# Date 2008-01-16 Time 05:19:40 PST -0800 (1200489580.36 s)
#phil __OFF__

Command line arguments: "../690.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1322
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 690

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00064
Completeness in resolution range: 0.963078
Completeness with d_max=infinity: 0.960057

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0006

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00064
Completeness in resolution range: 0.963078
Completeness with d_max=infinity: 0.960057

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2803 [2146/2173]  1930   216  10.1%
  bin  2:  4.2803 -  3.4104 [2037/2053]  1836   201   9.9%
  bin  3:  3.4104 -  2.9831 [2037/2056]  1832   205  10.1%
  bin  4:  2.9831 -  2.7121 [2000/2030]  1798   202  10.1%
  bin  5:  2.7121 -  2.5187 [1994/2013]  1793   201  10.1%
  bin  6:  2.5187 -  2.3708 [1985/2010]  1791   194   9.8%
  bin  7:  2.3708 -  2.2525 [1971/2005]  1777   194   9.8%
  bin  8:  2.2525 -  2.1547 [1975/2005]  1774   201  10.2%
  bin  9:  2.1547 -  2.0720 [1937/1979]  1742   195  10.1%
  bin 10:  2.0720 -  2.0006 [1507/2016]  1357   150  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/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: 13
        2.42 -     3.04: 2162
        3.04 -     3.66: 4604
        3.66 -     4.28: 8899
        4.28 -     4.90: 12285
  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 "  1.831 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.076 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  2.098 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  2.098 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27958 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_690/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3456   r_free= 0.3359   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.092716                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1390  153 0.2855 0.2888      6.3485      6.2896|
|  2:  4.7738 -  3.8093 0.99   1326  151 0.2657 0.2692      6.4793      6.5128|
|  3:  3.8093 -  3.3337 0.99   1317  146 0.3067 0.2850      6.4217      6.3822|
|  4:  3.3337 -  3.0316 0.99   1296  137 0.3294 0.3422      6.3047       6.284|
|  5:  3.0316 -  2.8159 0.99   1293  145 0.3569 0.2833      6.1645      6.0459|
|  6:  2.8159 -  2.6508 0.99   1285  148 0.3585 0.3904      6.0745       6.074|
|  7:  2.6508 -  2.5187 0.99   1282  145 0.3601 0.3515      6.0404      5.9936|
|  8:  2.5187 -  2.4095 0.98   1290  135 0.3898 0.3633      6.0472      6.0092|
|  9:  2.4095 -  2.3171 0.98   1259  146 0.3838 0.3368      5.9416      5.9122|
| 10:  2.3171 -  2.2374 0.98   1266  140 0.4105 0.3481      6.0186      5.8688|
| 11:  2.2374 -  2.1676 0.99   1270  141 0.4030 0.4237      5.9031      5.9516|
| 12:  2.1676 -  2.1059 0.97   1264  138 0.3998 0.4173      5.8509      5.9682|
| 13:  2.1059 -  2.0506 0.99   1266  139 0.4153 0.3808      5.7978      5.7238|
| 14:  2.0506 -  2.0006 0.65    826   95 0.3897 0.4259      5.7105      5.7123|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1390   153  0.79  25.94   0.86     0.81      42803.86|
|  2:  4.7738 -  3.8093  1326   151  0.83  23.16   0.96     0.89      50250.56|
|  3:  3.8093 -  3.3337  1317   146  0.79  27.23   0.96     0.91      48671.06|
|  4:  3.3337 -  3.0316  1296   137  0.76  30.06   0.96     0.88      42544.54|
|  5:  3.0316 -  2.8159  1293   145  0.71  34.81   0.98     0.86      34049.95|
|  6:  2.8159 -  2.6508  1285   148  0.69  36.81   0.96     0.84      31973.97|
|  7:  2.6508 -  2.5187  1282   145  0.68  37.40   1.00     0.84      29415.86|
|  8:  2.5187 -  2.4095  1290   135  0.68  37.31   0.97     0.86      27517.17|
|  9:  2.4095 -  2.3171  1259   146  0.69  36.93   0.99     0.89      23859.58|
| 10:  2.3171 -  2.2374  1266   140  0.68  37.20   1.01     0.89      22403.09|
| 11:  2.2374 -  2.1676  1270   141  0.65  40.23   0.99     0.88      23209.66|
| 12:  2.1676 -  2.1059  1264   138  0.62  42.82   1.01     0.85      24237.07|
| 13:  2.1059 -  2.0506  1266   139  0.58  45.81   0.98     0.80      23516.07|
| 14:  2.0506 -  2.0006   826    95  0.55  48.35   1.02     0.75      21064.82|
|alpha:            min =        0.75 max =            0.91 mean =         0.86|
|beta:             min =    21064.82 max =        50250.56 mean =     32295.68|
|figures of merit: min =        0.00 max =            1.00 mean =         0.70|
|phase err.(work): min =        0.00 max =           89.94 mean =        35.55|
|phase err.(test): min =        0.00 max =           89.97 mean =        35.42|
|-----------------------------------------------------------------------------|

============================== 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 = 5.095930              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.327   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.726096              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.953   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      182 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1980 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1828 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2776 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4581 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4318 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5588 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6697 |
|-----------------------------------------------------------------------------|
|-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 |        0.163 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.166 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    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: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3456   r_free= 0.3359   ksol= 0.00   Bsol= 0.00   scale= 0.951    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.092716                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3320   r_free= 0.3232   ksol= 0.30   Bsol= 50.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.53,0.24,2.25,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.070312                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.617749              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.119   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.422157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3320      final r-factor (work) = 0.1897          |
| start r-factor (free) = 0.3232      final r-factor (free) = 0.2102          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1893 = 4.62 * 0.50 * 6.0749 + 1.00 * 0.1632                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4171 = 4.62 * 0.50 * 5.7796 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1748          |
| start r-factor (free) = 0.2102      final r-factor (free) = 0.2129          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4465 = 0.42 * 1.00 * 5.7796 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3602 = 0.42 * 1.00 * 5.5019 + 1.00 * 0.0375                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.03   16.51    None  None   None       |
|    all(noH): 2823   0      0.00    64.03   16.51    None  None   None       |
|    Sol.    : 438    0      7.42    64.03   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    55.74   12.61    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 -   6.403:  290   |   5:    32.014 -  38.416:   88        |
|      1:     6.403 -  12.806: 1219   |   6:    38.416 -  44.819:  111        |
|      2:    12.806 -  19.208:  625   |   7:    44.819 -  51.222:   77        |
|      3:    19.208 -  25.611:  217   |   8:    51.222 -  57.625:   56        |
|      4:    25.611 -  32.014:  122   |   9:    57.625 -  64.027:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1748 r_free = 0.2129             target_work(ml) = 5.507         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1745 r_free = 0.2129             target_work(ml) = 5.506         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1745   r_free= 0.2129   ksol= 0.30   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.53,0.24,2.25,0.00,0.00,0.00); trace/3= -0.34                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.505978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1724   r_free= 0.2097   ksol= 0.33   Bsol= 69.68   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-1.39,-0.19,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.497917                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.743782              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.743   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340812              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.012   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1724      final r-factor (work) = 0.1378          |
| start r-factor (free) = 0.2097      final r-factor (free) = 0.1709          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8779 = 1.74 * 0.50 * 5.5111 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7590 = 1.74 * 0.50 * 5.3964 + 1.00 * 0.0540                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8611 = 0.34 * 1.00 * 5.3964 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8017 = 0.34 * 1.00 * 5.2597 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.71    74.89   16.89    None  None   None       |
|    all(noH): 2823   0      0.71    74.89   16.89    None  None   None       |
|    Sol.    : 438    0      5.86    72.08   39.48    None  None   None       |
|    Mac.    : 2385   0      0.71    74.89   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.709 -   8.127:  614   |   5:    37.800 -  45.218:  102        |
|      1:     8.127 -  15.545: 1286   |   6:    45.218 -  52.636:   94        |
|      2:    15.545 -  22.963:  378   |   7:    52.636 -  60.054:   73        |
|      3:    22.963 -  30.382:  128   |   8:    60.054 -  67.472:   36        |
|      4:    30.382 -  37.800:  107   |   9:    67.472 -  74.890:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1676             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1299 r_free = 0.1675             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1675   ksol= 0.33   Bsol= 69.68   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.30,-1.39,-0.19,-0.00,-0.00,-0.00); trace/3= -1.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.250686                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1673   ksol= 0.33   Bsol= 67.97   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.61,-0.39,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.249764                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.291356              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.190  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.268955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.319  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1298      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1673      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0792 = 2.29 * 0.50 * 5.2591 + 1.00 * 0.0540                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0214 = 2.29 * 0.50 * 5.1986 + 1.00 * 0.0655                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1598      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6058 = 1.27 * 1.00 * 5.1986 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5609 = 1.27 * 1.00 * 5.1619 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.80   17.08    None  None   None       |
|    all(noH): 2823   0      0.00    90.80   17.08    None  None   None       |
|    Sol.    : 438    0      0.00    83.96   41.08    None  None   None       |
|    Mac.    : 2385   0      0.00    90.80   12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.081:  909   |   5:    45.402 -  54.483:   90        |
|      1:     9.081 -  18.161: 1202   |   6:    54.483 -  63.563:   76        |
|      2:    18.161 -  27.241:  246   |   7:    63.563 -  72.644:   40        |
|      3:    27.241 -  36.322:  128   |   8:    72.644 -  81.724:   12        |
|      4:    36.322 -  45.402:  115   |   9:    81.724 -  90.805:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1590             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1141 r_free = 0.1589             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1589   ksol= 0.33   Bsol= 67.97   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.61,-0.39,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.160170                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1587   ksol= 0.33   Bsol= 67.97   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.49,-0.29,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.159828                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.902782              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.515  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.237607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.822  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1139      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5583 = 2.90 * 0.50 * 5.1625 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5408 = 2.90 * 0.50 * 5.1457 + 1.00 * 0.0724                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1585      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2332 = 0.24 * 1.00 * 5.1457 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2312 = 0.24 * 1.00 * 5.1453 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.69    88.64   16.37    None  None   None       |
|    all(noH): 2823   0      0.69    88.64   16.37    None  None   None       |
|    Sol.    : 438    0      1.53    81.31   38.36    None  None   None       |
|    Mac.    : 2385   0      0.69    88.64   12.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.693 -   9.488: 1038   |   5:    44.664 -  53.459:   85        |
|      1:     9.488 -  18.282: 1106   |   6:    53.459 -  62.253:   62        |
|      2:    18.282 -  27.076:  232   |   7:    62.253 -  71.047:   27        |
|      3:    27.076 -  35.870:  135   |   8:    71.047 -  79.841:    6        |
|      4:    35.870 -  44.664:  128   |   9:    79.841 -  88.635:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1566             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1566             target_work(ml) = 5.140         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1566   ksol= 0.33   Bsol= 67.97   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.49,-0.29,-0.00,-0.00,-0.00); trace/3= -1.36                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.139785                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1566   ksol= 0.32   Bsol= 59.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.41,-0.19,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.139741                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.680655              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.423  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.706604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.586  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5417 = 3.68 * 0.50 * 5.1454 + 1.00 * 0.0724                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5233 = 3.68 * 0.50 * 5.1288 + 1.00 * 0.0846                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6327 = 0.71 * 1.00 * 5.1288 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6314 = 0.71 * 1.00 * 5.1260 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    89.04   16.27    None  None   None       |
|    all(noH): 2823   0      0.01    89.04   16.27    None  None   None       |
|    Sol.    : 438    0      2.98    81.15   38.69    None  None   None       |
|    Mac.    : 2385   0      0.01    89.04   12.16    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:     0.009 -   8.911:  950   |   5:    44.523 -  53.426:   87        |
|      1:     8.911 -  17.814: 1167   |   6:    53.426 -  62.329:   66        |
|      2:    17.814 -  26.717:  250   |   7:    62.329 -  71.232:   28        |
|      3:    26.717 -  35.620:  132   |   8:    71.232 -  80.135:    6        |
|      4:    35.620 -  44.523:  133   |   9:    80.135 -  89.038:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1583             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1076 r_free = 0.1583             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1076   r_free= 0.1583   ksol= 0.32   Bsol= 59.52   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.41,-0.19,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.129854                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1390  153 0.1007 0.1359      5.4175      5.5546|
|  2:  4.7738 -  3.8093 0.99   1326  151 0.0833 0.1110      5.4335      5.6409|
|  3:  3.8093 -  3.3337 0.99   1317  146 0.1015 0.1514      5.4523      5.8475|
|  4:  3.3337 -  3.0316 0.99   1296  137 0.1151 0.1477      5.4229      5.5638|
|  5:  3.0316 -  2.8159 0.99   1293  145 0.1287 0.1763      5.3138      5.5551|
|  6:  2.8159 -  2.6508 0.99   1285  148 0.1181 0.2023      5.2078      5.5099|
|  7:  2.6508 -  2.5187 0.99   1282  145 0.1198 0.1624       5.147      5.3318|
|  8:  2.5187 -  2.4095 0.98   1290  135 0.1081 0.1641      5.0458      5.3237|
|  9:  2.4095 -  2.3171 0.98   1259  146 0.1114 0.1768      5.0022      5.2877|
| 10:  2.3171 -  2.2374 0.98   1266  140 0.1083 0.1648      4.9614      5.2036|
| 11:  2.2374 -  2.1676 0.99   1270  141 0.1111 0.1907      4.9281      5.2768|
| 12:  2.1676 -  2.1059 0.97   1264  138 0.1082 0.1609      4.8637      5.1697|
| 13:  2.1059 -  2.0506 0.99   1266  139 0.1034 0.1753      4.7557      5.0299|
| 14:  2.0506 -  2.0006 0.65    826   95 0.0938 0.1765      4.6235      4.9528|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1390   153  0.93   9.86   0.97     0.94       8066.66|
|  2:  4.7738 -  3.8093  1326   151  0.95   8.13   1.00     0.99       9331.90|
|  3:  3.8093 -  3.3337  1317   146  0.94  11.06   1.01     1.01      10192.70|
|  4:  3.3337 -  3.0316  1296   137  0.92  13.16   1.00     0.98       9937.91|
|  5:  3.0316 -  2.8159  1293   145  0.90  15.81   0.99     0.96       8281.27|
|  6:  2.8159 -  2.6508  1285   148  0.90  16.25   0.97     0.95       7218.85|
|  7:  2.6508 -  2.5187  1282   145  0.91  15.33   0.98     0.95       6158.48|
|  8:  2.5187 -  2.4095  1290   135  0.91  14.84   0.99     0.96       5253.69|
|  9:  2.4095 -  2.3171  1259   146  0.91  15.26   0.99     0.95       4875.77|
| 10:  2.3171 -  2.2374  1266   140  0.90  15.79   0.98     0.94       4502.07|
| 11:  2.2374 -  2.1676  1270   141  0.90  16.30   0.98     0.95       4403.90|
| 12:  2.1676 -  2.1059  1264   138  0.91  15.38   0.99     0.98       3938.52|
| 13:  2.1059 -  2.0506  1266   139  0.91  15.29   0.98     0.96       3220.26|
| 14:  2.0506 -  2.0006   826    95  0.92  14.00   0.95     0.91       2416.34|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2416.34 max =        10192.70 mean =      6411.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.98|
|phase err.(test): min =        0.00 max =           89.03 mean =        13.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1569   ksol= 0.32   Bsol= 59.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.25,-0.02,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.127148                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1569   ksol= 0.32   Bsol= 59.52   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.90,-1.25,-0.02,-0.00,-0.00,-0.00); trace/3= -1.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.127148                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1390  153 0.1015 0.1251      5.4025      5.5044|
|  2:  4.7738 -  3.8093 0.99   1326  151 0.0837 0.1093      5.4217      5.6277|
|  3:  3.8093 -  3.3337 0.99   1317  146 0.1016 0.1496      5.4483      5.8364|
|  4:  3.3337 -  3.0316 0.99   1296  137 0.1146 0.1478      5.4184      5.5615|
|  5:  3.0316 -  2.8159 0.99   1293  145 0.1286 0.1765      5.3115      5.5553|
|  6:  2.8159 -  2.6508 0.99   1285  148 0.1181 0.2014      5.2073      5.5081|
|  7:  2.6508 -  2.5187 0.99   1282  145 0.1195 0.1625       5.147      5.3314|
|  8:  2.5187 -  2.4095 0.98   1290  135 0.1081 0.1645       5.046      5.3254|
|  9:  2.4095 -  2.3171 0.98   1259  146 0.1115 0.1769      5.0029      5.2871|
| 10:  2.3171 -  2.2374 0.98   1266  140 0.1082 0.1648      4.9619      5.2054|
| 11:  2.2374 -  2.1676 0.99   1270  141 0.1111 0.1907      4.9285      5.2777|
| 12:  2.1676 -  2.1059 0.97   1264  138 0.1081 0.1607      4.8639      5.1694|
| 13:  2.1059 -  2.0506 0.99   1266  139 0.1033 0.1755       4.756      5.0312|
| 14:  2.0506 -  2.0006 0.65    826   95 0.0938 0.1765      4.6242      4.9533|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0544 -  4.7738  1390   153  0.94   9.29   0.97     0.94       7265.82|
|  2:  4.7738 -  3.8093  1326   151  0.95   7.88   1.00     0.99       8807.28|
|  3:  3.8093 -  3.3337  1317   146  0.94  10.91   1.02     1.01       9972.29|
|  4:  3.3337 -  3.0316  1296   137  0.92  13.10   1.00     0.99       9842.59|
|  5:  3.0316 -  2.8159  1293   145  0.90  15.78   1.00     0.97       8244.70|
|  6:  2.8159 -  2.6508  1285   148  0.90  16.22   0.98     0.95       7202.61|
|  7:  2.6508 -  2.5187  1282   145  0.91  15.33   0.99     0.96       6159.04|
|  8:  2.5187 -  2.4095  1290   135  0.91  14.84   0.99     0.97       5255.95|
|  9:  2.4095 -  2.3171  1259   146  0.91  15.28   1.00     0.96       4884.15|
| 10:  2.3171 -  2.2374  1266   140  0.90  15.80   0.99     0.95       4505.73|
| 11:  2.2374 -  2.1676  1270   141  0.90  16.31   0.99     0.96       4409.11|
| 12:  2.1676 -  2.1059  1264   138  0.91  15.40   1.00     0.99       3944.58|
| 13:  2.1059 -  2.0506  1266   139  0.91  15.29   0.99     0.97       3224.15|
| 14:  2.0506 -  2.0006   826    95  0.92  14.01   0.96     0.92       2420.37|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2420.37 max =         9972.29 mean =      6283.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           90.00 mean =        13.90|
|phase err.(test): min =        0.00 max =           88.30 mean =        13.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.170)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    89.04   16.28    None  None   None       |
|    all(noH): 2823   0      0.01    89.04   16.28    None  None   None       |
|    Sol.    : 438    0      2.98    81.15   38.69    None  None   None       |
|    Mac.    : 2385   0      0.01    89.04   12.16    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:     0.011 -   8.914:  950   |   5:    44.526 -  53.429:   87        |
|      1:     8.914 -  17.817: 1167   |   6:    53.429 -  62.332:   66        |
|      2:    17.817 -  26.720:  250   |   7:    62.332 -  71.235:   28        |
|      3:    26.720 -  35.623:  132   |   8:    71.235 -  80.138:    6        |
|      4:    35.623 -  44.526:  133   |   9:    80.138 -  89.041:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.476 - 4.967
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 283 from: 288
   mapped sites are within: 0.719 - 4.967

peak=    5.727 closest distance to " O   HOH Z 113 " =    2.292
peak=    5.095 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.976 closest distance to " CB  GLN A 223 " =    1.444
peak=    4.846 closest distance to " CG  PRO A  54 " =    1.269
peak=    4.833 closest distance to " CB  SER A  63 " =    1.151
peak=    4.786 closest distance to " CB  ARG A  79 " =    1.308
peak=    4.744 closest distance to " CB  ARG A 190 " =    1.725
peak=    4.696 closest distance to " CB  ARG A 275 " =    0.925
peak=    4.661 closest distance to " NE2 GLN A  11 " =    1.104
peak=    4.641 closest distance to " O   HOH Z 126 " =    1.767
peak=    4.453 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.444 closest distance to " CB  GLU A 152 " =    1.162
peak=    4.417 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.394 closest distance to " O   HOH Z 298 " =    1.881
peak=    4.347 closest distance to " O   HOH Z  15 " =    2.116
peak=    4.339 closest distance to " O   HOH Z  63 " =    1.981
peak=    4.329 closest distance to " O   HOH Z 369 " =    2.366
peak=    4.320 closest distance to " O   HOH Z  40 " =    1.854
peak=    4.312 closest distance to " CB  ASN A 148 " =    1.449
peak=    4.227 closest distance to " O   HOH Z  78 " =    1.622
peak=    4.169 closest distance to " CZ  PHE A 218 " =    1.121
peak=    4.167 closest distance to " C   PRO A 198 " =    1.453
peak=    4.163 closest distance to " O   HOH Z 287 " =    2.184
peak=    4.161 closest distance to " O   HOH Z 158 " =    3.140
peak=    4.134 closest distance to " O   SER A  87 " =    2.251
peak=    4.124 closest distance to " CB  GLU A 277 " =    3.663
peak=    4.117 closest distance to " O   HOH Z 142 " =    1.537
peak=    4.117 closest distance to " O   HOH Z 303 " =    2.155
peak=    4.111 closest distance to " O   HOH Z  43 " =    1.897
peak=    4.103 closest distance to " O   HOH Z 189 " =    2.687
peak=    4.062 closest distance to " CD2 TRP A 179 " =    1.341
peak=    4.054 closest distance to " CB  TYR A 169 " =    0.809
peak=    4.052 closest distance to " O   HOH Z 250 " =    1.451
peak=    4.042 closest distance to " O   HOH Z 346 " =    1.658
peak=    4.038 closest distance to " O   HOH Z 147 " =    1.862
peak=    4.026 closest distance to " O   HOH Z 368 " =    2.137
peak=    4.018 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.015 closest distance to " O   HOH Z 427 " =    3.014
peak=    4.007 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.998 closest distance to " CB  VAL A 265 " =    1.268
peak=    3.987 closest distance to " O   HOH Z 272 " =    1.926
peak=    3.985 closest distance to " O   HOH Z  61 " =    1.650
peak=    3.980 closest distance to " O   HOH Z 203 " =    1.691
peak=    3.976 closest distance to " O   HOH Z 234 " =    3.817
peak=    3.948 closest distance to " O   HOH Z  19 " =    2.157
peak=    3.936 closest distance to " CD  ARG A  66 " =    2.436
peak=    3.927 closest distance to " CG  PRO A 213 " =    1.140
peak=    3.917 closest distance to " CD  LYS A 166 " =    1.316
peak=    3.916 closest distance to " O   HOH Z 406 " =    1.602
peak=    3.905 closest distance to " O   HOH Z 209 " =    2.231
peak=    3.901 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.899 closest distance to " O   HOH Z 265 " =    2.217
peak=    3.888 closest distance to " O   HOH Z 214 " =    2.068
peak=    3.872 closest distance to " O   HOH Z 193 " =    1.860
peak=    3.869 closest distance to " CB  ASP A 140 " =    1.039
peak=    3.847 closest distance to " CA  TYR A  30 " =    1.030
peak=    3.846 closest distance to " O   HOH Z 197 " =    2.929
peak=    3.840 closest distance to " OG BSER A 164 " =    2.313
peak=    3.831 closest distance to " CB  PRO A  54 " =    0.864
peak=    3.828 closest distance to " ND2 ASN A 187 " =    1.432
peak=    3.825 closest distance to " O   HOH Z 148 " =    3.338
peak=    3.819 closest distance to " CA  ALA A  51 " =    0.934
peak=    3.819 closest distance to " CA  ASN A 215 " =    1.118
peak=    3.815 closest distance to " O   HOH Z 423 " =    2.034
peak=    3.806 closest distance to " CD  ARG A 269 " =    0.940
peak=    3.793 closest distance to " CG2AVAL A  72 " =    1.771
peak=    3.793 closest distance to " O   HOH Z 299 " =    4.386
peak=    3.792 closest distance to " O   HOH Z  21 " =    1.870
peak=    3.782 closest distance to " OD1 ASN A  69 " =    2.616
peak=    3.773 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.769 closest distance to " NH1AARG A 145 " =    1.315
peak=    3.768 closest distance to " CE  LYS A  76 " =    0.842
peak=    3.764 closest distance to " CG  MET A 185 " =    1.125
peak=    3.760 closest distance to " O   HOH Z 213 " =    1.946
peak=    3.735 closest distance to " O   HOH Z 180 " =    2.131
peak=    3.733 closest distance to " CG2 VAL A 257 " =    0.827
peak=    3.729 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.728 closest distance to " O  BHOH Z 338 " =    2.367
peak=    3.724 closest distance to " O   HOH Z 128 " =    2.328
peak=    3.719 closest distance to " O   HOH Z 403 " =    1.503
peak=    3.715 closest distance to " O   HOH Z 421 " =    1.764
peak=    3.713 closest distance to " CB  GLU A  46 " =    0.977
peak=    3.700 closest distance to " NZ  LYS A 117 " =    3.293
peak=    3.694 closest distance to " O   HOH Z 380 " =    1.970
peak=    3.693 closest distance to " CB  VAL A 202 " =    1.502
peak=    3.683 closest distance to " O   HOH Z  59 " =    2.273
peak=    3.675 closest distance to " NH2 ARG A 156 " =    1.168
peak=    3.673 closest distance to " O   HOH Z 403 " =    1.424
peak=    3.657 closest distance to " CG  PRO A 198 " =    1.304
peak=    3.655 closest distance to " C   ILE A 106 " =    1.951
peak=    3.652 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.649 closest distance to " CA  ARG A  36 " =    1.100
peak=    3.648 closest distance to " O   HOH Z 128 " =    2.050
peak=    3.638 closest distance to " O   HOH Z 362 " =    3.707
peak=    3.633 closest distance to " CG2 ILE A 120 " =    1.035
peak=    3.628 closest distance to " CB  GLU A 128 " =    1.031
peak=    3.614 closest distance to " NH2AARG A 275 " =    3.599
peak=    3.607 closest distance to " O   HOH Z  66 " =    2.181
peak=    3.606 closest distance to " CD1 LEU A 300 " =    1.203
peak=    3.600 closest distance to " O   HOH Z 133 " =    2.470
peak=    3.597 closest distance to " O   HOH Z 126 " =    1.637
peak=    3.587 closest distance to " O   HOH Z   1 " =    2.224
peak=    3.582 closest distance to " O   HOH Z 291 " =    1.569
peak=    3.571 closest distance to " CB  ASN A  39 " =    0.856
peak=    3.570 closest distance to " O   HOH Z 313 " =    1.999
peak=    3.569 closest distance to " O   ALA A 165 " =    1.482
peak=    3.566 closest distance to " O   HOH Z 245 " =    1.328
peak=    3.565 closest distance to " CB  SER A   3 " =    1.293
peak=    3.565 closest distance to " O   HOH Z 316 " =    3.091
peak=    3.565 closest distance to " O   HOH Z 261 " =    1.950
peak=    3.558 closest distance to " O   HOH Z  66 " =    2.252
peak=    3.555 closest distance to " CD  ARG A  66 " =    2.402
peak=    3.534 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.531 closest distance to " CB  TRP A 179 " =    1.381
peak=    3.529 closest distance to " CG2 ILE A  20 " =    1.257
peak=    3.525 closest distance to " CZ  PHE A  38 " =    1.291
peak=    3.522 closest distance to " CD2 LEU A 297 " =    0.824
peak=    3.516 closest distance to " CG  PRO A 243 " =    1.067
peak=    3.513 closest distance to " OD2 ASP A 298 " =    3.961
peak=    3.512 closest distance to " CB  GLN A  88 " =    1.188
peak=    3.509 closest distance to " O   ASN A  74 " =    1.531
peak=    3.508 closest distance to " CA  THR A 264 " =    0.927
peak=    3.507 closest distance to " CA  ASN A 176 " =    1.427
peak=    3.502 closest distance to " CB  SER A 212 " =    1.096
peak=    3.497 closest distance to " O   HOH Z 261 " =    1.733
peak=    3.494 closest distance to " CA  MET A 105 " =    0.990
peak=    3.483 closest distance to " O   HOH Z 248 " =    1.669
peak=    3.483 closest distance to " O   HOH Z 371 " =    3.141
peak=    3.475 closest distance to " O   HOH Z 193 " =    2.160
peak=    3.474 closest distance to " O   HOH Z 402 " =    1.397
peak=    3.474 closest distance to " O   HOH Z 389 " =    1.868
peak=    3.469 closest distance to " O   HOH Z 271 " =    2.810
peak=    3.455 closest distance to " O   HOH Z 417 " =    3.400
peak=    3.455 closest distance to " O   HOH Z 412 " =    3.892
peak=    3.452 closest distance to " O   HOH Z 426 " =    1.603
peak=    3.452 closest distance to " O   HOH Z  44 " =    1.675
peak=    3.452 closest distance to " O   HOH Z 359 " =    1.552
peak=    3.448 closest distance to " O   HOH Z  54 " =    1.656
peak=    3.447 closest distance to " CA  ALA A 291 " =    0.782
peak=    3.443 closest distance to " O   HOH Z 325 " =    2.436
peak=    3.442 closest distance to " CB  LEU A  83 " =    0.770
peak=    3.440 closest distance to " O   HOH Z  62 " =    2.198
peak=    3.429 closest distance to " N   ASN A  39 " =    1.291
peak=    3.426 closest distance to " OG1 THR A 294 " =    2.413
peak=    3.420 closest distance to " O   HOH Z 353 " =    2.667
peak=    3.418 closest distance to " CB  ASN A 142 " =    1.074
peak=    3.415 closest distance to " O   HOH Z 365 " =    2.898
peak=    3.410 closest distance to " O   HOH Z 185 " =    1.854
peak=    3.409 closest distance to " CB  TYR A 116 " =    0.721
peak=    3.407 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.406 closest distance to " CA  VAL A 125 " =    1.171
peak=    3.406 closest distance to " CG BARG A 275 " =    1.356
peak=    3.404 closest distance to " O   HOH Z 383 " =    2.203
peak=    3.403 closest distance to " CB  THR A  31 " =    1.718
peak=    3.396 closest distance to " O   HOH Z  10 " =    1.776
peak=    3.388 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.387 closest distance to " O   HOH Z 425 " =    2.000
peak=    3.386 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.386 closest distance to " O   HOH Z 294 " =    1.511
peak=    3.369 closest distance to " O   HOH Z 285 " =    1.775
peak=    3.362 closest distance to " CB  ILE A 120 " =    1.263
peak=    3.362 closest distance to " CG2 ILE A 234 " =    0.846
peak=    3.357 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.357 closest distance to " O   HOH Z 273 " =    2.863
peak=    3.356 closest distance to " CG  GLN A  11 " =    1.624
peak=    3.355 closest distance to " CB  ASN A 110 " =    1.146
peak=    3.354 closest distance to " CB  ASN A 215 " =    1.127
peak=    3.353 closest distance to " CA  ALA A  84 " =    1.265
peak=    3.352 closest distance to " O   HOH Z 193 " =    1.682
peak=    3.350 closest distance to " CG  GLN A  58 " =    2.798
peak=    3.349 closest distance to " NE  ARG A  79 " =    1.056
peak=    3.349 closest distance to " O   HOH Z  97 " =    2.421
peak=    3.349 closest distance to " NH2BARG A 145 " =    2.183
peak=    3.348 closest distance to " OE1 GLN A  11 " =    2.145
peak=    3.346 closest distance to " CZ2 TRP A 179 " =    1.745
peak=    3.344 closest distance to " CB  GLN A 103 " =    0.837
peak=    3.343 closest distance to " CA  ASP A 162 " =    1.048
peak=    3.339 closest distance to " CB  ARG A 139 " =    1.010
peak=    3.338 closest distance to " CB  GLN A 205 " =    1.073
peak=    3.337 closest distance to " CG  LEU A 167 " =    1.273
peak=    3.337 closest distance to " O   HOH Z  88 " =    2.453
peak=    3.335 closest distance to " CB  ASP A 298 " =    1.198
peak=    3.333 closest distance to " CG  PRO A  90 " =    1.291
peak=    3.322 closest distance to " O   HOH Z 327 " =    1.656
peak=    3.319 closest distance to " O   HOH Z  88 " =    3.402
peak=    3.310 closest distance to " O   HOH Z 285 " =    2.528
peak=    3.308 closest distance to " CB  ALA A   1 " =    4.967
peak=    3.305 closest distance to " OG BSER A 134 " =    2.955
peak=    3.305 closest distance to " CB  GLN A  89 " =    1.335
peak=    3.304 closest distance to " N   ARG A 156 " =    1.399
peak=    3.301 closest distance to " CB  ALA A 291 " =    1.280
peak=    3.296 closest distance to " CA  ALA A  21 " =    1.210
peak=    3.294 closest distance to " O   HOH Z 422 " =    2.695
peak=    3.293 closest distance to " O   HOH Z 419 " =    1.933
peak=    3.288 closest distance to " CD1AILE A 234 " =    0.913
peak=    3.287 closest distance to " N   GLY A  98 " =    1.143
peak=    3.286 closest distance to " CB  ALA A   9 " =    1.579
peak=    3.284 closest distance to " O   HOH Z  80 " =    1.605
peak=    3.281 closest distance to " CB  SER A  26 " =    1.723
peak=    3.280 closest distance to " CB  SER A 141 " =    1.019
peak=    3.275 closest distance to " CA  THR A 221 " =    0.971
peak=    3.272 closest distance to " ND1 HIS A  81 " =    1.704
peak=    3.271 closest distance to " NE2 HIS A 207 " =    1.294
peak=    3.269 closest distance to " O   THR A 220 " =    1.237
peak=    3.264 closest distance to " O   HOH Z 329 " =    4.103
peak=    3.263 closest distance to " OG BSER A  99 " =    2.411
peak=    3.262 closest distance to " CB  PHE A 204 " =    0.742
peak=    3.262 closest distance to " CB  ALA A 227 " =    1.065
peak=    3.262 closest distance to " CD  LYS A  76 " =    1.997
peak=    3.261 closest distance to " O   HOH Z 305 " =    3.698
peak=    3.261 closest distance to " CA  SER A  87 " =    1.072
peak=    3.260 closest distance to " O   HOH Z 345 " =    1.688
peak=    3.258 closest distance to " O   HOH Z 258 " =    2.106
peak=    3.258 closest distance to " CB  TYR A 169 " =    0.888
peak=    3.257 closest distance to " OG  SER A  22 " =    2.695
peak=    3.256 closest distance to " O   HOH Z 344 " =    3.252
peak=    3.255 closest distance to " O   HOH Z 171 " =    3.950
peak=    3.248 closest distance to " CG2 VAL A 197 " =    1.131
peak=    3.242 closest distance to " O   HOH Z 407 " =    2.667
peak=    3.242 closest distance to " O   HOH Z  48 " =    1.674
peak=    3.239 closest distance to " CG AARG A 275 " =    1.078
peak=    3.236 closest distance to " ND2 ASN A 110 " =    1.615
peak=    3.235 closest distance to " CD1 ILE A 106 " =    0.850
peak=    3.234 closest distance to " CA  TYR A 116 " =    1.364
peak=    3.233 closest distance to " O   HOH Z 384 " =    2.925
peak=    3.230 closest distance to " CA  ALA A 154 " =    0.984
peak=    3.230 closest distance to " CG  GLU A  37 " =    0.862
peak=    3.225 closest distance to " NE2 GLN A  77 " =    3.376
peak=    3.225 closest distance to " NZ  LYS A  48 " =    1.285
peak=    3.211 closest distance to " O   HOH Z 171 " =    2.025
peak=    3.202 closest distance to " O   HOH Z  85 " =    2.385
peak=    3.202 closest distance to " O   HOH Z 188 " =    2.220
peak=    3.201 closest distance to " CG BARG A 102 " =    1.782
peak=    3.197 closest distance to " CA  ARG A 159 " =    1.245
peak=    3.197 closest distance to " CD BLYS A 290 " =    0.958
peak=    3.196 closest distance to " CA  ASP A 140 " =    1.197
peak=    3.194 closest distance to " CG1 VAL A 189 " =    2.059
peak=    3.193 closest distance to " CB  ARG A 138 " =    0.992
peak=    3.190 closest distance to " CZ3 TRP A 266 " =    1.107
peak=    3.187 closest distance to " O   HOH Z 391 " =    2.870
peak=    3.184 closest distance to " N   CYS A 260 " =    0.840
peak=    3.183 closest distance to " CE1 HIS A 115 " =    3.839
peak=    3.182 closest distance to " O   HOH Z 394 " =    3.982
peak=    3.178 closest distance to " OG  SER A  28 " =    1.478
peak=    3.174 closest distance to " CD1 ILE A 199 " =    0.990
peak=    3.173 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.170 closest distance to " CA  ALA A 295 " =    1.047
peak=    3.170 closest distance to " O   HOH Z 250 " =    1.399
peak=    3.168 closest distance to " O   GLU A   2 " =    1.702
peak=    3.161 closest distance to " O   HOH Z 295 " =    1.487
peak=    3.159 closest distance to " O   HOH Z 248 " =    2.056
peak=    3.157 closest distance to " CB  ASN A 224 " =    0.997
peak=    3.157 closest distance to " OE1 GLU A   2 " =    2.123
peak=    3.156 closest distance to " O   HOH Z 132 " =    2.620
peak=    3.155 closest distance to " CG  LYS A  76 " =    0.985
peak=    3.154 closest distance to " CB  ASN A 187 " =    1.071
peak=    3.153 closest distance to " O   HOH Z 258 " =    1.674
peak=    3.150 closest distance to " CG1 ILE A 151 " =    1.011
peak=    3.147 closest distance to " O   TRP A 274 " =    1.878
peak=    3.146 closest distance to " CE1 TYR A 116 " =    1.288
peak=    3.144 closest distance to " O   HOH Z  49 " =    2.188
peak=    3.131 closest distance to " CB  THR A  52 " =    0.719
peak=    3.124 closest distance to " N   ASN A 127 " =    1.320
peak=    3.122 closest distance to " O   HOH Z 227 " =    2.028
peak=    3.118 closest distance to " CA  ASN A 252 " =    1.916
peak=    3.117 closest distance to " CA  ALA A 158 " =    1.251
peak=    3.115 closest distance to " OE2 GLU A  53 " =    2.102
peak=    3.111 closest distance to " O   HOH Z 267 " =    2.020
peak=    3.111 closest distance to " O   HOH Z 430 " =    1.512
peak=    3.107 closest distance to " CA  ALA A 233 " =    1.352
peak=    3.105 closest distance to " N   ALA A 158 " =    1.498
peak=    3.104 closest distance to " O   HOH Z   9 " =    2.180
peak=    3.104 closest distance to " CG  MET A 185 " =    1.015
peak=    3.101 closest distance to " O   THR A 251 " =    1.053
peak=    3.100 closest distance to " O   HOH Z 248 " =    1.669
peak=    3.091 closest distance to " CG1 ILE A  49 " =    1.526
peak=    3.083 closest distance to " CA  ASP A 191 " =    0.889
peak=    3.078 closest distance to " N   PHE A 130 " =    1.256
peak=    3.074 closest distance to " O   HOH Z  85 " =    1.927
peak=    3.070 closest distance to " O   HOH Z 417 " =    2.033
peak=    3.038 closest distance to " O   SER A 164 " =    1.168
peak=    3.023 closest distance to " O   HOH Z 383 " =    1.631
peak=    3.019 closest distance to " O   HOH Z 213 " =    2.746

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.762 - 5.814
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 205
   mapped sites are within: 0.762 - 5.814

peak=   -4.841 closest distance to " CD  GLN A  58 " =    0.938
peak=   -4.687 closest distance to " O   HOH Z 266 " =    5.305
peak=   -4.543 closest distance to " CD  ARG A  14 " =    3.471
peak=   -4.524 closest distance to " CB  PRO A 243 " =    2.675
peak=   -4.500 closest distance to " O   VAL A  67 " =    2.773
peak=   -4.425 closest distance to " CD  ARG A 156 " =    2.143
peak=   -4.194 closest distance to " O   HOH Z 196 " =    1.972
peak=   -4.186 closest distance to " C   HIS A 108 " =    1.135
peak=   -4.163 closest distance to " O   HOH Z 231 " =    2.286
peak=   -4.105 closest distance to " CB  ALA A 161 " =    2.588
peak=   -4.092 closest distance to " OG  SER A  97 " =    2.283
peak=   -4.088 closest distance to " CZ3 TRP A 179 " =    1.200
peak=   -4.022 closest distance to " CE2 TYR A  30 " =    2.708
peak=   -4.007 closest distance to " OE1 GLN A 223 " =    2.033
peak=   -3.996 closest distance to " O   HOH Z  10 " =    1.530
peak=   -3.990 closest distance to " CD1 LEU A 101 " =    2.429
peak=   -3.973 closest distance to " CE2 PHE A  61 " =    2.595
peak=   -3.967 closest distance to " O   HOH Z  73 " =    2.377
peak=   -3.962 closest distance to " C   ILE A 239 " =    2.166
peak=   -3.938 closest distance to " OXT GLY A 302 " =    2.878
peak=   -3.926 closest distance to " O   HOH Z 198 " =    2.121
peak=   -3.902 closest distance to " CD2 TYR A 293 " =    2.051
peak=   -3.891 closest distance to " N   ALA A  43 " =    2.611
peak=   -3.891 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -3.883 closest distance to " CA  VAL A  67 " =    2.931
peak=   -3.881 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.860 closest distance to " NE2 GLN A  88 " =    1.817
peak=   -3.851 closest distance to " CG1 VAL A 112 " =    2.600
peak=   -3.841 closest distance to " OG BSER A 134 " =    1.355
peak=   -3.835 closest distance to " O   HOH Z 211 " =    1.520
peak=   -3.822 closest distance to " CG1 VAL A 112 " =    2.830
peak=   -3.808 closest distance to " O   PRO A 198 " =    1.326
peak=   -3.783 closest distance to " CB  ALA A 291 " =    2.304
peak=   -3.765 closest distance to " O   HOH Z 290 " =    1.287
peak=   -3.748 closest distance to " CB  PHE A 192 " =    2.056
peak=   -3.737 closest distance to " CG1 VAL A 250 " =    2.679
peak=   -3.733 closest distance to " O   HOH Z 389 " =    1.884
peak=   -3.729 closest distance to " O   HOH Z  37 " =    1.798
peak=   -3.716 closest distance to " O   HOH Z 185 " =    2.337
peak=   -3.714 closest distance to " O   SER A 210 " =    1.926
peak=   -3.697 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.696 closest distance to " CE  MET A 105 " =    2.482
peak=   -3.696 closest distance to " O   HOH Z 114 " =    3.172
peak=   -3.693 closest distance to " O   PRO A 163 " =    2.098
peak=   -3.692 closest distance to " O   HOH Z  60 " =    1.943
peak=   -3.681 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.679 closest distance to " O   HOH Z 372 " =    2.311
peak=   -3.670 closest distance to " CD1 ILE A 151 " =    2.416
peak=   -3.645 closest distance to " O   HOH Z 166 " =    1.815
peak=   -3.645 closest distance to " NE2 GLN A 194 " =    1.865
peak=   -3.634 closest distance to " CG2 ILE A  49 " =    2.726
peak=   -3.627 closest distance to " CG  ARG A  66 " =    2.475
peak=   -3.618 closest distance to " CG  ASP A 132 " =    2.340
peak=   -3.602 closest distance to " NH2 ARG A  79 " =    1.592
peak=   -3.597 closest distance to " ND2 ASN A  45 " =    1.799
peak=   -3.570 closest distance to " CB  ASN A  39 " =    2.355
peak=   -3.570 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.562 closest distance to " CA  GLY A 241 " =    3.253
peak=   -3.556 closest distance to " NE2 GLN A  11 " =    1.789
peak=   -3.554 closest distance to " C   SER A 206 " =    1.492
peak=   -3.545 closest distance to " OD1 ASP A 171 " =    1.635
peak=   -3.544 closest distance to " CB  ALA A 291 " =    2.365
peak=   -3.540 closest distance to " CG2 ILE A 263 " =    2.331
peak=   -3.532 closest distance to " ND2 ASN A 249 " =    2.443
peak=   -3.517 closest distance to " O   HOH Z 348 " =    2.248
peak=   -3.511 closest distance to " O   ALA A  10 " =    1.690
peak=   -3.494 closest distance to " CG2 VAL A 189 " =    2.191
peak=   -3.491 closest distance to " O   PHE A 218 " =    1.572
peak=   -3.483 closest distance to " NH2AARG A 275 " =    5.327
peak=   -3.480 closest distance to " CA  GLY A 203 " =    2.412
peak=   -3.470 closest distance to " O   VAL A 189 " =    2.677
peak=   -3.456 closest distance to " OE1 GLN A 223 " =    2.156
peak=   -3.452 closest distance to " O   HOH Z  15 " =    1.475
peak=   -3.450 closest distance to " CG  ARG A 269 " =    2.571
peak=   -3.449 closest distance to " CG  HIS A  86 " =    1.119
peak=   -3.444 closest distance to " N   ALA A 248 " =    1.619
peak=   -3.442 closest distance to " CG  PHE A 283 " =    2.644
peak=   -3.435 closest distance to " CE3 TRP A 150 " =    2.279
peak=   -3.432 closest distance to " NE2 GLN A 103 " =    1.760
peak=   -3.428 closest distance to " N   THR A  52 " =    1.697
peak=   -3.428 closest distance to " CA  GLY A 241 " =    2.370
peak=   -3.427 closest distance to " O   HOH Z 407 " =    3.153
peak=   -3.422 closest distance to " O   HOH Z 311 " =    3.795
peak=   -3.413 closest distance to " CD  ARG A 139 " =    1.617
peak=   -3.406 closest distance to " O   HOH Z 243 " =    1.936
peak=   -3.406 closest distance to " ND2 ASN A  45 " =    1.158
peak=   -3.404 closest distance to " CD  ARG A 195 " =    5.180
peak=   -3.400 closest distance to " SG ACYS A 201 " =    1.983
peak=   -3.398 closest distance to " N   ALA A 226 " =    2.097
peak=   -3.390 closest distance to " O   HOH Z 234 " =    4.295
peak=   -3.390 closest distance to " CG  LEU A  83 " =    1.999
peak=   -3.388 closest distance to " NH2 ARG A 159 " =    2.399
peak=   -3.385 closest distance to " CD2 TYR A 247 " =    2.382
peak=   -3.384 closest distance to " O   HOH Z 323 " =    1.467
peak=   -3.382 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.382 closest distance to " N   MET A 188 " =    1.913
peak=   -3.374 closest distance to " C   MET A 188 " =    1.405
peak=   -3.362 closest distance to " CE BMET A  47 " =    1.782
peak=   -3.360 closest distance to " O   HOH Z 216 " =    1.736
peak=   -3.360 closest distance to " CZ  PHE A 155 " =    1.246
peak=   -3.357 closest distance to " O   ALA A   1 " =    1.830
peak=   -3.357 closest distance to " CG  GLU A 277 " =    1.137
peak=   -3.355 closest distance to " CE3 TRP A 274 " =    2.486
peak=   -3.351 closest distance to " CB  PRO A 163 " =    2.415
peak=   -3.343 closest distance to " CB  ALA A 248 " =    2.309
peak=   -3.343 closest distance to " CG1AVAL A  41 " =    2.792
peak=   -3.336 closest distance to " O   SER A  95 " =    1.670
peak=   -3.335 closest distance to " CD  GLN A 223 " =    0.973
peak=   -3.334 closest distance to " CB  ASP A 286 " =    2.068
peak=   -3.331 closest distance to " O   HOH Z   6 " =    2.298
peak=   -3.330 closest distance to " CB  ALA A  43 " =    2.585
peak=   -3.324 closest distance to " C   LEU A 143 " =    1.072
peak=   -3.324 closest distance to " OD2 ASP A 191 " =    1.483
peak=   -3.322 closest distance to " O   HOH Z 292 " =    4.671
peak=   -3.320 closest distance to " OG BSER A 134 " =    1.857
peak=   -3.309 closest distance to " O   HOH Z 134 " =    3.024
peak=   -3.308 closest distance to " O   HOH Z 393 " =    1.358
peak=   -3.307 closest distance to " ND2 ASN A 187 " =    1.540
peak=   -3.298 closest distance to " O   HOH Z  38 " =    1.503
peak=   -3.297 closest distance to " CB  TYR A  15 " =    2.216
peak=   -3.295 closest distance to " O   HOH Z 177 " =    1.774
peak=   -3.291 closest distance to " CG  GLU A  53 " =    1.589
peak=   -3.282 closest distance to " CB  TRP A  85 " =    2.602
peak=   -3.281 closest distance to " O   HOH Z 353 " =    2.198
peak=   -3.281 closest distance to " O   ALA A  34 " =    2.406
peak=   -3.281 closest distance to " CA  GLY A 133 " =    2.337
peak=   -3.280 closest distance to " O   HOH Z 111 " =    1.746
peak=   -3.279 closest distance to " CZ  PHE A  59 " =    1.655
peak=   -3.275 closest distance to " O   HOH Z 414 " =    1.509
peak=   -3.272 closest distance to " O   HOH Z   6 " =    1.508
peak=   -3.272 closest distance to " O   HOH Z 313 " =    1.951
peak=   -3.268 closest distance to " CG1 VAL A 125 " =    1.932
peak=   -3.262 closest distance to " O   HOH Z 435 " =    2.806
peak=   -3.258 closest distance to " O   HOH Z  44 " =    2.314
peak=   -3.258 closest distance to " CD1 LEU A   5 " =    2.570
peak=   -3.250 closest distance to " O   HOH Z 264 " =    1.758
peak=   -3.247 closest distance to " O   HOH Z  52 " =    1.494
peak=   -3.240 closest distance to " O   HOH Z 426 " =    1.602
peak=   -3.238 closest distance to " O   HOH Z  13 " =    1.745
peak=   -3.236 closest distance to " CB  ALA A 248 " =    2.227
peak=   -3.231 closest distance to " O   HOH Z 275 " =    1.487
peak=   -3.227 closest distance to " CD1 LEU A 101 " =    2.896
peak=   -3.227 closest distance to " CD2 LEU A 237 " =    2.748
peak=   -3.224 closest distance to " O   HOH Z 174 " =    2.506
peak=   -3.223 closest distance to " O   SER A 135 " =    1.473
peak=   -3.220 closest distance to " O   HOH Z 106 " =    1.861
peak=   -3.217 closest distance to " CG  PRO A 243 " =    1.859
peak=   -3.217 closest distance to " ND2BASN A 224 " =    1.780
peak=   -3.206 closest distance to " O   HOH Z 357 " =    2.036
peak=   -3.202 closest distance to " CG2 THR A 221 " =    2.323
peak=   -3.199 closest distance to " O   HOH Z 165 " =    1.870
peak=   -3.199 closest distance to " O   HOH Z  47 " =    1.628
peak=   -3.197 closest distance to " C   THR A 264 " =    1.405
peak=   -3.196 closest distance to " OD1 ASP A 191 " =    1.720
peak=   -3.192 closest distance to " CE1 TYR A 247 " =    2.772
peak=   -3.191 closest distance to " CG  ASP A 231 " =    0.762
peak=   -3.191 closest distance to " O   HOH Z 322 " =    1.716
peak=   -3.186 closest distance to " OG BSER A 210 " =    2.159
peak=   -3.182 closest distance to " O   VAL A 189 " =    1.607
peak=   -3.173 closest distance to " NE2 GLN A 278 " =    1.699
peak=   -3.170 closest distance to " CD  PRO A 243 " =    2.155
peak=   -3.170 closest distance to " O   HOH Z 100 " =    1.339
peak=   -3.167 closest distance to " O   HOH Z  11 " =    1.697
peak=   -3.166 closest distance to " O   GLY A 196 " =    1.145
peak=   -3.162 closest distance to " O   HOH Z 200 " =    3.595
peak=   -3.161 closest distance to " O   HOH Z 193 " =    1.830
peak=   -3.157 closest distance to " O   HOH Z 421 " =    3.333
peak=   -3.152 closest distance to " O   ALA A  34 " =    2.118
peak=   -3.146 closest distance to " O   HOH Z 171 " =    1.940
peak=   -3.145 closest distance to " O   PRO A 198 " =    1.843
peak=   -3.145 closest distance to " O   GLY A  80 " =    2.570
peak=   -3.139 closest distance to " ND2 ASN A  60 " =    1.353
peak=   -3.139 closest distance to " CG1 VAL A  67 " =    3.017
peak=   -3.135 closest distance to " CD2 TYR A 293 " =    2.152
peak=   -3.134 closest distance to " O   HOH Z  71 " =    2.130
peak=   -3.129 closest distance to " CZ  PHE A  38 " =    1.966
peak=   -3.127 closest distance to " O   HOH Z 266 " =    5.212
peak=   -3.120 closest distance to " O   GLN A 240 " =    2.465
peak=   -3.120 closest distance to " O   HOH Z  43 " =    1.647
peak=   -3.120 closest distance to " CB  PHE A  16 " =    2.586
peak=   -3.105 closest distance to " O   HOH Z 166 " =    1.578
peak=   -3.102 closest distance to " OD1 ASN A 301 " =    1.950
peak=   -3.100 closest distance to " O   HOH Z 191 " =    5.814
peak=   -3.100 closest distance to " O   HOH Z 396 " =    2.041
peak=   -3.100 closest distance to " O   PRO A 198 " =    1.346
peak=   -3.092 closest distance to " CD1 LEU A 228 " =    2.282
peak=   -3.085 closest distance to " CD  PRO A 213 " =    2.165
peak=   -3.084 closest distance to " OH  TYR A 247 " =    1.915
peak=   -3.076 closest distance to " O   HOH Z 283 " =    5.489
peak=   -3.073 closest distance to " C   ALA A 158 " =    1.316
peak=   -3.070 closest distance to " CG2BVAL A  41 " =    2.038
peak=   -3.068 closest distance to " O   SER A  62 " =    2.192
peak=   -3.066 closest distance to " O   HOH Z 139 " =    3.061
peak=   -3.065 closest distance to " N   SER A 276 " =    1.401
peak=   -3.063 closest distance to " CD  GLN A  88 " =    0.905
peak=   -3.063 closest distance to " O   HOH Z 351 " =    1.358
peak=   -3.055 closest distance to " CA  GLY A 241 " =    2.863
peak=   -3.055 closest distance to " O   TRP A  92 " =    1.804
peak=   -3.051 closest distance to " OD2 ASP A 171 " =    1.848
peak=   -3.050 closest distance to " CD  GLN A  11 " =    0.922
peak=   -3.043 closest distance to " CD  GLN A  73 " =    0.890
peak=   -3.038 closest distance to " CE3 TRP A  70 " =    1.772
peak=   -3.036 closest distance to " O   HOH Z 236 " =    1.560
peak=   -3.036 closest distance to " O   HOH Z 139 " =    4.792
peak=   -3.031 closest distance to " CD1 TYR A 247 " =    2.632

================= 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    :  0.3456 0.3359   6.092716e+00   6.064451e+00
   1_bss:  0.3320 0.3232   6.070312e+00   6.038978e+00
   1_xyz:  0.1897 0.2102   5.558150e+00   5.654213e+00
   1_adp:  0.1748 0.2129   5.506852e+00   5.669393e+00
   1_occ:  0.1745 0.2129   5.505978e+00   5.669550e+00
   2_bss:  0.1724 0.2097   5.497917e+00   5.659508e+00
   2_xyz:  0.1378 0.1709   5.291422e+00   5.467583e+00
   2_adp:  0.1301 0.1676   5.251167e+00   5.446282e+00
   2_occ:  0.1299 0.1675   5.250686e+00   5.446010e+00
   3_bss:  0.1298 0.1673   5.249764e+00   5.445335e+00
   3_xyz:  0.1162 0.1598   5.172063e+00   5.399612e+00
   3_adp:  0.1141 0.1590   5.160288e+00   5.395216e+00
   3_occ:  0.1141 0.1589   5.160170e+00   5.395339e+00
   4_bss:  0.1139 0.1587   5.159828e+00   5.395177e+00
   4_xyz:  0.1104 0.1585   5.142697e+00   5.391522e+00
   4_adp:  0.1109 0.1566   5.139860e+00   5.383507e+00
   4_occ:  0.1108 0.1566   5.139785e+00   5.383795e+00
   5_bss:  0.1107 0.1566   5.139741e+00   5.384039e+00
   5_xyz:  0.1080 0.1575   5.129229e+00   5.385109e+00
   5_adp:  0.1076 0.1583   5.129827e+00   5.389337e+00
   5_occ:  0.1076 0.1583   5.129854e+00   5.389474e+00
   5_bss:  0.1075 0.1569   5.127148e+00   5.383763e+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:  0.300  50.000  -3.534   0.245   2.255   0.000   0.000   0.000
   1_xyz:  0.300  50.000  -3.534   0.245   2.255   0.000   0.000   0.000
   1_adp:  0.300  50.000  -3.534   0.245   2.255   0.000   0.000   0.000
   1_occ:  0.300  50.000  -3.534   0.245   2.255   0.000   0.000   0.000
   2_bss:  0.333  69.678  -3.298  -1.392  -0.190  -0.000  -0.000  -0.000
   2_xyz:  0.333  69.678  -3.298  -1.392  -0.190  -0.000  -0.000  -0.000
   2_adp:  0.333  69.678  -3.298  -1.392  -0.190  -0.000  -0.000  -0.000
   2_occ:  0.333  69.678  -3.298  -1.392  -0.190  -0.000  -0.000  -0.000
   3_bss:  0.331  67.971  -2.764  -1.610  -0.394  -0.000  -0.000  -0.000
   3_xyz:  0.331  67.971  -2.764  -1.610  -0.394  -0.000  -0.000  -0.000
   3_adp:  0.331  67.971  -2.764  -1.610  -0.394  -0.000  -0.000  -0.000
   3_occ:  0.331  67.971  -2.764  -1.610  -0.394  -0.000  -0.000  -0.000
   4_bss:  0.329  67.971  -2.306  -1.491  -0.292  -0.000  -0.000  -0.000
   4_xyz:  0.329  67.971  -2.306  -1.491  -0.292  -0.000  -0.000  -0.000
   4_adp:  0.329  67.971  -2.306  -1.491  -0.292  -0.000  -0.000  -0.000
   4_occ:  0.329  67.971  -2.306  -1.491  -0.292  -0.000  -0.000  -0.000
   5_bss:  0.322  59.521  -2.111  -1.414  -0.192  -0.000  -0.000  -0.000
   5_xyz:  0.322  59.521  -2.111  -1.414  -0.192  -0.000  -0.000  -0.000
   5_adp:  0.322  59.521  -2.111  -1.414  -0.192  -0.000  -0.000  -0.000
   5_occ:  0.322  59.521  -2.111  -1.414  -0.192  -0.000  -0.000  -0.000
   5_bss:  0.322  59.524  -1.896  -1.254  -0.020  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  35.535 0.6979  0.8566    32293.680
   1_bss:  34.442 0.7086  0.8605    29345.044
   1_xyz:  20.303 0.8596  0.9927    11342.922
   1_adp:  20.776 0.8544  0.9834    11702.921
   1_occ:  20.794 0.8542  0.9831    11703.880
   2_bss:  20.398 0.8583  0.9452    11436.909
   2_xyz:  15.821 0.8996  0.9666     7433.815
   2_adp:  15.285 0.9045  0.9604     7124.854
   2_occ:  15.278 0.9046  0.9603     7121.949
   3_bss:  15.247 0.9049  0.9624     7126.186
   3_xyz:  14.305 0.9125  0.9680     6517.848
   3_adp:  14.167 0.9139  0.9603     6455.027
   3_occ:  14.169 0.9138  0.9602     6455.254
   4_bss:  14.158 0.9139  0.9683     6455.559
   4_xyz:  14.056 0.9147  0.9693     6413.977
   4_adp:  13.851 0.9165  0.9638     6329.912
   4_occ:  13.854 0.9165  0.9636     6331.555
   5_bss:  13.857 0.9164  0.9679     6330.316
   5_xyz:  13.862 0.9165  0.9684     6376.331
   5_adp:  13.931 0.9160  0.9608     6409.571
   5_occ:  13.933 0.9159  0.9607     6410.576
   5_bss:  13.851 0.9165  0.9670     6282.976
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6318e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6318e-01
   1_xyz:   1.145  0.009  0.073 15.126  0.004  4.115   7.2841e-02
   1_adp:   1.145  0.009  0.073 15.126  0.004  4.115   7.2841e-02
   1_occ:   1.145  0.009  0.073 15.126  0.004  4.115   7.2841e-02
   2_bss:   1.145  0.009  0.073 15.126  0.004  4.115   7.2841e-02
   2_xyz:   0.961  0.007  0.070 14.473  0.004  4.128   5.3969e-02
   2_adp:   0.961  0.007  0.070 14.473  0.004  4.128   5.3969e-02
   2_occ:   0.961  0.007  0.070 14.473  0.004  4.128   5.3969e-02
   3_bss:   0.961  0.007  0.070 14.473  0.004  4.128   5.3969e-02
   3_xyz:   1.046  0.009  0.078 14.640  0.004  4.115   6.5463e-02
   3_adp:   1.046  0.009  0.078 14.640  0.004  4.115   6.5463e-02
   3_occ:   1.046  0.009  0.078 14.640  0.004  4.115   6.5463e-02
   4_bss:   1.046  0.009  0.078 14.640  0.004  4.115   6.5463e-02
   4_xyz:   1.089  0.010  0.084 14.685  0.004  4.118   7.2368e-02
   4_adp:   1.089  0.010  0.084 14.685  0.004  4.118   7.2368e-02
   4_occ:   1.089  0.010  0.084 14.685  0.004  4.118   7.2368e-02
   5_bss:   1.089  0.010  0.084 14.685  0.004  4.118   7.2368e-02
   5_xyz:   1.160  0.012  0.090 14.900  0.005  4.121   8.4553e-02
   5_adp:   1.160  0.012  0.090 14.900  0.005  4.121   8.4553e-02
   5_occ:   1.160  0.012  0.090 14.900  0.005  4.121   8.4553e-02
   5_bss:   1.160  0.012  0.090 14.900  0.005  4.121   8.4553e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4318e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4318e-01
   1_xyz:   8.011  0.053  0.281 83.055  0.032  2.271   7.3054e-02
   1_adp:   8.011  0.053  0.281 83.055  0.032  2.271   7.3054e-02
   1_occ:   8.011  0.053  0.281 83.055  0.032  2.271   7.3054e-02
   2_bss:   8.011  0.053  0.281 83.055  0.032  2.271   7.3054e-02
   2_xyz:   6.631  0.033  0.208 82.289  0.048  2.398   6.0219e-02
   2_adp:   6.631  0.033  0.208 82.289  0.048  2.398   6.0219e-02
   2_occ:   6.631  0.033  0.208 82.289  0.048  2.398   6.0219e-02
   3_bss:   6.631  0.033  0.208 82.289  0.048  2.398   6.0219e-02
   3_xyz:   7.718  0.047  0.257 83.280  0.041  2.388   5.5728e-02
   3_adp:   7.718  0.047  0.257 83.280  0.041  2.388   5.5728e-02
   3_occ:   7.718  0.047  0.257 83.280  0.041  2.388   5.5728e-02
   4_bss:   7.718  0.047  0.257 83.280  0.041  2.388   5.5728e-02
   4_xyz:   7.782  0.052  0.290 82.176  0.039  2.340   5.4447e-02
   4_adp:   7.782  0.052  0.290 82.176  0.039  2.340   5.4447e-02
   4_occ:   7.782  0.052  0.290 82.176  0.039  2.340   5.4447e-02
   5_bss:   7.782  0.052  0.290 82.176  0.039  2.340   5.4447e-02
   5_xyz:   8.096  0.063  0.311 82.699  0.038  2.250   6.7792e-02
   5_adp:   8.096  0.063  0.311 82.699  0.038  2.250   6.7792e-02
   5_occ:   8.096  0.063  0.311 82.699  0.038  2.250   6.7792e-02
   5_bss:   8.096  0.063  0.311 82.699  0.038  2.250   6.7792e-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:  64.03   0.00  16.51  55.74   0.00  12.61  64.03   7.42  37.74
   1_occ:  64.03   0.00  16.51  55.74   0.00  12.61  64.03   7.42  37.74
   2_bss:  64.03   0.00  16.51  55.74   0.00  12.61  64.03   7.42  37.74
   2_xyz:  64.03   0.00  16.51  55.74   0.00  12.61  64.03   7.42  37.74
   2_adp:  74.89   0.71  16.89  74.89   0.71  12.74  72.08   5.86  39.48
   2_occ:  74.89   0.71  16.89  74.89   0.71  12.74  72.08   5.86  39.48
   3_bss:  74.89   0.71  16.89  74.89   0.71  12.74  72.08   5.86  39.48
   3_xyz:  74.89   0.71  16.89  74.89   0.71  12.74  72.08   5.86  39.48
   3_adp:  90.80   0.00  17.08  90.80   0.00  12.67  83.96   0.00  41.08
   3_occ:  90.80   0.00  17.08  90.80   0.00  12.67  83.96   0.00  41.08
   4_bss:  90.80   0.00  17.08  90.80   0.00  12.67  83.96   0.00  41.08
   4_xyz:  90.80   0.00  17.08  90.80   0.00  12.67  83.96   0.00  41.08
   4_adp:  88.64   0.69  16.37  88.64   0.69  12.33  81.31   1.53  38.36
   4_occ:  88.64   0.69  16.37  88.64   0.69  12.33  81.31   1.53  38.36
   5_bss:  88.64   0.69  16.37  88.64   0.69  12.33  81.31   1.53  38.36
   5_xyz:  88.64   0.69  16.37  88.64   0.69  12.33  81.31   1.53  38.36
   5_adp:  89.04   0.01  16.27  89.04   0.01  12.16  81.15   2.98  38.69
   5_occ:  89.04   0.01  16.27  89.04   0.01  12.16  81.15   2.98  38.69
   5_bss:  89.04   0.01  16.28  89.04   0.01  12.16  81.15   2.98  38.69
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.099    0.015    0.345
   1_adp:    1.099    0.015    0.345
   1_occ:    1.099    0.015    0.345
   2_bss:    1.099    0.015    0.345
   2_xyz:    0.917    0.046    0.389
   2_adp:    0.917    0.046    0.389
   2_occ:    0.917    0.046    0.389
   3_bss:    0.917    0.046    0.389
   3_xyz:    1.014    0.033    0.433
   3_adp:    1.014    0.033    0.433
   3_occ:    1.014    0.033    0.433
   4_bss:    1.014    0.033    0.433
   4_xyz:    1.169    0.056    0.445
   4_adp:    1.169    0.056    0.445
   4_occ:    1.169    0.056    0.445
   5_bss:    1.169    0.056    0.445
   5_xyz:    1.189    0.063    0.454
   5_adp:    1.189    0.063    0.454
   5_occ:    1.189    0.063    0.454
   5_bss:    1.189    0.063    0.454
------------------------------------------------------------------------

CPU time actual refinement: 330.63


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/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_690/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_690/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.49 
  Macro-tasks:
    bulk solvent and scale       = 40.40  
    individual site refinement   = 131.87 
    weights calculation          = 29.66  
    collect and process          = 6.83   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 208.88 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 104.60 
    alpha_beta                      = 7.97   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.60 
    fmodel                         = 6.74   
    r_factors                      = 0.24   
    phase_errors                   = 11.14  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 246.46 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.709 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    648 calls, 104.21 s
gradients_fft:          593 calls,  99.41 s

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

# Date 2008-01-16 Time 05:25:24 PST -0800 (1200489924.12 s)
Start R-work = 0.3456, R-free = 0.3359 (no bulk solvent and anisotropic scale)
Final R-work = 0.1279, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.3320, R-free = 0.3232
Final R-work = 0.1075, R-free = 0.1569