# Date 2008-01-16 Time 05:32:18 PST -0800 (1200490338.32 s)
#phil __OFF__

Command line arguments: "../778.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7918
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 778

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.6953, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.99239
Completeness in resolution range: 0.960292
Completeness with d_max=infinity: 0.957336

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9924

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.6953, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.99239
Completeness in resolution range: 0.960292
Completeness with d_max=infinity: 0.957336

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2633 [2147/2171]  1929   218  10.2%
  bin  2:  4.2633 -  3.3966 [2046/2066]  1845   201   9.8%
  bin  3:  3.3966 -  2.9709 [2040/2059]  1834   206  10.1%
  bin  4:  2.9709 -  2.7010 [2006/2036]  1806   200  10.0%
  bin  5:  2.7010 -  2.5083 [2009/2028]  1811   198   9.9%
  bin  6:  2.5083 -  2.3610 [1981/2006]  1778   203  10.2%
  bin  7:  2.3610 -  2.2432 [1986/2014]  1787   199  10.0%
  bin  8:  2.2432 -  2.1458 [1970/2006]  1776   194   9.8%
  bin  9:  2.1458 -  2.0634 [1961/2003]  1767   194   9.9%
  bin 10:  2.0634 -  1.9924 [1443/2010]  1297   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 14
        2.42 -     3.04: 2176
        3.04 -     3.66: 4641
        3.66 -     4.28: 8942
        4.28 -     4.90: 12310
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.961 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.119 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.140 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.154 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28078 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_778/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.69535 87.68585 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: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3113   r_free= 0.3022   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.011788                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7552 0.99   1394  154 0.2779 0.2584      6.3413      6.2328|
|  2:  4.7552 -  3.7940 0.99   1336  151 0.2369 0.2424      6.3744      6.3706|
|  3:  3.7940 -  3.3202 0.99   1308  143 0.2628 0.2473      6.2969      6.3159|
|  4:  3.3202 -  3.0193 0.99   1306  148 0.2860 0.2972      6.1959       6.219|
|  5:  3.0193 -  2.8043 0.99   1302  146 0.3236 0.2703      6.0779       5.971|
|  6:  2.8043 -  2.6399 0.99   1296  141 0.3137 0.3380      5.9653      5.9199|
|  7:  2.6399 -  2.5083 0.99   1283  140 0.3304 0.3277       5.964      5.9955|
|  8:  2.5083 -  2.3996 0.98   1272  145 0.3448 0.3090      5.9648      5.9205|
|  9:  2.3996 -  2.3076 0.98   1263  140 0.3457 0.3275      5.8927      5.8513|
| 10:  2.3076 -  2.2282 1.00   1292  144 0.3676 0.3518      5.9207      5.8455|
| 11:  2.2282 -  2.1587 0.97   1257  137 0.3747 0.3703      5.8505      5.8853|
| 12:  2.1587 -  2.0972 0.98   1253  144 0.3540 0.3586      5.7794      5.8128|
| 13:  2.0972 -  2.0421 0.99   1305  134 0.3702 0.3496      5.6847      5.6482|
| 14:  2.0421 -  1.9924 0.60    763   92 0.3449 0.3919      5.6543      5.6361|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7552  1394   154  0.82  23.38   0.86     0.83      35064.00|
|  2:  4.7552 -  3.7940  1336   151  0.86  19.99   0.97     0.93      39625.33|
|  3:  3.7940 -  3.3202  1308   143  0.83  23.66   0.99     0.95      38419.68|
|  4:  3.3202 -  3.0193  1306   148  0.81  25.73   0.99     0.94      32856.23|
|  5:  3.0193 -  2.8043  1302   146  0.76  30.28   1.00     0.91      26540.73|
|  6:  2.8043 -  2.6399  1296   141  0.75  31.15   0.99     0.89      23889.32|
|  7:  2.6399 -  2.5083  1283   140  0.74  32.31   1.01     0.89      22829.33|
|  8:  2.5083 -  2.3996  1272   145  0.74  32.63   1.00     0.91      21466.19|
|  9:  2.3996 -  2.3076  1263   140  0.75  32.03   1.02     0.93      19700.84|
| 10:  2.3076 -  2.2282  1292   144  0.72  34.30   1.04     0.93      19152.81|
| 11:  2.2282 -  2.1587  1257   137  0.70  35.95   1.02     0.93      19663.06|
| 12:  2.1587 -  2.0972  1253   144  0.69  36.74   1.05     0.92      19224.27|
| 13:  2.0972 -  2.0421  1305   134  0.66  39.00   1.02     0.91      16661.77|
| 14:  2.0421 -  1.9924   763    92  0.72  34.70   1.06     0.90      13018.68|
|alpha:            min =        0.83 max =            0.95 mean =         0.91|
|beta:             min =    13018.68 max =        39625.33 mean =     25365.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.75|
|phase err.(work): min =        0.00 max =           89.99 mean =        30.63|
|phase err.(test): min =        0.00 max =           89.72 mean =        30.19|
|-----------------------------------------------------------------------------|

============================== 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 = 3.933585              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.121   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.561584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.994   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      193 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1983 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1836 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2805 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4586 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4356 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5645 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6665 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.806 |       0.159 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    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: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3113   r_free= 0.3022   ksol= 0.00   Bsol= 0.00   scale= 0.970    |
|                                                                             |
| 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:   0.35 A                  |
| x-ray target function (ml) for work reflections: 6.011788                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2962   r_free= 0.2894   ksol= 0.33   Bsol= 60.48   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.43,2.44,-0.00,0.00,0.00); trace/3= -0.94                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.984668                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.441924              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.023   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.307223              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.742   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2962      final r-factor (work) = 0.1699          |
| start r-factor (free) = 0.2894      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4681 = 3.44 * 0.50 * 5.9885 + 1.00 * 0.1621                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8232 = 3.44 * 0.50 * 5.6713 + 1.00 * 0.0630                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1699      final r-factor (work) = 0.1580          |
| start r-factor (free) = 0.1955      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7490 = 0.31 * 1.00 * 5.6713 + 1.00 * 0.0067                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7488 = 0.31 * 1.00 * 5.4104 + 1.00 * 0.0866                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.33   16.36    None  None   None       |
|    all(noH): 2823   0      0.00    86.33   16.36    None  None   None       |
|    Sol.    : 438    0      5.13    62.84   37.32    None  None   None       |
|    Mac.    : 2385   0      0.00    86.33   12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.633:  618   |   5:    43.166 -  51.800:   94        |
|      1:     8.633 -  17.267: 1452   |   6:    51.800 -  60.433:   58        |
|      2:    17.267 -  25.900:  308   |   7:    60.433 -  69.066:    5        |
|      3:    25.900 -  34.533:  150   |   8:    69.066 -  77.700:    0        |
|      4:    34.533 -  43.166:  137   |   9:    77.700 -  86.333:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1580 r_free = 0.1982             target_work(ml) = 5.417         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1575 r_free = 0.1980             target_work(ml) = 5.415         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1575   r_free= 0.1980   ksol= 0.33   Bsol= 60.48   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.84,-2.43,2.44,-0.00,0.00,0.00); trace/3= -0.94                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.415143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1557   r_free= 0.1954   ksol= 0.33   Bsol= 63.50   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.72,-0.23,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.407416                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.372295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.638  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.490389              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.694   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1557      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1954      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4894 = 2.37 * 0.50 * 5.4179 + 1.00 * 0.0630                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3552 = 2.37 * 0.50 * 5.3085 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1182          |
| start r-factor (free) = 0.1618      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6366 = 0.49 * 1.00 * 5.3085 + 1.00 * 0.0334                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5518 = 0.49 * 1.00 * 5.1851 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    78.60   17.11    None  None   None       |
|    all(noH): 2823   0      0.79    78.60   17.11    None  None   None       |
|    Sol.    : 438    0      4.42    78.60   40.23    None  None   None       |
|    Mac.    : 2385   0      0.79    77.63   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:     0.791 -   8.571:  676   |   5:    39.694 -  47.474:   96        |
|      1:     8.571 -  16.352: 1312   |   6:    47.474 -  55.255:   78        |
|      2:    16.352 -  24.132:  318   |   7:    55.255 -  63.035:   73        |
|      3:    24.132 -  31.913:  135   |   8:    63.035 -  70.816:   27        |
|      4:    31.913 -  39.694:   96   |   9:    70.816 -  78.597:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1182 r_free = 0.1611             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1610             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1610   ksol= 0.33   Bsol= 63.50   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.72,-0.23,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180075                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1179   r_free= 0.1603   ksol= 0.33   Bsol= 63.50   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.47,-0.52,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.178285                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.977344              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.968  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.675  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1603      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7767 = 2.98 * 0.50 * 5.1846 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7362 = 2.98 * 0.50 * 5.1487 + 1.00 * 0.0715                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9411 = 0.18 * 1.00 * 5.1487 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9377 = 0.18 * 1.00 * 5.1384 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    77.15   16.55    None  None   None       |
|    all(noH): 2823   0      1.53    77.15   16.55    None  None   None       |
|    Sol.    : 438    0      2.75    74.28   37.80    None  None   None       |
|    Mac.    : 2385   0      1.53    77.15   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.526 -   9.088:  830   |   5:    39.338 -  46.900:   93        |
|      1:     9.088 -  16.651: 1189   |   6:    46.900 -  54.463:   89        |
|      2:    16.651 -  24.213:  306   |   7:    54.463 -  62.025:   38        |
|      3:    24.213 -  31.775:  124   |   8:    62.025 -  69.587:   20        |
|      4:    31.775 -  39.338:  127   |   9:    69.587 -  77.150:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1553             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1101 r_free = 0.1553             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1553   ksol= 0.33   Bsol= 63.50   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.47,-0.52,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.132883                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1554   ksol= 0.32   Bsol= 54.48   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.30,-0.53,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132853                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.081238              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.823  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.208358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.562  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1112          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4186 = 2.08 * 0.50 * 5.1384 + 1.00 * 0.0715                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4073 = 2.08 * 0.50 * 5.1372 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1112      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0779 = 0.21 * 1.00 * 5.1372 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0786 = 0.21 * 1.00 * 5.1402 + 1.00 * 0.0076                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    77.26   16.40    None  None   None       |
|    all(noH): 2823   0      1.37    77.26   16.40    None  None   None       |
|    Sol.    : 438    0      3.17    74.01   37.60    None  None   None       |
|    Mac.    : 2385   0      1.37    77.26   12.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.374 -   8.963:  829   |   5:    39.318 -  46.907:   92        |
|      1:     8.963 -  16.551: 1196   |   6:    46.907 -  54.496:   92        |
|      2:    16.551 -  24.140:  301   |   7:    54.496 -  62.084:   35        |
|      3:    24.140 -  31.729:  126   |   8:    62.084 -  69.673:   19        |
|      4:    31.729 -  39.318:  126   |   9:    69.673 -  77.262:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1111 r_free = 0.1560             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1561             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1561   ksol= 0.32   Bsol= 54.48   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.38,-2.30,-0.53,-0.00,-0.00,-0.00); trace/3= -1.74                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141141                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1560   ksol= 0.32   Bsol= 54.48   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.21,-0.49,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141171                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.689208              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 167.776  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.854772              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1560      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9732 = 2.69 * 0.50 * 5.1404 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9707 = 2.69 * 0.50 * 5.1321 + 1.00 * 0.0701                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1088      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3943 = 0.85 * 1.00 * 5.1321 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3912 = 0.85 * 1.00 * 5.1266 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    83.83   16.55    None  None   None       |
|    all(noH): 2823   0      0.34    83.83   16.55    None  None   None       |
|    Sol.    : 438    0      4.09    77.08   38.93    None  None   None       |
|    Mac.    : 2385   0      0.34    83.83   12.44    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:     0.344 -   8.692:  838   |   5:    42.085 -  50.434:  100        |
|      1:     8.692 -  17.041: 1224   |   6:    50.434 -  58.782:   80        |
|      2:    17.041 -  25.389:  284   |   7:    58.782 -  67.130:   35        |
|      3:    25.389 -  33.737:  123   |   8:    67.130 -  75.478:   18        |
|      4:    33.737 -  42.085:  118   |   9:    75.478 -  83.826:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1080 r_free = 0.1575             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1079 r_free = 0.1576             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1079   r_free= 0.1576   ksol= 0.32   Bsol= 54.48   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.29,-2.21,-0.49,-0.00,-0.00,-0.00); trace/3= -1.66                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130968                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7552 0.99   1394  154 0.0981 0.1319      5.3963      5.5598|
|  2:  4.7552 -  3.7940 0.99   1336  151 0.0836 0.1139      5.4351      5.6382|
|  3:  3.7940 -  3.3202 0.99   1308  143 0.1030 0.1480      5.4643      5.8441|
|  4:  3.3202 -  3.0193 0.99   1306  148 0.1172 0.1667      5.4327      5.5971|
|  5:  3.0193 -  2.8043 0.99   1302  146 0.1284 0.1672      5.3101       5.565|
|  6:  2.8043 -  2.6399 0.99   1296  141 0.1168 0.2012      5.1947      5.4858|
|  7:  2.6399 -  2.5083 0.99   1283  140 0.1236 0.1520      5.1552      5.3087|
|  8:  2.5083 -  2.3996 0.98   1272  145 0.1089 0.1655      5.0459      5.3065|
|  9:  2.3996 -  2.3076 0.98   1263  140 0.1117 0.1687      5.0097      5.2658|
| 10:  2.3076 -  2.2282 1.00   1292  144 0.1085 0.1753      4.9395      5.2188|
| 11:  2.2282 -  2.1587 0.97   1257  137 0.1099 0.1754      4.9211      5.2745|
| 12:  2.1587 -  2.0972 0.98   1253  144 0.1065 0.1763      4.8669      5.2039|
| 13:  2.0972 -  2.0421 0.99   1305  134 0.1061 0.1671      4.7635      5.0173|
| 14:  2.0421 -  1.9924 0.60    763   92 0.0943 0.1675      4.6458      4.8913|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7552  1394   154  0.94   9.51   0.97     0.94       7634.79|
|  2:  4.7552 -  3.7940  1336   151  0.95   7.98   1.01     0.99       9403.06|
|  3:  3.7940 -  3.3202  1308   143  0.93  11.23   1.02     1.01      10285.09|
|  4:  3.3202 -  3.0193  1306   148  0.92  13.41   1.00     0.97      10012.21|
|  5:  3.0193 -  2.8043  1302   146  0.90  15.64   0.99     0.97       8259.14|
|  6:  2.8043 -  2.6399  1296   141  0.90  16.00   0.98     0.95       7005.13|
|  7:  2.6399 -  2.5083  1283   140  0.91  15.59   0.98     0.95       6178.08|
|  8:  2.5083 -  2.3996  1272   145  0.91  14.86   0.98     0.96       5174.47|
|  9:  2.3996 -  2.3076  1263   140  0.92  14.75   0.99     0.95       4841.16|
| 10:  2.3076 -  2.2282  1292   144  0.90  15.87   0.99     0.96       4382.77|
| 11:  2.2282 -  2.1587  1257   137  0.90  16.17   0.97     0.93       4276.84|
| 12:  2.1587 -  2.0972  1253   144  0.91  15.38   0.99     0.98       3994.10|
| 13:  2.0972 -  2.0421  1305   134  0.90  16.17   0.98     0.96       3303.61|
| 14:  2.0421 -  1.9924   763    92  0.92  13.60   0.96     0.93       2543.21|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2543.21 max =        10285.09 mean =      6380.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.97|
|phase err.(test): min =        0.00 max =           88.01 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1574   ksol= 0.32   Bsol= 54.47   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.94,-0.26,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130873                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1574   ksol= 0.32   Bsol= 54.47   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.94,-0.26,-0.00,-0.00,-0.00); trace/3= -1.40                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130873                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7552 0.99   1394  154 0.0980 0.1320      5.3949      5.5599|
|  2:  4.7552 -  3.7940 0.99   1336  151 0.0837 0.1139      5.4358      5.6385|
|  3:  3.7940 -  3.3202 0.99   1308  143 0.1030 0.1480      5.4644      5.8444|
|  4:  3.3202 -  3.0193 0.99   1306  148 0.1172 0.1667      5.4326      5.5969|
|  5:  3.0193 -  2.8043 0.99   1302  146 0.1283 0.1671      5.3097      5.5641|
|  6:  2.8043 -  2.6399 0.99   1296  141 0.1168 0.2013      5.1945       5.486|
|  7:  2.6399 -  2.5083 0.99   1283  140 0.1236 0.1520      5.1552      5.3089|
|  8:  2.5083 -  2.3996 0.98   1272  145 0.1090 0.1654       5.046      5.3061|
|  9:  2.3996 -  2.3076 0.98   1263  140 0.1116 0.1689      5.0097      5.2661|
| 10:  2.3076 -  2.2282 1.00   1292  144 0.1085 0.1752      4.9396      5.2182|
| 11:  2.2282 -  2.1587 0.97   1257  137 0.1099 0.1753      4.9211      5.2743|
| 12:  2.1587 -  2.0972 0.98   1253  144 0.1065 0.1761      4.8666      5.2034|
| 13:  2.0972 -  2.0421 0.99   1305  134 0.1060 0.1672      4.7635      5.0175|
| 14:  2.0421 -  1.9924 0.60    763   92 0.0943 0.1674      4.6462      4.8913|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7552  1394   154  0.94   9.50   0.97     0.94       7612.89|
|  2:  4.7552 -  3.7940  1336   151  0.95   7.98   1.01     1.00       9400.88|
|  3:  3.7940 -  3.3202  1308   143  0.93  11.24   1.02     1.01      10288.90|
|  4:  3.3202 -  3.0193  1306   148  0.92  13.41   1.00     0.98      10006.78|
|  5:  3.0193 -  2.8043  1302   146  0.90  15.64   1.00     0.98       8255.06|
|  6:  2.8043 -  2.6399  1296   141  0.90  16.00   0.98     0.96       7000.87|
|  7:  2.6399 -  2.5083  1283   140  0.91  15.59   0.99     0.96       6177.31|
|  8:  2.5083 -  2.3996  1272   145  0.91  14.86   0.99     0.97       5174.81|
|  9:  2.3996 -  2.3076  1263   140  0.92  14.75   1.00     0.96       4842.83|
| 10:  2.3076 -  2.2282  1292   144  0.90  15.86   1.00     0.97       4381.28|
| 11:  2.2282 -  2.1587  1257   137  0.90  16.16   0.99     0.94       4274.10|
| 12:  2.1587 -  2.0972  1253   144  0.91  15.38   1.01     0.99       3991.60|
| 13:  2.0972 -  2.0421  1305   134  0.90  16.17   0.99     0.97       3303.33|
| 14:  2.0421 -  1.9924   763    92  0.92  13.61   0.97     0.94       2544.77|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2544.77 max =        10288.90 mean =      6377.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.97|
|phase err.(test): min =        0.00 max =           88.03 mean =        13.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.063)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.33    83.82   16.54    None  None   None       |
|    all(noH): 2823   0      0.33    83.82   16.54    None  None   None       |
|    Sol.    : 438    0      4.08    77.07   38.92    None  None   None       |
|    Mac.    : 2385   0      0.33    83.82   12.43    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:     0.334 -   8.682:  838   |   5:    42.075 -  50.424:  100        |
|      1:     8.682 -  17.031: 1224   |   6:    50.424 -  58.772:   80        |
|      2:    17.031 -  25.379:  284   |   7:    58.772 -  67.120:   35        |
|      3:    25.379 -  33.727:  123   |   8:    67.120 -  75.468:   18        |
|      4:    33.727 -  42.075:  118   |   9:    75.468 -  83.816:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.436 - 4.786
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 291
   mapped sites are within: 0.707 - 4.786

peak=    5.759 closest distance to " NH2 ARG A  56 " =    2.220
peak=    5.225 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.208 closest distance to " CG  PRO A  54 " =    1.290
peak=    5.101 closest distance to " O   HOH Z 232 " =    2.363
peak=    5.058 closest distance to " O   HOH Z 126 " =    1.966
peak=    5.052 closest distance to " CB  GLN A 223 " =    1.439
peak=    4.910 closest distance to " O   HOH Z 144 " =    1.756
peak=    4.784 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.694 closest distance to " CB  ARG A 190 " =    1.656
peak=    4.681 closest distance to " CB  ARG A 275 " =    0.910
peak=    4.664 closest distance to " CB  ARG A  79 " =    1.419
peak=    4.591 closest distance to " O   HOH Z 298 " =    1.965
peak=    4.564 closest distance to " O   HOH Z  15 " =    2.149
peak=    4.563 closest distance to " O   HOH Z 369 " =    2.150
peak=    4.559 closest distance to " CB  SER A  63 " =    1.204
peak=    4.538 closest distance to " O   HOH Z  78 " =    1.724
peak=    4.432 closest distance to " CG  PRO A 213 " =    1.164
peak=    4.374 closest distance to " C   PRO A 198 " =    1.473
peak=    4.365 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.356 closest distance to " O   HOH Z 303 " =    2.117
peak=    4.330 closest distance to " CB  PRO A  54 " =    0.932
peak=    4.314 closest distance to " O   HOH Z 427 " =    2.964
peak=    4.297 closest distance to " CB  LEU A 228 " =    1.103
peak=    4.277 closest distance to " O   HOH Z 287 " =    2.245
peak=    4.271 closest distance to " CB  GLU A 152 " =    1.234
peak=    4.235 closest distance to " O   HOH Z 158 " =    3.105
peak=    4.218 closest distance to " CZ  PHE A 218 " =    1.066
peak=    4.207 closest distance to " O   HOH Z 250 " =    1.503
peak=    4.207 closest distance to " O   HOH Z 189 " =    2.739
peak=    4.160 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.153 closest distance to " O   HOH Z  61 " =    1.632
peak=    4.126 closest distance to " CE  LYS A  76 " =    0.851
peak=    4.108 closest distance to " ND2 ASN A 187 " =    1.442
peak=    4.094 closest distance to " O   HOH Z 392 " =    3.127
peak=    4.084 closest distance to " OD1 ASN A  69 " =    2.622
peak=    4.074 closest distance to " CB  VAL A 265 " =    1.274
peak=    4.074 closest distance to " O   HOH Z 346 " =    1.674
peak=    4.067 closest distance to " CD  ARG A 159 " =    0.771
peak=    4.063 closest distance to " CB  TRP A 266 " =    1.012
peak=    4.061 closest distance to " O   HOH Z 193 " =    1.892
peak=    4.053 closest distance to " O   HOH Z 234 " =    3.764
peak=    4.049 closest distance to " CG  PRO A 198 " =    1.230
peak=    4.003 closest distance to " CB  TYR A 169 " =    0.776
peak=    4.000 closest distance to " O   HOH Z 313 " =    1.984
peak=    3.993 closest distance to " CD2 TRP A 179 " =    1.316
peak=    3.977 closest distance to " NZ  LYS A 117 " =    3.230
peak=    3.967 closest distance to " CG2 VAL A 257 " =    0.868
peak=    3.966 closest distance to " O   HOH Z  78 " =    2.140
peak=    3.958 closest distance to " O   HOH Z 214 " =    2.150
peak=    3.949 closest distance to " CA  ASN A 215 " =    1.112
peak=    3.946 closest distance to " O   HOH Z 265 " =    2.331
peak=    3.913 closest distance to " O   SER A  87 " =    2.267
peak=    3.913 closest distance to " O   HOH Z 406 " =    1.606
peak=    3.880 closest distance to " CB  SER A 212 " =    1.131
peak=    3.860 closest distance to " O   HOH Z  53 " =    2.563
peak=    3.857 closest distance to " CB  ASP A 140 " =    1.020
peak=    3.846 closest distance to " O   HOH Z 180 " =    2.143
peak=    3.843 closest distance to " O   HOH Z 272 " =    1.834
peak=    3.838 closest distance to " NH1AARG A 145 " =    1.280
peak=    3.836 closest distance to " CB  GLU A 277 " =    3.663
peak=    3.828 closest distance to " O   HOH Z 368 " =    2.138
peak=    3.818 closest distance to " CA  ALA A  51 " =    0.932
peak=    3.815 closest distance to " O   HOH Z 172 " =    3.113
peak=    3.804 closest distance to " CB  ASP A 124 " =    0.707
peak=    3.792 closest distance to " CB  ASN A 142 " =    1.029
peak=    3.782 closest distance to " OG ASER A 258 " =    3.135
peak=    3.755 closest distance to " CD  ARG A  66 " =    2.437
peak=    3.749 closest distance to " O   HOH Z 133 " =    2.546
peak=    3.747 closest distance to " O   HOH Z   1 " =    1.872
peak=    3.747 closest distance to " O   HOH Z 389 " =    1.905
peak=    3.746 closest distance to " CB  VAL A 202 " =    1.594
peak=    3.736 closest distance to " CB  ASN A  39 " =    0.920
peak=    3.735 closest distance to " O   HOH Z  10 " =    1.851
peak=    3.730 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.715 closest distance to " CG  LEU A 167 " =    1.270
peak=    3.715 closest distance to " O   HOH Z  21 " =    1.759
peak=    3.701 closest distance to " O  BHOH Z 338 " =    2.288
peak=    3.692 closest distance to " CB  GLU A 128 " =    0.949
peak=    3.691 closest distance to " O   HOH Z 209 " =    2.318
peak=    3.682 closest distance to " CA  THR A 264 " =    0.887
peak=    3.680 closest distance to " CB  GLU A  46 " =    0.972
peak=    3.659 closest distance to " O   HOH Z 423 " =    1.893
peak=    3.656 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.655 closest distance to " CA  ARG A 195 " =    1.206
peak=    3.627 closest distance to " CA  ARG A  36 " =    1.040
peak=    3.612 closest distance to " CA  TYR A  30 " =    1.044
peak=    3.611 closest distance to " CD2 LEU A 297 " =    0.853
peak=    3.608 closest distance to " NE2 HIS A 207 " =    1.282
peak=    3.606 closest distance to " CD1 LEU A 300 " =    1.181
peak=    3.596 closest distance to " CB  ASN A 187 " =    1.053
peak=    3.595 closest distance to " O   HOH Z 353 " =    2.677
peak=    3.585 closest distance to " CB  ASN A 110 " =    1.087
peak=    3.583 closest distance to " CG  PRO A 243 " =    1.021
peak=    3.580 closest distance to " O   HOH Z  40 " =    1.763
peak=    3.570 closest distance to " CG  MET A 185 " =    1.154
peak=    3.569 closest distance to " O   HOH Z 291 " =    1.584
peak=    3.567 closest distance to " OG BSER A 164 " =    2.318
peak=    3.562 closest distance to " O   HOH Z 371 " =    2.955
peak=    3.559 closest distance to " CD  LYS A 166 " =    1.234
peak=    3.551 closest distance to " O   HOH Z 280 " =    2.986
peak=    3.545 closest distance to " O   HOH Z 371 " =    1.874
peak=    3.522 closest distance to " O   HOH Z   9 " =    1.992
peak=    3.515 closest distance to " ND1 HIS A  86 " =    1.763
peak=    3.515 closest distance to " O   HOH Z 411 " =    3.938
peak=    3.514 closest distance to " O   HOH Z 368 " =    3.623
peak=    3.513 closest distance to " CB  TYR A 116 " =    0.773
peak=    3.510 closest distance to " CA  THR A 221 " =    1.016
peak=    3.509 closest distance to " CB  SER A   3 " =    1.332
peak=    3.507 closest distance to " O   HOH Z 419 " =    2.104
peak=    3.503 closest distance to " OG  SER A  22 " =    2.773
peak=    3.498 closest distance to " CD  ARG A 269 " =    0.881
peak=    3.497 closest distance to " O   HOH Z 359 " =    1.487
peak=    3.492 closest distance to " CB  ALA A  34 " =    0.912
peak=    3.492 closest distance to " CA  SER A  87 " =    1.003
peak=    3.488 closest distance to " O   HOH Z  43 " =    1.875
peak=    3.480 closest distance to " CB  PRO A  90 " =    1.165
peak=    3.478 closest distance to " O   HOH Z 245 " =    1.259
peak=    3.477 closest distance to " CG1 VAL A 153 " =    1.006
peak=    3.476 closest distance to " O   HOH Z 305 " =    3.533
peak=    3.468 closest distance to " CG2AVAL A  72 " =    1.617
peak=    3.464 closest distance to " CG2 THR A 221 " =    1.043
peak=    3.463 closest distance to " CZ3 TRP A 266 " =    1.121
peak=    3.462 closest distance to " O   HOH Z 248 " =    1.568
peak=    3.458 closest distance to " O   HOH Z 147 " =    1.847
peak=    3.457 closest distance to " N   ARG A 156 " =    1.348
peak=    3.456 closest distance to " O   HOH Z 185 " =    1.878
peak=    3.453 closest distance to " CB  GLN A  88 " =    1.197
peak=    3.445 closest distance to " CA  TYR A 116 " =    1.305
peak=    3.440 closest distance to " O   HOH Z 203 " =    1.709
peak=    3.439 closest distance to " CG1 ILE A  33 " =    1.200
peak=    3.436 closest distance to " O   HOH Z 425 " =    2.034
peak=    3.435 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.432 closest distance to " OD2 ASP A 286 " =    2.860
peak=    3.429 closest distance to " O   HOH Z 325 " =    3.970
peak=    3.423 closest distance to " CB  ARG A 139 " =    1.042
peak=    3.420 closest distance to " CB  ALA A 291 " =    1.297
peak=    3.418 closest distance to " O   ASN A  74 " =    1.479
peak=    3.414 closest distance to " N   ASN A  39 " =    1.295
peak=    3.414 closest distance to " N   PHE A 130 " =    1.235
peak=    3.412 closest distance to " O   HOH Z 426 " =    1.883
peak=    3.408 closest distance to " CG2 ILE A 120 " =    1.095
peak=    3.407 closest distance to " O   HOH Z  88 " =    3.318
peak=    3.406 closest distance to " O   MET A 105 " =    1.901
peak=    3.406 closest distance to " O   HOH Z 213 " =    1.892
peak=    3.400 closest distance to " NE2 GLN A  73 " =    3.891
peak=    3.395 closest distance to " CE1 TYR A 186 " =    1.342
peak=    3.394 closest distance to " O   HOH Z 403 " =    1.597
peak=    3.394 closest distance to " CB  PHE A 204 " =    0.709
peak=    3.389 closest distance to " CA  ALA A 158 " =    1.244
peak=    3.384 closest distance to " CB  THR A  31 " =    1.604
peak=    3.381 closest distance to " O   HOH Z 285 " =    2.468
peak=    3.379 closest distance to " CB  ASN A 215 " =    1.128
peak=    3.375 closest distance to " O   HOH Z 128 " =    2.143
peak=    3.373 closest distance to " CB  ALA A   1 " =    4.786
peak=    3.373 closest distance to " O   HOH Z 403 " =    1.447
peak=    3.370 closest distance to " O   HOH Z 329 " =    4.027
peak=    3.367 closest distance to " CD1 LEU A  96 " =    0.757
peak=    3.365 closest distance to " O   HOH Z 128 " =    2.318
peak=    3.362 closest distance to " O   HOH Z 116 " =    3.097
peak=    3.356 closest distance to " CA  ASN A 217 " =    1.199
peak=    3.356 closest distance to " CG2 ILE A  20 " =    1.442
peak=    3.354 closest distance to " CA  MET A 105 " =    0.989
peak=    3.354 closest distance to " O   HOH Z 175 " =    2.139
peak=    3.352 closest distance to " O   HOH Z 148 " =    3.412
peak=    3.349 closest distance to " O   HOH Z 193 " =    1.697
peak=    3.348 closest distance to " CA  ALA A 160 " =    0.975
peak=    3.346 closest distance to " CB  TRP A 179 " =    1.399
peak=    3.346 closest distance to " CB  LEU A  83 " =    0.784
peak=    3.342 closest distance to " CB  ARG A 138 " =    0.979
peak=    3.341 closest distance to " O   HOH Z 391 " =    2.887
peak=    3.339 closest distance to " NH2 ARG A 156 " =    1.188
peak=    3.337 closest distance to " CE1 PHE A 218 " =    0.960
peak=    3.336 closest distance to " CZ2 TRP A 179 " =    1.738
peak=    3.336 closest distance to " O   HOH Z 227 " =    1.792
peak=    3.335 closest distance to " NH2BARG A 145 " =    2.121
peak=    3.326 closest distance to " O   HOH Z 287 " =    2.278
peak=    3.324 closest distance to " O   HOH Z   1 " =    1.644
peak=    3.323 closest distance to " CD2 LEU A 255 " =    1.506
peak=    3.321 closest distance to " CG  GLN A  11 " =    1.746
peak=    3.319 closest distance to " N   ASN A 127 " =    1.266
peak=    3.315 closest distance to " O   HOH Z 234 " =    1.871
peak=    3.313 closest distance to " CA  VAL A 125 " =    1.093
peak=    3.312 closest distance to " CB  ALA A 248 " =    0.924
peak=    3.307 closest distance to " CB  THR A  82 " =    1.396
peak=    3.294 closest distance to " OG1 THR A 294 " =    2.456
peak=    3.293 closest distance to " O   HOH Z  66 " =    2.206
peak=    3.292 closest distance to " O   THR A 220 " =    1.259
peak=    3.290 closest distance to " O   HOH Z 365 " =    2.877
peak=    3.287 closest distance to " CG1 VAL A 189 " =    1.945
peak=    3.283 closest distance to " O   HOH Z  59 " =    1.852
peak=    3.281 closest distance to " CA  MET A  40 " =    1.184
peak=    3.279 closest distance to " O   HOH Z 325 " =    2.523
peak=    3.278 closest distance to " CG  GLU A  37 " =    0.866
peak=    3.278 closest distance to " CG  LYS A  76 " =    0.952
peak=    3.278 closest distance to " CD BLYS A 290 " =    1.046
peak=    3.277 closest distance to " CE1 PHE A  38 " =    1.242
peak=    3.277 closest distance to " CB  ILE A 120 " =    1.283
peak=    3.276 closest distance to " O   HOH Z 273 " =    2.923
peak=    3.276 closest distance to " O   HOH Z  97 " =    2.692
peak=    3.274 closest distance to " O   HOH Z 188 " =    1.996
peak=    3.274 closest distance to " O   HOH Z 417 " =    3.415
peak=    3.272 closest distance to " O   HOH Z 132 " =    2.571
peak=    3.268 closest distance to " CD1 ILE A 263 " =    1.313
peak=    3.267 closest distance to " CB  LYS A 117 " =    1.210
peak=    3.264 closest distance to " CB  SER A 141 " =    0.997
peak=    3.264 closest distance to " CA  ALA A 233 " =    1.283
peak=    3.264 closest distance to " O   HOH Z 422 " =    2.677
peak=    3.264 closest distance to " O   HOH Z 402 " =    1.369
peak=    3.263 closest distance to " NH2AARG A 275 " =    3.611
peak=    3.262 closest distance to " CA  GLU A  46 " =    0.789
peak=    3.261 closest distance to " O   ALA A 165 " =    1.585
peak=    3.257 closest distance to " CB  ASP A 298 " =    1.131
peak=    3.256 closest distance to " O   TYR A 116 " =    1.335
peak=    3.251 closest distance to " CA  PHE A  59 " =    1.017
peak=    3.248 closest distance to " O   HOH Z  40 " =    1.992
peak=    3.246 closest distance to " CA  ALA A  84 " =    1.357
peak=    3.242 closest distance to " OD1BASN A 224 " =    2.338
peak=    3.241 closest distance to " O   HOH Z 218 " =    4.583
peak=    3.237 closest distance to " O   HOH Z 409 " =    2.821
peak=    3.235 closest distance to " O   HOH Z 421 " =    2.022
peak=    3.234 closest distance to " OG BSER A  99 " =    2.236
peak=    3.233 closest distance to " O   HOH Z 345 " =    1.653
peak=    3.232 closest distance to " CG2 VAL A 197 " =    1.079
peak=    3.231 closest distance to " CA  ALA A  21 " =    1.184
peak=    3.229 closest distance to " O   HOH Z  44 " =    2.895
peak=    3.229 closest distance to " CG2 ILE A 234 " =    0.780
peak=    3.228 closest distance to " O   THR A 251 " =    1.160
peak=    3.228 closest distance to " CB  ASN A 224 " =    0.976
peak=    3.222 closest distance to " O   HOH Z  61 " =    1.426
peak=    3.222 closest distance to " CB  THR A 235 " =    1.214
peak=    3.220 closest distance to " CD  ARG A 219 " =    1.174
peak=    3.215 closest distance to " CB  THR A 157 " =    1.144
peak=    3.207 closest distance to " CA  ARG A 102 " =    1.095
peak=    3.203 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.195 closest distance to " O   HOH Z 299 " =    4.388
peak=    3.195 closest distance to " O   HOH Z 344 " =    3.199
peak=    3.192 closest distance to " O   HOH Z 294 " =    1.494
peak=    3.189 closest distance to " CG1 ILE A  49 " =    1.474
peak=    3.188 closest distance to " CB  MET A  40 " =    0.798
peak=    3.187 closest distance to " O   HOH Z 171 " =    4.064
peak=    3.186 closest distance to " CE  LYS A  48 " =    1.125
peak=    3.184 closest distance to " O   PHE A 192 " =    1.406
peak=    3.182 closest distance to " O   HOH Z 193 " =    2.046
peak=    3.179 closest distance to " CA  ARG A 159 " =    1.262
peak=    3.179 closest distance to " CB  LYS A 290 " =    1.023
peak=    3.174 closest distance to " ND2 ASN A 110 " =    1.660
peak=    3.173 closest distance to " CB  SER A 216 " =    0.842
peak=    3.172 closest distance to " O   HOH Z 116 " =    1.808
peak=    3.169 closest distance to " O   HOH Z 345 " =    3.492
peak=    3.168 closest distance to " CB  SER A  97 " =    0.885
peak=    3.164 closest distance to " CA  ILE A 234 " =    0.959
peak=    3.163 closest distance to " N   GLN A 278 " =    1.340
peak=    3.162 closest distance to " CB  ALA A   9 " =    1.574
peak=    3.161 closest distance to " NZ  LYS A  48 " =    1.286
peak=    3.150 closest distance to " NE  ARG A  79 " =    1.098
peak=    3.149 closest distance to " NH1BARG A 145 " =    1.038
peak=    3.138 closest distance to " O   HOH Z 248 " =    1.635
peak=    3.135 closest distance to " CD1 ILE A 106 " =    0.743
peak=    3.134 closest distance to " O   HOH Z 423 " =    2.919
peak=    3.129 closest distance to " O   HOH Z 332 " =    1.509
peak=    3.128 closest distance to " CB  SER A 210 " =    0.735
peak=    3.125 closest distance to " CA  SER A 146 " =    1.655
peak=    3.122 closest distance to " CB  GLN A 103 " =    0.889
peak=    3.121 closest distance to " O   HOH Z  97 " =    1.979
peak=    3.120 closest distance to " CB  VAL A 268 " =    0.832
peak=    3.117 closest distance to " CB  MET A  47 " =    1.227
peak=    3.114 closest distance to " O   HOH Z 407 " =    2.404
peak=    3.113 closest distance to " CD  ARG A 195 " =    3.443
peak=    3.112 closest distance to " O   HOH Z 285 " =    1.882
peak=    3.110 closest distance to " O   HOH Z 173 " =    1.719
peak=    3.106 closest distance to " O   HOH Z 302 " =    1.999
peak=    3.105 closest distance to " N   GLY A  98 " =    1.070
peak=    3.100 closest distance to " O   SER A 164 " =    1.320
peak=    3.097 closest distance to " O   HOH Z 327 " =    1.696
peak=    3.089 closest distance to " O   HOH Z 336 " =    1.779
peak=    3.085 closest distance to " O   HOH Z 384 " =    2.974
peak=    3.072 closest distance to " O   HOH Z 298 " =    2.389
peak=    3.066 closest distance to " CB  LYS A 193 " =    0.961
peak=    3.064 closest distance to " O   ALA A 158 " =    1.302
peak=    3.051 closest distance to " OG  SER A  62 " =    3.013
peak=    3.047 closest distance to " CB  ALA A 114 " =    0.723
peak=    3.040 closest distance to " CB  ALA A  43 " =    0.785
peak=    3.037 closest distance to " O   HOH Z  88 " =    2.726
peak=    3.026 closest distance to " O   HOH Z 188 " =    2.498
peak=    3.012 closest distance to " CA  ALA A 299 " =    0.888

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.720 - 5.662
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.720 - 5.662

peak=   -4.687 closest distance to " CD  ARG A  14 " =    3.495
peak=   -4.512 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.442 closest distance to " O   HOH Z 266 " =    5.342
peak=   -4.436 closest distance to " CB  PRO A 243 " =    2.663
peak=   -4.391 closest distance to " CD  GLN A  58 " =    0.985
peak=   -4.380 closest distance to " O   HOH Z 231 " =    2.290
peak=   -4.360 closest distance to " O   HOH Z 377 " =    2.179
peak=   -4.340 closest distance to " CG1 VAL A 112 " =    2.644
peak=   -4.301 closest distance to " O   VAL A  67 " =    2.764
peak=   -4.245 closest distance to " CG  GLN A 223 " =    2.065
peak=   -4.176 closest distance to " N   ALA A  43 " =    2.666
peak=   -4.165 closest distance to " OG BSER A 134 " =    1.269
peak=   -4.143 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -4.142 closest distance to " CD2 PHE A 192 " =    2.057
peak=   -4.135 closest distance to " O   HOH Z  73 " =    2.194
peak=   -4.067 closest distance to " O   HOH Z 372 " =    2.453
peak=   -4.023 closest distance to " CG1 VAL A 112 " =    2.894
peak=   -3.986 closest distance to " C   HIS A 108 " =    1.139
peak=   -3.969 closest distance to " CE  MET A 105 " =    2.460
peak=   -3.968 closest distance to " O   HOH Z 389 " =    2.000
peak=   -3.943 closest distance to " O   HOH Z 198 " =    2.016
peak=   -3.907 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.891 closest distance to " CE2 TYR A  30 " =    2.762
peak=   -3.881 closest distance to " CB  ALA A  43 " =    2.603
peak=   -3.874 closest distance to " CA  VAL A  67 " =    2.939
peak=   -3.853 closest distance to " O   ILE A 109 " =    2.540
peak=   -3.845 closest distance to " CB  ALA A 291 " =    2.264
peak=   -3.832 closest distance to " O   HOH Z  10 " =    1.474
peak=   -3.818 closest distance to " CD1 PHE A  59 " =    1.973
peak=   -3.815 closest distance to " O   HOH Z 407 " =    3.200
peak=   -3.799 closest distance to " O   HOH Z 435 " =    2.885
peak=   -3.794 closest distance to " O   HOH Z  38 " =    1.474
peak=   -3.792 closest distance to " O   HOH Z 114 " =    3.049
peak=   -3.770 closest distance to " O   HOH Z 313 " =    1.933
peak=   -3.769 closest distance to " CE BMET A  47 " =    1.447
peak=   -3.756 closest distance to " O   HOH Z 185 " =    2.232
peak=   -3.748 closest distance to " OG  SER A  97 " =    2.242
peak=   -3.742 closest distance to " ND2 ASN A  45 " =    1.817
peak=   -3.736 closest distance to " O   HOH Z 351 " =    1.476
peak=   -3.724 closest distance to " CG  ARG A 269 " =    2.398
peak=   -3.720 closest distance to " CG2 ILE A 263 " =    2.316
peak=   -3.716 closest distance to " OD1 ASP A 171 " =    1.670
peak=   -3.709 closest distance to " O   HOH Z 196 " =    2.075
peak=   -3.688 closest distance to " CB  ALA A 291 " =    2.253
peak=   -3.687 closest distance to " CA  GLY A 203 " =    2.434
peak=   -3.669 closest distance to " OXT GLY A 302 " =    2.913
peak=   -3.666 closest distance to " CD  ARG A 139 " =    1.611
peak=   -3.657 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.646 closest distance to " CG1 VAL A 250 " =    2.689
peak=   -3.640 closest distance to " NH2AARG A 275 " =    5.407
peak=   -3.632 closest distance to " CE2 PHE A  61 " =    2.626
peak=   -3.622 closest distance to " CB  ASN A  39 " =    2.334
peak=   -3.609 closest distance to " O   HOH Z  51 " =    1.637
peak=   -3.604 closest distance to " ND2 ASN A 249 " =    2.380
peak=   -3.604 closest distance to " OD1 ASN A 148 " =    1.479
peak=   -3.595 closest distance to " O   HOH Z 290 " =    1.339
peak=   -3.584 closest distance to " CB  ALA A 248 " =    2.409
peak=   -3.566 closest distance to " N   ALA A 248 " =    1.598
peak=   -3.559 closest distance to " O   VAL A 189 " =    2.641
peak=   -3.557 closest distance to " ND2 ASN A  45 " =    1.260
peak=   -3.554 closest distance to " CD2 LEU A 237 " =    2.846
peak=   -3.538 closest distance to " O   PRO A 163 " =    2.092
peak=   -3.527 closest distance to " O   HOH Z 394 " =    1.458
peak=   -3.521 closest distance to " O   PHE A 218 " =    1.590
peak=   -3.511 closest distance to " CD2 PHE A  61 " =    2.060
peak=   -3.509 closest distance to " CG2 THR A 178 " =    2.303
peak=   -3.501 closest distance to " CD2 TYR A 293 " =    1.983
peak=   -3.494 closest distance to " NE2 GLN A 194 " =    1.827
peak=   -3.493 closest distance to " CG  PHE A 283 " =    2.714
peak=   -3.482 closest distance to " O   HOH Z 198 " =    1.457
peak=   -3.480 closest distance to " O   HOH Z  11 " =    1.722
peak=   -3.472 closest distance to " CB  ASP A 286 " =    2.057
peak=   -3.471 closest distance to " O   HOH Z  52 " =    1.339
peak=   -3.466 closest distance to " O   HOH Z 359 " =    3.204
peak=   -3.461 closest distance to " CB  TRP A  85 " =    2.528
peak=   -3.451 closest distance to " O   HOH Z 253 " =    3.936
peak=   -3.449 closest distance to " NH2BARG A 275 " =    1.863
peak=   -3.442 closest distance to " O   HOH Z 211 " =    1.523
peak=   -3.440 closest distance to " CZ  PHE A 155 " =    1.301
peak=   -3.439 closest distance to " O   HOH Z  43 " =    1.664
peak=   -3.427 closest distance to " CA  GLY A 241 " =    2.317
peak=   -3.420 closest distance to " CG2 ILE A  49 " =    2.736
peak=   -3.415 closest distance to " CA  GLY A 241 " =    3.080
peak=   -3.413 closest distance to " C   ASN A 285 " =    2.407
peak=   -3.410 closest distance to " NE2 GLN A 278 " =    1.675
peak=   -3.409 closest distance to " O   HOH Z 353 " =    2.162
peak=   -3.409 closest distance to " CG1BVAL A  41 " =    2.740
peak=   -3.408 closest distance to " OD2 ASP A 191 " =    1.440
peak=   -3.402 closest distance to " CB  ASP A 132 " =    2.299
peak=   -3.398 closest distance to " CB  PHE A 208 " =    2.260
peak=   -3.398 closest distance to " N   THR A 157 " =    1.539
peak=   -3.395 closest distance to " CB  ALA A 244 " =    2.086
peak=   -3.393 closest distance to " CG1 VAL A 125 " =    1.908
peak=   -3.391 closest distance to " O   HOH Z 311 " =    3.775
peak=   -3.389 closest distance to " CD1 LEU A 101 " =    2.363
peak=   -3.383 closest distance to " ND2 ASN A  60 " =    1.536
peak=   -3.370 closest distance to " O   ALA A  10 " =    1.680
peak=   -3.367 closest distance to " O   HOH Z   6 " =    1.411
peak=   -3.366 closest distance to " CB  PRO A 163 " =    2.474
peak=   -3.362 closest distance to " CB  ALA A 248 " =    2.194
peak=   -3.362 closest distance to " CE3 TRP A 150 " =    2.184
peak=   -3.360 closest distance to " OH  TYR A 247 " =    2.099
peak=   -3.352 closest distance to " CE2 PHE A 218 " =    2.480
peak=   -3.346 closest distance to " CE3 TRP A 274 " =    2.429
peak=   -3.344 closest distance to " O   HOH Z  13 " =    1.744
peak=   -3.342 closest distance to " CD1 LEU A   5 " =    2.616
peak=   -3.340 closest distance to " CG  HIS A  86 " =    1.094
peak=   -3.337 closest distance to " CG  GLU A 277 " =    1.219
peak=   -3.327 closest distance to " N   SER A 212 " =    2.043
peak=   -3.327 closest distance to " N   THR A  52 " =    1.707
peak=   -3.323 closest distance to " O   HOH Z 243 " =    1.978
peak=   -3.320 closest distance to " OD1 ASN A 187 " =    1.518
peak=   -3.310 closest distance to " O   HOH Z 322 " =    1.250
peak=   -3.307 closest distance to " C   ALA A 158 " =    1.418
peak=   -3.306 closest distance to " CB  ALA A 114 " =    2.559
peak=   -3.301 closest distance to " CB  TYR A  15 " =    2.208
peak=   -3.301 closest distance to " O   HOH Z 191 " =    5.603
peak=   -3.298 closest distance to " O   ARG A 145 " =    1.561
peak=   -3.293 closest distance to " CZ  PHE A  59 " =    1.572
peak=   -3.289 closest distance to " NE2 GLN A  88 " =    1.875
peak=   -3.286 closest distance to " CZ  TYR A 169 " =    1.740
peak=   -3.286 closest distance to " NH2 ARG A  79 " =    1.540
peak=   -3.280 closest distance to " O   SER A 135 " =    1.428
peak=   -3.278 closest distance to " SD  MET A 188 " =    2.126
peak=   -3.277 closest distance to " O   GLY A  17 " =    1.152
peak=   -3.277 closest distance to " O   HOH Z 426 " =    1.586
peak=   -3.277 closest distance to " OD2 ASP A 171 " =    1.859
peak=   -3.275 closest distance to " CD  ARG A 195 " =    5.216
peak=   -3.269 closest distance to " O   HOH Z 102 " =    1.595
peak=   -3.268 closest distance to " O   HOH Z 128 " =    2.655
peak=   -3.267 closest distance to " CD1 LEU A 228 " =    2.302
peak=   -3.266 closest distance to " O   HOH Z 298 " =    1.290
peak=   -3.266 closest distance to " O   HOH Z 126 " =    1.924
peak=   -3.264 closest distance to " CG1 VAL A 197 " =    2.238
peak=   -3.263 closest distance to " ND2 ASN A 187 " =    1.495
peak=   -3.262 closest distance to " O   HOH Z  60 " =    1.879
peak=   -3.261 closest distance to " OD2 ASP A 171 " =    2.332
peak=   -3.261 closest distance to " O   ALA A  34 " =    2.566
peak=   -3.258 closest distance to " ND2 ASN A  60 " =    4.163
peak=   -3.257 closest distance to " O   HOH Z 174 " =    2.599
peak=   -3.254 closest distance to " CG  TRP A 266 " =    1.865
peak=   -3.252 closest distance to " C   MET A 188 " =    1.381
peak=   -3.251 closest distance to " OE1 GLN A  88 " =    1.072
peak=   -3.247 closest distance to " O   HOH Z 357 " =    2.046
peak=   -3.247 closest distance to " O   HOH Z  37 " =    1.874
peak=   -3.243 closest distance to " O   HOH Z 421 " =    3.066
peak=   -3.242 closest distance to " O   VAL A 189 " =    1.603
peak=   -3.240 closest distance to " O   GLY A 211 " =    1.404
peak=   -3.239 closest distance to " CB  ASN A 252 " =    1.633
peak=   -3.236 closest distance to " CB  CYS A 201 " =    2.644
peak=   -3.235 closest distance to " CB  GLN A  11 " =    1.822
peak=   -3.234 closest distance to " C   LEU A 222 " =    0.720
peak=   -3.231 closest distance to " OG BSER A 134 " =    1.760
peak=   -3.227 closest distance to " O   HOH Z 134 " =    3.082
peak=   -3.225 closest distance to " O   ALA A 292 " =    2.131
peak=   -3.217 closest distance to " CA  SER A 135 " =    1.340
peak=   -3.209 closest distance to " CA  TRP A 274 " =    1.434
peak=   -3.206 closest distance to " O   HOH Z 244 " =    2.010
peak=   -3.204 closest distance to " O   PRO A 198 " =    1.359
peak=   -3.203 closest distance to " O   HOH Z 140 " =    1.846
peak=   -3.200 closest distance to " C   LEU A 143 " =    1.119
peak=   -3.199 closest distance to " CD2 TYR A 247 " =    2.428
peak=   -3.198 closest distance to " OD1 ASP A 191 " =    1.840
peak=   -3.197 closest distance to " N   ASP A 171 " =    2.345
peak=   -3.194 closest distance to " O   GLN A 240 " =    2.508
peak=   -3.193 closest distance to " NH2 ARG A  24 " =    1.891
peak=   -3.191 closest distance to " O   HOH Z 310 " =    1.849
peak=   -3.190 closest distance to " O   TRP A  70 " =    1.437
peak=   -3.189 closest distance to " O   ALA A  51 " =    1.303
peak=   -3.189 closest distance to " CD1 LEU A 297 " =    2.422
peak=   -3.185 closest distance to " OE1 GLN A 223 " =    2.032
peak=   -3.184 closest distance to " CD  GLN A 223 " =    0.796
peak=   -3.178 closest distance to " OD2 ASP A  50 " =    1.736
peak=   -3.175 closest distance to " O   HOH Z 365 " =    1.961
peak=   -3.170 closest distance to " CG2 ILE A  20 " =    2.763
peak=   -3.163 closest distance to " CB  ALA A 129 " =    2.462
peak=   -3.163 closest distance to " O   HOH Z 281 " =    2.729
peak=   -3.160 closest distance to " O   ALA A 180 " =    1.287
peak=   -3.158 closest distance to " O   ALA A 161 " =    1.780
peak=   -3.151 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.150 closest distance to " N   SER A 276 " =    1.309
peak=   -3.150 closest distance to " CD2 HIS A 207 " =    2.368
peak=   -3.150 closest distance to " O   HOH Z 350 " =    2.057
peak=   -3.146 closest distance to " O   HOH Z 348 " =    1.955
peak=   -3.146 closest distance to " CG  ARG A 269 " =    2.039
peak=   -3.131 closest distance to " O   HOH Z 177 " =    1.730
peak=   -3.129 closest distance to " O   HOH Z  71 " =    2.161
peak=   -3.124 closest distance to " CA  HIS A  86 " =    2.362
peak=   -3.118 closest distance to " OE2 GLU A 152 " =    1.181
peak=   -3.116 closest distance to " CE  LYS A  76 " =    2.683
peak=   -3.110 closest distance to " O   HOH Z 175 " =    4.215
peak=   -3.108 closest distance to " CB  ALA A 100 " =    2.163
peak=   -3.098 closest distance to " O   HOH Z 189 " =    1.916
peak=   -3.097 closest distance to " OD1AASN A 224 " =    1.789
peak=   -3.090 closest distance to " CG  PRO A 163 " =    2.584
peak=   -3.085 closest distance to " O   HOH Z 266 " =    5.104
peak=   -3.084 closest distance to " CG2 VAL A 189 " =    2.033
peak=   -3.078 closest distance to " CZ  PHE A  38 " =    1.969
peak=   -3.075 closest distance to " CB  ASP A 132 " =    2.402
peak=   -3.052 closest distance to " O   HOH Z 262 " =    2.905
peak=   -3.044 closest distance to " O   HOH Z 283 " =    5.662
peak=   -3.014 closest distance to " C   GLN A  58 " =    1.973

================= 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    :  0.3113 0.3022   6.011788e+00   5.987417e+00
   1_bss:  0.2962 0.2894   5.984668e+00   5.955867e+00
   1_xyz:  0.1699 0.1955   5.463117e+00   5.564210e+00
   1_adp:  0.1580 0.1982   5.417157e+00   5.583981e+00
   1_occ:  0.1575 0.1980   5.415143e+00   5.583086e+00
   2_bss:  0.1557 0.1954   5.407416e+00   5.575645e+00
   2_xyz:  0.1257 0.1618   5.217065e+00   5.415471e+00
   2_adp:  0.1182 0.1611   5.180064e+00   5.403104e+00
   2_occ:  0.1181 0.1610   5.180075e+00   5.403417e+00
   3_bss:  0.1179 0.1603   5.178285e+00   5.400354e+00
   3_xyz:  0.1100 0.1569   5.137093e+00   5.381925e+00
   3_adp:  0.1103 0.1553   5.132865e+00   5.373159e+00
   3_occ:  0.1101 0.1553   5.132883e+00   5.373598e+00
   4_bss:  0.1101 0.1554   5.132853e+00   5.374004e+00
   4_xyz:  0.1112 0.1561   5.141425e+00   5.381612e+00
   4_adp:  0.1111 0.1560   5.140978e+00   5.381713e+00
   4_occ:  0.1110 0.1561   5.141141e+00   5.382069e+00
   5_bss:  0.1110 0.1560   5.141171e+00   5.382100e+00
   5_xyz:  0.1088 0.1564   5.131793e+00   5.382358e+00
   5_adp:  0.1080 0.1575   5.130761e+00   5.386721e+00
   5_occ:  0.1079 0.1576   5.130968e+00   5.387091e+00
   5_bss:  0.1078 0.1574   5.130873e+00   5.386993e+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:  0.327  60.478  -2.835  -2.433   2.445  -0.000   0.000   0.000
   1_xyz:  0.327  60.478  -2.835  -2.433   2.445  -0.000   0.000   0.000
   1_adp:  0.327  60.478  -2.835  -2.433   2.445  -0.000   0.000   0.000
   1_occ:  0.327  60.478  -2.835  -2.433   2.445  -0.000   0.000   0.000
   2_bss:  0.333  63.498  -2.937  -2.723  -0.230  -0.000  -0.000  -0.000
   2_xyz:  0.333  63.498  -2.937  -2.723  -0.230  -0.000  -0.000  -0.000
   2_adp:  0.333  63.498  -2.937  -2.723  -0.230  -0.000  -0.000  -0.000
   2_occ:  0.333  63.498  -2.937  -2.723  -0.230  -0.000  -0.000  -0.000
   3_bss:  0.333  63.498  -2.593  -2.469  -0.522  -0.000  -0.000  -0.000
   3_xyz:  0.333  63.498  -2.593  -2.469  -0.522  -0.000  -0.000  -0.000
   3_adp:  0.333  63.498  -2.593  -2.469  -0.522  -0.000  -0.000  -0.000
   3_occ:  0.333  63.498  -2.593  -2.469  -0.522  -0.000  -0.000  -0.000
   4_bss:  0.323  54.478  -2.383  -2.301  -0.529  -0.000  -0.000  -0.000
   4_xyz:  0.323  54.478  -2.383  -2.301  -0.529  -0.000  -0.000  -0.000
   4_adp:  0.323  54.478  -2.383  -2.301  -0.529  -0.000  -0.000  -0.000
   4_occ:  0.323  54.478  -2.383  -2.301  -0.529  -0.000  -0.000  -0.000
   5_bss:  0.323  54.478  -2.287  -2.208  -0.488  -0.000  -0.000  -0.000
   5_xyz:  0.323  54.478  -2.287  -2.208  -0.488  -0.000  -0.000  -0.000
   5_adp:  0.323  54.478  -2.287  -2.208  -0.488  -0.000  -0.000  -0.000
   5_occ:  0.323  54.478  -2.287  -2.208  -0.488  -0.000  -0.000  -0.000
   5_bss:  0.317  54.468  -2.006  -1.943  -0.265  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  30.584 0.7550  0.9126    25366.434
   1_bss:  29.340 0.7670  0.8999    22646.969
   1_xyz:  17.883 0.8825  0.9946     9372.711
   1_adp:  18.404 0.8772  0.9886     9689.074
   1_occ:  18.382 0.8774  0.9883     9659.741
   2_bss:  18.097 0.8803  0.9567     9565.142
   2_xyz:  14.626 0.9098  0.9706     6735.648
   2_adp:  14.379 0.9119  0.9663     6550.606
   2_occ:  14.381 0.9118  0.9660     6549.401
   3_bss:  14.319 0.9123  0.9697     6499.842
   3_xyz:  13.869 0.9161  0.9722     6298.798
   3_adp:  13.668 0.9179  0.9682     6206.776
   3_occ:  13.677 0.9178  0.9681     6210.313
   4_bss:  13.683 0.9178  0.9722     6210.120
   4_xyz:  13.812 0.9169  0.9714     6315.512
   4_adp:  13.808 0.9169  0.9660     6317.419
   4_occ:  13.817 0.9168  0.9659     6320.054
   5_bss:  13.818 0.9168  0.9686     6320.909
   5_xyz:  13.820 0.9168  0.9690     6348.519
   5_adp:  13.921 0.9160  0.9616     6377.207
   5_occ:  13.925 0.9159  0.9615     6380.492
   5_bss:  13.924 0.9159  0.9699     6377.516
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6211e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6211e-01
   1_xyz:   1.030  0.008  0.072 15.344  0.004  4.119   6.2991e-02
   1_adp:   1.030  0.008  0.072 15.344  0.004  4.119   6.2991e-02
   1_occ:   1.030  0.008  0.072 15.344  0.004  4.119   6.2991e-02
   2_bss:   1.030  0.008  0.072 15.344  0.004  4.119   6.2991e-02
   2_xyz:   0.984  0.008  0.075 14.961  0.004  4.125   5.8591e-02
   2_adp:   0.984  0.008  0.075 14.961  0.004  4.125   5.8591e-02
   2_occ:   0.984  0.008  0.075 14.961  0.004  4.125   5.8591e-02
   3_bss:   0.984  0.008  0.075 14.961  0.004  4.125   5.8591e-02
   3_xyz:   1.072  0.010  0.083 15.049  0.004  4.113   7.1463e-02
   3_adp:   1.072  0.010  0.083 15.049  0.004  4.113   7.1463e-02
   3_occ:   1.072  0.010  0.083 15.049  0.004  4.113   7.1463e-02
   4_bss:   1.072  0.010  0.083 15.049  0.004  4.113   7.1463e-02
   4_xyz:   0.990  0.008  0.078 14.811  0.004  4.113   6.1415e-02
   4_adp:   0.990  0.008  0.078 14.811  0.004  4.113   6.1415e-02
   4_occ:   0.990  0.008  0.078 14.811  0.004  4.113   6.1415e-02
   5_bss:   0.990  0.008  0.078 14.811  0.004  4.113   6.1415e-02
   5_xyz:   1.065  0.010  0.083 14.956  0.004  4.115   7.0124e-02
   5_adp:   1.065  0.010  0.083 14.956  0.004  4.115   7.0124e-02
   5_occ:   1.065  0.010  0.083 14.956  0.004  4.115   7.0124e-02
   5_bss:   1.065  0.010  0.083 14.956  0.004  4.115   7.0124e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4233e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4233e-01
   1_xyz:   8.247  0.043  0.238 83.274  0.038  2.286   5.8598e-02
   1_adp:   8.247  0.043  0.238 83.274  0.038  2.286   5.8598e-02
   1_occ:   8.247  0.043  0.238 83.274  0.038  2.286   5.8598e-02
   2_bss:   8.247  0.043  0.238 83.274  0.038  2.286   5.8598e-02
   2_xyz:   7.124  0.040  0.248 81.662  0.033  2.334   3.9721e-02
   2_adp:   7.124  0.040  0.248 81.662  0.033  2.334   3.9721e-02
   2_occ:   7.124  0.040  0.248 81.662  0.033  2.334   3.9721e-02
   3_bss:   7.124  0.040  0.248 81.662  0.033  2.334   3.9721e-02
   3_xyz:   6.987  0.051  0.294 83.457  0.038  2.328   5.5353e-02
   3_adp:   6.987  0.051  0.294 83.457  0.038  2.328   5.5353e-02
   3_occ:   6.987  0.051  0.294 83.457  0.038  2.328   5.5353e-02
   4_bss:   6.987  0.051  0.294 83.457  0.038  2.328   5.5353e-02
   4_xyz:   6.872  0.047  0.252 83.091  0.036  2.329   4.3034e-02
   4_adp:   6.872  0.047  0.252 83.091  0.036  2.329   4.3034e-02
   4_occ:   6.872  0.047  0.252 83.091  0.036  2.329   4.3034e-02
   5_bss:   6.872  0.047  0.252 83.091  0.036  2.329   4.3034e-02
   5_xyz:   7.034  0.052  0.278 83.811  0.036  2.292   5.1355e-02
   5_adp:   7.034  0.052  0.278 83.811  0.036  2.292   5.1355e-02
   5_occ:   7.034  0.052  0.278 83.811  0.036  2.292   5.1355e-02
   5_bss:   7.034  0.052  0.278 83.811  0.036  2.292   5.1355e-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:  86.33   0.00  16.36  86.33   0.00  12.51  62.84   5.13  37.32
   1_occ:  86.33   0.00  16.36  86.33   0.00  12.51  62.84   5.13  37.32
   2_bss:  86.33   0.00  16.36  86.33   0.00  12.51  62.84   5.13  37.32
   2_xyz:  86.33   0.00  16.36  86.33   0.00  12.51  62.84   5.13  37.32
   2_adp:  78.60   0.79  17.11  77.63   0.79  12.87  78.60   4.42  40.23
   2_occ:  78.60   0.79  17.11  77.63   0.79  12.87  78.60   4.42  40.23
   3_bss:  78.60   0.79  17.11  77.63   0.79  12.87  78.60   4.42  40.23
   3_xyz:  78.60   0.79  17.11  77.63   0.79  12.87  78.60   4.42  40.23
   3_adp:  77.15   1.53  16.55  77.15   1.53  12.65  74.28   2.75  37.80
   3_occ:  77.15   1.53  16.55  77.15   1.53  12.65  74.28   2.75  37.80
   4_bss:  77.15   1.53  16.55  77.15   1.53  12.65  74.28   2.75  37.80
   4_xyz:  77.15   1.53  16.55  77.15   1.53  12.65  74.28   2.75  37.80
   4_adp:  77.26   1.37  16.40  77.26   1.37  12.51  74.01   3.17  37.60
   4_occ:  77.26   1.37  16.40  77.26   1.37  12.51  74.01   3.17  37.60
   5_bss:  77.26   1.37  16.40  77.26   1.37  12.51  74.01   3.17  37.60
   5_xyz:  77.26   1.37  16.40  77.26   1.37  12.51  74.01   3.17  37.60
   5_adp:  83.83   0.34  16.55  83.83   0.34  12.44  77.08   4.09  38.93
   5_occ:  83.83   0.34  16.55  83.83   0.34  12.44  77.08   4.09  38.93
   5_bss:  83.82   0.33  16.54  83.82   0.33  12.43  77.07   4.08  38.92
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.923    0.006    0.289
   1_adp:    0.923    0.006    0.289
   1_occ:    0.923    0.006    0.289
   2_bss:    0.923    0.006    0.289
   2_xyz:    0.871    0.029    0.334
   2_adp:    0.871    0.029    0.334
   2_occ:    0.871    0.029    0.334
   3_bss:    0.871    0.029    0.334
   3_xyz:    1.135    0.027    0.358
   3_adp:    1.135    0.027    0.358
   3_occ:    1.135    0.027    0.358
   4_bss:    1.135    0.027    0.358
   4_xyz:    1.290    0.028    0.363
   4_adp:    1.290    0.028    0.363
   4_occ:    1.290    0.028    0.363
   5_bss:    1.290    0.028    0.363
   5_xyz:    1.388    0.048    0.370
   5_adp:    1.388    0.048    0.370
   5_occ:    1.388    0.048    0.370
   5_bss:    1.388    0.048    0.370
------------------------------------------------------------------------

CPU time actual refinement: 310.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/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_778/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_778/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 310.62 
  Macro-tasks:
    bulk solvent and scale       = 36.71  
    individual site refinement   = 124.06 
    weights calculation          = 28.78  
    collect and process          = 6.57   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 196.26 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 98.01  
    alpha_beta                      = 8.13   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 105.92 
    fmodel                         = 6.36   
    r_factors                      = 0.23   
    phase_errors                   = 11.34  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 232.57 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.486 micro seconds
Total CPU time: 5.40 minutes
from_scatterers_fft:    623 calls, 97.75 s
gradients_fft:          568 calls, 93.20 s

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

# Date 2008-01-16 Time 05:37:41 PST -0800 (1200490661.47 s)
Start R-work = 0.3113, R-free = 0.3022 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.2962, R-free = 0.2894
Final R-work = 0.1078, R-free = 0.1574