# Date 2008-01-16 Time 06:10:06 PST -0800 (1200492606.47 s)
#phil __OFF__

Command line arguments: "../1030.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7955
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1030

-------------------------------------------------------------------------------
  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, 46.93, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, 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, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.00252
Completeness in resolution range: 0.965689
Completeness with d_max=infinity: 0.962699

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0025

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, 46.93, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.00252
Completeness in resolution range: 0.965689
Completeness with d_max=infinity: 0.962699

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2851 [2126/2150]  1913   213  10.0%
  bin  2:  4.2851 -  3.4139 [2041/2061]  1837   204  10.0%
  bin  3:  3.4139 -  2.9861 [2028/2047]  1825   203  10.0%
  bin  4:  2.9861 -  2.7147 [2006/2036]  1809   197   9.8%
  bin  5:  2.7147 -  2.5211 [2002/2021]  1803   199   9.9%
  bin  6:  2.5211 -  2.3730 [1960/1985]  1758   202  10.3%
  bin  7:  2.3730 -  2.2546 [1967/1995]  1768   199  10.1%
  bin  8:  2.2546 -  2.1567 [1974/2010]  1781   193   9.8%
  bin  9:  2.1567 -  2.0739 [1958/2000]  1762   196  10.0%
  bin 10:  2.0739 -  2.0025 [1527/1980]  1374   153  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/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:
        1.81 -     2.42: 8
        2.42 -     3.04: 2173
        3.04 -     3.66: 4598
        3.66 -     4.28: 8923
        4.28 -     4.90: 12258
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.981 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 27955 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_1030/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/model_refine_001.geo

CPU time processing inputs: 9.22


============================ 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 46.93 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3052   r_free= 0.2974   ksol= 0.00   Bsol= 0.00   scale= 0.968    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.986985                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7794 0.99   1385  154 0.2746 0.2544      6.3191      6.2165|
|  2:  4.7794 -  3.8133 0.99   1333  148 0.2400 0.2169      6.3714      6.3134|
|  3:  3.8133 -  3.3371 0.99   1306  143 0.2603 0.2464      6.2584      6.2955|
|  4:  3.3371 -  3.0346 0.99   1294  146 0.2684 0.2942      6.1452      6.1668|
|  5:  3.0346 -  2.8186 0.99   1286  145 0.3177 0.3060      6.0679      6.0884|
|  6:  2.8186 -  2.6533 0.99   1299  139 0.3053 0.3066      5.9605      5.8935|
|  7:  2.6533 -  2.5211 0.99   1284  141 0.3317 0.3321      5.9669      6.0481|
|  8:  2.5211 -  2.4118 0.98   1257  145 0.3338 0.3007      5.9317      5.8614|
|  9:  2.4118 -  2.3193 0.98   1271  140 0.3396 0.3342      5.8667      5.8457|
| 10:  2.3193 -  2.2395 1.00   1258  141 0.3444 0.3195      5.8649      5.8413|
| 11:  2.2395 -  2.1697 0.98   1269  140 0.3597 0.3641      5.8383      5.8818|
| 12:  2.1697 -  2.1078 0.98   1245  142 0.3596 0.3640      5.7634      5.8471|
| 13:  2.1078 -  2.0525 0.99   1288  138 0.3592 0.3584      5.6686      5.6129|
| 14:  2.0525 -  2.0025 0.68    855   97 0.3464 0.3634        5.61      5.6179|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7794  1385   154  0.81  23.85   0.86     0.83      35882.96|
|  2:  4.7794 -  3.8133  1333   148  0.87  19.58   0.97     0.92      37026.86|
|  3:  3.8133 -  3.3371  1306   143  0.83  23.44   0.99     0.94      36841.32|
|  4:  3.3371 -  3.0346  1294   146  0.81  25.98   0.99     0.92      33212.71|
|  5:  3.0346 -  2.8186  1286   145  0.74  31.79   0.99     0.90      29160.98|
|  6:  2.8186 -  2.6533  1299   139  0.75  31.18   1.00     0.89      24628.49|
|  7:  2.6533 -  2.5211  1284   141  0.74  32.28   1.00     0.89      22886.69|
|  8:  2.5211 -  2.4118  1257   145  0.74  32.02   1.01     0.92      20992.21|
|  9:  2.4118 -  2.3193  1271   140  0.74  32.50   1.02     0.93      20057.29|
| 10:  2.3193 -  2.2395  1258   141  0.71  34.72   1.05     0.91      19320.66|
| 11:  2.2395 -  2.1697  1269   140  0.70  35.74   1.03     0.90      19504.58|
| 12:  2.1697 -  2.1078  1245   142  0.69  36.34   1.03     0.92      18519.31|
| 13:  2.1078 -  2.0525  1288   138  0.68  37.18   1.04     0.93      15755.04|
| 14:  2.0525 -  2.0025   855    97  0.73  33.52   1.03     0.91      11628.98|
|alpha:            min =        0.83 max =            0.94 mean =         0.91|
|beta:             min =    11628.98 max =        37026.86 mean =     25142.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.76|
|phase err.(work): min =        0.00 max =           89.92 mean =        30.55|
|phase err.(test): min =        0.00 max =           89.85 mean =        30.11|
|-----------------------------------------------------------------------------|

============================== 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 = 4.479567              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.746   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.822   (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 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        6 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      174 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1999 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1817 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2781 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4591 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4332 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5577 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6681 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.136 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3052   r_free= 0.2974   ksol= 0.00   Bsol= 0.00   scale= 0.968    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.986985                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2907   r_free= 0.2862   ksol= 0.30   Bsol= 50.00   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-3.20,0.34,-0.00,0.00,0.00); trace/3= -1.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.962451                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.068779              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.829   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.323460              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.550   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2907      final r-factor (work) = 0.1629          |
| start r-factor (free) = 0.2862      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3061 = 4.07 * 0.50 * 5.9698 + 1.00 * 0.1611                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5896 = 4.07 * 0.50 * 5.6643 + 1.00 * 0.0663                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1629      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8384 = 0.32 * 1.00 * 5.6643 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7596 = 0.32 * 1.00 * 5.3584 + 1.00 * 0.0264                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.51   16.74    None  None   None       |
|    all(noH): 2823   0      0.00    64.51   16.74    None  None   None       |
|    Sol.    : 438    0      4.64    64.51   37.83    None  None   None       |
|    Mac.    : 2385   0      0.00    56.46   12.87    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 -   6.451:  242   |   5:    32.254 -  38.705:   88        |
|      1:     6.451 -  12.902: 1250   |   6:    38.705 -  45.156:  111        |
|      2:    12.902 -  19.353:  651   |   7:    45.156 -  51.607:   79        |
|      3:    19.353 -  25.804:  213   |   8:    51.607 -  58.058:   57        |
|      4:    25.804 -  32.254:  117   |   9:    58.058 -  64.509:   15        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1495 r_free = 0.1888             target_work(ml) = 5.367         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.1885             target_work(ml) = 5.365         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.1885   ksol= 0.30   Bsol= 50.00   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,-3.20,0.34,-0.00,0.00,0.00); trace/3= -1.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.364879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1474   r_free= 0.1860   ksol= 0.33   Bsol= 64.62   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-3.13,-1.05,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.359759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.048175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.278  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213082              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.833   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1474      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1860      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5656 = 2.05 * 0.50 * 5.3697 + 1.00 * 0.0666                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4676 = 2.05 * 0.50 * 5.2812 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1453 = 0.21 * 1.00 * 5.2812 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1157 = 0.21 * 1.00 * 5.1998 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    72.62   16.92    None  None   None       |
|    all(noH): 2823   0      1.57    72.62   16.92    None  None   None       |
|    Sol.    : 438    0      6.39    72.62   38.36    None  None   None       |
|    Mac.    : 2385   0      1.57    71.86   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.566 -   8.672:  625   |   5:    37.095 -  44.200:  114        |
|      1:     8.672 -  15.777: 1283   |   6:    44.200 -  51.306:   86        |
|      2:    15.777 -  22.883:  371   |   7:    51.306 -  58.412:   74        |
|      3:    22.883 -  29.989:  138   |   8:    58.412 -  65.517:   26        |
|      4:    29.989 -  37.095:   99   |   9:    65.517 -  72.623:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1601             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1600             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1600   ksol= 0.33   Bsol= 64.62   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-3.13,-1.05,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.187588                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1599   ksol= 0.33   Bsol= 64.62   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.75,-1.12,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.065434              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.492  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.164453              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.395  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0278 = 3.07 * 0.50 * 5.1990 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9766 = 3.07 * 0.50 * 5.1537 + 1.00 * 0.0774                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8552 = 0.16 * 1.00 * 5.1537 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8533 = 0.16 * 1.00 * 5.1450 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.82    73.61   16.67    None  None   None       |
|    all(noH): 2823   0      1.82    73.61   16.67    None  None   None       |
|    Sol.    : 438    0      5.13    73.61   37.56    None  None   None       |
|    Mac.    : 2385   0      1.82    72.00   12.84    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.816 -   8.995:  726   |   5:    37.711 -  44.890:  106        |
|      1:     8.995 -  16.174: 1238   |   6:    44.890 -  52.069:   87        |
|      2:    16.174 -  23.353:  345   |   7:    52.069 -  59.248:   64        |
|      3:    23.353 -  30.532:  124   |   8:    59.248 -  66.427:   17        |
|      4:    30.532 -  37.711:  111   |   9:    66.427 -  73.606:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1569             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1111 r_free = 0.1570             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1570   ksol= 0.33   Bsol= 64.62   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.75,-1.12,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140922                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1558   ksol= 0.33   Bsol= 64.62   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.59,-1.11,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138539                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.276317              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.000665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.551  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9327 = 2.28 * 0.50 * 5.1445 + 1.00 * 0.0774                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9196 = 2.28 * 0.50 * 5.1418 + 1.00 * 0.0674                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1523 = 1.00 * 1.00 * 5.1418 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1532 = 1.00 * 1.00 * 5.1406 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.45    78.91   16.97    None  None   None       |
|    all(noH): 2823   0      0.45    78.91   16.97    None  None   None       |
|    Sol.    : 438    0      5.94    77.50   39.57    None  None   None       |
|    Mac.    : 2385   0      0.45    78.91   12.82    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:     0.445 -   8.292:  635   |   5:    39.679 -  47.526:  100        |
|      1:     8.292 -  16.139: 1320   |   6:    47.526 -  55.372:   88        |
|      2:    16.139 -  23.985:  347   |   7:    55.372 -  63.219:   61        |
|      3:    23.985 -  31.832:  134   |   8:    63.219 -  71.066:   24        |
|      4:    31.832 -  39.679:  107   |   9:    71.066 -  78.913:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1585             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1586             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1586   ksol= 0.33   Bsol= 64.62   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.59,-1.11,-0.00,-0.00,-0.00); trace/3= -2.01                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145544                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1585   ksol= 0.33   Bsol= 64.62   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.34,-0.92,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.145342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.462264              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.741  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.516708              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.375  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3969 = 2.46 * 0.50 * 5.1412 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3988 = 2.46 * 0.50 * 5.1416 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1608          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9492 = 2.52 * 1.00 * 5.1416 + 1.00 * 0.0092                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9522 = 2.52 * 1.00 * 5.1423 + 1.00 * 0.0106                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.54   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    89.54   17.04    None  None   None       |
|    Sol.    : 438    0      5.39    81.63   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    89.54   12.73    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.954:  874   |   5:    44.770 -  53.724:   94        |
|      1:     8.954 -  17.908: 1215   |   6:    53.724 -  62.678:   79        |
|      2:    17.908 -  26.862:  264   |   7:    62.678 -  71.632:   34        |
|      3:    26.862 -  35.816:  138   |   8:    71.632 -  80.586:   15        |
|      4:    35.816 -  44.770:  105   |   9:    80.586 -  89.540:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1095 r_free = 0.1608             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1609             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1609   ksol= 0.33   Bsol= 64.62   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.16,-2.34,-0.92,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.145950                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7794 0.99   1385  154 0.0970 0.1301      5.3889       5.538|
|  2:  4.7794 -  3.8133 0.99   1333  148 0.0827 0.1092      5.4207      5.6166|
|  3:  3.8133 -  3.3371 0.99   1306  143 0.1023 0.1479      5.4556      5.8578|
|  4:  3.3371 -  3.0346 0.99   1294  146 0.1177 0.1623      5.4463      5.5896|
|  5:  3.0346 -  2.8186 0.99   1286  145 0.1313 0.1794      5.3333      5.5891|
|  6:  2.8186 -  2.6533 0.99   1299  139 0.1187 0.1981      5.2258      5.4988|
|  7:  2.6533 -  2.5211 0.99   1284  141 0.1266 0.1589      5.1772      5.3529|
|  8:  2.5211 -  2.4118 0.98   1257  145 0.1121 0.1763      5.0635      5.3533|
|  9:  2.4118 -  2.3193 0.98   1271  140 0.1138 0.1779       5.033      5.2953|
| 10:  2.3193 -  2.2395 1.00   1258  141 0.1090 0.1780       4.958      5.2711|
| 11:  2.2395 -  2.1697 0.98   1269  140 0.1102 0.1828      4.9464      5.2889|
| 12:  2.1697 -  2.1078 0.98   1245  142 0.1092 0.1678      4.8937       5.163|
| 13:  2.1078 -  2.0525 0.99   1288  138 0.1122 0.1817      4.8037      5.0799|
| 14:  2.0525 -  2.0025 0.68    855   97 0.1047 0.1778      4.6911      4.9631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7794  1385   154  0.94   9.45   0.97     0.93       7509.29|
|  2:  4.7794 -  3.8133  1333   148  0.95   7.86   1.00     0.99       9062.48|
|  3:  3.8133 -  3.3371  1306   143  0.94  11.01   1.01     1.01      10047.26|
|  4:  3.3371 -  3.0346  1294   146  0.92  13.85   1.00     0.98      10413.42|
|  5:  3.0346 -  2.8186  1286   145  0.90  16.26   0.99     0.96       8735.13|
|  6:  2.8186 -  2.6533  1299   139  0.90  16.35   0.98     0.95       7574.37|
|  7:  2.6533 -  2.5211  1284   141  0.90  16.11   0.98     0.95       6530.98|
|  8:  2.5211 -  2.4118  1257   145  0.91  15.36   0.98     0.95       5396.37|
|  9:  2.4118 -  2.3193  1271   140  0.91  15.22   0.98     0.94       5059.40|
| 10:  2.3193 -  2.2395  1258   141  0.90  15.82   0.98     0.94       4533.96|
| 11:  2.2395 -  2.1697  1269   140  0.90  16.47   0.96     0.92       4447.00|
| 12:  2.1697 -  2.1078  1245   142  0.91  15.44   0.99     0.98       4197.55|
| 13:  2.1078 -  2.0525  1288   138  0.90  16.77   0.97     0.94       3547.47|
| 14:  2.0525 -  2.0025   855    97  0.91  15.07   0.94     0.91       2787.01|
|alpha:            min =        0.91 max =            1.01 mean =         0.95|
|beta:             min =     2787.01 max =        10413.42 mean =      6538.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.29|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1607   ksol= 0.33   Bsol= 64.62   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.00,-0.64,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.146138                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1607   ksol= 0.33   Bsol= 64.62   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-2.00,-0.64,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.146138                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7794 0.99   1385  154 0.0971 0.1303        5.39      5.5397|
|  2:  4.7794 -  3.8133 0.99   1333  148 0.0827 0.1092      5.4212      5.6163|
|  3:  3.8133 -  3.3371 0.99   1306  143 0.1023 0.1479      5.4555       5.858|
|  4:  3.3371 -  3.0346 0.99   1294  146 0.1177 0.1623      5.4462      5.5897|
|  5:  3.0346 -  2.8186 0.99   1286  145 0.1312 0.1794      5.3333      5.5889|
|  6:  2.8186 -  2.6533 0.99   1299  139 0.1188 0.1983       5.226      5.4991|
|  7:  2.6533 -  2.5211 0.99   1284  141 0.1266 0.1589      5.1774       5.353|
|  8:  2.5211 -  2.4118 0.98   1257  145 0.1121 0.1763      5.0637      5.3533|
|  9:  2.4118 -  2.3193 0.98   1271  140 0.1137 0.1780      5.0332      5.2957|
| 10:  2.3193 -  2.2395 1.00   1258  141 0.1090 0.1779      4.9581        5.27|
| 11:  2.2395 -  2.1697 0.98   1269  140 0.1102 0.1827      4.9465      5.2888|
| 12:  2.1697 -  2.1078 0.98   1245  142 0.1093 0.1678      4.8934      5.1627|
| 13:  2.1078 -  2.0525 0.99   1288  138 0.1122 0.1817      4.8038      5.0797|
| 14:  2.0525 -  2.0025 0.68    855   97 0.1047 0.1779      4.6917      4.9641|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7794  1385   154  0.94   9.47   0.97     0.94       7531.07|
|  2:  4.7794 -  3.8133  1333   148  0.95   7.87   1.00     0.99       9074.25|
|  3:  3.8133 -  3.3371  1306   143  0.94  11.01   1.02     1.01      10044.89|
|  4:  3.3371 -  3.0346  1294   146  0.92  13.85   1.01     0.98      10412.67|
|  5:  3.0346 -  2.8186  1286   145  0.90  16.27   1.00     0.97       8737.57|
|  6:  2.8186 -  2.6533  1299   139  0.90  16.36   0.99     0.96       7575.52|
|  7:  2.6533 -  2.5211  1284   141  0.90  16.11   0.99     0.96       6532.26|
|  8:  2.5211 -  2.4118  1257   145  0.91  15.36   0.99     0.96       5397.41|
|  9:  2.4118 -  2.3193  1271   140  0.91  15.22   0.99     0.95       5060.27|
| 10:  2.3193 -  2.2395  1258   141  0.90  15.82   1.00     0.96       4532.50|
| 11:  2.2395 -  2.1697  1269   140  0.90  16.47   0.98     0.93       4443.98|
| 12:  2.1697 -  2.1078  1245   142  0.91  15.44   1.00     1.00       4193.99|
| 13:  2.1078 -  2.0525  1288   138  0.90  16.77   0.98     0.96       3547.60|
| 14:  2.0525 -  2.0025   855    97  0.91  15.09   0.96     0.93       2791.10|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2791.10 max =        10412.67 mean =      6541.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.29|
|phase err.(test): min =        0.00 max =           89.71 mean =        13.80|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.210)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.54   17.04    None  None   None       |
|    all(noH): 2823   0      0.00    89.54   17.04    None  None   None       |
|    Sol.    : 438    0      5.39    81.63   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    89.54   12.73    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 -   8.957:  874   |   5:    44.773 -  53.727:   94        |
|      1:     8.957 -  17.911: 1215   |   6:    53.727 -  62.681:   79        |
|      2:    17.911 -  26.865:  264   |   7:    62.681 -  71.635:   34        |
|      3:    26.865 -  35.819:  138   |   8:    71.635 -  80.589:   15        |
|      4:    35.819 -  44.773:  105   |   9:    80.589 -  89.543:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.501 - 4.745
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 288
   mapped sites are within: 0.710 - 4.745

peak=    5.724 closest distance to " NH2 ARG A  56 " =    2.265
peak=    5.415 closest distance to " CG  PRO A  54 " =    1.314
peak=    5.233 closest distance to " CB  GLN A 223 " =    1.435
peak=    5.121 closest distance to " NE2 GLN A  11 " =    1.103
peak=    4.869 closest distance to " CB  SER A  63 " =    1.230
peak=    4.855 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.808 closest distance to " CG  PRO A 213 " =    1.176
peak=    4.769 closest distance to " O   HOH Z 298 " =    1.981
peak=    4.727 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.665 closest distance to " O   HOH Z 126 " =    1.903
peak=    4.627 closest distance to " CB  ARG A  79 " =    1.362
peak=    4.582 closest distance to " O   HOH Z  78 " =    1.643
peak=    4.574 closest distance to " CB  ARG A 190 " =    1.646
peak=    4.565 closest distance to " O   HOH Z 369 " =    2.157
peak=    4.534 closest distance to " O   HOH Z  15 " =    2.199
peak=    4.491 closest distance to " CB  PRO A  54 " =    0.923
peak=    4.481 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.477 closest distance to " CB  LEU A 228 " =    1.131
peak=    4.423 closest distance to " CG  PRO A 198 " =    1.192
peak=    4.356 closest distance to " CA  TYR A  30 " =    0.975
peak=    4.329 closest distance to " C   PRO A 198 " =    1.489
peak=    4.323 closest distance to " CB  ASN A 148 " =    1.396
peak=    4.306 closest distance to " O   HOH Z 142 " =    1.676
peak=    4.242 closest distance to " O   HOH Z 250 " =    1.530
peak=    4.229 closest distance to " CZ  PHE A 218 " =    1.057
peak=    4.224 closest distance to " O   HOH Z 189 " =    2.665
peak=    4.161 closest distance to " CE  LYS A  76 " =    0.836
peak=    4.129 closest distance to " O   HOH Z 427 " =    3.073
peak=    4.118 closest distance to " O   HOH Z 368 " =    2.134
peak=    4.099 closest distance to " O   HOH Z  54 " =    2.387
peak=    4.082 closest distance to " OD1 ASN A  69 " =    2.626
peak=    4.058 closest distance to " CD  ARG A 159 " =    0.778
peak=    4.056 closest distance to " CB  TYR A 169 " =    0.773
peak=    4.040 closest distance to " O   HOH Z 180 " =    2.160
peak=    4.034 closest distance to " CB  GLU A 128 " =    1.012
peak=    4.028 closest distance to " CB  ASP A 124 " =    0.732
peak=    4.025 closest distance to " NZ  LYS A 117 " =    3.283
peak=    4.022 closest distance to " O   HOH Z 234 " =    3.872
peak=    4.014 closest distance to " O   HOH Z 287 " =    2.170
peak=    4.012 closest distance to " O   HOH Z 261 " =    1.908
peak=    3.996 closest distance to " CB  TRP A 266 " =    1.025
peak=    3.993 closest distance to " ND2 ASN A 187 " =    1.319
peak=    3.979 closest distance to " O   HOH Z 193 " =    1.902
peak=    3.966 closest distance to " NH1AARG A 145 " =    1.308
peak=    3.961 closest distance to " O   HOH Z 303 " =    2.135
peak=    3.958 closest distance to " O   HOH Z 392 " =    3.067
peak=    3.958 closest distance to " O   HOH Z 316 " =    3.153
peak=    3.945 closest distance to " CB  ASP A 140 " =    1.045
peak=    3.943 closest distance to " CG2 VAL A 257 " =    0.908
peak=    3.942 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.939 closest distance to " CB  GLU A 277 " =    3.705
peak=    3.934 closest distance to " O   HOH Z 133 " =    2.343
peak=    3.911 closest distance to " CB  VAL A 202 " =    1.632
peak=    3.904 closest distance to " CG1 ILE A  33 " =    1.213
peak=    3.903 closest distance to " O   HOH Z 158 " =    3.026
peak=    3.892 closest distance to " CB  GLU A 152 " =    1.224
peak=    3.881 closest distance to " CB  VAL A 265 " =    1.249
peak=    3.868 closest distance to " O   HOH Z 214 " =    2.086
peak=    3.862 closest distance to " CB  SER A 212 " =    1.100
peak=    3.846 closest distance to " O   HOH Z 346 " =    1.657
peak=    3.816 closest distance to " CA  ALA A  51 " =    0.942
peak=    3.816 closest distance to " O   HOH Z  53 " =    2.515
peak=    3.812 closest distance to " CD  ARG A 269 " =    0.911
peak=    3.806 closest distance to " CD  ARG A  66 " =    2.383
peak=    3.804 closest distance to " CD BLYS A 290 " =    0.964
peak=    3.796 closest distance to " O   HOH Z 193 " =    1.718
peak=    3.796 closest distance to " CA  ARG A 195 " =    1.219
peak=    3.794 closest distance to " CA  ASN A 215 " =    1.191
peak=    3.769 closest distance to " CG  PRO A 243 " =    1.036
peak=    3.767 closest distance to " O   HOH Z 126 " =    1.961
peak=    3.765 closest distance to " O   HOH Z  61 " =    1.622
peak=    3.763 closest distance to " O   HOH Z 406 " =    1.604
peak=    3.753 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.752 closest distance to " CG  LEU A 167 " =    1.270
peak=    3.748 closest distance to " O   HOH Z  21 " =    1.785
peak=    3.746 closest distance to " CB  SER A   3 " =    1.335
peak=    3.737 closest distance to " CD  LYS A 166 " =    1.282
peak=    3.730 closest distance to " O   HOH Z   1 " =    2.054
peak=    3.729 closest distance to " CD2 LEU A 297 " =    0.867
peak=    3.724 closest distance to " CD2 TRP A 179 " =    1.358
peak=    3.724 closest distance to " C   ILE A 106 " =    1.924
peak=    3.680 closest distance to " CA  MET A  40 " =    1.181
peak=    3.665 closest distance to " O   HOH Z 272 " =    1.850
peak=    3.661 closest distance to " CA  MET A 105 " =    1.026
peak=    3.660 closest distance to " NE2 HIS A 207 " =    1.316
peak=    3.655 closest distance to " O   HOH Z 313 " =    1.904
peak=    3.650 closest distance to " O   HOH Z 411 " =    3.892
peak=    3.649 closest distance to " CB  ASN A  39 " =    0.915
peak=    3.635 closest distance to " CG2 THR A 221 " =    1.049
peak=    3.634 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.628 closest distance to " N   ASN A 127 " =    1.270
peak=    3.626 closest distance to " CA  THR A 264 " =    0.893
peak=    3.621 closest distance to " CB  GLU A  46 " =    0.962
peak=    3.621 closest distance to " O   HOH Z  43 " =    1.848
peak=    3.619 closest distance to " CA  ARG A  36 " =    1.117
peak=    3.615 closest distance to " CB  TYR A 116 " =    0.777
peak=    3.603 closest distance to " O   HOH Z 423 " =    1.863
peak=    3.599 closest distance to " CB  ASN A 187 " =    1.465
peak=    3.586 closest distance to " O   HOH Z 135 " =    1.706
peak=    3.578 closest distance to " CB  ALA A  34 " =    0.972
peak=    3.577 closest distance to " NH2 ARG A 156 " =    1.220
peak=    3.575 closest distance to " O   HOH Z 368 " =    3.696
peak=    3.572 closest distance to " ND2 ASN A 249 " =    0.850
peak=    3.571 closest distance to " O   HOH Z 172 " =    3.410
peak=    3.567 closest distance to " O   HOH Z 291 " =    1.613
peak=    3.562 closest distance to " O   HOH Z  59 " =    2.016
peak=    3.559 closest distance to " O   HOH Z 285 " =    2.467
peak=    3.552 closest distance to " O   HOH Z 128 " =    2.378
peak=    3.551 closest distance to " O   HOH Z 147 " =    1.799
peak=    3.543 closest distance to " O   HOH Z 280 " =    2.979
peak=    3.541 closest distance to " O   HOH Z 426 " =    1.634
peak=    3.536 closest distance to " O   HOH Z 391 " =    2.878
peak=    3.533 closest distance to " O   HOH Z   9 " =    2.083
peak=    3.532 closest distance to " CA  ALA A 158 " =    1.215
peak=    3.532 closest distance to " N   ARG A 156 " =    1.372
peak=    3.528 closest distance to " CB  THR A  82 " =    1.414
peak=    3.527 closest distance to " CA  THR A 221 " =    0.992
peak=    3.523 closest distance to " OG BSER A 164 " =    2.291
peak=    3.516 closest distance to " O   THR A 251 " =    1.260
peak=    3.514 closest distance to " CB  ASN A 142 " =    1.018
peak=    3.512 closest distance to " ND2 ASN A 249 " =    1.921
peak=    3.503 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.500 closest distance to " O   HOH Z 353 " =    2.667
peak=    3.498 closest distance to " O   HOH Z 359 " =    1.488
peak=    3.492 closest distance to " O   HOH Z 371 " =    3.061
peak=    3.492 closest distance to " O   HOH Z 344 " =    3.166
peak=    3.492 closest distance to " ND1 HIS A  86 " =    1.718
peak=    3.489 closest distance to " OD2 ASP A 286 " =    2.864
peak=    3.485 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.485 closest distance to " CB  MET A  47 " =    1.019
peak=    3.482 closest distance to " O   SER A  87 " =    2.284
peak=    3.482 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.482 closest distance to " CA  ALA A 154 " =    1.002
peak=    3.479 closest distance to " O   HOH Z 203 " =    1.790
peak=    3.477 closest distance to " O   HOH Z 403 " =    1.654
peak=    3.471 closest distance to " O   HOH Z 425 " =    1.919
peak=    3.470 closest distance to " CA  TYR A  30 " =    1.049
peak=    3.468 closest distance to " O   HOH Z  10 " =    1.833
peak=    3.465 closest distance to " O   HOH Z 166 " =    3.805
peak=    3.446 closest distance to " O   HOH Z 213 " =    1.941
peak=    3.446 closest distance to " CD  ARG A  66 " =    2.275
peak=    3.445 closest distance to " O   HOH Z  66 " =    2.192
peak=    3.443 closest distance to " O   HOH Z  88 " =    3.709
peak=    3.441 closest distance to " CD2 LEU A 255 " =    1.663
peak=    3.440 closest distance to " O   HOH Z  20 " =    1.737
peak=    3.435 closest distance to " O   HOH Z 108 " =    2.728
peak=    3.432 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.426 closest distance to " OG  SER A  22 " =    2.798
peak=    3.425 closest distance to " O   HOH Z 305 " =    3.677
peak=    3.424 closest distance to " CA  SER A  87 " =    1.054
peak=    3.423 closest distance to " CB  GLN A  88 " =    1.252
peak=    3.423 closest distance to " CA  ALA A 160 " =    0.931
peak=    3.421 closest distance to " CG2 ILE A 120 " =    1.057
peak=    3.419 closest distance to " O   HOH Z 227 " =    1.735
peak=    3.413 closest distance to " CA  GLY A 267 " =    1.133
peak=    3.410 closest distance to " CA  ALA A 295 " =    1.055
peak=    3.410 closest distance to " O   HOH Z 329 " =    3.959
peak=    3.408 closest distance to " O   HOH Z 245 " =    1.226
peak=    3.405 closest distance to " CG  MET A 185 " =    1.198
peak=    3.400 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.390 closest distance to " CG1 VAL A 153 " =    0.954
peak=    3.386 closest distance to " O   TYR A 116 " =    1.285
peak=    3.386 closest distance to " CB  ARG A 138 " =    1.003
peak=    3.385 closest distance to " CB  MET A  40 " =    0.793
peak=    3.385 closest distance to " NE  ARG A  79 " =    1.147
peak=    3.371 closest distance to " O   ASN A  74 " =    1.558
peak=    3.370 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.368 closest distance to " CA  ASN A 176 " =    1.724
peak=    3.365 closest distance to " N   ASN A  39 " =    1.372
peak=    3.364 closest distance to " O   THR A 220 " =    1.251
peak=    3.360 closest distance to " CA  VAL A 125 " =    1.119
peak=    3.355 closest distance to " CA  GLY A 241 " =    0.739
peak=    3.355 closest distance to " CB  ALA A   1 " =    4.745
peak=    3.346 closest distance to " CB  GLN A  89 " =    1.231
peak=    3.345 closest distance to " CD  ARG A 219 " =    1.144
peak=    3.334 closest distance to " CZ3 TRP A 266 " =    1.133
peak=    3.331 closest distance to " CB  LYS A 117 " =    1.183
peak=    3.331 closest distance to " CB  ASN A 110 " =    1.150
peak=    3.329 closest distance to " CA  ALA A 291 " =    0.808
peak=    3.327 closest distance to " CB  PRO A  90 " =    1.199
peak=    3.326 closest distance to " O   HOH Z 193 " =    2.121
peak=    3.325 closest distance to " CG2AVAL A  72 " =    1.713
peak=    3.324 closest distance to " CB  SER A 141 " =    1.021
peak=    3.323 closest distance to " CB  LEU A 143 " =    1.139
peak=    3.319 closest distance to " O   HOH Z 403 " =    1.413
peak=    3.318 closest distance to " O   HOH Z 290 " =    0.916
peak=    3.316 closest distance to " O   HOH Z 109 " =    2.617
peak=    3.312 closest distance to " ND2 ASN A 110 " =    1.638
peak=    3.310 closest distance to " CB  SER A 216 " =    0.903
peak=    3.310 closest distance to " O   HOH Z 218 " =    4.679
peak=    3.310 closest distance to " O   ALA A 158 " =    1.276
peak=    3.306 closest distance to " CD  GLU A 152 " =    0.799
peak=    3.306 closest distance to " O   HOH Z 273 " =    2.858
peak=    3.304 closest distance to " CB  ALA A 291 " =    1.259
peak=    3.303 closest distance to " O   HOH Z 422 " =    2.712
peak=    3.300 closest distance to " N   PHE A 130 " =    1.247
peak=    3.299 closest distance to " O   HOH Z 132 " =    2.673
peak=    3.294 closest distance to " O   HOH Z 282 " =    1.919
peak=    3.283 closest distance to " NH2BARG A 145 " =    2.152
peak=    3.277 closest distance to " O   HOH Z 133 " =    1.664
peak=    3.277 closest distance to " OE1 GLN A  11 " =    2.176
peak=    3.276 closest distance to " O   HOH Z 148 " =    3.410
peak=    3.274 closest distance to " CG2 ILE A 234 " =    0.792
peak=    3.271 closest distance to " CA  ALA A 233 " =    1.386
peak=    3.271 closest distance to " CB  ALA A   9 " =    1.601
peak=    3.270 closest distance to " O   HOH Z  66 " =    2.181
peak=    3.268 closest distance to " O   HOH Z 409 " =    2.950
peak=    3.265 closest distance to " O   HOH Z 185 " =    1.939
peak=    3.262 closest distance to " O   HOH Z 417 " =    3.258
peak=    3.261 closest distance to " CB  HIS A 108 " =    0.784
peak=    3.260 closest distance to " O   HOH Z 171 " =    3.910
peak=    3.257 closest distance to " O   HOH Z 411 " =    1.708
peak=    3.257 closest distance to " O   HOH Z 248 " =    1.711
peak=    3.256 closest distance to " O   HOH Z 126 " =    1.624
peak=    3.256 closest distance to " CE  LYS A  48 " =    1.099
peak=    3.252 closest distance to " O   HOH Z 421 " =    2.096
peak=    3.249 closest distance to " ND1 HIS A  81 " =    1.606
peak=    3.247 closest distance to " CB  LEU A  83 " =    0.774
peak=    3.246 closest distance to " CB  ILE A 120 " =    1.298
peak=    3.246 closest distance to " CZ  PHE A  38 " =    1.237
peak=    3.244 closest distance to " CA  ILE A 234 " =    1.004
peak=    3.239 closest distance to " CA  ALA A  21 " =    1.186
peak=    3.236 closest distance to " O   HOH Z 365 " =    2.961
peak=    3.231 closest distance to " O   GLN A 278 " =    1.286
peak=    3.229 closest distance to " O   ALA A 165 " =    1.526
peak=    3.224 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.219 closest distance to " OD1BASN A 224 " =    2.374
peak=    3.216 closest distance to " CA  ASN A 217 " =    1.227
peak=    3.216 closest distance to " CA  LYS A 290 " =    1.307
peak=    3.208 closest distance to " CG2 VAL A 197 " =    1.159
peak=    3.208 closest distance to " CA  LEU A 101 " =    1.362
peak=    3.206 closest distance to " CG1 ILE A 151 " =    1.007
peak=    3.204 closest distance to " CB  TRP A 150 " =    1.244
peak=    3.199 closest distance to " O   HOH Z  96 " =    1.963
peak=    3.191 closest distance to " CD  LYS A 119 " =    1.234
peak=    3.189 closest distance to " CG BARG A 275 " =    1.445
peak=    3.188 closest distance to " O   HOH Z  44 " =    3.027
peak=    3.187 closest distance to " CB  PHE A 204 " =    0.870
peak=    3.186 closest distance to " O   HOH Z 325 " =    2.490
peak=    3.186 closest distance to " O   HOH Z 383 " =    2.184
peak=    3.184 closest distance to " CB  LYS A 193 " =    0.984
peak=    3.184 closest distance to " CB  ASP A 200 " =    1.100
peak=    3.183 closest distance to " O   HOH Z 425 " =    1.237
peak=    3.183 closest distance to " CZ2 TRP A 179 " =    1.691
peak=    3.182 closest distance to " N   VAL A 126 " =    1.285
peak=    3.181 closest distance to " CD1 ILE A 106 " =    0.781
peak=    3.181 closest distance to " CG  GLN A  11 " =    1.615
peak=    3.181 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.180 closest distance to " N   GLY A  98 " =    1.107
peak=    3.171 closest distance to " CG  ARG A 159 " =    0.906
peak=    3.171 closest distance to " CA  ARG A 102 " =    1.131
peak=    3.162 closest distance to " NH2AARG A 275 " =    3.625
peak=    3.162 closest distance to " O   HOH Z 271 " =    2.360
peak=    3.159 closest distance to " CB  ASN A 224 " =    0.958
peak=    3.158 closest distance to " CA  GLU A  46 " =    0.753
peak=    3.157 closest distance to " CB  LEU A  96 " =    1.258
peak=    3.154 closest distance to " CA  SER A 146 " =    1.726
peak=    3.151 closest distance to " CB  SER A 210 " =    0.773
peak=    3.143 closest distance to " O   HOH Z 116 " =    1.885
peak=    3.142 closest distance to " O   HOH Z 188 " =    2.100
peak=    3.140 closest distance to " CB  ALA A 248 " =    0.925
peak=    3.134 closest distance to " CG1 VAL A 189 " =    2.047
peak=    3.129 closest distance to " CD1AILE A 234 " =    0.943
peak=    3.128 closest distance to " O   HOH Z 419 " =    1.974
peak=    3.120 closest distance to " CB  ASN A 215 " =    1.124
peak=    3.113 closest distance to " CB  PHE A 204 " =    0.712
peak=    3.108 closest distance to " CB  ALA A  43 " =    0.848
peak=    3.108 closest distance to " CA  ASN A 127 " =    1.090
peak=    3.106 closest distance to " O   HOH Z  97 " =    2.024
peak=    3.097 closest distance to " O   HOH Z  88 " =    2.891
peak=    3.095 closest distance to " O   HOH Z 234 " =    1.768
peak=    3.088 closest distance to " OG  SER A  62 " =    2.998
peak=    3.086 closest distance to " CB  GLN A 103 " =    0.849
peak=    3.084 closest distance to " CB  GLN A 205 " =    1.021
peak=    3.078 closest distance to " NZ  LYS A  48 " =    1.377
peak=    3.078 closest distance to " CB  ALA A 227 " =    1.008
peak=    3.069 closest distance to " OD2 ASP A 200 " =    1.241
peak=    3.067 closest distance to " O   HOH Z 248 " =    1.592
peak=    3.063 closest distance to " O   HOH Z 124 " =    1.925
peak=    3.062 closest distance to " NH1BARG A 145 " =    0.988
peak=    3.058 closest distance to " CG  LYS A  76 " =    0.982
peak=    3.053 closest distance to " O   HOH Z 384 " =    2.885
peak=    3.043 closest distance to " O   HOH Z 183 " =    1.329
peak=    3.036 closest distance to " O   HOH Z 302 " =    2.014

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.500
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.779 - 5.500

peak=   -4.561 closest distance to " CD  ARG A  14 " =    3.465
peak=   -4.453 closest distance to " CD  ARG A 156 " =    2.093
peak=   -4.447 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -4.422 closest distance to " CB  PRO A 243 " =    2.648
peak=   -4.389 closest distance to " O   HOH Z 231 " =    2.270
peak=   -4.369 closest distance to " O   HOH Z 266 " =    5.285
peak=   -4.357 closest distance to " O   HOH Z 377 " =    2.076
peak=   -4.270 closest distance to " O   VAL A  67 " =    2.792
peak=   -4.196 closest distance to " OE1 GLN A 223 " =    2.074
peak=   -4.185 closest distance to " CZ3 TRP A 179 " =    1.147
peak=   -4.127 closest distance to " CD  GLN A  58 " =    0.995
peak=   -4.077 closest distance to " O   HOH Z 198 " =    2.176
peak=   -4.059 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -4.050 closest distance to " N   ALA A  43 " =    2.644
peak=   -4.016 closest distance to " C   HIS A 108 " =    1.109
peak=   -4.002 closest distance to " O   ILE A 109 " =    2.606
peak=   -3.983 closest distance to " OG BSER A 134 " =    1.241
peak=   -3.967 closest distance to " O   HOH Z  73 " =    2.134
peak=   -3.935 closest distance to " O   PRO A 198 " =    1.301
peak=   -3.927 closest distance to " CG1 VAL A 112 " =    2.939
peak=   -3.910 closest distance to " O   HOH Z  10 " =    1.505
peak=   -3.903 closest distance to " O   HOH Z 372 " =    2.408
peak=   -3.872 closest distance to " OG  SER A  97 " =    2.233
peak=   -3.864 closest distance to " CE  MET A 105 " =    2.364
peak=   -3.863 closest distance to " O   HOH Z 389 " =    1.992
peak=   -3.859 closest distance to " CD1 PHE A  59 " =    1.933
peak=   -3.852 closest distance to " CG1 VAL A 250 " =    2.684
peak=   -3.805 closest distance to " O   HOH Z 196 " =    2.064
peak=   -3.770 closest distance to " CA  GLY A 203 " =    2.387
peak=   -3.770 closest distance to " CB  ALA A 291 " =    2.353
peak=   -3.766 closest distance to " O   HOH Z  38 " =    1.364
peak=   -3.753 closest distance to " OXT GLY A 302 " =    2.982
peak=   -3.721 closest distance to " NE2 GLN A  88 " =    1.927
peak=   -3.721 closest distance to " CB  ALA A 291 " =    2.306
peak=   -3.717 closest distance to " O   HOH Z 114 " =    3.222
peak=   -3.712 closest distance to " CB  ALA A  43 " =    2.668
peak=   -3.697 closest distance to " O   HOH Z 394 " =    1.485
peak=   -3.690 closest distance to " CD  ARG A 139 " =    1.555
peak=   -3.687 closest distance to " O   HOH Z 435 " =    2.795
peak=   -3.682 closest distance to " O   HOH Z 407 " =    3.245
peak=   -3.677 closest distance to " N   MET A 188 " =    1.926
peak=   -3.660 closest distance to " O   HOH Z  51 " =    1.711
peak=   -3.652 closest distance to " O   HOH Z 290 " =    1.362
peak=   -3.648 closest distance to " CD1 LEU A 101 " =    2.410
peak=   -3.643 closest distance to " OD1 ASN A 148 " =    1.514
peak=   -3.638 closest distance to " NH2AARG A 275 " =    5.500
peak=   -3.628 closest distance to " CA  GLY A 241 " =    3.212
peak=   -3.623 closest distance to " O   HOH Z  43 " =    1.637
peak=   -3.612 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.610 closest distance to " ND2 ASN A  45 " =    1.868
peak=   -3.594 closest distance to " O   HOH Z 185 " =    2.316
peak=   -3.593 closest distance to " ND2 ASN A  45 " =    1.113
peak=   -3.580 closest distance to " O   PRO A 163 " =    2.146
peak=   -3.580 closest distance to " O   HOH Z  52 " =    1.372
peak=   -3.579 closest distance to " C   ASN A 285 " =    2.518
peak=   -3.579 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.561 closest distance to " O   HOH Z 426 " =    1.619
peak=   -3.555 closest distance to " O   VAL A 189 " =    2.593
peak=   -3.551 closest distance to " CG2 ILE A 263 " =    2.364
peak=   -3.551 closest distance to " CB  ASN A  39 " =    2.327
peak=   -3.544 closest distance to " CG2 ILE A  49 " =    2.708
peak=   -3.536 closest distance to " CB  PHE A 192 " =    2.048
peak=   -3.526 closest distance to " O   GLY A 211 " =    1.428
peak=   -3.522 closest distance to " CG  PHE A 283 " =    2.632
peak=   -3.520 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.518 closest distance to " O   PHE A 218 " =    1.517
peak=   -3.509 closest distance to " C   LEU A 222 " =    0.779
peak=   -3.507 closest distance to " O   HOH Z 393 " =    1.401
peak=   -3.491 closest distance to " O   HOH Z  60 " =    2.412
peak=   -3.488 closest distance to " O   HOH Z 313 " =    1.974
peak=   -3.483 closest distance to " CD1 ILE A 151 " =    2.418
peak=   -3.479 closest distance to " CA  VAL A  67 " =    2.909
peak=   -3.478 closest distance to " O   HOH Z 198 " =    1.489
peak=   -3.460 closest distance to " CD1 LEU A 228 " =    2.384
peak=   -3.460 closest distance to " OD1 ASP A 171 " =    1.596
peak=   -3.452 closest distance to " O   HOH Z 243 " =    2.062
peak=   -3.452 closest distance to " CB  TRP A  85 " =    2.459
peak=   -3.443 closest distance to " C   GLY A  17 " =    1.197
peak=   -3.441 closest distance to " NE2 GLN A 194 " =    1.827
peak=   -3.440 closest distance to " ND2 ASN A 249 " =    2.507
peak=   -3.433 closest distance to " O   HOH Z 353 " =    2.129
peak=   -3.431 closest distance to " CG  PRO A 243 " =    1.799
peak=   -3.431 closest distance to " CB  PHE A 208 " =    2.262
peak=   -3.430 closest distance to " O   HOH Z 166 " =    1.893
peak=   -3.425 closest distance to " OD1 ASP A 191 " =    1.739
peak=   -3.416 closest distance to " CE2 PHE A  61 " =    2.623
peak=   -3.414 closest distance to " O   ALA A  10 " =    1.676
peak=   -3.411 closest distance to " O   HOH Z 253 " =    4.040
peak=   -3.411 closest distance to " CG  HIS A  86 " =    1.075
peak=   -3.409 closest distance to " O   HOH Z   6 " =    1.484
peak=   -3.403 closest distance to " NH2 ARG A  79 " =    1.497
peak=   -3.401 closest distance to " O   HOH Z 350 " =    1.823
peak=   -3.388 closest distance to " ND2 ASN A  60 " =    1.618
peak=   -3.386 closest distance to " C   ALA A 158 " =    1.390
peak=   -3.385 closest distance to " CZ  PHE A  59 " =    1.633
peak=   -3.383 closest distance to " CB  PRO A  54 " =    2.496
peak=   -3.383 closest distance to " O   HOH Z  11 " =    1.704
peak=   -3.381 closest distance to " CE3 TRP A 150 " =    2.165
peak=   -3.370 closest distance to " CA  GLY A 241 " =    2.869
peak=   -3.370 closest distance to " O   HOH Z 292 " =    1.845
peak=   -3.368 closest distance to " CG  ARG A  66 " =    2.211
peak=   -3.365 closest distance to " CD2 PHE A  61 " =    2.089
peak=   -3.364 closest distance to " O   SER A 135 " =    1.460
peak=   -3.362 closest distance to " O   HOH Z 211 " =    1.603
peak=   -3.351 closest distance to " O   HOH Z 311 " =    3.838
peak=   -3.347 closest distance to " CG2 THR A 178 " =    2.309
peak=   -3.342 closest distance to " CE BMET A  47 " =    1.806
peak=   -3.339 closest distance to " N   ALA A 248 " =    1.604
peak=   -3.338 closest distance to " CG  MET A 105 " =    0.983
peak=   -3.334 closest distance to " CG  ARG A 269 " =    2.463
peak=   -3.332 closest distance to " O   HOH Z 359 " =    3.156
peak=   -3.325 closest distance to " N   THR A 157 " =    1.572
peak=   -3.319 closest distance to " OE1 GLN A  88 " =    1.187
peak=   -3.318 closest distance to " O   TYR A 247 " =    2.889
peak=   -3.318 closest distance to " CG1 VAL A 125 " =    1.932
peak=   -3.317 closest distance to " N   THR A 264 " =    1.324
peak=   -3.316 closest distance to " NH2BARG A 275 " =    1.812
peak=   -3.314 closest distance to " O   HOH Z 103 " =    1.831
peak=   -3.312 closest distance to " OD1 ASN A 187 " =    1.556
peak=   -3.311 closest distance to " CD  ARG A 195 " =    5.139
peak=   -3.310 closest distance to " CG1 VAL A 197 " =    2.287
peak=   -3.304 closest distance to " CG  TRP A 266 " =    1.814
peak=   -3.304 closest distance to " CD2 TYR A 247 " =    2.413
peak=   -3.303 closest distance to " CG2 VAL A 189 " =    2.144
peak=   -3.298 closest distance to " CB  PRO A 163 " =    2.525
peak=   -3.292 closest distance to " CG1BVAL A  41 " =    2.771
peak=   -3.277 closest distance to " O   HOH Z 298 " =    1.310
peak=   -3.270 closest distance to " OD2 ASP A 171 " =    1.811
peak=   -3.269 closest distance to " O   HOH Z 281 " =    2.648
peak=   -3.267 closest distance to " C   LEU A 143 " =    1.237
peak=   -3.263 closest distance to " CG  GLU A 277 " =    1.181
peak=   -3.259 closest distance to " O   VAL A 174 " =    2.079
peak=   -3.259 closest distance to " CB  TYR A  15 " =    2.199
peak=   -3.258 closest distance to " CD1 LEU A 297 " =    2.505
peak=   -3.252 closest distance to " O   HOH Z 189 " =    1.928
peak=   -3.251 closest distance to " O   SER A  62 " =    2.265
peak=   -3.251 closest distance to " C   MET A 188 " =    1.378
peak=   -3.249 closest distance to " OG BSER A 134 " =    1.798
peak=   -3.247 closest distance to " CB  ALA A   7 " =    2.291
peak=   -3.245 closest distance to " CE2 PHE A 218 " =    2.401
peak=   -3.244 closest distance to " ND2BASN A 224 " =    1.733
peak=   -3.240 closest distance to " OE1 GLN A 223 " =    2.176
peak=   -3.229 closest distance to " ND2 ASN A  69 " =    1.731
peak=   -3.227 closest distance to " O   HOH Z  71 " =    1.956
peak=   -3.225 closest distance to " O   HOH Z 174 " =    2.982
peak=   -3.225 closest distance to " O   HOH Z 295 " =    1.511
peak=   -3.224 closest distance to " CB  ALA A 100 " =    2.158
peak=   -3.224 closest distance to " O   HOH Z 322 " =    1.303
peak=   -3.224 closest distance to " O   HOH Z 114 " =    1.507
peak=   -3.223 closest distance to " O   TRP A  70 " =    1.450
peak=   -3.220 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.218 closest distance to " O   HOH Z 298 " =    2.529
peak=   -3.218 closest distance to " CG  LEU A  83 " =    1.976
peak=   -3.218 closest distance to " O   HOH Z 111 " =    1.415
peak=   -3.217 closest distance to " O   HOH Z 232 " =    1.690
peak=   -3.212 closest distance to " CB  ALA A 248 " =    2.462
peak=   -3.206 closest distance to " NH2 ARG A 159 " =    2.386
peak=   -3.205 closest distance to " CA  ASP A  27 " =    2.528
peak=   -3.203 closest distance to " CB  ALA A 114 " =    2.562
peak=   -3.200 closest distance to " CB  GLN A  11 " =    1.770
peak=   -3.198 closest distance to " O   HOH Z 139 " =    2.920
peak=   -3.198 closest distance to " ND2 ASN A  60 " =    4.162
peak=   -3.197 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.196 closest distance to " O   HOH Z 234 " =    4.357
peak=   -3.196 closest distance to " OH  TYR A 247 " =    2.129
peak=   -3.195 closest distance to " CB  ASP A 286 " =    2.117
peak=   -3.189 closest distance to " O   HOH Z 207 " =    2.236
peak=   -3.189 closest distance to " O   HOH Z 275 " =    1.598
peak=   -3.189 closest distance to " CZ  TYR A 169 " =    1.686
peak=   -3.184 closest distance to " O   ALA A  34 " =    2.146
peak=   -3.184 closest distance to " CD2 PHE A 225 " =    1.146
peak=   -3.182 closest distance to " N   ASP A 171 " =    2.374
peak=   -3.174 closest distance to " O   PRO A 198 " =    1.379
peak=   -3.174 closest distance to " CA  SER A 135 " =    1.352
peak=   -3.173 closest distance to " N   SER A 276 " =    1.355
peak=   -3.168 closest distance to " CG1 VAL A 125 " =    2.363
peak=   -3.165 closest distance to " O   HOH Z  13 " =    1.632
peak=   -3.165 closest distance to " O   HOH Z  47 " =    1.626
peak=   -3.164 closest distance to " O   HOH Z 177 " =    1.667
peak=   -3.163 closest distance to " O   HOH Z 265 " =    2.253
peak=   -3.158 closest distance to " CG  GLU A   2 " =    1.947
peak=   -3.158 closest distance to " CE3 TRP A 274 " =    2.449
peak=   -3.156 closest distance to " CB  ASN A 252 " =    1.631
peak=   -3.155 closest distance to " O   HOH Z 396 " =    1.698
peak=   -3.154 closest distance to " CG2 ILE A  20 " =    2.843
peak=   -3.152 closest distance to " O   GLN A 240 " =    2.525
peak=   -3.151 closest distance to " O   HOH Z 134 " =    2.872
peak=   -3.151 closest distance to " O   HOH Z 193 " =    1.622
peak=   -3.148 closest distance to " CD2 PHE A  59 " =    2.503
peak=   -3.144 closest distance to " O   TYR A 186 " =    1.732
peak=   -3.143 closest distance to " CA  GLY A 133 " =    2.329
peak=   -3.141 closest distance to " C   SER A 206 " =    1.530
peak=   -3.139 closest distance to " C   GLY A  13 " =    1.006
peak=   -3.135 closest distance to " O   ALA A 292 " =    2.063
peak=   -3.135 closest distance to " O   HOH Z 106 " =    1.927
peak=   -3.133 closest distance to " CB  PHE A  16 " =    2.556
peak=   -3.130 closest distance to " O   VAL A 189 " =    1.582
peak=   -3.128 closest distance to " N   ALA A 226 " =    2.224
peak=   -3.126 closest distance to " CB  ALA A  10 " =    2.250
peak=   -3.125 closest distance to " CD2 LEU A 222 " =    2.196
peak=   -3.123 closest distance to " OD2 ASP A 191 " =    1.580
peak=   -3.118 closest distance to " CB  ALA A 248 " =    2.077
peak=   -3.114 closest distance to " CA  HIS A  86 " =    2.395
peak=   -3.112 closest distance to " SG ACYS A 201 " =    2.051
peak=   -3.099 closest distance to " O   HOH Z 216 " =    1.910
peak=   -3.098 closest distance to " OH  TYR A 247 " =    1.833
peak=   -3.093 closest distance to " SD  MET A 188 " =    2.307
peak=   -3.084 closest distance to " O   ALA A 180 " =    1.451
peak=   -3.083 closest distance to " O   HOH Z 111 " =    2.237
peak=   -3.070 closest distance to " O   SER A 210 " =    2.008
peak=   -3.067 closest distance to " OD1 ASN A 301 " =    1.999
peak=   -3.063 closest distance to " CG  PRO A 163 " =    2.475
peak=   -3.055 closest distance to " OG  SER A 206 " =    1.867
peak=   -3.046 closest distance to " NE1 TRP A  70 " =    1.114

================= 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    :  0.3052 0.2974   5.986985e+00   5.978728e+00
   1_bss:  0.2907 0.2862   5.962451e+00   5.951008e+00
   1_xyz:  0.1629 0.1847   5.421489e+00   5.520987e+00
   1_adp:  0.1495 0.1888   5.366990e+00   5.544517e+00
   1_occ:  0.1490 0.1885   5.364879e+00   5.543514e+00
   2_bss:  0.1474 0.1860   5.359759e+00   5.537557e+00
   2_xyz:  0.1244 0.1643   5.218579e+00   5.426138e+00
   2_adp:  0.1200 0.1601   5.187960e+00   5.403337e+00
   2_occ:  0.1199 0.1600   5.187588e+00   5.403272e+00
   3_bss:  0.1198 0.1599   5.186728e+00   5.402406e+00
   3_xyz:  0.1112 0.1578   5.145648e+00   5.389460e+00
   3_adp:  0.1111 0.1569   5.140881e+00   5.382560e+00
   3_occ:  0.1111 0.1570   5.140922e+00   5.382807e+00
   4_bss:  0.1111 0.1558   5.138539e+00   5.377588e+00
   4_xyz:  0.1120 0.1575   5.148106e+00   5.388687e+00
   4_adp:  0.1107 0.1585   5.145352e+00   5.393092e+00
   4_occ:  0.1107 0.1586   5.145544e+00   5.393550e+00
   5_bss:  0.1106 0.1585   5.145342e+00   5.393406e+00
   5_xyz:  0.1097 0.1598   5.145300e+00   5.399409e+00
   5_adp:  0.1095 0.1608   5.145820e+00   5.402535e+00
   5_occ:  0.1095 0.1609   5.145950e+00   5.402855e+00
   5_bss:  0.1093 0.1607   5.146138e+00   5.402972e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -0.154  -3.198   0.338  -0.000   0.000   0.000
   1_xyz:  0.300  50.000  -0.154  -3.198   0.338  -0.000   0.000   0.000
   1_adp:  0.300  50.000  -0.154  -3.198   0.338  -0.000   0.000   0.000
   1_occ:  0.300  50.000  -0.154  -3.198   0.338  -0.000   0.000   0.000
   2_bss:  0.333  64.621  -1.985  -3.134  -1.052  -0.000  -0.000  -0.000
   2_xyz:  0.333  64.621  -1.985  -3.134  -1.052  -0.000  -0.000  -0.000
   2_adp:  0.333  64.621  -1.985  -3.134  -1.052  -0.000  -0.000  -0.000
   2_occ:  0.333  64.621  -1.985  -3.134  -1.052  -0.000  -0.000  -0.000
   3_bss:  0.333  64.621  -2.287  -2.747  -1.116  -0.000  -0.000  -0.000
   3_xyz:  0.333  64.621  -2.287  -2.747  -1.116  -0.000  -0.000  -0.000
   3_adp:  0.333  64.621  -2.287  -2.747  -1.116  -0.000  -0.000  -0.000
   3_occ:  0.333  64.621  -2.287  -2.747  -1.116  -0.000  -0.000  -0.000
   4_bss:  0.333  64.621  -2.336  -2.588  -1.108  -0.000  -0.000  -0.000
   4_xyz:  0.333  64.621  -2.336  -2.588  -1.108  -0.000  -0.000  -0.000
   4_adp:  0.333  64.621  -2.336  -2.588  -1.108  -0.000  -0.000  -0.000
   4_occ:  0.333  64.621  -2.336  -2.588  -1.108  -0.000  -0.000  -0.000
   5_bss:  0.325  64.621  -2.156  -2.338  -0.923  -0.000  -0.000  -0.000
   5_xyz:  0.325  64.621  -2.156  -2.338  -0.923  -0.000  -0.000  -0.000
   5_adp:  0.325  64.621  -2.156  -2.338  -0.923  -0.000  -0.000  -0.000
   5_occ:  0.325  64.621  -2.156  -2.338  -0.923  -0.000  -0.000  -0.000
   5_bss:  0.325  64.624  -1.849  -1.997  -0.639  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.505 0.7556  0.9068    25141.452
   1_bss:  29.485 0.7653  0.8925    22851.592
   1_xyz:  16.699 0.8933  0.9983     8468.689
   1_adp:  17.310 0.8873  0.9987     8820.776
   1_occ:  17.287 0.8875  0.9984     8776.315
   2_bss:  17.127 0.8890  0.9627     8689.315
   2_xyz:  14.805 0.9086  0.9703     6889.043
   2_adp:  14.280 0.9130  0.9671     6552.080
   2_occ:  14.277 0.9130  0.9669     6546.090
   3_bss:  14.258 0.9131  0.9670     6532.200
   3_xyz:  13.962 0.9155  0.9693     6416.240
   3_adp:  13.792 0.9170  0.9655     6348.683
   3_occ:  13.799 0.9170  0.9654     6349.358
   4_bss:  13.732 0.9174  0.9663     6234.014
   4_xyz:  13.921 0.9160  0.9647     6383.128
   4_adp:  14.037 0.9150  0.9571     6409.442
   4_occ:  14.046 0.9150  0.9570     6414.468
   5_bss:  14.043 0.9150  0.9638     6409.160
   5_xyz:  14.157 0.9141  0.9636     6506.649
   5_adp:  14.235 0.9135  0.9548     6535.127
   5_occ:  14.238 0.9134  0.9547     6538.261
   5_bss:  14.242 0.9134  0.9653     6540.759
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6107e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6107e-01
   1_xyz:   1.071  0.009  0.074 15.213  0.004  4.126   6.6334e-02
   1_adp:   1.071  0.009  0.074 15.213  0.004  4.126   6.6334e-02
   1_occ:   1.071  0.009  0.074 15.213  0.004  4.126   6.6334e-02
   2_bss:   1.071  0.009  0.074 15.213  0.004  4.126   6.6334e-02
   2_xyz:   0.997  0.008  0.075 14.784  0.004  4.127   5.9155e-02
   2_adp:   0.997  0.008  0.075 14.784  0.004  4.127   5.9155e-02
   2_occ:   0.997  0.008  0.075 14.784  0.004  4.127   5.9155e-02
   3_bss:   0.997  0.008  0.075 14.784  0.004  4.127   5.9155e-02
   3_xyz:   1.116  0.011  0.085 15.061  0.004  4.134   7.7404e-02
   3_adp:   1.116  0.011  0.085 15.061  0.004  4.134   7.7404e-02
   3_occ:   1.116  0.011  0.085 15.061  0.004  4.134   7.7404e-02
   4_bss:   1.116  0.011  0.085 15.061  0.004  4.134   7.7404e-02
   4_xyz:   1.040  0.010  0.080 14.830  0.004  4.135   6.7400e-02
   4_adp:   1.040  0.010  0.080 14.830  0.004  4.135   6.7400e-02
   4_occ:   1.040  0.010  0.080 14.830  0.004  4.135   6.7400e-02
   5_bss:   1.040  0.010  0.080 14.830  0.004  4.135   6.7400e-02
   5_xyz:   1.062  0.010  0.081 14.868  0.004  4.136   6.8824e-02
   5_adp:   1.062  0.010  0.081 14.868  0.004  4.136   6.8824e-02
   5_occ:   1.062  0.010  0.081 14.868  0.004  4.136   6.8824e-02
   5_bss:   1.062  0.010  0.081 14.868  0.004  4.136   6.8824e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4317e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4317e-01
   1_xyz:   9.378  0.042  0.211 83.191  0.036  2.366   6.6141e-02
   1_adp:   9.378  0.042  0.211 83.191  0.036  2.366   6.6141e-02
   1_occ:   9.378  0.042  0.211 83.191  0.036  2.366   6.6141e-02
   2_bss:   9.378  0.042  0.211 83.191  0.036  2.366   6.6141e-02
   2_xyz:   7.882  0.036  0.226 81.918  0.033  2.372   3.7913e-02
   2_adp:   7.882  0.036  0.226 81.918  0.033  2.372   3.7913e-02
   2_occ:   7.882  0.036  0.226 81.918  0.033  2.372   3.7913e-02
   3_bss:   7.882  0.036  0.226 81.918  0.033  2.372   3.7913e-02
   3_xyz:   7.693  0.050  0.286 83.426  0.038  2.308   6.2787e-02
   3_adp:   7.693  0.050  0.286 83.426  0.038  2.308   6.2787e-02
   3_occ:   7.693  0.050  0.286 83.426  0.038  2.308   6.2787e-02
   4_bss:   7.693  0.050  0.286 83.426  0.038  2.308   6.2787e-02
   4_xyz:   7.466  0.048  0.258 83.556  0.037  2.355   5.5226e-02
   4_adp:   7.466  0.048  0.258 83.556  0.037  2.355   5.5226e-02
   4_occ:   7.466  0.048  0.258 83.556  0.037  2.355   5.5226e-02
   5_bss:   7.466  0.048  0.258 83.556  0.037  2.355   5.5226e-02
   5_xyz:   7.661  0.048  0.259 83.330  0.038  2.333   4.8932e-02
   5_adp:   7.661  0.048  0.259 83.330  0.038  2.333   4.8932e-02
   5_occ:   7.661  0.048  0.259 83.330  0.038  2.333   4.8932e-02
   5_bss:   7.661  0.048  0.259 83.330  0.038  2.333   4.8932e-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:  64.51   0.00  16.74  56.46   0.00  12.87  64.51   4.64  37.83
   1_occ:  64.51   0.00  16.74  56.46   0.00  12.87  64.51   4.64  37.83
   2_bss:  64.51   0.00  16.74  56.46   0.00  12.87  64.51   4.64  37.83
   2_xyz:  64.51   0.00  16.74  56.46   0.00  12.87  64.51   4.64  37.83
   2_adp:  72.62   1.57  16.92  71.86   1.57  12.98  72.62   6.39  38.36
   2_occ:  72.62   1.57  16.92  71.86   1.57  12.98  72.62   6.39  38.36
   3_bss:  72.62   1.57  16.92  71.86   1.57  12.98  72.62   6.39  38.36
   3_xyz:  72.62   1.57  16.92  71.86   1.57  12.98  72.62   6.39  38.36
   3_adp:  73.61   1.82  16.67  72.00   1.82  12.84  73.61   5.13  37.56
   3_occ:  73.61   1.82  16.67  72.00   1.82  12.84  73.61   5.13  37.56
   4_bss:  73.61   1.82  16.67  72.00   1.82  12.84  73.61   5.13  37.56
   4_xyz:  73.61   1.82  16.67  72.00   1.82  12.84  73.61   5.13  37.56
   4_adp:  78.91   0.45  16.97  78.91   0.45  12.82  77.50   5.94  39.57
   4_occ:  78.91   0.45  16.97  78.91   0.45  12.82  77.50   5.94  39.57
   5_bss:  78.91   0.45  16.97  78.91   0.45  12.82  77.50   5.94  39.57
   5_xyz:  78.91   0.45  16.97  78.91   0.45  12.82  77.50   5.94  39.57
   5_adp:  89.54   0.00  17.04  89.54   0.00  12.73  81.63   5.39  40.54
   5_occ:  89.54   0.00  17.04  89.54   0.00  12.73  81.63   5.39  40.54
   5_bss:  89.54   0.00  17.04  89.54   0.00  12.73  81.63   5.39  40.54
------------------------------------------------------------------------
 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:    0.833    0.008    0.284
   1_adp:    0.833    0.008    0.284
   1_occ:    0.833    0.008    0.284
   2_bss:    0.833    0.008    0.284
   2_xyz:    0.799    0.021    0.314
   2_adp:    0.799    0.021    0.314
   2_occ:    0.799    0.021    0.314
   3_bss:    0.799    0.021    0.314
   3_xyz:    0.990    0.033    0.340
   3_adp:    0.990    0.033    0.340
   3_occ:    0.990    0.033    0.340
   4_bss:    0.990    0.033    0.340
   4_xyz:    1.126    0.044    0.348
   4_adp:    1.126    0.044    0.348
   4_occ:    1.126    0.044    0.348
   5_bss:    1.126    0.044    0.348
   5_xyz:    1.145    0.043    0.354
   5_adp:    1.145    0.043    0.354
   5_occ:    1.145    0.043    0.354
   5_bss:    1.145    0.043    0.354
------------------------------------------------------------------------

CPU time actual refinement: 331.45


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/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_1030/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1030/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.29 
  Macro-tasks:
    bulk solvent and scale       = 37.96  
    individual site refinement   = 140.19 
    weights calculation          = 29.61  
    collect and process          = 6.64   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 214.53 
  Micro-tasks:
    mask                            = 1.23   
    f_calc                          = 105.85 
    alpha_beta                      = 7.92   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 116.07 
    fmodel                         = 6.74   
    r_factors                      = 0.16   
    phase_errors                   = 11.07  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 250.45 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.646 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    654 calls, 105.42 s
gradients_fft:          599 calls, 102.02 s

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

# Date 2008-01-16 Time 06:15:50 PST -0800 (1200492950.55 s)
Start R-work = 0.3052, R-free = 0.2974 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.2907, R-free = 0.2862
Final R-work = 0.1093, R-free = 0.1607