET A  40 " =    1.166
peak=    3.722 closest distance to " O   HOH Z 163 " =    1.659
peak=    3.714 closest distance to " O   HOH Z 247 " =    1.405
peak=    3.713 closest distance to " O   HOH Z 279 " =    2.286
peak=    3.709 closest distance to " O   HOH Z 316 " =    3.116
peak=    3.706 closest distance to " NH1AARG A 145 " =    1.154
peak=    3.701 closest distance to " O   HOH Z  97 " =    2.041
peak=    3.699 closest distance to " ND2 ASN A 249 " =    1.989
peak=    3.689 closest distance to " CG2BVAL A  41 " =    0.879
peak=    3.686 closest distance to " O   HOH Z 383 " =    2.108
peak=    3.686 closest distance to " O   HOH Z 427 " =    3.167
peak=    3.685 closest distance to " ND2 ASN A 187 " =    1.410
peak=    3.685 closest distance to " O   SER A  87 " =    2.331
peak=    3.679 closest distance to " O   HOH Z  63 " =    1.887
peak=    3.678 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.677 closest distance to " CD  LYS A 166 " =    1.322
peak=    3.674 closest distance to " O   HOH Z 303 " =    2.175
peak=    3.671 closest distance to " CB  SER A   3 " =    1.376
peak=    3.667 closest distance to " O   HOH Z  80 " =    1.711
peak=    3.665 closest distance to " O   HOH Z 285 " =    3.071
peak=    3.660 closest distance to " CA  GLU A 152 " =    0.865
peak=    3.655 closest distance to " O   HOH Z 391 " =    2.937
peak=    3.647 closest distance to " O   HOH Z 102 " =    1.293
peak=    3.647 closest distance to " O   HOH Z 371 " =    3.338
peak=    3.646 closest distance to " CE  LYS A  76 " =    0.835
peak=    3.624 closest distance to " O   HOH Z 374 " =    2.860
peak=    3.624 closest distance to " O   HOH Z 272 " =    1.876
peak=    3.623 closest distance to " O   HOH Z 147 " =    1.764
peak=    3.620 closest distance to " NZ  LYS A 117 " =    3.184
peak=    3.613 closest distance to " CE1 TYR A 186 " =    1.361
peak=    3.608 closest distance to " O   HOH Z 155 " =    3.339
peak=    3.602 closest distance to " O   HOH Z 295 " =    1.510
peak=    3.599 closest distance to " CA  ALA A 160 " =    0.868
peak=    3.595 closest distance to " CA  ALA A 295 " =    1.167
peak=    3.593 closest distance to " CB  SER A 212 " =    1.041
peak=    3.587 closest distance to " OD1 ASN A 217 " =    1.759
peak=    3.587 closest distance to " CA  ASP A 124 " =    0.724
peak=    3.586 closest distance to " N   VAL A 126 " =    1.491
peak=    3.585 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.579 closest distance to " CD1 ILE A 106 " =    0.832
peak=    3.561 closest distance to " O   HOH Z 135 " =    1.963
peak=    3.561 closest distance to " O   HOH Z 423 " =    1.875
peak=    3.547 closest distance to " O   HOH Z 346 " =    1.568
peak=    3.545 closest distance to " O   HOH Z 426 " =    1.564
peak=    3.543 closest distance to " NH2BARG A 145 " =    2.112
peak=    3.542 closest distance to " CB  SER A 141 " =    1.024
peak=    3.536 closest distance to " CB  ASN A  39 " =    0.863
peak=    3.528 closest distance to " CB  ASN A 187 " =    1.176
peak=    3.526 closest distance to " O   HOH Z 132 " =    2.705
peak=    3.526 closest distance to " CZ  PHE A 192 " =    0.982
peak=    3.525 closest distance to " N   ASN A  39 " =    1.369
peak=    3.515 closest distance to " CA  VAL A 125 " =    1.259
peak=    3.512 closest distance to " O   HOH Z 250 " =    1.496
peak=    3.510 closest distance to " O   HOH Z  59 " =    2.370
peak=    3.509 closest distance to " O   HOH Z  88 " =    3.588
peak=    3.506 closest distance to " O   HOH Z 406 " =    1.571
peak=    3.502 closest distance to " CG  GLU A  37 " =    0.909
peak=    3.497 closest distance to " CA  SER A  87 " =    1.048
peak=    3.497 closest distance to " CB  SER A  62 " =    0.768
peak=    3.486 closest distance to " O   HOH Z 142 " =    1.405
peak=    3.482 closest distance to " N   ASN A 127 " =    1.272
peak=    3.481 closest distance to " O   ASN A  74 " =    1.624
peak=    3.476 closest distance to " NE2 HIS A 115 " =    1.032
peak=    3.473 closest distance to " OE1 GLN A  11 " =    1.990
peak=    3.466 closest distance to " CB  MET A  47 " =    0.986
peak=    3.461 closest distance to " O   HOH Z 126 " =    1.573
peak=    3.459 closest distance to " O   HOH Z 433 " =    1.503
peak=    3.451 closest distance to " O   HOH Z 145 " =    2.507
peak=    3.446 closest distance to " O   THR A 220 " =    1.189
peak=    3.443 closest distance to " CB  ALA A 291 " =    1.307
peak=    3.442 closest distance to " O   HOH Z 174 " =    2.324
peak=    3.439 closest distance to " N   ILE A  33 " =    1.071
peak=    3.434 closest distance to " O   ALA A 158 " =    1.230
peak=    3.431 closest distance to " O   HOH Z 353 " =    2.745
peak=    3.427 closest distance to " O   HOH Z 387 " =    2.926
peak=    3.423 closest distance to " CG  GLN A  58 " =    2.536
peak=    3.421 closest distance to " CB  PRO A 198 " =    1.085
peak=    3.417 closest distance to " O   HOH Z 344 " =    3.232
peak=    3.417 closest distance to " CB  ALA A 100 " =    1.372
peak=    3.417 closest distance to " CG2 VAL A 197 " =    1.199
peak=    3.417 closest distance to " O   HOH Z 422 " =    2.637
peak=    3.411 closest distance to " CD1 LEU A  96 " =    0.708
peak=    3.406 closest distance to " CG2 VAL A 257 " =    0.900
peak=    3.402 closest distance to " O   HOH Z 421 " =    1.562
peak=    3.390 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.388 closest distance to " CB  ASN A 148 " =    1.978
peak=    3.387 closest distance to " O   HOH Z 294 " =    1.584
peak=    3.386 closest distance to " CD2 LEU A 255 " =    1.510
peak=    3.384 closest distance to " OG BSER A 164 " =    2.366
peak=    3.383 closest distance to " CA  MET A 105 " =    1.080
peak=    3.383 closest distance to " OD2 ASP A 298 " =    3.955
peak=    3.374 closest distance to " CA  THR A 221 " =    1.335
peak=    3.366 closest distance to " CA  ASN A 215 " =    1.132
peak=    3.366 closest distance to " O   HOH Z 245 " =    1.263
peak=    3.365 closest distance to " CB  ASN A 142 " =    1.093
peak=    3.365 closest distance to " O   HOH Z 132 " =    3.226
peak=    3.362 closest distance to " CA  ARG A 102 " =    1.209
peak=    3.360 closest distance to " CA  GLU A  46 " =    0.767
peak=    3.358 closest distance to " O   HOH Z 281 " =    4.712
peak=    3.358 closest distance to " O   HOH Z  47 " =    1.275
peak=    3.357 closest distance to " OD2 ASP A 286 " =    2.939
peak=    3.356 closest distance to " C   TYR A 214 " =    1.475
peak=    3.346 closest distance to " CB  ARG A 139 " =    0.868
peak=    3.344 closest distance to " O   HOH Z 116 " =    1.829
peak=    3.344 closest distance to " CB  MET A  40 " =    0.834
peak=    3.344 closest distance to " CG2 THR A  29 " =    1.456
peak=    3.343 closest distance to " CB  ASN A 285 " =    0.895
peak=    3.340 closest distance to " CD  ARG A  66 " =    2.504
peak=    3.339 closest distance to " CA  GLY A 241 " =    0.766
peak=    3.338 closest distance to " ND1 HIS A  81 " =    1.654
peak=    3.336 closest distance to " O   HOH Z 404 " =    1.477
peak=    3.334 closest distance to " N   ASN A 252 " =    1.232
peak=    3.333 closest distance to " CB  ALA A   9 " =    1.550
peak=    3.331 closest distance to " O   HOH Z 299 " =    4.491
peak=    3.329 closest distance to " CB  GLN A  89 " =    1.256
peak=    3.326 closest distance to " O   ASP A 124 " =    1.275
peak=    3.323 closest distance to " O   HOH Z 291 " =    1.498
peak=    3.318 closest distance to " CA  ASP A 162 " =    1.163
peak=    3.311 closest distance to " O   HOH Z 345 " =    1.678
peak=    3.311 closest distance to " O   HOH Z 197 " =    1.994
peak=    3.303 closest distance to " CG  LEU A 167 " =    1.142
peak=    3.297 closest distance to " CG1BVAL A  72 " =    1.822
peak=    3.295 closest distance to " O   HOH Z  88 " =    1.806
peak=    3.295 closest distance to " CB  TYR A 169 " =    0.839
peak=    3.292 closest distance to " O   HOH Z 437 " =    1.216
peak=    3.292 closest distance to " CB  ALA A 242 " =    0.907
peak=    3.290 closest distance to " CB  ALA A  34 " =    0.928
peak=    3.288 closest distance to " O   HOH Z 128 " =    2.393
peak=    3.287 closest distance to " CB  ILE A 120 " =    1.359
peak=    3.285 closest distance to " CB  TYR A 116 " =    0.991
peak=    3.284 closest distance to " CA  ASP A 140 " =    1.229
peak=    3.283 closest distance to " N   ARG A 156 " =    1.396
peak=    3.283 closest distance to " O   HOH Z   1 " =    2.536
peak=    3.277 closest distance to " CZ  PHE A  38 " =    1.319
peak=    3.274 closest distance to " CA  LYS A 117 " =    1.236
peak=    3.273 closest distance to " O   HOH Z 109 " =    2.721
peak=    3.272 closest distance to " CG AARG A 275 " =    1.225
peak=    3.270 closest distance to " C   GLY A  80 " =    1.041
peak=    3.264 closest distance to " O   HOH Z  44 " =    1.707
peak=    3.262 closest distance to " CZ3 TRP A  85 " =    0.916
peak=    3.259 closest distance to " CG2 VAL A  78 " =    0.942
peak=    3.258 closest distance to " CA  ASN A 217 " =    1.251
peak=    3.256 closest distance to " CG1 ILE A 151 " =    0.954
peak=    3.253 closest distance to " OG1 THR A 294 " =    2.447
peak=    3.252 closest distance to " CB  GLU A  46 " =    1.007
peak=    3.250 closest distance to " O   HOH Z 357 " =    2.068
peak=    3.249 closest distance to " CD  LYS A 119 " =    1.345
peak=    3.247 closest distance to " CB  GLN A 103 " =    0.947
peak=    3.243 closest distance to " O   HOH Z 329 " =    3.782
peak=    3.242 closest distance to " CA  GLN A  88 " =    1.409
peak=    3.237 closest distance to " CG2 ILE A  20 " =    1.326
peak=    3.234 closest distance to " O   HOH Z 171 " =    2.539
peak=    3.232 closest distance to " O   HOH Z 171 " =    3.875
peak=    3.227 closest distance to " O   HOH Z 423 " =    3.223
peak=    3.226 closest distance to " O   HOH Z 305 " =    3.749
peak=    3.224 closest distance to " O  BHOH Z 338 " =    2.221
peak=    3.222 closest distance to " O   HOH Z 130 " =    2.229
peak=    3.222 closest distance to " NZ  LYS A  48 " =    1.332
peak=    3.221 closest distance to " O   HOH Z 403 " =    1.349
peak=    3.219 closest distance to " O   HOH Z 189 " =    3.167
peak=    3.218 closest distance to " CD  GLU A 152 " =    0.835
peak=    3.217 closest distance to " CA  ILE A 106 " =    0.876
peak=    3.214 closest distance to " CD1 TRP A 266 " =    1.173
peak=    3.213 closest distance to " O   HOH Z 365 " =    2.955
peak=    3.213 closest distance to " NH2AARG A 275 " =    3.615
peak=    3.212 closest distance to " O   HOH Z 261 " =    1.487
peak=    3.207 closest distance to " O   HOH Z 193 " =    2.315
peak=    3.205 closest distance to " CG  ARG A 219 " =    1.167
peak=    3.203 closest distance to " N   CYS A 260 " =    0.813
peak=    3.202 closest distance to " O   TRP A 274 " =    1.791
peak=    3.198 closest distance to " O   HOH Z 325 " =    2.304
peak=    3.198 closest distance to " CB  GLN A  88 " =    1.273
peak=    3.197 closest distance to " CA  ALA A 291 " =    0.839
peak=    3.195 closest distance to " CA  ALA A 154 " =    1.047
peak=    3.195 closest distance to " O   HOH Z 425 " =    2.039
peak=    3.194 closest distance to " CG2AVAL A 121 " =    2.221
peak=    3.193 closest distance to " O   HOH Z 114 " =    1.206
peak=    3.191 closest distance to " O   HOH Z 227 " =    1.651
peak=    3.187 closest distance to " CB  ASN A 215 " =    1.226
peak=    3.183 closest distance to " O   HOH Z 141 " =    1.602
peak=    3.179 closest distance to " OG  SER A  62 " =    3.056
peak=    3.179 closest distance to " CG  LYS A  76 " =    1.058
peak=    3.178 closest distance to " CB  TRP A 150 " =    0.952
peak=    3.177 closest distance to " O   HOH Z 359 " =    1.434
peak=    3.176 closest distance to " O   HOH Z  44 " =    3.278
peak=    3.175 closest distance to " O   HOH Z 393 " =    3.288
peak=    3.175 closest distance to " N   TYR A  15 " =    0.774
peak=    3.173 closest distance to " NH2BARG A 190 " =    1.813
peak=    3.163 closest distance to " CA  GLU A 152 " =    1.403
peak=    3.159 closest distance to " CB  MET A 105 " =    1.026
peak=    3.158 closest distance to " CG2 ILE A 120 " =    1.003
peak=    3.154 closest distance to " CB  LEU A  83 " =    0.887
peak=    3.154 closest distance to " N   GLY A  98 " =    1.172
peak=    3.152 closest distance to " O   HOH Z 327 " =    1.908
peak=    3.152 closest distance to " O   HOH Z 271 " =    2.571
peak=    3.152 closest distance to " O   HOH Z 250 " =    1.517
peak=    3.148 closest distance to " O   THR A 251 " =    2.163
peak=    3.147 closest distance to " O   TYR A 116 " =    1.297
peak=    3.147 closest distance to " O   HOH Z 394 " =    1.596
peak=    3.143 closest distance to " CG2 ILE A 234 " =    0.874
peak=    3.143 closest distance to " O   HOH Z  10 " =    1.845
peak=    3.140 closest distance to " OG  SER A  97 " =    3.562
peak=    3.139 closest distance to " CA  ALA A 233 " =    1.672
peak=    3.136 closest distance to " CZ2 TRP A 179 " =    1.747
peak=    3.135 closest distance to " OH  TYR A  30 " =    1.250
peak=    3.133 closest distance to " NZ  LYS A 117 " =    1.624
peak=    3.133 closest distance to " CD  ARG A 195 " =    0.907
peak=    3.132 closest distance to " O   HOH Z 234 " =    1.880
peak=    3.130 closest distance to " O   HOH Z  32 " =    1.690
peak=    3.127 closest distance to " CG  MET A 185 " =    1.214
peak=    3.125 closest distance to " CE2 TYR A 186 " =    0.861
peak=    3.121 closest distance to " CA  ALA A  84 " =    1.344
peak=    3.119 closest distance to " OD2 ASP A 200 " =    1.262
peak=    3.115 closest distance to " O   HOH Z 134 " =    2.499
peak=    3.111 closest distance to " NE1 TRP A 266 " =    1.380
peak=    3.100 closest distance to " O   HOH Z 417 " =    3.151
peak=    3.100 closest distance to " CB  HIS A 108 " =    0.829
peak=    3.094 closest distance to " O   HOH Z 148 " =    3.305
peak=    3.093 closest distance to " O   HOH Z 167 " =    1.772
peak=    3.091 closest distance to " OG  SER A  28 " =    1.524
peak=    3.084 closest distance to " CB  ARG A 138 " =    1.003
peak=    3.083 closest distance to " O   HOH Z  88 " =    2.990
peak=    3.082 closest distance to " CA  ALA A 158 " =    1.076
peak=    3.078 closest distance to " OE1 GLU A   2 " =    2.161
peak=    3.076 closest distance to " CB  ALA A  43 " =    0.834
peak=    3.073 closest distance to " N   GLN A 278 " =    1.139
peak=    3.067 closest distance to " ND2 ASN A 110 " =    1.538
peak=    3.064 closest distance to " CB  ALA A 256 " =    1.434
peak=    3.010 closest distance to " O   ASP A 124 " =    1.791
peak=    2.987 closest distance to " ND2 ASN A 301 " =    1.703

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.701 - 5.957
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 225 from: 225
   mapped sites are within: 0.701 - 5.957

peak=   -4.715 closest distance to " O   HOH Z 266 " =    5.045
peak=   -4.413 closest distance to " O   HOH Z  10 " =    1.656
peak=   -4.386 closest distance to " CD  ARG A 156 " =    2.067
peak=   -4.217 closest distance to " CG1 VAL A 250 " =    2.672
peak=   -4.182 closest distance to " CB  PRO A 243 " =    2.666
peak=   -4.108 closest distance to " O   VAL A  67 " =    2.712
peak=   -4.069 closest distance to " O   HOH Z 377 " =    1.972
peak=   -4.054 closest distance to " N   ALA A  43 " =    2.719
peak=   -4.049 closest distance to " OG  SER A  97 " =    2.229
peak=   -4.045 closest distance to " O   HOH Z  73 " =    2.277
peak=   -4.023 closest distance to " CA  ASP A 298 " =    1.061
peak=   -4.009 closest distance to " CD  GLN A 223 " =    1.317
peak=   -3.994 closest distance to " CG1 VAL A 112 " =    2.582
peak=   -3.968 closest distance to " O   HOH Z 196 " =    2.283
peak=   -3.966 closest distance to " O   HOH Z 231 " =    2.316
peak=   -3.924 closest distance to " O   PRO A 198 " =    1.305
peak=   -3.916 closest distance to " O   ILE A 109 " =    2.683
peak=   -3.904 closest distance to " O   HOH Z 292 " =    4.555
peak=   -3.887 closest distance to " O   HOH Z  52 " =    1.601
peak=   -3.886 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -3.885 closest distance to " O   HOH Z  38 " =    1.248
peak=   -3.857 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -3.851 closest distance to " C   HIS A 108 " =    1.113
peak=   -3.826 closest distance to " CD  GLN A  58 " =    1.019
peak=   -3.826 closest distance to " NH2 ARG A  66 " =    1.724
peak=   -3.826 closest distance to " O   HOH Z  13 " =    1.691
peak=   -3.809 closest distance to " O   PRO A 163 " =    2.199
peak=   -3.805 closest distance to " O   HOH Z  43 " =    1.476
peak=   -3.804 closest distance to " C   ASN A 285 " =    2.502
peak=   -3.796 closest distance to " ND2 ASN A  45 " =    1.814
peak=   -3.784 closest distance to " CD1 LEU A 101 " =    2.521
peak=   -3.782 closest distance to " CZ3 TRP A 179 " =    1.203
peak=   -3.776 closest distance to " CD  ARG A  14 " =    3.436
peak=   -3.771 closest distance to " OD1 ASN A 148 " =    1.518
peak=   -3.738 closest distance to " O   HOH Z 372 " =    2.523
peak=   -3.730 closest distance to " OXT GLY A 302 " =    3.018
peak=   -3.727 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.721 closest distance to " C   ASN A 187 " =    1.935
peak=   -3.712 closest distance to " O   HOH Z 210 " =    0.898
peak=   -3.696 closest distance to " O   HOH Z  19 " =    2.064
peak=   -3.677 closest distance to " CG2 ILE A 263 " =    2.371
peak=   -3.671 closest distance to " OE1 GLN A 223 " =    2.110
peak=   -3.664 closest distance to " O   HOH Z 166 " =    1.661
peak=   -3.662 closest distance to " CE2 PHE A  61 " =    2.594
peak=   -3.656 closest distance to " CG  GLU A  53 " =    1.387
peak=   -3.646 closest distance to " O   HOH Z 353 " =    2.224
peak=   -3.636 closest distance to " CG  GLU A 277 " =    1.206
peak=   -3.635 closest distance to " O   HOH Z 128 " =    2.541
peak=   -3.634 closest distance to " OG BSER A 134 " =    1.333
peak=   -3.632 closest distance to " OD1 ASP A 191 " =    1.604
peak=   -3.607 closest distance to " ND2 ASN A  45 " =    1.065
peak=   -3.600 closest distance to " O   HOH Z 290 " =    1.187
peak=   -3.598 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.597 closest distance to " O   HOH Z 252 " =    4.096
peak=   -3.587 closest distance to " O   HOH Z 185 " =    2.416
peak=   -3.582 closest distance to " CD  ARG A 139 " =    1.568
peak=   -3.576 closest distance to " O   HOH Z 198 " =    2.409
peak=   -3.573 closest distance to " CD2 PHE A 225 " =    1.247
peak=   -3.568 closest distance to " O   HOH Z 394 " =    1.610
peak=   -3.565 closest distance to " CG  ARG A  66 " =    2.458
peak=   -3.564 closest distance to " O   ALA A  10 " =    1.750
peak=   -3.557 closest distance to " O   HOH Z 393 " =    1.499
peak=   -3.555 closest distance to " CB  TRP A  85 " =    2.418
peak=   -3.555 closest distance to " O   HOH Z  37 " =    1.910
peak=   -3.554 closest distance to " CA  GLY A 203 " =    2.287
peak=   -3.549 closest distance to " O   HOH Z 407 " =    3.566
peak=   -3.534 closest distance to " NH2AARG A 275 " =    5.455
peak=   -3.530 closest distance to " C   SER A 206 " =    1.474
peak=   -3.519 closest distance to " C   ALA A 158 " =    1.317
peak=   -3.514 closest distance to " O   HOH Z 348 " =    2.249
peak=   -3.509 closest distance to " O   HOH Z 177 " =    1.728
peak=   -3.503 closest distance to " O   ALA A  34 " =    2.516
peak=   -3.502 closest distance to " O   HOH Z 150 " =    2.222
peak=   -3.494 closest distance to " NE2 GLN A 103 " =    1.826
peak=   -3.489 closest distance to " CD1 ILE A 151 " =    2.383
peak=   -3.479 closest distance to " O   HOH Z 377 " =    1.307
peak=   -3.475 closest distance to " CD2 TYR A 293 " =    2.028
peak=   -3.475 closest distance to " O   HOH Z 308 " =    1.744
peak=   -3.475 closest distance to " CE3 TRP A 150 " =    2.080
peak=   -3.473 closest distance to " OG BSER A 134 " =    1.944
peak=   -3.472 closest distance to " O   HOH Z   6 " =    1.535
peak=   -3.470 closest distance to " CD1 LEU A 228 " =    2.392
peak=   -3.468 closest distance to " CG2 VAL A 189 " =    2.206
peak=   -3.467 closest distance to " NE1 TRP A 266 " =    2.267
peak=   -3.466 closest distance to " OD2 ASP A 171 " =    1.841
peak=   -3.464 closest distance to " O   HOH Z 275 " =    1.576
peak=   -3.452 closest distance to " O   HOH Z 418 " =    1.284
peak=   -3.444 closest distance to " CA  GLY A 133 " =    2.312
peak=   -3.440 closest distance to " O   HOH Z 253 " =    4.237
peak=   -3.435 closest distance to " O   HOH Z 111 " =    2.028
peak=   -3.433 closest distance to " C   LEU A 143 " =    1.223
peak=   -3.431 closest distance to " CA  VAL A  67 " =    2.928
peak=   -3.430 closest distance to " O   HOH Z  71 " =    1.628
peak=   -3.427 closest distance to " SG  CYS A 168 " =    1.118
peak=   -3.426 closest distance to " CA  GLY A 241 " =    2.316
peak=   -3.423 closest distance to " CE BMET A  47 " =    2.172
peak=   -3.414 closest distance to " O   HOH Z 275 " =    1.855
peak=   -3.412 closest distance to " CD  PRO A 213 " =    2.223
peak=   -3.408 closest distance to " CD1 PHE A  16 " =    2.617
peak=   -3.407 closest distance to " CH2 TRP A 177 " =    2.069
peak=   -3.401 closest distance to " O   HOH Z 197 " =    2.062
peak=   -3.398 closest distance to " CG  ARG A 269 " =    2.362
peak=   -3.396 closest distance to " O   HOH Z 166 " =    1.703
peak=   -3.395 closest distance to " N   SER A 276 " =    1.481
peak=   -3.393 closest distance to " N   ALA A 226 " =    2.092
peak=   -3.392 closest distance to " CD2 PHE A  59 " =    2.553
peak=   -3.389 closest distance to " OH  TYR A 169 " =    0.999
peak=   -3.383 closest distance to " O   HOH Z 189 " =    1.873
peak=   -3.374 closest distance to " O   HOH Z 426 " =    1.790
peak=   -3.369 closest distance to " CD  ARG A 195 " =    5.042
peak=   -3.367 closest distance to " CG  ASP A 231 " =    0.850
peak=   -3.366 closest distance to " CD  GLN A  88 " =    0.924
peak=   -3.361 closest distance to " ND2BASN A 224 " =    1.802
peak=   -3.361 closest distance to " O   HOH Z  51 " =    1.577
peak=   -3.357 closest distance to " O   GLY A 118 " =    2.232
peak=   -3.356 closest distance to " O   HOH Z 311 " =    3.827
peak=   -3.355 closest distance to " O   HOH Z 389 " =    1.887
peak=   -3.351 closest distance to " O   SER A 210 " =    1.896
peak=   -3.347 closest distance to " O   HOH Z 102 " =    1.589
peak=   -3.344 closest distance to " ND2 ASN A  60 " =    1.567
peak=   -3.342 closest distance to " CG1 VAL A 112 " =    3.011
peak=   -3.334 closest distance to " CG  MET A 105 " =    0.913
peak=   -3.329 closest distance to " O   ASP A  27 " =    2.129
peak=   -3.326 closest distance to " OH  TYR A 247 " =    2.203
peak=   -3.326 closest distance to " CB  ALA A   9 " =    2.671
peak=   -3.324 closest distance to " O   PHE A 218 " =    1.539
peak=   -3.318 closest distance to " N   THR A 157 " =    1.619
peak=   -3.317 closest distance to " OG BSER A 210 " =    1.338
peak=   -3.311 closest distance to " OE1 GLN A  88 " =    1.017
peak=   -3.311 closest distance to " O   HOH Z 396 " =    1.636
peak=   -3.310 closest distance to " CB  ALA A  43 " =    2.623
peak=   -3.309 closest distance to " O   HOH Z 350 " =    1.841
peak=   -3.306 closest distance to " CB  ASP A 286 " =    2.216
peak=   -3.305 closest distance to " CB  ALA A 291 " =    2.324
peak=   -3.302 closest distance to " CB  ALA A  10 " =    2.129
peak=   -3.299 closest distance to " O   HOH Z 111 " =    1.481
peak=   -3.297 closest distance to " NE2 GLN A 194 " =    1.885
peak=   -3.295 closest distance to " O   HOH Z 234 " =    4.380
peak=   -3.289 closest distance to " OE2 GLU A   2 " =    1.605
peak=   -3.288 closest distance to " OD1 ASN A 187 " =    1.598
peak=   -3.286 closest distance to " O   HOH Z 298 " =    2.620
peak=   -3.285 closest distance to " O   HOH Z 191 " =    5.745
peak=   -3.284 closest distance to " CA  GLY A  98 " =    2.187
peak=   -3.284 closest distance to " O   HOH Z 118 " =    3.556
peak=   -3.283 closest distance to " O   HOH Z 414 " =    1.629
peak=   -3.282 closest distance to " O   HOH Z  11 " =    2.145
peak=   -3.281 closest distance to " NH1 ARG A 195 " =    2.708
peak=   -3.274 closest distance to " CE  MET A  93 " =    1.519
peak=   -3.271 closest distance to " CZ  TYR A 169 " =    1.833
peak=   -3.269 closest distance to " O   HOH Z 165 " =    1.910
peak=   -3.267 closest distance to " NH2 ARG A  79 " =    2.058
peak=   -3.264 closest distance to " O   HOH Z 323 " =    1.468
peak=   -3.263 closest distance to " O   ASN A 301 " =    1.393
peak=   -3.263 closest distance to " OG  SER A  26 " =    1.471
peak=   -3.251 closest distance to " N   GLN A  58 " =    1.608
peak=   -3.248 closest distance to " CZ  PHE A  38 " =    2.398
peak=   -3.247 closest distance to " O   HOH Z 200 " =    1.540
peak=   -3.244 closest distance to " OG ASER A 134 " =    1.223
peak=   -3.241 closest distance to " OH  TYR A 247 " =    1.766
peak=   -3.232 closest distance to " CG2 THR A 221 " =    2.257
peak=   -3.232 closest distance to " O   VAL A 125 " =    2.276
peak=   -3.230 closest distance to " CG1 VAL A 125 " =    2.041
peak=   -3.230 closest distance to " O   HOH Z 113 " =    2.183
peak=   -3.229 closest distance to " O   HOH Z 123 " =    2.408
peak=   -3.222 closest distance to " O   SER A 276 " =    1.666
peak=   -3.222 closest distance to " CD1 TRP A 179 " =    1.139
peak=   -3.220 closest distance to " NE2 GLN A  88 " =    1.973
peak=   -3.218 closest distance to " CE3 TRP A  70 " =    1.823
peak=   -3.214 closest distance to " O   HOH Z 117 " =    4.476
peak=   -3.211 closest distance to " ND2 ASN A  60 " =    1.845
peak=   -3.209 closest distance to " N   THR A 235 " =    1.284
peak=   -3.208 closest distance to " OG  SER A  62 " =    1.665
peak=   -3.205 closest distance to " O   HOH Z 351 " =    1.589
peak=   -3.201 closest distance to " CD2 PHE A  61 " =    2.050
peak=   -3.197 closest distance to " O   VAL A 189 " =    2.578
peak=   -3.196 closest distance to " O   HOH Z  93 " =    2.402
peak=   -3.189 closest distance to " CZ  PHE A  59 " =    1.970
peak=   -3.185 closest distance to " O   HOH Z 283 " =    5.957
peak=   -3.180 closest distance to " O   HOH Z 137 " =    2.368
peak=   -3.180 closest distance to " CE3 TRP A 274 " =    2.494
peak=   -3.179 closest distance to " CB  CYS A 254 " =    2.411
peak=   -3.177 closest distance to " NH2 ARG A  79 " =    1.602
peak=   -3.176 closest distance to " O   HOH Z 399 " =    2.266
peak=   -3.174 closest distance to " CB  ALA A 131 " =    1.979
peak=   -3.170 closest distance to " OD1 ASP A 171 " =    1.526
peak=   -3.170 closest distance to " NH2 ARG A 159 " =    2.439
peak=   -3.169 closest distance to " O   ALA A 160 " =    1.541
peak=   -3.164 closest distance to " O   GLY A 211 " =    1.395
peak=   -3.161 closest distance to " CB  ALA A 291 " =    2.277
peak=   -3.157 closest distance to " CG1 VAL A 197 " =    2.320
peak=   -3.155 closest distance to " O   HOH Z 198 " =    1.522
peak=   -3.152 closest distance to " CZ  PHE A  38 " =    1.909
peak=   -3.149 closest distance to " O   HOH Z 149 " =    2.083
peak=   -3.148 closest distance to " CD1 ILE A 263 " =    2.029
peak=   -3.142 closest distance to " O   HOH Z 423 " =    2.265
peak=   -3.138 closest distance to " O   ALA A   1 " =    1.964
peak=   -3.138 closest distance to " SD  MET A 188 " =    2.393
peak=   -3.136 closest distance to " O   HOH Z  90 " =    1.785
peak=   -3.130 closest distance to " O   HOH Z 114 " =    1.560
peak=   -3.126 closest distance to " O   HOH Z 211 " =    1.615
peak=   -3.123 closest distance to " CG  PRO A 163 " =    2.266
peak=   -3.123 closest distance to " CA  VAL A 197 " =    1.034
peak=   -3.119 closest distance to " O   HOH Z  17 " =    1.526
peak=   -3.115 closest distance to " O   HOH Z 264 " =    1.853
peak=   -3.114 closest distance to " O   HOH Z 380 " =    4.781
peak=   -3.109 closest distance to " OD1 ASN A  39 " =    2.278
peak=   -3.106 closest distance to " O   HOH Z 236 " =    1.516
peak=   -3.105 closest distance to " OE2 GLU A 152 " =    2.304
peak=   -3.104 closest distance to " O   HOH Z 184 " =    1.521
peak=   -3.100 closest distance to " O   HOH Z 387 " =    3.907
peak=   -3.089 closest distance to " O   HOH Z 421 " =    3.536
peak=   -3.088 closest distance to " O   HOH Z 259 " =    2.121
peak=   -3.084 closest distance to " C   GLU A  46 " =    0.952
peak=   -3.080 closest distance to " N   MET A 105 " =    2.783
peak=   -3.071 closest distance to " CE  MET A 105 " =    2.189
peak=   -3.065 closest distance to " O   HOH Z 312 " =    1.462
peak=   -3.064 closest distance to " O   HOH Z 106 " =    2.005
peak=   -3.062 closest distance to " OD2 ASP A  50 " =    2.192
peak=   -3.062 closest distance to " O   HOH Z 145 " =    2.134
peak=   -3.056 closest distance to " O   HOH Z  39 " =    0.701
peak=   -3.053 closest distance to " O   HOH Z 431 " =    1.943
peak=   -3.052 closest distance to " NE2 GLN A 223 " =    1.370
peak=   -3.036 closest distance to " CD2 TYR A 293 " =    2.174
peak=   -3.029 closest distance to " NH2 ARG A  66 " =    1.462
peak=   -3.020 closest distance to " C   GLY A 262 " =    2.187

================= 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    :  0.3726 0.3635   6.152873e+00   6.133757e+00
   1_bss:  0.3613 0.3531   6.136483e+00   6.113619e+00
   1_xyz:  0.2520 0.2769   5.828409e+00   5.900426e+00
   1_adp:  0.2305 0.2805   5.770510e+00   5.917377e+00
   1_occ:  0.2301 0.2803   5.769734e+00   5.916927e+00
   2_bss:  0.2287 0.2783   5.766603e+00   5.913285e+00
   2_xyz:  0.1680 0.2095   5.481231e+00   5.667085e+00
   2_adp:  0.1565 0.1946   5.419512e+00   5.603719e+00
   2_occ:  0.1564 0.1947   5.418940e+00   5.603357e+00
   3_bss:  0.1562 0.1948   5.418109e+00   5.600767e+00
   3_xyz:  0.1287 0.1702   5.255368e+00   5.473392e+00
   3_adp:  0.1228 0.1669   5.221596e+00   5.451015e+00
   3_occ:  0.1228 0.1669   5.221443e+00   5.450947e+00
   4_bss:  0.1231 0.1668   5.222021e+00   5.449473e+00
   4_xyz:  0.1215 0.1659   5.213409e+00   5.441002e+00
   4_adp:  0.1208 0.1665   5.210522e+00   5.441532e+00
   4_occ:  0.1208 0.1665   5.210697e+00   5.441878e+00
   5_bss:  0.1207 0.1664   5.210660e+00   5.441901e+00
   5_xyz:  0.1148 0.1640   5.178253e+00   5.425799e+00
   5_adp:  0.1143 0.1642   5.176735e+00   5.427067e+00
   5_occ:  0.1143 0.1642   5.176635e+00   5.427063e+00
   5_bss:  0.1141 0.1641   5.176720e+00   5.427164e+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:  0.300  50.000  -0.665   2.948  -1.968   0.000  -0.000  -0.000
   1_xyz:  0.300  50.000  -0.665   2.948  -1.968   0.000  -0.000  -0.000
   1_adp:  0.300  50.000  -0.665   2.948  -1.968   0.000  -0.000  -0.000
   1_occ:  0.300  50.000  -0.665   2.948  -1.968   0.000  -0.000  -0.000
   2_bss:  0.328  71.376  -1.531   0.328  -1.490   0.000  -0.000  -0.000
   2_xyz:  0.328  71.376  -1.531   0.328  -1.490   0.000  -0.000  -0.000
   2_adp:  0.328  71.376  -1.531   0.328  -1.490   0.000  -0.000  -0.000
   2_occ:  0.328  71.376  -1.531   0.328  -1.490   0.000  -0.000  -0.000
   3_bss:  0.329  71.376  -1.882  -0.866  -1.215  -0.000  -0.000  -0.000
   3_xyz:  0.329  71.376  -1.882  -0.866  -1.215  -0.000  -0.000  -0.000
   3_adp:  0.329  71.376  -1.882  -0.866  -1.215  -0.000  -0.000  -0.000
   3_occ:  0.329  71.376  -1.882  -0.866  -1.215  -0.000  -0.000  -0.000
   4_bss:  0.328  69.098  -1.886  -1.264  -1.040  -0.000  -0.000  -0.000
   4_xyz:  0.328  69.098  -1.886  -1.264  -1.040  -0.000  -0.000  -0.000
   4_adp:  0.328  69.098  -1.886  -1.264  -1.040  -0.000  -0.000  -0.000
   4_occ:  0.328  69.098  -1.886  -1.264  -1.040  -0.000  -0.000  -0.000
   5_bss:  0.323  66.820  -1.729  -1.250  -0.803  -0.000  -0.000  -0.000
   5_xyz:  0.323  66.820  -1.729  -1.250  -0.803  -0.000  -0.000  -0.000
   5_adp:  0.323  66.820  -1.729  -1.250  -0.803  -0.000  -0.000  -0.000
   5_occ:  0.323  66.820  -1.729  -1.250  -0.803  -0.000  -0.000  -0.000
   5_bss:  0.321  65.393  -1.416  -1.034  -0.506  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  40.434 0.6396  0.8021    40114.060
   1_bss:  39.535 0.6486  0.8184    37370.221
   1_xyz:  28.351 0.7770  0.9435    20512.853
   1_adp:  28.898 0.7703  0.9300    21272.228
   1_occ:  28.905 0.7702  0.9294    21245.618
   2_bss:  28.617 0.7733  0.9031    20956.311
   2_xyz:  20.715 0.8538  0.9660    11327.085
   2_adp:  18.787 0.8732  0.9690     9841.033
   2_occ:  18.778 0.8733  0.9690     9839.795
   3_bss:  18.707 0.8740  0.9554     9769.691
   3_xyz:  15.823 0.8996  0.9707     7426.495
   3_adp:  15.222 0.9051  0.9657     7131.518
   3_occ:  15.215 0.9052  0.9655     7129.231
   4_bss:  15.198 0.9053  0.9632     7108.927
   4_xyz:  15.001 0.9070  0.9637     6969.463
   4_adp:  14.989 0.9072  0.9559     6999.061
   4_occ:  14.996 0.9072  0.9558     7002.320
   5_bss:  14.997 0.9072  0.9605     7002.162
   5_xyz:  14.715 0.9093  0.9627     6783.778
   5_adp:  14.736 0.9092  0.9546     6802.805
   5_occ:  14.733 0.9092  0.9545     6803.364
   5_bss:  14.735 0.9092  0.9640     6804.738
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6454e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6454e-01
   1_xyz:   1.300  0.010  0.079 15.214  0.005  4.116   9.2840e-02
   1_adp:   1.300  0.010  0.079 15.214  0.005  4.116   9.2840e-02
   1_occ:   1.300  0.010  0.079 15.214  0.005  4.116   9.2840e-02
   2_bss:   1.300  0.010  0.079 15.214  0.005  4.116   9.2840e-02
   2_xyz:   1.119  0.008  0.078 14.395  0.004  4.132   6.6138e-02
   2_adp:   1.119  0.008  0.078 14.395  0.004  4.132   6.6138e-02
   2_occ:   1.119  0.008  0.078 14.395  0.004  4.132   6.6138e-02
   3_bss:   1.119  0.008  0.078 14.395  0.004  4.132   6.6138e-02
   3_xyz:   1.035  0.008  0.075 14.510  0.004  4.141   6.2593e-02
   3_adp:   1.035  0.008  0.075 14.510  0.004  4.141   6.2593e-02
   3_occ:   1.035  0.008  0.075 14.510  0.004  4.141   6.2593e-02
   4_bss:   1.035  0.008  0.075 14.510  0.004  4.141   6.2593e-02
   4_xyz:   0.916  0.006  0.070 14.312  0.003  4.126   5.0460e-02
   4_adp:   0.916  0.006  0.070 14.312  0.003  4.126   5.0460e-02
   4_occ:   0.916  0.006  0.070 14.312  0.003  4.126   5.0460e-02
   5_bss:   0.916  0.006  0.070 14.312  0.003  4.126   5.0460e-02
   5_xyz:   1.040  0.009  0.078 14.542  0.004  4.131   6.3585e-02
   5_adp:   1.040  0.009  0.078 14.542  0.004  4.131   6.3585e-02
   5_occ:   1.040  0.009  0.078 14.542  0.004  4.131   6.3585e-02
   5_bss:   1.040  0.009  0.078 14.542  0.004  4.131   6.3585e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.519   2.4390e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.519   2.4390e-01
   1_xyz:  10.807  0.050  0.386 88.883  0.034  2.110   1.6821e-01
   1_adp:  10.807  0.050  0.386 88.883  0.034  2.110   1.6821e-01
   1_occ:  10.807  0.050  0.386 88.883  0.034  2.110   1.6821e-01
   2_bss:  10.807  0.050  0.386 88.883  0.034  2.110   1.6821e-01
   2_xyz:   7.888  0.047  0.244 88.798  0.041  2.311   6.6586e-02
   2_adp:   7.888  0.047  0.244 88.798  0.041  2.311   6.6586e-02
   2_occ:   7.888  0.047  0.244 88.798  0.041  2.311   6.6586e-02
   3_bss:   7.888  0.047  0.244 88.798  0.041  2.311   6.6586e-02
   3_xyz:   7.526  0.045  0.233 81.976  0.040  2.313   6.0125e-02
   3_adp:   7.526  0.045  0.233 81.976  0.040  2.313   6.0125e-02
   3_occ:   7.526  0.045  0.233 81.976  0.040  2.313   6.0125e-02
   4_bss:   7.526  0.045  0.233 81.976  0.040  2.313   6.0125e-02
   4_xyz:   7.393  0.038  0.222 82.704  0.039  2.423   2.8541e-02
   4_adp:   7.393  0.038  0.222 82.704  0.039  2.423   2.8541e-02
   4_occ:   7.393  0.038  0.222 82.704  0.039  2.423   2.8541e-02
   5_bss:   7.393  0.038  0.222 82.704  0.039  2.423   2.8541e-02
   5_xyz:   7.693  0.044  0.246 82.036  0.040  2.317   4.1430e-02
   5_adp:   7.693  0.044  0.246 82.036  0.040  2.317   4.1430e-02
   5_occ:   7.693  0.044  0.246 82.036  0.040  2.317   4.1430e-02
   5_bss:   7.693  0.044  0.246 82.036  0.040  2.317   4.1430e-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:  89.10   0.00  17.41  79.38   0.00  13.38  89.10   2.94  39.34
   1_occ:  89.10   0.00  17.41  79.38   0.00  13.38  89.10   2.94  39.34
   2_bss:  89.10   0.00  17.41  79.38   0.00  13.38  89.10   2.94  39.34
   2_xyz:  89.10   0.00  17.41  79.38   0.00  13.38  89.10   2.94  39.34
   2_adp:  88.58   0.91  17.13  82.03   0.91  12.93  88.58   4.54  40.01
   2_occ:  88.58   0.91  17.13  82.03   0.91  12.93  88.58   4.54  40.01
   3_bss:  88.58   0.91  17.13  82.03   0.91  12.93  88.58   4.54  40.01
   3_xyz:  88.58   0.91  17.13  82.03   0.91  12.93  88.58   4.54  40.01
   3_adp:  91.87   0.00  17.19  91.87   0.00  12.70  89.68   5.15  41.65
   3_occ:  91.87   0.00  17.19  91.87   0.00  12.70  89.68   5.15  41.65
   4_bss:  91.87   0.00  17.19  91.87   0.00  12.70  89.68   5.15  41.65
   4_xyz:  91.87   0.00  17.19  91.87   0.00  12.70  89.68   5.15  41.65
   4_adp:  92.64   0.00  17.01  92.64   0.00  12.50  89.94   4.90  41.55
   4_occ:  92.64   0.00  17.01  92.64   0.00  12.50  89.94   4.90  41.55
   5_bss:  92.64   0.00  17.01  92.64   0.00  12.50  89.94   4.90  41.55
   5_xyz:  92.64   0.00  17.01  92.64   0.00  12.50  89.94   4.90  41.55
   5_adp: 103.96   0.00  16.92 103.96   0.00  12.36  92.53   4.73  41.75
   5_occ: 103.96   0.00  16.92 103.96   0.00  12.36  92.53   4.73  41.75
   5_bss: 103.97   0.00  16.92 103.97   0.00  12.36  92.54   4.73  41.75
------------------------------------------------------------------------
 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:    1.755    0.014    0.315
   1_adp:    1.755    0.014    0.315
   1_occ:    1.755    0.014    0.315
   2_bss:    1.755    0.014    0.315
   2_xyz:    1.147    0.035    0.418
   2_adp:    1.147    0.035    0.418
   2_occ:    1.147    0.035    0.418
   3_bss:    1.147    0.035    0.418
   3_xyz:    1.011    0.031    0.506
   3_adp:    1.011    0.031    0.506
   3_occ:    1.011    0.031    0.506
   4_bss:    1.011    0.031    0.506
   4_xyz:    1.037    0.029    0.522
   4_adp:    1.037    0.029    0.522
   4_occ:    1.037    0.029    0.522
   5_bss:    1.037    0.029    0.522
   5_xyz:    1.028    0.048    0.537
   5_adp:    1.028    0.048    0.537
   5_occ:    1.028    0.048    0.537
   5_bss:    1.028    0.048    0.537
------------------------------------------------------------------------

CPU time actual refinement: 334.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/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_1061/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1061/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.29 
  Macro-tasks:
    bulk solvent and scale       = 39.49  
    individual site refinement   = 140.11 
    weights calculation          = 29.57  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 215.90 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 106.00 
    alpha_beta                      = 8.24   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 116.19 
    fmodel                         = 6.53   
    r_factors                      = 0.14   
    phase_errors                   = 11.14  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 251.36 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.672 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    660 calls, 105.65 s
gradients_fft:          605 calls, 101.97 s

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

# Date 2008-01-16 Time 06:19:16 PST -0800 (1200493156.80 s)
Start R-work = 0.3726, R-free = 0.3635 (no bulk solvent and anisotropic scale)
Final R-work = 0.1325, R-free = 0.1798 (no bulk solvent and anisotropic scale)

Start R-work = 0.3613, R-free = 0.3531
Final R-work = 0.1141, R-free = 0.1641