# Date 2008-01-16 Time 03:59:18 PST -0800 (1200484758.96 s)
#phil __OFF__

Command line arguments: "../132.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22276
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 132

-------------------------------------------------------------------------------
  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: (68.845, 45.9914, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


================================== 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: (68.845, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95099
Completeness in resolution range: 0.977544
Completeness with d_max=infinity: 0.974432

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             d_min =   1.9510

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: (68.845, 45.9914, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95099
Completeness in resolution range: 0.977544
Completeness with d_max=infinity: 0.974432

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1741 [2101/2125]  1892   209   9.9%
  bin  2:  4.1741 -  3.3258 [2030/2049]  1826   204  10.0%
  bin  3:  3.3258 -  2.9091 [1992/2011]  1790   202  10.1%
  bin  4:  2.9091 -  2.6448 [1971/2001]  1777   194   9.8%
  bin  5:  2.6448 -  2.4562 [1962/1981]  1765   197  10.0%
  bin  6:  2.4562 -  2.3119 [1953/1978]  1757   196  10.0%
  bin  7:  2.3119 -  2.1966 [1968/1996]  1771   197  10.0%
  bin  8:  2.1966 -  2.1012 [1928/1964]  1737   191   9.9%
  bin  9:  2.1012 -  2.0206 [1915/1957]  1725   190   9.9%
  bin 10:  2.0206 -  1.9510 [1769/1977]  1590   179  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/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: 0.11 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:
        0.74 -     1.57: 6
        1.57 -     2.40: 80
        2.40 -     3.24: 3495
        3.24 -     4.07: 9757
        4.07 -     4.90: 16017
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.741 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.209 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.222 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.227 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.404 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29350 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_132/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/model_refine_001.geo

CPU time processing inputs: 7.92


============================ 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 = 68.845 45.9914 84.23025 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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5022   r_free= 0.5092   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.299967                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.4099 0.4040      6.6113      6.6121|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.4493 0.4418      6.8538      6.8534|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.4856 0.5000      6.7405       6.811|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.4946 0.4851      6.5742       6.541|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.5306 0.5094      6.4057      6.3897|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.5419 0.5862      6.3181       6.285|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.5295 0.5022      6.2649      6.1957|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.5351 0.5490       6.211      6.2251|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.5561 0.5587       6.135      6.1602|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.5317 0.5459       6.133       6.136|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.5329 0.5882      6.0537      6.1023|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.5371 0.5508      5.9998      6.0301|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.5235 0.5603      5.8985      5.8974|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.5391 0.4919      5.8594      5.7566|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6552  1372   153  0.64  39.03   0.82     0.70      87424.38|
|  2:  4.6552 -  3.7147  1314   145  0.63  41.47   0.88     0.75     138600.39|
|  3:  3.7147 -  3.2510  1287   144  0.50  51.99   0.92     0.69     149487.29|
|  4:  3.2510 -  2.9564  1278   143  0.37  61.96   0.92     0.54     134680.29|
|  5:  2.9564 -  2.7460  1274   141  0.24  71.72   0.87     0.35     104276.20|
|  6:  2.7460 -  2.5850  1274   139  0.15  79.08   0.87     0.21      91213.74|
|  7:  2.5850 -  2.4562  1251   141  0.12  81.24   0.89     0.16      81100.55|
|  8:  2.4562 -  2.3497  1265   139  0.15  78.56   0.93     0.23      73289.14|
|  9:  2.3497 -  2.2596  1258   139  0.20  74.85   0.89     0.31      64234.87|
| 10:  2.2596 -  2.1819  1232   137  0.23  72.73   0.96     0.35      57176.73|
| 11:  2.1819 -  2.1138  1252   143  0.20  75.14   0.95     0.31      54084.69|
| 12:  2.1138 -  2.0536  1237   133  0.21  74.16   0.98     0.35      49640.92|
| 13:  2.0536 -  1.9997  1239   143  0.26  70.60   0.95     0.42      40693.54|
| 14:  1.9997 -  1.9510  1097   119  0.38  61.34   0.96     0.56      28200.37|
|alpha:            min =        0.16 max =            0.75 mean =         0.43|
|beta:             min =    28200.37 max =       149487.29 mean =     83467.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.45|
|phase err.(test): min =        0.00 max =           89.91 mean =        66.78|
|-----------------------------------------------------------------------------|

============================== 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 = 21.377567             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.474   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.586254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.503   (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 |  0.741 -  1.157:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.157 -  1.573:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.573 -  1.989:       21 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  1.989 -  2.405:       59 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.405 -  2.821:      937 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.821 -  3.236:     2558 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.236 -  3.652:     3567 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.652 -  4.068:     6190 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.068 -  4.484:     6939 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.484 -  4.900:     9078 |
|-----------------------------------------------------------------------------|
|-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 |        0.251 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.104    4.900  0.741 |       1.588 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5022   r_free= 0.5092   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.93 A                  |
| x-ray target function (ml) for work reflections: 6.299967                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4942   r_free= 0.4980   ksol= 0.35   Bsol= 0.00   scale= 0.917    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,0.68,1.60,0.00,0.00,0.00); trace/3= 0.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.297844                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.095271             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.560   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.105860              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.231   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4942      final r-factor (work) = 0.4147          |
| start r-factor (free) = 0.4980      final r-factor (free) = 0.4440          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.7567 = 15.10 * 0.50 * 6.2941 + 1.00 * 0.2513                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.1284 = 15.10 * 0.50 * 6.2256 + 1.00 * 0.1396                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4147      final r-factor (work) = 0.3745          |
| start r-factor (free) = 0.4440      final r-factor (free) = 0.4438          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.1165 = 2.11 * 1.00 * 6.2256 + 1.00 * 0.0062                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.9704 = 2.11 * 1.00 * 6.1463 + 1.00 * 0.0271                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.35   20.37    None  None   None       |
|    all(noH): 2823   0      0.00    99.35   20.37    None  None   None       |
|    Sol.    : 438    0      0.00    99.35   35.73    None  None   None       |
|    Mac.    : 2385   0      0.00    85.54   17.55    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 -   9.935:  835   |   5:    49.675 -  59.610:   94        |
|      1:     9.935 -  19.870:  781   |   6:    59.610 -  69.545:   40        |
|      2:    19.870 -  29.805:  543   |   7:    69.545 -  79.479:   15        |
|      3:    29.805 -  39.740:  321   |   8:    79.479 -  89.414:    7        |
|      4:    39.740 -  49.675:  183   |   9:    89.414 -  99.349:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3745 r_free = 0.4438             target_work(ml) = 6.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3741 r_free = 0.4439             target_work(ml) = 6.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3741   r_free= 0.4439   ksol= 0.35   Bsol= 0.00   scale= 1.006    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.61,0.68,1.60,0.00,0.00,0.00); trace/3= 0.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.147218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3715   r_free= 0.4435   ksol= 0.35   Bsol= 40.09   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.96,1.14,0.00,0.00,0.00); trace/3= 0.47                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.144721                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.297777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.079  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.728953              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.748  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3715      final r-factor (work) = 0.3162          |
| start r-factor (free) = 0.4435      final r-factor (free) = 0.3850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.7190 = 9.30 * 0.50 * 6.1476 + 1.00 * 0.1396                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.3932 = 9.30 * 0.50 * 6.0890 + 1.00 * 0.0863                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3162      final r-factor (work) = 0.3002          |
| start r-factor (free) = 0.3850      final r-factor (free) = 0.3732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4654 = 0.73 * 1.00 * 6.0890 + 1.00 * 0.0268                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3897 = 0.73 * 1.00 * 6.0012 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.25   19.17    None  None   None       |
|    all(noH): 2823   0      0.00    99.25   19.17    None  None   None       |
|    Sol.    : 438    0      0.00    99.25   36.98    None  None   None       |
|    Mac.    : 2385   0      0.00    88.35   15.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.925:  860   |   5:    49.627 -  59.552:   79        |
|      1:     9.925 -  19.851:  921   |   6:    59.552 -  69.477:   30        |
|      2:    19.851 -  29.776:  494   |   7:    69.477 -  79.402:    9        |
|      3:    29.776 -  39.701:  257   |   8:    79.402 -  89.328:    9        |
|      4:    39.701 -  49.627:  161   |   9:    89.328 -  99.253:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3002 r_free = 0.3732             target_work(ml) = 5.987         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2999 r_free = 0.3733             target_work(ml) = 5.987         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2999   r_free= 0.3733   ksol= 0.35   Bsol= 40.09   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.96,1.14,0.00,0.00,0.00); trace/3= 0.47                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.986839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2999   r_free= 0.3719   ksol= 0.34   Bsol= 40.09   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.22,0.15,-0.00,0.00,0.00); trace/3= -0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.985085                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.475149              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.655   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665910              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.163  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2999      final r-factor (work) = 0.2481          |
| start r-factor (free) = 0.3719      final r-factor (free) = 0.3222          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5128 = 4.48 * 0.50 * 6.0005 + 1.00 * 0.0863                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2863 = 4.48 * 0.50 * 5.9095 + 1.00 * 0.0634                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2481      final r-factor (work) = 0.2328          |
| start r-factor (free) = 0.3222      final r-factor (free) = 0.3083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9505 = 0.67 * 1.00 * 5.9095 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1880 = 0.67 * 1.00 * 5.8131 + 1.00 * 0.3170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.64  18.52    None  None   None       |
|    all(noH): 2823   0      0.00    101.64  18.52    None  None   None       |
|    Sol.    : 438    0      3.31    101.64  40.59    None  None   None       |
|    Mac.    : 2385   0      0.00    98.05   14.47    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 -  10.164: 1005   |   5:    50.819 -  60.983:   92        |
|      1:    10.164 -  20.328:  960   |   6:    60.983 -  71.146:   40        |
|      2:    20.328 -  30.491:  341   |   7:    71.146 -  81.310:   11        |
|      3:    30.491 -  40.655:  217   |   8:    81.310 -  91.474:    4        |
|      4:    40.655 -  50.819:  148   |   9:    91.474 - 101.638:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2328 r_free = 0.3083             target_work(ml) = 5.790         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2326 r_free = 0.3081             target_work(ml) = 5.789         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2326   r_free= 0.3081   ksol= 0.34   Bsol= 40.09   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.22,0.15,-0.00,0.00,0.00); trace/3= -0.36                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.789240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2327   r_free= 0.3074   ksol= 0.33   Bsol= 37.52   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.11,-0.50,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.789001                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.991399              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.552  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 30.511587             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.993   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2327      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3074      final r-factor (free) = 0.2425          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7600 = 2.99 * 0.50 * 5.8145 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5842 = 2.99 * 0.50 * 5.6992 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2425      final r-factor (free) = 0.2284          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 173.9061 = 30.51 * 1.00 * 5.6992 + 1.00 * 0.0147                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 168.6521 = 30.51 * 1.00 * 5.5269 + 1.00 * 0.0161                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.60  19.11    None  None   None       |
|    all(noH): 2823   0      0.00    112.60  19.11    None  None   None       |
|    Sol.    : 438    0      2.94    106.70  48.54    None  None   None       |
|    Mac.    : 2385   0      0.00    112.60  13.71    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 -  11.260: 1293   |   5:    56.299 -  67.558:  106        |
|      1:    11.260 -  22.519:  874   |   6:    67.558 -  78.818:   65        |
|      2:    22.519 -  33.779:  201   |   7:    78.818 -  90.078:   27        |
|      3:    33.779 -  45.039:  122   |   8:    90.078 - 101.337:   10        |
|      4:    45.039 -  56.299:  121   |   9:   101.337 - 112.597:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1669 r_free = 0.2284             target_work(ml) = 5.493         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1667 r_free = 0.2278             target_work(ml) = 5.492         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2278   ksol= 0.33   Bsol= 37.52   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-1.11,-0.50,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.491891                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2274   ksol= 0.31   Bsol= 37.52   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.60,-0.85,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.489555                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.530934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.432   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.188455              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1430          |
| start r-factor (free) = 0.2274      final r-factor (free) = 0.2026          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0548 = 2.53 * 0.50 * 5.5275 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9206 = 2.53 * 0.50 * 5.4249 + 1.00 * 0.0555                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1430      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1864          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0384 = 0.19 * 1.00 * 5.4249 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0239 = 0.19 * 1.00 * 5.3535 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.98  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    104.98  17.56    None  None   None       |
|    Sol.    : 438    0      5.66    101.42  43.09    None  None   None       |
|    Mac.    : 2385   0      0.00    104.98  12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.498: 1207   |   5:    52.488 -  62.986:   97        |
|      1:    10.498 -  20.995: 1005   |   6:    62.986 -  73.483:   45        |
|      2:    20.995 -  31.493:  200   |   7:    73.483 -  83.981:   23        |
|      3:    31.493 -  41.990:  136   |   8:    83.981 -  94.478:    5        |
|      4:    41.990 -  52.488:   99   |   9:    94.478 - 104.976:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1381 r_free = 0.1864             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1377 r_free = 0.1855             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1855   ksol= 0.31   Bsol= 37.52   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.60,-0.85,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.307279                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.1088 0.1440        5.48      5.6521|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.1032 0.1404      5.6069      5.8608|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.1338 0.1708      5.7011      5.9691|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.1542 0.2134       5.663      5.8855|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.1550 0.1950      5.4754      5.6354|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.1453 0.1875      5.3517      5.4784|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.1481 0.1986      5.2951      5.5283|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.1559 0.2023      5.2828      5.5208|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.1519 0.2109      5.2254      5.4303|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.1418 0.2214      5.1472      5.3972|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.1442 0.2011      5.0964      5.3812|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.1405 0.1739      5.0261      5.2382|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.1394 0.2028      4.9413      5.1866|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.1434 0.2012      4.8958      5.1141|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6552  1372   153  0.92  11.25   0.99     0.97       9552.44|
|  2:  4.6552 -  3.7147  1314   145  0.94  10.34   1.05     1.03      12702.63|
|  3:  3.7147 -  3.2510  1287   144  0.91  14.73   1.06     1.05      15908.82|
|  4:  3.2510 -  2.9564  1278   143  0.89  17.27   1.04     1.03      15355.37|
|  5:  2.9564 -  2.7460  1274   141  0.88  17.96   1.02     0.98      10688.32|
|  6:  2.7460 -  2.5850  1274   139  0.89  17.81   1.01     0.99       8928.91|
|  7:  2.5850 -  2.4562  1251   141  0.88  18.85   1.02     0.98       8005.59|
|  8:  2.4562 -  2.3497  1265   139  0.88  18.20   1.03     1.02       7485.32|
|  9:  2.3497 -  2.2596  1258   139  0.88  18.70   1.04     1.03       7024.87|
| 10:  2.2596 -  2.1819  1232   137  0.87  18.92   1.03     0.99       6203.09|
| 11:  2.1819 -  2.1138  1252   143  0.88  18.86   1.04     1.00       5635.35|
| 12:  2.1138 -  2.0536  1237   133  0.89  17.34   1.05     1.04       4820.78|
| 13:  2.0536 -  1.9997  1239   143  0.88  17.97   1.05     1.04       4194.74|
| 14:  1.9997 -  1.9510  1097   119  0.88  18.72   1.02     0.99       3872.90|
|alpha:            min =        0.97 max =            1.05 mean =         1.01|
|beta:             min =     3872.90 max =        15908.82 mean =      8696.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.88 mean =        16.84|
|phase err.(test): min =        0.00 max =           89.34 mean =        16.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1856   ksol= 0.31   Bsol= 33.13   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-1.93,-1.15,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.307410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1856   ksol= 0.31   Bsol= 33.13   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-1.93,-1.15,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.307410                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6552 0.99   1372  153 0.1092 0.1437       5.475      5.6393|
|  2:  4.6552 -  3.7147 0.99   1314  145 0.1034 0.1414       5.606      5.8612|
|  3:  3.7147 -  3.2510 0.99   1287  144 0.1336 0.1691       5.699      5.9613|
|  4:  3.2510 -  2.9564 0.99   1278  143 0.1541 0.2126      5.6633      5.8872|
|  5:  2.9564 -  2.7460 0.99   1274  141 0.1553 0.1968      5.4765      5.6384|
|  6:  2.7460 -  2.5850 0.99   1274  139 0.1450 0.1868      5.3521      5.4747|
|  7:  2.5850 -  2.4562 0.99   1251  141 0.1481 0.1984      5.2963      5.5302|
|  8:  2.4562 -  2.3497 0.98   1265  139 0.1558 0.2016      5.2833      5.5207|
|  9:  2.3497 -  2.2596 0.98   1258  139 0.1518 0.2106      5.2258       5.431|
| 10:  2.2596 -  2.1819 0.99   1232  137 0.1419 0.2213      5.1489      5.3991|
| 11:  2.1819 -  2.1138 0.98   1252  143 0.1439 0.2013      5.0967      5.3836|
| 12:  2.1138 -  2.0536 0.97   1237  133 0.1405 0.1749      5.0277      5.2404|
| 13:  2.0536 -  1.9997 1.00   1239  143 0.1393 0.2034      4.9429      5.1896|
| 14:  1.9997 -  1.9510 0.85   1097  119 0.1435 0.2009      4.8974      5.1142|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6741 -  4.6552  1372   153  0.93  11.00   0.98     0.96       9297.41|
|  2:  4.6552 -  3.7147  1314   145  0.94  10.19   1.05     1.03      12488.33|
|  3:  3.7147 -  3.2510  1287   144  0.91  14.68   1.06     1.05      15813.59|
|  4:  3.2510 -  2.9564  1278   143  0.89  17.26   1.03     1.02      15356.10|
|  5:  2.9564 -  2.7460  1274   141  0.88  18.03   1.01     0.97      10736.35|
|  6:  2.7460 -  2.5850  1274   139  0.89  17.84   1.00     0.97       8955.89|
|  7:  2.5850 -  2.4562  1251   141  0.88  18.87   1.01     0.97       8021.73|
|  8:  2.4562 -  2.3497  1265   139  0.88  18.25   1.01     1.00       7520.70|
|  9:  2.3497 -  2.2596  1258   139  0.88  18.73   1.03     1.01       7048.15|
| 10:  2.2596 -  2.1819  1232   137  0.87  18.95   1.02     0.97       6230.40|
| 11:  2.1819 -  2.1138  1252   143  0.88  18.90   1.02     0.98       5660.70|
| 12:  2.1138 -  2.0536  1237   133  0.89  17.41   1.03     1.02       4848.59|
| 13:  2.0536 -  1.9997  1239   143  0.88  18.02   1.02     1.02       4218.76|
| 14:  1.9997 -  1.9510  1097   119  0.88  18.75   1.00     0.97       3888.24|
|alpha:            min =        0.96 max =            1.05 mean =         1.00|
|beta:             min =     3888.24 max =        15813.59 mean =      8672.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.84|
|phase err.(test): min =        0.00 max =           89.79 mean =        16.36|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.107)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.98  17.56    None  None   None       |
|    all(noH): 2823   0      0.00    104.98  17.56    None  None   None       |
|    Sol.    : 438    0      5.66    101.42  43.09    None  None   None       |
|    Mac.    : 2385   0      0.00    104.98  12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.501: 1207   |   5:    52.491 -  62.989:   97        |
|      1:    10.501 -  20.998: 1005   |   6:    62.989 -  73.486:   45        |
|      2:    20.998 -  31.496:  200   |   7:    73.486 -  83.984:   23        |
|      3:    31.496 -  41.993:  136   |   8:    83.984 -  94.481:    5        |
|      4:    41.993 -  52.491:   99   |   9:    94.481 - 104.979:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.642 - 5.623
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 348
   mapped sites are within: 0.716 - 5.623

peak=    8.236 closest distance to " O   HOH Z 400 " =    1.234
peak=    6.940 closest distance to " O   HOH Z 179 " =    1.293
peak=    6.775 closest distance to " OD1 ASN A  60 " =    1.179
peak=    6.708 closest distance to " C   SER A  62 " =    1.153
peak=    6.461 closest distance to " O   HOH Z  65 " =    1.756
peak=    6.363 closest distance to " O   HOH Z 130 " =    1.235
peak=    6.315 closest distance to " O   HOH Z 385 " =    1.608
peak=    5.932 closest distance to " O   HOH Z 138 " =    1.127
peak=    5.863 closest distance to " O   HOH Z 138 " =    2.104
peak=    5.762 closest distance to " O   HOH Z 126 " =    1.974
peak=    5.681 closest distance to " O   HOH Z 375 " =    1.525
peak=    5.622 closest distance to " O   HOH Z 390 " =    1.122
peak=    5.622 closest distance to " O   HOH Z 363 " =    1.300
peak=    5.612 closest distance to " O   HOH Z 199 " =    1.537
peak=    5.553 closest distance to " O   HOH Z 245 " =    1.381
peak=    5.524 closest distance to " O   HOH Z  61 " =    1.286
peak=    5.486 closest distance to " O   HOH Z  37 " =    1.458
peak=    5.372 closest distance to " O   HOH Z 403 " =    1.745
peak=    5.365 closest distance to " O   HOH Z 278 " =    1.628
peak=    5.362 closest distance to " CG  PRO A  54 " =    1.242
peak=    5.345 closest distance to " O   HOH Z 214 " =    1.545
peak=    5.299 closest distance to " O   HOH Z 244 " =    1.725
peak=    5.284 closest distance to " NH2 ARG A  56 " =    2.012
peak=    5.220 closest distance to " O   HOH Z 279 " =    1.203
peak=    5.205 closest distance to " NE2 GLN A  11 " =    1.433
peak=    5.193 closest distance to " O   HOH Z 431 " =    1.406
peak=    5.188 closest distance to " NE2 GLN A  55 " =    1.305
peak=    5.132 closest distance to " O   HOH Z 236 " =    1.733
peak=    5.126 closest distance to " CB  ARG A 275 " =    1.108
peak=    5.119 closest distance to " O   HOH Z 103 " =    1.029
peak=    5.071 closest distance to " O   HOH Z 112 " =    2.013
peak=    5.070 closest distance to " O   HOH Z 429 " =    1.129
peak=    5.005 closest distance to " O   HOH Z 116 " =    1.405
peak=    4.999 closest distance to " O   HOH Z 410 " =    1.403
peak=    4.976 closest distance to " O   HOH Z 276 " =    1.693
peak=    4.904 closest distance to " O   HOH Z 426 " =    1.243
peak=    4.896 closest distance to " O   HOH Z 427 " =    1.304
peak=    4.889 closest distance to " O   PRO A 198 " =    1.342
peak=    4.881 closest distance to " CG  PRO A  90 " =    1.285
peak=    4.864 closest distance to " N   ASN A  60 " =    1.138
peak=    4.858 closest distance to " O   HOH Z   7 " =    1.541
peak=    4.732 closest distance to " O   HOH Z 316 " =    2.563
peak=    4.716 closest distance to " O   HOH Z 109 " =    1.508
peak=    4.714 closest distance to " O   HOH Z 124 " =    1.799
peak=    4.711 closest distance to " O   HOH Z  92 " =    1.609
peak=    4.665 closest distance to " O   HOH Z 427 " =    1.850
peak=    4.661 closest distance to " CG  PRO A 213 " =    1.260
peak=    4.652 closest distance to " O   HOH Z  24 " =    1.712
peak=    4.622 closest distance to " O   HOH Z 344 " =    1.509
peak=    4.610 closest distance to " O   HOH Z 192 " =    1.590
peak=    4.600 closest distance to " O   HOH Z 134 " =    1.359
peak=    4.560 closest distance to " O   HOH Z 332 " =    1.310
peak=    4.550 closest distance to " O   HOH Z 207 " =    1.861
peak=    4.516 closest distance to " O   HOH Z  47 " =    1.680
peak=    4.494 closest distance to " CB  ASN A  60 " =    0.861
peak=    4.470 closest distance to " NE1 TRP A 266 " =    1.740
peak=    4.469 closest distance to " O   HOH Z  28 " =    1.491
peak=    4.439 closest distance to " O   HOH Z 414 " =    1.646
peak=    4.438 closest distance to " O   HOH Z 234 " =    3.548
peak=    4.425 closest distance to " O   HOH Z 358 " =    1.289
peak=    4.392 closest distance to " O   HOH Z  97 " =    1.304
peak=    4.373 closest distance to " O   HOH Z 117 " =    1.440
peak=    4.336 closest distance to " O   HOH Z  49 " =    1.357
peak=    4.314 closest distance to " CB  ARG A 102 " =    0.950
peak=    4.290 closest distance to " O   HOH Z 282 " =    1.565
peak=    4.255 closest distance to " O   HOH Z 222 " =    1.135
peak=    4.246 closest distance to " O   HOH Z 202 " =    2.078
peak=    4.246 closest distance to " O   HOH Z 269 " =    1.350
peak=    4.240 closest distance to " CE AMET A  47 " =    0.781
peak=    4.226 closest distance to " O   HOH Z 193 " =    1.830
peak=    4.225 closest distance to " O   HOH Z 352 " =    1.670
peak=    4.203 closest distance to " O   HOH Z 139 " =    1.454
peak=    4.197 closest distance to " N   PHE A  59 " =    0.752
peak=    4.195 closest distance to " CG  GLN A  11 " =    2.186
peak=    4.195 closest distance to " O   HOH Z 183 " =    2.019
peak=    4.178 closest distance to " O   HOH Z 393 " =    1.447
peak=    4.164 closest distance to " O   HOH Z 425 " =    1.820
peak=    4.152 closest distance to " O   HOH Z 126 " =    1.385
peak=    4.120 closest distance to " CB  PRO A  54 " =    1.141
peak=    4.110 closest distance to " CA  LEU A 282 " =    1.214
peak=    4.102 closest distance to " O   HOH Z 272 " =    1.764
peak=    4.098 closest distance to " O   HOH Z  59 " =    1.625
peak=    4.095 closest distance to " O   HOH Z  11 " =    1.549
peak=    4.059 closest distance to " O   HOH Z 423 " =    1.530
peak=    4.039 closest distance to " CB  ARG A 275 " =    0.849
peak=    4.038 closest distance to " O   HOH Z 257 " =    1.422
peak=    4.019 closest distance to " O   HOH Z 212 " =    1.720
peak=    4.015 closest distance to " CA  TYR A  30 " =    1.088
peak=    4.001 closest distance to " O   HOH Z 220 " =    1.487
peak=    3.993 closest distance to " CB  ASN A 148 " =    1.475
peak=    3.993 closest distance to " O   HOH Z 215 " =    1.706
peak=    3.987 closest distance to " O   HOH Z 381 " =    1.484
peak=    3.984 closest distance to " CG AARG A 275 " =    1.234
peak=    3.971 closest distance to " OD1 ASP A 286 " =    1.208
peak=    3.967 closest distance to " SD BMET A  47 " =    1.563
peak=    3.954 closest distance to " O   HOH Z 371 " =    2.093
peak=    3.954 closest distance to " CB  ALA A   1 " =    1.034
peak=    3.946 closest distance to " CB  TRP A 179 " =    1.060
peak=    3.942 closest distance to " CB  SER A   3 " =    1.290
peak=    3.940 closest distance to " O   HOH Z 145 " =    1.370
peak=    3.919 closest distance to " O   HOH Z 289 " =    1.226
peak=    3.908 closest distance to " N   GLU A   2 " =    1.300
peak=    3.906 closest distance to " O   HOH Z 269 " =    3.049
peak=    3.882 closest distance to " O   HOH Z 136 " =    1.143
peak=    3.863 closest distance to " O   HOH Z 334 " =    1.686
peak=    3.863 closest distance to " NH2 ARG A 219 " =    1.831
peak=    3.861 closest distance to " O   HOH Z 369 " =    2.035
peak=    3.845 closest distance to " NZ  LYS A 117 " =    3.462
peak=    3.844 closest distance to " O   HOH Z  93 " =    1.786
peak=    3.810 closest distance to " O   HOH Z 213 " =    2.024
peak=    3.806 closest distance to " N   ASN A 148 " =    1.286
peak=    3.796 closest distance to " O   HOH Z 250 " =    1.163
peak=    3.779 closest distance to " O   HOH Z 334 " =    1.673
peak=    3.766 closest distance to " O   HOH Z  97 " =    2.169
peak=    3.761 closest distance to " O   HOH Z   6 " =    2.096
peak=    3.760 closest distance to " OG ASER A 134 " =    1.413
peak=    3.760 closest distance to " O   HOH Z 158 " =    1.564
peak=    3.758 closest distance to " O   HOH Z 290 " =    1.113
peak=    3.756 closest distance to " O   HOH Z 302 " =    1.445
peak=    3.748 closest distance to " O   HOH Z 211 " =    1.215
peak=    3.738 closest distance to " CG  PRO A 243 " =    1.207
peak=    3.721 closest distance to " CD  GLN A  58 " =    5.623
peak=    3.718 closest distance to " O   HOH Z 132 " =    1.370
peak=    3.717 closest distance to " NE1 TRP A 274 " =    1.104
peak=    3.712 closest distance to " O   SER A  87 " =    2.205
peak=    3.706 closest distance to " O   HOH Z 278 " =    1.603
peak=    3.698 closest distance to " CB  ASP A 200 " =    0.923
peak=    3.684 closest distance to " CA  PHE A 283 " =    1.070
peak=    3.683 closest distance to " O   HOH Z 193 " =    1.288
peak=    3.679 closest distance to " O   HOH Z 196 " =    1.641
peak=    3.674 closest distance to " CG2 THR A 220 " =    0.892
peak=    3.673 closest distance to " O   HOH Z 188 " =    1.206
peak=    3.667 closest distance to " O   HOH Z 258 " =    1.143
peak=    3.649 closest distance to " CB  LEU A 300 " =    1.118
peak=    3.633 closest distance to " O   HOH Z 158 " =    2.983
peak=    3.624 closest distance to " O   ASP A 286 " =    2.350
peak=    3.621 closest distance to " O   HOH Z 223 " =    1.199
peak=    3.620 closest distance to " O   HOH Z 250 " =    2.144
peak=    3.613 closest distance to " O   HOH Z 261 " =    1.952
peak=    3.610 closest distance to " NZ  LYS A 117 " =    1.050
peak=    3.576 closest distance to " O   HOH Z  69 " =    2.116
peak=    3.572 closest distance to " O   HOH Z 380 " =    1.970
peak=    3.563 closest distance to " O   HOH Z 269 " =    1.156
peak=    3.555 closest distance to " O   HOH Z 140 " =    1.820
peak=    3.553 closest distance to " O   HOH Z 291 " =    1.677
peak=    3.541 closest distance to " O   HOH Z  32 " =    2.002
peak=    3.538 closest distance to " CG  LEU A 167 " =    1.259
peak=    3.536 closest distance to " OD1 ASP A 238 " =    0.920
peak=    3.533 closest distance to " O   HOH Z 258 " =    1.477
peak=    3.527 closest distance to " O   HOH Z 181 " =    1.652
peak=    3.527 closest distance to " O   HOH Z  88 " =    2.671
peak=    3.525 closest distance to " O   HOH Z   1 " =    1.616
peak=    3.523 closest distance to " NE2 GLN A  73 " =    1.640
peak=    3.513 closest distance to " O   HOH Z 286 " =    2.176
peak=    3.512 closest distance to " O   HOH Z 222 " =    2.333
peak=    3.508 closest distance to " O   HOH Z 298 " =    1.736
peak=    3.508 closest distance to " O   HOH Z 248 " =    2.198
peak=    3.508 closest distance to " CB  VAL A 202 " =    1.558
peak=    3.505 closest distance to " O   HOH Z  50 " =    1.541
peak=    3.505 closest distance to " N   GLN A 278 " =    0.990
peak=    3.501 closest distance to " CB  ALA A  34 " =    1.002
peak=    3.497 closest distance to " O   HOH Z 227 " =    1.996
peak=    3.497 closest distance to " NH1AARG A 145 " =    0.753
peak=    3.496 closest distance to " CG  TRP A 179 " =    2.069
peak=    3.494 closest distance to " CB  GLN A 223 " =    1.429
peak=    3.489 closest distance to " O   HOH Z 311 " =    1.501
peak=    3.487 closest distance to " O   HOH Z 325 " =    1.518
peak=    3.485 closest distance to " O   HOH Z  53 " =    2.233
peak=    3.481 closest distance to " O   HOH Z 260 " =    1.431
peak=    3.476 closest distance to " CE  MET A  93 " =    1.425
peak=    3.468 closest distance to " O   SER A  26 " =    1.737
peak=    3.465 closest distance to " CG  GLN A 240 " =    3.478
peak=    3.464 closest distance to " O   HOH Z 125 " =    2.110
peak=    3.456 closest distance to " O   HOH Z 226 " =    1.154
peak=    3.455 closest distance to " CA  ASN A 127 " =    0.835
peak=    3.452 closest distance to " O   HOH Z 411 " =    3.232
peak=    3.450 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.446 closest distance to " O   HOH Z  65 " =    1.564
peak=    3.442 closest distance to " CB  GLN A 183 " =    1.078
peak=    3.441 closest distance to " O   HOH Z 100 " =    1.396
peak=    3.434 closest distance to " O   HOH Z 132 " =    2.519
peak=    3.432 closest distance to " O   HOH Z  63 " =    1.634
peak=    3.432 closest distance to " O   HOH Z  54 " =    1.451
peak=    3.427 closest distance to " O   HOH Z 166 " =    1.699
peak=    3.425 closest distance to " CG  GLU A 277 " =    2.012
peak=    3.421 closest distance to " CG2 THR A 279 " =    1.388
peak=    3.419 closest distance to " O   HOH Z 130 " =    2.524
peak=    3.415 closest distance to " O   HOH Z 257 " =    1.910
peak=    3.413 closest distance to " CG2 THR A 294 " =    1.166
peak=    3.412 closest distance to " O   HOH Z  59 " =    1.927
peak=    3.406 closest distance to " O   HOH Z 406 " =    1.350
peak=    3.404 closest distance to " O   HOH Z  68 " =    1.749
peak=    3.402 closest distance to " O   ALA A 165 " =    1.064
peak=    3.401 closest distance to " CG  ASN A 301 " =    0.845
peak=    3.397 closest distance to " CA  THR A 264 " =    0.779
peak=    3.391 closest distance to " O   HOH Z  18 " =    1.951
peak=    3.389 closest distance to " O   HOH Z 384 " =    1.139
peak=    3.387 closest distance to " OG BSER A 258 " =    0.774
peak=    3.387 closest distance to " O   HOH Z 305 " =    3.489
peak=    3.385 closest distance to " NE2 GLN A 278 " =    3.700
peak=    3.383 closest distance to " OD2 ASP A 286 " =    2.283
peak=    3.379 closest distance to " O   HOH Z 123 " =    1.383
peak=    3.377 closest distance to " OG1 THR A 246 " =    1.222
peak=    3.377 closest distance to " O   HOH Z 104 " =    1.409
peak=    3.374 closest distance to " O  BHOH Z  74 " =    1.412
peak=    3.374 closest distance to " O   HOH Z 227 " =    2.062
peak=    3.368 closest distance to " O   HOH Z 217 " =    1.273
peak=    3.368 closest distance to " O   HOH Z  44 " =    1.661
peak=    3.367 closest distance to " CG  GLN A  77 " =    1.057
peak=    3.367 closest distance to " C   ALA A 299 " =    0.970
peak=    3.366 closest distance to " CB  PRO A 198 " =    1.023
peak=    3.365 closest distance to " O   HOH Z  89 " =    1.519
peak=    3.365 closest distance to " N   TYR A  15 " =    1.304
peak=    3.363 closest distance to " O   HOH Z   5 " =    1.512
peak=    3.360 closest distance to " O   HOH Z 152 " =    2.734
peak=    3.359 closest distance to " CG2 VAL A 257 " =    0.946
peak=    3.358 closest distance to " O   HOH Z 264 " =    1.346
peak=    3.356 closest distance to " O   HOH Z 273 " =    1.188
peak=    3.353 closest distance to " O   HOH Z 366 " =    2.404
peak=    3.352 closest distance to " CG2 THR A 221 " =    1.329
peak=    3.350 closest distance to " O   HOH Z 216 " =    1.979
peak=    3.349 closest distance to " O   HOH Z  97 " =    3.717
peak=    3.345 closest distance to " O   HOH Z 148 " =    1.743
peak=    3.343 closest distance to " CB  ALA A  84 " =    1.738
peak=    3.337 closest distance to " O   HOH Z 340 " =    1.721
peak=    3.331 closest distance to " OD1 ASN A  45 " =    1.283
peak=    3.323 closest distance to " O   HOH Z 313 " =    1.763
peak=    3.316 closest distance to " N   TRP A 177 " =    1.661
peak=    3.311 closest distance to " O   HOH Z 287 " =    1.621
peak=    3.310 closest distance to " O   HOH Z 108 " =    1.730
peak=    3.304 closest distance to " CG1 VAL A 153 " =    0.799
peak=    3.304 closest distance to " NZ  LYS A  76 " =    1.515
peak=    3.301 closest distance to " O   HOH Z  88 " =    2.617
peak=    3.301 closest distance to " CB  GLN A 278 " =    0.797
peak=    3.301 closest distance to " O   HOH Z 119 " =    1.554
peak=    3.300 closest distance to " O   HOH Z 155 " =    2.232
peak=    3.300 closest distance to " CD2 LEU A 167 " =    1.319
peak=    3.299 closest distance to " CG  LEU A 297 " =    0.893
peak=    3.299 closest distance to " CG2BVAL A  41 " =    0.716
peak=    3.296 closest distance to " NH1BARG A 145 " =    1.331
peak=    3.296 closest distance to " O   HOH Z 365 " =    2.072
peak=    3.294 closest distance to " O   HOH Z 162 " =    1.793
peak=    3.292 closest distance to " O   HOH Z 303 " =    1.788
peak=    3.290 closest distance to " CG1 ILE A 120 " =    1.487
peak=    3.290 closest distance to " O   HOH Z 328 " =    2.012
peak=    3.286 closest distance to " CG  PRO A 280 " =    0.797
peak=    3.285 closest distance to " CG  LYS A 119 " =    0.956
peak=    3.283 closest distance to " CG  GLN A  88 " =    1.004
peak=    3.282 closest distance to " O   HOH Z 435 " =    1.878
peak=    3.278 closest distance to " CG  PRO A 198 " =    1.436
peak=    3.277 closest distance to " NH2BARG A 145 " =    2.039
peak=    3.276 closest distance to " N   SER A  63 " =    1.000
peak=    3.272 closest distance to " N   GLN A  89 " =    1.067
peak=    3.272 closest distance to " CA  PRO A 243 " =    1.353
peak=    3.272 closest distance to " O   HOH Z 365 " =    5.041
peak=    3.271 closest distance to " O   HOH Z 128 " =    1.964
peak=    3.270 closest distance to " O   SER A 164 " =    1.125
peak=    3.266 closest distance to " CB  ALA A 131 " =    1.868
peak=    3.259 closest distance to " O   GLY A 302 " =    1.598
peak=    3.259 closest distance to " CB  LYS A 290 " =    1.555
peak=    3.258 closest distance to " CB  VAL A 126 " =    1.211
peak=    3.258 closest distance to " CZ  PHE A  59 " =    1.200
peak=    3.257 closest distance to " CG1 ILE A  33 " =    1.260
peak=    3.257 closest distance to " CZ  PHE A  38 " =    1.283
peak=    3.257 closest distance to " O   HOH Z  69 " =    1.175
peak=    3.257 closest distance to " NH2 ARG A 269 " =    1.218
peak=    3.255 closest distance to " O   HOH Z 392 " =    1.277
peak=    3.254 closest distance to " O   HOH Z  43 " =    2.394
peak=    3.253 closest distance to " N   PHE A 130 " =    1.320
peak=    3.252 closest distance to " O   HOH Z 156 " =    2.715
peak=    3.252 closest distance to " CE  LYS A 119 " =    1.092
peak=    3.251 closest distance to " NE  ARG A  56 " =    1.183
peak=    3.250 closest distance to " O   HOH Z 207 " =    1.887
peak=    3.248 closest distance to " O   HOH Z 423 " =    1.848
peak=    3.248 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.245 closest distance to " NH2AARG A 190 " =    1.420
peak=    3.244 closest distance to " O   HOH Z 106 " =    1.918
peak=    3.243 closest distance to " O   HOH Z 189 " =    1.767
peak=    3.241 closest distance to " N   PHE A  59 " =    1.215
peak=    3.239 closest distance to " CG2AVAL A  72 " =    2.920
peak=    3.239 closest distance to " CG1BVAL A 121 " =    1.983
peak=    3.238 closest distance to " O   HOH Z 185 " =    1.558
peak=    3.235 closest distance to " CA  ALA A  21 " =    1.179
peak=    3.228 closest distance to " O   HOH Z 369 " =    1.212
peak=    3.227 closest distance to " CG  MET A 185 " =    1.423
peak=    3.227 closest distance to " O   HOH Z 378 " =    1.127
peak=    3.224 closest distance to " O   HOH Z 137 " =    1.845
peak=    3.223 closest distance to " O   HOH Z 118 " =    1.871
peak=    3.206 closest distance to " CD  PRO A  54 " =    1.048
peak=    3.206 closest distance to " O   HOH Z 128 " =    2.089
peak=    3.202 closest distance to " CD1 LEU A 228 " =    1.652
peak=    3.202 closest distance to " CE  LYS A 117 " =    1.515
peak=    3.197 closest distance to " O   HOH Z 344 " =    2.892
peak=    3.194 closest distance to " CG1 VAL A 202 " =    2.054
peak=    3.193 closest distance to " O   HOH Z 214 " =    1.957
peak=    3.193 closest distance to " OG BSER A  12 " =    0.998
peak=    3.187 closest distance to " CA  ILE A  20 " =    0.833
peak=    3.187 closest distance to " CB  ALA A   7 " =    1.211
peak=    3.184 closest distance to " O   HOH Z 305 " =    1.669
peak=    3.180 closest distance to " CB  GLU A 152 " =    1.456
peak=    3.179 closest distance to " O   HOH Z 329 " =    1.642
peak=    3.175 closest distance to " O   HOH Z 389 " =    1.421
peak=    3.175 closest distance to " O   HOH Z 144 " =    2.259
peak=    3.175 closest distance to " O   HOH Z 247 " =    1.203
peak=    3.173 closest distance to " CB  VAL A 265 " =    1.164
peak=    3.169 closest distance to " O   HOH Z 296 " =    1.670
peak=    3.168 closest distance to " CG  LYS A 166 " =    1.448
peak=    3.167 closest distance to " O   HOH Z 172 " =    2.632
peak=    3.163 closest distance to " OE2 GLU A 236 " =    1.314
peak=    3.161 closest distance to " CA  PHE A 208 " =    0.892
peak=    3.156 closest distance to " O   HOH Z 329 " =    1.379
peak=    3.151 closest distance to " CA  ALA A 227 " =    1.323
peak=    3.151 closest distance to " O   PRO A 213 " =    1.399
peak=    3.151 closest distance to " CG2 ILE A 120 " =    1.308
peak=    3.150 closest distance to " CB  MET A 188 " =    1.717
peak=    3.147 closest distance to " NE AARG A 275 " =    1.412
peak=    3.147 closest distance to " CZ3 TRP A  70 " =    1.016
peak=    3.142 closest distance to " CG2 ILE A  20 " =    1.233
peak=    3.141 closest distance to " CA  SER A  32 " =    1.559
peak=    3.134 closest distance to " O   HOH Z 289 " =    1.532
peak=    3.130 closest distance to " O   GLN A 278 " =    1.422
peak=    3.129 closest distance to " O   HOH Z 200 " =    2.550
peak=    3.128 closest distance to " CB  ALA A 160 " =    1.762
peak=    3.127 closest distance to " O   HOH Z 419 " =    1.976
peak=    3.125 closest distance to " CE  MET A  40 " =    1.070
peak=    3.120 closest distance to " O   HOH Z 326 " =    1.329
peak=    3.120 closest distance to " NE2 GLN A  58 " =    3.255
peak=    3.116 closest distance to " O   HOH Z 362 " =    2.105
peak=    3.109 closest distance to " CD1 LEU A   5 " =    1.905
peak=    3.104 closest distance to " O   HOH Z 128 " =    2.038
peak=    3.100 closest distance to " O   HOH Z 249 " =    1.437
peak=    3.099 closest distance to " O   HOH Z 425 " =    1.486
peak=    3.098 closest distance to " O   HOH Z 365 " =    1.739
peak=    3.095 closest distance to " O   HOH Z 212 " =    1.162
peak=    3.093 closest distance to " CA  PHE A 130 " =    1.102
peak=    3.091 closest distance to " CE  MET A 188 " =    1.115
peak=    3.090 closest distance to " CB  ALA A 114 " =    1.697
peak=    3.089 closest distance to " CB  ASN A 215 " =    1.047
peak=    3.082 closest distance to " CH2 TRP A  92 " =    2.024
peak=    3.080 closest distance to " CD  LYS A 166 " =    1.691
peak=    3.066 closest distance to " O   HOH Z  39 " =    2.234
peak=    3.058 closest distance to " O   HOH Z  43 " =    1.644
peak=    3.055 closest distance to " CA  GLY A 241 " =    4.248
peak=    3.048 closest distance to " O   HOH Z 345 " =    3.332
peak=    3.044 closest distance to " O   HOH Z 325 " =    1.293
peak=    3.026 closest distance to " N   SER A  32 " =    1.368

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 183         
Filter by distance & map next to the model:
   mapped sites are within: 0.297 - 4.989
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 173 from: 183
   mapped sites are within: 0.705 - 4.989

peak=   -6.481 closest distance to " O   SER A  62 " =    0.773
peak=   -4.910 closest distance to " O   HOH Z  52 " =    0.705
peak=   -4.887 closest distance to " O   PRO A 198 " =    1.048
peak=   -4.883 closest distance to " O   HOH Z 244 " =    1.120
peak=   -4.512 closest distance to " CG  GLN A  88 " =    0.989
peak=   -4.419 closest distance to " N   ASN A  60 " =    0.900
peak=   -4.387 closest distance to " O   HOH Z 179 " =    0.948
peak=   -4.354 closest distance to " N   GLN A  58 " =    1.037
peak=   -4.105 closest distance to " O   HOH Z 290 " =    0.992
peak=   -4.094 closest distance to " CD1 TRP A 179 " =    1.042
peak=   -4.081 closest distance to " CA  GLY A 133 " =    1.911
peak=   -4.051 closest distance to " O   SER A 135 " =    1.574
peak=   -4.035 closest distance to " O   ILE A  49 " =    1.644
peak=   -4.028 closest distance to " CD  ARG A  14 " =    3.128
peak=   -4.017 closest distance to " O   HOH Z  54 " =    0.775
peak=   -4.004 closest distance to " O   ALA A  51 " =    1.176
peak=   -3.983 closest distance to " O   HOH Z  24 " =    1.149
peak=   -3.965 closest distance to " O   HOH Z 400 " =    0.919
peak=   -3.951 closest distance to " O   SER A  22 " =    1.170
peak=   -3.937 closest distance to " OE1 GLU A 277 " =    2.004
peak=   -3.889 closest distance to " O   HOH Z 407 " =    2.836
peak=   -3.874 closest distance to " O   HOH Z  61 " =    0.760
peak=   -3.870 closest distance to " O   HOH Z 250 " =    1.197
peak=   -3.833 closest distance to " OG  SER A  97 " =    2.203
peak=   -3.829 closest distance to " O   HOH Z 220 " =    1.149
peak=   -3.786 closest distance to " O   HOH Z  88 " =    1.927
peak=   -3.776 closest distance to " CG  ASP A 231 " =    0.743
peak=   -3.768 closest distance to " NH2 ARG A  79 " =    1.910
peak=   -3.764 closest distance to " C   HIS A 108 " =    1.206
peak=   -3.759 closest distance to " O   HOH Z 197 " =    2.077
peak=   -3.758 closest distance to " CG  PRO A 243 " =    0.920
peak=   -3.758 closest distance to " O   HOH Z  13 " =    1.142
peak=   -3.738 closest distance to " O   HOH Z 298 " =    1.179
peak=   -3.730 closest distance to " CG2 ILE A  20 " =    2.877
peak=   -3.713 closest distance to " O   HOH Z 413 " =    4.283
peak=   -3.701 closest distance to " O   ALA A 161 " =    1.875
peak=   -3.652 closest distance to " O   VAL A  67 " =    2.779
peak=   -3.626 closest distance to " O   HOH Z  93 " =    1.331
peak=   -3.616 closest distance to " O   HOH Z 117 " =    1.050
peak=   -3.596 closest distance to " CG2 THR A  52 " =    2.843
peak=   -3.593 closest distance to " CD2 LEU A 237 " =    2.747
peak=   -3.585 closest distance to " C   ASN A 285 " =    2.059
peak=   -3.574 closest distance to " CD  GLU A 277 " =    0.867
peak=   -3.556 closest distance to " O   VAL A 197 " =    0.987
peak=   -3.529 closest distance to " O   HOH Z 198 " =    1.270
peak=   -3.524 closest distance to " O   HOH Z  29 " =    0.732
peak=   -3.520 closest distance to " O   HOH Z 287 " =    1.005
peak=   -3.515 closest distance to " O   HOH Z 388 " =    1.795
peak=   -3.508 closest distance to " CG  ASN A  39 " =    2.004
peak=   -3.508 closest distance to " O   HOH Z  79 " =    1.527
peak=   -3.503 closest distance to " O   HOH Z 300 " =    1.167
peak=   -3.500 closest distance to " O   HOH Z 266 " =    4.379
peak=   -3.487 closest distance to " CG  GLN A  77 " =    1.199
peak=   -3.486 closest distance to " CB  CYS A 201 " =    2.207
peak=   -3.486 closest distance to " CD  PRO A 198 " =    1.385
peak=   -3.484 closest distance to " O   SER A 245 " =    1.392
peak=   -3.483 closest distance to " CB  PHE A 283 " =    2.516
peak=   -3.483 closest distance to " OG1 THR A 246 " =    1.295
peak=   -3.476 closest distance to " O   HOH Z 134 " =    1.522
peak=   -3.472 closest distance to " CA  GLY A  98 " =    1.715
peak=   -3.468 closest distance to " CG1 ILE A 263 " =    1.918
peak=   -3.466 closest distance to " O   HOH Z 124 " =    1.438
peak=   -3.466 closest distance to " O   HOH Z 395 " =    0.834
peak=   -3.464 closest distance to " NE1 TRP A  70 " =    1.427
peak=   -3.446 closest distance to " OG BSER A 134 " =    1.331
peak=   -3.442 closest distance to " O   GLN A  73 " =    1.570
peak=   -3.442 closest distance to " C   ASN A 187 " =    1.918
peak=   -3.442 closest distance to " CB  ALA A 227 " =    2.280
peak=   -3.441 closest distance to " CD1 ILE A 239 " =    2.478
peak=   -3.441 closest distance to " O   VAL A  72 " =    1.246
peak=   -3.439 closest distance to " O   HOH Z 221 " =    0.957
peak=   -3.437 closest distance to " CG  LEU A  83 " =    2.021
peak=   -3.433 closest distance to " OG BSER A 134 " =    1.788
peak=   -3.429 closest distance to " O   HOH Z 397 " =    1.462
peak=   -3.423 closest distance to " O   HOH Z 103 " =    0.745
peak=   -3.421 closest distance to " CB  SER A 146 " =    2.202
peak=   -3.419 closest distance to " N   GLN A  58 " =    2.106
peak=   -3.405 closest distance to " O   HOH Z 208 " =    0.913
peak=   -3.401 closest distance to " O   THR A 235 " =    1.223
peak=   -3.391 closest distance to " O   HOH Z  28 " =    0.753
peak=   -3.388 closest distance to " CD2 TYR A 293 " =    1.911
peak=   -3.386 closest distance to " C   SER A  63 " =    1.191
peak=   -3.384 closest distance to " N   HIS A 115 " =    2.102
peak=   -3.372 closest distance to " ND2 ASN A 209 " =    1.569
peak=   -3.369 closest distance to " O   PHE A 218 " =    1.530
peak=   -3.364 closest distance to " N   SER A 206 " =    2.004
peak=   -3.334 closest distance to " OG  SER A 245 " =    1.312
peak=   -3.324 closest distance to " CE3 TRP A 274 " =    2.471
peak=   -3.324 closest distance to " C   ILE A 239 " =    2.084
peak=   -3.320 closest distance to " OD2 ASP A  50 " =    1.435
peak=   -3.320 closest distance to " O   HOH Z 186 " =    0.955
peak=   -3.319 closest distance to " O   HOH Z 393 " =    3.056
peak=   -3.313 closest distance to " CG  LEU A 281 " =    1.700
peak=   -3.311 closest distance to " O   HOH Z 219 " =    2.730
peak=   -3.309 closest distance to " O   HOH Z 185 " =    1.443
peak=   -3.301 closest distance to " CB  SER A 258 " =    1.989
peak=   -3.298 closest distance to " NH2AARG A 275 " =    4.989
peak=   -3.292 closest distance to " O   HOH Z 256 " =    1.179
peak=   -3.289 closest distance to " CG  MET A 105 " =    0.903
peak=   -3.287 closest distance to " CG1 VAL A 296 " =    2.137
peak=   -3.280 closest distance to " O   HOH Z 367 " =    4.400
peak=   -3.279 closest distance to " OG ASER A 134 " =    1.331
peak=   -3.277 closest distance to " CG  ARG A 219 " =    2.620
peak=   -3.274 closest distance to " CG  LYS A 193 " =    2.436
peak=   -3.274 closest distance to " CG1 VAL A 197 " =    1.716
peak=   -3.273 closest distance to " O   VAL A 189 " =    2.503
peak=   -3.269 closest distance to " O   HOH Z 419 " =    0.844
peak=   -3.268 closest distance to " CG  PRO A 198 " =    1.449
peak=   -3.266 closest distance to " O   HOH Z 234 " =    4.593
peak=   -3.265 closest distance to " O   HOH Z 279 " =    1.147
peak=   -3.259 closest distance to " O   LYS A 289 " =    1.300
peak=   -3.258 closest distance to " C   GLN A 144 " =    0.896
peak=   -3.258 closest distance to " CB  ALA A 100 " =    2.504
peak=   -3.254 closest distance to " CG1 VAL A 268 " =    2.343
peak=   -3.251 closest distance to " CG  ASN A 301 " =    2.030
peak=   -3.246 closest distance to " O   HOH Z  46 " =    1.488
peak=   -3.245 closest distance to " OG  SER A  62 " =    1.873
peak=   -3.245 closest distance to " O   HOH Z 426 " =    2.133
peak=   -3.243 closest distance to " O   HOH Z 139 " =    2.918
peak=   -3.242 closest distance to " O   HOH Z 435 " =    2.451
peak=   -3.241 closest distance to " O   HOH Z 437 " =    0.816
peak=   -3.238 closest distance to " O   HOH Z 401 " =    1.013
peak=   -3.238 closest distance to " O   HOH Z  56 " =    1.375
peak=   -3.234 closest distance to " O   HOH Z 153 " =    1.254
peak=   -3.232 closest distance to " CB  ALA A 100 " =    1.985
peak=   -3.229 closest distance to " O   HOH Z 211 " =    2.021
peak=   -3.229 closest distance to " CG BLYS A 290 " =    1.368
peak=   -3.221 closest distance to " OE2 GLU A   2 " =    0.809
peak=   -3.221 closest distance to " O   HOH Z 249 " =    0.805
peak=   -3.215 closest distance to " CZ3 TRP A 274 " =    1.024
peak=   -3.209 closest distance to " CE2 TRP A 274 " =    1.205
peak=   -3.206 closest distance to " O   HOH Z 305 " =    1.271
peak=   -3.200 closest distance to " OD1 ASP A 200 " =    0.879
peak=   -3.199 closest distance to " O   HOH Z 141 " =    0.753
peak=   -3.199 closest distance to " CG  PRO A 163 " =    2.634
peak=   -3.198 closest distance to " OG BSER A  12 " =    1.181
peak=   -3.196 closest distance to " OG  SER A   3 " =    1.054
peak=   -3.191 closest distance to " O   HOH Z 406 " =    0.840
peak=   -3.188 closest distance to " O   HOH Z 220 " =    1.762
peak=   -3.186 closest distance to " O   HOH Z 438 " =    0.764
peak=   -3.185 closest distance to " OD2 ASP A  27 " =    1.277
peak=   -3.185 closest distance to " NZ  LYS A 117 " =    0.987
peak=   -3.183 closest distance to " O   HOH Z 166 " =    1.550
peak=   -3.176 closest distance to " CG2 ILE A 239 " =    2.158
peak=   -3.175 closest distance to " OD1 ASP A 191 " =    1.810
peak=   -3.170 closest distance to " O   PRO A  54 " =    1.495
peak=   -3.163 closest distance to " CG  ARG A 139 " =    0.905
peak=   -3.161 closest distance to " O   HOH Z 373 " =    1.135
peak=   -3.158 closest distance to " N   ASP A 200 " =    1.803
peak=   -3.157 closest distance to " O   HOH Z 258 " =    0.940
peak=   -3.156 closest distance to " O   SER A 216 " =    1.685
peak=   -3.142 closest distance to " C   ASP A 124 " =    2.035
peak=   -3.135 closest distance to " N   ARG A 275 " =    0.846
peak=   -3.128 closest distance to " O   HOH Z  69 " =    1.883
peak=   -3.127 closest distance to " O   HOH Z 355 " =    0.883
peak=   -3.123 closest distance to " CE1 HIS A 115 " =    0.949
peak=   -3.121 closest distance to " C   TYR A  30 " =    1.743
peak=   -3.121 closest distance to " O   HOH Z 317 " =    3.047
peak=   -3.118 closest distance to " CB  PRO A 213 " =    1.596
peak=   -3.110 closest distance to " O   HOH Z 198 " =    1.481
peak=   -3.107 closest distance to " CG2 ILE A 120 " =    0.870
peak=   -3.106 closest distance to " O   HOH Z 233 " =    2.418
peak=   -3.095 closest distance to " C   LYS A 119 " =    1.968
peak=   -3.089 closest distance to " O   HOH Z 165 " =    1.991
peak=   -3.079 closest distance to " CB  ALA A  43 " =    1.861
peak=   -3.071 closest distance to " CG  PRO A 213 " =    0.740
peak=   -3.069 closest distance to " O   TRP A  92 " =    1.484
peak=   -3.066 closest distance to " N   SER A 276 " =    0.996
peak=   -3.056 closest distance to " O   HOH Z 289 " =    0.742
peak=   -3.049 closest distance to " CD  ARG A 156 " =    1.897
peak=   -3.036 closest distance to " CB  TYR A 172 " =    1.797
peak=   -3.022 closest distance to " O   HOH Z 417 " =    1.865
peak=   -3.019 closest distance to " O   VAL A 153 " =    2.413

================= 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    :  0.5022 0.5092   6.299967e+00   6.296517e+00
   1_bss:  0.4942 0.4980   6.297844e+00   6.282893e+00
   1_xyz:  0.4147 0.4440   6.193879e+00   6.229435e+00
   1_adp:  0.3745 0.4438   6.147368e+00   6.232840e+00
   1_occ:  0.3741 0.4439   6.147218e+00   6.233441e+00
   2_bss:  0.3715 0.4435   6.144721e+00   6.233441e+00
   2_xyz:  0.3162 0.3850   6.019704e+00   6.148441e+00
   2_adp:  0.3002 0.3732   5.986848e+00   6.126922e+00
   2_occ:  0.2999 0.3733   5.986839e+00   6.127213e+00
   3_bss:  0.2999 0.3719   5.985085e+00   6.123908e+00
   3_xyz:  0.2481 0.3222   5.839150e+00   6.020270e+00
   3_adp:  0.2328 0.3083   5.790073e+00   5.981234e+00
   3_occ:  0.2326 0.3081   5.789240e+00   5.980628e+00
   4_bss:  0.2327 0.3074   5.789001e+00   5.978844e+00
   4_xyz:  0.1858 0.2425   5.575633e+00   5.780802e+00
   4_adp:  0.1669 0.2284   5.493228e+00   5.724865e+00
   4_occ:  0.1667 0.2278   5.491891e+00   5.722626e+00
   5_bss:  0.1671 0.2274   5.489555e+00   5.720462e+00
   5_xyz:  0.1430 0.2026   5.362341e+00   5.609643e+00
   5_adp:  0.1381 0.1864   5.310336e+00   5.531847e+00
   5_occ:  0.1377 0.1855   5.307279e+00   5.528019e+00
   5_bss:  0.1378 0.1856   5.307410e+00   5.527437e+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:  0.347   0.000  -1.613   0.684   1.604   0.000   0.000   0.000
   1_xyz:  0.347   0.000  -1.613   0.684   1.604   0.000   0.000   0.000
   1_adp:  0.347   0.000  -1.613   0.684   1.604   0.000   0.000   0.000
   1_occ:  0.347   0.000  -1.613   0.684   1.604   0.000   0.000   0.000
   2_bss:  0.347  40.091  -0.688   0.960   1.139   0.000   0.000   0.000
   2_xyz:  0.347  40.091  -0.688   0.960   1.139   0.000   0.000   0.000
   2_adp:  0.347  40.091  -0.688   0.960   1.139   0.000   0.000   0.000
   2_occ:  0.347  40.091  -0.688   0.960   1.139   0.000   0.000   0.000
   3_bss:  0.339  40.091  -1.015  -0.224   0.153  -0.000   0.000   0.000
   3_xyz:  0.339  40.091  -1.015  -0.224   0.153  -0.000   0.000   0.000
   3_adp:  0.339  40.091  -1.015  -0.224   0.153  -0.000   0.000   0.000
   3_occ:  0.339  40.091  -1.015  -0.224   0.153  -0.000   0.000   0.000
   4_bss:  0.326  37.524  -1.667  -1.114  -0.500  -0.000  -0.000  -0.000
   4_xyz:  0.326  37.524  -1.667  -1.114  -0.500  -0.000  -0.000  -0.000
   4_adp:  0.326  37.524  -1.667  -1.114  -0.500  -0.000  -0.000  -0.000
   4_occ:  0.326  37.524  -1.667  -1.114  -0.500  -0.000  -0.000  -0.000
   5_bss:  0.314  37.524  -1.880  -1.600  -0.850  -0.000  -0.000  -0.000
   5_xyz:  0.314  37.524  -1.880  -1.600  -0.850  -0.000  -0.000  -0.000
   5_adp:  0.314  37.524  -1.880  -1.600  -0.850  -0.000  -0.000  -0.000
   5_occ:  0.314  37.524  -1.880  -1.600  -0.850  -0.000  -0.000  -0.000
   5_bss:  0.312  33.129  -2.275  -1.931  -1.147  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.487 0.3090  0.4255    83468.288
   1_bss:  65.211 0.3239  0.4506    78941.077
   1_xyz:  51.648 0.4993  0.6861    59452.964
   1_adp:  51.289 0.5037  0.6987    59243.236
   1_occ:  51.413 0.5021  0.6957    59403.401
   2_bss:  51.247 0.5040  0.7142    59265.846
   2_xyz:  41.861 0.6200  0.8741    41966.491
   2_adp:  39.590 0.6477  0.8969    38681.180
   2_occ:  39.597 0.6477  0.8967    38740.098
   3_bss:  39.433 0.6493  0.8710    38247.881
   3_xyz:  33.265 0.7207  0.9522    27805.965
   3_adp:  30.857 0.7486  0.9607    24959.123
   3_occ:  30.808 0.7492  0.9612    24915.424
   4_bss:  30.722 0.7500  0.9362    24737.368
   4_xyz:  23.525 0.8268  0.9981    14934.830
   4_adp:  21.484 0.8480  1.0000    13115.980
   4_occ:  21.430 0.8485  1.0002    13036.832
   5_bss:  21.344 0.8491  0.9878    12903.380
   5_xyz:  18.787 0.8732  1.0022    10103.590
   5_adp:  16.876 0.8913  1.0101     8785.850
   5_occ:  16.790 0.8920  1.0102     8696.613
   5_bss:  16.789 0.8919  0.9971     8672.958
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.104   2.5132e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.104   2.5132e-01
   1_xyz:   1.530  0.013  0.098 16.003  0.007  4.102   1.3958e-01
   1_adp:   1.530  0.013  0.098 16.003  0.007  4.102   1.3958e-01
   1_occ:   1.530  0.013  0.098 16.003  0.007  4.102   1.3958e-01
   2_bss:   1.530  0.013  0.098 16.003  0.007  4.102   1.3958e-01
   2_xyz:   1.232  0.009  0.085 15.099  0.005  4.104   8.6305e-02
   2_adp:   1.232  0.009  0.085 15.099  0.005  4.104   8.6305e-02
   2_occ:   1.232  0.009  0.085 15.099  0.005  4.104   8.6305e-02
   3_bss:   1.232  0.009  0.085 15.099  0.005  4.104   8.6305e-02
   3_xyz:   1.011  0.007  0.067 14.366  0.004  4.109   6.3427e-02
   3_adp:   1.011  0.007  0.067 14.366  0.004  4.109   6.3427e-02
   3_occ:   1.011  0.007  0.067 14.366  0.004  4.109   6.3427e-02
   4_bss:   1.011  0.007  0.067 14.366  0.004  4.109   6.3427e-02
   4_xyz:   0.992  0.006  0.066 14.194  0.004  4.105   5.9890e-02
   4_adp:   0.992  0.006  0.066 14.194  0.004  4.105   5.9890e-02
   4_occ:   0.992  0.006  0.066 14.194  0.004  4.105   5.9890e-02
   5_bss:   0.992  0.006  0.066 14.194  0.004  4.105   5.9890e-02
   5_xyz:   0.973  0.006  0.065 14.396  0.003  4.103   5.5544e-02
   5_adp:   0.973  0.006  0.065 14.396  0.003  4.103   5.5544e-02
   5_occ:   0.973  0.006  0.065 14.396  0.003  4.103   5.5544e-02
   5_bss:   0.973  0.006  0.065 14.396  0.003  4.103   5.5544e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.741   2.4085e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.741   2.4085e-01
   1_xyz:   9.572  0.080  0.438 83.917  0.057  1.738   9.6753e-02
   1_adp:   9.572  0.080  0.438 83.917  0.057  1.738   9.6753e-02
   1_occ:   9.572  0.080  0.438 83.917  0.057  1.738   9.6753e-02
   2_bss:   9.572  0.080  0.438 83.917  0.057  1.738   9.6753e-02
   2_xyz:   9.052  0.057  0.309 79.550  0.034  2.264   9.8826e-02
   2_adp:   9.052  0.057  0.309 79.550  0.034  2.264   9.8826e-02
   2_occ:   9.052  0.057  0.309 79.550  0.034  2.264   9.8826e-02
   3_bss:   9.052  0.057  0.309 79.550  0.034  2.264   9.8826e-02
   3_xyz:   8.236  0.051  0.270 76.262  0.028  2.360   4.6304e-02
   3_adp:   8.236  0.051  0.270 76.262  0.028  2.360   4.6304e-02
   3_occ:   8.236  0.051  0.270 76.262  0.028  2.360   4.6304e-02
   4_bss:   8.236  0.051  0.270 76.262  0.028  2.360   4.6304e-02
   4_xyz:   6.373  0.033  0.196 75.136  0.034  2.347   9.6919e-02
   4_adp:   6.373  0.033  0.196 75.136  0.034  2.347   9.6919e-02
   4_occ:   6.373  0.033  0.196 75.136  0.034  2.347   9.6919e-02
   5_bss:   6.373  0.033  0.196 75.136  0.034  2.347   9.6919e-02
   5_xyz:   7.568  0.038  0.232 82.179  0.028  2.290   3.4687e-02
   5_adp:   7.568  0.038  0.232 82.179  0.028  2.290   3.4687e-02
   5_occ:   7.568  0.038  0.232 82.179  0.028  2.290   3.4687e-02
   5_bss:   7.568  0.038  0.232 82.179  0.028  2.290   3.4687e-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:  99.35   0.00  20.37  85.54   0.00  17.55  99.35   0.00  35.73
   1_occ:  99.35   0.00  20.37  85.54   0.00  17.55  99.35   0.00  35.73
   2_bss:  99.35   0.00  20.37  85.54   0.00  17.55  99.35   0.00  35.73
   2_xyz:  99.35   0.00  20.37  85.54   0.00  17.55  99.35   0.00  35.73
   2_adp:  99.25   0.00  19.17  88.35   0.00  15.90  99.25   0.00  36.98
   2_occ:  99.25   0.00  19.17  88.35   0.00  15.90  99.25   0.00  36.98
   3_bss:  99.25   0.00  19.17  88.35   0.00  15.90  99.25   0.00  36.98
   3_xyz:  99.25   0.00  19.17  88.35   0.00  15.90  99.25   0.00  36.98
   3_adp: 101.64   0.00  18.52  98.05   0.00  14.47 101.64   3.31  40.59
   3_occ: 101.64   0.00  18.52  98.05   0.00  14.47 101.64   3.31  40.59
   4_bss: 101.64   0.00  18.52  98.05   0.00  14.47 101.64   3.31  40.59
   4_xyz: 101.64   0.00  18.52  98.05   0.00  14.47 101.64   3.31  40.59
   4_adp: 112.60   0.00  19.11 112.60   0.00  13.71 106.70   2.94  48.54
   4_occ: 112.60   0.00  19.11 112.60   0.00  13.71 106.70   2.94  48.54
   5_bss: 112.60   0.00  19.11 112.60   0.00  13.71 106.70   2.94  48.54
   5_xyz: 112.60   0.00  19.11 112.60   0.00  13.71 106.70   2.94  48.54
   5_adp: 104.98   0.00  17.56 104.98   0.00  12.87 101.42   5.66  43.09
   5_occ: 104.98   0.00  17.56 104.98   0.00  12.87 101.42   5.66  43.09
   5_bss: 104.98   0.00  17.56 104.98   0.00  12.87 101.42   5.66  43.09
------------------------------------------------------------------------
 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:    3.161    0.010    0.357
   1_adp:    3.161    0.010    0.357
   1_occ:    3.161    0.010    0.357
   2_bss:    3.161    0.010    0.357
   2_xyz:    2.307    0.065    0.533
   2_adp:    2.307    0.065    0.533
   2_occ:    2.307    0.065    0.533
   3_bss:    2.307    0.065    0.533
   3_xyz:    2.368    0.096    0.664
   3_adp:    2.368    0.096    0.664
   3_occ:    2.368    0.096    0.664
   4_bss:    2.368    0.096    0.664
   4_xyz:    2.291    0.075    0.804
   4_adp:    2.291    0.075    0.804
   4_occ:    2.291    0.075    0.804
   5_bss:    2.291    0.075    0.804
   5_xyz:    2.192    0.070    0.848
   5_adp:    2.192    0.070    0.848
   5_occ:    2.192    0.070    0.848
   5_bss:    2.192    0.070    0.848
------------------------------------------------------------------------

CPU time actual refinement: 293.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/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_132/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_132/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 293.12 
  Macro-tasks:
    bulk solvent and scale       = 37.23  
    individual site refinement   = 122.20 
    weights calculation          = 24.90  
    collect and process          = 5.30   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 189.71 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 94.11  
    alpha_beta                      = 7.13   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 101.24 
    fmodel                         = 6.00   
    r_factors                      = 0.28   
    phase_errors                   = 8.26   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 220.68 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.183 micro seconds
Total CPU time: 5.08 minutes
from_scatterers_fft:    639 calls, 93.76 s
gradients_fft:          584 calls, 90.39 s

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

# Date 2008-01-16 Time 04:04:22 PST -0800 (1200485062.76 s)
Start R-work = 0.5022, R-free = 0.5092 (no bulk solvent and anisotropic scale)
Final R-work = 0.1586, R-free = 0.2035 (no bulk solvent and anisotropic scale)

Start R-work = 0.4942, R-free = 0.4980
Final R-work = 0.1378, R-free = 0.1856