# Date 2008-01-16 Time 06:36:44 PST -0800 (1200494204.37 s)
#phil __OFF__

Command line arguments: "../1215.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9982
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1215

-------------------------------------------------------------------------------
  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, 45.7567, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.95459
Completeness in resolution range: 0.921532
Completeness with d_max=infinity: 0.918938

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   1.9546

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, 45.7567, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.95459
Completeness in resolution range: 0.921532
Completeness with d_max=infinity: 0.918938

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.1848 [2230/2257]  2007   223  10.0%
  bin  2:  4.1848 -  3.3330 [2152/2172]  1940   212   9.9%
  bin  3:  3.3330 -  2.9150 [2124/2143]  1907   217  10.2%
  bin  4:  2.9150 -  2.6500 [2083/2113]  1876   207   9.9%
  bin  5:  2.6500 -  2.4609 [2094/2113]  1891   203   9.7%
  bin  6:  2.4609 -  2.3163 [2077/2102]  1858   219  10.5%
  bin  7:  2.3163 -  2.2007 [2065/2093]  1849   216  10.5%
  bin  8:  2.2007 -  2.1051 [2058/2094]  1866   192   9.3%
  bin  9:  2.1051 -  2.0243 [1971/2091]  1780   191   9.7%
  bin 10:  2.0243 -  1.9546 [ 735/2079]   656    79  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.48 -     2.16: 21
        2.16 -     2.85: 1107
        2.85 -     3.53: 4449
        3.53 -     4.22: 9320
        4.22 -     4.90: 13489
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.481 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " OG BSER A 216 " - " O   HOH Z 113 "  1.781 3.040 -x+1/2,-y+1,z-1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28381 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_1215/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 45.75675 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4757   ksol= 0.00   Bsol= 0.00   scale= 0.879    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.292109                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.6687 0.99   1445  163 0.4006 0.4052      6.6036      6.6238|
|  2:  4.6687 -  3.7234 0.99   1401  155 0.4272 0.4233      6.8474      6.8371|
|  3:  3.7234 -  3.2580 0.99   1364  144 0.4522 0.4440      6.6831      6.6908|
|  4:  3.2580 -  2.9625 0.99   1356  160 0.4758 0.5024      6.5326      6.5466|
|  5:  2.9625 -  2.7514 0.99   1363  145 0.4981 0.5312      6.3755      6.3745|
|  6:  2.7514 -  2.5901 0.99   1340  156 0.5053 0.4984      6.2862      6.2354|
|  7:  2.5901 -  2.4609 0.99   1352  139 0.5167 0.4832      6.2345      6.1555|
|  8:  2.4609 -  2.3542 0.98   1327  158 0.5157 0.5501      6.1586      6.2152|
|  9:  2.3542 -  2.2639 0.98   1316  147 0.4962 0.5128      6.1249      6.1592|
| 10:  2.2639 -  2.1860 1.00   1339  152 0.5349 0.4852      6.0778      6.0453|
| 11:  2.1860 -  2.1178 0.98   1323  137 0.5119 0.5250      6.0152      6.0549|
| 12:  2.1178 -  2.0574 0.98   1309  150 0.5044 0.4856      5.9298      5.9263|
| 13:  2.0574 -  2.0034 0.82   1084  122 0.5172 0.4605      5.8754       5.795|
| 14:  2.0034 -  1.9546 0.23    311   31 0.4928 0.4898      5.8456      5.9068|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.6687  1445   163  0.68  35.82   0.80     0.75      79125.59|
|  2:  4.6687 -  3.7234  1401   155  0.66  38.76   0.89     0.78     123860.33|
|  3:  3.7234 -  3.2580  1364   144  0.51  50.93   0.90     0.69     137326.90|
|  4:  3.2580 -  2.9625  1356   160  0.38  60.96   0.88     0.56     130599.15|
|  5:  2.9625 -  2.7514  1363   145  0.29  68.24   0.88     0.43     101435.60|
|  6:  2.7514 -  2.5901  1340   156  0.27  69.48   0.88     0.40      85547.20|
|  7:  2.5901 -  2.4609  1352   139  0.28  68.80   0.90     0.40      71640.60|
|  8:  2.4609 -  2.3542  1327   158  0.29  68.05   0.90     0.44      63933.52|
|  9:  2.3542 -  2.2639  1316   147  0.31  66.83   0.93     0.45      57448.50|
| 10:  2.2639 -  2.1860  1339   152  0.30  67.76   0.92     0.46      51816.78|
| 11:  2.1860 -  2.1178  1323   137  0.31  66.87   0.94     0.49      49306.71|
| 12:  2.1178 -  2.0574  1309   150  0.33  65.53   0.94     0.52      42861.60|
| 13:  2.0574 -  2.0034  1084   122  0.35  63.70   0.93     0.58      35293.34|
| 14:  2.0034 -  1.9546   311    31  0.46  55.45   1.02     0.65      25685.49|
|alpha:            min =        0.40 max =            0.78 mean =         0.54|
|beta:             min =    25685.49 max =       137326.90 mean =     79377.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.51|
|phase err.(test): min =        0.00 max =           89.84 mean =        60.71|
|-----------------------------------------------------------------------------|

============================== 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 = 22.505124             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.603   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.291767              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.702   (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 |  1.481 -  1.823:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.823 -  2.165:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.165 -  2.507:       35 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.507 -  2.849:     1072 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.849 -  3.191:     1992 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.191 -  3.532:     2457 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.532 -  3.874:     4674 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.874 -  4.216:     4646 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.216 -  4.558:     6113 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.558 -  4.900:     7376 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.481 |       0.539 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    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: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4757   ksol= 0.00   Bsol= 0.00   scale= 0.879    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.292109                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4680   r_free= 0.4669   ksol= 0.34   Bsol= 50.00   scale= 0.909   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.59,-2.16,0.00,-0.00,-0.00); trace/3= 0.20                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.288297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.423698             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.591   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.542742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.433   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4680      final r-factor (work) = 0.3827          |
| start r-factor (free) = 0.4669      final r-factor (free) = 0.4311          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.0793 = 18.42 * 0.50 * 6.2846 + 1.00 * 0.1866                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.3217 = 18.42 * 0.50 * 6.2040 + 1.00 * 0.1716                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3827      final r-factor (work) = 0.3547          |
| start r-factor (free) = 0.4311      final r-factor (free) = 0.4330          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5774 = 1.54 * 1.00 * 6.2040 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4952 = 1.54 * 1.00 * 6.1280 + 1.00 * 0.0413                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.92  17.31    None  None   None       |
|    all(noH): 2823   0      0.00    106.92  17.31    None  None   None       |
|    Sol.    : 438    0      0.00    65.32   36.08    None  None   None       |
|    Mac.    : 2385   0      0.00    106.92  13.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.692:  997   |   5:    53.460 -  64.152:   40        |
|      1:    10.692 -  21.384:  988   |   6:    64.152 -  74.844:    2        |
|      2:    21.384 -  32.076:  471   |   7:    74.844 -  85.536:    0        |
|      3:    32.076 -  42.768:  207   |   8:    85.536 -  96.228:    0        |
|      4:    42.768 -  53.460:  117   |   9:    96.228 - 106.920:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3547 r_free = 0.4330             target_work(ml) = 6.131         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3543 r_free = 0.4327             target_work(ml) = 6.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3543   r_free= 0.4327   ksol= 0.34   Bsol= 50.00   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.18,1.59,-2.16,0.00,-0.00,-0.00); trace/3= 0.20                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.129715                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3541   r_free= 0.4298   ksol= 0.36   Bsol= 79.93   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.40,-0.24,0.00,-0.00,-0.00); trace/3= 0.20                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.129805                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.378332             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.053  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.105156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.620   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3541      final r-factor (work) = 0.2843          |
| start r-factor (free) = 0.4298      final r-factor (free) = 0.3554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1106 = 12.38 * 0.50 * 6.1299 + 1.00 * 0.1716                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.6217 = 12.38 * 0.50 * 6.0603 + 1.00 * 0.1133                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2843      final r-factor (work) = 0.2626          |
| start r-factor (free) = 0.3554      final r-factor (free) = 0.3498          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7160 = 1.11 * 1.00 * 6.0603 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5648 = 1.11 * 1.00 * 5.9234 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.00   18.89    None  None   None       |
|    all(noH): 2823   0      0.00    88.00   18.89    None  None   None       |
|    Sol.    : 438    0      0.00    88.00   40.90    None  None   None       |
|    Mac.    : 2385   0      0.00    74.70   14.85    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 -   8.800:  855   |   5:    44.001 -  52.801:  117        |
|      1:     8.800 -  17.600:  851   |   6:    52.801 -  61.601:   77        |
|      2:    17.600 -  26.401:  437   |   7:    61.601 -  70.401:   41        |
|      3:    26.401 -  35.201:  265   |   8:    70.401 -  79.202:   14        |
|      4:    35.201 -  44.001:  163   |   9:    79.202 -  88.002:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2626 r_free = 0.3498             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2626 r_free = 0.3495             target_work(ml) = 5.916         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2626   r_free= 0.3495   ksol= 0.36   Bsol= 79.93   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,0.40,-0.24,0.00,-0.00,-0.00); trace/3= 0.20                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.915926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2630   r_free= 0.3485   ksol= 0.36   Bsol= 80.89   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.31,-0.24,0.35,-0.00,0.00,0.00); trace/3= 0.14                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.913460                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.750749              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.955   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.400639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.889  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2630      final r-factor (work) = 0.2202          |
| start r-factor (free) = 0.3485      final r-factor (free) = 0.2970          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1839 = 4.75 * 0.50 * 5.9235 + 1.00 * 0.1133                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9521 = 4.75 * 0.50 * 5.8478 + 1.00 * 0.0613                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2202      final r-factor (work) = 0.2057          |
| start r-factor (free) = 0.2970      final r-factor (free) = 0.2820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2092 = 1.40 * 1.00 * 5.8478 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0480 = 1.40 * 1.00 * 5.7328 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.70   19.07    None  None   None       |
|    all(noH): 2823   0      0.00    98.70   19.07    None  None   None       |
|    Sol.    : 438    0      3.71    98.70   46.75    None  None   None       |
|    Mac.    : 2385   0      0.00    89.32   13.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.871: 1054   |   5:    49.352 -  59.223:  126        |
|      1:     9.871 -  19.741:  905   |   6:    59.223 -  69.093:   89        |
|      2:    19.741 -  29.611:  316   |   7:    69.093 -  78.964:   37        |
|      3:    29.611 -  39.482:  161   |   8:    78.964 -  88.834:   18        |
|      4:    39.482 -  49.352:  113   |   9:    88.834 -  98.704:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2057 r_free = 0.2820             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2054 r_free = 0.2813             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2054   r_free= 0.2813   ksol= 0.36   Bsol= 80.89   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.31,-0.24,0.35,-0.00,0.00,0.00); trace/3= 0.14                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.706506                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2057   r_free= 0.2811   ksol= 0.34   Bsol= 73.11   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.94,0.17,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.705589                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.787405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.234  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.933867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.513  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2057      final r-factor (work) = 0.1670          |
| start r-factor (free) = 0.2811      final r-factor (free) = 0.2340          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7848 = 4.79 * 0.50 * 5.7331 + 1.00 * 0.0614                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5294 = 4.79 * 0.50 * 5.6257 + 1.00 * 0.0632                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1670      final r-factor (work) = 0.1523          |
| start r-factor (free) = 0.2340      final r-factor (free) = 0.2136          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2718 = 0.93 * 1.00 * 5.6257 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1349 = 0.93 * 1.00 * 5.4832 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.40  18.25    None  None   None       |
|    all(noH): 2823   0      0.00    100.40  18.25    None  None   None       |
|    Sol.    : 438    0      1.51    100.40  47.89    None  None   None       |
|    Mac.    : 2385   0      0.00    93.76   12.81    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 -  10.040: 1196   |   5:    50.200 -  60.241:  110        |
|      1:    10.040 -  20.080:  927   |   6:    60.241 -  70.281:   82        |
|      2:    20.080 -  30.120:  227   |   7:    70.281 -  80.321:   51        |
|      3:    30.120 -  40.160:  123   |   8:    80.321 -  90.361:   16        |
|      4:    40.160 -  50.200:   87   |   9:    90.361 - 100.401:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1523 r_free = 0.2136             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1521 r_free = 0.2132             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1521   r_free= 0.2132   ksol= 0.34   Bsol= 73.11   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.94,0.17,-0.00,0.00,0.00); trace/3= -0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.432374                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1523   r_free= 0.2130   ksol= 0.33   Bsol= 64.35   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-1.62,-0.18,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.431889                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.642122              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.017  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.386713              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.832  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1523      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.2130      final r-factor (free) = 0.1907          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7932 = 4.64 * 0.50 * 5.4845 + 1.00 * 0.0632                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5620 = 4.64 * 0.50 * 5.3816 + 1.00 * 0.0711                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1907      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4768 = 1.39 * 1.00 * 5.3816 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3502 = 1.39 * 1.00 * 5.2910 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.85  17.77    None  None   None       |
|    all(noH): 2823   0      0.00    103.85  17.77    None  None   None       |
|    Sol.    : 438    0      1.12    103.85  47.45    None  None   None       |
|    Mac.    : 2385   0      0.00    102.08  12.32    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 -  10.386: 1320   |   5:    51.927 -  62.313:   98        |
|      1:    10.386 -  20.771:  869   |   6:    62.313 -  72.698:   59        |
|      2:    20.771 -  31.156:  218   |   7:    72.698 -  83.084:   51        |
|      3:    31.156 -  41.542:   93   |   8:    83.084 -  93.469:   11        |
|      4:    41.542 -  51.927:   92   |   9:    93.469 - 103.854:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1261 r_free = 0.1811             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1809             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1809   ksol= 0.33   Bsol= 64.35   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-1.62,-0.18,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264941                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.6687 0.99   1445  163 0.0952 0.1427      5.3875      5.6734|
|  2:  4.6687 -  3.7234 0.99   1401  155 0.0857 0.1235      5.4782      5.7377|
|  3:  3.7234 -  3.2580 0.99   1364  144 0.1173 0.1655       5.563      5.8592|
|  4:  3.2580 -  2.9625 0.99   1356  160 0.1456 0.1981      5.5844      5.7839|
|  5:  2.9625 -  2.7514 0.99   1363  145 0.1520 0.2084      5.4496      5.6856|
|  6:  2.7514 -  2.5901 0.99   1340  156 0.1431 0.2092      5.3222      5.5469|
|  7:  2.5901 -  2.4609 0.99   1352  139 0.1403 0.1976      5.2668      5.4713|
|  8:  2.4609 -  2.3542 0.98   1327  158 0.1376 0.1875      5.1956      5.4224|
|  9:  2.3542 -  2.2639 0.98   1316  147 0.1406 0.2039      5.1695      5.4173|
| 10:  2.2639 -  2.1860 1.00   1339  152 0.1328 0.1954      5.0813      5.3096|
| 11:  2.1860 -  2.1178 0.98   1323  137 0.1294 0.2071      5.0471      5.4147|
| 12:  2.1178 -  2.0574 0.98   1309  150 0.1258 0.2146        4.98      5.2471|
| 13:  2.0574 -  2.0034 0.82   1084  122 0.1350 0.1834      4.9149      5.1363|
| 14:  2.0034 -  1.9546 0.23    311   31 0.1224 0.1697      4.8071      5.1031|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.6687  1445   163  0.93  10.17   0.97     0.94       8282.60|
|  2:  4.6687 -  3.7234  1401   155  0.95   9.12   1.02     1.01      10837.98|
|  3:  3.7234 -  3.2580  1364   144  0.92  13.64   1.05     1.04      13011.47|
|  4:  3.2580 -  2.9625  1356   160  0.89  17.67   1.03     1.01      14138.01|
|  5:  2.9625 -  2.7514  1363   145  0.88  18.33   1.01     0.99      10840.38|
|  6:  2.7514 -  2.5901  1340   156  0.87  19.42   0.99     0.95       8919.68|
|  7:  2.5901 -  2.4609  1352   139  0.88  18.25   1.01     0.98       8014.28|
|  8:  2.4609 -  2.3542  1327   158  0.88  18.49   0.99     0.96       7053.02|
|  9:  2.3542 -  2.2639  1316   147  0.87  19.03   1.01     0.96       6649.21|
| 10:  2.2639 -  2.1860  1339   152  0.87  19.02   1.00     0.97       5875.18|
| 11:  2.1860 -  2.1178  1323   137  0.88  19.08   0.99     0.95       5629.69|
| 12:  2.1178 -  2.0574  1309   150  0.87  19.36   1.01     0.99       5248.83|
| 13:  2.0574 -  2.0034  1084   122  0.87  19.96   0.99     0.97       4503.02|
| 14:  2.0034 -  1.9546   311    31  0.89  17.44   0.98     0.95       3539.49|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     3539.49 max =        14138.01 mean =      8389.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        16.93|
|phase err.(test): min =        0.00 max =           89.26 mean =        16.19|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1804   ksol= 0.32   Bsol= 64.35   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-1.62,-0.18,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.263723                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1804   ksol= 0.32   Bsol= 64.35   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,-1.62,-0.18,-0.00,-0.00,-0.00); trace/3= -0.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.263723                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.6687 0.99   1445  163 0.0966 0.1387      5.3742      5.6502|
|  2:  4.6687 -  3.7234 0.99   1401  155 0.0862 0.1233      5.4759      5.7405|
|  3:  3.7234 -  3.2580 0.99   1364  144 0.1181 0.1657      5.5639      5.8625|
|  4:  3.2580 -  2.9625 0.99   1356  160 0.1454 0.1977       5.585      5.7842|
|  5:  2.9625 -  2.7514 0.99   1363  145 0.1522 0.2079      5.4506      5.6853|
|  6:  2.7514 -  2.5901 0.99   1340  156 0.1430 0.2089      5.3222      5.5461|
|  7:  2.5901 -  2.4609 0.99   1352  139 0.1403 0.1972      5.2663      5.4699|
|  8:  2.4609 -  2.3542 0.98   1327  158 0.1377 0.1873      5.1954      5.4221|
|  9:  2.3542 -  2.2639 0.98   1316  147 0.1406 0.2038       5.169      5.4172|
| 10:  2.2639 -  2.1860 1.00   1339  152 0.1327 0.1954      5.0812      5.3097|
| 11:  2.1860 -  2.1178 0.98   1323  137 0.1294 0.2070      5.0468      5.4145|
| 12:  2.1178 -  2.0574 0.98   1309  150 0.1258 0.2146      4.9798       5.247|
| 13:  2.0574 -  2.0034 0.82   1084  122 0.1350 0.1834      4.9149      5.1362|
| 14:  2.0034 -  1.9546 0.23    311   31 0.1223 0.1696      4.8069      5.1025|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2649 -  4.6687  1445   163  0.93   9.94   0.96     0.95       7840.93|
|  2:  4.6687 -  3.7234  1401   155  0.95   8.92   1.02     1.01      10537.59|
|  3:  3.7234 -  3.2580  1364   144  0.92  13.57   1.05     1.04      12939.96|
|  4:  3.2580 -  2.9625  1356   160  0.88  17.69   1.03     1.01      14181.90|
|  5:  2.9625 -  2.7514  1363   145  0.88  18.34   1.01     0.99      10860.55|
|  6:  2.7514 -  2.5901  1340   156  0.87  19.40   0.99     0.94       8908.44|
|  7:  2.5901 -  2.4609  1352   139  0.88  18.23   1.01     0.98       8001.41|
|  8:  2.4609 -  2.3542  1327   158  0.88  18.48   0.99     0.96       7043.69|
|  9:  2.3542 -  2.2639  1316   147  0.87  19.01   1.01     0.96       6641.59|
| 10:  2.2639 -  2.1860  1339   152  0.87  19.02   1.00     0.97       5874.03|
| 11:  2.1860 -  2.1178  1323   137  0.88  19.08   0.99     0.95       5626.38|
| 12:  2.1178 -  2.0574  1309   150  0.87  19.36   1.01     0.99       5247.76|
| 13:  2.0574 -  2.0034  1084   122  0.87  19.96   0.99     0.97       4502.78|
| 14:  2.0034 -  1.9546   311    31  0.89  17.44   0.98     0.95       3538.90|
|alpha:            min =        0.94 max =            1.04 mean =         0.98|
|beta:             min =     3538.90 max =        14181.90 mean =      8325.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.88|
|phase err.(test): min =        0.00 max =           89.33 mean =        16.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.830)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.86  17.78    None  None   None       |
|    all(noH): 2823   0      0.00    103.86  17.78    None  None   None       |
|    Sol.    : 438    0      1.12    103.86  47.46    None  None   None       |
|    Mac.    : 2385   0      0.00    102.09  12.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.388: 1320   |   5:    51.930 -  62.316:   98        |
|      1:    10.388 -  20.774:  869   |   6:    62.316 -  72.701:   59        |
|      2:    20.774 -  31.159:  218   |   7:    72.701 -  83.087:   51        |
|      3:    31.159 -  41.545:   93   |   8:    83.087 -  93.472:   11        |
|      4:    41.545 -  51.930:   92   |   9:    93.472 - 103.857:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.713 - 4.792
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 346
   mapped sites are within: 0.713 - 4.792

peak=    8.012 closest distance to " O   HOH Z 390 " =    1.267
peak=    6.738 closest distance to " O   HOH Z 120 " =    1.352
peak=    6.326 closest distance to " O   HOH Z 431 " =    1.628
peak=    6.224 closest distance to " NE2 GLN A  11 " =    1.420
peak=    5.646 closest distance to " O   HOH Z 245 " =    1.245
peak=    5.618 closest distance to " O   HOH Z 214 " =    1.880
peak=    5.618 closest distance to " O   HOH Z  65 " =    1.530
peak=    5.294 closest distance to " O   HOH Z   7 " =    2.029
peak=    5.293 closest distance to " O   HOH Z 385 " =    1.087
peak=    5.134 closest distance to " O   HOH Z 417 " =    2.554
peak=    5.120 closest distance to " O   HOH Z  27 " =    1.101
peak=    5.088 closest distance to " O   HOH Z 222 " =    1.394
peak=    5.080 closest distance to " O   HOH Z 139 " =    1.458
peak=    5.071 closest distance to " O   HOH Z 403 " =    1.575
peak=    5.050 closest distance to " O   HOH Z 427 " =    1.371
peak=    5.019 closest distance to " CG  PRO A  54 " =    1.352
peak=    4.985 closest distance to " O   HOH Z 427 " =    2.190
peak=    4.899 closest distance to " O   HOH Z 375 " =    1.047
peak=    4.831 closest distance to " O   HOH Z 183 " =    1.635
peak=    4.815 closest distance to " O   HOH Z 144 " =    1.666
peak=    4.793 closest distance to " O   HOH Z   9 " =    1.491
peak=    4.741 closest distance to " CB  PRO A  54 " =    1.127
peak=    4.713 closest distance to " O   HOH Z 316 " =    3.048
peak=    4.680 closest distance to " O   HOH Z 126 " =    1.545
peak=    4.678 closest distance to " O   HOH Z  97 " =    1.447
peak=    4.650 closest distance to " CB  GLN A 223 " =    1.502
peak=    4.646 closest distance to " O   HOH Z   4 " =    1.146
peak=    4.602 closest distance to " O   HOH Z 239 " =    1.538
peak=    4.601 closest distance to " O   HOH Z 186 " =    1.252
peak=    4.538 closest distance to " CB  SER A  63 " =    1.394
peak=    4.483 closest distance to " O   HOH Z 287 " =    2.149
peak=    4.479 closest distance to " O   HOH Z  11 " =    1.220
peak=    4.442 closest distance to " O   HOH Z 193 " =    2.088
peak=    4.427 closest distance to " CB  SER A 216 " =    1.087
peak=    4.423 closest distance to " O   PRO A 198 " =    1.295
peak=    4.383 closest distance to " CG  PRO A 213 " =    1.297
peak=    4.366 closest distance to " O   HOH Z 369 " =    2.004
peak=    4.353 closest distance to " O   HOH Z 158 " =    1.294
peak=    4.327 closest distance to " O   HOH Z  63 " =    1.704
peak=    4.315 closest distance to " O   HOH Z 112 " =    1.144
peak=    4.312 closest distance to " O   HOH Z 211 " =    1.283
peak=    4.274 closest distance to " O   HOH Z 133 " =    2.503
peak=    4.227 closest distance to " O   HOH Z 175 " =    3.671
peak=    4.226 closest distance to " CG  PRO A  90 " =    1.291
peak=    4.212 closest distance to " O   HOH Z 147 " =    1.223
peak=    4.194 closest distance to " O   HOH Z  57 " =    2.240
peak=    4.188 closest distance to " O   HOH Z 298 " =    2.268
peak=    4.170 closest distance to " O   HOH Z 416 " =    1.296
peak=    4.164 closest distance to " O   HOH Z 170 " =    1.402
peak=    4.160 closest distance to " CA  TYR A  30 " =    1.113
peak=    4.157 closest distance to " O   HOH Z 232 " =    2.149
peak=    4.156 closest distance to " O   HOH Z 126 " =    2.315
peak=    4.151 closest distance to " O   HOH Z 363 " =    1.193
peak=    4.140 closest distance to " CB  VAL A 202 " =    1.558
peak=    4.121 closest distance to " CB  ARG A 275 " =    1.106
peak=    4.120 closest distance to " O   HOH Z  91 " =    2.405
peak=    4.117 closest distance to " O   HOH Z 414 " =    1.668
peak=    4.114 closest distance to " O   HOH Z  29 " =    1.147
peak=    4.109 closest distance to " CB  GLN A 183 " =    1.132
peak=    4.104 closest distance to " O   HOH Z 380 " =    2.152
peak=    4.103 closest distance to " O   HOH Z 209 " =    2.316
peak=    4.096 closest distance to " NH1AARG A 145 " =    1.216
peak=    4.085 closest distance to " O   HOH Z  49 " =    1.388
peak=    4.080 closest distance to " O   HOH Z 359 " =    1.571
peak=    4.065 closest distance to " CG  PRO A 198 " =    1.363
peak=    4.057 closest distance to " O   HOH Z  61 " =    1.732
peak=    4.052 closest distance to " O   HOH Z 155 " =    1.904
peak=    4.041 closest distance to " O   HOH Z  88 " =    3.365
peak=    4.034 closest distance to " CB  ASN A 148 " =    1.306
peak=    4.009 closest distance to " O   HOH Z 424 " =    1.295
peak=    4.003 closest distance to " CB  SER A   3 " =    1.494
peak=    4.002 closest distance to " CG  LEU A 167 " =    1.356
peak=    3.980 closest distance to " O   HOH Z 293 " =    1.445
peak=    3.977 closest distance to " CB  TRP A 266 " =    1.049
peak=    3.976 closest distance to " O   HOH Z 423 " =    1.903
peak=    3.975 closest distance to " C   ASN A 209 " =    1.547
peak=    3.970 closest distance to " O   HOH Z 401 " =    1.021
peak=    3.942 closest distance to " CB  ASP A 124 " =    0.912
peak=    3.935 closest distance to " OG BSER A 258 " =    0.974
peak=    3.931 closest distance to " O   HOH Z 399 " =    0.783
peak=    3.927 closest distance to " OE1 GLN A  11 " =    1.947
peak=    3.924 closest distance to " CD2 TRP A 179 " =    2.176
peak=    3.921 closest distance to " O   HOH Z 390 " =    2.657
peak=    3.916 closest distance to " O   HOH Z 130 " =    0.798
peak=    3.904 closest distance to " CE  MET A  93 " =    1.461
peak=    3.903 closest distance to " O   HOH Z 272 " =    1.911
peak=    3.902 closest distance to " O   HOH Z 217 " =    2.420
peak=    3.877 closest distance to " CG2 THR A 221 " =    1.121
peak=    3.875 closest distance to " O   HOH Z 392 " =    1.405
peak=    3.868 closest distance to " CB  GLU A 128 " =    1.140
peak=    3.858 closest distance to " ND2 ASN A  60 " =    3.020
peak=    3.858 closest distance to " N   TYR A  15 " =    1.071
peak=    3.850 closest distance to " CA  ASN A 127 " =    1.062
peak=    3.850 closest distance to " O   HOH Z   9 " =    2.256
peak=    3.850 closest distance to " O   HOH Z 128 " =    2.284
peak=    3.846 closest distance to " O   HOH Z 394 " =    1.828
peak=    3.842 closest distance to " N   GLN A 278 " =    1.177
peak=    3.841 closest distance to " O   HOH Z 284 " =    1.257
peak=    3.831 closest distance to " CE3 TRP A 274 " =    1.365
peak=    3.828 closest distance to " O   HOH Z 115 " =    1.998
peak=    3.824 closest distance to " O   HOH Z 145 " =    2.359
peak=    3.817 closest distance to " CA  GLY A 267 " =    1.267
peak=    3.814 closest distance to " NZ  LYS A 117 " =    1.248
peak=    3.798 closest distance to " O   HOH Z 361 " =    1.429
peak=    3.792 closest distance to " O   HOH Z  44 " =    2.640
peak=    3.786 closest distance to " CG  ARG A 159 " =    0.815
peak=    3.786 closest distance to " CB  TRP A 179 " =    1.480
peak=    3.785 closest distance to " CZ  PHE A 192 " =    1.017
peak=    3.782 closest distance to " O   HOH Z 104 " =    1.725
peak=    3.779 closest distance to " O   HOH Z 134 " =    1.261
peak=    3.778 closest distance to " O   HOH Z  20 " =    2.076
peak=    3.777 closest distance to " CB  MET A  47 " =    1.143
peak=    3.767 closest distance to " O   HOH Z 148 " =    1.573
peak=    3.759 closest distance to " O   HOH Z  57 " =    1.605
peak=    3.754 closest distance to " O   HOH Z   2 " =    1.750
peak=    3.753 closest distance to " O   HOH Z 422 " =    2.545
peak=    3.748 closest distance to " O   HOH Z  17 " =    1.975
peak=    3.744 closest distance to " CD  ARG A 159 " =    0.795
peak=    3.742 closest distance to " ND2 ASN A 249 " =    2.062
peak=    3.738 closest distance to " O   HOH Z 105 " =    1.292
peak=    3.736 closest distance to " O   HOH Z  59 " =    2.184
peak=    3.731 closest distance to " O   HOH Z 409 " =    1.966
peak=    3.728 closest distance to " O   HOH Z  39 " =    1.160
peak=    3.724 closest distance to " CB  MET A 105 " =    1.442
peak=    3.722 closest distance to " O   HOH Z  59 " =    1.523
peak=    3.715 closest distance to " O   HOH Z 171 " =    1.779
peak=    3.714 closest distance to " CD BLYS A 290 " =    1.080
peak=    3.710 closest distance to " CB  GLU A 152 " =    1.185
peak=    3.706 closest distance to " O   HOH Z 236 " =    1.463
peak=    3.699 closest distance to " CD1 ILE A  33 " =    1.751
peak=    3.698 closest distance to " CG  GLN A 278 " =    3.758
peak=    3.697 closest distance to " O   HOH Z  55 " =    1.876
peak=    3.696 closest distance to " O   HOH Z 159 " =    0.904
peak=    3.675 closest distance to " O   HOH Z 278 " =    1.083
peak=    3.674 closest distance to " CD  LYS A 166 " =    1.662
peak=    3.674 closest distance to " O   HOH Z 411 " =    3.316
peak=    3.672 closest distance to " O   HOH Z 135 " =    1.719
peak=    3.672 closest distance to " CA  ASP A  50 " =    1.227
peak=    3.669 closest distance to " O   HOH Z   9 " =    1.500
peak=    3.666 closest distance to " CA  ARG A  36 " =    1.397
peak=    3.663 closest distance to " O   HOH Z 207 " =    2.365
peak=    3.662 closest distance to " N   CYS A 260 " =    0.907
peak=    3.657 closest distance to " O   HOH Z  78 " =    1.637
peak=    3.657 closest distance to " CD1 LEU A 300 " =    1.216
peak=    3.653 closest distance to " CB  SER A 276 " =    1.020
peak=    3.651 closest distance to " NZ ALYS A 290 " =    0.961
peak=    3.644 closest distance to " O   HOH Z 405 " =    1.839
peak=    3.634 closest distance to " O   HOH Z 281 " =    1.890
peak=    3.633 closest distance to " O   HOH Z 288 " =    1.877
peak=    3.628 closest distance to " O   HOH Z  92 " =    1.218
peak=    3.616 closest distance to " CB  ALA A  43 " =    0.981
peak=    3.609 closest distance to " O   HOH Z 234 " =    3.920
peak=    3.606 closest distance to " CB  LEU A 228 " =    1.115
peak=    3.591 closest distance to " CB  GLU A 277 " =    3.642
peak=    3.591 closest distance to " O   HOH Z 217 " =    1.787
peak=    3.591 closest distance to " O   HOH Z 410 " =    1.662
peak=    3.588 closest distance to " O   HOH Z  51 " =    1.754
peak=    3.585 closest distance to " OE1 GLN A 240 " =    1.619
peak=    3.577 closest distance to " O   HOH Z  22 " =    1.854
peak=    3.576 closest distance to " CB  ARG A 190 " =    1.865
peak=    3.576 closest distance to " NE1 TRP A 274 " =    1.008
peak=    3.562 closest distance to " O   HOH Z 302 " =    1.490
peak=    3.559 closest distance to " CA  ALA A  51 " =    1.150
peak=    3.559 closest distance to " O   HOH Z  30 " =    1.845
peak=    3.557 closest distance to " CA  ILE A 234 " =    1.102
peak=    3.552 closest distance to " O   HOH Z 386 " =    1.242
peak=    3.549 closest distance to " CA  SER A  32 " =    1.708
peak=    3.549 closest distance to " O   HOH Z 122 " =    1.878
peak=    3.545 closest distance to " CG  GLN A  88 " =    1.017
peak=    3.539 closest distance to " OD2 ASP A 286 " =    2.794
peak=    3.539 closest distance to " O   HOH Z 411 " =    1.194
peak=    3.538 closest distance to " O   HOH Z 145 " =    3.491
peak=    3.534 closest distance to " O   HOH Z 282 " =    1.522
peak=    3.531 closest distance to " O   HOH Z 313 " =    2.080
peak=    3.522 closest distance to " CD  LYS A  76 " =    1.758
peak=    3.522 closest distance to " CA  SER A  95 " =    0.963
peak=    3.521 closest distance to " O   MET A 105 " =    1.754
peak=    3.520 closest distance to " O   HOH Z  67 " =    1.877
peak=    3.511 closest distance to " OD1 ASN A 217 " =    1.560
peak=    3.502 closest distance to " ND1 HIS A  81 " =    1.562
peak=    3.499 closest distance to " O   HOH Z 437 " =    2.253
peak=    3.498 closest distance to " O   HOH Z 258 " =    2.008
peak=    3.497 closest distance to " O   HOH Z 119 " =    4.066
peak=    3.486 closest distance to " NZ  LYS A  76 " =    1.435
peak=    3.486 closest distance to " CB  GLU A 236 " =    1.476
peak=    3.484 closest distance to " CA  ARG A 195 " =    1.499
peak=    3.481 closest distance to " O   HOH Z 113 " =    1.771
peak=    3.477 closest distance to " CA  MET A 105 " =    0.892
peak=    3.476 closest distance to " O   HOH Z  57 " =    1.345
peak=    3.473 closest distance to " NE AARG A 275 " =    1.685
peak=    3.470 closest distance to " O   HOH Z 145 " =    2.048
peak=    3.467 closest distance to " O   HOH Z 108 " =    1.914
peak=    3.464 closest distance to " CD  ARG A 195 " =    3.507
peak=    3.459 closest distance to " NE2 GLN A  58 " =    3.777
peak=    3.459 closest distance to " O   HOH Z 299 " =    2.927
peak=    3.453 closest distance to " O   HOH Z 371 " =    2.841
peak=    3.452 closest distance to " CA  GLU A 152 " =    1.144
peak=    3.445 closest distance to " CZ  PHE A 218 " =    1.191
peak=    3.442 closest distance to " CB  VAL A 265 " =    1.418
peak=    3.430 closest distance to " O   HOH Z 380 " =    3.205
peak=    3.428 closest distance to " O   HOH Z 417 " =    1.862
peak=    3.424 closest distance to " O   HOH Z 111 " =    1.442
peak=    3.423 closest distance to " NH1 ARG A  56 " =    1.324
peak=    3.417 closest distance to " O   HOH Z  40 " =    2.083
peak=    3.416 closest distance to " O   HOH Z 368 " =    3.780
peak=    3.413 closest distance to " O   GLY A 302 " =    2.428
peak=    3.412 closest distance to " CB  TRP A 274 " =    1.384
peak=    3.407 closest distance to " O   HOH Z   6 " =    1.968
peak=    3.407 closest distance to " CA  ALA A 160 " =    0.847
peak=    3.406 closest distance to " O   HOH Z 213 " =    2.080
peak=    3.404 closest distance to " O   HOH Z   7 " =    3.021
peak=    3.404 closest distance to " CB  PHE A 225 " =    1.440
peak=    3.403 closest distance to " O   HOH Z 334 " =    2.762
peak=    3.401 closest distance to " O   HOH Z 193 " =    2.079
peak=    3.400 closest distance to " NH2 ARG A 219 " =    1.719
peak=    3.400 closest distance to " O   HOH Z  47 " =    1.672
peak=    3.397 closest distance to " OE1 GLN A  88 " =    0.919
peak=    3.397 closest distance to " OG BSER A  99 " =    2.378
peak=    3.395 closest distance to " O   HOH Z 334 " =    1.574
peak=    3.395 closest distance to " OG BSER A 134 " =    2.652
peak=    3.394 closest distance to " O   THR A 220 " =    1.539
peak=    3.393 closest distance to " CB  ARG A 156 " =    1.041
peak=    3.393 closest distance to " O   HOH Z 258 " =    1.524
peak=    3.389 closest distance to " O   ALA A 165 " =    1.351
peak=    3.386 closest distance to " CA  ARG A 102 " =    1.112
peak=    3.385 closest distance to " O   HOH Z 329 " =    3.778
peak=    3.381 closest distance to " OE2 GLU A  53 " =    2.017
peak=    3.380 closest distance to " CB  ALA A  21 " =    1.161
peak=    3.378 closest distance to " O   HOH Z 225 " =    1.406
peak=    3.376 closest distance to " CD2 TRP A 179 " =    1.329
peak=    3.369 closest distance to " O   HOH Z  80 " =    1.480
peak=    3.369 closest distance to " CB  TRP A 150 " =    0.939
peak=    3.364 closest distance to " CG1 ILE A 120 " =    1.496
peak=    3.361 closest distance to " CZ3 TRP A 266 " =    1.177
peak=    3.358 closest distance to " CA  LEU A 282 " =    1.051
peak=    3.357 closest distance to " CA  TYR A 116 " =    1.372
peak=    3.357 closest distance to " O   HOH Z 182 " =    1.063
peak=    3.356 closest distance to " CB  ALA A 184 " =    1.085
peak=    3.345 closest distance to " CB  ALA A 114 " =    1.075
peak=    3.345 closest distance to " OG  SER A  22 " =    3.012
peak=    3.343 closest distance to " O   HOH Z  77 " =    1.332
peak=    3.341 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.336 closest distance to " CG1 ILE A  33 " =    1.273
peak=    3.333 closest distance to " O   HOH Z  61 " =    1.652
peak=    3.333 closest distance to " O   GLN A  55 " =    1.863
peak=    3.333 closest distance to " O   HOH Z 166 " =    1.401
peak=    3.332 closest distance to " CG2 ILE A 234 " =    0.883
peak=    3.331 closest distance to " CZ  PHE A  38 " =    1.483
peak=    3.329 closest distance to " O   HOH Z 148 " =    2.237
peak=    3.328 closest distance to " CG  PRO A 280 " =    0.959
peak=    3.325 closest distance to " CG  GLN A  11 " =    2.261
peak=    3.324 closest distance to " CG2 VAL A 257 " =    0.921
peak=    3.321 closest distance to " N   VAL A  72 " =    1.674
peak=    3.321 closest distance to " ND1 HIS A  86 " =    1.797
peak=    3.318 closest distance to " CA  TYR A 186 " =    1.531
peak=    3.311 closest distance to " O   HOH Z  42 " =    1.563
peak=    3.309 closest distance to " N   ASN A 127 " =    1.458
peak=    3.306 closest distance to " CB  ALA A  84 " =    0.713
peak=    3.304 closest distance to " O  BHOH Z  74 " =    1.440
peak=    3.301 closest distance to " O   HOH Z 222 " =    2.344
peak=    3.299 closest distance to " O   HOH Z 362 " =    1.721
peak=    3.293 closest distance to " O   HOH Z 222 " =    1.870
peak=    3.288 closest distance to " O   HOH Z 108 " =    1.659
peak=    3.288 closest distance to " O   HOH Z 276 " =    1.041
peak=    3.287 closest distance to " CG1 ILE A 151 " =    1.038
peak=    3.282 closest distance to " O   HOH Z 426 " =    0.990
peak=    3.280 closest distance to " CA  ASP A 124 " =    0.769
peak=    3.279 closest distance to " O   HOH Z 311 " =    2.156
peak=    3.277 closest distance to " CG  GLN A  89 " =    1.476
peak=    3.275 closest distance to " O   HOH Z 239 " =    1.540
peak=    3.269 closest distance to " O   HOH Z  57 " =    1.765
peak=    3.268 closest distance to " O   HOH Z 415 " =    1.761
peak=    3.267 closest distance to " O   HOH Z 133 " =    2.340
peak=    3.266 closest distance to " CB  ALA A   1 " =    4.529
peak=    3.265 closest distance to " CA  TRP A  92 " =    1.010
peak=    3.264 closest distance to " CA  THR A 264 " =    0.896
peak=    3.264 closest distance to " CE3 TRP A 274 " =    2.321
peak=    3.263 closest distance to " CG2 ILE A  20 " =    1.644
peak=    3.255 closest distance to " O   HOH Z 189 " =    2.292
peak=    3.251 closest distance to " CB  PRO A 243 " =    1.108
peak=    3.251 closest distance to " NE  ARG A  66 " =    3.069
peak=    3.247 closest distance to " CA  PRO A 280 " =    1.500
peak=    3.242 closest distance to " CB  ASN A 285 " =    0.907
peak=    3.241 closest distance to " CB  ALA A 114 " =    1.533
peak=    3.239 closest distance to " O   HOH Z 373 " =    1.413
peak=    3.239 closest distance to " O   HOH Z 189 " =    3.245
peak=    3.237 closest distance to " CB  LEU A 237 " =    0.804
peak=    3.227 closest distance to " CB  ASN A  60 " =    0.973
peak=    3.226 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.226 closest distance to " O   HOH Z 153 " =    3.800
peak=    3.226 closest distance to " O   HOH Z  37 " =    1.289
peak=    3.224 closest distance to " O   HOH Z  76 " =    1.052
peak=    3.224 closest distance to " N   SER A  97 " =    0.851
peak=    3.223 closest distance to " CB  ALA A  10 " =    1.089
peak=    3.222 closest distance to " O   HOH Z 158 " =    2.471
peak=    3.222 closest distance to " O   HOH Z  50 " =    1.901
peak=    3.215 closest distance to " CA  VAL A 125 " =    1.134
peak=    3.214 closest distance to " CE3 TRP A  85 " =    0.858
peak=    3.214 closest distance to " N   PHE A 130 " =    1.272
peak=    3.214 closest distance to " CG2 THR A 279 " =    0.949
peak=    3.213 closest distance to " O   HOH Z  44 " =    1.801
peak=    3.210 closest distance to " CD  ARG A 269 " =    0.949
peak=    3.201 closest distance to " O   HOH Z 146 " =    1.617
peak=    3.197 closest distance to " OG BSER A 210 " =    1.318
peak=    3.196 closest distance to " O   HOH Z 216 " =    2.787
peak=    3.196 closest distance to " CB  ASP A 140 " =    0.938
peak=    3.193 closest distance to " O   HOH Z 368 " =    4.792
peak=    3.184 closest distance to " O   HOH Z 393 " =    1.359
peak=    3.183 closest distance to " O   HOH Z 124 " =    1.742
peak=    3.181 closest distance to " NH2 ARG A  14 " =    1.857
peak=    3.179 closest distance to " O   HOH Z 156 " =    3.019
peak=    3.174 closest distance to " O   HOH Z  32 " =    2.319
peak=    3.174 closest distance to " CG2 ILE A 151 " =    1.001
peak=    3.168 closest distance to " CB  MET A  40 " =    0.759
peak=    3.168 closest distance to " N   SER A 271 " =    1.122
peak=    3.167 closest distance to " NE  ARG A 138 " =    0.975
peak=    3.166 closest distance to " O   HOH Z 306 " =    1.057
peak=    3.163 closest distance to " CG  GLU A 277 " =    1.991
peak=    3.162 closest distance to " CD  LYS A 119 " =    1.210
peak=    3.162 closest distance to " O   HOH Z 345 " =    1.902
peak=    3.158 closest distance to " CB  THR A 235 " =    0.904
peak=    3.156 closest distance to " CB  THR A  31 " =    1.562
peak=    3.152 closest distance to " CB  LEU A 300 " =    0.915
peak=    3.145 closest distance to " O   ALA A 158 " =    1.512
peak=    3.137 closest distance to " C   GLU A 277 " =    1.471
peak=    3.134 closest distance to " CA  SER A  87 " =    1.011
peak=    3.134 closest distance to " CB  ASN A  39 " =    1.002
peak=    3.134 closest distance to " CB  TYR A 116 " =    1.200
peak=    3.127 closest distance to " O   HOH Z 431 " =    1.270
peak=    3.114 closest distance to " O   HOH Z 407 " =    2.081
peak=    3.113 closest distance to " O   HOH Z 116 " =    1.782
peak=    3.113 closest distance to " O   HOH Z 213 " =    1.982
peak=    3.110 closest distance to " CG  GLN A 278 " =    1.113
peak=    3.109 closest distance to " O   HOH Z 158 " =    2.868
peak=    3.104 closest distance to " O   HOH Z 374 " =    1.134
peak=    3.100 closest distance to " O   HOH Z 154 " =    2.019
peak=    3.099 closest distance to " CG1 VAL A 189 " =    1.126
peak=    3.096 closest distance to " ND2 ASN A 187 " =    1.447
peak=    3.080 closest distance to " O   ALA A 242 " =    1.125
peak=    3.066 closest distance to " O   HOH Z 196 " =    1.135
peak=    3.066 closest distance to " OE2 GLU A 277 " =    2.182
peak=    3.053 closest distance to " O   HOH Z 104 " =    1.798
peak=    3.045 closest distance to " O   TYR A 116 " =    1.293
peak=    3.031 closest distance to " CG  PRO A 280 " =    2.159
peak=    3.003 closest distance to " O   HOH Z  30 " =    1.602

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 226         
Filter by distance & map next to the model:
   mapped sites are within: 0.406 - 5.665
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 226
   mapped sites are within: 0.774 - 5.665

peak=   -4.530 closest distance to " CG  GLN A  88 " =    0.892
peak=   -4.526 closest distance to " CD  ARG A  14 " =    3.344
peak=   -4.517 closest distance to " O   HOH Z 404 " =    0.885
peak=   -4.429 closest distance to " OG BSER A 134 " =    1.739
peak=   -4.357 closest distance to " O   PRO A 198 " =    1.349
peak=   -4.098 closest distance to " CZ3 TRP A 179 " =    1.270
peak=   -4.047 closest distance to " O   HOH Z 198 " =    2.312
peak=   -4.038 closest distance to " O   HOH Z  60 " =    1.757
peak=   -4.027 closest distance to " CG  PRO A 163 " =    2.390
peak=   -4.001 closest distance to " O   HOH Z  28 " =    1.389
peak=   -3.985 closest distance to " O   HOH Z 102 " =    1.747
peak=   -3.977 closest distance to " O   HOH Z 377 " =    2.009
peak=   -3.967 closest distance to " N   THR A 157 " =    1.632
peak=   -3.948 closest distance to " CB  ASP A  27 " =    2.481
peak=   -3.901 closest distance to " N   ALA A  43 " =    2.380
peak=   -3.894 closest distance to " CD1 TRP A 179 " =    1.234
peak=   -3.879 closest distance to " OG  SER A  87 " =    1.219
peak=   -3.873 closest distance to " CG  MET A 105 " =    0.921
peak=   -3.866 closest distance to " CA  GLY A  23 " =    2.869
peak=   -3.859 closest distance to " O   HOH Z  39 " =    1.048
peak=   -3.844 closest distance to " CD  LYS A 289 " =    2.285
peak=   -3.836 closest distance to " O   HOH Z  88 " =    1.781
peak=   -3.831 closest distance to " OE1 GLN A 223 " =    2.424
peak=   -3.813 closest distance to " OG  SER A  97 " =    2.175
peak=   -3.810 closest distance to " O   HOH Z 290 " =    1.328
peak=   -3.807 closest distance to " CB  TYR A  15 " =    2.029
peak=   -3.806 closest distance to " O   HOH Z 385 " =    1.481
peak=   -3.790 closest distance to " O   HOH Z 407 " =    3.308
peak=   -3.784 closest distance to " CB  ALA A 291 " =    1.916
peak=   -3.783 closest distance to " O   HOH Z 426 " =    1.595
peak=   -3.773 closest distance to " OE1 GLN A  88 " =    1.063
peak=   -3.763 closest distance to " O   ASP A 191 " =    2.012
peak=   -3.751 closest distance to " O   GLY A  80 " =    2.463
peak=   -3.751 closest distance to " CB  PRO A 243 " =    2.497
peak=   -3.729 closest distance to " O   HOH Z 163 " =    1.377
peak=   -3.728 closest distance to " O   HOH Z 371 " =    2.235
peak=   -3.717 closest distance to " O   ALA A   1 " =    1.204
peak=   -3.717 closest distance to " CA  GLY A 133 " =    1.980
peak=   -3.704 closest distance to " O   HOH Z  49 " =    1.389
peak=   -3.699 closest distance to " CB  ALA A 100 " =    2.138
peak=   -3.680 closest distance to " OD1 ASN A  60 " =    0.877
peak=   -3.659 closest distance to " CA  GLY A 203 " =    2.302
peak=   -3.650 closest distance to " CA  GLY A 241 " =    2.188
peak=   -3.644 closest distance to " OE1 GLN A 183 " =    1.631
peak=   -3.636 closest distance to " OG  SER A 245 " =    1.293
peak=   -3.617 closest distance to " O   ASN A 301 " =    1.165
peak=   -3.611 closest distance to " O   HOH Z 185 " =    2.126
peak=   -3.601 closest distance to " CG1BVAL A  41 " =    2.683
peak=   -3.601 closest distance to " O   HOH Z 401 " =    0.996
peak=   -3.599 closest distance to " ND2 ASN A 209 " =    1.950
peak=   -3.586 closest distance to " O   HOH Z 166 " =    1.353
peak=   -3.586 closest distance to " O   HOH Z 138 " =    0.947
peak=   -3.585 closest distance to " O   HOH Z  88 " =    2.492
peak=   -3.582 closest distance to " NH2 ARG A 219 " =    1.883
peak=   -3.575 closest distance to " O   HOH Z  13 " =    1.165
peak=   -3.574 closest distance to " NH2BARG A 275 " =    1.829
peak=   -3.573 closest distance to " O   HOH Z 111 " =    1.958
peak=   -3.551 closest distance to " OG ASER A 134 " =    1.195
peak=   -3.537 closest distance to " O   HOH Z  43 " =    1.285
peak=   -3.529 closest distance to " O   HOH Z  90 " =    2.786
peak=   -3.527 closest distance to " O   LEU A 300 " =    2.322
peak=   -3.525 closest distance to " O   ALA A  10 " =    1.702
peak=   -3.519 closest distance to " N   ARG A 159 " =    1.856
peak=   -3.519 closest distance to " OG  SER A 206 " =    2.032
peak=   -3.514 closest distance to " OD2 ASP A 270 " =    1.428
peak=   -3.513 closest distance to " O   ILE A 106 " =    2.201
peak=   -3.506 closest distance to " OD2 ASP A 171 " =    2.083
peak=   -3.501 closest distance to " O   HOH Z 231 " =    2.063
peak=   -3.500 closest distance to " NH1 ARG A 195 " =    2.292
peak=   -3.499 closest distance to " O   HOH Z 118 " =    1.139
peak=   -3.497 closest distance to " O   HOH Z 418 " =    1.306
peak=   -3.492 closest distance to " O   HOH Z 410 " =    2.327
peak=   -3.486 closest distance to " CZ  PHE A  59 " =    1.455
peak=   -3.472 closest distance to " OE1 GLU A  44 " =    1.776
peak=   -3.470 closest distance to " O   HOH Z   1 " =    1.370
peak=   -3.467 closest distance to " O   VAL A 125 " =    2.249
peak=   -3.466 closest distance to " CG1 VAL A  78 " =    2.411
peak=   -3.464 closest distance to " O   SER A 135 " =    1.485
peak=   -3.464 closest distance to " O   HOH Z 275 " =    1.718
peak=   -3.456 closest distance to " O   HOH Z 323 " =    2.118
peak=   -3.452 closest distance to " CE  MET A 113 " =    2.222
peak=   -3.448 closest distance to " O   HOH Z 411 " =    1.327
peak=   -3.446 closest distance to " CB  ALA A 248 " =    1.983
peak=   -3.443 closest distance to " CB  ASN A 285 " =    2.364
peak=   -3.442 closest distance to " CE2 TYR A 186 " =    1.791
peak=   -3.437 closest distance to " O   SER A  87 " =    1.950
peak=   -3.436 closest distance to " CB  TRP A  85 " =    2.580
peak=   -3.431 closest distance to " CG1 VAL A 265 " =    2.365
peak=   -3.424 closest distance to " O   HOH Z  27 " =    1.164
peak=   -3.419 closest distance to " CG  ARG A 269 " =    2.403
peak=   -3.418 closest distance to " CD2 TYR A 116 " =    2.204
peak=   -3.416 closest distance to " CG1BVAL A  41 " =    2.894
peak=   -3.415 closest distance to " CD  GLN A 223 " =    1.611
peak=   -3.413 closest distance to " O   HOH Z  51 " =    0.862
peak=   -3.407 closest distance to " O   HOH Z  73 " =    2.152
peak=   -3.405 closest distance to " O   HOH Z 389 " =    2.206
peak=   -3.405 closest distance to " CB  PRO A  54 " =    2.331
peak=   -3.394 closest distance to " CB  ALA A   9 " =    2.378
peak=   -3.394 closest distance to " OE1 GLU A   2 " =    1.969
peak=   -3.384 closest distance to " CA  GLY A  98 " =    1.869
peak=   -3.383 closest distance to " CG2 THR A 178 " =    2.004
peak=   -3.381 closest distance to " O   HOH Z 139 " =    2.831
peak=   -3.377 closest distance to " N   ARG A 138 " =    1.598
peak=   -3.375 closest distance to " O   HOH Z 147 " =    1.007
peak=   -3.375 closest distance to " O   HOH Z 308 " =    2.029
peak=   -3.374 closest distance to " C   VAL A  72 " =    1.058
peak=   -3.368 closest distance to " O   HOH Z  60 " =    2.561
peak=   -3.365 closest distance to " OH  TYR A 214 " =    1.170
peak=   -3.365 closest distance to " O   HOH Z 369 " =    2.307
peak=   -3.364 closest distance to " NH2 ARG A  79 " =    1.920
peak=   -3.359 closest distance to " OE2 GLU A 152 " =    1.050
peak=   -3.359 closest distance to " O   HOH Z  65 " =    1.229
peak=   -3.355 closest distance to " O   HOH Z  38 " =    1.262
peak=   -3.350 closest distance to " O   ASP A 253 " =    1.758
peak=   -3.349 closest distance to " O   HOH Z 351 " =    1.598
peak=   -3.346 closest distance to " O   VAL A 174 " =    2.235
peak=   -3.346 closest distance to " NE1 TRP A  70 " =    2.369
peak=   -3.345 closest distance to " O   HOH Z 386 " =    3.210
peak=   -3.345 closest distance to " CG  LEU A 281 " =    1.874
peak=   -3.343 closest distance to " O   HOH Z  24 " =    1.243
peak=   -3.332 closest distance to " O   HOH Z  52 " =    1.587
peak=   -3.326 closest distance to " CG2 ILE A  49 " =    2.737
peak=   -3.323 closest distance to " N   ALA A   1 " =    3.136
peak=   -3.322 closest distance to " O   HOH Z 251 " =    1.336
peak=   -3.318 closest distance to " O   HOH Z 424 " =    0.875
peak=   -3.318 closest distance to " O   HOH Z 140 " =    4.987
peak=   -3.317 closest distance to " N   ARG A 156 " =    1.073
peak=   -3.316 closest distance to " OE1 GLN A  89 " =    1.775
peak=   -3.310 closest distance to " OXT GLY A 302 " =    3.316
peak=   -3.308 closest distance to " O   SER A 216 " =    2.081
peak=   -3.306 closest distance to " O   ILE A  49 " =    1.630
peak=   -3.305 closest distance to " O   HOH Z 211 " =    1.525
peak=   -3.303 closest distance to " O   HOH Z 399 " =    2.238
peak=   -3.299 closest distance to " ND2 ASN A 285 " =    1.948
peak=   -3.298 closest distance to " O   PHE A 218 " =    1.446
peak=   -3.291 closest distance to " O   HOH Z 352 " =    2.086
peak=   -3.284 closest distance to " CD2 TYR A 293 " =    1.761
peak=   -3.277 closest distance to " O   HOH Z 414 " =    1.153
peak=   -3.270 closest distance to " O   HOH Z 234 " =    4.951
peak=   -3.268 closest distance to " CD2 TYR A 169 " =    2.501
peak=   -3.267 closest distance to " O   HOH Z 425 " =    0.972
peak=   -3.264 closest distance to " N   HIS A 115 " =    2.182
peak=   -3.255 closest distance to " O   HOH Z 276 " =    1.052
peak=   -3.254 closest distance to " CE3 TRP A 150 " =    2.122
peak=   -3.251 closest distance to " CE3 TRP A  70 " =    1.609
peak=   -3.250 closest distance to " OG  SER A  63 " =    1.374
peak=   -3.250 closest distance to " OE1 GLN A  58 " =    2.853
peak=   -3.248 closest distance to " NE2 GLN A  55 " =    0.774
peak=   -3.247 closest distance to " CG1BVAL A  72 " =    2.114
peak=   -3.245 closest distance to " CG  LEU A  83 " =    2.192
peak=   -3.244 closest distance to " O   HOH Z 388 " =    1.891
peak=   -3.243 closest distance to " OD2 ASP A 132 " =    2.331
peak=   -3.237 closest distance to " O   HOH Z 130 " =    0.982
peak=   -3.235 closest distance to " CG2BVAL A  72 " =    1.804
peak=   -3.233 closest distance to " C   LYS A 290 " =    1.430
peak=   -3.233 closest distance to " CB  ALA A  43 " =    2.402
peak=   -3.232 closest distance to " O   HOH Z 428 " =    2.284
peak=   -3.228 closest distance to " O   HOH Z   1 " =    3.715
peak=   -3.226 closest distance to " O   PRO A 163 " =    1.973
peak=   -3.220 closest distance to " CG  ARG A  66 " =    1.718
peak=   -3.219 closest distance to " CE3 TRP A 274 " =    2.498
peak=   -3.218 closest distance to " O   PRO A 243 " =    2.354
peak=   -3.218 closest distance to " O   LEU A 143 " =    1.475
peak=   -3.215 closest distance to " CG2BVAL A  41 " =    2.789
peak=   -3.215 closest distance to " CB  PHE A 130 " =    1.185
peak=   -3.211 closest distance to " CD1 LEU A 101 " =    2.317
peak=   -3.209 closest distance to " O   MET A  47 " =    2.642
peak=   -3.208 closest distance to " CB  ALA A 248 " =    2.387
peak=   -3.207 closest distance to " ND2 ASN A  60 " =    4.097
peak=   -3.203 closest distance to " OE1 GLN A 278 " =    1.169
peak=   -3.197 closest distance to " OD1 ASN A 301 " =    2.034
peak=   -3.197 closest distance to " O   ALA A 292 " =    2.207
peak=   -3.196 closest distance to " O   HOH Z 196 " =    1.601
peak=   -3.193 closest distance to " O   HOH Z  30 " =    1.719
peak=   -3.193 closest distance to " O   HOH Z 247 " =    1.691
peak=   -3.189 closest distance to " CD2 LEU A 237 " =    2.838
peak=   -3.188 closest distance to " O   GLY A 211 " =    1.258
peak=   -3.185 closest distance to " CB  ALA A 114 " =    2.424
peak=   -3.181 closest distance to " CB  LEU A 167 " =    1.734
peak=   -3.180 closest distance to " CG  GLN A  88 " =    1.129
peak=   -3.180 closest distance to " ND2 ASN A 215 " =    2.257
peak=   -3.180 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.180 closest distance to " CA  ASN A 148 " =    1.756
peak=   -3.176 closest distance to " O   HOH Z 416 " =    1.339
peak=   -3.169 closest distance to " O   HOH Z 390 " =    1.080
peak=   -3.169 closest distance to " O   HOH Z 298 " =    2.419
peak=   -3.168 closest distance to " CZ  ARG A  24 " =    1.976
peak=   -3.162 closest distance to " OD2 ASP A  27 " =    1.876
peak=   -3.157 closest distance to " CB  SER A  62 " =    2.427
peak=   -3.145 closest distance to " O   HOH Z  27 " =    1.629
peak=   -3.145 closest distance to " C   VAL A 265 " =    0.967
peak=   -3.143 closest distance to " CG2 VAL A 232 " =    2.085
peak=   -3.141 closest distance to " O   HOH Z 417 " =    1.661
peak=   -3.139 closest distance to " O   HOH Z   4 " =    1.275
peak=   -3.133 closest distance to " CB  CYS A 254 " =    1.954
peak=   -3.132 closest distance to " CB  ASN A 285 " =    2.129
peak=   -3.129 closest distance to " O   HOH Z 275 " =    1.900
peak=   -3.126 closest distance to " O   HOH Z  95 " =    1.531
peak=   -3.126 closest distance to " OH  TYR A 247 " =    1.466
peak=   -3.121 closest distance to " ND2 ASN A  60 " =    1.911
peak=   -3.120 closest distance to " C   ASN A 187 " =    1.768
peak=   -3.117 closest distance to " O   HOH Z 389 " =    1.133
peak=   -3.116 closest distance to " O   HOH Z 166 " =    1.649
peak=   -3.112 closest distance to " O   HOH Z 198 " =    1.904
peak=   -3.110 closest distance to " O   HOH Z 209 " =    2.695
peak=   -3.106 closest distance to " CA  LYS A 290 " =    1.405
peak=   -3.105 closest distance to " O   HOH Z 359 " =    1.436
peak=   -3.104 closest distance to " CA  SER A 271 " =    1.061
peak=   -3.103 closest distance to " O   HOH Z 128 " =    2.444
peak=   -3.102 closest distance to " O   HOH Z 433 " =    2.011
peak=   -3.100 closest distance to " O   HOH Z 336 " =    5.665
peak=   -3.094 closest distance to " CD  ARG A 156 " =    1.836
peak=   -3.093 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.088 closest distance to " C   GLU A 277 " =    2.214
peak=   -3.088 closest distance to " O   HOH Z  29 " =    0.959
peak=   -3.086 closest distance to " O   HOH Z 313 " =    1.409
peak=   -3.084 closest distance to " CZ  TYR A 169 " =    1.854
peak=   -3.077 closest distance to " O   HOH Z 124 " =    1.414
peak=   -3.070 closest distance to " O   HOH Z 350 " =    1.766
peak=   -3.057 closest distance to " O   HOH Z  52 " =    1.853
peak=   -3.031 closest distance to " O   HOH Z   2 " =    1.079
peak=   -3.026 closest distance to " CB  ASN A  39 " =    1.957

================= 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    :  0.4766 0.4757   6.292109e+00   6.287813e+00
   1_bss:  0.4680 0.4669   6.288297e+00   6.282186e+00
   1_xyz:  0.3827 0.4311   6.161844e+00   6.222651e+00
   1_adp:  0.3547 0.4330   6.130639e+00   6.225583e+00
   1_occ:  0.3543 0.4327   6.129715e+00   6.225519e+00
   2_bss:  0.3541 0.4298   6.129805e+00   6.224834e+00
   2_xyz:  0.2843 0.3554   5.956744e+00   6.091821e+00
   2_adp:  0.2626 0.3498   5.916797e+00   6.081638e+00
   2_occ:  0.2626 0.3495   5.915926e+00   6.081218e+00
   3_bss:  0.2630 0.3485   5.913460e+00   6.078965e+00
   3_xyz:  0.2202 0.2970   5.758950e+00   5.954941e+00
   3_adp:  0.2057 0.2820   5.707559e+00   5.917662e+00
   3_occ:  0.2054 0.2813   5.706506e+00   5.916439e+00
   4_bss:  0.2057 0.2811   5.705589e+00   5.914915e+00
   4_xyz:  0.1670 0.2340   5.514041e+00   5.750972e+00
   4_adp:  0.1523 0.2136   5.433215e+00   5.671465e+00
   4_occ:  0.1521 0.2132   5.432374e+00   5.670475e+00
   5_bss:  0.1523 0.2130   5.431889e+00   5.669340e+00
   5_xyz:  0.1323 0.1907   5.307995e+00   5.557449e+00
   5_adp:  0.1261 0.1811   5.265472e+00   5.517131e+00
   5_occ:  0.1260 0.1809   5.264941e+00   5.516765e+00
   5_bss:  0.1265 0.1804   5.263723e+00   5.515067e+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:  0.342  50.000   1.180   1.585  -2.161   0.000  -0.000  -0.000
   1_xyz:  0.342  50.000   1.180   1.585  -2.161   0.000  -0.000  -0.000
   1_adp:  0.342  50.000   1.180   1.585  -2.161   0.000  -0.000  -0.000
   1_occ:  0.342  50.000   1.180   1.585  -2.161   0.000  -0.000  -0.000
   2_bss:  0.360  79.932   0.437   0.401  -0.237   0.000  -0.000  -0.000
   2_xyz:  0.360  79.932   0.437   0.401  -0.237   0.000  -0.000  -0.000
   2_adp:  0.360  79.932   0.437   0.401  -0.237   0.000  -0.000  -0.000
   2_occ:  0.360  79.932   0.437   0.401  -0.237   0.000  -0.000  -0.000
   3_bss:  0.358  80.894   0.314  -0.243   0.345  -0.000   0.000   0.000
   3_xyz:  0.358  80.894   0.314  -0.243   0.345  -0.000   0.000   0.000
   3_adp:  0.358  80.894   0.314  -0.243   0.345  -0.000   0.000   0.000
   3_occ:  0.358  80.894   0.314  -0.243   0.345  -0.000   0.000   0.000
   4_bss:  0.338  73.112  -0.327  -0.942   0.174  -0.000   0.000   0.000
   4_xyz:  0.338  73.112  -0.327  -0.942   0.174  -0.000   0.000   0.000
   4_adp:  0.338  73.112  -0.327  -0.942   0.174  -0.000   0.000   0.000
   4_occ:  0.338  73.112  -0.327  -0.942   0.174  -0.000   0.000   0.000
   5_bss:  0.328  64.352  -0.696  -1.616  -0.181  -0.000  -0.000  -0.000
   5_xyz:  0.328  64.352  -0.696  -1.616  -0.181  -0.000  -0.000  -0.000
   5_adp:  0.328  64.352  -0.696  -1.616  -0.181  -0.000  -0.000  -0.000
   5_occ:  0.328  64.352  -0.696  -1.616  -0.181  -0.000  -0.000  -0.000
   5_bss:  0.322  64.355  -0.699  -1.619  -0.184  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.533 0.3869  0.5385    79376.989
   1_bss:  59.906 0.3940  0.5578    77485.021
   1_xyz:  50.650 0.5113  0.7046    57374.554
   1_adp:  51.038 0.5061  0.6893    57791.399
   1_occ:  51.080 0.5055  0.6874    57790.507
   2_bss:  50.675 0.5105  0.6954    57060.102
   2_xyz:  38.872 0.6547  0.8655    35547.134
   2_adp:  37.859 0.6667  0.8733    34659.850
   2_occ:  37.831 0.6670  0.8731    34562.091
   3_bss:  37.653 0.6688  0.8725    34124.958
   3_xyz:  31.073 0.7443  0.9452    23818.672
   3_adp:  29.000 0.7679  0.9512    21398.751
   3_occ:  28.955 0.7684  0.9511    21326.441
   4_bss:  28.907 0.7688  0.9346    21222.671
   4_xyz:  23.464 0.8255  0.9768    14139.353
   4_adp:  20.982 0.8513  0.9820    11850.910
   4_occ:  20.948 0.8516  0.9819    11816.931
   5_bss:  20.912 0.8519  0.9659    11768.498
   5_xyz:  17.966 0.8801  0.9807     9136.428
   5_adp:  16.864 0.8906  0.9785     8405.583
   5_occ:  16.852 0.8907  0.9783     8390.282
   5_bss:  16.806 0.8910  0.9787     8326.056
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8662e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8662e-01
   1_xyz:   1.721  0.013  0.123 16.930  0.006  4.107   1.7164e-01
   1_adp:   1.721  0.013  0.123 16.930  0.006  4.107   1.7164e-01
   1_occ:   1.721  0.013  0.123 16.930  0.006  4.107   1.7164e-01
   2_bss:   1.721  0.013  0.123 16.930  0.006  4.107   1.7164e-01
   2_xyz:   1.405  0.011  0.100 15.457  0.006  4.110   1.1332e-01
   2_adp:   1.405  0.011  0.100 15.457  0.006  4.110   1.1332e-01
   2_occ:   1.405  0.011  0.100 15.457  0.006  4.110   1.1332e-01
   3_bss:   1.405  0.011  0.100 15.457  0.006  4.110   1.1332e-01
   3_xyz:   0.978  0.007  0.067 14.280  0.004  4.121   6.1331e-02
   3_adp:   0.978  0.007  0.067 14.280  0.004  4.121   6.1331e-02
   3_occ:   0.978  0.007  0.067 14.280  0.004  4.121   6.1331e-02
   4_bss:   0.978  0.007  0.067 14.280  0.004  4.121   6.1331e-02
   4_xyz:   1.037  0.007  0.075 14.185  0.004  4.118   6.3213e-02
   4_adp:   1.037  0.007  0.075 14.185  0.004  4.118   6.3213e-02
   4_occ:   1.037  0.007  0.075 14.185  0.004  4.118   6.3213e-02
   5_bss:   1.037  0.007  0.075 14.185  0.004  4.118   6.3213e-02
   5_xyz:   1.105  0.009  0.078 14.411  0.004  4.111   7.1052e-02
   5_adp:   1.105  0.009  0.078 14.411  0.004  4.111   7.1052e-02
   5_occ:   1.105  0.009  0.078 14.411  0.004  4.111   7.1052e-02
   5_bss:   1.105  0.009  0.078 14.411  0.004  4.111   7.1052e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.481   2.4139e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.481   2.4139e-01
   1_xyz:  10.265  0.098  0.578 84.739  0.026  1.915   1.3159e-01
   1_adp:  10.265  0.098  0.578 84.739  0.026  1.915   1.3159e-01
   1_occ:  10.265  0.098  0.578 84.739  0.026  1.915   1.3159e-01
   2_bss:  10.265  0.098  0.578 84.739  0.026  1.915   1.3159e-01
   2_xyz:   7.649  0.087  0.307 79.786  0.036  2.125   1.4391e-01
   2_adp:   7.649  0.087  0.307 79.786  0.036  2.125   1.4391e-01
   2_occ:   7.649  0.087  0.307 79.786  0.036  2.125   1.4391e-01
   3_bss:   7.649  0.087  0.307 79.786  0.036  2.125   1.4391e-01
   3_xyz:   8.957  0.044  0.267 74.559  0.036  2.270   6.3638e-02
   3_adp:   8.957  0.044  0.267 74.559  0.036  2.270   6.3638e-02
   3_occ:   8.957  0.044  0.267 74.559  0.036  2.270   6.3638e-02
   4_bss:   8.957  0.044  0.267 74.559  0.036  2.270   6.3638e-02
   4_xyz:   8.707  0.046  0.236 78.910  0.031  2.296   5.3078e-02
   4_adp:   8.707  0.046  0.236 78.910  0.031  2.296   5.3078e-02
   4_occ:   8.707  0.046  0.236 78.910  0.031  2.296   5.3078e-02
   5_bss:   8.707  0.046  0.236 78.910  0.031  2.296   5.3078e-02
   5_xyz:   8.992  0.044  0.249 82.962  0.032  2.248   5.7296e-02
   5_adp:   8.992  0.044  0.249 82.962  0.032  2.248   5.7296e-02
   5_occ:   8.992  0.044  0.249 82.962  0.032  2.248   5.7296e-02
   5_bss:   8.992  0.044  0.249 82.962  0.032  2.248   5.7296e-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: 106.92   0.00  17.31 106.92   0.00  13.87  65.32   0.00  36.08
   1_occ: 106.92   0.00  17.31 106.92   0.00  13.87  65.32   0.00  36.08
   2_bss: 106.92   0.00  17.31 106.92   0.00  13.87  65.32   0.00  36.08
   2_xyz: 106.92   0.00  17.31 106.92   0.00  13.87  65.32   0.00  36.08
   2_adp:  88.00   0.00  18.89  74.70   0.00  14.85  88.00   0.00  40.90
   2_occ:  88.00   0.00  18.89  74.70   0.00  14.85  88.00   0.00  40.90
   3_bss:  88.00   0.00  18.89  74.70   0.00  14.85  88.00   0.00  40.90
   3_xyz:  88.00   0.00  18.89  74.70   0.00  14.85  88.00   0.00  40.90
   3_adp:  98.70   0.00  19.07  89.32   0.00  13.98  98.70   3.71  46.75
   3_occ:  98.70   0.00  19.07  89.32   0.00  13.98  98.70   3.71  46.75
   4_bss:  98.70   0.00  19.07  89.32   0.00  13.98  98.70   3.71  46.75
   4_xyz:  98.70   0.00  19.07  89.32   0.00  13.98  98.70   3.71  46.75
   4_adp: 100.40   0.00  18.25  93.76   0.00  12.81 100.40   1.51  47.89
   4_occ: 100.40   0.00  18.25  93.76   0.00  12.81 100.40   1.51  47.89
   5_bss: 100.40   0.00  18.25  93.76   0.00  12.81 100.40   1.51  47.89
   5_xyz: 100.40   0.00  18.25  93.76   0.00  12.81 100.40   1.51  47.89
   5_adp: 103.85   0.00  17.77 102.08   0.00  12.32 103.85   1.12  47.45
   5_occ: 103.85   0.00  17.77 102.08   0.00  12.32 103.85   1.12  47.45
   5_bss: 103.86   0.00  17.78 102.09   0.00  12.33 103.86   1.12  47.46
------------------------------------------------------------------------
 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:    1.798    0.009    0.415
   1_adp:    1.798    0.009    0.415
   1_occ:    1.798    0.009    0.415
   2_bss:    1.798    0.009    0.415
   2_xyz:    1.750    0.067    0.615
   2_adp:    1.750    0.067    0.615
   2_occ:    1.750    0.067    0.615
   3_bss:    1.750    0.067    0.615
   3_xyz:    1.966    0.042    0.725
   3_adp:    1.966    0.042    0.725
   3_occ:    1.966    0.042    0.725
   4_bss:    1.966    0.042    0.725
   4_xyz:    2.050    0.073    0.834
   4_adp:    2.050    0.073    0.834
   4_occ:    2.050    0.073    0.834
   5_bss:    2.050    0.073    0.834
   5_xyz:    2.146    0.061    0.875
   5_adp:    2.146    0.061    0.875
   5_occ:    2.146    0.061    0.875
   5_bss:    2.146    0.061    0.875
------------------------------------------------------------------------

CPU time actual refinement: 353.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/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_1215/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1215/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.61 
  Macro-tasks:
    bulk solvent and scale       = 49.09  
    individual site refinement   = 141.68 
    weights calculation          = 30.62  
    collect and process          = 6.45   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 227.95 
  Micro-tasks:
    mask                            = 3.02   
    f_calc                          = 112.20 
    alpha_beta                      = 8.01   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 119.22 
    fmodel                         = 8.15   
    r_factors                      = 0.22   
    phase_errors                   = 10.26  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 262.52 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.065 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    621 calls, 111.89 s
gradients_fft:          566 calls, 106.64 s

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

# Date 2008-01-16 Time 06:42:51 PST -0800 (1200494571.25 s)
Start R-work = 0.4766, R-free = 0.4757 (no bulk solvent and anisotropic scale)
Final R-work = 0.1434, R-free = 0.1960 (no bulk solvent and anisotropic scale)

Start R-work = 0.4680, R-free = 0.4669
Final R-work = 0.1265, R-free = 0.1804