# Date 2008-01-16 Time 05:11:54 PST -0800 (1200489114.54 s)
#phil __OFF__

Command line arguments: "../629.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16231
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 629

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.2261, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97037
Completeness in resolution range: 0.971628
Completeness with d_max=infinity: 0.96865

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97037
Completeness in resolution range: 0.971628
Completeness with d_max=infinity: 0.96865

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2162 [2112/2137]  1902   210   9.9%
  bin  2:  4.2162 -  3.3590 [2038/2058]  1833   205  10.1%
  bin  3:  3.3590 -  2.9381 [2005/2024]  1802   203  10.1%
  bin  4:  2.9381 -  2.6711 [1989/2019]  1797   192   9.7%
  bin  5:  2.6711 -  2.4806 [1984/2003]  1786   198  10.0%
  bin  6:  2.4806 -  2.3349 [1969/1994]  1769   200  10.2%
  bin  7:  2.3349 -  2.2184 [1942/1970]  1743   199  10.2%
  bin  8:  2.2184 -  2.1221 [1961/1997]  1767   194   9.9%
  bin  9:  2.1221 -  2.0406 [1948/1990]  1757   191   9.8%
  bin 10:  2.0406 -  1.9704 [1641/1969]  1474   167  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/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: 0.12 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: 41
        2.42 -     3.04: 2224
        3.04 -     3.66: 4799
        3.66 -     4.28: 9151
        4.28 -     4.90: 12523
  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 204 " - " O   HOH Z 296 "  1.942 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.958 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.998 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  ... (remaining 28733 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_629/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/model_refine_001.geo

CPU time processing inputs: 8.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.22605 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3959   r_free= 0.3919   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.187712                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7025 0.99   1380  154 0.3243 0.3189      6.4482      6.4197|
|  2:  4.7025 -  3.7520 0.99   1325  146 0.3263 0.3064      6.6452      6.5828|
|  3:  3.7520 -  3.2835 0.99   1289  142 0.3493 0.3456      6.5318      6.6409|
|  4:  3.2835 -  2.9859 0.99   1282  147 0.3621 0.3957      6.4114       6.413|
|  5:  2.9859 -  2.7733 0.99   1292  140 0.4150 0.3804      6.2768      6.2234|
|  6:  2.7733 -  2.6107 0.99   1278  142 0.4156 0.4371      6.1988       6.192|
|  7:  2.6107 -  2.4806 0.99   1274  137 0.4255 0.4044      6.1546      6.1273|
|  8:  2.4806 -  2.3731 0.98   1256  146 0.4373 0.4248      6.1186      6.1254|
|  9:  2.3731 -  2.2821 0.98   1255  137 0.4419 0.4266       6.066      6.0519|
| 10:  2.2821 -  2.2036 1.00   1269  142 0.4377 0.4409       6.032      6.0334|
| 11:  2.2036 -  2.1349 0.97   1248  136 0.4584 0.4527      5.9902      6.0416|
| 12:  2.1349 -  2.0740 0.98   1243  142 0.4531 0.4710      5.9366      5.9645|
| 13:  2.0740 -  2.0195 1.00   1258  137 0.4512 0.4476      5.8399      5.7946|
| 14:  2.0195 -  1.9704 0.77    981  111 0.4865 0.4427      5.8312      5.7262|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7025  1380   154  0.76  29.17   0.85     0.79      53001.10|
|  2:  4.7025 -  3.7520  1325   146  0.79  27.56   0.95     0.89      70631.45|
|  3:  3.7520 -  3.2835  1289   142  0.72  33.67   0.98     0.91      74728.49|
|  4:  3.2835 -  2.9859  1282   147  0.66  38.82   0.98     0.86      68689.12|
|  5:  2.9859 -  2.7733  1292   140  0.59  44.40   0.94     0.80      56032.31|
|  6:  2.7733 -  2.6107  1278   142  0.58  45.74   0.96     0.77      49871.70|
|  7:  2.6107 -  2.4806  1274   137  0.57  46.63   0.96     0.78      45172.26|
|  8:  2.4806 -  2.3731  1256   146  0.56  47.63   0.97     0.78      41538.65|
|  9:  2.3731 -  2.2821  1255   137  0.56  46.98   0.97     0.77      37333.05|
| 10:  2.2821 -  2.2036  1269   142  0.55  48.38   1.00     0.77      35249.34|
| 11:  2.2036 -  2.1349  1248   136  0.52  50.61   1.01     0.76      34228.88|
| 12:  2.1349 -  2.0740  1243   142  0.52  50.76   1.02     0.78      31717.29|
| 13:  2.0740 -  2.0195  1258   137  0.50  52.04   1.01     0.75      27178.19|
| 14:  2.0195 -  1.9704   981   111  0.52  50.71   0.99     0.71      22047.13|
|alpha:            min =        0.71 max =            0.91 mean =         0.80|
|beta:             min =    22047.13 max =        74728.49 mean =     46880.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.60|
|phase err.(work): min =        0.00 max =           90.00 mean =        43.50|
|phase err.(test): min =        0.00 max =           89.80 mean =        43.53|
|-----------------------------------------------------------------------------|

============================== 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 = 8.764224              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.646   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.328744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.357   (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:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       35 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      210 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2014 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1924 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2875 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4694 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4457 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5686 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6837 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.806 |       0.275 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3959   r_free= 0.3919   ksol= 0.00   Bsol= 0.00   scale= 0.948    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.187712                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3822   r_free= 0.3781   ksol= 0.34   Bsol= 27.11   scale= 0.967   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,1.81,0.65,0.00,0.00,0.00); trace/3= -0.25                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.176733                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.169082              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.633   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664783              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.215   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3822      final r-factor (work) = 0.2233          |
| start r-factor (free) = 0.3781      final r-factor (free) = 0.2530          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2932 = 7.17 * 0.50 * 6.1727 + 1.00 * 0.1670                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.3278 = 7.17 * 0.50 * 5.9243 + 1.00 * 0.0918                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2233      final r-factor (work) = 0.2043          |
| start r-factor (free) = 0.2530      final r-factor (free) = 0.2641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9444 = 0.66 * 1.00 * 5.9243 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7707 = 0.66 * 1.00 * 5.6542 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.72   17.68    None  None   None       |
|    all(noH): 2823   0      0.00    79.72   17.68    None  None   None       |
|    Sol.    : 438    0      6.80    79.72   41.11    None  None   None       |
|    Mac.    : 2385   0      0.00    78.86   13.37    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 -   7.972:  589   |   5:    39.859 -  47.831:  118        |
|      1:     7.972 -  15.944: 1207   |   6:    47.831 -  55.803:   92        |
|      2:    15.944 -  23.916:  448   |   7:    55.803 -  63.775:   63        |
|      3:    23.916 -  31.888:  153   |   8:    63.775 -  71.747:   21        |
|      4:    31.888 -  39.859:  125   |   9:    71.747 -  79.719:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2043 r_free = 0.2641             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2040 r_free = 0.2636             target_work(ml) = 5.669         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2040   r_free= 0.2636   ksol= 0.34   Bsol= 27.11   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.22,1.81,0.65,0.00,0.00,0.00); trace/3= -0.25                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.668775                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2012   r_free= 0.2596   ksol= 0.33   Bsol= 41.96   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.37,-1.11,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.657328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.503154              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.831   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.154640              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.890  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2012      final r-factor (work) = 0.1454          |
| start r-factor (free) = 0.2596      final r-factor (free) = 0.1919          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0073 = 3.50 * 0.50 * 5.6609 + 1.00 * 0.0918                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7403 = 3.50 * 0.50 * 5.5283 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1454      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.1919      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8667 = 0.15 * 1.00 * 5.5283 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8357 = 0.15 * 1.00 * 5.3249 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.79   17.08    None  None   None       |
|    all(noH): 2823   0      0.00    78.79   17.08    None  None   None       |
|    Sol.    : 438    0      5.90    76.90   39.46    None  None   None       |
|    Mac.    : 2385   0      0.00    78.79   12.97    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 -   7.879:  498   |   5:    39.396 -  47.275:  122        |
|      1:     7.879 -  15.759: 1400   |   6:    47.275 -  55.155:   86        |
|      2:    15.759 -  23.638:  397   |   7:    55.155 -  63.034:   49        |
|      3:    23.638 -  31.517:  130   |   8:    63.034 -  70.913:   19        |
|      4:    31.517 -  39.396:  116   |   9:    70.913 -  78.792:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1336 r_free = 0.1756             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1334 r_free = 0.1755             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1755   ksol= 0.33   Bsol= 41.96   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.37,-1.11,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.279316                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1758   ksol= 0.32   Bsol= 41.39   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.23,-1.42,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.277851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.387083              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219235              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.460   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4115 = 2.39 * 0.50 * 5.3244 + 1.00 * 0.0566                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2843 = 2.39 * 0.50 * 5.2188 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1144          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1533 = 0.22 * 1.00 * 5.2188 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1371 = 0.22 * 1.00 * 5.1524 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.25    81.49   16.87    None  None   None       |
|    all(noH): 2823   0      1.25    81.49   16.87    None  None   None       |
|    Sol.    : 438    0      4.61    76.01   39.12    None  None   None       |
|    Mac.    : 2385   0      1.25    81.49   12.79    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:     1.250 -   9.274:  826   |   5:    41.370 -  49.394:  104        |
|      1:     9.274 -  17.298: 1228   |   6:    49.394 -  57.418:   78        |
|      2:    17.298 -  25.322:  284   |   7:    57.418 -  65.442:   42        |
|      3:    25.322 -  33.346:  121   |   8:    65.442 -  73.466:   10        |
|      4:    33.346 -  41.370:  126   |   9:    73.466 -  81.490:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1144 r_free = 0.1559             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1143 r_free = 0.1558             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1558   ksol= 0.32   Bsol= 41.39   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-2.23,-1.42,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.140457                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1143   r_free= 0.1557   ksol= 0.32   Bsol= 41.39   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.45,-1.56,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.139964                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.321908              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.438  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.003481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.301  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1143      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4608 = 1.32 * 0.50 * 5.1521 + 1.00 * 0.0555                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.4412 = 1.32 * 0.50 * 5.1360 + 1.00 * 0.0465                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1614 = 1.00 * 1.00 * 5.1360 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1514 = 1.00 * 1.00 * 5.1247 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    88.46   17.04    None  None   None       |
|    all(noH): 2823   0      0.55    88.46   17.04    None  None   None       |
|    Sol.    : 438    0      5.74    79.83   40.21    None  None   None       |
|    Mac.    : 2385   0      0.55    88.46   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.549 -   9.340:  899   |   5:    44.503 -  53.294:  108        |
|      1:     9.340 -  18.131: 1195   |   6:    53.294 -  62.085:   59        |
|      2:    18.131 -  26.922:  261   |   7:    62.085 -  70.876:   37        |
|      3:    26.922 -  35.712:  128   |   8:    70.876 -  79.667:   11        |
|      4:    35.712 -  44.503:  122   |   9:    79.667 -  88.457:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1112 r_free = 0.1553             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1112 r_free = 0.1553             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1112   r_free= 0.1553   ksol= 0.32   Bsol= 41.39   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-2.45,-1.56,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130439                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1111   r_free= 0.1553   ksol= 0.32   Bsol= 43.50   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.36,-1.43,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.130436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.999017              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.239813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.621  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1688 = 2.00 * 0.50 * 5.1248 + 1.00 * 0.0465                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1651 = 2.00 * 0.50 * 5.1115 + 1.00 * 0.0561                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1544          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.5693 = 3.24 * 1.00 * 5.1115 + 1.00 * 0.0089                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.5384 = 3.24 * 1.00 * 5.1017 + 1.00 * 0.0099                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.98   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    98.98   17.07    None  None   None       |
|    Sol.    : 438    0      6.07    86.13   40.62    None  None   None       |
|    Mac.    : 2385   0      0.00    98.98   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.898: 1062   |   5:    49.491 -  59.389:   89        |
|      1:     9.898 -  19.796: 1117   |   6:    59.389 -  69.287:   37        |
|      2:    19.796 -  29.695:  218   |   7:    69.287 -  79.186:   23        |
|      3:    29.695 -  39.593:  135   |   8:    79.186 -  89.084:   13        |
|      4:    39.593 -  49.491:  127   |   9:    89.084 -  98.982:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1544             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1545             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1545   ksol= 0.32   Bsol= 43.50   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-2.36,-1.43,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105201                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7025 0.99   1380  154 0.0940 0.1216      5.3378      5.4817|
|  2:  4.7025 -  3.7520 0.99   1325  146 0.0821 0.1124      5.4043      5.6081|
|  3:  3.7520 -  3.2835 0.99   1289  142 0.1019 0.1500      5.4498      5.8463|
|  4:  3.2835 -  2.9859 0.99   1282  147 0.1180 0.1551      5.4353      5.5768|
|  5:  2.9859 -  2.7733 0.99   1292  140 0.1249 0.1747      5.2841      5.5295|
|  6:  2.7733 -  2.6107 0.99   1278  142 0.1101 0.1649      5.1601      5.3556|
|  7:  2.6107 -  2.4806 0.99   1274  137 0.1204 0.1563      5.1222      5.3589|
|  8:  2.4806 -  2.3731 0.98   1256  146 0.1096 0.1703      5.0132      5.3343|
|  9:  2.3731 -  2.2821 0.98   1255  137 0.1118 0.1604      5.0027      5.2277|
| 10:  2.2821 -  2.2036 1.00   1269  142 0.1034 0.1835      4.9192      5.2651|
| 11:  2.2036 -  2.1349 0.97   1248  136 0.1071 0.1611      4.9218        5.23|
| 12:  2.1349 -  2.0740 0.98   1243  142 0.1081 0.1684      4.8604      5.1896|
| 13:  2.0740 -  2.0195 1.00   1258  137 0.1065 0.1784      4.7653      5.0842|
| 14:  2.0195 -  1.9704 0.77    981  111 0.1007 0.1663      4.6298      4.8721|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7025  1380   154  0.95   8.39   0.98     0.95       6398.48|
|  2:  4.7025 -  3.7520  1325   146  0.95   7.58   1.03     1.02       8537.47|
|  3:  3.7520 -  3.2835  1289   142  0.94  10.81   1.04     1.03       9937.32|
|  4:  3.2835 -  2.9859  1282   147  0.92  13.21   1.02     1.00       9972.92|
|  5:  2.9859 -  2.7733  1292   140  0.90  15.35   1.00     0.97       7754.64|
|  6:  2.7733 -  2.6107  1278   142  0.91  14.82   0.99     0.97       6550.84|
|  7:  2.6107 -  2.4806  1274   137  0.91  14.98   0.99     0.95       5693.53|
|  8:  2.4806 -  2.3731  1256   146  0.91  14.32   0.99     0.97       4755.02|
|  9:  2.3731 -  2.2821  1255   137  0.92  14.42   1.00     0.98       4694.65|
| 10:  2.2821 -  2.2036  1269   142  0.91  14.64   1.00     0.96       4073.20|
| 11:  2.2036 -  2.1349  1248   136  0.90  16.31   1.00     0.97       4355.11|
| 12:  2.1349 -  2.0740  1243   142  0.92  14.60   1.00     0.98       3829.57|
| 13:  2.0740 -  2.0195  1258   137  0.91  15.53   1.00     0.99       3241.03|
| 14:  2.0195 -  1.9704   981   111  0.92  13.77   0.99     0.96       2379.48|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2379.48 max =         9972.92 mean =      5956.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.24 mean =        13.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1544   ksol= 0.32   Bsol= 44.41   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.18,-1.24,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105338                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1064   r_free= 0.1544   ksol= 0.32   Bsol= 44.41   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.10,-2.18,-1.24,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105338                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7025 0.99   1380  154 0.0941 0.1219      5.3401      5.4847|
|  2:  4.7025 -  3.7520 0.99   1325  146 0.0822 0.1124      5.4053      5.6081|
|  3:  3.7520 -  3.2835 0.99   1289  142 0.1019 0.1501      5.4501      5.8469|
|  4:  3.2835 -  2.9859 0.99   1282  147 0.1180 0.1551      5.4352      5.5768|
|  5:  2.9859 -  2.7733 0.99   1292  140 0.1248 0.1745      5.2837      5.5287|
|  6:  2.7733 -  2.6107 0.99   1278  142 0.1101 0.1648      5.1597      5.3553|
|  7:  2.6107 -  2.4806 0.99   1274  137 0.1204 0.1563      5.1221      5.3592|
|  8:  2.4806 -  2.3731 0.98   1256  146 0.1096 0.1701      5.0131      5.3334|
|  9:  2.3731 -  2.2821 0.98   1255  137 0.1118 0.1605      5.0026      5.2279|
| 10:  2.2821 -  2.2036 1.00   1269  142 0.1034 0.1835      4.9193      5.2654|
| 11:  2.2036 -  2.1349 0.97   1248  136 0.1071 0.1610      4.9217      5.2296|
| 12:  2.1349 -  2.0740 0.98   1243  142 0.1081 0.1684        4.86      5.1896|
| 13:  2.0740 -  2.0195 1.00   1258  137 0.1065 0.1782       4.765      5.0832|
| 14:  2.0195 -  1.9704 0.77    981  111 0.1007 0.1662      4.6296      4.8718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7025  1380   154  0.94   8.44   0.98     0.96       6440.23|
|  2:  4.7025 -  3.7520  1325   146  0.95   7.61   1.03     1.02       8566.22|
|  3:  3.7520 -  3.2835  1289   142  0.94  10.82   1.04     1.03       9944.47|
|  4:  3.2835 -  2.9859  1282   147  0.92  13.20   1.02     1.01       9969.54|
|  5:  2.9859 -  2.7733  1292   140  0.90  15.35   1.01     0.98       7748.33|
|  6:  2.7733 -  2.6107  1278   142  0.91  14.82   1.00     0.98       6544.72|
|  7:  2.6107 -  2.4806  1274   137  0.91  14.97   1.00     0.96       5690.14|
|  8:  2.4806 -  2.3731  1256   146  0.91  14.32   1.00     0.98       4752.47|
|  9:  2.3731 -  2.2821  1255   137  0.92  14.43   1.01     0.99       4694.74|
| 10:  2.2821 -  2.2036  1269   142  0.91  14.64   1.01     0.97       4072.98|
| 11:  2.2036 -  2.1349  1248   136  0.90  16.30   1.01     0.98       4354.34|
| 12:  2.1349 -  2.0740  1243   142  0.92  14.58   1.02     1.00       3825.72|
| 13:  2.0740 -  2.0195  1258   137  0.91  15.52   1.02     1.00       3237.60|
| 14:  2.0195 -  1.9704   981   111  0.92  13.76   1.00     0.97       2377.42|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2377.42 max =         9969.54 mean =      5960.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.42|
|phase err.(test): min =        0.00 max =           89.25 mean =        13.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.570)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.98   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    98.98   17.07    None  None   None       |
|    Sol.    : 438    0      6.07    86.13   40.63    None  None   None       |
|    Mac.    : 2385   0      0.00    98.98   12.74    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 -   9.901: 1062   |   5:    49.494 -  59.392:   89        |
|      1:     9.901 -  19.799: 1117   |   6:    59.392 -  69.290:   37        |
|      2:    19.799 -  29.698:  218   |   7:    69.290 -  79.188:   23        |
|      3:    29.698 -  39.596:  135   |   8:    79.188 -  89.087:   13        |
|      4:    39.596 -  49.494:  127   |   9:    89.087 -  98.985:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.411 - 4.586
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 295
   mapped sites are within: 0.753 - 4.586

peak=    6.229 closest distance to " NE2 GLN A  11 " =    1.212
peak=    5.857 closest distance to " O   HOH Z 126 " =    1.910
peak=    5.654 closest distance to " CG  PRO A  54 " =    1.226
peak=    5.502 closest distance to " NH2 ARG A  56 " =    2.162
peak=    5.493 closest distance to " O   HOH Z 144 " =    1.659
peak=    5.069 closest distance to " CB  SER A  63 " =    1.218
peak=    5.044 closest distance to " CG  PRO A 213 " =    1.249
peak=    4.881 closest distance to " CB  GLN A 223 " =    1.518
peak=    4.873 closest distance to " O   HOH Z  78 " =    1.790
peak=    4.847 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.794 closest distance to " CB  GLN A 183 " =    1.225
peak=    4.694 closest distance to " O   HOH Z 427 " =    2.675
peak=    4.623 closest distance to " O   HOH Z 193 " =    1.800
peak=    4.591 closest distance to " C   PRO A 198 " =    1.470
peak=    4.581 closest distance to " CB  PRO A  54 " =    0.958
peak=    4.570 closest distance to " O   HOH Z 369 " =    2.154
peak=    4.493 closest distance to " O   HOH Z 298 " =    1.890
peak=    4.473 closest distance to " O   HOH Z  63 " =    1.505
peak=    4.452 closest distance to " O   HOH Z 287 " =    2.015
peak=    4.449 closest distance to " CB  ASN A 148 " =    1.376
peak=    4.442 closest distance to " O   HOH Z 209 " =    2.194
peak=    4.414 closest distance to " O   HOH Z 232 " =    2.361
peak=    4.376 closest distance to " CG  PRO A  90 " =    1.070
peak=    4.376 closest distance to " O   HOH Z   9 " =    2.376
peak=    4.369 closest distance to " CG  ARG A  66 " =    2.430
peak=    4.364 closest distance to " O   HOH Z 423 " =    1.534
peak=    4.350 closest distance to " CB  GLU A 128 " =    1.059
peak=    4.339 closest distance to " CB  GLU A 152 " =    1.301
peak=    4.333 closest distance to " O   HOH Z 203 " =    1.855
peak=    4.284 closest distance to " O   HOH Z 234 " =    3.631
peak=    4.263 closest distance to " O   HOH Z 217 " =    3.040
peak=    4.249 closest distance to " O   HOH Z  78 " =    2.128
peak=    4.241 closest distance to " O   HOH Z 419 " =    2.181
peak=    4.238 closest distance to " O   HOH Z  44 " =    1.770
peak=    4.210 closest distance to " CB  LEU A 228 " =    1.102
peak=    4.202 closest distance to " O   HOH Z 316 " =    3.029
peak=    4.202 closest distance to " CB  SER A   3 " =    1.319
peak=    4.198 closest distance to " CG  TRP A 179 " =    2.218
peak=    4.169 closest distance to " O   HOH Z   1 " =    1.900
peak=    4.160 closest distance to " ND2 ASN A 187 " =    1.362
peak=    4.142 closest distance to " OD1 ASN A  69 " =    2.661
peak=    4.133 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.125 closest distance to " O   HOH Z 425 " =    1.317
peak=    4.118 closest distance to " O   HOH Z 371 " =    1.803
peak=    4.109 closest distance to " O   HOH Z 368 " =    3.623
peak=    4.107 closest distance to " O   HOH Z 261 " =    2.078
peak=    4.084 closest distance to " O   HOH Z 236 " =    1.450
peak=    4.080 closest distance to " OG BSER A 164 " =    2.348
peak=    4.060 closest distance to " CB  VAL A 265 " =    1.376
peak=    4.051 closest distance to " CG2 VAL A 257 " =    0.862
peak=    4.042 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.038 closest distance to " CG1 ILE A  33 " =    1.225
peak=    4.020 closest distance to " O   HOH Z 132 " =    2.283
peak=    4.006 closest distance to " CB  ARG A 139 " =    1.032
peak=    3.996 closest distance to " O   HOH Z  61 " =    1.672
peak=    3.979 closest distance to " O   HOH Z  61 " =    1.518
peak=    3.968 closest distance to " CB  TYR A 169 " =    0.813
peak=    3.966 closest distance to " CB  ARG A  79 " =    1.403
peak=    3.966 closest distance to " O   HOH Z 158 " =    3.004
peak=    3.963 closest distance to " O   HOH Z 344 " =    3.101
peak=    3.946 closest distance to " O   HOH Z 207 " =    1.664
peak=    3.944 closest distance to " O   HOH Z 272 " =    1.778
peak=    3.943 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.918 closest distance to " O   HOH Z 437 " =    1.657
peak=    3.894 closest distance to " O   HOH Z 128 " =    2.103
peak=    3.877 closest distance to " O   HOH Z 425 " =    1.972
peak=    3.867 closest distance to " CD BLYS A 290 " =    1.190
peak=    3.839 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.836 closest distance to " O   HOH Z 368 " =    1.923
peak=    3.834 closest distance to " ND1 HIS A  86 " =    1.778
peak=    3.825 closest distance to " O   SER A  87 " =    2.222
peak=    3.815 closest distance to " OD2 ASP A 286 " =    2.739
peak=    3.813 closest distance to " CA  ASN A 215 " =    1.247
peak=    3.798 closest distance to " CA  ALA A  21 " =    1.123
peak=    3.780 closest distance to " O   HOH Z 214 " =    2.100
peak=    3.779 closest distance to " O   HOH Z   1 " =    1.763
peak=    3.771 closest distance to " O   HOH Z  59 " =    1.631
peak=    3.766 closest distance to " O   HOH Z 250 " =    1.446
peak=    3.760 closest distance to " CD2 TRP A 179 " =    1.373
peak=    3.760 closest distance to " O   HOH Z 405 " =    1.169
peak=    3.750 closest distance to " O   HOH Z  66 " =    2.088
peak=    3.746 closest distance to " O   HOH Z 289 " =    1.662
peak=    3.743 closest distance to " O   HOH Z 180 " =    2.160
peak=    3.743 closest distance to " O   HOH Z   3 " =    1.919
peak=    3.729 closest distance to " CA  THR A 264 " =    0.819
peak=    3.710 closest distance to " CB  TRP A 266 " =    1.027
peak=    3.703 closest distance to " CG2 THR A 221 " =    1.152
peak=    3.695 closest distance to " OD1BASN A 224 " =    2.254
peak=    3.690 closest distance to " O   HOH Z  43 " =    1.901
peak=    3.680 closest distance to " O   HOH Z  93 " =    2.190
peak=    3.678 closest distance to " O   HOH Z  10 " =    1.780
peak=    3.677 closest distance to " N   PHE A 130 " =    1.237
peak=    3.675 closest distance to " O   HOH Z 403 " =    1.669
peak=    3.675 closest distance to " NH2BARG A 145 " =    2.036
peak=    3.672 closest distance to " O   HOH Z 263 " =    2.303
peak=    3.670 closest distance to " CB  ARG A 190 " =    1.619
peak=    3.670 closest distance to " O   HOH Z 327 " =    1.698
peak=    3.667 closest distance to " O   HOH Z 389 " =    1.770
peak=    3.663 closest distance to " O   HOH Z  40 " =    1.948
peak=    3.659 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.645 closest distance to " O   MET A 105 " =    1.841
peak=    3.632 closest distance to " O   HOH Z 286 " =    2.316
peak=    3.627 closest distance to " O   HOH Z 371 " =    2.927
peak=    3.626 closest distance to " O   HOH Z 108 " =    1.333
peak=    3.625 closest distance to " CB  SER A 216 " =    0.798
peak=    3.616 closest distance to " O   HOH Z 392 " =    3.153
peak=    3.605 closest distance to " CA  GLY A 241 " =    3.787
peak=    3.604 closest distance to " CB  GLU A 277 " =    3.503
peak=    3.578 closest distance to " O   HOH Z 108 " =    2.008
peak=    3.574 closest distance to " O   HOH Z 175 " =    2.195
peak=    3.566 closest distance to " O   HOH Z 147 " =    1.706
peak=    3.563 closest distance to " CD2 LEU A 297 " =    0.979
peak=    3.562 closest distance to " CG  PRO A 243 " =    1.111
peak=    3.560 closest distance to " O   HOH Z 284 " =    2.924
peak=    3.549 closest distance to " O   HOH Z  88 " =    2.865
peak=    3.541 closest distance to " O   HOH Z 245 " =    1.258
peak=    3.535 closest distance to " NH1BARG A 145 " =    1.276
peak=    3.524 closest distance to " O   HOH Z 133 " =    2.369
peak=    3.522 closest distance to " O   HOH Z 380 " =    1.559
peak=    3.520 closest distance to " O   HOH Z 124 " =    1.354
peak=    3.515 closest distance to " O   HOH Z 172 " =    3.118
peak=    3.513 closest distance to " CB  THR A 157 " =    1.094
peak=    3.512 closest distance to " OG  SER A  62 " =    2.936
peak=    3.510 closest distance to " O   HOH Z 407 " =    2.221
peak=    3.506 closest distance to " CB  ALA A  21 " =    1.806
peak=    3.505 closest distance to " O   HOH Z 426 " =    1.672
peak=    3.504 closest distance to " O   HOH Z 409 " =    2.499
peak=    3.491 closest distance to " O   HOH Z  40 " =    1.980
peak=    3.488 closest distance to " O   HOH Z 133 " =    1.498
peak=    3.488 closest distance to " O   HOH Z 271 " =    2.332
peak=    3.479 closest distance to " CA  MET A  40 " =    1.089
peak=    3.477 closest distance to " OG  SER A  22 " =    2.760
peak=    3.468 closest distance to " O   HOH Z 298 " =    2.605
peak=    3.466 closest distance to " O   HOH Z 227 " =    1.743
peak=    3.465 closest distance to " O   HOH Z 193 " =    1.793
peak=    3.456 closest distance to " O   HOH Z 357 " =    1.833
peak=    3.449 closest distance to " CB  ALA A  34 " =    1.060
peak=    3.448 closest distance to " O   HOH Z 189 " =    1.901
peak=    3.445 closest distance to " O   HOH Z 391 " =    2.909
peak=    3.442 closest distance to " O   HOH Z 305 " =    3.536
peak=    3.440 closest distance to " O   HOH Z 290 " =    0.913
peak=    3.438 closest distance to " OE2 GLU A  53 " =    2.078
peak=    3.433 closest distance to " O   HOH Z 345 " =    3.373
peak=    3.431 closest distance to " O   HOH Z 128 " =    2.049
peak=    3.430 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.428 closest distance to " NH1AARG A 145 " =    1.102
peak=    3.424 closest distance to " O   HOH Z 211 " =    2.686
peak=    3.422 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.417 closest distance to " CB  VAL A 202 " =    1.653
peak=    3.414 closest distance to " CB  SER A  62 " =    1.269
peak=    3.410 closest distance to " CA  LYS A 290 " =    1.324
peak=    3.394 closest distance to " O   HOH Z 281 " =    1.762
peak=    3.393 closest distance to " O   HOH Z 217 " =    1.521
peak=    3.391 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.390 closest distance to " CB  LEU A 143 " =    1.106
peak=    3.390 closest distance to " O   HOH Z 227 " =    2.168
peak=    3.389 closest distance to " CB  TYR A 116 " =    0.825
peak=    3.387 closest distance to " CG2 ILE A 120 " =    1.147
peak=    3.385 closest distance to " O   HOH Z 365 " =    2.784
peak=    3.384 closest distance to " CB  THR A  31 " =    1.777
peak=    3.383 closest distance to " O   HOH Z  21 " =    1.693
peak=    3.377 closest distance to " CB  ALA A   1 " =    4.586
peak=    3.376 closest distance to " O   HOH Z  97 " =    1.932
peak=    3.369 closest distance to " CB  GLN A  89 " =    1.380
peak=    3.365 closest distance to " O   HOH Z 423 " =    2.323
peak=    3.358 closest distance to " NH2 ARG A 219 " =    1.865
peak=    3.355 closest distance to " CD  PRO A 243 " =    1.594
peak=    3.353 closest distance to " O   HOH Z 128 " =    2.013
peak=    3.349 closest distance to " CA  ALA A 233 " =    1.002
peak=    3.349 closest distance to " CA  ALA A 158 " =    1.114
peak=    3.348 closest distance to " NH2AARG A 275 " =    3.600
peak=    3.348 closest distance to " O   HOH Z 336 " =    1.995
peak=    3.347 closest distance to " O   HOH Z 261 " =    2.248
peak=    3.346 closest distance to " O   HOH Z   6 " =    2.002
peak=    3.345 closest distance to " CA  PHE A 283 " =    1.287
peak=    3.344 closest distance to " CD2 LEU A 255 " =    1.467
peak=    3.342 closest distance to " CB  MET A  47 " =    1.250
peak=    3.333 closest distance to " O   HOH Z 219 " =    2.256
peak=    3.333 closest distance to " CB  SER A  26 " =    1.568
peak=    3.331 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.328 closest distance to " O   HOH Z 258 " =    2.208
peak=    3.327 closest distance to " N   ALA A   1 " =    2.068
peak=    3.325 closest distance to " O   HOH Z 146 " =    1.652
peak=    3.325 closest distance to " CB  ALA A 291 " =    1.448
peak=    3.323 closest distance to " N   ASN A 127 " =    1.280
peak=    3.321 closest distance to " CA  SER A  32 " =    1.633
peak=    3.316 closest distance to " O   HOH Z 135 " =    1.631
peak=    3.311 closest distance to " CB  SER A 212 " =    0.972
peak=    3.304 closest distance to " O   HOH Z 266 " =    3.092
peak=    3.304 closest distance to " O   HOH Z 402 " =    1.402
peak=    3.296 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.293 closest distance to " N   ARG A 156 " =    1.279
peak=    3.292 closest distance to " O   HOH Z 373 " =    1.423
peak=    3.292 closest distance to " NE2 GLN A  73 " =    3.554
peak=    3.292 closest distance to " CB  ILE A 120 " =    1.369
peak=    3.290 closest distance to " O   HOH Z 313 " =    1.915
peak=    3.286 closest distance to " O   HOH Z 432 " =    1.719
peak=    3.285 closest distance to " CG  MET A 113 " =    1.186
peak=    3.278 closest distance to " O   HOH Z 435 " =    1.878
peak=    3.275 closest distance to " O   HOH Z 417 " =    3.495
peak=    3.275 closest distance to " O   HOH Z   2 " =    1.349
peak=    3.274 closest distance to " ND1 HIS A  81 " =    1.597
peak=    3.274 closest distance to " O   HOH Z 126 " =    1.513
peak=    3.268 closest distance to " N   SER A 134 " =    1.396
peak=    3.267 closest distance to " N   ASN A  39 " =    1.254
peak=    3.263 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.262 closest distance to " O   HOH Z 422 " =    2.617
peak=    3.255 closest distance to " N   GLN A 278 " =    1.122
peak=    3.253 closest distance to " CB  SER A 276 " =    1.084
peak=    3.250 closest distance to " CA  THR A 221 " =    1.000
peak=    3.250 closest distance to " O   HOH Z 265 " =    2.189
peak=    3.249 closest distance to " CB  ASP A 132 " =    4.081
peak=    3.249 closest distance to " CA  ASP A 162 " =    1.077
peak=    3.248 closest distance to " O   HOH Z 394 " =    1.553
peak=    3.247 closest distance to " O   SER A  26 " =    1.570
peak=    3.247 closest distance to " O   HOH Z 286 " =    2.369
peak=    3.246 closest distance to " OG BSER A  99 " =    2.180
peak=    3.240 closest distance to " O  BHOH Z 338 " =    2.361
peak=    3.239 closest distance to " CE AMET A  47 " =    1.389
peak=    3.239 closest distance to " CZ  PHE A 218 " =    0.997
peak=    3.238 closest distance to " CG  GLU A 277 " =    2.038
peak=    3.236 closest distance to " O   HOH Z  44 " =    3.092
peak=    3.227 closest distance to " O   HOH Z 153 " =    1.627
peak=    3.226 closest distance to " OH  TYR A 116 " =    1.005
peak=    3.225 closest distance to " CA  ILE A 234 " =    1.004
peak=    3.225 closest distance to " CB  ALA A 114 " =    1.472
peak=    3.224 closest distance to " CG1 ILE A 151 " =    0.919
peak=    3.221 closest distance to " N   SER A 146 " =    1.741
peak=    3.216 closest distance to " O   HOH Z 291 " =    1.586
peak=    3.216 closest distance to " CG  GLN A  89 " =    1.485
peak=    3.214 closest distance to " CB  GLN A  88 " =    1.268
peak=    3.212 closest distance to " O   HOH Z  71 " =    2.052
peak=    3.210 closest distance to " CG1BVAL A  72 " =    1.383
peak=    3.206 closest distance to " O   HOH Z 151 " =    1.422
peak=    3.203 closest distance to " O   HOH Z  49 " =    1.986
peak=    3.201 closest distance to " O   HOH Z 359 " =    1.327
peak=    3.196 closest distance to " CD  ARG A  79 " =    2.297
peak=    3.195 closest distance to " CA  LEU A 101 " =    1.593
peak=    3.192 closest distance to " CA  ASN A 127 " =    1.014
peak=    3.189 closest distance to " O   HOH Z  88 " =    2.333
peak=    3.188 closest distance to " O   HOH Z 213 " =    2.101
peak=    3.187 closest distance to " CG  GLN A  77 " =    2.337
peak=    3.187 closest distance to " CB  VAL A 268 " =    0.827
peak=    3.186 closest distance to " CB  ASP A 140 " =    0.882
peak=    3.181 closest distance to " O   HOH Z 403 " =    1.281
peak=    3.181 closest distance to " CA  ASN A  74 " =    1.284
peak=    3.180 closest distance to " O   HOH Z 273 " =    2.709
peak=    3.178 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.175 closest distance to " CA  ALA A 291 " =    0.899
peak=    3.171 closest distance to " O   HOH Z 110 " =    1.681
peak=    3.171 closest distance to " O   HOH Z 392 " =    1.381
peak=    3.169 closest distance to " CD1 LEU A 300 " =    1.250
peak=    3.169 closest distance to " O   HOH Z  53 " =    2.515
peak=    3.169 closest distance to " CG BARG A 102 " =    1.791
peak=    3.168 closest distance to " O   HOH Z 173 " =    1.881
peak=    3.166 closest distance to " O   HOH Z  99 " =    1.782
peak=    3.162 closest distance to " O   HOH Z  64 " =    2.050
peak=    3.161 closest distance to " O   HOH Z 291 " =    1.823
peak=    3.161 closest distance to " NZ  LYS A  76 " =    1.427
peak=    3.161 closest distance to " O   HOH Z 329 " =    3.619
peak=    3.158 closest distance to " O   HOH Z 132 " =    3.632
peak=    3.154 closest distance to " O  BHOH Z  74 " =    1.390
peak=    3.153 closest distance to " O   HOH Z  15 " =    1.399
peak=    3.149 closest distance to " CB  VAL A 126 " =    1.143
peak=    3.149 closest distance to " CG1 VAL A 189 " =    1.897
peak=    3.144 closest distance to " O   HOH Z 374 " =    2.540
peak=    3.137 closest distance to " N   ALA A 154 " =    0.952
peak=    3.137 closest distance to " NE2 GLN A  58 " =    3.370
peak=    3.136 closest distance to " CB  SER A  62 " =    0.790
peak=    3.134 closest distance to " N   TYR A  15 " =    0.819
peak=    3.131 closest distance to " O   HOH Z 303 " =    1.674
peak=    3.129 closest distance to " O   HOH Z 189 " =    2.098
peak=    3.120 closest distance to " O   HOH Z 248 " =    1.557
peak=    3.114 closest distance to " CD  LYS A 166 " =    1.294
peak=    3.109 closest distance to " OG  SER A  62 " =    3.012
peak=    3.104 closest distance to " CD  ARG A 195 " =    3.476
peak=    3.101 closest distance to " O   HOH Z 379 " =    1.948
peak=    3.098 closest distance to " O   HOH Z 346 " =    1.419
peak=    3.097 closest distance to " O   HOH Z 433 " =    1.770
peak=    3.095 closest distance to " CB  ALA A  71 " =    1.409
peak=    3.091 closest distance to " O   HOH Z 130 " =    3.793
peak=    3.090 closest distance to " CA  ALA A 248 " =    1.200
peak=    3.076 closest distance to " CD  ARG A 138 " =    0.760
peak=    3.068 closest distance to " CB  LEU A 255 " =    0.753
peak=    3.063 closest distance to " CB  ASN A 110 " =    1.123
peak=    3.062 closest distance to " N   CYS A 260 " =    0.842
peak=    3.056 closest distance to " NZ  LYS A 119 " =    1.244
peak=    3.051 closest distance to " O   HOH Z  30 " =    1.567
peak=    3.042 closest distance to " O   HOH Z 285 " =    1.594
peak=    3.033 closest distance to " CA  ALA A  51 " =    0.987
peak=    3.020 closest distance to " CA  ALA A 299 " =    0.907

                           ----------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: 0.681 - 5.951
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 214
   mapped sites are within: 0.768 - 5.951

peak=   -4.695 closest distance to " O   HOH Z 377 " =    2.000
peak=   -4.487 closest distance to " O   HOH Z 266 " =    4.501
peak=   -4.441 closest distance to " C   HIS A 108 " =    1.110
peak=   -4.391 closest distance to " CB  PRO A 243 " =    2.573
peak=   -4.390 closest distance to " CD  ARG A 156 " =    1.982
peak=   -4.352 closest distance to " CG  GLN A 223 " =    1.905
peak=   -4.308 closest distance to " SG  CYS A 254 " =    3.316
peak=   -4.292 closest distance to " OG BSER A 134 " =    1.201
peak=   -4.176 closest distance to " O   VAL A  67 " =    2.677
peak=   -4.174 closest distance to " CG1 VAL A 112 " =    2.854
peak=   -4.079 closest distance to " CE2 PHE A 218 " =    2.491
peak=   -4.068 closest distance to " O   HOH Z 198 " =    1.965
peak=   -4.062 closest distance to " O   HOH Z 231 " =    2.101
peak=   -4.041 closest distance to " CA  GLY A  98 " =    1.847
peak=   -4.022 closest distance to " CG  LYS A 193 " =    2.446
peak=   -4.014 closest distance to " O   SER A 135 " =    1.462
peak=   -4.004 closest distance to " N   GLN A  58 " =    1.689
peak=   -3.998 closest distance to " CE  MET A 105 " =    2.230
peak=   -3.992 closest distance to " CZ  PHE A  59 " =    1.500
peak=   -3.989 closest distance to " O   HOH Z 313 " =    1.889
peak=   -3.979 closest distance to " O   HOH Z 389 " =    1.791
peak=   -3.944 closest distance to " CD1 LEU A 255 " =    2.901
peak=   -3.931 closest distance to " O   HOH Z  13 " =    1.485
peak=   -3.926 closest distance to " O   ARG A 145 " =    1.548
peak=   -3.881 closest distance to " ND2 ASN A  45 " =    1.036
peak=   -3.871 closest distance to " CG  PHE A 283 " =    2.639
peak=   -3.869 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.847 closest distance to " O   VAL A  67 " =    2.696
peak=   -3.835 closest distance to " O   HOH Z 102 " =    1.644
peak=   -3.821 closest distance to " O   PRO A 198 " =    1.334
peak=   -3.815 closest distance to " CB  TYR A  15 " =    2.163
peak=   -3.813 closest distance to " CE2 TYR A  30 " =    2.802
peak=   -3.813 closest distance to " CB  ALA A 291 " =    2.125
peak=   -3.811 closest distance to " O   HOH Z 351 " =    1.617
peak=   -3.810 closest distance to " O   HOH Z 290 " =    1.239
peak=   -3.809 closest distance to " OD1 ASN A 187 " =    1.571
peak=   -3.797 closest distance to " CB  ALA A 161 " =    2.566
peak=   -3.790 closest distance to " O   HOH Z  43 " =    1.779
peak=   -3.776 closest distance to " O   HOH Z 316 " =    1.867
peak=   -3.771 closest distance to " O   PRO A 163 " =    1.968
peak=   -3.743 closest distance to " O   HOH Z 152 " =    4.963
peak=   -3.741 closest distance to " N   ALA A  43 " =    2.544
peak=   -3.734 closest distance to " N   ASP A 286 " =    2.438
peak=   -3.732 closest distance to " OXT GLY A 302 " =    2.831
peak=   -3.724 closest distance to " ND2 ASN A  45 " =    1.618
peak=   -3.711 closest distance to " O   HOH Z 385 " =    1.927
peak=   -3.707 closest distance to " O   HOH Z 407 " =    3.094
peak=   -3.706 closest distance to " O   HOH Z 263 " =    2.849
peak=   -3.694 closest distance to " CG  ASP A 231 " =    0.768
peak=   -3.684 closest distance to " CA  GLY A 203 " =    2.158
peak=   -3.667 closest distance to " OD1 ASP A 171 " =    1.542
peak=   -3.662 closest distance to " CZ  TYR A 169 " =    1.575
peak=   -3.643 closest distance to " O   HOH Z 185 " =    2.065
peak=   -3.639 closest distance to " O   HOH Z 198 " =    1.535
peak=   -3.633 closest distance to " OD2 ASP A 191 " =    1.478
peak=   -3.630 closest distance to " O   HOH Z 388 " =    1.994
peak=   -3.613 closest distance to " O   HOH Z  24 " =    1.270
peak=   -3.612 closest distance to " CB  ASN A  39 " =    2.261
peak=   -3.610 closest distance to " CB  ALA A 291 " =    2.310
peak=   -3.608 closest distance to " N   MET A 188 " =    1.898
peak=   -3.598 closest distance to " O   HOH Z  52 " =    1.306
peak=   -3.598 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.595 closest distance to " CD  ARG A 139 " =    1.542
peak=   -3.580 closest distance to " N   ALA A 248 " =    1.500
peak=   -3.575 closest distance to " O   HOH Z 298 " =    1.232
peak=   -3.570 closest distance to " O   HOH Z 409 " =    5.951
peak=   -3.555 closest distance to " CD1 LEU A 228 " =    2.128
peak=   -3.552 closest distance to " C   ALA A 158 " =    1.284
peak=   -3.544 closest distance to " CZ3 TRP A 179 " =    1.228
peak=   -3.542 closest distance to " O   SER A  95 " =    1.401
peak=   -3.530 closest distance to " NE  ARG A  36 " =    1.876
peak=   -3.528 closest distance to " CA  GLY A 133 " =    1.921
peak=   -3.513 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.512 closest distance to " O   HOH Z 193 " =    1.858
peak=   -3.510 closest distance to " NH2BARG A 275 " =    1.770
peak=   -3.508 closest distance to " OD1 ASN A 148 " =    1.591
peak=   -3.503 closest distance to " NH2 ARG A  79 " =    1.924
peak=   -3.501 closest distance to " O   HOH Z  93 " =    2.001
peak=   -3.498 closest distance to " O   PHE A 218 " =    1.523
peak=   -3.478 closest distance to " OD1 ASP A 191 " =    1.440
peak=   -3.472 closest distance to " O   PRO A 243 " =    2.456
peak=   -3.466 closest distance to " O   HOH Z  60 " =    2.088
peak=   -3.453 closest distance to " CA  ASP A  27 " =    2.447
peak=   -3.449 closest distance to " CB  ALA A   7 " =    2.025
peak=   -3.447 closest distance to " CG  MET A 105 " =    0.947
peak=   -3.444 closest distance to " O   ALA A 161 " =    1.546
peak=   -3.436 closest distance to " C   LEU A 143 " =    1.122
peak=   -3.434 closest distance to " ND2 ASN A  69 " =    1.502
peak=   -3.432 closest distance to " CB  PHE A 192 " =    1.888
peak=   -3.432 closest distance to " CB  ALA A 248 " =    1.932
peak=   -3.430 closest distance to " O   HOH Z 166 " =    1.275
peak=   -3.429 closest distance to " O   VAL A 174 " =    2.206
peak=   -3.428 closest distance to " OG  SER A  87 " =    1.266
peak=   -3.420 closest distance to " O   VAL A 153 " =    2.293
peak=   -3.420 closest distance to " CD1 LEU A 101 " =    2.304
peak=   -3.415 closest distance to " O   HOH Z 137 " =    1.447
peak=   -3.415 closest distance to " CB  CYS A 254 " =    2.266
peak=   -3.414 closest distance to " O   SER A  22 " =    2.456
peak=   -3.410 closest distance to " OD1 ASN A 176 " =    1.210
peak=   -3.406 closest distance to " O   HOH Z 393 " =    3.533
peak=   -3.401 closest distance to " O   VAL A 189 " =    2.456
peak=   -3.398 closest distance to " NH1 ARG A 195 " =    2.640
peak=   -3.394 closest distance to " O   HOH Z  63 " =    1.954
peak=   -3.391 closest distance to " OD2 ASP A 171 " =    2.061
peak=   -3.389 closest distance to " NH2AARG A 275 " =    5.255
peak=   -3.387 closest distance to " O   HOH Z 211 " =    1.516
peak=   -3.382 closest distance to " O   HOH Z 266 " =    4.310
peak=   -3.380 closest distance to " O   SER A 146 " =    0.996
peak=   -3.374 closest distance to " O   HOH Z  60 " =    2.025
peak=   -3.369 closest distance to " CE3 TRP A 123 " =    1.309
peak=   -3.367 closest distance to " CB  PRO A 163 " =    2.442
peak=   -3.362 closest distance to " O   HOH Z 140 " =    1.896
peak=   -3.358 closest distance to " O   HOH Z  90 " =    2.470
peak=   -3.357 closest distance to " O   ALA A  10 " =    1.722
peak=   -3.356 closest distance to " CG2 THR A 178 " =    2.163
peak=   -3.355 closest distance to " CB  ILE A  33 " =    2.799
peak=   -3.355 closest distance to " CG  GLN A  58 " =    1.211
peak=   -3.351 closest distance to " OG  SER A 245 " =    1.282
peak=   -3.351 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.351 closest distance to " CE3 TRP A 274 " =    2.292
peak=   -3.347 closest distance to " CD2 LEU A 237 " =    2.690
peak=   -3.342 closest distance to " CG2 VAL A 189 " =    1.958
peak=   -3.341 closest distance to " O   HOH Z 114 " =    2.821
peak=   -3.337 closest distance to " N   HIS A 115 " =    2.053
peak=   -3.330 closest distance to " O   HOH Z 213 " =    1.357
peak=   -3.327 closest distance to " O   MET A  40 " =    2.720
peak=   -3.319 closest distance to " O   HOH Z 103 " =    1.693
peak=   -3.312 closest distance to " OG  SER A  97 " =    2.038
peak=   -3.291 closest distance to " OG  SER A  26 " =    1.199
peak=   -3.289 closest distance to " O   HOH Z 131 " =    4.136
peak=   -3.285 closest distance to " O   HOH Z 359 " =    3.325
peak=   -3.283 closest distance to " O   HOH Z 281 " =    2.803
peak=   -3.281 closest distance to " CD  LYS A 289 " =    2.339
peak=   -3.278 closest distance to " N   SER A 212 " =    1.853
peak=   -3.276 closest distance to " CE  LYS A  76 " =    2.789
peak=   -3.273 closest distance to " O   HOH Z 250 " =    1.431
peak=   -3.273 closest distance to " CG1 VAL A 230 " =    1.922
peak=   -3.272 closest distance to " CA  ASP A 298 " =    1.001
peak=   -3.272 closest distance to " OE1 GLN A 223 " =    2.001
peak=   -3.271 closest distance to " O   HOH Z 345 " =    1.933
peak=   -3.271 closest distance to " NH1 ARG A  36 " =    2.010
peak=   -3.271 closest distance to " O   ASN A 249 " =    1.473
peak=   -3.269 closest distance to " CB  ASP A 286 " =    2.289
peak=   -3.269 closest distance to " N   THR A 235 " =    1.367
peak=   -3.266 closest distance to " ND2 ASN A 187 " =    1.562
peak=   -3.265 closest distance to " C   PRO A  90 " =    1.497
peak=   -3.259 closest distance to " O   HOH Z  51 " =    1.203
peak=   -3.258 closest distance to " SD BMET A  47 " =    1.027
peak=   -3.256 closest distance to " CG  GLN A  88 " =    0.826
peak=   -3.252 closest distance to " NZ  LYS A 119 " =    3.327
peak=   -3.247 closest distance to " O   HOH Z 111 " =    4.597
peak=   -3.247 closest distance to " O   ALA A 180 " =    1.175
peak=   -3.234 closest distance to " NH1AARG A 275 " =    1.771
peak=   -3.231 closest distance to " O   ALA A  51 " =    1.306
peak=   -3.231 closest distance to " O   HOH Z  38 " =    1.691
peak=   -3.230 closest distance to " O   HOH Z 322 " =    1.739
peak=   -3.229 closest distance to " CB  ALA A 131 " =    1.943
peak=   -3.225 closest distance to " O   HOH Z 326 " =    1.687
peak=   -3.220 closest distance to " OD1 ASP A 200 " =    1.375
peak=   -3.219 closest distance to " CG1 VAL A 197 " =    2.160
peak=   -3.217 closest distance to " CB  ASP A 132 " =    2.227
peak=   -3.215 closest distance to " O   HOH Z 234 " =    3.930
peak=   -3.214 closest distance to " CB  TRP A  85 " =    2.449
peak=   -3.211 closest distance to " CE1 TYR A 169 " =    2.495
peak=   -3.207 closest distance to " ND2 ASN A  39 " =    1.473
peak=   -3.203 closest distance to " O   TRP A  70 " =    1.479
peak=   -3.202 closest distance to " O   GLY A  80 " =    2.398
peak=   -3.201 closest distance to " CD1 ILE A 151 " =    2.129
peak=   -3.195 closest distance to " CG  GLU A 152 " =    1.214
peak=   -3.194 closest distance to " CB  ALA A 248 " =    2.294
peak=   -3.184 closest distance to " CD2 LEU A 143 " =    2.615
peak=   -3.182 closest distance to " O   HOH Z 191 " =    5.487
peak=   -3.177 closest distance to " CE  MET A  93 " =    1.193
peak=   -3.173 closest distance to " NH1 ARG A  56 " =    2.497
peak=   -3.172 closest distance to " CG  TRP A 266 " =    1.746
peak=   -3.170 closest distance to " OG ASER A 134 " =    1.023
peak=   -3.166 closest distance to " CB  PHE A 208 " =    2.195
peak=   -3.164 closest distance to " O   HOH Z 350 " =    1.291
peak=   -3.164 closest distance to " OG1 THR A 178 " =    1.207
peak=   -3.156 closest distance to " ND2BASN A 224 " =    1.849
peak=   -3.154 closest distance to " OH  TYR A 214 " =    1.270
peak=   -3.152 closest distance to " O   GLY A 111 " =    1.313
peak=   -3.149 closest distance to " O   HOH Z 166 " =    1.976
peak=   -3.147 closest distance to " CB  ALA A  51 " =    1.847
peak=   -3.145 closest distance to " O   HOH Z 137 " =    1.430
peak=   -3.144 closest distance to " CD  PRO A 198 " =    1.601
peak=   -3.142 closest distance to " CA  GLY A  57 " =    2.094
peak=   -3.140 closest distance to " OD2 ASP A  50 " =    1.491
peak=   -3.135 closest distance to " CD2 LEU A 300 " =    2.818
peak=   -3.126 closest distance to " C   LYS A  76 " =    1.605
peak=   -3.126 closest distance to " O   HOH Z 394 " =    1.430
peak=   -3.124 closest distance to " CD2 TYR A 293 " =    1.974
peak=   -3.123 closest distance to " OG BSER A 134 " =    1.604
peak=   -3.122 closest distance to " O   HOH Z  97 " =    1.666
peak=   -3.120 closest distance to " O   ALA A 292 " =    1.948
peak=   -3.120 closest distance to " CZ2 TRP A 274 " =    0.974
peak=   -3.113 closest distance to " O   HOH Z 438 " =    1.095
peak=   -3.112 closest distance to " CG  PRO A 163 " =    2.535
peak=   -3.104 closest distance to " O   HOH Z 298 " =    2.424
peak=   -3.100 closest distance to " O   ALA A  34 " =    2.835
peak=   -3.098 closest distance to " CZ3 TRP A 123 " =    1.783
peak=   -3.097 closest distance to " O   HOH Z   9 " =    2.080
peak=   -3.096 closest distance to " O   HOH Z 236 " =    1.915
peak=   -3.084 closest distance to " O   HOH Z 168 " =    1.749
peak=   -3.077 closest distance to " OE1 GLN A  58 " =    3.042
peak=   -3.063 closest distance to " O   HOH Z 281 " =    2.968
peak=   -3.062 closest distance to " CB  ASP A 286 " =    1.766
peak=   -3.057 closest distance to " SG ACYS A 201 " =    1.791
peak=   -3.047 closest distance to " O   ASN A 127 " =    2.192
peak=   -3.042 closest distance to " CD  GLN A  77 " =    1.623
peak=   -3.029 closest distance to " O   HOH Z 357 " =    2.061
peak=   -3.026 closest distance to " CD  GLN A 223 " =    1.406
peak=   -2.972 closest distance to " CG1BVAL A  41 " =    2.730

================= 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    :  0.3959 0.3919   6.187712e+00   6.178491e+00
   1_bss:  0.3822 0.3781   6.176733e+00   6.154182e+00
   1_xyz:  0.2233 0.2530   5.718011e+00   5.814651e+00
   1_adp:  0.2043 0.2641   5.670184e+00   5.854333e+00
   1_occ:  0.2040 0.2636   5.668775e+00   5.852984e+00
   2_bss:  0.2012 0.2596   5.657328e+00   5.842539e+00
   2_xyz:  0.1454 0.1919   5.358095e+00   5.576850e+00
   2_adp:  0.1336 0.1756   5.279880e+00   5.492597e+00
   2_occ:  0.1334 0.1755   5.279316e+00   5.492195e+00
   3_bss:  0.1336 0.1758   5.277851e+00   5.490643e+00
   3_xyz:  0.1176 0.1598   5.165447e+00   5.395934e+00
   3_adp:  0.1144 0.1559   5.140407e+00   5.372308e+00
   3_occ:  0.1143 0.1558   5.140457e+00   5.372722e+00
   4_bss:  0.1143 0.1557   5.139964e+00   5.372358e+00
   4_xyz:  0.1128 0.1541   5.131934e+00   5.362594e+00
   4_adp:  0.1112 0.1553   5.130581e+00   5.370864e+00
   4_occ:  0.1112 0.1553   5.130439e+00   5.370761e+00
   5_bss:  0.1111 0.1553   5.130436e+00   5.370173e+00
   5_xyz:  0.1070 0.1537   5.104842e+00   5.360633e+00
   5_adp:  0.1066 0.1544   5.104989e+00   5.364424e+00
   5_occ:  0.1065 0.1545   5.105201e+00   5.364945e+00
   5_bss:  0.1064 0.1544   5.105338e+00   5.364995e+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:  0.335  27.108  -3.216   1.806   0.654   0.000   0.000   0.000
   1_xyz:  0.335  27.108  -3.216   1.806   0.654   0.000   0.000   0.000
   1_adp:  0.335  27.108  -3.216   1.806   0.654   0.000   0.000   0.000
   1_occ:  0.335  27.108  -3.216   1.806   0.654   0.000   0.000   0.000
   2_bss:  0.330  41.957  -2.747  -1.366  -1.110  -0.000  -0.000  -0.000
   2_xyz:  0.330  41.957  -2.747  -1.366  -1.110  -0.000  -0.000  -0.000
   2_adp:  0.330  41.957  -2.747  -1.366  -1.110  -0.000  -0.000  -0.000
   2_occ:  0.330  41.957  -2.747  -1.366  -1.110  -0.000  -0.000  -0.000
   3_bss:  0.321  41.385  -2.612  -2.230  -1.418  -0.000  -0.000  -0.000
   3_xyz:  0.321  41.385  -2.612  -2.230  -1.418  -0.000  -0.000  -0.000
   3_adp:  0.321  41.385  -2.612  -2.230  -1.418  -0.000  -0.000  -0.000
   3_occ:  0.321  41.385  -2.612  -2.230  -1.418  -0.000  -0.000  -0.000
   4_bss:  0.321  41.385  -2.558  -2.448  -1.556  -0.000  -0.000  -0.000
   4_xyz:  0.321  41.385  -2.558  -2.448  -1.556  -0.000  -0.000  -0.000
   4_adp:  0.321  41.385  -2.558  -2.448  -1.556  -0.000  -0.000  -0.000
   4_occ:  0.321  41.385  -2.558  -2.448  -1.556  -0.000  -0.000  -0.000
   5_bss:  0.319  43.503  -2.338  -2.358  -1.429  -0.000  -0.000  -0.000
   5_xyz:  0.319  43.503  -2.338  -2.358  -1.429  -0.000  -0.000  -0.000
   5_adp:  0.319  43.503  -2.338  -2.358  -1.429  -0.000  -0.000  -0.000
   5_occ:  0.319  43.503  -2.338  -2.358  -1.429  -0.000  -0.000  -0.000
   5_bss:  0.321  44.408  -2.104  -2.180  -1.236  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  43.499 0.6029  0.7965    46879.463
   1_bss:  41.931 0.6196  0.8092    42403.860
   1_xyz:  24.405 0.8197  1.0007    16394.216
   1_adp:  25.878 0.8032  0.9851    17755.988
   1_occ:  25.844 0.8036  0.9848    17688.323
   2_bss:  25.338 0.8087  0.9414    17108.294
   2_xyz:  18.299 0.8770  0.9905     9217.943
   2_adp:  16.137 0.8971  0.9984     7884.306
   2_occ:  16.131 0.8972  0.9983     7868.312
   3_bss:  16.084 0.8976  0.9857     7859.188
   3_xyz:  14.089 0.9139  0.9919     6358.195
   3_adp:  13.579 0.9181  0.9900     6103.226
   3_occ:  13.584 0.9181  0.9899     6103.301
   4_bss:  13.570 0.9182  0.9863     6099.785
   4_xyz:  13.340 0.9203  0.9862     5950.640
   4_adp:  13.478 0.9194  0.9803     6029.068
   4_occ:  13.477 0.9194  0.9802     6028.431
   5_bss:  13.476 0.9194  0.9858     6021.117
   5_xyz:  13.295 0.9206  0.9864     5917.750
   5_adp:  13.371 0.9201  0.9796     5950.349
   5_occ:  13.379 0.9200  0.9795     5956.697
   5_bss:  13.381 0.9200  0.9870     5960.375
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.6699e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.6699e-01
   1_xyz:   1.304  0.010  0.084 15.178  0.006  4.105   9.1767e-02
   1_adp:   1.304  0.010  0.084 15.178  0.006  4.105   9.1767e-02
   1_occ:   1.304  0.010  0.084 15.178  0.006  4.105   9.1767e-02
   2_bss:   1.304  0.010  0.084 15.178  0.006  4.105   9.1767e-02
   2_xyz:   0.995  0.006  0.072 14.440  0.004  4.111   5.7056e-02
   2_adp:   0.995  0.006  0.072 14.440  0.004  4.111   5.7056e-02
   2_occ:   0.995  0.006  0.072 14.440  0.004  4.111   5.7056e-02
   3_bss:   0.995  0.006  0.072 14.440  0.004  4.111   5.7056e-02
   3_xyz:   0.963  0.006  0.070 14.590  0.004  4.114   5.5486e-02
   3_adp:   0.963  0.006  0.070 14.590  0.004  4.114   5.5486e-02
   3_occ:   0.963  0.006  0.070 14.590  0.004  4.114   5.5486e-02
   4_bss:   0.963  0.006  0.070 14.590  0.004  4.114   5.5486e-02
   4_xyz:   0.855  0.004  0.065 14.249  0.003  4.114   4.6503e-02
   4_adp:   0.855  0.004  0.065 14.249  0.003  4.114   4.6503e-02
   4_occ:   0.855  0.004  0.065 14.249  0.003  4.114   4.6503e-02
   5_bss:   0.855  0.004  0.065 14.249  0.003  4.114   4.6503e-02
   5_xyz:   0.973  0.006  0.071 14.555  0.004  4.115   5.6107e-02
   5_adp:   0.973  0.006  0.071 14.555  0.004  4.115   5.6107e-02
   5_occ:   0.973  0.006  0.071 14.555  0.004  4.115   5.6107e-02
   5_bss:   0.973  0.006  0.071 14.555  0.004  4.115   5.6107e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3808e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3808e-01
   1_xyz:   8.730  0.053  0.447 86.119  0.041  2.156   9.3580e-02
   1_adp:   8.730  0.053  0.447 86.119  0.041  2.156   9.3580e-02
   1_occ:   8.730  0.053  0.447 86.119  0.041  2.156   9.3580e-02
   2_bss:   8.730  0.053  0.447 86.119  0.041  2.156   9.3580e-02
   2_xyz:   7.518  0.032  0.201 83.116  0.048  2.330   5.7350e-02
   2_adp:   7.518  0.032  0.201 83.116  0.048  2.330   5.7350e-02
   2_occ:   7.518  0.032  0.201 83.116  0.048  2.330   5.7350e-02
   3_bss:   7.518  0.032  0.201 83.116  0.048  2.330   5.7350e-02
   3_xyz:   7.110  0.045  0.215 85.388  0.036  2.306   4.2515e-02
   3_adp:   7.110  0.045  0.215 85.388  0.036  2.306   4.2515e-02
   3_occ:   7.110  0.045  0.215 85.388  0.036  2.306   4.2515e-02
   4_bss:   7.110  0.045  0.215 85.388  0.036  2.306   4.2515e-02
   4_xyz:   6.756  0.040  0.201 84.460  0.037  2.370   2.7821e-02
   4_adp:   6.756  0.040  0.201 84.460  0.037  2.370   2.7821e-02
   4_occ:   6.756  0.040  0.201 84.460  0.037  2.370   2.7821e-02
   5_bss:   6.756  0.040  0.201 84.460  0.037  2.370   2.7821e-02
   5_xyz:   6.596  0.039  0.229 84.329  0.033  2.269   3.8460e-02
   5_adp:   6.596  0.039  0.229 84.329  0.033  2.269   3.8460e-02
   5_occ:   6.596  0.039  0.229 84.329  0.033  2.269   3.8460e-02
   5_bss:   6.596  0.039  0.229 84.329  0.033  2.269   3.8460e-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:  79.72   0.00  17.68  78.86   0.00  13.37  79.72   6.80  41.11
   1_occ:  79.72   0.00  17.68  78.86   0.00  13.37  79.72   6.80  41.11
   2_bss:  79.72   0.00  17.68  78.86   0.00  13.37  79.72   6.80  41.11
   2_xyz:  79.72   0.00  17.68  78.86   0.00  13.37  79.72   6.80  41.11
   2_adp:  78.79   0.00  17.08  78.79   0.00  12.97  76.90   5.90  39.46
   2_occ:  78.79   0.00  17.08  78.79   0.00  12.97  76.90   5.90  39.46
   3_bss:  78.79   0.00  17.08  78.79   0.00  12.97  76.90   5.90  39.46
   3_xyz:  78.79   0.00  17.08  78.79   0.00  12.97  76.90   5.90  39.46
   3_adp:  81.49   1.25  16.87  81.49   1.25  12.79  76.01   4.61  39.12
   3_occ:  81.49   1.25  16.87  81.49   1.25  12.79  76.01   4.61  39.12
   4_bss:  81.49   1.25  16.87  81.49   1.25  12.79  76.01   4.61  39.12
   4_xyz:  81.49   1.25  16.87  81.49   1.25  12.79  76.01   4.61  39.12
   4_adp:  88.46   0.55  17.04  88.46   0.55  12.78  79.83   5.74  40.21
   4_occ:  88.46   0.55  17.04  88.46   0.55  12.78  79.83   5.74  40.21
   5_bss:  88.46   0.55  17.04  88.46   0.55  12.78  79.83   5.74  40.21
   5_xyz:  88.46   0.55  17.04  88.46   0.55  12.78  79.83   5.74  40.21
   5_adp:  98.98   0.00  17.07  98.98   0.00  12.74  86.13   6.07  40.62
   5_occ:  98.98   0.00  17.07  98.98   0.00  12.74  86.13   6.07  40.62
   5_bss:  98.98   0.00  17.07  98.98   0.00  12.74  86.13   6.07  40.63
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.402    0.031    0.411
   1_adp:    1.402    0.031    0.411
   1_occ:    1.402    0.031    0.411
   2_bss:    1.402    0.031    0.411
   2_xyz:    1.051    0.040    0.501
   2_adp:    1.051    0.040    0.501
   2_occ:    1.051    0.040    0.501
   3_bss:    1.051    0.040    0.501
   3_xyz:    0.951    0.045    0.539
   3_adp:    0.951    0.045    0.539
   3_occ:    0.951    0.045    0.539
   4_bss:    0.951    0.045    0.539
   4_xyz:    1.070    0.060    0.557
   4_adp:    1.070    0.060    0.557
   4_occ:    1.070    0.060    0.557
   5_bss:    1.070    0.060    0.557
   5_xyz:    1.166    0.024    0.568
   5_adp:    1.166    0.024    0.568
   5_occ:    1.166    0.024    0.568
   5_bss:    1.166    0.024    0.568
------------------------------------------------------------------------

CPU time actual refinement: 278.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/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_629/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_629/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 278.58 
  Macro-tasks:
    bulk solvent and scale       = 31.23  
    individual site refinement   = 115.62 
    weights calculation          = 25.29  
    collect and process          = 5.54   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 177.78 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 89.33  
    alpha_beta                      = 7.20   
    target                          = 1.06   
    gradients_wrt_atomic_parameters = 97.13  
    fmodel                         = 5.59   
    r_factors                      = 0.15   
    phase_errors                   = 8.89   
    foms                           = 0.16   
    TOTAL for micro-tasks          = 211.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.955 micro seconds
Total CPU time: 4.84 minutes
from_scatterers_fft:    641 calls, 89.13 s
gradients_fft:          586 calls, 85.53 s

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

# Date 2008-01-16 Time 05:16:44 PST -0800 (1200489404.10 s)
Start R-work = 0.3959, R-free = 0.3919 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1734 (no bulk solvent and anisotropic scale)

Start R-work = 0.3822, R-free = 0.3781
Final R-work = 0.1064, R-free = 0.1544