# Date 2008-01-16 Time 06:41:09 PST -0800 (1200494469.19 s)
#phil __OFF__

Command line arguments: "../1239.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9349
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1239

-------------------------------------------------------------------------------
  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: (72.0062, 46.2261, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.97409
Completeness in resolution range: 0.929931
Completeness with d_max=infinity: 0.92729

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3069
                             d_min =   1.9741

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: (72.0062, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3069 1.97409
Completeness in resolution range: 0.929931
Completeness with d_max=infinity: 0.92729

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3073 -  4.2260 [2215/2242]  1994   221  10.0%
  bin  2:  4.2260 -  3.3660 [2130/2150]  1917   213  10.0%
  bin  3:  3.3660 -  2.9440 [2097/2116]  1886   211  10.1%
  bin  4:  2.9440 -  2.6764 [2063/2093]  1853   210  10.2%
  bin  5:  2.6764 -  2.4854 [2073/2092]  1879   194   9.4%
  bin  6:  2.4854 -  2.3394 [2075/2100]  1857   218  10.5%
  bin  7:  2.3394 -  2.2226 [2022/2050]  1811   211  10.4%
  bin  8:  2.2226 -  2.1261 [2047/2083]  1847   200   9.8%
  bin  9:  2.1261 -  2.0445 [2025/2074]  1831   194   9.6%
  bin 10:  2.0445 -  1.9741 [ 842/2065]   755    87  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 29
        2.42 -     3.04: 2171
        3.04 -     3.66: 4669
        3.66 -     4.28: 8978
        4.28 -     4.90: 12239
  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 201 " - " O   HOH Z 349 "  2.017 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.049 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
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  ... (remaining 28081 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_1239/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 = 72.00625 46.22605 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4474   r_free= 0.4442   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255380                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7144 0.99   1431  161 0.3527 0.3373      6.5148      6.4645|
|  2:  4.7144 -  3.7602 0.99   1385  152 0.3829 0.3585      6.7841      6.7247|
|  3:  3.7602 -  3.2903 0.99   1346  148 0.4031 0.3921      6.5973       6.614|
|  4:  3.2903 -  2.9919 0.99   1355  154 0.4423 0.4712        6.48      6.4988|
|  5:  2.9919 -  2.7788 0.99   1342  145 0.4660 0.4660      6.3396      6.3528|
|  6:  2.7788 -  2.6158 0.99   1342  152 0.4663 0.4488      6.2295      6.1865|
|  7:  2.6158 -  2.4854 0.99   1328  137 0.4960 0.4643      6.2228      6.1679|
|  8:  2.4854 -  2.3776 0.98   1307  157 0.4993 0.5320       6.152      6.1622|
|  9:  2.3776 -  2.2864 0.98   1316  145 0.4979 0.5055      6.1151      6.1449|
| 10:  2.2864 -  2.2078 1.00   1315  158 0.5079 0.4774      6.0641       6.025|
| 11:  2.2078 -  2.1389 0.98   1313  129 0.5117 0.5182      6.0302      6.0487|
| 12:  2.1389 -  2.0779 0.98   1299  156 0.5041 0.5391      5.9294      5.9546|
| 13:  2.0779 -  2.0233 0.91   1201  125 0.5168 0.4764      5.8639      5.7898|
| 14:  2.0233 -  1.9741 0.26    350   40 0.4967 0.5997      5.8479      5.8852|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7144  1431   161  0.75  29.32   0.83     0.80      55213.73|
|  2:  4.7144 -  3.7602  1385   152  0.75  30.55   0.91     0.85      83650.80|
|  3:  3.7602 -  3.2903  1346   148  0.64  40.61   0.93     0.82      96402.08|
|  4:  3.2903 -  2.9919  1355   154  0.55  48.11   0.90     0.74      91764.07|
|  5:  2.9919 -  2.7788  1342   145  0.46  54.69   0.90     0.65      76014.44|
|  6:  2.7788 -  2.6158  1342   152  0.45  56.24   0.91     0.62      64252.90|
|  7:  2.6158 -  2.4854  1328   137  0.43  57.91   0.91     0.58      58726.41|
|  8:  2.4854 -  2.3776  1307   157  0.41  58.96   0.89     0.57      53640.63|
|  9:  2.3776 -  2.2864  1316   145  0.40  59.72   0.94     0.57      49391.39|
| 10:  2.2864 -  2.2078  1315   158  0.40  59.96   0.92     0.58      44757.32|
| 11:  2.2078 -  2.1389  1313   129  0.38  61.49   0.93     0.57      44636.50|
| 12:  2.1389 -  2.0779  1299   156  0.34  64.53   0.93     0.53      41341.46|
| 13:  2.0779 -  2.0233  1201   125  0.31  66.89   0.92     0.50      37607.68|
| 14:  2.0233 -  1.9741   350    40  0.35  64.07   0.94     0.48      30720.16|
|alpha:            min =        0.48 max =            0.85 mean =         0.65|
|beta:             min =    30720.16 max =        96402.08 mean =     61110.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.85|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.90|
|-----------------------------------------------------------------------------|

============================== 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 = 16.010482             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.918   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.266193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.283   (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:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      189 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1982 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1864 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4615 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4363 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5580 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6659 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.210 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    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 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4474   r_free= 0.4442   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255380                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4395   r_free= 0.4380   ksol= 0.33   Bsol= 59.01   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,0.53,-0.22,0.00,-0.00,-0.00); trace/3= 0.82                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.248528                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.743039             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.037   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.066150              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.986   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4395      final r-factor (work) = 0.2723          |
| start r-factor (free) = 0.4380      final r-factor (free) = 0.3056          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0727 = 13.74 * 0.50 * 6.2442 + 1.00 * 0.1656                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.8360 = 13.74 * 0.50 * 6.0693 + 1.00 * 0.1309                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2723      final r-factor (work) = 0.2502          |
| start r-factor (free) = 0.3056      final r-factor (free) = 0.3155          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4774 = 1.07 * 1.00 * 6.0693 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2777 = 1.07 * 1.00 * 5.8322 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.45   17.30    None  None   None       |
|    all(noH): 2823   0      0.00    79.45   17.30    None  None   None       |
|    Sol.    : 438    0      2.12    65.16   39.48    None  None   None       |
|    Mac.    : 2385   0      0.00    79.45   13.23    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 -   7.945:  648   |   5:    39.723 -  47.667:  138        |
|      1:     7.945 -  15.889: 1057   |   6:    47.667 -  55.612:   87        |
|      2:    15.889 -  23.834:  519   |   7:    55.612 -  63.556:   37        |
|      3:    23.834 -  31.778:  196   |   8:    63.556 -  71.501:    5        |
|      4:    31.778 -  39.723:  135   |   9:    71.501 -  79.445:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2502 r_free = 0.3155             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2496 r_free = 0.3155             target_work(ml) = 5.844         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2496   r_free= 0.3155   ksol= 0.33   Bsol= 59.01   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,0.53,-0.22,0.00,-0.00,-0.00); trace/3= 0.82                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.844149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2480   r_free= 0.3146   ksol= 0.33   Bsol= 59.01   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-1.62,-0.72,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.842465                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.829493              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.042   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.763787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.147   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2480      final r-factor (work) = 0.1780          |
| start r-factor (free) = 0.3146      final r-factor (free) = 0.2333          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2386 = 4.83 * 0.50 * 5.8423 + 1.00 * 0.1309                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8822 = 4.83 * 0.50 * 5.7210 + 1.00 * 0.0674                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1780      final r-factor (work) = 0.1598          |
| start r-factor (free) = 0.2333      final r-factor (free) = 0.2145          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3852 = 0.76 * 1.00 * 5.7210 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2161 = 0.76 * 1.00 * 5.5046 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.08   17.78    None  None   None       |
|    all(noH): 2823   0      0.00    80.08   17.78    None  None   None       |
|    Sol.    : 438    0      5.58    80.08   42.88    None  None   None       |
|    Mac.    : 2385   0      0.00    70.03   13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.008:  648   |   5:    40.039 -  48.046:  103        |
|      1:     8.008 -  16.015: 1206   |   6:    48.046 -  56.054:   93        |
|      2:    16.015 -  24.023:  380   |   7:    56.054 -  64.062:   81        |
|      3:    24.023 -  32.031:  171   |   8:    64.062 -  72.069:   35        |
|      4:    32.031 -  40.039:   98   |   9:    72.069 -  80.077:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1598 r_free = 0.2145             target_work(ml) = 5.463         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1597 r_free = 0.2147             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1597   r_free= 0.2147   ksol= 0.33   Bsol= 59.01   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.51,-1.62,-0.72,-0.00,-0.00,-0.00); trace/3= -0.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.462464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1596   r_free= 0.2145   ksol= 0.34   Bsol= 67.53   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-2.08,-0.67,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.460705                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.000386              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.895  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.103816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.580  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1596      final r-factor (work) = 0.1390          |
| start r-factor (free) = 0.2145      final r-factor (free) = 0.1896          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5732 = 2.00 * 0.50 * 5.5047 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4573 = 2.00 * 0.50 * 5.4045 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1335          |
| start r-factor (free) = 0.1896      final r-factor (free) = 0.1855          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3819 = 2.10 * 1.00 * 5.4045 + 1.00 * 0.0118                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2005 = 2.10 * 1.00 * 5.3176 + 1.00 * 0.0132                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.18  18.30    None  None   None       |
|    all(noH): 2823   0      0.00    109.18  18.30    None  None   None       |
|    Sol.    : 438    0      2.54    109.18  46.54    None  None   None       |
|    Mac.    : 2385   0      0.00    91.29   13.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.918: 1243   |   5:    54.588 -  65.506:   93        |
|      1:    10.918 -  21.835:  960   |   6:    65.506 -  76.423:   62        |
|      2:    21.835 -  32.753:  212   |   7:    76.423 -  87.341:   31        |
|      3:    32.753 -  43.670:  123   |   8:    87.341 -  98.258:    8        |
|      4:    43.670 -  54.588:   89   |   9:    98.258 - 109.176:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1335 r_free = 0.1855             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1335 r_free = 0.1855             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1855   ksol= 0.34   Bsol= 67.53   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,-2.08,-0.67,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1855   ksol= 0.33   Bsol= 70.31   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-2.36,-0.76,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305172                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.767448              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.421  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.779  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1334      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1855      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7510 = 1.77 * 0.50 * 5.3176 + 1.00 * 0.0517                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7169 = 1.77 * 0.50 * 5.2778 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7127 = 0.70 * 1.00 * 5.2778 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6900 = 0.70 * 1.00 * 5.2471 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.66  17.91    None  None   None       |
|    all(noH): 2823   0      0.00    109.66  17.91    None  None   None       |
|    Sol.    : 438    0      0.00    109.66  45.14    None  None   None       |
|    Mac.    : 2385   0      0.00    92.78   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.966: 1281   |   5:    54.832 -  65.798:   91        |
|      1:    10.966 -  21.933:  949   |   6:    65.798 -  76.765:   48        |
|      2:    21.933 -  32.899:  211   |   7:    76.765 -  87.731:   28        |
|      3:    32.899 -  43.866:  114   |   8:    87.731 -  98.697:    9        |
|      4:    43.866 -  54.832:   90   |   9:    98.697 - 109.664:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1727             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1726             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1726   ksol= 0.33   Bsol= 70.31   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-2.36,-0.76,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236674                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1720   ksol= 0.33   Bsol= 70.31   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-2.36,-0.76,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236299                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.843351              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.629  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324883              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.997  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1369 = 3.84 * 0.50 * 5.2476 + 1.00 * 0.0528                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0742 = 3.84 * 0.50 * 5.2003 + 1.00 * 0.0808                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7013 = 0.32 * 1.00 * 5.2003 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6916 = 0.32 * 1.00 * 5.1769 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.89   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    95.89   17.21    None  None   None       |
|    Sol.    : 438    0      0.98    95.89   41.91    None  None   None       |
|    Mac.    : 2385   0      0.00    93.60   12.68    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 -   9.589: 1012   |   5:    47.944 -  57.533:   93        |
|      1:     9.589 -  19.178: 1141   |   6:    57.533 -  67.122:   47        |
|      2:    19.178 -  28.767:  240   |   7:    67.122 -  76.711:   32        |
|      3:    28.767 -  38.356:  124   |   8:    76.711 -  86.300:   15        |
|      4:    38.356 -  47.944:  111   |   9:    86.300 -  95.889:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1632             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1632             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1632   ksol= 0.33   Bsol= 70.31   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,-2.36,-0.76,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167173                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7144 0.99   1431  161 0.0933 0.1343      5.3451      5.6038|
|  2:  4.7144 -  3.7602 0.99   1385  152 0.0834 0.1073      5.4335      5.6061|
|  3:  3.7602 -  3.2903 0.99   1346  148 0.1069 0.1643      5.4828      5.8675|
|  4:  3.2903 -  2.9919 0.99   1355  154 0.1283 0.1737        5.48      5.6265|
|  5:  2.9919 -  2.7788 0.99   1342  145 0.1328 0.1806      5.3323       5.628|
|  6:  2.7788 -  2.6158 0.99   1342  152 0.1285 0.1873      5.2173       5.458|
|  7:  2.6158 -  2.4854 0.99   1328  137 0.1287 0.1756       5.183      5.3728|
|  8:  2.4854 -  2.3776 0.98   1307  157 0.1214 0.1738      5.0954      5.3285|
|  9:  2.3776 -  2.2864 0.98   1316  145 0.1235 0.1931       5.076      5.3477|
| 10:  2.2864 -  2.2078 1.00   1315  158 0.1137 0.1656      4.9522      5.1794|
| 11:  2.2078 -  2.1389 0.98   1313  129 0.1123 0.1930      4.9391      5.3932|
| 12:  2.1389 -  2.0779 0.98   1299  156 0.1161 0.1781       4.881      5.1131|
| 13:  2.0779 -  2.0233 0.91   1201  125 0.1164 0.1642      4.8002      5.0045|
| 14:  2.0233 -  1.9741 0.26    350   40 0.1048 0.1605      4.6707       4.957|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7144  1431   161  0.94   9.06   0.97     0.95       7073.72|
|  2:  4.7144 -  3.7602  1385   152  0.95   8.16   1.01     1.00       9403.26|
|  3:  3.7602 -  3.2903  1346   148  0.93  11.70   1.02     1.02      10855.12|
|  4:  3.2903 -  2.9919  1355   154  0.90  15.40   1.01     0.98      11192.60|
|  5:  2.9919 -  2.7788  1342   145  0.90  15.90   1.00     0.99       8505.60|
|  6:  2.7788 -  2.6158  1342   152  0.89  16.49   0.98     0.97       7119.51|
|  7:  2.6158 -  2.4854  1328   137  0.90  15.72   1.00     0.98       6431.61|
|  8:  2.4854 -  2.3776  1307   157  0.90  16.16   0.98     0.95       5626.05|
|  9:  2.3776 -  2.2864  1316   145  0.89  16.75   1.00     0.96       5468.31|
| 10:  2.2864 -  2.2078  1315   158  0.90  16.14   1.00     0.97       4500.86|
| 11:  2.2078 -  2.1389  1313   129  0.90  15.89   0.98     0.93       4263.55|
| 12:  2.1389 -  2.0779  1299   156  0.90  16.35   1.00     1.01       4080.82|
| 13:  2.0779 -  2.0233  1201   125  0.89  17.14   0.99     0.97       3507.63|
| 14:  2.0233 -  1.9741   350    40  0.92  14.58   0.97     0.95       2676.70|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2676.70 max =        11192.60 mean =      6747.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1631   ksol= 0.32   Bsol= 60.82   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.38,-0.69,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167153                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1631   ksol= 0.32   Bsol= 60.82   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.38,-0.69,-0.00,-0.00,-0.00); trace/3= -1.54                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167153                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3073 -  4.7144 0.99   1431  161 0.0928 0.1337      5.3419      5.5975|
|  2:  4.7144 -  3.7602 0.99   1385  152 0.0829 0.1069      5.4286      5.6026|
|  3:  3.7602 -  3.2903 0.99   1346  148 0.1066 0.1636        5.48      5.8645|
|  4:  3.2903 -  2.9919 0.99   1355  154 0.1284 0.1741      5.4806      5.6279|
|  5:  2.9919 -  2.7788 0.99   1342  145 0.1332 0.1812      5.3345      5.6302|
|  6:  2.7788 -  2.6158 0.99   1342  152 0.1288 0.1875      5.2189      5.4595|
|  7:  2.6158 -  2.4854 0.99   1328  137 0.1288 0.1758      5.1849      5.3741|
|  8:  2.4854 -  2.3776 0.98   1307  157 0.1215 0.1743      5.0965      5.3293|
|  9:  2.3776 -  2.2864 0.98   1316  145 0.1235 0.1929      5.0769       5.347|
| 10:  2.2864 -  2.2078 1.00   1315  158 0.1138 0.1662      4.9533      5.1816|
| 11:  2.2078 -  2.1389 0.98   1313  129 0.1123 0.1931      4.9399       5.394|
| 12:  2.1389 -  2.0779 0.98   1299  156 0.1162 0.1784      4.8818      5.1144|
| 13:  2.0779 -  2.0233 0.91   1201  125 0.1165 0.1639      4.8004      5.0034|
| 14:  2.0233 -  1.9741 0.26    350   40 0.1048 0.1608      4.6704      4.9578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3073 -  4.7144  1431   161  0.94   9.02   0.97     0.95       7021.34|
|  2:  4.7144 -  3.7602  1385   152  0.95   8.11   1.01     1.00       9318.65|
|  3:  3.7602 -  3.2903  1346   148  0.93  11.64   1.02     1.02      10780.30|
|  4:  3.2903 -  2.9919  1355   154  0.90  15.38   1.01     0.98      11187.58|
|  5:  2.9919 -  2.7788  1342   145  0.90  15.94   1.00     0.99       8532.96|
|  6:  2.7788 -  2.6158  1342   152  0.89  16.53   0.98     0.97       7147.26|
|  7:  2.6158 -  2.4854  1328   137  0.90  15.75   1.00     0.98       6456.70|
|  8:  2.4854 -  2.3776  1307   157  0.90  16.18   0.98     0.95       5639.06|
|  9:  2.3776 -  2.2864  1316   145  0.89  16.76   1.00     0.95       5476.65|
| 10:  2.2864 -  2.2078  1315   158  0.90  16.17   1.00     0.97       4511.90|
| 11:  2.2078 -  2.1389  1313   129  0.90  15.91   0.98     0.93       4276.15|
| 12:  2.1389 -  2.0779  1299   156  0.90  16.38   1.00     1.01       4091.57|
| 13:  2.0779 -  2.0233  1201   125  0.89  17.15   0.99     0.97       3510.25|
| 14:  2.0233 -  1.9741   350    40  0.92  14.58   0.97     0.95       2675.58|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2675.58 max =        11187.58 mean =      6740.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.38 mean =        14.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.096)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.89   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    95.89   17.22    None  None   None       |
|    Sol.    : 438    0      0.99    95.89   41.91    None  None   None       |
|    Mac.    : 2385   0      0.00    93.61   12.68    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 -   9.592: 1012   |   5:    47.947 -  57.536:   93        |
|      1:     9.592 -  19.181: 1141   |   6:    57.536 -  67.125:   47        |
|      2:    19.181 -  28.770:  240   |   7:    67.125 -  76.714:   32        |
|      3:    28.770 -  38.358:  124   |   8:    76.714 -  86.303:   15        |
|      4:    38.358 -  47.947:  111   |   9:    86.303 -  95.892:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.723 - 4.994
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 338
   mapped sites are within: 0.723 - 4.994

peak=    6.429 closest distance to " NE2 GLN A  11 " =    1.227
peak=    5.229 closest distance to " CB  GLN A 223 " =    1.535
peak=    5.201 closest distance to " O   HOH Z 144 " =    1.766
peak=    5.198 closest distance to " O   HOH Z 232 " =    2.219
peak=    5.068 closest distance to " O   HOH Z 111 " =    1.847
peak=    5.066 closest distance to " O   HOH Z   7 " =    1.470
peak=    5.016 closest distance to " CG  PRO A  54 " =    1.285
peak=    4.970 closest distance to " O   HOH Z 417 " =    1.550
peak=    4.936 closest distance to " CB  SER A  63 " =    1.318
peak=    4.865 closest distance to " O   HOH Z 126 " =    1.578
peak=    4.812 closest distance to " O   HOH Z 369 " =    2.086
peak=    4.684 closest distance to " O   HOH Z 298 " =    2.259
peak=    4.655 closest distance to " O   HOH Z 222 " =    1.250
peak=    4.637 closest distance to " O   HOH Z 423 " =    1.991
peak=    4.626 closest distance to " O   HOH Z 425 " =    1.521
peak=    4.523 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.476 closest distance to " O   HOH Z 183 " =    1.578
peak=    4.443 closest distance to " O   HOH Z   2 " =    1.697
peak=    4.427 closest distance to " C   PRO A 198 " =    1.556
peak=    4.420 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.420 closest distance to " O   HOH Z 126 " =    1.998
peak=    4.399 closest distance to " CB  LEU A 228 " =    1.073
peak=    4.393 closest distance to " O   HOH Z  63 " =    1.443
peak=    4.355 closest distance to " O   HOH Z 427 " =    2.662
peak=    4.310 closest distance to " O   HOH Z 287 " =    2.274
peak=    4.234 closest distance to " CB  ARG A 190 " =    1.596
peak=    4.231 closest distance to " O   HOH Z 437 " =    1.685
peak=    4.217 closest distance to " NH1AARG A 145 " =    1.270
peak=    4.207 closest distance to " CG  PRO A 213 " =    1.282
peak=    4.196 closest distance to " O   HOH Z 380 " =    1.759
peak=    4.164 closest distance to " O   HOH Z 180 " =    2.087
peak=    4.154 closest distance to " CB  PRO A  54 " =    0.952
peak=    4.137 closest distance to " CB  ARG A 275 " =    1.015
peak=    4.128 closest distance to " O   HOH Z 272 " =    1.850
peak=    4.089 closest distance to " O   HOH Z  58 " =    1.893
peak=    4.084 closest distance to " O   HOH Z 133 " =    2.503
peak=    4.079 closest distance to " ND1 HIS A  86 " =    1.795
peak=    4.064 closest distance to " O   HOH Z  78 " =    1.710
peak=    4.061 closest distance to " CB  GLU A 128 " =    1.042
peak=    4.059 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.055 closest distance to " O   HOH Z 193 " =    1.740
peak=    4.043 closest distance to " ND2 ASN A 187 " =    1.408
peak=    4.021 closest distance to " CE  LYS A  76 " =    0.898
peak=    4.014 closest distance to " CG2 THR A 221 " =    0.968
peak=    4.013 closest distance to " CB  TRP A 266 " =    1.037
peak=    4.009 closest distance to " CG  LEU A 167 " =    1.281
peak=    4.006 closest distance to " O   HOH Z 316 " =    3.096
peak=    4.002 closest distance to " CD  ARG A 159 " =    0.790
peak=    3.976 closest distance to " CD  ARG A  66 " =    2.078
peak=    3.971 closest distance to " O   HOH Z   1 " =    1.890
peak=    3.953 closest distance to " CB  ASP A 132 " =    4.033
peak=    3.949 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.939 closest distance to " O   HOH Z  21 " =    1.728
peak=    3.931 closest distance to " CB  SER A 212 " =    1.162
peak=    3.917 closest distance to " O   HOH Z   9 " =    2.084
peak=    3.906 closest distance to " O   HOH Z 250 " =    1.456
peak=    3.903 closest distance to " CG  TRP A 179 " =    2.249
peak=    3.901 closest distance to " CB  SER A   3 " =    1.543
peak=    3.887 closest distance to " O   HOH Z 258 " =    2.101
peak=    3.867 closest distance to " O   HOH Z 214 " =    2.058
peak=    3.862 closest distance to " CZ  PHE A 218 " =    1.047
peak=    3.847 closest distance to " CA  ALA A 158 " =    1.087
peak=    3.840 closest distance to " O   HOH Z   1 " =    1.658
peak=    3.833 closest distance to " O   HOH Z  78 " =    1.990
peak=    3.832 closest distance to " CB  ARG A  79 " =    1.354
peak=    3.831 closest distance to " CD1 LEU A 300 " =    1.248
peak=    3.827 closest distance to " O   HOH Z 209 " =    2.325
peak=    3.823 closest distance to " O   HOH Z 158 " =    2.929
peak=    3.811 closest distance to " O   HOH Z  61 " =    1.551
peak=    3.800 closest distance to " O   HOH Z 132 " =    2.358
peak=    3.798 closest distance to " CD ALYS A 290 " =    0.999
peak=    3.781 closest distance to " CB  ASN A 187 " =    1.013
peak=    3.779 closest distance to " O   HOH Z 391 " =    2.862
peak=    3.769 closest distance to " O   HOH Z  40 " =    1.933
peak=    3.769 closest distance to " CA  MET A  40 " =    1.248
peak=    3.765 closest distance to " CB  ASN A 142 " =    0.919
peak=    3.764 closest distance to " CB  TRP A 150 " =    1.090
peak=    3.763 closest distance to " O   HOH Z 368 " =    1.960
peak=    3.761 closest distance to " CG BARG A 275 " =    1.488
peak=    3.759 closest distance to " O   HOH Z 135 " =    1.703
peak=    3.749 closest distance to " N   ALA A   1 " =    2.083
peak=    3.746 closest distance to " N   ASN A 127 " =    1.305
peak=    3.745 closest distance to " CB  ASP A 124 " =    0.766
peak=    3.743 closest distance to " O   HOH Z 261 " =    1.850
peak=    3.740 closest distance to " CB  GLU A 152 " =    1.198
peak=    3.739 closest distance to " CA  SER A  87 " =    1.024
peak=    3.734 closest distance to " O   TYR A 116 " =    1.288
peak=    3.726 closest distance to " CB  SER A 216 " =    0.960
peak=    3.725 closest distance to " CB  VAL A 265 " =    1.429
peak=    3.723 closest distance to " CA  ARG A 102 " =    1.149
peak=    3.720 closest distance to " CA  TYR A  30 " =    1.052
peak=    3.697 closest distance to " O   HOH Z  10 " =    1.791
peak=    3.675 closest distance to " O   ASN A 209 " =    1.429
peak=    3.667 closest distance to " O   HOH Z 362 " =    2.364
peak=    3.667 closest distance to " O   HOH Z 325 " =    4.009
peak=    3.666 closest distance to " O   HOH Z 213 " =    2.129
peak=    3.660 closest distance to " CG2 VAL A 257 " =    0.933
peak=    3.660 closest distance to " O   HOH Z 373 " =    1.564
peak=    3.646 closest distance to " O   HOH Z 403 " =    1.310
peak=    3.644 closest distance to " CB  VAL A 202 " =    1.660
peak=    3.636 closest distance to " O   HOH Z 409 " =    2.317
peak=    3.634 closest distance to " CG  PRO A 280 " =    0.723
peak=    3.631 closest distance to " O   HOH Z 193 " =    1.796
peak=    3.623 closest distance to " O   HOH Z 217 " =    2.904
peak=    3.613 closest distance to " OH  TYR A 186 " =    1.079
peak=    3.613 closest distance to " O   HOH Z 116 " =    1.816
peak=    3.603 closest distance to " O   HOH Z 128 " =    2.203
peak=    3.601 closest distance to " O   HOH Z 346 " =    1.672
peak=    3.599 closest distance to " CB  TYR A 169 " =    0.818
peak=    3.595 closest distance to " CA  GLY A 241 " =    0.810
peak=    3.593 closest distance to " O   HOH Z 145 " =    1.755
peak=    3.592 closest distance to " O   HOH Z  59 " =    1.952
peak=    3.591 closest distance to " CB  MET A  47 " =    1.141
peak=    3.578 closest distance to " CB  ASP A 140 " =    0.855
peak=    3.577 closest distance to " CB  GLU A 277 " =    3.663
peak=    3.571 closest distance to " O   HOH Z 234 " =    3.862
peak=    3.570 closest distance to " O   HOH Z 326 " =    2.359
peak=    3.570 closest distance to " O   HOH Z 133 " =    1.668
peak=    3.569 closest distance to " OG  SER A  62 " =    3.031
peak=    3.568 closest distance to " CA  SER A  95 " =    0.992
peak=    3.565 closest distance to " O   HOH Z 365 " =    2.803
peak=    3.563 closest distance to " CA  TYR A 116 " =    1.390
peak=    3.560 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    3.558 closest distance to " CD2 TRP A 179 " =    1.244
peak=    3.558 closest distance to " CB  LEU A 237 " =    0.813
peak=    3.557 closest distance to " O   HOH Z  85 " =    2.185
peak=    3.553 closest distance to " O   HOH Z 368 " =    4.345
peak=    3.551 closest distance to " CB  ASN A  39 " =    0.957
peak=    3.547 closest distance to " CA  THR A 264 " =    0.855
peak=    3.542 closest distance to " CD  GLN A 240 " =    1.680
peak=    3.540 closest distance to " CB  ALA A 104 " =    0.739
peak=    3.539 closest distance to " O   HOH Z 188 " =    2.074
peak=    3.536 closest distance to " O   HOH Z 170 " =    1.201
peak=    3.535 closest distance to " O   HOH Z 193 " =    2.221
peak=    3.534 closest distance to " O   HOH Z  98 " =    1.852
peak=    3.532 closest distance to " O   HOH Z  80 " =    1.489
peak=    3.532 closest distance to " O   HOH Z 411 " =    3.556
peak=    3.531 closest distance to " CG1 ILE A 151 " =    1.080
peak=    3.526 closest distance to " O   HOH Z 207 " =    2.216
peak=    3.519 closest distance to " O   HOH Z 419 " =    1.903
peak=    3.519 closest distance to " CB  SER A 276 " =    1.140
peak=    3.518 closest distance to " CA  PRO A  54 " =    1.372
peak=    3.517 closest distance to " O   MET A 105 " =    1.795
peak=    3.510 closest distance to " CA  ALA A  51 " =    0.964
peak=    3.508 closest distance to " CD2 LEU A 255 " =    1.744
peak=    3.506 closest distance to " O   HOH Z 147 " =    1.770
peak=    3.506 closest distance to " CZ3 TRP A 123 " =    1.325
peak=    3.505 closest distance to " CD  LYS A 166 " =    1.464
peak=    3.505 closest distance to " CB  TYR A 116 " =    0.957
peak=    3.496 closest distance to " O   HOH Z 406 " =    1.617
peak=    3.496 closest distance to " CD1 ILE A  33 " =    1.695
peak=    3.491 closest distance to " O   HOH Z 290 " =    1.078
peak=    3.490 closest distance to " OD1 ASN A  69 " =    2.617
peak=    3.486 closest distance to " CA  ALA A 233 " =    1.230
peak=    3.484 closest distance to " CA  ALA A 160 " =    0.949
peak=    3.479 closest distance to " CA  ARG A 195 " =    1.329
peak=    3.479 closest distance to " NE AARG A 275 " =    1.457
peak=    3.476 closest distance to " O   HOH Z 218 " =    4.663
peak=    3.475 closest distance to " O   HOH Z 148 " =    3.413
peak=    3.472 closest distance to " CB  ALA A   1 " =    4.653
peak=    3.471 closest distance to " O   HOH Z 184 " =    1.517
peak=    3.470 closest distance to " CA  VAL A 125 " =    1.186
peak=    3.470 closest distance to " CA  GLU A  46 " =    0.834
peak=    3.466 closest distance to " O   HOH Z 302 " =    1.735
peak=    3.464 closest distance to " CG1 VAL A 189 " =    1.942
peak=    3.464 closest distance to " O   HOH Z 286 " =    2.321
peak=    3.461 closest distance to " CB  ARG A 138 " =    0.991
peak=    3.455 closest distance to " CA  ILE A 234 " =    1.053
peak=    3.451 closest distance to " O   HOH Z 389 " =    1.930
peak=    3.451 closest distance to " CG  ARG A 159 " =    0.847
peak=    3.447 closest distance to " O   HOH Z 115 " =    1.869
peak=    3.445 closest distance to " CB  TYR A 169 " =    0.988
peak=    3.445 closest distance to " O   HOH Z 285 " =    2.442
peak=    3.444 closest distance to " O   HOH Z  30 " =    1.747
peak=    3.443 closest distance to " N   PHE A 130 " =    1.210
peak=    3.441 closest distance to " O   HOH Z 432 " =    1.723
peak=    3.439 closest distance to " CG  PRO A 243 " =    1.081
peak=    3.437 closest distance to " O   HOH Z 359 " =    4.112
peak=    3.429 closest distance to " O   HOH Z  91 " =    2.521
peak=    3.425 closest distance to " CA  LEU A 101 " =    1.433
peak=    3.422 closest distance to " CG  PRO A  90 " =    1.342
peak=    3.419 closest distance to " OG BSER A  99 " =    2.334
peak=    3.418 closest distance to " O   HOH Z  44 " =    2.674
peak=    3.413 closest distance to " O   HOH Z 130 " =    3.794
peak=    3.403 closest distance to " O   HOH Z 189 " =    2.786
peak=    3.403 closest distance to " O   HOH Z 286 " =    2.335
peak=    3.401 closest distance to " O   HOH Z 172 " =    2.915
peak=    3.401 closest distance to " CB  ILE A 120 " =    1.391
peak=    3.399 closest distance to " OD2 ASP A  65 " =    3.063
peak=    3.398 closest distance to " CG2 VAL A 197 " =    1.125
peak=    3.394 closest distance to " CB  THR A  82 " =    1.251
peak=    3.393 closest distance to " C   ARG A 145 " =    1.697
peak=    3.391 closest distance to " CG  LYS A  76 " =    1.889
peak=    3.389 closest distance to " O   HOH Z  57 " =    1.331
peak=    3.388 closest distance to " CA  MET A 105 " =    0.933
peak=    3.374 closest distance to " N   TYR A  15 " =    0.886
peak=    3.374 closest distance to " O   HOH Z 112 " =    1.385
peak=    3.369 closest distance to " CA  ALA A 291 " =    0.902
peak=    3.366 closest distance to " CB  LEU A 143 " =    1.132
peak=    3.360 closest distance to " O   HOH Z 422 " =    2.697
peak=    3.359 closest distance to " OD1 ASN A 217 " =    1.501
peak=    3.358 closest distance to " OD1BASN A 224 " =    2.325
peak=    3.356 closest distance to " O   HOH Z 265 " =    1.884
peak=    3.355 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.355 closest distance to " NE  ARG A  79 " =    1.165
peak=    3.353 closest distance to " O   HOH Z 108 " =    2.617
peak=    3.353 closest distance to " CA  ALA A 154 " =    0.989
peak=    3.348 closest distance to " CB  GLU A  46 " =    0.958
peak=    3.346 closest distance to " O   HOH Z  64 " =    2.327
peak=    3.344 closest distance to " CE3 TRP A 274 " =    1.256
peak=    3.341 closest distance to " O   HOH Z 327 " =    2.034
peak=    3.340 closest distance to " O   HOH Z   9 " =    1.454
peak=    3.339 closest distance to " O   HOH Z 128 " =    1.402
peak=    3.339 closest distance to " CB  GLN A  88 " =    1.294
peak=    3.337 closest distance to " O   HOH Z  68 " =    2.085
peak=    3.337 closest distance to " CG  GLN A  88 " =    1.064
peak=    3.332 closest distance to " O   HOH Z 305 " =    3.749
peak=    3.329 closest distance to " O   HOH Z 371 " =    2.066
peak=    3.329 closest distance to " CG2 ILE A  20 " =    1.463
peak=    3.328 closest distance to " NH2 ARG A 219 " =    1.834
peak=    3.327 closest distance to " O   HOH Z 185 " =    2.044
peak=    3.321 closest distance to " CG  GLN A 278 " =    1.355
peak=    3.319 closest distance to " ND2 ASN A 110 " =    1.694
peak=    3.315 closest distance to " O   ASN A  74 " =    1.543
peak=    3.314 closest distance to " O   HOH Z 176 " =    2.094
peak=    3.311 closest distance to " CB  ALA A 114 " =    1.452
peak=    3.310 closest distance to " O   HOH Z 352 " =    1.695
peak=    3.308 closest distance to " CD  ARG A 269 " =    0.973
peak=    3.307 closest distance to " O   HOH Z 153 " =    1.662
peak=    3.301 closest distance to " CB  GLU A 236 " =    1.227
peak=    3.298 closest distance to " CA  ASP A 124 " =    0.780
peak=    3.298 closest distance to " O   HOH Z 175 " =    3.709
peak=    3.294 closest distance to " OD2 ASP A 286 " =    2.874
peak=    3.293 closest distance to " O   HOH Z 345 " =    3.551
peak=    3.293 closest distance to " O   HOH Z 282 " =    1.948
peak=    3.292 closest distance to " NE2 GLN A  73 " =    3.922
peak=    3.291 closest distance to " CG1 ILE A  33 " =    1.201
peak=    3.289 closest distance to " N   SER A 271 " =    0.908
peak=    3.289 closest distance to " CD  PRO A 243 " =    1.737
peak=    3.287 closest distance to " CG  GLN A 144 " =    0.857
peak=    3.286 closest distance to " C   GLU A 277 " =    1.413
peak=    3.286 closest distance to " O   HOH Z 280 " =    3.082
peak=    3.284 closest distance to " O   HOH Z 273 " =    2.838
peak=    3.277 closest distance to " CG  GLN A  89 " =    1.528
peak=    3.274 closest distance to " O   ALA A 291 " =    1.466
peak=    3.272 closest distance to " O   HOH Z 394 " =    1.641
peak=    3.271 closest distance to " CB  PRO A  90 " =    1.211
peak=    3.268 closest distance to " OG  SER A  62 " =    3.134
peak=    3.266 closest distance to " O   HOH Z  68 " =    1.701
peak=    3.266 closest distance to " NH2AARG A 190 " =    1.769
peak=    3.266 closest distance to " O  BHOH Z 338 " =    2.234
peak=    3.263 closest distance to " O   HOH Z 434 " =    1.371
peak=    3.259 closest distance to " CA  LYS A 290 " =    1.399
peak=    3.256 closest distance to " CB  ALA A  34 " =    1.197
peak=    3.255 closest distance to " O   HOH Z 386 " =    2.997
peak=    3.255 closest distance to " O   THR A 182 " =    1.542
peak=    3.254 closest distance to " O   HOH Z 189 " =    3.277
peak=    3.254 closest distance to " CG  MET A 113 " =    1.545
peak=    3.249 closest distance to " CA  ASN A  74 " =    1.318
peak=    3.247 closest distance to " CG2 ILE A 151 " =    0.864
peak=    3.246 closest distance to " O   HOH Z 109 " =    2.579
peak=    3.246 closest distance to " OG BSER A 164 " =    2.429
peak=    3.245 closest distance to " CB  MET A  40 " =    0.824
peak=    3.244 closest distance to " CD2 LEU A 297 " =    0.931
peak=    3.243 closest distance to " CG  GLU A 277 " =    1.943
peak=    3.234 closest distance to " CB  ASP A 171 " =    1.187
peak=    3.228 closest distance to " O   HOH Z 329 " =    4.004
peak=    3.227 closest distance to " O   HOH Z 369 " =    1.603
peak=    3.227 closest distance to " O   HOH Z 371 " =    2.726
peak=    3.225 closest distance to " CB  ALA A 248 " =    0.961
peak=    3.221 closest distance to " O   HOH Z 154 " =    1.980
peak=    3.217 closest distance to " CB  LEU A 300 " =    0.927
peak=    3.217 closest distance to " O   HOH Z 345 " =    1.751
peak=    3.214 closest distance to " CE2 TYR A 186 " =    0.893
peak=    3.210 closest distance to " N   GLU A   2 " =    1.373
peak=    3.208 closest distance to " CA  ASP A 140 " =    1.317
peak=    3.207 closest distance to " O   HOH Z 132 " =    3.731
peak=    3.206 closest distance to " CB  ALA A   9 " =    1.642
peak=    3.201 closest distance to " O   HOH Z 386 " =    3.118
peak=    3.201 closest distance to " CG1 VAL A 153 " =    0.939
peak=    3.198 closest distance to " CB  ARG A 139 " =    1.065
peak=    3.198 closest distance to " O   HOH Z 291 " =    2.051
peak=    3.196 closest distance to " O   HOH Z 407 " =    1.545
peak=    3.196 closest distance to " CB  SER A 210 " =    0.848
peak=    3.195 closest distance to " O   HOH Z 116 " =    3.138
peak=    3.189 closest distance to " CA  THR A 221 " =    0.961
peak=    3.188 closest distance to " NH1 ARG A  56 " =    1.132
peak=    3.183 closest distance to " O   THR A 220 " =    1.453
peak=    3.180 closest distance to " N   ARG A 156 " =    1.348
peak=    3.180 closest distance to " O   HOH Z 359 " =    1.435
peak=    3.179 closest distance to " CB  TYR A  30 " =    1.137
peak=    3.175 closest distance to " O   HOH Z 124 " =    1.914
peak=    3.175 closest distance to " O   LEU A 300 " =    1.437
peak=    3.174 closest distance to " CB  SER A  99 " =    0.997
peak=    3.174 closest distance to " CG  LYS A 119 " =    1.199
peak=    3.173 closest distance to " O   HOH Z  88 " =    3.566
peak=    3.172 closest distance to " CA  ALA A 299 " =    0.900
peak=    3.169 closest distance to " OG BSER A 134 " =    3.091
peak=    3.168 closest distance to " O   HOH Z 368 " =    3.723
peak=    3.166 closest distance to " CA  TYR A 186 " =    1.565
peak=    3.165 closest distance to " O   HOH Z 235 " =    1.668
peak=    3.160 closest distance to " N   CYS A 260 " =    0.846
peak=    3.152 closest distance to " CD2 PHE A  59 " =    1.722
peak=    3.149 closest distance to " CA  ASN A 127 " =    1.109
peak=    3.148 closest distance to " CA  TRP A  92 " =    1.129
peak=    3.147 closest distance to " CB  PRO A 243 " =    1.264
peak=    3.147 closest distance to " O   HOH Z  53 " =    2.481
peak=    3.146 closest distance to " CB  ASN A 285 " =    0.862
peak=    3.146 closest distance to " ND1 HIS A  81 " =    1.653
peak=    3.143 closest distance to " O   HOH Z 407 " =    1.935
peak=    3.140 closest distance to " O   HOH Z 122 " =    1.704
peak=    3.137 closest distance to " NH1 ARG A  66 " =    1.684
peak=    3.127 closest distance to " O   HOH Z 423 " =    2.028
peak=    3.121 closest distance to " CG BARG A 102 " =    1.888
peak=    3.114 closest distance to " O   HOH Z 380 " =    4.994
peak=    3.113 closest distance to " NE2 GLN A  58 " =    3.869
peak=    3.113 closest distance to " CB  THR A 157 " =    1.204
peak=    3.111 closest distance to " O   HOH Z 274 " =    2.056
peak=    3.102 closest distance to " CB  GLU A 152 " =    1.453
peak=    3.101 closest distance to " O   HOH Z 149 " =    2.145
peak=    3.100 closest distance to " O   HOH Z 356 " =    2.654
peak=    3.098 closest distance to " O   HOH Z  29 " =    2.332
peak=    3.094 closest distance to " O   HOH Z 415 " =    3.851
peak=    3.084 closest distance to " CA  ILE A 106 " =    0.839
peak=    3.083 closest distance to " O   HOH Z 425 " =    2.028
peak=    3.078 closest distance to " NH2BARG A 145 " =    1.068
peak=    3.076 closest distance to " CB  ALA A  43 " =    0.786
peak=    3.070 closest distance to " NE2 HIS A 207 " =    1.286
peak=    3.068 closest distance to " O   HOH Z 153 " =    3.764
peak=    3.062 closest distance to " CA  TYR A  30 " =    1.048
peak=    3.055 closest distance to " CE3 TRP A  85 " =    0.951
peak=    3.053 closest distance to " CG  GLU A 277 " =    3.549
peak=    3.043 closest distance to " CB  ALA A 184 " =    1.075
peak=    3.037 closest distance to " NE2 GLN A  73 " =    1.732
peak=    3.019 closest distance to " O   HOH Z 113 " =    2.054

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.530 - 5.740
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 208
   mapped sites are within: 0.768 - 5.740

peak=   -4.542 closest distance to " O   HOH Z 377 " =    1.776
peak=   -4.453 closest distance to " CB  PRO A 243 " =    2.549
peak=   -4.435 closest distance to " O   HOH Z  52 " =    1.169
peak=   -4.352 closest distance to " CD  ARG A  14 " =    3.444
peak=   -4.200 closest distance to " O   PRO A 198 " =    1.287
peak=   -4.184 closest distance to " O   HOH Z 231 " =    2.021
peak=   -4.172 closest distance to " O   HOH Z  38 " =    1.233
peak=   -4.122 closest distance to " CD  ARG A 156 " =    2.150
peak=   -4.117 closest distance to " C   ALA A 158 " =    1.582
peak=   -4.092 closest distance to " N   ALA A  43 " =    2.504
peak=   -4.040 closest distance to " CD1 TYR A 247 " =    2.878
peak=   -3.962 closest distance to " CG  GLN A 223 " =    2.337
peak=   -3.939 closest distance to " CZ3 TRP A 179 " =    1.146
peak=   -3.938 closest distance to " O   HOH Z 389 " =    2.122
peak=   -3.891 closest distance to " CB  ASP A  27 " =    2.466
peak=   -3.887 closest distance to " CB  TRP A  85 " =    2.486
peak=   -3.884 closest distance to " O   HOH Z 407 " =    3.403
peak=   -3.840 closest distance to " CG2 ILE A  49 " =    2.690
peak=   -3.830 closest distance to " O   HOH Z 290 " =    1.193
peak=   -3.827 closest distance to " CA  GLY A  98 " =    1.877
peak=   -3.799 closest distance to " CB  ALA A  43 " =    2.518
peak=   -3.787 closest distance to " CB  PRO A  54 " =    2.458
peak=   -3.776 closest distance to " O   HOH Z 111 " =    1.761
peak=   -3.771 closest distance to " OG BSER A 134 " =    1.370
peak=   -3.770 closest distance to " CG  MET A 105 " =    0.962
peak=   -3.763 closest distance to " O   HOH Z 351 " =    1.638
peak=   -3.759 closest distance to " O   HOH Z 266 " =    5.180
peak=   -3.751 closest distance to " CD2 LEU A 143 " =    2.614
peak=   -3.751 closest distance to " CB  ALA A   9 " =    2.432
peak=   -3.735 closest distance to " O   HOH Z 337 " =    1.353
peak=   -3.734 closest distance to " CG1 VAL A 250 " =    2.674
peak=   -3.709 closest distance to " CD  LYS A 289 " =    2.336
peak=   -3.708 closest distance to " CD  GLN A  88 " =    0.869
peak=   -3.706 closest distance to " CA  GLY A 241 " =    2.313
peak=   -3.699 closest distance to " OE1 GLN A  88 " =    1.160
peak=   -3.684 closest distance to " C   LEU A 143 " =    1.520
peak=   -3.676 closest distance to " O   HOH Z 281 " =    2.744
peak=   -3.668 closest distance to " OD1 ASP A 191 " =    1.917
peak=   -3.663 closest distance to " O   HOH Z 211 " =    1.189
peak=   -3.656 closest distance to " O   HOH Z 313 " =    1.740
peak=   -3.653 closest distance to " NH2AARG A 275 " =    5.740
peak=   -3.653 closest distance to " O   HOH Z 435 " =    2.930
peak=   -3.630 closest distance to " ND2 ASN A 249 " =    2.116
peak=   -3.624 closest distance to " O   PRO A 243 " =    2.316
peak=   -3.611 closest distance to " O   HOH Z  65 " =    1.268
peak=   -3.608 closest distance to " O   HOH Z  73 " =    1.906
peak=   -3.608 closest distance to " C   LEU A 222 " =    0.810
peak=   -3.603 closest distance to " CA  GLY A 203 " =    2.337
peak=   -3.596 closest distance to " NH1AARG A 275 " =    2.004
peak=   -3.595 closest distance to " CB  ALA A 291 " =    2.251
peak=   -3.595 closest distance to " O   VAL A  67 " =    2.781
peak=   -3.594 closest distance to " CA  GLY A 241 " =    3.060
peak=   -3.591 closest distance to " O   HOH Z 131 " =    4.223
peak=   -3.584 closest distance to " CG2 THR A 178 " =    2.251
peak=   -3.563 closest distance to " OXT GLY A 302 " =    3.196
peak=   -3.561 closest distance to " CE2 TYR A  30 " =    2.649
peak=   -3.559 closest distance to " O   HOH Z 166 " =    1.218
peak=   -3.557 closest distance to " O   ALA A  10 " =    1.745
peak=   -3.556 closest distance to " CG1 VAL A 112 " =    2.998
peak=   -3.552 closest distance to " O   VAL A 189 " =    2.478
peak=   -3.536 closest distance to " O   HOH Z 185 " =    2.160
peak=   -3.524 closest distance to " O   GLY A 211 " =    1.332
peak=   -3.522 closest distance to " CE BMET A  47 " =    1.469
peak=   -3.522 closest distance to " CG2 THR A  18 " =    2.903
peak=   -3.517 closest distance to " ND2 ASN A  45 " =    2.101
peak=   -3.516 closest distance to " O   HOH Z 152 " =    5.077
peak=   -3.512 closest distance to " ND2 ASN A  45 " =    1.363
peak=   -3.508 closest distance to " O   SER A 135 " =    1.427
peak=   -3.506 closest distance to " CD1 LEU A 101 " =    2.327
peak=   -3.499 closest distance to " O   PHE A 218 " =    1.366
peak=   -3.497 closest distance to " CG2 ILE A 151 " =    2.629
peak=   -3.484 closest distance to " O   HOH Z 198 " =    1.662
peak=   -3.484 closest distance to " O   VAL A 125 " =    2.283
peak=   -3.482 closest distance to " CG1 VAL A 112 " =    2.542
peak=   -3.480 closest distance to " O   HOH Z 282 " =    4.606
peak=   -3.473 closest distance to " O   SER A  22 " =    2.728
peak=   -3.463 closest distance to " CD2 TYR A 293 " =    1.935
peak=   -3.462 closest distance to " O   HOH Z  22 " =    2.339
peak=   -3.459 closest distance to " C   ASN A 285 " =    2.451
peak=   -3.456 closest distance to " O   HOH Z 118 " =    1.079
peak=   -3.455 closest distance to " CB  CYS A 254 " =    2.107
peak=   -3.442 closest distance to " O   HOH Z 198 " =    2.021
peak=   -3.442 closest distance to " O   HOH Z  51 " =    1.165
peak=   -3.436 closest distance to " O   HOH Z 275 " =    1.751
peak=   -3.435 closest distance to " NH2 ARG A  79 " =    2.012
peak=   -3.432 closest distance to " O   HOH Z   9 " =    1.908
peak=   -3.432 closest distance to " O   HOH Z 426 " =    1.669
peak=   -3.429 closest distance to " O   HOH Z 243 " =    1.981
peak=   -3.423 closest distance to " CE2 PHE A 218 " =    2.466
peak=   -3.423 closest distance to " CZ BARG A 275 " =    1.794
peak=   -3.420 closest distance to " ND2 ASN A  69 " =    1.670
peak=   -3.414 closest distance to " OD1 ASP A 171 " =    1.655
peak=   -3.407 closest distance to " O   HOH Z  60 " =    1.804
peak=   -3.406 closest distance to " OE1 GLN A  58 " =    3.255
peak=   -3.403 closest distance to " NZ  LYS A 166 " =    1.245
peak=   -3.399 closest distance to " O   HOH Z 184 " =    1.835
peak=   -3.396 closest distance to " O   HOH Z  53 " =    1.741
peak=   -3.387 closest distance to " N   ASP A 171 " =    2.439
peak=   -3.383 closest distance to " O   PRO A 163 " =    2.017
peak=   -3.380 closest distance to " OG BSER A 134 " =    1.733
peak=   -3.372 closest distance to " OH  TYR A 172 " =    1.711
peak=   -3.365 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.362 closest distance to " CD1 PHE A  59 " =    1.966
peak=   -3.357 closest distance to " CE  MET A 105 " =    2.449
peak=   -3.349 closest distance to " CG  TRP A 266 " =    1.732
peak=   -3.347 closest distance to " O   VAL A 197 " =    1.780
peak=   -3.345 closest distance to " O   HOH Z 384 " =    2.940
peak=   -3.342 closest distance to " O   HOH Z 118 " =    1.429
peak=   -3.336 closest distance to " N   SER A 141 " =    1.884
peak=   -3.330 closest distance to " O   HOH Z 406 " =    2.160
peak=   -3.329 closest distance to " CG  PRO A 163 " =    2.445
peak=   -3.327 closest distance to " O   GLY A  17 " =    1.218
peak=   -3.322 closest distance to " OG  SER A  87 " =    1.303
peak=   -3.318 closest distance to " O   HOH Z 298 " =    1.198
peak=   -3.313 closest distance to " NE  ARG A  36 " =    1.934
peak=   -3.310 closest distance to " CD1 TRP A 179 " =    1.083
peak=   -3.309 closest distance to " N   THR A 157 " =    1.534
peak=   -3.306 closest distance to " CB  ASP A 132 " =    2.375
peak=   -3.303 closest distance to " O   ILE A  49 " =    1.688
peak=   -3.301 closest distance to " O   ASN A 301 " =    1.331
peak=   -3.300 closest distance to " O   HOH Z 357 " =    1.960
peak=   -3.296 closest distance to " O   HOH Z  90 " =    2.905
peak=   -3.292 closest distance to " O   HOH Z 241 " =    1.298
peak=   -3.292 closest distance to " ND2 ASN A 187 " =    1.651
peak=   -3.287 closest distance to " O   HOH Z   1 " =    1.475
peak=   -3.281 closest distance to " O   HOH Z 394 " =    1.482
peak=   -3.276 closest distance to " O   HOH Z 266 " =    5.009
peak=   -3.273 closest distance to " CA  SER A  62 " =    2.727
peak=   -3.269 closest distance to " CB  ALA A 248 " =    2.414
peak=   -3.269 closest distance to " CG1 VAL A 112 " =    2.638
peak=   -3.267 closest distance to " OG  SER A 245 " =    1.341
peak=   -3.266 closest distance to " CG2BVAL A  41 " =    1.161
peak=   -3.257 closest distance to " O   HOH Z  43 " =    1.457
peak=   -3.254 closest distance to " CG1 VAL A  78 " =    2.466
peak=   -3.250 closest distance to " CD  PRO A 213 " =    2.141
peak=   -3.248 closest distance to " CB  PRO A 163 " =    2.483
peak=   -3.243 closest distance to " C   GLY A  13 " =    0.896
peak=   -3.243 closest distance to " CB  SER A  63 " =    3.420
peak=   -3.231 closest distance to " O   HOH Z 372 " =    2.546
peak=   -3.231 closest distance to " CB  SER A 245 " =    2.299
peak=   -3.226 closest distance to " O   HOH Z  32 " =    1.695
peak=   -3.223 closest distance to " O   PRO A 198 " =    1.407
peak=   -3.221 closest distance to " CG  ARG A 269 " =    2.564
peak=   -3.219 closest distance to " CB  ASP A 286 " =    2.243
peak=   -3.216 closest distance to " O   HOH Z 350 " =    1.312
peak=   -3.215 closest distance to " OH  TYR A 247 " =    1.807
peak=   -3.213 closest distance to " CD1 LEU A 228 " =    2.396
peak=   -3.211 closest distance to " O   HOH Z 174 " =    2.704
peak=   -3.209 closest distance to " ND2 ASN A 285 " =    2.154
peak=   -3.208 closest distance to " CD2 PHE A 130 " =    2.951
peak=   -3.204 closest distance to " CB  ASN A  39 " =    2.220
peak=   -3.202 closest distance to " O   HOH Z   2 " =    1.583
peak=   -3.200 closest distance to " CD1 ILE A 199 " =    2.668
peak=   -3.197 closest distance to " OG ASER A 134 " =    1.270
peak=   -3.196 closest distance to " CZ2 TRP A 274 " =    0.976
peak=   -3.195 closest distance to " CB  ALA A  10 " =    2.281
peak=   -3.193 closest distance to " CA  GLY A 241 " =    2.882
peak=   -3.190 closest distance to " CB  ALA A 227 " =    2.380
peak=   -3.187 closest distance to " O   HOH Z 298 " =    2.392
peak=   -3.179 closest distance to " CG2 THR A 157 " =    2.259
peak=   -3.177 closest distance to " O   HOH Z 377 " =    0.768
peak=   -3.174 closest distance to " O   HOH Z 345 " =    2.333
peak=   -3.170 closest distance to " SD  MET A 113 " =    3.029
peak=   -3.169 closest distance to " CB  PHE A 130 " =    1.220
peak=   -3.162 closest distance to " SD  MET A 105 " =    2.618
peak=   -3.161 closest distance to " O   HOH Z 417 " =    2.982
peak=   -3.160 closest distance to " O   HOH Z 253 " =    4.239
peak=   -3.153 closest distance to " CA  HIS A  86 " =    2.219
peak=   -3.148 closest distance to " CG1 VAL A 197 " =    2.347
peak=   -3.142 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.141 closest distance to " OH  TYR A 247 " =    2.164
peak=   -3.137 closest distance to " O   HOH Z 295 " =    1.687
peak=   -3.134 closest distance to " O   HOH Z  76 " =    1.332
peak=   -3.132 closest distance to " N   ARG A 159 " =    2.083
peak=   -3.132 closest distance to " CE  MET A  93 " =    1.239
peak=   -3.127 closest distance to " O   HOH Z 359 " =    3.180
peak=   -3.122 closest distance to " O   HOH Z 414 " =    2.277
peak=   -3.119 closest distance to " OD2 ASP A 171 " =    2.179
peak=   -3.116 closest distance to " O   HOH Z 109 " =    1.740
peak=   -3.114 closest distance to " OD1 ASN A 148 " =    1.627
peak=   -3.114 closest distance to " CE  LYS A  76 " =    2.761
peak=   -3.111 closest distance to " O   HOH Z 318 " =    1.860
peak=   -3.110 closest distance to " O   HOH Z 145 " =    1.516
peak=   -3.109 closest distance to " CD2 TRP A 274 " =    2.593
peak=   -3.106 closest distance to " N   LYS A 166 " =    1.844
peak=   -3.106 closest distance to " CB  ALA A 100 " =    2.238
peak=   -3.103 closest distance to " OD2 ASP A 171 " =    1.824
peak=   -3.097 closest distance to " O   HOH Z 322 " =    1.196
peak=   -3.095 closest distance to " O   HOH Z 252 " =    3.990
peak=   -3.091 closest distance to " OD2 ASP A 171 " =    2.954
peak=   -3.091 closest distance to " O   HOH Z 292 " =    1.556
peak=   -3.089 closest distance to " O   HOH Z 193 " =    1.533
peak=   -3.084 closest distance to " O   HOH Z 383 " =    1.678
peak=   -3.083 closest distance to " O   HOH Z 111 " =    1.317
peak=   -3.082 closest distance to " CG  PHE A 283 " =    2.842
peak=   -3.082 closest distance to " CD1 LEU A 297 " =    2.642
peak=   -3.072 closest distance to " O   HOH Z 114 " =    1.672
peak=   -3.070 closest distance to " O   HOH Z 353 " =    2.066
peak=   -3.063 closest distance to " O   HOH Z 128 " =    2.655
peak=   -3.061 closest distance to " N   ALA A 226 " =    2.119
peak=   -3.059 closest distance to " O   GLY A  80 " =    2.461
peak=   -3.057 closest distance to " O   ASP A 272 " =    2.463
peak=   -3.055 closest distance to " CD1 ILE A 239 " =    2.333
peak=   -3.045 closest distance to " OD1 ASN A 187 " =    1.557
peak=   -3.041 closest distance to " O   MET A  47 " =    2.709

================= 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    :  0.4474 0.4442   6.255380e+00   6.241901e+00
   1_bss:  0.4395 0.4380   6.248528e+00   6.233649e+00
   1_xyz:  0.2723 0.3056   5.889063e+00   5.966999e+00
   1_adp:  0.2502 0.3155   5.845432e+00   5.995270e+00
   1_occ:  0.2496 0.3155   5.844149e+00   5.994491e+00
   2_bss:  0.2480 0.3146   5.842465e+00   5.989824e+00
   2_xyz:  0.1780 0.2333   5.551380e+00   5.751612e+00
   2_adp:  0.1598 0.2145   5.462518e+00   5.676671e+00
   2_occ:  0.1597 0.2147   5.462464e+00   5.677289e+00
   3_bss:  0.1596 0.2145   5.460705e+00   5.675496e+00
   3_xyz:  0.1390 0.1896   5.334446e+00   5.556890e+00
   3_adp:  0.1335 0.1855   5.305862e+00   5.533410e+00
   3_occ:  0.1335 0.1855   5.305778e+00   5.533447e+00
   4_bss:  0.1334 0.1855   5.305172e+00   5.533343e+00
   4_xyz:  0.1252 0.1758   5.250190e+00   5.488443e+00
   4_adp:  0.1239 0.1727   5.236943e+00   5.471894e+00
   4_occ:  0.1238 0.1726   5.236674e+00   5.471576e+00
   5_bss:  0.1243 0.1720   5.236299e+00   5.469110e+00
   5_xyz:  0.1138 0.1661   5.177354e+00   5.434342e+00
   5_adp:  0.1133 0.1632   5.167501e+00   5.420682e+00
   5_occ:  0.1133 0.1632   5.167173e+00   5.420381e+00
   5_bss:  0.1132 0.1631   5.167153e+00   5.420122e+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:  0.332  59.009   2.144   0.532  -0.216   0.000  -0.000  -0.000
   1_xyz:  0.332  59.009   2.144   0.532  -0.216   0.000  -0.000  -0.000
   1_adp:  0.332  59.009   2.144   0.532  -0.216   0.000  -0.000  -0.000
   1_occ:  0.332  59.009   2.144   0.532  -0.216   0.000  -0.000  -0.000
   2_bss:  0.332  59.009  -0.513  -1.616  -0.716  -0.000  -0.000  -0.000
   2_xyz:  0.332  59.009  -0.513  -1.616  -0.716  -0.000  -0.000  -0.000
   2_adp:  0.332  59.009  -0.513  -1.616  -0.716  -0.000  -0.000  -0.000
   2_occ:  0.332  59.009  -0.513  -1.616  -0.716  -0.000  -0.000  -0.000
   3_bss:  0.336  67.534  -1.189  -2.077  -0.668  -0.000  -0.000  -0.000
   3_xyz:  0.336  67.534  -1.189  -2.077  -0.668  -0.000  -0.000  -0.000
   3_adp:  0.336  67.534  -1.189  -2.077  -0.668  -0.000  -0.000  -0.000
   3_occ:  0.336  67.534  -1.189  -2.077  -0.668  -0.000  -0.000  -0.000
   4_bss:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   4_xyz:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   4_adp:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   4_occ:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   5_bss:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   5_xyz:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   5_adp:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   5_occ:  0.329  70.306  -1.496  -2.356  -0.755  -0.000  -0.000  -0.000
   5_bss:  0.321  60.822  -1.553  -2.375  -0.686  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.854 0.4846  0.6451    61106.450
   1_bss:  52.256 0.4910  0.6788    59494.047
   1_xyz:  31.214 0.7454  0.9600    24843.577
   1_adp:  32.758 0.7269  0.9375    26372.196
   1_occ:  32.762 0.7267  0.9362    26284.622
   2_bss:  32.484 0.7298  0.8845    25941.258
   2_xyz:  23.232 0.8283  0.9673    13914.043
   2_adp:  20.906 0.8525  0.9766    11921.491
   2_occ:  20.924 0.8523  0.9762    11935.243
   3_bss:  20.863 0.8528  0.9637    11859.622
   3_xyz:  17.854 0.8813  0.9792     9025.437
   3_adp:  17.230 0.8875  0.9760     8638.337
   3_occ:  17.230 0.8875  0.9759     8636.034
   4_bss:  17.221 0.8875  0.9684     8630.140
   4_xyz:  16.156 0.8969  0.9733     7776.235
   4_adp:  15.709 0.9010  0.9709     7533.386
   4_occ:  15.705 0.9010  0.9709     7528.421
   5_bss:  15.669 0.9012  0.9709     7471.590
   5_xyz:  14.895 0.9076  0.9753     6936.640
   5_adp:  14.550 0.9106  0.9738     6755.483
   5_occ:  14.549 0.9107  0.9737     6746.858
   5_bss:  14.552 0.9106  0.9736     6740.244
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6561e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6561e-01
   1_xyz:   1.496  0.013  0.101 16.365  0.007  4.115   1.3091e-01
   1_adp:   1.496  0.013  0.101 16.365  0.007  4.115   1.3091e-01
   1_occ:   1.496  0.013  0.101 16.365  0.007  4.115   1.3091e-01
   2_bss:   1.496  0.013  0.101 16.365  0.007  4.115   1.3091e-01
   2_xyz:   1.094  0.008  0.078 14.313  0.004  4.111   6.7427e-02
   2_adp:   1.094  0.008  0.078 14.313  0.004  4.111   6.7427e-02
   2_occ:   1.094  0.008  0.078 14.313  0.004  4.111   6.7427e-02
   3_bss:   1.094  0.008  0.078 14.313  0.004  4.111   6.7427e-02
   3_xyz:   0.935  0.006  0.067 14.143  0.003  4.117   5.1699e-02
   3_adp:   0.935  0.006  0.067 14.143  0.003  4.117   5.1699e-02
   3_occ:   0.935  0.006  0.067 14.143  0.003  4.117   5.1699e-02
   4_bss:   0.935  0.006  0.067 14.143  0.003  4.117   5.1699e-02
   4_xyz:   0.937  0.007  0.070 14.099  0.003  4.122   5.2781e-02
   4_adp:   0.937  0.007  0.070 14.099  0.003  4.122   5.2781e-02
   4_occ:   0.937  0.007  0.070 14.099  0.003  4.122   5.2781e-02
   5_bss:   0.937  0.007  0.070 14.099  0.003  4.122   5.2781e-02
   5_xyz:   1.170  0.011  0.084 14.710  0.004  4.130   8.0823e-02
   5_adp:   1.170  0.011  0.084 14.710  0.004  4.130   8.0823e-02
   5_occ:   1.170  0.011  0.084 14.710  0.004  4.130   8.0823e-02
   5_bss:   1.170  0.011  0.084 14.710  0.004  4.130   8.0823e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4237e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4237e-01
   1_xyz:  10.484  0.087  0.346 84.686  0.056  1.985   1.3548e-01
   1_adp:  10.484  0.087  0.346 84.686  0.056  1.985   1.3548e-01
   1_occ:  10.484  0.087  0.346 84.686  0.056  1.985   1.3548e-01
   2_bss:  10.484  0.087  0.346 84.686  0.056  1.985   1.3548e-01
   2_xyz:   7.836  0.073  0.263 82.081  0.030  2.321   5.9687e-02
   2_adp:   7.836  0.073  0.263 82.081  0.030  2.321   5.9687e-02
   2_occ:   7.836  0.073  0.263 82.081  0.030  2.321   5.9687e-02
   3_bss:   7.836  0.073  0.263 82.081  0.030  2.321   5.9687e-02
   3_xyz:   8.930  0.038  0.224 80.397  0.028  2.368   3.6829e-02
   3_adp:   8.930  0.038  0.224 80.397  0.028  2.368   3.6829e-02
   3_occ:   8.930  0.038  0.224 80.397  0.028  2.368   3.6829e-02
   4_bss:   8.930  0.038  0.224 80.397  0.028  2.368   3.6829e-02
   4_xyz:   8.733  0.052  0.217 81.403  0.029  2.359   4.7443e-02
   4_adp:   8.733  0.052  0.217 81.403  0.029  2.359   4.7443e-02
   4_occ:   8.733  0.052  0.217 81.403  0.029  2.359   4.7443e-02
   5_bss:   8.733  0.052  0.217 81.403  0.029  2.359   4.7443e-02
   5_xyz:   8.999  0.058  0.268 83.197  0.034  2.264   6.3749e-02
   5_adp:   8.999  0.058  0.268 83.197  0.034  2.264   6.3749e-02
   5_occ:   8.999  0.058  0.268 83.197  0.034  2.264   6.3749e-02
   5_bss:   8.999  0.058  0.268 83.197  0.034  2.264   6.3749e-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:  79.45   0.00  17.30  79.45   0.00  13.23  65.16   2.12  39.48
   1_occ:  79.45   0.00  17.30  79.45   0.00  13.23  65.16   2.12  39.48
   2_bss:  79.45   0.00  17.30  79.45   0.00  13.23  65.16   2.12  39.48
   2_xyz:  79.45   0.00  17.30  79.45   0.00  13.23  65.16   2.12  39.48
   2_adp:  80.08   0.00  17.78  70.03   0.00  13.17  80.08   5.58  42.88
   2_occ:  80.08   0.00  17.78  70.03   0.00  13.17  80.08   5.58  42.88
   3_bss:  80.08   0.00  17.78  70.03   0.00  13.17  80.08   5.58  42.88
   3_xyz:  80.08   0.00  17.78  70.03   0.00  13.17  80.08   5.58  42.88
   3_adp: 109.18   0.00  18.30  91.29   0.00  13.12 109.18   2.54  46.54
   3_occ: 109.18   0.00  18.30  91.29   0.00  13.12 109.18   2.54  46.54
   4_bss: 109.18   0.00  18.30  91.29   0.00  13.12 109.18   2.54  46.54
   4_xyz: 109.18   0.00  18.30  91.29   0.00  13.12 109.18   2.54  46.54
   4_adp: 109.66   0.00  17.91  92.78   0.00  12.91 109.66   0.00  45.14
   4_occ: 109.66   0.00  17.91  92.78   0.00  12.91 109.66   0.00  45.14
   5_bss: 109.66   0.00  17.91  92.78   0.00  12.91 109.66   0.00  45.14
   5_xyz: 109.66   0.00  17.91  92.78   0.00  12.91 109.66   0.00  45.14
   5_adp:  95.89   0.00  17.21  93.60   0.00  12.68  95.89   0.98  41.91
   5_occ:  95.89   0.00  17.21  93.60   0.00  12.68  95.89   0.98  41.91
   5_bss:  95.89   0.00  17.22  93.61   0.00  12.68  95.89   0.99  41.91
------------------------------------------------------------------------
 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:    1.334    0.009    0.483
   1_adp:    1.334    0.009    0.483
   1_occ:    1.334    0.009    0.483
   2_bss:    1.334    0.009    0.483
   2_xyz:    1.207    0.025    0.585
   2_adp:    1.207    0.025    0.585
   2_occ:    1.207    0.025    0.585
   3_bss:    1.207    0.025    0.585
   3_xyz:    1.251    0.024    0.638
   3_adp:    1.251    0.024    0.638
   3_occ:    1.251    0.024    0.638
   4_bss:    1.251    0.024    0.638
   4_xyz:    1.337    0.059    0.660
   4_adp:    1.337    0.059    0.660
   4_occ:    1.337    0.059    0.660
   5_bss:    1.337    0.059    0.660
   5_xyz:    1.480    0.059    0.682
   5_adp:    1.480    0.059    0.682
   5_occ:    1.480    0.059    0.682
   5_bss:    1.480    0.059    0.682
------------------------------------------------------------------------

CPU time actual refinement: 356.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/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_1239/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1239/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.31 
  Macro-tasks:
    bulk solvent and scale       = 38.87  
    individual site refinement   = 152.79 
    weights calculation          = 30.33  
    collect and process          = 6.59   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 228.69 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 117.56 
    alpha_beta                      = 8.30   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 126.71 
    fmodel                         = 6.87   
    r_factors                      = 0.17   
    phase_errors                   = 10.83  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 273.76 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.980 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    664 calls, 117.24 s
gradients_fft:          609 calls, 112.73 s

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

# Date 2008-01-16 Time 06:47:18 PST -0800 (1200494838.79 s)
Start R-work = 0.4474, R-free = 0.4442 (no bulk solvent and anisotropic scale)
Final R-work = 0.1352, R-free = 0.1821 (no bulk solvent and anisotropic scale)

Start R-work = 0.4395, R-free = 0.4380
Final R-work = 0.1132, R-free = 0.1631