# Date 2008-01-16 Time 06:13:38 PST -0800 (1200492818.02 s)
#phil __OFF__

Command line arguments: "../1062.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9518
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1062

-------------------------------------------------------------------------------
  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, 86.822, 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: 3.30, per 1000 atoms: 1.17


================================== 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, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.0111
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0111

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, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.0111
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.3030 [2117/2144]  1906   211  10.0%
  bin  2:  4.3030 -  3.4283 [2041/2057]  1836   205  10.0%
  bin  3:  3.4283 -  2.9988 [2018/2037]  1814   204  10.1%
  bin  4:  2.9988 -  2.7263 [1999/2029]  1804   195   9.8%
  bin  5:  2.7263 -  2.5319 [1979/1998]  1779   200  10.1%
  bin  6:  2.5319 -  2.3832 [1960/1985]  1768   192   9.8%
  bin  7:  2.3832 -  2.2642 [1970/2002]  1769   201  10.2%
  bin  8:  2.2642 -  2.1660 [1955/1987]  1760   195  10.0%
  bin  9:  2.1660 -  2.0828 [1961/2003]  1766   195   9.9%
  bin 10:  2.0828 -  2.0111 [1589/1994]  1428   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 5
        2.20 -     2.87: 1199
        2.87 -     3.55: 4354
        3.55 -     4.22: 9046
        4.22 -     4.90: 13219
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.525 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 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.151 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27818 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_1062/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/model_refine_001.geo

CPU time processing inputs: 9.81


============================ 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 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3832   r_free= 0.3725   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.164918                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.3073 0.3146      6.4019      6.3419|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.3052 0.3078      6.6074      6.6263|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.3331 0.3135      6.4895      6.4522|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.3721 0.3392       6.399      6.3093|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.3959 0.3872      6.2371      6.2573|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.4138 0.3944      6.1836      6.1214|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.4093 0.3874      6.1247       6.078|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.4299 0.4004      6.0986      6.0678|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.4291 0.4267      6.0418      6.0665|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.4407 0.4168      6.0326       6.039|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.4388 0.4316      5.9787      6.0009|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.4541 0.4463       5.936      5.9475|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.4525 0.4559      5.8353      5.8047|
| 14:  2.0613 -  2.0111 0.73    938  101 0.4362 0.4641      5.7732      5.7578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.77  28.17   0.85     0.79      49180.31|
|  2:  4.7991 -  3.8294  1334   145  0.81  25.48   0.94     0.87      59498.08|
|  3:  3.8294 -  3.3512  1300   146  0.76  30.56   0.95     0.88      61483.50|
|  4:  3.3512 -  3.0475  1291   145  0.71  34.45   0.94     0.84      55179.68|
|  5:  3.0475 -  2.8306  1280   141  0.63  41.53   0.94     0.80      47606.26|
|  6:  2.8306 -  2.6647  1285   143  0.62  42.17   0.94     0.78      41815.26|
|  7:  2.6647 -  2.5319  1271   141  0.60  43.86   0.96     0.77      39246.95|
|  8:  2.5319 -  2.4221  1272   142  0.58  45.58   0.95     0.77      37689.50|
|  9:  2.4221 -  2.3292  1269   139  0.57  46.42   0.96     0.76      35919.26|
| 10:  2.3292 -  2.2491  1247   144  0.55  48.20   0.97     0.75      34026.43|
| 11:  2.2491 -  2.1790  1275   139  0.55  48.34   0.97     0.76      32087.64|
| 12:  2.1790 -  2.1169  1241   137  0.53  49.58   0.96     0.76      30943.36|
| 13:  2.1169 -  2.0613  1249   142  0.50  52.33   0.95     0.72      27826.88|
| 14:  2.0613 -  2.0111   938   101  0.49  53.31   0.96     0.63      23692.99|
|alpha:            min =        0.63 max =            0.88 mean =         0.78|
|beta:             min =    23692.99 max =        61483.50 mean =     41696.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.73|
|phase err.(test): min =        0.00 max =           89.94 mean =        41.83|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.275157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.145   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.123677              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.340   (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 |  1.525 -  1.862:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.862 -  2.200:        3 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.200 -  2.537:       15 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.537 -  2.875:     1184 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.875 -  3.212:     1885 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.212 -  3.550:     2469 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.550 -  3.887:     4586 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.887 -  4.225:     4460 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.225 -  4.562:     6009 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.562 -  4.900:     7210 |
|-----------------------------------------------------------------------------|
|-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 |        0.164 |
| 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  1.525 |       0.171 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3832   r_free= 0.3725   ksol= 0.00   Bsol= 0.00   scale= 0.928    |
|                                                                             |
| 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:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.164918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3733   r_free= 0.3629   ksol= 0.30   Bsol= 58.45   scale= 0.961   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,2.90,-1.17,0.00,-0.00,-0.00); trace/3= 0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.150374                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.860304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.175   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.604672              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.095   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3733      final r-factor (work) = 0.2606          |
| start r-factor (free) = 0.3629      final r-factor (free) = 0.2825          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0409 = 3.86 * 0.50 * 6.1533 + 1.00 * 0.1642                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5769 = 3.86 * 0.50 * 5.9537 + 1.00 * 0.0853                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2606      final r-factor (work) = 0.2411          |
| start r-factor (free) = 0.2825      final r-factor (free) = 0.2864          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6070 = 0.60 * 1.00 * 5.9537 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6460 = 0.60 * 1.00 * 5.7982 + 1.00 * 0.1399                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.72  16.86    None  None   None       |
|    all(noH): 2823   0      0.00    101.72  16.86    None  None   None       |
|    Sol.    : 438    0      2.53    69.91   37.61    None  None   None       |
|    Mac.    : 2385   0      0.00    101.72  13.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.172: 1019   |   5:    50.858 -  61.030:   81        |
|      1:    10.172 -  20.343: 1069   |   6:    61.030 -  71.201:    5        |
|      2:    20.343 -  30.515:  337   |   7:    71.201 -  81.373:    0        |
|      3:    30.515 -  40.687:  174   |   8:    81.373 -  91.545:    0        |
|      4:    40.687 -  50.858:  137   |   9:    91.545 - 101.716:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2411 r_free = 0.2864             target_work(ml) = 5.802         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2407 r_free = 0.2858             target_work(ml) = 5.801         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2407   r_free= 0.2858   ksol= 0.30   Bsol= 58.45   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,2.90,-1.17,0.00,-0.00,-0.00); trace/3= 0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.800758                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2398   r_free= 0.2846   ksol= 0.33   Bsol= 69.45   scale= 0.984   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,0.41,-1.24,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.800003                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.433355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.144   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.313446              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2398      final r-factor (work) = 0.1710          |
| start r-factor (free) = 0.2846      final r-factor (free) = 0.2069          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0436 = 3.43 * 0.50 * 5.8009 + 1.00 * 0.0853                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7831 = 3.43 * 0.50 * 5.6576 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1710      final r-factor (work) = 0.1528          |
| start r-factor (free) = 0.2069      final r-factor (free) = 0.1950          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4771 = 1.31 * 1.00 * 5.6576 + 1.00 * 0.0461                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1514 = 1.31 * 1.00 * 5.4344 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.69   17.82    None  None   None       |
|    all(noH): 2823   0      0.00    93.69   17.82    None  None   None       |
|    Sol.    : 438    0      3.74    93.69   43.65    None  None   None       |
|    Mac.    : 2385   0      0.00    92.65   13.08    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 -   9.369:  983   |   5:    46.844 -  56.213:   87        |
|      1:     9.369 -  18.738: 1091   |   6:    56.213 -  65.582:   85        |
|      2:    18.738 -  28.106:  265   |   7:    65.582 -  74.950:   51        |
|      3:    28.106 -  37.475:  141   |   8:    74.950 -  84.319:   16        |
|      4:    37.475 -  46.844:   96   |   9:    84.319 -  93.688:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1528 r_free = 0.1950             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1527 r_free = 0.1946             target_work(ml) = 5.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1527   r_free= 0.1946   ksol= 0.33   Bsol= 69.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.58,0.41,-1.24,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.404321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1526   r_free= 0.1951   ksol= 0.33   Bsol= 79.27   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.57,-0.77,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.403568                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.766071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.175  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.035332              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.139  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1951      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5864 = 2.77 * 0.50 * 5.4341 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4327 = 2.77 * 0.50 * 5.3265 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1699          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8547 = 2.04 * 1.00 * 5.3265 + 1.00 * 0.0135                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6905 = 2.04 * 1.00 * 5.2459 + 1.00 * 0.0132                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.83  17.45    None  None   None       |
|    all(noH): 2823   0      0.00    104.83  17.45    None  None   None       |
|    Sol.    : 438    0      0.00    98.82   43.75    None  None   None       |
|    Mac.    : 2385   0      0.00    104.83  12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.483: 1267   |   5:    52.415 -  62.898:   94        |
|      1:    10.483 -  20.966:  950   |   6:    62.898 -  73.381:   62        |
|      2:    20.966 -  31.449:  189   |   7:    73.381 -  83.864:   20        |
|      3:    31.449 -  41.932:  136   |   8:    83.864 -  94.347:   10        |
|      4:    41.932 -  52.415:   89   |   9:    94.347 - 104.830:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1228 r_free = 0.1699             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1227 r_free = 0.1698             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1698   ksol= 0.33   Bsol= 79.27   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-0.57,-0.77,-0.00,-0.00,-0.00); trace/3= -0.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1693   ksol= 0.33   Bsol= 74.31   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.73,-0.31,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.226812                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.809959              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.986  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.842865              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.020  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1693      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4381 = 2.81 * 0.50 * 5.2472 + 1.00 * 0.0660                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3798 = 2.81 * 0.50 * 5.2013 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1161      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3971 = 0.84 * 1.00 * 5.2013 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3792 = 0.84 * 1.00 * 5.1813 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.91  16.93    None  None   None       |
|    all(noH): 2823   0      0.00    107.91  16.93    None  None   None       |
|    Sol.    : 438    0      0.00    98.29   42.30    None  None   None       |
|    Mac.    : 2385   0      0.00    107.91  12.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.791: 1390   |   5:    53.955 -  64.746:   77        |
|      1:    10.791 -  21.582:  861   |   6:    64.746 -  75.537:   50        |
|      2:    21.582 -  32.373:  189   |   7:    75.537 -  86.328:   15        |
|      3:    32.373 -  43.164:  126   |   8:    86.328 -  97.119:    6        |
|      4:    43.164 -  53.955:  104   |   9:    97.119 - 107.910:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1635             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1635             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1635   ksol= 0.33   Bsol= 74.31   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.32,-0.73,-0.31,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.176074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1635   ksol= 0.32   Bsol= 68.43   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,-0.86,-0.23,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.175896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.534891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.399  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.450252              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.102  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6388 = 2.53 * 0.50 * 5.1810 + 1.00 * 0.0721                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6240 = 2.53 * 0.50 * 5.1716 + 1.00 * 0.0692                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1639      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3405 = 0.45 * 1.00 * 5.1716 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3391 = 0.45 * 1.00 * 5.1718 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.50  16.24    None  None   None       |
|    all(noH): 2823   0      0.00    107.50  16.24    None  None   None       |
|    Sol.    : 438    0      2.20    92.08   39.89    None  None   None       |
|    Mac.    : 2385   0      0.00    107.50  11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.750: 1428   |   5:    53.750 -  64.500:   80        |
|      1:    10.750 -  21.500:  839   |   6:    64.500 -  75.249:   29        |
|      2:    21.500 -  32.250:  189   |   7:    75.249 -  85.999:    9        |
|      3:    32.250 -  43.000:  140   |   8:    85.999 -  96.749:    6        |
|      4:    43.000 -  53.750:  100   |   9:    96.749 - 107.499:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1624             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1624             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1624   ksol= 0.32   Bsol= 68.43   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,-0.86,-0.23,-0.00,-0.00,-0.00); trace/3= -0.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.0986 0.1331      5.3841      5.5385|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.0841 0.1062      5.4226      5.6092|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.1016 0.1513      5.4535      5.8676|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.1221 0.1542      5.4748      5.6043|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.1395 0.1872       5.372      5.5983|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.1264 0.1892       5.263      5.4746|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.1279 0.1797      5.1984      5.4524|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.1194 0.1740      5.1088       5.373|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.1198 0.1800      5.0651      5.3162|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.1165 0.1855      5.0153      5.2777|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.1199 0.1909      4.9823      5.3212|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.1140 0.1700      4.9278      5.1923|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.1181 0.1882      4.8234      5.1389|
| 14:  2.0613 -  2.0111 0.73    938  101 0.1097 0.1736      4.6891      4.9372|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.94   9.34   0.96     0.94       7375.39|
|  2:  4.7991 -  3.8294  1334   145  0.95   7.92   1.00     0.98       8892.31|
|  3:  3.8294 -  3.3512  1300   146  0.93  11.15   1.01     1.00      10243.83|
|  4:  3.3512 -  3.0475  1291   145  0.92  13.79   1.00     0.98      10793.81|
|  5:  3.0475 -  2.8306  1280   141  0.89  16.78   0.99     0.96       9113.36|
|  6:  2.8306 -  2.6647  1285   143  0.89  16.75   0.98     0.95       7911.42|
|  7:  2.6647 -  2.5319  1271   141  0.90  16.48   0.98     0.95       6736.24|
|  8:  2.5319 -  2.4221  1272   142  0.90  15.89   0.98     0.96       5885.79|
|  9:  2.4221 -  2.3292  1269   139  0.90  16.02   0.98     0.94       5381.97|
| 10:  2.3292 -  2.2491  1247   144  0.90  16.30   0.98     0.93       4903.70|
| 11:  2.2491 -  2.1790  1275   139  0.89  17.19   0.97     0.93       4711.21|
| 12:  2.1790 -  2.1169  1241   137  0.91  15.75   0.98     0.97       4396.81|
| 13:  2.1169 -  2.0613  1249   142  0.90  16.66   0.97     0.96       3607.57|
| 14:  2.0613 -  2.0111   938   101  0.91  14.87   0.95     0.91       2618.57|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2618.57 max =        10793.81 mean =      6723.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.56|
|phase err.(test): min =        0.00 max =           89.23 mean =        14.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1624   ksol= 0.32   Bsol= 65.29   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.75,-0.03,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168957                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1624   ksol= 0.32   Bsol= 65.29   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-0.75,-0.03,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.168957                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.0985 0.1332      5.3834      5.5381|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.0840 0.1058      5.4213      5.6067|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.1015 0.1514      5.4529      5.8683|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.1222 0.1542      5.4754      5.6046|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.1396 0.1874      5.3728      5.5989|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.1265 0.1890      5.2635      5.4745|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.1279 0.1798      5.1987      5.4531|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.1194 0.1741       5.109       5.373|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.1197 0.1798      5.0653      5.3161|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.1165 0.1857      5.0159      5.2786|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.1199 0.1911      4.9827      5.3217|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.1140 0.1702       4.928      5.1931|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.1181 0.1883      4.8233      5.1391|
| 14:  2.0613 -  2.0111 0.73    938  101 0.1097 0.1734      4.6888       4.936|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.94   9.34   0.96     0.94       7371.37|
|  2:  4.7991 -  3.8294  1334   145  0.95   7.91   1.00     0.98       8873.76|
|  3:  3.8294 -  3.3512  1300   146  0.93  11.14   1.02     1.01      10224.30|
|  4:  3.3512 -  3.0475  1291   145  0.92  13.79   1.00     0.98      10802.63|
|  5:  3.0475 -  2.8306  1280   141  0.89  16.79   0.99     0.97       9119.69|
|  6:  2.8306 -  2.6647  1285   143  0.89  16.76   0.98     0.96       7917.56|
|  7:  2.6647 -  2.5319  1271   141  0.90  16.48   0.99     0.96       6738.10|
|  8:  2.5319 -  2.4221  1272   142  0.90  15.89   0.98     0.96       5887.57|
|  9:  2.4221 -  2.3292  1269   139  0.90  16.03   0.99     0.95       5385.59|
| 10:  2.3292 -  2.2491  1247   144  0.90  16.31   0.99     0.94       4909.28|
| 11:  2.2491 -  2.1790  1275   139  0.89  17.21   0.98     0.94       4718.08|
| 12:  2.1790 -  2.1169  1241   137  0.91  15.77   0.99     0.98       4401.49|
| 13:  2.1169 -  2.0613  1249   142  0.90  16.65   0.98     0.97       3605.94|
| 14:  2.0613 -  2.0111   938   101  0.91  14.84   0.96     0.92       2613.52|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2613.52 max =        10802.63 mean =      6722.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.57|
|phase err.(test): min =        0.00 max =           89.29 mean =        14.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.50  16.24    None  None   None       |
|    all(noH): 2823   0      0.00    107.50  16.24    None  None   None       |
|    Sol.    : 438    0      2.20    92.08   39.89    None  None   None       |
|    Mac.    : 2385   0      0.00    107.50  11.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.753: 1428   |   5:    53.753 -  64.502:   80        |
|      1:    10.753 -  21.503:  839   |   6:    64.502 -  75.252:   29        |
|      2:    21.503 -  32.253:  189   |   7:    75.252 -  86.002:    9        |
|      3:    32.253 -  43.003:  140   |   8:    86.002 -  96.752:    6        |
|      4:    43.003 -  53.753:  100   |   9:    96.752 - 107.502:    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)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.504 - 4.805
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 312
   mapped sites are within: 0.706 - 4.805

peak=    5.936 closest distance to " O   HOH Z 111 " =    2.125
peak=    5.703 closest distance to " CB  GLN A 223 " =    1.420
peak=    5.174 closest distance to " CG  PRO A  54 " =    1.335
peak=    5.031 closest distance to " O   HOH Z 232 " =    2.323
peak=    4.867 closest distance to " CB  SER A  63 " =    1.279
peak=    4.763 closest distance to " CB  ARG A 190 " =    1.699
peak=    4.590 closest distance to " CB  PRO A  54 " =    0.906
peak=    4.520 closest distance to " CG  PRO A 213 " =    1.173
peak=    4.504 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.486 closest distance to " CG  PRO A 198 " =    1.286
peak=    4.461 closest distance to " CB  ARG A 275 " =    0.894
peak=    4.438 closest distance to " CB  GLU A 128 " =    1.095
peak=    4.436 closest distance to " CZ  PHE A 218 " =    1.099
peak=    4.432 closest distance to " C   PRO A 198 " =    1.514
peak=    4.404 closest distance to " CB  LEU A 228 " =    1.080
peak=    4.397 closest distance to " O   HOH Z 298 " =    2.024
peak=    4.371 closest distance to " CA  TYR A  30 " =    0.929
peak=    4.277 closest distance to " CB  VAL A 202 " =    1.586
peak=    4.267 closest distance to " O   HOH Z 369 " =    2.132
peak=    4.244 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.233 closest distance to " CD  ARG A 269 " =    0.907
peak=    4.233 closest distance to " NH2 ARG A 156 " =    1.164
peak=    4.216 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.185 closest distance to " CB  GLU A 277 " =    3.766
peak=    4.179 closest distance to " O   HOH Z  44 " =    2.214
peak=    4.176 closest distance to " OD1 ASN A  69 " =    2.522
peak=    4.159 closest distance to " O   HOH Z  15 " =    2.118
peak=    4.156 closest distance to " CD1 LEU A 300 " =    1.211
peak=    4.143 closest distance to " O   HOH Z  21 " =    1.793
peak=    4.137 closest distance to " CB  TRP A 266 " =    0.968
peak=    4.137 closest distance to " O   HOH Z 234 " =    3.841
peak=    4.123 closest distance to " NE2 GLN A  11 " =    1.029
peak=    4.111 closest distance to " C   ILE A 106 " =    1.864
peak=    4.101 closest distance to " CA  ALA A  51 " =    0.959
peak=    4.080 closest distance to " O   HOH Z 368 " =    2.185
peak=    4.060 closest distance to " O   HOH Z 236 " =    2.058
peak=    4.056 closest distance to " O   HOH Z 265 " =    2.221
peak=    4.051 closest distance to " ND2 ASN A 187 " =    1.450
peak=    4.046 closest distance to " CB  TYR A 169 " =    0.796
peak=    4.021 closest distance to " O   HOH Z 134 " =    1.448
peak=    4.006 closest distance to " O   HOH Z 403 " =    1.703
peak=    3.996 closest distance to " O   HOH Z  68 " =    1.890
peak=    3.984 closest distance to " O   HOH Z 189 " =    2.666
peak=    3.973 closest distance to " CB  ARG A  79 " =    1.218
peak=    3.968 closest distance to " CA  PRO A  54 " =    1.364
peak=    3.959 closest distance to " CG1 ILE A  33 " =    1.240
peak=    3.955 closest distance to " O   HOH Z  19 " =    2.106
peak=    3.928 closest distance to " O   HOH Z  40 " =    1.869
peak=    3.928 closest distance to " O   HOH Z 303 " =    2.188
peak=    3.928 closest distance to " O   HOH Z 133 " =    2.358
peak=    3.927 closest distance to " O   HOH Z 126 " =    2.024
peak=    3.927 closest distance to " O   HOH Z 261 " =    1.900
peak=    3.922 closest distance to " CG2 THR A 221 " =    1.063
peak=    3.914 closest distance to " O   HOH Z 158 " =    3.059
peak=    3.913 closest distance to " O   HOH Z 423 " =    1.905
peak=    3.909 closest distance to " CB  ASN A 148 " =    1.426
peak=    3.905 closest distance to " CD  LYS A 166 " =    1.300
peak=    3.887 closest distance to " O   HOH Z 412 " =    3.741
peak=    3.875 closest distance to " O   HOH Z 214 " =    2.141
peak=    3.870 closest distance to " CD ALYS A 290 " =    1.034
peak=    3.863 closest distance to " O   HOH Z  20 " =    1.762
peak=    3.859 closest distance to " CB  ASP A 140 " =    0.947
peak=    3.855 closest distance to " CA  ARG A 195 " =    1.186
peak=    3.838 closest distance to " O   HOH Z  43 " =    1.832
peak=    3.829 closest distance to " CA  ARG A  36 " =    1.201
peak=    3.815 closest distance to " O   HOH Z  97 " =    2.015
peak=    3.813 closest distance to " O   HOH Z 271 " =    2.793
peak=    3.801 closest distance to " O   HOH Z  63 " =    1.886
peak=    3.800 closest distance to " O   HOH Z 352 " =    1.921
peak=    3.796 closest distance to " O   HOH Z 406 " =    1.626
peak=    3.793 closest distance to " O   HOH Z 426 " =    1.594
peak=    3.785 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.785 closest distance to " CA  THR A 221 " =    0.888
peak=    3.782 closest distance to " CB  VAL A 265 " =    1.255
peak=    3.781 closest distance to " ND2 ASN A 249 " =    2.040
peak=    3.774 closest distance to " O   HOH Z 346 " =    1.534
peak=    3.773 closest distance to " O   HOH Z 427 " =    3.138
peak=    3.764 closest distance to " O   ALA A 165 " =    1.419
peak=    3.750 closest distance to " CA  ASP A 191 " =    0.840
peak=    3.749 closest distance to " O   SER A  87 " =    2.243
peak=    3.749 closest distance to " O   THR A 251 " =    1.220
peak=    3.739 closest distance to " NH1AARG A 145 " =    1.276
peak=    3.732 closest distance to " O   HOH Z  80 " =    1.671
peak=    3.732 closest distance to " CA  ALA A 160 " =    0.908
peak=    3.732 closest distance to " CG2 VAL A 257 " =    0.956
peak=    3.725 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.723 closest distance to " CG1 VAL A 153 " =    1.009
peak=    3.723 closest distance to " O   HOH Z  78 " =    1.625
peak=    3.722 closest distance to " O   HOH Z 250 " =    1.497
peak=    3.722 closest distance to " O   HOH Z 180 " =    2.150
peak=    3.718 closest distance to " O   HOH Z 294 " =    1.558
peak=    3.711 closest distance to " CB  GLU A  46 " =    0.996
peak=    3.708 closest distance to " O   HOH Z 272 " =    1.934
peak=    3.707 closest distance to " CA  ALA A  21 " =    1.304
peak=    3.707 closest distance to " CZ  PHE A 192 " =    0.979
peak=    3.702 closest distance to " O   HOH Z 193 " =    2.009
peak=    3.698 closest distance to " O   HOH Z 126 " =    1.589
peak=    3.694 closest distance to " O   HOH Z 383 " =    2.126
peak=    3.682 closest distance to " O   HOH Z 285 " =    2.918
peak=    3.679 closest distance to " CD  ARG A  66 " =    2.491
peak=    3.673 closest distance to " O   HOH Z 280 " =    2.983
peak=    3.665 closest distance to " O   HOH Z 361 " =    3.651
peak=    3.663 closest distance to " O   HOH Z 147 " =    1.821
peak=    3.646 closest distance to " CD2 LEU A 297 " =    0.900
peak=    3.638 closest distance to " CG2BVAL A  41 " =    0.859
peak=    3.637 closest distance to " CB  TRP A 179 " =    1.513
peak=    3.633 closest distance to " OD2 ASP A 298 " =    3.948
peak=    3.632 closest distance to " O   HOH Z 421 " =    1.541
peak=    3.632 closest distance to " N   ASN A  39 " =    1.333
peak=    3.627 closest distance to " CB  SER A   3 " =    1.387
peak=    3.627 closest distance to " CB  ASN A 187 " =    1.159
peak=    3.625 closest distance to " NH2BARG A 145 " =    2.167
peak=    3.619 closest distance to " CE  LYS A  76 " =    0.844
peak=    3.617 closest distance to " O   HOH Z 402 " =    1.454
peak=    3.605 closest distance to " CG  GLU A  37 " =    0.880
peak=    3.605 closest distance to " CD1 LEU A  96 " =    0.706
peak=    3.603 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.601 closest distance to " O   HOH Z 279 " =    2.377
peak=    3.600 closest distance to " CD  ARG A 159 " =    0.827
peak=    3.597 closest distance to " NZ  LYS A 117 " =    3.266
peak=    3.592 closest distance to " O   HOH Z 295 " =    1.486
peak=    3.588 closest distance to " O   HOH Z 425 " =    1.320
peak=    3.586 closest distance to " CB  ILE A 120 " =    1.230
peak=    3.584 closest distance to " CA  SER A  87 " =    1.065
peak=    3.584 closest distance to " OD1 ASN A 217 " =    1.670
peak=    3.582 closest distance to " CD1 ILE A 106 " =    0.867
peak=    3.575 closest distance to " CB  SER A 141 " =    1.002
peak=    3.567 closest distance to " N   ASN A 127 " =    1.278
peak=    3.562 closest distance to " CB  MET A  40 " =    0.829
peak=    3.562 closest distance to " CA  ALA A 295 " =    1.114
peak=    3.561 closest distance to " O   ASN A  74 " =    1.571
peak=    3.555 closest distance to " NE2 GLN A  77 " =    3.401
peak=    3.552 closest distance to " O   HOH Z 316 " =    3.152
peak=    3.547 closest distance to " O   HOH Z 163 " =    1.655
peak=    3.544 closest distance to " CA  MET A  40 " =    1.193
peak=    3.541 closest distance to " O   HOH Z   1 " =    2.329
peak=    3.540 closest distance to " O   HOH Z 391 " =    2.945
peak=    3.538 closest distance to " O   HOH Z 174 " =    2.348
peak=    3.534 closest distance to " CB  SER A 212 " =    1.115
peak=    3.532 closest distance to " O   HOH Z  61 " =    1.592
peak=    3.524 closest distance to " CA  GLY A 241 " =    0.802
peak=    3.503 closest distance to " CB  MET A  47 " =    0.984
peak=    3.502 closest distance to " ND1 HIS A  81 " =    1.669
peak=    3.491 closest distance to " O   HOH Z 135 " =    1.908
peak=    3.476 closest distance to " CB  TYR A 116 " =    0.964
peak=    3.475 closest distance to " O   HOH Z 353 " =    2.728
peak=    3.465 closest distance to " CA  ASN A 215 " =    1.118
peak=    3.460 closest distance to " O   HOH Z 171 " =    3.890
peak=    3.456 closest distance to " C   SER A  32 " =    1.066
peak=    3.455 closest distance to " OG BSER A 164 " =    2.418
peak=    3.453 closest distance to " O   HOH Z 411 " =    1.737
peak=    3.451 closest distance to " CB  ALA A 104 " =    0.757
peak=    3.451 closest distance to " O   HOH Z  48 " =    1.896
peak=    3.450 closest distance to " O   HOH Z 371 " =    3.155
peak=    3.445 closest distance to " CA  GLU A 152 " =    0.879
peak=    3.442 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.433 closest distance to " CA  THR A 264 " =    0.841
peak=    3.424 closest distance to " CB  ASN A 142 " =    1.078
peak=    3.419 closest distance to " CB  ALA A 248 " =    1.064
peak=    3.415 closest distance to " CG2 ILE A 120 " =    0.976
peak=    3.415 closest distance to " CZ  PHE A  38 " =    1.280
peak=    3.414 closest distance to " CB  GLN A 103 " =    0.928
peak=    3.412 closest distance to " OE1 GLN A  11 " =    2.013
peak=    3.408 closest distance to " CA  MET A 105 " =    1.018
peak=    3.407 closest distance to " O   HOH Z  49 " =    2.544
peak=    3.407 closest distance to " CE1 TYR A 186 " =    1.272
peak=    3.406 closest distance to " O   HOH Z 374 " =    2.827
peak=    3.403 closest distance to " O   HOH Z  88 " =    3.479
peak=    3.395 closest distance to " CB  ALA A   1 " =    4.805
peak=    3.391 closest distance to " O   HOH Z 132 " =    2.745
peak=    3.389 closest distance to " O   HOH Z 102 " =    1.277
peak=    3.389 closest distance to " O   HOH Z  59 " =    2.292
peak=    3.383 closest distance to " CA  ILE A 106 " =    0.847
peak=    3.378 closest distance to " O   HOH Z  10 " =    1.839
peak=    3.377 closest distance to " CB  TYR A 169 " =    0.856
peak=    3.373 closest distance to " C   TYR A 214 " =    1.556
peak=    3.372 closest distance to " O   HOH Z 291 " =    1.507
peak=    3.369 closest distance to " CG2 VAL A 197 " =    1.145
peak=    3.365 closest distance to " OG BSER A 134 " =    2.842
peak=    3.361 closest distance to " CA  ASP A 124 " =    0.733
peak=    3.358 closest distance to " CB  ALA A 291 " =    1.302
peak=    3.358 closest distance to " CD  ARG A  66 " =    2.468
peak=    3.355 closest distance to " O   GLN A 278 " =    1.303
peak=    3.355 closest distance to " O   ALA A 158 " =    1.232
peak=    3.354 closest distance to " CB  SER A  62 " =    0.746
peak=    3.354 closest distance to " OD2 ASP A 286 " =    2.914
peak=    3.354 closest distance to " CB  GLN A  88 " =    1.255
peak=    3.351 closest distance to " NE2 HIS A 115 " =    1.013
peak=    3.350 closest distance to " CA  ALA A 233 " =    1.601
peak=    3.349 closest distance to " O   HOH Z 325 " =    2.317
peak=    3.348 closest distance to " O   THR A 220 " =    1.183
peak=    3.343 closest distance to " O   HOH Z 142 " =    1.528
peak=    3.341 closest distance to " O   HOH Z 359 " =    1.487
peak=    3.340 closest distance to " O   HOH Z 403 " =    2.213
peak=    3.339 closest distance to " O  BHOH Z 338 " =    2.255
peak=    3.337 closest distance to " CA  GLY A  98 " =    1.177
peak=    3.336 closest distance to " O   HOH Z 345 " =    1.736
peak=    3.333 closest distance to " CG1BVAL A  72 " =    1.895
peak=    3.332 closest distance to " O   HOH Z 234 " =    1.856
peak=    3.332 closest distance to " O   HOH Z 128 " =    2.379
peak=    3.325 closest distance to " CA  THR A 221 " =    1.320
peak=    3.325 closest distance to " O   HOH Z 213 " =    1.789
peak=    3.324 closest distance to " O   HOH Z 327 " =    2.105
peak=    3.322 closest distance to " O   HOH Z 193 " =    1.625
peak=    3.322 closest distance to " O   HOH Z 403 " =    1.401
peak=    3.322 closest distance to " O   HOH Z 109 " =    2.725
peak=    3.320 closest distance to " CB  TRP A 150 " =    1.470
peak=    3.320 closest distance to " CB  ASN A 215 " =    1.202
peak=    3.315 closest distance to " CA  GLN A  88 " =    1.368
peak=    3.313 closest distance to " O   TRP A 274 " =    1.834
peak=    3.312 closest distance to " O   HOH Z 305 " =    3.794
peak=    3.310 closest distance to " O   HOH Z 197 " =    2.686
peak=    3.310 closest distance to " CG BARG A 275 " =    1.374
peak=    3.303 closest distance to " CB  ASP A 298 " =    1.257
peak=    3.302 closest distance to " O   HOH Z 245 " =    1.303
peak=    3.302 closest distance to " CG1 ILE A 151 " =    1.002
peak=    3.297 closest distance to " CD  ARG A 219 " =    1.049
peak=    3.294 closest distance to " OG1 THR A 294 " =    2.465
peak=    3.294 closest distance to " CA  ALA A 291 " =    0.832
peak=    3.294 closest distance to " O   HOH Z 285 " =    1.452
peak=    3.290 closest distance to " NH2AARG A 275 " =    3.526
peak=    3.290 closest distance to " N   CYS A 260 " =    0.808
peak=    3.290 closest distance to " CG  LEU A 167 " =    1.177
peak=    3.289 closest distance to " CB  LEU A  83 " =    0.823
peak=    3.286 closest distance to " ND2 ASN A 249 " =    0.853
peak=    3.286 closest distance to " CG2 THR A  29 " =    1.376
peak=    3.286 closest distance to " O   HOH Z 422 " =    2.642
peak=    3.284 closest distance to " O   HOH Z 387 " =    2.867
peak=    3.280 closest distance to " CG  MET A 185 " =    1.214
peak=    3.279 closest distance to " CA  ASP A 162 " =    1.143
peak=    3.273 closest distance to " CB  ALA A 100 " =    1.338
peak=    3.269 closest distance to " CA  VAL A 125 " =    1.138
peak=    3.267 closest distance to " O   ASP A 124 " =    1.258
peak=    3.267 closest distance to " O   HOH Z 130 " =    2.254
peak=    3.265 closest distance to " O   HOH Z 344 " =    3.213
peak=    3.265 closest distance to " CA  ALA A 154 " =    1.020
peak=    3.264 closest distance to " CB  ALA A 242 " =    0.842
peak=    3.261 closest distance to " CZ3 TRP A 266 " =    1.084
peak=    3.261 closest distance to " O   HOH Z 357 " =    2.061
peak=    3.260 closest distance to " O   HOH Z 148 " =    3.280
peak=    3.260 closest distance to " CG AARG A 275 " =    1.156
peak=    3.253 closest distance to " O   HOH Z  66 " =    2.105
peak=    3.252 closest distance to " OD2 ASP A 200 " =    1.271
peak=    3.252 closest distance to " CA  LYS A 117 " =    1.246
peak=    3.239 closest distance to " O   HOH Z 146 " =    2.333
peak=    3.237 closest distance to " CB  MET A 113 " =    1.814
peak=    3.234 closest distance to " CA  ALA A  84 " =    1.313
peak=    3.230 closest distance to " O   HOH Z 227 " =    1.658
peak=    3.227 closest distance to " OG  SER A  22 " =    2.791
peak=    3.225 closest distance to " N   VAL A 126 " =    1.518
peak=    3.216 closest distance to " CA  ASN A 217 " =    1.274
peak=    3.214 closest distance to " O   HOH Z 247 " =    1.414
peak=    3.211 closest distance to " O   HOH Z 199 " =    1.591
peak=    3.210 closest distance to " O   HOH Z 355 " =    1.630
peak=    3.207 closest distance to " O   TYR A 116 " =    1.287
peak=    3.202 closest distance to " CA  ASP A 140 " =    1.258
peak=    3.202 closest distance to " O   HOH Z 365 " =    2.916
peak=    3.199 closest distance to " CB  PHE A 204 " =    0.904
peak=    3.195 closest distance to " CB  SER A  28 " =    1.102
peak=    3.194 closest distance to " OG  SER A 245 " =    1.669
peak=    3.192 closest distance to " CA  ARG A 102 " =    1.170
peak=    3.190 closest distance to " CD2 LEU A 255 " =    1.660
peak=    3.188 closest distance to " O   THR A 251 " =    1.945
peak=    3.183 closest distance to " O   HOH Z  44 " =    3.322
peak=    3.178 closest distance to " CB  GLN A  89 " =    1.149
peak=    3.177 closest distance to " O   HOH Z 193 " =    2.265
peak=    3.176 closest distance to " NZ  LYS A  48 " =    1.323
peak=    3.175 closest distance to " O   HOH Z 185 " =    1.875
peak=    3.175 closest distance to " CD  PRO A  54 " =    1.091
peak=    3.171 closest distance to " CA  GLU A  46 " =    0.790
peak=    3.169 closest distance to " O   HOH Z 141 " =    1.688
peak=    3.168 closest distance to " CB  ARG A 139 " =    0.911
peak=    3.168 closest distance to " O   HOH Z 273 " =    2.882
peak=    3.158 closest distance to " CB  SER A 273 " =    0.862
peak=    3.156 closest distance to " CG2 ILE A  20 " =    1.287
peak=    3.156 closest distance to " ND2 ASN A 110 " =    1.542
peak=    3.152 closest distance to " CG  MET A 185 " =    1.068
peak=    3.152 closest distance to " O   HOH Z 116 " =    1.802
peak=    3.151 closest distance to " O   HOH Z 197 " =    1.990
peak=    3.150 closest distance to " CA  LEU A  83 " =    1.476
peak=    3.144 closest distance to " CB  PRO A 243 " =    1.559
peak=    3.142 closest distance to " CG ALYS A 290 " =    1.155
peak=    3.140 closest distance to " CA  ALA A 158 " =    1.150
peak=    3.139 closest distance to " CB  MET A 105 " =    0.928
peak=    3.139 closest distance to " O   GLU A   2 " =    1.616
peak=    3.138 closest distance to " O   HOH Z 167 " =    1.752
peak=    3.137 closest distance to " CG1 ILE A  49 " =    1.549
peak=    3.136 closest distance to " CB  ARG A 138 " =    1.035
peak=    3.130 closest distance to " CB  ALA A  34 " =    0.884
peak=    3.129 closest distance to " N   TYR A  15 " =    0.760
peak=    3.125 closest distance to " O   HOH Z 329 " =    3.817
peak=    3.125 closest distance to " CD1AILE A 234 " =    0.912
peak=    3.122 closest distance to " O   HOH Z 299 " =    4.494
peak=    3.119 closest distance to " NH1 ARG A  14 " =    1.087
peak=    3.114 closest distance to " CG BARG A 102 " =    1.937
peak=    3.114 closest distance to " CB  SER A 216 " =    0.844
peak=    3.108 closest distance to " OG  SER A  62 " =    3.061
peak=    3.108 closest distance to " CG  ARG A 219 " =    1.106
peak=    3.105 closest distance to " O   HOH Z 251 " =    1.628
peak=    3.101 closest distance to " O   HOH Z 271 " =    2.464
peak=    3.099 closest distance to " O   HOH Z 271 " =    2.125
peak=    3.096 closest distance to " CB  THR A 157 " =    1.123
peak=    3.096 closest distance to " O   HOH Z 423 " =    3.242
peak=    3.068 closest distance to " O   HOH Z 173 " =    2.096
peak=    3.062 closest distance to " O   HOH Z 417 " =    3.180
peak=    3.045 closest distance to " CA  GLN A 223 " =    0.895
peak=    3.030 closest distance to " CB  ALA A  43 " =    0.843

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.844 - 5.844
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 216
   mapped sites are within: 0.844 - 5.844

peak=   -4.548 closest distance to " O   HOH Z 266 " =    5.118
peak=   -4.458 closest distance to " CB  PRO A 243 " =    2.672
peak=   -4.428 closest distance to " CD  ARG A 156 " =    2.085
peak=   -4.300 closest distance to " CG1 VAL A 250 " =    2.694
peak=   -4.227 closest distance to " O   HOH Z  10 " =    1.612
peak=   -4.209 closest distance to " O   VAL A  67 " =    2.622
peak=   -4.178 closest distance to " CG1 VAL A 112 " =    2.603
peak=   -4.119 closest distance to " O   HOH Z 290 " =    1.197
peak=   -3.995 closest distance to " CD  GLN A 223 " =    1.263
peak=   -3.984 closest distance to " O   HOH Z 196 " =    2.205
peak=   -3.972 closest distance to " C   HIS A 108 " =    1.128
peak=   -3.965 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.942 closest distance to " O   HOH Z  73 " =    2.297
peak=   -3.939 closest distance to " CD  ARG A  14 " =    3.433
peak=   -3.926 closest distance to " ND2 ASN A  45 " =    1.883
peak=   -3.924 closest distance to " CD1 PHE A 130 " =    2.380
peak=   -3.890 closest distance to " OE1 GLN A 223 " =    1.809
peak=   -3.889 closest distance to " CZ3 TRP A 179 " =    1.183
peak=   -3.867 closest distance to " CD  GLN A  58 " =    1.008
peak=   -3.859 closest distance to " CD1 LEU A 101 " =    2.492
peak=   -3.856 closest distance to " OG  SER A  97 " =    2.239
peak=   -3.852 closest distance to " O   HOH Z 394 " =    1.499
peak=   -3.841 closest distance to " O   HOH Z 377 " =    1.916
peak=   -3.828 closest distance to " CE2 PHE A  61 " =    2.565
peak=   -3.824 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.819 closest distance to " O   PRO A 198 " =    1.299
peak=   -3.815 closest distance to " O   HOH Z 292 " =    4.641
peak=   -3.812 closest distance to " CB  ALA A 161 " =    2.685
peak=   -3.809 closest distance to " OXT GLY A 302 " =    3.007
peak=   -3.797 closest distance to " CB  ASP A 132 " =    2.377
peak=   -3.791 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.783 closest distance to " O   HOH Z  52 " =    1.636
peak=   -3.776 closest distance to " CD1 PHE A  59 " =    1.940
peak=   -3.765 closest distance to " CE2 TYR A  30 " =    2.705
peak=   -3.753 closest distance to " O   HOH Z 377 " =    1.273
peak=   -3.736 closest distance to " NH2 ARG A  66 " =    1.865
peak=   -3.714 closest distance to " O   HOH Z 372 " =    2.550
peak=   -3.708 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.708 closest distance to " NE2 GLN A 103 " =    1.819
peak=   -3.698 closest distance to " O   HOH Z 353 " =    2.269
peak=   -3.679 closest distance to " O   HOH Z  38 " =    1.264
peak=   -3.672 closest distance to " CG1 VAL A 265 " =    2.419
peak=   -3.668 closest distance to " C   ASN A 285 " =    2.475
peak=   -3.660 closest distance to " O   HOH Z 348 " =    2.263
peak=   -3.653 closest distance to " ND2 ASN A 249 " =    2.440
peak=   -3.650 closest distance to " CA  GLY A 241 " =    2.364
peak=   -3.637 closest distance to " NH2AARG A 275 " =    5.482
peak=   -3.635 closest distance to " O   HOH Z 166 " =    1.759
peak=   -3.635 closest distance to " O   HOH Z  19 " =    2.175
peak=   -3.629 closest distance to " O   PRO A 163 " =    2.209
peak=   -3.621 closest distance to " OD1 ASN A 148 " =    1.538
peak=   -3.617 closest distance to " OG BSER A 134 " =    1.370
peak=   -3.615 closest distance to " O   HOH Z 185 " =    2.384
peak=   -3.606 closest distance to " CA  GLY A 241 " =    3.177
peak=   -3.584 closest distance to " O   HOH Z  13 " =    1.654
peak=   -3.584 closest distance to " CD  PRO A 213 " =    2.239
peak=   -3.581 closest distance to " C   ALA A 158 " =    1.407
peak=   -3.558 closest distance to " O   ALA A  10 " =    1.696
peak=   -3.549 closest distance to " CB  TRP A  85 " =    2.439
peak=   -3.542 closest distance to " CG  ARG A  66 " =    2.365
peak=   -3.540 closest distance to " O   HOH Z 275 " =    1.568
peak=   -3.533 closest distance to " O   HOH Z 128 " =    2.525
peak=   -3.531 closest distance to " O   HOH Z 393 " =    1.478
peak=   -3.528 closest distance to " O   SER A 210 " =    1.983
peak=   -3.526 closest distance to " CG2 VAL A 189 " =    2.234
peak=   -3.525 closest distance to " O   HOH Z 118 " =    3.714
peak=   -3.523 closest distance to " C   SER A 206 " =    1.496
peak=   -3.512 closest distance to " C   ASN A 187 " =    1.892
peak=   -3.507 closest distance to " C   LEU A 143 " =    1.162
peak=   -3.506 closest distance to " OD1 ASP A 191 " =    1.569
peak=   -3.499 closest distance to " CE3 TRP A 150 " =    2.068
peak=   -3.496 closest distance to " NH2 ARG A 159 " =    2.360
peak=   -3.496 closest distance to " NH2 ARG A  79 " =    2.059
peak=   -3.493 closest distance to " O   HOH Z 150 " =    2.246
peak=   -3.492 closest distance to " ND2 ASN A  45 " =    1.104
peak=   -3.491 closest distance to " CG  GLU A  53 " =    1.522
peak=   -3.481 closest distance to " NH2 ARG A  79 " =    1.555
peak=   -3.476 closest distance to " CH2 TRP A 177 " =    2.102
peak=   -3.475 closest distance to " O   VAL A  67 " =    2.927
peak=   -3.474 closest distance to " CA  GLY A 133 " =    2.314
peak=   -3.473 closest distance to " CB  ALA A  10 " =    2.183
peak=   -3.470 closest distance to " CD1 LEU A 228 " =    2.397
peak=   -3.465 closest distance to " O   HOH Z 350 " =    2.027
peak=   -3.462 closest distance to " O   HOH Z 264 " =    1.779
peak=   -3.461 closest distance to " CD2 LEU A 167 " =    1.880
peak=   -3.450 closest distance to " N   SER A 276 " =    1.472
peak=   -3.450 closest distance to " CE BMET A  47 " =    2.119
peak=   -3.449 closest distance to " CD1 PHE A  16 " =    2.642
peak=   -3.440 closest distance to " O   HOH Z   6 " =    1.559
peak=   -3.432 closest distance to " CG  ASP A 231 " =    0.844
peak=   -3.428 closest distance to " O   HOH Z  43 " =    1.513
peak=   -3.428 closest distance to " O   HOH Z 198 " =    2.421
peak=   -3.428 closest distance to " O   HOH Z 177 " =    1.762
peak=   -3.428 closest distance to " NE1 TRP A 266 " =    2.345
peak=   -3.427 closest distance to " O   HOH Z 426 " =    1.729
peak=   -3.425 closest distance to " O   HOH Z 234 " =    4.424
peak=   -3.420 closest distance to " OD2 ASP A 171 " =    1.880
peak=   -3.418 closest distance to " CB  ALA A  43 " =    2.634
peak=   -3.414 closest distance to " CG  GLU A 277 " =    1.174
peak=   -3.413 closest distance to " CB  ALA A   9 " =    2.649
peak=   -3.398 closest distance to " O   HOH Z 166 " =    1.728
peak=   -3.391 closest distance to " O   HOH Z 123 " =    2.453
peak=   -3.391 closest distance to " OE1 GLN A  88 " =    1.296
peak=   -3.389 closest distance to " O   HOH Z 351 " =    1.536
peak=   -3.387 closest distance to " O   HOH Z 111 " =    1.969
peak=   -3.386 closest distance to " O   HOH Z 311 " =    3.839
peak=   -3.380 closest distance to " O   HOH Z  11 " =    2.338
peak=   -3.374 closest distance to " O   HOH Z 232 " =    1.636
peak=   -3.373 closest distance to " OG BSER A 134 " =    1.966
peak=   -3.368 closest distance to " O   HOH Z 114 " =    1.432
peak=   -3.367 closest distance to " O   ALA A  34 " =    2.575
peak=   -3.365 closest distance to " N   ALA A 226 " =    2.107
peak=   -3.365 closest distance to " ND2 ASN A 187 " =    1.705
peak=   -3.364 closest distance to " OG  SER A  62 " =    1.706
peak=   -3.361 closest distance to " CD1 ILE A 151 " =    2.415
peak=   -3.356 closest distance to " N   THR A 157 " =    1.587
peak=   -3.354 closest distance to " O   HOH Z 150 " =    1.261
peak=   -3.351 closest distance to " CA  GLY A 203 " =    2.399
peak=   -3.350 closest distance to " ND2BASN A 224 " =    1.812
peak=   -3.341 closest distance to " N   MET A 105 " =    2.698
peak=   -3.340 closest distance to " OH  TYR A 169 " =    0.991
peak=   -3.340 closest distance to " O   HOH Z 298 " =    2.572
peak=   -3.338 closest distance to " O   HOH Z 211 " =    1.591
peak=   -3.330 closest distance to " O   HOH Z  71 " =    1.638
peak=   -3.330 closest distance to " OG BSER A 210 " =    2.198
peak=   -3.329 closest distance to " CD2 PHE A 192 " =    2.097
peak=   -3.329 closest distance to " O   HOH Z 241 " =    1.325
peak=   -3.323 closest distance to " O   HOH Z 252 " =    4.010
peak=   -3.321 closest distance to " O   HOH Z 407 " =    3.547
peak=   -3.321 closest distance to " CG  MET A 105 " =    0.931
peak=   -3.321 closest distance to " O   HOH Z 389 " =    1.881
peak=   -3.312 closest distance to " N   THR A  52 " =    1.650
peak=   -3.305 closest distance to " O   HOH Z  37 " =    1.911
peak=   -3.302 closest distance to " O   HOH Z 253 " =    4.151
peak=   -3.297 closest distance to " O   VAL A 189 " =    2.659
peak=   -3.296 closest distance to " C   GLY A  17 " =    1.276
peak=   -3.291 closest distance to " O   TYR A 247 " =    2.906
peak=   -3.290 closest distance to " NH1 ARG A 195 " =    2.647
peak=   -3.289 closest distance to " CD1 ILE A 263 " =    1.968
peak=   -3.287 closest distance to " O   ASP A  27 " =    2.130
peak=   -3.279 closest distance to " NE2 GLN A 194 " =    1.883
peak=   -3.278 closest distance to " O   HOH Z 396 " =    1.628
peak=   -3.277 closest distance to " C   ILE A 234 " =    1.222
peak=   -3.272 closest distance to " O   HOH Z 236 " =    1.445
peak=   -3.270 closest distance to " O   HOH Z 198 " =    1.462
peak=   -3.266 closest distance to " CG2BVAL A  41 " =    1.690
peak=   -3.265 closest distance to " O   HOH Z  90 " =    1.790
peak=   -3.264 closest distance to " CD2 PHE A 225 " =    1.277
peak=   -3.262 closest distance to " CG1 VAL A 125 " =    2.028
peak=   -3.259 closest distance to " O   GLY A 211 " =    1.429
peak=   -3.257 closest distance to " O   HOH Z 200 " =    1.610
peak=   -3.255 closest distance to " O   ASN A 301 " =    1.399
peak=   -3.255 closest distance to " O   HOH Z  11 " =    1.829
peak=   -3.253 closest distance to " CD2 PHE A  59 " =    2.561
peak=   -3.253 closest distance to " CB  ALA A 291 " =    2.343
peak=   -3.242 closest distance to " O   HOH Z 102 " =    1.568
peak=   -3.240 closest distance to " O   ALA A   1 " =    1.928
peak=   -3.239 closest distance to " O   HOH Z  78 " =    1.855
peak=   -3.236 closest distance to " CD1 TRP A 179 " =    1.064
peak=   -3.233 closest distance to " NE2 GLN A  88 " =    1.902
peak=   -3.233 closest distance to " ND2 ASN A  60 " =    1.343
peak=   -3.233 closest distance to " O   HOH Z 323 " =    1.404
peak=   -3.229 closest distance to " CE3 TRP A  70 " =    1.913
peak=   -3.229 closest distance to " O   HOH Z 421 " =    3.519
peak=   -3.228 closest distance to " CG  ARG A 269 " =    2.397
peak=   -3.221 closest distance to " O   HOH Z  60 " =    2.463
peak=   -3.219 closest distance to " CB  ALA A 291 " =    2.190
peak=   -3.219 closest distance to " OD1 ASN A 187 " =    1.569
peak=   -3.217 closest distance to " O   HOH Z 165 " =    1.887
peak=   -3.214 closest distance to " O   HOH Z 216 " =    2.162
peak=   -3.210 closest distance to " CB  ASP A 286 " =    2.139
peak=   -3.209 closest distance to " CB  PRO A 163 " =    2.597
peak=   -3.206 closest distance to " CZ  PHE A  38 " =    1.957
peak=   -3.204 closest distance to " CB  PRO A  54 " =    2.629
peak=   -3.203 closest distance to " OH  TYR A 247 " =    1.814
peak=   -3.197 closest distance to " CE3 TRP A 274 " =    2.552
peak=   -3.197 closest distance to " O   HOH Z 283 " =    5.844
peak=   -3.195 closest distance to " O   HOH Z 139 " =    2.991
peak=   -3.195 closest distance to " CE  MET A  93 " =    1.723
peak=   -3.193 closest distance to " O   HOH Z 435 " =    2.588
peak=   -3.190 closest distance to " O   HOH Z  51 " =    1.819
peak=   -3.190 closest distance to " CG1 VAL A 112 " =    3.016
peak=   -3.189 closest distance to " C   GLY A 262 " =    2.112
peak=   -3.189 closest distance to " O   HOH Z 136 " =    2.076
peak=   -3.185 closest distance to " O   PHE A 218 " =    1.561
peak=   -3.184 closest distance to " CG  PRO A 163 " =    2.361
peak=   -3.173 closest distance to " N   ALA A 248 " =    1.725
peak=   -3.172 closest distance to " O   HOH Z 106 " =    1.966
peak=   -3.167 closest distance to " CG  TRP A 266 " =    1.813
peak=   -3.166 closest distance to " CB  ALA A 248 " =    2.084
peak=   -3.166 closest distance to " O   HOH Z 256 " =    2.338
peak=   -3.166 closest distance to " OD1 ASP A 171 " =    1.604
peak=   -3.165 closest distance to " CE  MET A 105 " =    2.255
peak=   -3.165 closest distance to " CG  LEU A  83 " =    1.992
peak=   -3.158 closest distance to " ND2 ASN A  60 " =    1.914
peak=   -3.157 closest distance to " CZ  PHE A  59 " =    1.975
peak=   -3.153 closest distance to " OG ASER A 134 " =    1.341
peak=   -3.141 closest distance to " O   HOH Z 313 " =    1.249
peak=   -3.141 closest distance to " O   HOH Z 133 " =    1.411
peak=   -3.134 closest distance to " O   HOH Z  17 " =    1.548
peak=   -3.131 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.122 closest distance to " O   HOH Z 322 " =    1.413
peak=   -3.118 closest distance to " O   HOH Z 357 " =    2.000
peak=   -3.117 closest distance to " CG  ASN A 301 " =    2.014
peak=   -3.114 closest distance to " CB  ARG A  79 " =    2.605
peak=   -3.110 closest distance to " CZ  TYR A 169 " =    1.856
peak=   -3.108 closest distance to " CG2 THR A 221 " =    2.221
peak=   -3.105 closest distance to " O   HOH Z 189 " =    1.816
peak=   -3.103 closest distance to " O   HOH Z 176 " =    0.890
peak=   -3.102 closest distance to " CD  GLN A  88 " =    0.876
peak=   -3.081 closest distance to " O   HOH Z 326 " =    5.053
peak=   -3.077 closest distance to " O   HOH Z 423 " =    2.318
peak=   -3.073 closest distance to " O   HOH Z 117 " =    4.449
peak=   -3.071 closest distance to " CA  GLY A  98 " =    2.166
peak=   -3.067 closest distance to " CG1 VAL A  78 " =    2.772
peak=   -3.016 closest distance to " O   HOH Z 357 " =    2.112

================= 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    :  0.3832 0.3725   6.164918e+00   6.145075e+00
   1_bss:  0.3733 0.3629   6.150374e+00   6.126854e+00
   1_xyz:  0.2606 0.2825   5.855485e+00   5.919475e+00
   1_adp:  0.2411 0.2864   5.801773e+00   5.935580e+00
   1_occ:  0.2407 0.2858   5.800758e+00   5.935310e+00
   2_bss:  0.2398 0.2846   5.800003e+00   5.933755e+00
   2_xyz:  0.1710 0.2069   5.489686e+00   5.661675e+00
   2_adp:  0.1528 0.1950   5.405155e+00   5.601387e+00
   2_occ:  0.1527 0.1946   5.404321e+00   5.600627e+00
   3_bss:  0.1526 0.1951   5.403568e+00   5.598832e+00
   3_xyz:  0.1285 0.1753   5.266320e+00   5.496447e+00
   3_adp:  0.1228 0.1699   5.226990e+00   5.463137e+00
   3_occ:  0.1227 0.1698   5.226518e+00   5.462909e+00
   4_bss:  0.1231 0.1693   5.226812e+00   5.460691e+00
   4_xyz:  0.1161 0.1656   5.185573e+00   5.433925e+00
   4_adp:  0.1148 0.1635   5.176194e+00   5.424374e+00
   4_occ:  0.1148 0.1635   5.176074e+00   5.424446e+00
   5_bss:  0.1147 0.1635   5.175896e+00   5.424301e+00
   5_xyz:  0.1134 0.1639   5.172077e+00   5.424750e+00
   5_adp:  0.1135 0.1624   5.168891e+00   5.419833e+00
   5_occ:  0.1135 0.1624   5.168899e+00   5.420029e+00
   5_bss:  0.1134 0.1624   5.168957e+00   5.420071e+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:  0.304  58.454  -0.654   2.896  -1.167   0.000  -0.000  -0.000
   1_xyz:  0.304  58.454  -0.654   2.896  -1.167   0.000  -0.000  -0.000
   1_adp:  0.304  58.454  -0.654   2.896  -1.167   0.000  -0.000  -0.000
   1_occ:  0.304  58.454  -0.654   2.896  -1.167   0.000  -0.000  -0.000
   2_bss:  0.326  69.453  -1.576   0.405  -1.243   0.000  -0.000  -0.000
   2_xyz:  0.326  69.453  -1.576   0.405  -1.243   0.000  -0.000  -0.000
   2_adp:  0.326  69.453  -1.576   0.405  -1.243   0.000  -0.000  -0.000
   2_occ:  0.326  69.453  -1.576   0.405  -1.243   0.000  -0.000  -0.000
   3_bss:  0.334  79.267  -1.625  -0.572  -0.775  -0.000  -0.000  -0.000
   3_xyz:  0.334  79.267  -1.625  -0.572  -0.775  -0.000  -0.000  -0.000
   3_adp:  0.334  79.267  -1.625  -0.572  -0.775  -0.000  -0.000  -0.000
   3_occ:  0.334  79.267  -1.625  -0.572  -0.775  -0.000  -0.000  -0.000
   4_bss:  0.329  74.314  -1.319  -0.730  -0.315  -0.000  -0.000  -0.000
   4_xyz:  0.329  74.314  -1.319  -0.730  -0.315  -0.000  -0.000  -0.000
   4_adp:  0.329  74.314  -1.319  -0.730  -0.315  -0.000  -0.000  -0.000
   4_occ:  0.329  74.314  -1.319  -0.730  -0.315  -0.000  -0.000  -0.000
   5_bss:  0.322  68.434  -1.278  -0.856  -0.234  -0.000  -0.000  -0.000
   5_xyz:  0.322  68.434  -1.278  -0.856  -0.234  -0.000  -0.000  -0.000
   5_adp:  0.322  68.434  -1.278  -0.856  -0.234  -0.000  -0.000  -0.000
   5_occ:  0.322  68.434  -1.278  -0.856  -0.234  -0.000  -0.000  -0.000
   5_bss:  0.319  65.291  -1.119  -0.753  -0.030  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.736 0.6236  0.7794    41696.694
   1_bss:  40.914 0.6319  0.8031    39147.895
   1_xyz:  29.083 0.7691  0.9419    21514.160
   1_adp:  29.583 0.7631  0.9273    22273.194
   1_occ:  29.597 0.7628  0.9268    22266.237
   2_bss:  29.431 0.7647  0.8939    22145.948
   2_xyz:  20.709 0.8538  0.9640    11187.787
   2_adp:  18.888 0.8718  0.9606     9764.695
   2_occ:  18.864 0.8720  0.9604     9745.970
   3_bss:  18.811 0.8725  0.9547     9708.243
   3_xyz:  16.387 0.8946  0.9677     7763.828
   3_adp:  15.492 0.9028  0.9604     7302.905
   3_occ:  15.484 0.9029  0.9602     7297.130
   4_bss:  15.458 0.9031  0.9673     7261.005
   4_xyz:  14.921 0.9074  0.9708     6863.539
   4_adp:  14.665 0.9098  0.9627     6763.221
   4_occ:  14.663 0.9098  0.9626     6763.478
   5_bss:  14.662 0.9098  0.9627     6759.566
   5_xyz:  14.647 0.9100  0.9628     6766.299
   5_adp:  14.503 0.9113  0.9556     6720.763
   5_occ:  14.508 0.9112  0.9554     6723.320
   5_bss:  14.509 0.9112  0.9608     6723.077
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6418e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6418e-01
   1_xyz:   1.283  0.010  0.080 15.257  0.005  4.115   8.5317e-02
   1_adp:   1.283  0.010  0.080 15.257  0.005  4.115   8.5317e-02
   1_occ:   1.283  0.010  0.080 15.257  0.005  4.115   8.5317e-02
   2_bss:   1.283  0.010  0.080 15.257  0.005  4.115   8.5317e-02
   2_xyz:   1.137  0.009  0.080 14.735  0.004  4.136   7.0801e-02
   2_adp:   1.137  0.009  0.080 14.735  0.004  4.136   7.0801e-02
   2_occ:   1.137  0.009  0.080 14.735  0.004  4.136   7.0801e-02
   3_bss:   1.137  0.009  0.080 14.735  0.004  4.136   7.0801e-02
   3_xyz:   1.042  0.009  0.077 14.812  0.004  4.116   6.5955e-02
   3_adp:   1.042  0.009  0.077 14.812  0.004  4.116   6.5955e-02
   3_occ:   1.042  0.009  0.077 14.812  0.004  4.116   6.5955e-02
   4_bss:   1.042  0.009  0.077 14.812  0.004  4.116   6.5955e-02
   4_xyz:   1.095  0.010  0.082 14.913  0.004  4.122   7.2108e-02
   4_adp:   1.095  0.010  0.082 14.913  0.004  4.122   7.2108e-02
   4_occ:   1.095  0.010  0.082 14.913  0.004  4.122   7.2108e-02
   5_bss:   1.095  0.010  0.082 14.913  0.004  4.122   7.2108e-02
   5_xyz:   1.066  0.010  0.080 14.853  0.004  4.124   6.9199e-02
   5_adp:   1.066  0.010  0.080 14.853  0.004  4.124   6.9199e-02
   5_occ:   1.066  0.010  0.080 14.853  0.004  4.124   6.9199e-02
   5_bss:   1.066  0.010  0.080 14.853  0.004  4.124   6.9199e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.525   2.4428e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.525   2.4428e-01
   1_xyz:   9.790  0.051  0.396 88.451  0.033  2.093   7.9969e-02
   1_adp:   9.790  0.051  0.396 88.451  0.033  2.093   7.9969e-02
   1_occ:   9.790  0.051  0.396 88.451  0.033  2.093   7.9969e-02
   2_bss:   9.790  0.051  0.396 88.451  0.033  2.093   7.9969e-02
   2_xyz:   7.928  0.054  0.268 87.835  0.039  2.278   6.1347e-02
   2_adp:   7.928  0.054  0.268 87.835  0.039  2.278   6.1347e-02
   2_occ:   7.928  0.054  0.268 87.835  0.039  2.278   6.1347e-02
   3_bss:   7.928  0.054  0.268 87.835  0.039  2.278   6.1347e-02
   3_xyz:   7.452  0.047  0.237 81.372  0.038  2.322   6.2536e-02
   3_adp:   7.452  0.047  0.237 81.372  0.038  2.322   6.2536e-02
   3_occ:   7.452  0.047  0.237 81.372  0.038  2.322   6.2536e-02
   4_bss:   7.452  0.047  0.237 81.372  0.038  2.322   6.2536e-02
   4_xyz:   7.891  0.048  0.263 82.247  0.042  2.330   5.1057e-02
   4_adp:   7.891  0.048  0.263 82.247  0.042  2.330   5.1057e-02
   4_occ:   7.891  0.048  0.263 82.247  0.042  2.330   5.1057e-02
   5_bss:   7.891  0.048  0.263 82.247  0.042  2.330   5.1057e-02
   5_xyz:   7.750  0.047  0.256 81.378  0.039  2.350   4.7295e-02
   5_adp:   7.750  0.047  0.256 81.378  0.039  2.350   4.7295e-02
   5_occ:   7.750  0.047  0.256 81.378  0.039  2.350   4.7295e-02
   5_bss:   7.750  0.047  0.256 81.378  0.039  2.350   4.7295e-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: 101.72   0.00  16.86 101.72   0.00  13.05  69.91   2.53  37.61
   1_occ: 101.72   0.00  16.86 101.72   0.00  13.05  69.91   2.53  37.61
   2_bss: 101.72   0.00  16.86 101.72   0.00  13.05  69.91   2.53  37.61
   2_xyz: 101.72   0.00  16.86 101.72   0.00  13.05  69.91   2.53  37.61
   2_adp:  93.69   0.00  17.82  92.65   0.00  13.08  93.69   3.74  43.65
   2_occ:  93.69   0.00  17.82  92.65   0.00  13.08  93.69   3.74  43.65
   3_bss:  93.69   0.00  17.82  92.65   0.00  13.08  93.69   3.74  43.65
   3_xyz:  93.69   0.00  17.82  92.65   0.00  13.08  93.69   3.74  43.65
   3_adp: 104.83   0.00  17.45 104.83   0.00  12.62  98.82   0.00  43.75
   3_occ: 104.83   0.00  17.45 104.83   0.00  12.62  98.82   0.00  43.75
   4_bss: 104.83   0.00  17.45 104.83   0.00  12.62  98.82   0.00  43.75
   4_xyz: 104.83   0.00  17.45 104.83   0.00  12.62  98.82   0.00  43.75
   4_adp: 107.91   0.00  16.93 107.91   0.00  12.27  98.29   0.00  42.30
   4_occ: 107.91   0.00  16.93 107.91   0.00  12.27  98.29   0.00  42.30
   5_bss: 107.91   0.00  16.93 107.91   0.00  12.27  98.29   0.00  42.30
   5_xyz: 107.91   0.00  16.93 107.91   0.00  12.27  98.29   0.00  42.30
   5_adp: 107.50   0.00  16.24 107.50   0.00  11.90  92.08   2.20  39.89
   5_occ: 107.50   0.00  16.24 107.50   0.00  11.90  92.08   2.20  39.89
   5_bss: 107.50   0.00  16.24 107.50   0.00  11.90  92.08   2.20  39.89
------------------------------------------------------------------------
 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:    1.665    0.025    0.298
   1_adp:    1.665    0.025    0.298
   1_occ:    1.665    0.025    0.298
   2_bss:    1.665    0.025    0.298
   2_xyz:    1.047    0.050    0.445
   2_adp:    1.047    0.050    0.445
   2_occ:    1.047    0.050    0.445
   3_bss:    1.047    0.050    0.445
   3_xyz:    1.056    0.058    0.524
   3_adp:    1.056    0.058    0.524
   3_occ:    1.056    0.058    0.524
   4_bss:    1.056    0.058    0.524
   4_xyz:    1.021    0.044    0.542
   4_adp:    1.021    0.044    0.542
   4_occ:    1.021    0.044    0.542
   5_bss:    1.021    0.044    0.542
   5_xyz:    1.095    0.042    0.557
   5_adp:    1.095    0.042    0.557
   5_occ:    1.095    0.042    0.557
   5_bss:    1.095    0.042    0.557
------------------------------------------------------------------------

CPU time actual refinement: 343.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/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_1062/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1062/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.25 
  Macro-tasks:
    bulk solvent and scale       = 43.09  
    individual site refinement   = 142.70 
    weights calculation          = 29.56  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 222.11 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 108.41 
    alpha_beta                      = 8.17   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.27 
    fmodel                         = 7.61   
    r_factors                      = 0.24   
    phase_errors                   = 10.79  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 256.82 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.798 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    666 calls, 108.05 s
gradients_fft:          611 calls, 104.32 s

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

# Date 2008-01-16 Time 06:19:34 PST -0800 (1200493174.86 s)
Start R-work = 0.3832, R-free = 0.3725 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.3733, R-free = 0.3629
Final R-work = 0.1134, R-free = 0.1624