# Date 2008-01-16 Time 06:09:15 PST -0800 (1200492555.97 s)
#phil __OFF__

Command line arguments: "../1026.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7220
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1026

-------------------------------------------------------------------------------
  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: (71.3037, 46.93, 85.5261, 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: (71.3037, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98111
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951338

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9811

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: (71.3037, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98111
Completeness in resolution range: 0.954211
Completeness with d_max=infinity: 0.951338

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2397 [2153/2182]  1942   211   9.8%
  bin  2:  4.2397 -  3.3775 [2072/2088]  1862   210  10.1%
  bin  3:  3.3775 -  2.9542 [2033/2052]  1828   205  10.1%
  bin  4:  2.9542 -  2.6858 [2040/2070]  1838   202   9.9%
  bin  5:  2.6858 -  2.4942 [2021/2040]  1819   202  10.0%
  bin  6:  2.4942 -  2.3477 [1998/2023]  1792   206  10.3%
  bin  7:  2.3477 -  2.2305 [1986/2019]  1790   196   9.9%
  bin  8:  2.2305 -  2.1337 [1984/2015]  1790   194   9.8%
  bin  9:  2.1337 -  2.0517 [1985/2027]  1784   201  10.1%
  bin 10:  2.0517 -  1.9811 [1317/2013]  1185   132  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 14
        2.42 -     3.04: 2194
        3.04 -     3.66: 4663
        3.66 -     4.28: 9028
        4.28 -     4.90: 12338
  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 207 " - " O   HOH Z 341 "  2.009 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.117 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.176 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.197 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28232 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_1026/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/model_refine_001.geo

CPU time processing inputs: 9.67


============================ 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 = 71.30375 46.93 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3017   r_free= 0.3068   ksol= 0.00   Bsol= 0.00   scale= 0.978    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.979003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7290 0.99   1396  155 0.2761 0.2708      6.3222      6.2725|
|  2:  4.7290 -  3.7728 0.99   1349  146 0.2301 0.2266      6.3385      6.3203|
|  3:  3.7728 -  3.3016 0.99   1322  149 0.2593 0.2351      6.2412       6.309|
|  4:  3.3016 -  3.0023 0.99   1321  152 0.2654 0.3028      6.1311      6.1636|
|  5:  3.0023 -  2.7885 0.99   1305  141 0.2994 0.3109      6.0246      6.1102|
|  6:  2.7885 -  2.6250 0.99   1295  145 0.3227 0.3241      5.9792      5.9686|
|  7:  2.6250 -  2.4942 0.99   1301  142 0.3210 0.3072      5.9691      5.9534|
|  8:  2.4942 -  2.3860 0.98   1270  147 0.3393 0.3143      5.8976      5.8565|
|  9:  2.3860 -  2.2945 0.98   1289  146 0.3304 0.3392      5.8536      5.8652|
| 10:  2.2945 -  2.2156 0.99   1271  137 0.3357 0.4393      5.8473       6.011|
| 11:  2.2156 -  2.1465 0.99   1289  140 0.3544 0.3506       5.815      5.8426|
| 12:  2.1465 -  2.0853 0.97   1261  136 0.3612 0.3667      5.7658      5.8318|
| 13:  2.0853 -  2.0305 0.99   1269  143 0.3543 0.3605      5.6699      5.5814|
| 14:  2.0305 -  1.9811 0.53    692   80 0.3461 0.3812      5.6128      5.6222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7290  1396   155  0.81  24.47   0.87     0.82      38123.52|
|  2:  4.7290 -  3.7728  1349   146  0.86  20.53   0.98     0.92      39624.07|
|  3:  3.7728 -  3.3016  1322   149  0.82  24.65   1.00     0.95      39127.00|
|  4:  3.3016 -  3.0023  1321   152  0.80  26.98   1.00     0.94      35804.21|
|  5:  3.0023 -  2.7885  1305   141  0.73  32.55   0.99     0.91      31022.42|
|  6:  2.7885 -  2.6250  1295   145  0.73  32.72   1.02     0.91      26382.87|
|  7:  2.6250 -  2.4942  1301   142  0.75  31.18   1.01     0.93      23136.93|
|  8:  2.4942 -  2.3860  1270   147  0.73  33.01   1.00     0.95      21667.53|
|  9:  2.3860 -  2.2945  1289   146  0.72  33.92   1.05     0.94      21408.54|
| 10:  2.2945 -  2.2156  1271   137  0.69  36.26   1.05     0.93      22296.19|
| 11:  2.2156 -  2.1465  1289   140  0.68  37.78   1.06     0.92      21223.07|
| 12:  2.1465 -  2.0853  1261   136  0.69  37.12   1.04     0.95      19426.48|
| 13:  2.0853 -  2.0305  1269   143  0.68  37.62   1.03     0.93      15932.39|
| 14:  2.0305 -  1.9811   692    80  0.69  37.16   1.06     0.87      13206.47|
|alpha:            min =        0.82 max =            0.95 mean =         0.92|
|beta:             min =    13206.47 max =        39624.07 mean =     26948.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           90.00 mean =        31.55|
|phase err.(test): min =        0.00 max =           89.82 mean =        31.49|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.712654              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.812   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.604236              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.506   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      191 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2003 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1833 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2830 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4647 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4381 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5601 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6737 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.161 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3017   r_free= 0.3068   ksol= 0.00   Bsol= 0.00   scale= 0.978    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.979003                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2869   r_free= 0.2935   ksol= 0.32   Bsol= 42.60   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.14,-2.94,-0.45,-0.00,-0.00,-0.00); trace/3= -1.09                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.956083                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.239750              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.095   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.311215              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.145   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2869      final r-factor (work) = 0.1693          |
| start r-factor (free) = 0.2935      final r-factor (free) = 0.1892          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8254 = 3.24 * 0.50 * 5.9658 + 1.00 * 0.1616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2728 = 3.24 * 0.50 * 5.6879 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1693      final r-factor (work) = 0.1581          |
| start r-factor (free) = 0.1892      final r-factor (free) = 0.1918          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7768 = 0.31 * 1.00 * 5.6879 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7468 = 0.31 * 1.00 * 5.4095 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.46   16.48    None  None   None       |
|    all(noH): 2823   0      0.00    82.46   16.48    None  None   None       |
|    Sol.    : 438    0      5.35    62.81   37.33    None  None   None       |
|    Mac.    : 2385   0      0.00    82.46   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.246:  506   |   5:    41.230 -  49.476:  100        |
|      1:     8.246 -  16.492: 1497   |   6:    49.476 -  57.722:   78        |
|      2:    16.492 -  24.738:  346   |   7:    57.722 -  65.968:   13        |
|      3:    24.738 -  32.984:  156   |   8:    65.968 -  74.214:    0        |
|      4:    32.984 -  41.230:  126   |   9:    74.214 -  82.461:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1581 r_free = 0.1918             target_work(ml) = 5.416         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1576 r_free = 0.1918             target_work(ml) = 5.413         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1576   r_free= 0.1918   ksol= 0.32   Bsol= 42.60   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.14,-2.94,-0.45,-0.00,-0.00,-0.00); trace/3= -1.09                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.413368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1561   r_free= 0.1895   ksol= 0.33   Bsol= 50.53   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-3.04,-1.68,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.408625                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.415190              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.969   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420236              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.554   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1561      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3207 = 3.42 * 0.50 * 5.4237 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1064 = 3.42 * 0.50 * 5.2926 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1587      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2485 = 0.42 * 1.00 * 5.2926 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1754 = 0.42 * 1.00 * 5.1569 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.39    78.67   17.05    None  None   None       |
|    all(noH): 2823   0      1.39    78.67   17.05    None  None   None       |
|    Sol.    : 438    0      2.06    71.24   39.04    None  None   None       |
|    Mac.    : 2385   0      1.39    78.67   13.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.389 -   9.117:  731   |   5:    40.029 -  47.757:  112        |
|      1:     9.117 -  16.845: 1279   |   6:    47.757 -  55.485:   83        |
|      2:    16.845 -  24.573:  309   |   7:    55.485 -  63.213:   53        |
|      3:    24.573 -  32.301:  129   |   8:    63.213 -  70.941:   17        |
|      4:    32.301 -  40.029:  103   |   9:    70.941 -  78.669:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1561             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1560             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1560   ksol= 0.33   Bsol= 50.53   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.92,-3.04,-1.68,-0.00,-0.00,-0.00); trace/3= -2.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145218                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1555   ksol= 0.32   Bsol= 50.53   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.70,-1.69,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144036                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.403312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.379  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1555      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8421 = 3.40 * 0.50 * 5.1557 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7906 = 3.40 * 0.50 * 5.1222 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1073          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0829 = 0.21 * 1.00 * 5.1222 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0812 = 0.21 * 1.00 * 5.1165 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    78.85   16.88    None  None   None       |
|    all(noH): 2823   0      1.75    78.85   16.88    None  None   None       |
|    Sol.    : 438    0      2.43    71.49   38.48    None  None   None       |
|    Mac.    : 2385   0      1.75    78.85   12.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.750 -   9.460:  857   |   5:    40.301 -  48.011:  106        |
|      1:     9.460 -  17.171: 1176   |   6:    48.011 -  55.721:   85        |
|      2:    17.171 -  24.881:  299   |   7:    55.721 -  63.431:   45        |
|      3:    24.881 -  32.591:  125   |   8:    63.431 -  71.141:   15        |
|      4:    32.591 -  40.301:  109   |   9:    71.141 -  78.851:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1073 r_free = 0.1537             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1537             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1537   ksol= 0.32   Bsol= 50.53   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.70,-1.69,-0.00,-0.00,-0.00); trace/3= -2.19                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112746                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1537   ksol= 0.32   Bsol= 50.53   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.47,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112708                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.889860              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.759  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.149203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.366  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9092 = 1.89 * 0.50 * 5.1166 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8993 = 1.89 * 0.50 * 5.1234 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1096      final r-factor (work) = 0.1088          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8955 = 1.15 * 1.00 * 5.1234 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8979 = 1.15 * 1.00 * 5.1241 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.48    89.13   17.07    None  None   None       |
|    all(noH): 2823   0      0.48    89.13   17.07    None  None   None       |
|    Sol.    : 438    0      3.15    77.49   39.62    None  None   None       |
|    Mac.    : 2385   0      0.48    89.13   12.93    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:     0.480 -   9.345:  891   |   5:    44.805 -  53.670:  104        |
|      1:     9.345 -  18.210: 1208   |   6:    53.670 -  62.535:   62        |
|      2:    18.210 -  27.075:  260   |   7:    62.535 -  71.399:   26        |
|      3:    27.075 -  35.940:  137   |   8:    71.399 -  80.264:   11        |
|      4:    35.940 -  44.805:  118   |   9:    80.264 -  89.129:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1088 r_free = 0.1567             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1567             target_work(ml) = 5.132         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1567   ksol= 0.32   Bsol= 50.53   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.18,-2.47,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132055                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1567   ksol= 0.32   Bsol= 50.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.27,-1.46,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.132168                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.929412              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616028              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.293  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1082          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0018 = 1.93 * 0.50 * 5.1246 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0071 = 1.93 * 0.50 * 5.1301 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1082      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1695 = 0.62 * 1.00 * 5.1301 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1710 = 0.62 * 1.00 * 5.1323 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.37    89.72   16.90    None  None   None       |
|    all(noH): 2823   0      0.37    89.72   16.90    None  None   None       |
|    Sol.    : 438    0      4.79    77.69   39.44    None  None   None       |
|    Mac.    : 2385   0      0.37    89.72   12.76    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:     0.375 -   9.309:  935   |   5:    45.047 -  53.982:  101        |
|      1:     9.309 -  18.244: 1176   |   6:    53.982 -  62.917:   62        |
|      2:    18.244 -  27.178:  251   |   7:    62.917 -  71.851:   24        |
|      3:    27.178 -  36.113:  137   |   8:    71.851 -  80.786:   11        |
|      4:    36.113 -  45.047:  120   |   9:    80.786 -  89.720:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1083 r_free = 0.1580             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1082 r_free = 0.1581             target_work(ml) = 5.133         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1082   r_free= 0.1581   ksol= 0.32   Bsol= 50.53   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-2.27,-1.46,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133379                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7290 0.99   1396  155 0.0962 0.1288      5.3653       5.518|
|  2:  4.7290 -  3.7728 0.99   1349  146 0.0829 0.1082      5.4145      5.6033|
|  3:  3.7728 -  3.3016 0.99   1322  149 0.1028 0.1509      5.4521      5.8626|
|  4:  3.3016 -  3.0023 0.99   1321  152 0.1155 0.1552      5.4392      5.5853|
|  5:  3.0023 -  2.7885 0.99   1305  141 0.1307 0.1818      5.3223      5.5587|
|  6:  2.7885 -  2.6250 0.99   1295  145 0.1189 0.1786      5.2032      5.4457|
|  7:  2.6250 -  2.4942 0.99   1301  142 0.1203 0.1616      5.1533      5.3583|
|  8:  2.4942 -  2.3860 0.98   1270  147 0.1112 0.1756      5.0238      5.3203|
|  9:  2.3860 -  2.2945 0.98   1289  146 0.1113 0.1773      5.0077      5.3328|
| 10:  2.2945 -  2.2156 0.99   1271  137 0.1056 0.1792       4.933      5.2205|
| 11:  2.2156 -  2.1465 0.99   1289  140 0.1135 0.1806      4.9549      5.2994|
| 12:  2.1465 -  2.0853 0.97   1261  136 0.1077 0.1538      4.8777      5.0818|
| 13:  2.0853 -  2.0305 0.99   1269  143 0.1151 0.1816      4.7933      5.0851|
| 14:  2.0305 -  1.9811 0.53    692   80 0.0987 0.1681       4.626      4.9403|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7290  1396   155  0.94   8.91   0.97     0.95       6917.49|
|  2:  4.7290 -  3.7728  1349   146  0.95   7.85   1.01     1.00       8713.94|
|  3:  3.7728 -  3.3016  1322   149  0.93  11.17   1.02     1.02      10078.89|
|  4:  3.3016 -  3.0023  1321   152  0.92  13.51   1.00     0.98      10370.92|
|  5:  3.0023 -  2.7885  1305   141  0.89  16.37   0.99     0.97       8493.59|
|  6:  2.7885 -  2.6250  1295   145  0.90  15.93   0.98     0.96       7158.40|
|  7:  2.6250 -  2.4942  1301   142  0.91  15.20   0.98     0.95       6134.33|
|  8:  2.4942 -  2.3860  1270   147  0.91  14.96   0.99     0.96       4985.04|
|  9:  2.3860 -  2.2945  1289   146  0.91  14.85   0.99     0.97       4837.10|
| 10:  2.2945 -  2.2156  1271   137  0.90  15.31   0.98     0.95       4253.07|
| 11:  2.2156 -  2.1465  1289   140  0.90  16.72   0.99     0.96       4603.19|
| 12:  2.1465 -  2.0853  1261   136  0.91  15.24   0.99     0.97       4093.76|
| 13:  2.0853 -  2.0305  1269   143  0.90  16.64   0.99     0.98       3433.87|
| 14:  2.0305 -  1.9811   692    80  0.92  14.19   0.96     0.93       2412.34|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2412.34 max =        10370.92 mean =      6345.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.73 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1580   ksol= 0.32   Bsol= 50.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.04,-1.25,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1081   r_free= 0.1580   ksol= 0.32   Bsol= 50.52   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-2.04,-1.25,-0.00,-0.00,-0.00); trace/3= -1.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133514                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7290 0.99   1396  155 0.0962 0.1289      5.3662      5.5192|
|  2:  4.7290 -  3.7728 0.99   1349  146 0.0830 0.1082      5.4148      5.6029|
|  3:  3.7728 -  3.3016 0.99   1322  149 0.1027 0.1509      5.4518      5.8624|
|  4:  3.3016 -  3.0023 0.99   1321  152 0.1154 0.1552      5.4392      5.5854|
|  5:  3.0023 -  2.7885 0.99   1305  141 0.1307 0.1818      5.3224      5.5585|
|  6:  2.7885 -  2.6250 0.99   1295  145 0.1189 0.1786      5.2033      5.4457|
|  7:  2.6250 -  2.4942 0.99   1301  142 0.1203 0.1616      5.1534      5.3583|
|  8:  2.4942 -  2.3860 0.98   1270  147 0.1112 0.1756      5.0238      5.3202|
|  9:  2.3860 -  2.2945 0.98   1289  146 0.1113 0.1772      5.0078      5.3327|
| 10:  2.2945 -  2.2156 0.99   1271  137 0.1056 0.1793      4.9332      5.2203|
| 11:  2.2156 -  2.1465 0.99   1289  140 0.1135 0.1807       4.955      5.2997|
| 12:  2.1465 -  2.0853 0.97   1261  136 0.1077 0.1538      4.8777      5.0821|
| 13:  2.0853 -  2.0305 0.99   1269  143 0.1151 0.1816      4.7933      5.0848|
| 14:  2.0305 -  1.9811 0.53    692   80 0.0987 0.1682      4.6262      4.9407|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1149 -  4.7290  1396   155  0.94   8.93   0.98     0.95       6931.08|
|  2:  4.7290 -  3.7728  1349   146  0.95   7.86   1.01     1.00       8721.07|
|  3:  3.7728 -  3.3016  1322   149  0.93  11.17   1.03     1.02      10075.40|
|  4:  3.3016 -  3.0023  1321   152  0.92  13.51   1.01     0.98      10370.83|
|  5:  3.0023 -  2.7885  1305   141  0.89  16.37   1.00     0.97       8494.21|
|  6:  2.7885 -  2.6250  1295   145  0.90  15.93   0.99     0.96       7159.14|
|  7:  2.6250 -  2.4942  1301   142  0.91  15.20   0.99     0.96       6133.94|
|  8:  2.4942 -  2.3860  1270   147  0.91  14.96   1.00     0.97       4984.68|
|  9:  2.3860 -  2.2945  1289   146  0.91  14.85   1.00     0.97       4836.06|
| 10:  2.2945 -  2.2156  1271   137  0.90  15.32   0.99     0.95       4254.37|
| 11:  2.2156 -  2.1465  1289   140  0.90  16.73   1.00     0.97       4603.59|
| 12:  2.1465 -  2.0853  1261   136  0.91  15.24   1.00     0.98       4094.84|
| 13:  2.0853 -  2.0305  1269   143  0.90  16.64   1.00     0.99       3434.06|
| 14:  2.0305 -  1.9811   692    80  0.92  14.20   0.98     0.94       2413.71|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2413.71 max =        10370.83 mean =      6346.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.00|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.986)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.36    89.71   16.89    None  None   None       |
|    all(noH): 2823   0      0.36    89.71   16.89    None  None   None       |
|    Sol.    : 438    0      4.78    77.68   39.43    None  None   None       |
|    Mac.    : 2385   0      0.36    89.71   12.75    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:     0.364 -   9.298:  935   |   5:    45.036 -  53.971:  101        |
|      1:     9.298 -  18.233: 1176   |   6:    53.971 -  62.905:   62        |
|      2:    18.233 -  27.167:  251   |   7:    62.905 -  71.840:   24        |
|      3:    27.167 -  36.102:  137   |   8:    71.840 -  80.775:   11        |
|      4:    36.102 -  45.036:  120   |   9:    80.775 -  89.709:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.649 - 4.621
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 285 from: 289
   mapped sites are within: 0.709 - 4.621

peak=    5.912 closest distance to " NH2 ARG A  56 " =    2.231
peak=    5.662 closest distance to " CG  PRO A  54 " =    1.258
peak=    5.547 closest distance to " CB  GLN A 223 " =    1.443
peak=    5.208 closest distance to " CB  SER A  63 " =    1.238
peak=    5.188 closest distance to " O   HOH Z 126 " =    1.887
peak=    5.090 closest distance to " O   HOH Z 232 " =    2.280
peak=    4.978 closest distance to " CG  PRO A 213 " =    1.227
peak=    4.860 closest distance to " CB  PRO A  54 " =    0.933
peak=    4.827 closest distance to " NE2 GLN A  11 " =    1.118
peak=    4.804 closest distance to " CB  GLN A 183 " =    1.236
peak=    4.712 closest distance to " CB  ARG A 275 " =    0.900
peak=    4.695 closest distance to " CG  PRO A  90 " =    1.113
peak=    4.675 closest distance to " CB  LEU A 228 " =    1.081
peak=    4.628 closest distance to " C   PRO A 198 " =    1.544
peak=    4.592 closest distance to " O   HOH Z 298 " =    1.943
peak=    4.589 closest distance to " O   HOH Z  78 " =    1.676
peak=    4.562 closest distance to " CB  GLU A 128 " =    1.057
peak=    4.544 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.486 closest distance to " O   HOH Z 142 " =    1.672
peak=    4.465 closest distance to " O   HOH Z  15 " =    2.185
peak=    4.430 closest distance to " O   HOH Z 193 " =    1.884
peak=    4.395 closest distance to " CG  PRO A 198 " =    1.260
peak=    4.392 closest distance to " OD1 ASN A  69 " =    2.562
peak=    4.363 closest distance to " O   HOH Z 236 " =    2.007
peak=    4.345 closest distance to " CB  TYR A 169 " =    0.758
peak=    4.336 closest distance to " ND2 ASN A 187 " =    1.489
peak=    4.317 closest distance to " O   HOH Z 369 " =    2.065
peak=    4.279 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.231 closest distance to " CB  GLU A 152 " =    1.201
peak=    4.227 closest distance to " CG  PRO A 243 " =    1.137
peak=    4.203 closest distance to " O   HOH Z 261 " =    2.176
peak=    4.192 closest distance to " O   HOH Z 427 " =    2.957
peak=    4.192 closest distance to " CB  SER A   3 " =    1.378
peak=    4.081 closest distance to " CB  VAL A 265 " =    1.236
peak=    4.077 closest distance to " CB  ARG A  79 " =    1.393
peak=    4.074 closest distance to " O   HOH Z 316 " =    3.110
peak=    4.066 closest distance to " OD2 ASP A 286 " =    2.894
peak=    4.049 closest distance to " O   HOH Z 234 " =    3.769
peak=    4.048 closest distance to " CA  ALA A  21 " =    1.210
peak=    4.002 closest distance to " CG2 VAL A 257 " =    0.919
peak=    4.000 closest distance to " O   HOH Z 303 " =    2.106
peak=    3.994 closest distance to " O   HOH Z 368 " =    2.007
peak=    3.969 closest distance to " CB  ARG A 190 " =    1.628
peak=    3.964 closest distance to " NH2 ARG A 156 " =    1.217
peak=    3.959 closest distance to " CB  TRP A 179 " =    1.375
peak=    3.957 closest distance to " CD1 LEU A 300 " =    1.208
peak=    3.955 closest distance to " CG1 ILE A  33 " =    1.270
peak=    3.947 closest distance to " CA  THR A 264 " =    0.855
peak=    3.930 closest distance to " CZ  PHE A 218 " =    1.060
peak=    3.924 closest distance to " O   HOH Z 132 " =    2.497
peak=    3.920 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.901 closest distance to " O   HOH Z 203 " =    1.866
peak=    3.892 closest distance to " O   HOH Z 158 " =    2.960
peak=    3.883 closest distance to " CB  SER A 212 " =    1.111
peak=    3.882 closest distance to " O   HOH Z 214 " =    2.014
peak=    3.874 closest distance to " CD  ARG A  66 " =    2.320
peak=    3.873 closest distance to " CD  ARG A 159 " =    0.786
peak=    3.869 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.858 closest distance to " O   HOH Z 135 " =    1.668
peak=    3.857 closest distance to " NH1AARG A 145 " =    1.167
peak=    3.856 closest distance to " CA  MET A  40 " =    1.131
peak=    3.855 closest distance to " NZ  LYS A 117 " =    3.246
peak=    3.852 closest distance to " O   HOH Z 346 " =    1.648
peak=    3.850 closest distance to " CA  PRO A  54 " =    1.330
peak=    3.841 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.841 closest distance to " CB  VAL A 202 " =    1.617
peak=    3.840 closest distance to " O   HOH Z 272 " =    1.844
peak=    3.836 closest distance to " CB  GLU A 277 " =    3.645
peak=    3.835 closest distance to " O   HOH Z 425 " =    2.022
peak=    3.831 closest distance to " ND2 ASN A 249 " =    1.933
peak=    3.825 closest distance to " CG2 THR A 221 " =    1.095
peak=    3.824 closest distance to " O   MET A 105 " =    1.839
peak=    3.815 closest distance to " O   HOH Z 344 " =    3.145
peak=    3.815 closest distance to " ND1 HIS A  86 " =    1.730
peak=    3.810 closest distance to " O   HOH Z 180 " =    2.154
peak=    3.810 closest distance to " ND2 ASN A 110 " =    1.813
peak=    3.761 closest distance to " CD  ARG A 269 " =    0.939
peak=    3.759 closest distance to " CB  ASP A 140 " =    0.974
peak=    3.756 closest distance to " CA  THR A 221 " =    1.002
peak=    3.751 closest distance to " CA  ASN A 215 " =    1.180
peak=    3.748 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.722 closest distance to " O   HOH Z 133 " =    1.646
peak=    3.720 closest distance to " O   HOH Z 250 " =    1.428
peak=    3.720 closest distance to " O   HOH Z  10 " =    1.867
peak=    3.719 closest distance to " O   HOH Z 403 " =    1.688
peak=    3.713 closest distance to " CB  TYR A 169 " =    0.741
peak=    3.710 closest distance to " CB  SER A 216 " =    0.834
peak=    3.694 closest distance to " O   HOH Z 426 " =    1.585
peak=    3.690 closest distance to " CD2 LEU A 297 " =    0.885
peak=    3.666 closest distance to " O   HOH Z 197 " =    3.115
peak=    3.661 closest distance to " O   HOH Z 368 " =    3.630
peak=    3.655 closest distance to " CA  ALA A  51 " =    0.930
peak=    3.655 closest distance to " O   HOH Z 189 " =    2.364
peak=    3.654 closest distance to " O   HOH Z  21 " =    1.699
peak=    3.645 closest distance to " CG1BVAL A  72 " =    1.621
peak=    3.644 closest distance to " CD BLYS A 290 " =    1.001
peak=    3.629 closest distance to " O   HOH Z 411 " =    3.831
peak=    3.625 closest distance to " O   HOH Z 108 " =    2.378
peak=    3.623 closest distance to " O   HOH Z   1 " =    1.942
peak=    3.622 closest distance to " N   ARG A 156 " =    1.336
peak=    3.613 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.599 closest distance to " CD  LYS A 166 " =    1.260
peak=    3.598 closest distance to " O   HOH Z 245 " =    1.319
peak=    3.587 closest distance to " O   HOH Z  20 " =    1.612
peak=    3.568 closest distance to " CG  LEU A 167 " =    1.210
peak=    3.562 closest distance to " CD1 ILE A 106 " =    0.784
peak=    3.558 closest distance to " O   HOH Z 193 " =    2.075
peak=    3.556 closest distance to " NH2BARG A 145 " =    2.119
peak=    3.548 closest distance to " O   HOH Z 213 " =    1.826
peak=    3.542 closest distance to " O   HOH Z  61 " =    1.528
peak=    3.541 closest distance to " O   HOH Z  66 " =    2.146
peak=    3.538 closest distance to " O   HOH Z 280 " =    3.009
peak=    3.538 closest distance to " O   HOH Z 305 " =    3.634
peak=    3.537 closest distance to " ND1 HIS A  81 " =    1.622
peak=    3.534 closest distance to " O   HOH Z  88 " =    3.520
peak=    3.526 closest distance to " CA  ALA A 291 " =    0.914
peak=    3.525 closest distance to " O   HOH Z  40 " =    1.821
peak=    3.521 closest distance to " OD1 ASN A 217 " =    1.635
peak=    3.519 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.515 closest distance to " CD2 LEU A 255 " =    1.479
peak=    3.515 closest distance to " N   ASN A 127 " =    1.251
peak=    3.510 closest distance to " O   HOH Z 219 " =    1.943
peak=    3.504 closest distance to " O   HOH Z 172 " =    3.421
peak=    3.499 closest distance to " O   HOH Z 371 " =    3.211
peak=    3.498 closest distance to " CA  ASP A 140 " =    1.184
peak=    3.496 closest distance to " O   HOH Z 134 " =    1.314
peak=    3.494 closest distance to " CB  MET A  40 " =    0.818
peak=    3.491 closest distance to " CA  ARG A  36 " =    1.105
peak=    3.487 closest distance to " O   HOH Z  59 " =    2.011
peak=    3.481 closest distance to " CB  ALA A  34 " =    1.043
peak=    3.481 closest distance to " O   HOH Z  64 " =    2.150
peak=    3.481 closest distance to " O   HOH Z  44 " =    1.689
peak=    3.481 closest distance to " CD  ARG A 219 " =    1.006
peak=    3.479 closest distance to " O   HOH Z 291 " =    1.516
peak=    3.477 closest distance to " CA  ARG A 195 " =    1.263
peak=    3.476 closest distance to " O   HOH Z  49 " =    2.151
peak=    3.471 closest distance to " CB  MET A  47 " =    1.003
peak=    3.469 closest distance to " CB  ASN A  39 " =    0.927
peak=    3.467 closest distance to " O   HOH Z 402 " =    1.448
peak=    3.467 closest distance to " CB  LEU A 255 " =    0.778
peak=    3.462 closest distance to " O   HOH Z 295 " =    1.489
peak=    3.458 closest distance to " CD2 TRP A 179 " =    1.349
peak=    3.457 closest distance to " O   HOH Z  54 " =    2.399
peak=    3.456 closest distance to " CB  ARG A 139 " =    0.929
peak=    3.452 closest distance to " CA  ALA A  84 " =    1.459
peak=    3.448 closest distance to " CB  ASN A 142 " =    0.995
peak=    3.448 closest distance to " CG2 ILE A 120 " =    1.240
peak=    3.446 closest distance to " O   HOH Z 133 " =    2.422
peak=    3.444 closest distance to " CD  LYS A 119 " =    1.182
peak=    3.442 closest distance to " CG1 ILE A 151 " =    0.973
peak=    3.425 closest distance to " O   HOH Z  97 " =    1.925
peak=    3.425 closest distance to " O   HOH Z   9 " =    2.093
peak=    3.424 closest distance to " CB  GLN A  88 " =    1.264
peak=    3.423 closest distance to " CB  TYR A 116 " =    0.856
peak=    3.422 closest distance to " O   HOH Z 273 " =    2.718
peak=    3.421 closest distance to " CA  ALA A 154 " =    0.970
peak=    3.419 closest distance to " O   TRP A 274 " =    1.831
peak=    3.416 closest distance to " CG2BVAL A  41 " =    0.836
peak=    3.415 closest distance to " O   HOH Z 425 " =    1.244
peak=    3.414 closest distance to " CB  ALA A   1 " =    4.621
peak=    3.413 closest distance to " N   VAL A 126 " =    1.330
peak=    3.410 closest distance to " O   HOH Z 327 " =    2.021
peak=    3.408 closest distance to " OG BSER A 164 " =    2.398
peak=    3.404 closest distance to " CB  SER A 141 " =    0.964
peak=    3.399 closest distance to " O   HOH Z 345 " =    3.478
peak=    3.393 closest distance to " O   HOH Z 227 " =    1.624
peak=    3.389 closest distance to " O   THR A 251 " =    1.200
peak=    3.384 closest distance to " O   HOH Z 391 " =    2.927
peak=    3.382 closest distance to " CA  GLY A 267 " =    1.162
peak=    3.373 closest distance to " O   HOH Z  53 " =    2.561
peak=    3.372 closest distance to " O  BHOH Z 338 " =    2.353
peak=    3.371 closest distance to " O   HOH Z  93 " =    2.638
peak=    3.370 closest distance to " O   HOH Z 407 " =    2.482
peak=    3.370 closest distance to " O   HOH Z   6 " =    2.188
peak=    3.369 closest distance to " O   HOH Z 128 " =    2.147
peak=    3.369 closest distance to " CE1 TYR A 186 " =    1.299
peak=    3.369 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.368 closest distance to " O   SER A  87 " =    2.334
peak=    3.367 closest distance to " CB  ALA A 248 " =    1.043
peak=    3.366 closest distance to " CB  ALA A 291 " =    1.376
peak=    3.359 closest distance to " O   HOH Z 128 " =    2.328
peak=    3.353 closest distance to " CB  ALA A 248 " =    1.387
peak=    3.350 closest distance to " O   HOH Z  43 " =    1.766
peak=    3.349 closest distance to " O   HOH Z 329 " =    3.747
peak=    3.347 closest distance to " O   HOH Z 406 " =    1.618
peak=    3.345 closest distance to " O   HOH Z 209 " =    2.368
peak=    3.342 closest distance to " O   HOH Z 359 " =    3.877
peak=    3.338 closest distance to " O   HOH Z 423 " =    1.783
peak=    3.337 closest distance to " CB  HIS A 108 " =    0.832
peak=    3.336 closest distance to " CG  LYS A  76 " =    0.962
peak=    3.332 closest distance to " CA  ALA A 248 " =    1.272
peak=    3.330 closest distance to " CA  ASP A 191 " =    0.742
peak=    3.325 closest distance to " CD1 LEU A  96 " =    0.761
peak=    3.323 closest distance to " OG  SER A  22 " =    2.799
peak=    3.317 closest distance to " O   HOH Z  54 " =    1.686
peak=    3.304 closest distance to " CB  PHE A  16 " =    0.985
peak=    3.300 closest distance to " CA  SER A  87 " =    1.036
peak=    3.299 closest distance to " O   THR A 220 " =    1.310
peak=    3.293 closest distance to " CB  SER A  62 " =    1.206
peak=    3.293 closest distance to " O   HOH Z 359 " =    1.390
peak=    3.292 closest distance to " CZ  PHE A 192 " =    0.805
peak=    3.290 closest distance to " O   HOH Z 411 " =    1.803
peak=    3.286 closest distance to " O   HOH Z 409 " =    2.995
peak=    3.285 closest distance to " O   ALA A 158 " =    1.271
peak=    3.281 closest distance to " O   HOH Z 374 " =    2.666
peak=    3.279 closest distance to " O   ALA A 165 " =    1.417
peak=    3.274 closest distance to " CA  ARG A 102 " =    1.181
peak=    3.273 closest distance to " CA  ALA A 233 " =    1.336
peak=    3.272 closest distance to " N   ASN A  39 " =    1.330
peak=    3.269 closest distance to " CB  ILE A 120 " =    1.228
peak=    3.266 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.266 closest distance to " CA  MET A 105 " =    1.006
peak=    3.265 closest distance to " CB  ASN A 224 " =    1.052
peak=    3.263 closest distance to " CB  THR A 157 " =    1.109
peak=    3.255 closest distance to " NH2AARG A 275 " =    3.689
peak=    3.253 closest distance to " CZ  PHE A 208 " =    1.171
peak=    3.252 closest distance to " O   HOH Z 334 " =    1.459
peak=    3.251 closest distance to " O   HOH Z 353 " =    2.752
peak=    3.246 closest distance to " O   HOH Z 263 " =    1.735
peak=    3.243 closest distance to " O   HOH Z   1 " =    1.643
peak=    3.241 closest distance to " O   HOH Z 437 " =    1.360
peak=    3.240 closest distance to " CG  MET A 113 " =    1.419
peak=    3.240 closest distance to " O   HOH Z 403 " =    1.345
peak=    3.236 closest distance to " NZ  LYS A 166 " =    3.089
peak=    3.232 closest distance to " OG  SER A  97 " =    3.557
peak=    3.231 closest distance to " CA  LYS A 117 " =    1.188
peak=    3.224 closest distance to " O   HOH Z 234 " =    1.694
peak=    3.221 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.217 closest distance to " CZ2 TRP A 179 " =    1.659
peak=    3.216 closest distance to " O   HOH Z 185 " =    1.750
peak=    3.214 closest distance to " CA  GLU A  46 " =    0.709
peak=    3.212 closest distance to " CG  GLN A  11 " =    1.737
peak=    3.210 closest distance to " O   HOH Z  49 " =    2.878
peak=    3.210 closest distance to " CB  ALA A   9 " =    1.563
peak=    3.206 closest distance to " O   HOH Z 171 " =    2.084
peak=    3.200 closest distance to " O   HOH Z  66 " =    2.047
peak=    3.196 closest distance to " O   GLY A  57 " =    2.608
peak=    3.196 closest distance to " N   GLN A 278 " =    1.036
peak=    3.194 closest distance to " CB  ASN A 215 " =    1.094
peak=    3.191 closest distance to " O   HOH Z  40 " =    1.955
peak=    3.190 closest distance to " CG  MET A 185 " =    1.190
peak=    3.190 closest distance to " O   HOH Z 423 " =    2.906
peak=    3.188 closest distance to " CB  LYS A 193 " =    0.957
peak=    3.187 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.184 closest distance to " CA  SER A 146 " =    1.702
peak=    3.181 closest distance to " O   HOH Z  44 " =    3.244
peak=    3.180 closest distance to " CA  ILE A  33 " =    1.544
peak=    3.178 closest distance to " CG2 VAL A 197 " =    1.109
peak=    3.177 closest distance to " O   HOH Z 383 " =    1.807
peak=    3.177 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.174 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.172 closest distance to " O   HOH Z 261 " =    2.131
peak=    3.167 closest distance to " O   HOH Z  88 " =    2.959
peak=    3.165 closest distance to " O   HOH Z 183 " =    1.389
peak=    3.160 closest distance to " CB  GLU A 152 " =    1.473
peak=    3.158 closest distance to " O   HOH Z 271 " =    2.503
peak=    3.156 closest distance to " CA  ALA A  43 " =    1.224
peak=    3.154 closest distance to " O   HOH Z 211 " =    2.789
peak=    3.152 closest distance to " O   HOH Z 290 " =    1.030
peak=    3.149 closest distance to " CA  LEU A 282 " =    1.051
peak=    3.148 closest distance to " OE1 GLU A 152 " =    0.872
peak=    3.147 closest distance to " O   HOH Z 435 " =    1.937
peak=    3.136 closest distance to " N   ASN A 252 " =    1.382
peak=    3.131 closest distance to " O   HOH Z 236 " =    1.636
peak=    3.131 closest distance to " O   HOH Z 302 " =    1.902
peak=    3.130 closest distance to " OD1BASN A 224 " =    2.377
peak=    3.130 closest distance to " CA  TYR A 116 " =    1.417
peak=    3.125 closest distance to " O   HOH Z 417 " =    1.952
peak=    3.124 closest distance to " CB  ASN A 110 " =    1.189
peak=    3.121 closest distance to " O   HOH Z 148 " =    3.275
peak=    3.112 closest distance to " CG  MET A 185 " =    1.043
peak=    3.110 closest distance to " OG  SER A 206 " =    1.301
peak=    3.100 closest distance to " N   SER A 135 " =    1.317
peak=    3.097 closest distance to " CB  ARG A 138 " =    0.986
peak=    3.096 closest distance to " O   HOH Z 116 " =    1.766
peak=    3.084 closest distance to " NE2 HIS A 115 " =    1.105
peak=    3.084 closest distance to " O   HOH Z 368 " =    2.663
peak=    3.080 closest distance to " NH1BARG A 145 " =    0.952
peak=    3.076 closest distance to " O   TYR A 116 " =    1.288
peak=    3.074 closest distance to " O   HOH Z 144 " =    1.755
peak=    3.072 closest distance to " CA  LEU A  83 " =    1.530
peak=    3.058 closest distance to " NZ  LYS A  76 " =    1.270
peak=    3.052 closest distance to " CB  TRP A 150 " =    1.386
peak=    3.052 closest distance to " N   TYR A  15 " =    0.778
peak=    3.044 closest distance to " CG BARG A 102 " =    1.854

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.733 - 5.620
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 215 from: 216
   mapped sites are within: 0.733 - 5.620

peak=   -4.702 closest distance to " O   HOH Z 266 " =    4.782
peak=   -4.519 closest distance to " CB  PRO A 243 " =    2.621
peak=   -4.343 closest distance to " O   VAL A  67 " =    2.769
peak=   -4.337 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.276 closest distance to " CG  GLN A 223 " =    1.947
peak=   -4.208 closest distance to " N   ALA A  43 " =    2.608
peak=   -4.169 closest distance to " O   HOH Z 377 " =    2.029
peak=   -4.147 closest distance to " CE2 TYR A  30 " =    2.782
peak=   -4.142 closest distance to " O   HOH Z 372 " =    2.470
peak=   -4.142 closest distance to " O   ILE A 109 " =    2.590
peak=   -4.136 closest distance to " O   HOH Z 126 " =    1.871
peak=   -4.120 closest distance to " SG  CYS A 254 " =    3.462
peak=   -4.075 closest distance to " O   HOH Z 198 " =    2.140
peak=   -4.064 closest distance to " O   HOH Z 290 " =    1.147
peak=   -4.059 closest distance to " O   HOH Z  10 " =    1.522
peak=   -4.055 closest distance to " O   HOH Z 118 " =    3.113
peak=   -4.005 closest distance to " O   HOH Z 389 " =    1.867
peak=   -4.003 closest distance to " O   HOH Z 231 " =    2.170
peak=   -3.972 closest distance to " CG1 VAL A 112 " =    2.866
peak=   -3.963 closest distance to " O   HOH Z  43 " =    1.571
peak=   -3.961 closest distance to " C   HIS A 108 " =    1.096
peak=   -3.886 closest distance to " O   HOH Z 353 " =    2.149
peak=   -3.874 closest distance to " O   HOH Z  52 " =    1.383
peak=   -3.848 closest distance to " O   PRO A 163 " =    2.078
peak=   -3.847 closest distance to " CB  ALA A 291 " =    2.260
peak=   -3.837 closest distance to " OG BSER A 134 " =    1.216
peak=   -3.831 closest distance to " CZ3 TRP A 179 " =    1.128
peak=   -3.828 closest distance to " ND2 ASN A  45 " =    1.821
peak=   -3.804 closest distance to " CD  ARG A 139 " =    1.576
peak=   -3.793 closest distance to " O   HOH Z 185 " =    2.276
peak=   -3.791 closest distance to " O   PRO A 198 " =    1.283
peak=   -3.787 closest distance to " NH2AARG A 275 " =    5.457
peak=   -3.779 closest distance to " CG  ASP A 231 " =    0.804
peak=   -3.769 closest distance to " CD1 LEU A 228 " =    2.340
peak=   -3.767 closest distance to " CD1 PHE A  59 " =    1.813
peak=   -3.752 closest distance to " CG  ARG A 269 " =    2.550
peak=   -3.735 closest distance to " CG  PHE A 283 " =    2.840
peak=   -3.732 closest distance to " CE2 PHE A 218 " =    2.486
peak=   -3.730 closest distance to " O   HOH Z 435 " =    2.789
peak=   -3.701 closest distance to " CG2 ILE A 263 " =    2.332
peak=   -3.698 closest distance to " CZ  PHE A  59 " =    1.650
peak=   -3.685 closest distance to " SG ACYS A 201 " =    1.919
peak=   -3.681 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.676 closest distance to " ND2 ASN A  45 " =    1.017
peak=   -3.672 closest distance to " CA  GLY A 203 " =    2.341
peak=   -3.634 closest distance to " C   ASN A 285 " =    2.550
peak=   -3.634 closest distance to " O   HOH Z 313 " =    1.983
peak=   -3.631 closest distance to " O   HOH Z 407 " =    3.217
peak=   -3.622 closest distance to " CD2 PHE A 192 " =    2.086
peak=   -3.617 closest distance to " CD2 LEU A 300 " =    2.908
peak=   -3.608 closest distance to " CE  MET A 105 " =    2.280
peak=   -3.603 closest distance to " C   ALA A 158 " =    1.296
peak=   -3.602 closest distance to " CB  ALA A  43 " =    2.514
peak=   -3.602 closest distance to " CB  ALA A 291 " =    2.378
peak=   -3.598 closest distance to " CG  MET A 105 " =    0.998
peak=   -3.580 closest distance to " OXT GLY A 302 " =    2.869
peak=   -3.577 closest distance to " O   HOH Z  38 " =    1.475
peak=   -3.576 closest distance to " O   GLY A 211 " =    1.521
peak=   -3.565 closest distance to " CB  ASN A  39 " =    2.274
peak=   -3.559 closest distance to " O   HOH Z 351 " =    1.510
peak=   -3.552 closest distance to " O   HOH Z 211 " =    1.658
peak=   -3.549 closest distance to " NH1 ARG A 195 " =    2.597
peak=   -3.542 closest distance to " O   HOH Z 196 " =    2.141
peak=   -3.526 closest distance to " OG BSER A 134 " =    1.746
peak=   -3.524 closest distance to " CD  GLN A  58 " =    1.087
peak=   -3.524 closest distance to " ND2 ASN A 249 " =    2.120
peak=   -3.523 closest distance to " O   HOH Z 292 " =    4.598
peak=   -3.522 closest distance to " O   HOH Z 198 " =    1.439
peak=   -3.518 closest distance to " C   LEU A 143 " =    1.201
peak=   -3.514 closest distance to " NE2 GLN A  88 " =    1.923
peak=   -3.510 closest distance to " CB  TYR A  15 " =    2.172
peak=   -3.505 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.505 closest distance to " O   HOH Z 311 " =    3.649
peak=   -3.505 closest distance to " CG1 VAL A 250 " =    2.610
peak=   -3.501 closest distance to " OD2 ASP A 171 " =    1.772
peak=   -3.492 closest distance to " CZ  TYR A 169 " =    1.729
peak=   -3.491 closest distance to " CA  ASP A 298 " =    1.053
peak=   -3.490 closest distance to " O   HOH Z  11 " =    1.782
peak=   -3.489 closest distance to " CD2 LEU A 143 " =    2.690
peak=   -3.487 closest distance to " CD1 LEU A 101 " =    2.426
peak=   -3.482 closest distance to " N   SER A 212 " =    1.987
peak=   -3.469 closest distance to " OD1 ASP A 191 " =    1.751
peak=   -3.463 closest distance to " NH2BARG A 275 " =    1.892
peak=   -3.461 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.456 closest distance to " CD  ARG A 195 " =    5.201
peak=   -3.443 closest distance to " O   HOH Z  13 " =    1.648
peak=   -3.439 closest distance to " O   HOH Z  73 " =    2.209
peak=   -3.439 closest distance to " CB  PRO A 163 " =    2.535
peak=   -3.439 closest distance to " CA  GLY A 241 " =    3.073
peak=   -3.430 closest distance to " CA  VAL A  67 " =    2.636
peak=   -3.422 closest distance to " O   HOH Z   6 " =    2.210
peak=   -3.400 closest distance to " C   ILE A 234 " =    1.301
peak=   -3.396 closest distance to " O   HOH Z 243 " =    2.128
peak=   -3.381 closest distance to " CG  TRP A 266 " =    1.824
peak=   -3.380 closest distance to " N   ALA A 226 " =    2.164
peak=   -3.377 closest distance to " OD1 ASN A 187 " =    1.589
peak=   -3.372 closest distance to " O   HOH Z 111 " =    2.196
peak=   -3.367 closest distance to " O   SER A 135 " =    1.487
peak=   -3.360 closest distance to " O   VAL A 189 " =    2.520
peak=   -3.357 closest distance to " CB  CYS A 254 " =    2.303
peak=   -3.355 closest distance to " OE1 GLN A  88 " =    1.222
peak=   -3.354 closest distance to " ND2 ASN A  60 " =    1.443
peak=   -3.346 closest distance to " CA  ASP A  27 " =    2.500
peak=   -3.345 closest distance to " OG  SER A  62 " =    1.668
peak=   -3.344 closest distance to " CB  CYS A 201 " =    2.577
peak=   -3.339 closest distance to " CB  TRP A  85 " =    2.398
peak=   -3.339 closest distance to " O   HOH Z 394 " =    1.474
peak=   -3.337 closest distance to " CD  GLU A 236 " =    1.050
peak=   -3.334 closest distance to " O   GLY A 196 " =    1.109
peak=   -3.329 closest distance to " O   HOH Z 253 " =    3.955
peak=   -3.326 closest distance to " CD2 TYR A 293 " =    2.019
peak=   -3.325 closest distance to " O   PHE A 218 " =    1.597
peak=   -3.323 closest distance to " CB  ALA A 248 " =    1.992
peak=   -3.323 closest distance to " CD2 PHE A  61 " =    2.531
peak=   -3.319 closest distance to " O   HOH Z 281 " =    2.643
peak=   -3.316 closest distance to " OD1 ASP A 191 " =    1.597
peak=   -3.313 closest distance to " CD  LYS A 289 " =    2.452
peak=   -3.311 closest distance to " OD1 ASP A 171 " =    1.593
peak=   -3.305 closest distance to " O   HOH Z  98 " =    2.263
peak=   -3.303 closest distance to " O   HOH Z 317 " =    2.352
peak=   -3.302 closest distance to " O   HOH Z 168 " =    1.863
peak=   -3.296 closest distance to " O   HOH Z  93 " =    2.107
peak=   -3.295 closest distance to " CD2 TYR A 247 " =    2.431
peak=   -3.294 closest distance to " O   HOH Z 426 " =    1.687
peak=   -3.292 closest distance to " NH2 ARG A  79 " =    1.927
peak=   -3.292 closest distance to " O   HOH Z 207 " =    2.218
peak=   -3.291 closest distance to " CE3 TRP A 274 " =    2.442
peak=   -3.282 closest distance to " O   HOH Z 252 " =    4.228
peak=   -3.280 closest distance to " CG  ARG A  66 " =    2.363
peak=   -3.280 closest distance to " O   HOH Z 102 " =    1.639
peak=   -3.279 closest distance to " O   HOH Z 103 " =    1.932
peak=   -3.276 closest distance to " CB  PHE A 208 " =    2.247
peak=   -3.276 closest distance to " CA  GLY A 241 " =    2.284
peak=   -3.275 closest distance to " NH2 ARG A  79 " =    1.558
peak=   -3.274 closest distance to " O   HOH Z 417 " =    2.449
peak=   -3.268 closest distance to " CA  GLY A  98 " =    1.982
peak=   -3.267 closest distance to " CD1 LEU A 297 " =    2.517
peak=   -3.265 closest distance to " O   HOH Z  51 " =    1.688
peak=   -3.262 closest distance to " N   THR A 157 " =    1.554
peak=   -3.261 closest distance to " O   HOH Z 388 " =    2.000
peak=   -3.258 closest distance to " N   GLN A  58 " =    1.681
peak=   -3.256 closest distance to " O   HOH Z 166 " =    1.544
peak=   -3.255 closest distance to " CD1 ILE A 239 " =    2.113
peak=   -3.253 closest distance to " O   MET A  40 " =    2.773
peak=   -3.251 closest distance to " CG1 VAL A 197 " =    2.277
peak=   -3.251 closest distance to " C   LEU A 222 " =    0.733
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.303
peak=   -3.242 closest distance to " O   HOH Z 298 " =    2.590
peak=   -3.241 closest distance to " O   HOH Z 174 " =    2.964
peak=   -3.239 closest distance to " O   HOH Z 350 " =    1.732
peak=   -3.235 closest distance to " CG  PRO A 163 " =    2.471
peak=   -3.233 closest distance to " NH2 ARG A  66 " =    2.103
peak=   -3.230 closest distance to " CG  GLU A  53 " =    1.475
peak=   -3.227 closest distance to " O   LYS A 117 " =    1.736
peak=   -3.225 closest distance to " CB  ASP A 286 " =    2.178
peak=   -3.222 closest distance to " O   HOH Z 324 " =    2.260
peak=   -3.222 closest distance to " O   HOH Z 385 " =    2.104
peak=   -3.220 closest distance to " O   HOH Z 222 " =    1.197
peak=   -3.217 closest distance to " O   HOH Z 393 " =    1.442
peak=   -3.215 closest distance to " O   HOH Z 191 " =    5.620
peak=   -3.210 closest distance to " O   ALA A  34 " =    2.664
peak=   -3.210 closest distance to " OH  TYR A 247 " =    2.104
peak=   -3.207 closest distance to " O   HOH Z 275 " =    1.553
peak=   -3.207 closest distance to " O   HOH Z 322 " =    1.542
peak=   -3.206 closest distance to " O   HOH Z  88 " =    2.256
peak=   -3.201 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.199 closest distance to " O   HOH Z 166 " =    1.890
peak=   -3.197 closest distance to " O   VAL A 174 " =    2.048
peak=   -3.192 closest distance to " CE3 TRP A 150 " =    2.030
peak=   -3.191 closest distance to " CD2 PHE A 225 " =    1.169
peak=   -3.188 closest distance to " NE  ARG A  36 " =    1.965
peak=   -3.185 closest distance to " OG  SER A  87 " =    1.412
peak=   -3.184 closest distance to " CE  MET A  93 " =    1.277
peak=   -3.184 closest distance to " CG1 VAL A 125 " =    2.000
peak=   -3.182 closest distance to " CG2 VAL A 189 " =    2.067
peak=   -3.179 closest distance to " CE BMET A  47 " =    2.217
peak=   -3.178 closest distance to " O   HOH Z 298 " =    1.232
peak=   -3.176 closest distance to " CD1 ILE A 199 " =    2.556
peak=   -3.176 closest distance to " ND2BASN A 224 " =    1.634
peak=   -3.174 closest distance to " CG  GLU A   2 " =    1.846
peak=   -3.172 closest distance to " O   HOH Z  90 " =    1.705
peak=   -3.168 closest distance to " O   HOH Z  76 " =    1.864
peak=   -3.167 closest distance to " O   HOH Z  90 " =    2.982
peak=   -3.165 closest distance to " O   HOH Z 357 " =    2.062
peak=   -3.165 closest distance to " O   TRP A  70 " =    1.530
peak=   -3.162 closest distance to " N   ALA A 248 " =    1.568
peak=   -3.159 closest distance to " O   GLN A 240 " =    2.423
peak=   -3.153 closest distance to " O   HOH Z 380 " =    5.120
peak=   -3.151 closest distance to " CA  SER A 135 " =    1.330
peak=   -3.149 closest distance to " CD2 LEU A 237 " =    2.763
peak=   -3.148 closest distance to " CG  GLU A 277 " =    1.139
peak=   -3.142 closest distance to " CD2 PHE A  59 " =    2.539
peak=   -3.138 closest distance to " C   MET A 188 " =    1.456
peak=   -3.138 closest distance to " CE  LYS A  76 " =    2.696
peak=   -3.137 closest distance to " OH  TYR A 214 " =    1.233
peak=   -3.130 closest distance to " CG  PHE A 283 " =    2.673
peak=   -3.128 closest distance to " C   ALA A   8 " =    1.587
peak=   -3.126 closest distance to " CG  GLN A  88 " =    0.929
peak=   -3.121 closest distance to " CG  ASN A 301 " =    1.945
peak=   -3.101 closest distance to " OG  SER A  26 " =    1.304
peak=   -3.101 closest distance to " O   HOH Z 241 " =    1.407
peak=   -3.101 closest distance to " O   PRO A 198 " =    1.328
peak=   -3.100 closest distance to " O   HOH Z 128 " =    2.508
peak=   -3.099 closest distance to " O   GLY A 203 " =    2.448
peak=   -3.092 closest distance to " O   ALA A 161 " =    1.639
peak=   -3.091 closest distance to " O   HOH Z 234 " =    4.232
peak=   -3.084 closest distance to " O   HOH Z 377 " =    1.421
peak=   -3.082 closest distance to " O   HOH Z  51 " =    1.348
peak=   -3.068 closest distance to " O   HOH Z 414 " =    1.755
peak=   -3.066 closest distance to " O   LEU A 101 " =    2.286
peak=   -3.064 closest distance to " OD1 ASP A 200 " =    1.436
peak=   -3.053 closest distance to " O   HOH Z   6 " =    1.594
peak=   -3.049 closest distance to " O   HOH Z 210 " =    1.169
peak=   -3.049 closest distance to " O   HOH Z 139 " =    2.928
peak=   -3.033 closest distance to " O   HOH Z 323 " =    1.346

================= 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    :  0.3017 0.3068   5.979003e+00   5.994904e+00
   1_bss:  0.2869 0.2935   5.956083e+00   5.966140e+00
   1_xyz:  0.1693 0.1892   5.462839e+00   5.570610e+00
   1_adp:  0.1581 0.1918   5.415824e+00   5.587690e+00
   1_occ:  0.1576 0.1918   5.413368e+00   5.586023e+00
   2_bss:  0.1561 0.1895   5.408625e+00   5.579984e+00
   2_xyz:  0.1208 0.1587   5.188182e+00   5.401583e+00
   2_adp:  0.1135 0.1561   5.145547e+00   5.380669e+00
   2_occ:  0.1134 0.1560   5.145218e+00   5.380689e+00
   3_bss:  0.1135 0.1555   5.144036e+00   5.379008e+00
   3_xyz:  0.1075 0.1547   5.117448e+00   5.371000e+00
   3_adp:  0.1073 0.1537   5.112739e+00   5.364326e+00
   3_occ:  0.1072 0.1537   5.112746e+00   5.364771e+00
   4_bss:  0.1071 0.1537   5.112708e+00   5.364607e+00
   4_xyz:  0.1096 0.1546   5.128924e+00   5.374508e+00
   4_adp:  0.1088 0.1567   5.131936e+00   5.385010e+00
   4_occ:  0.1087 0.1567   5.132055e+00   5.385392e+00
   5_bss:  0.1087 0.1567   5.132168e+00   5.385414e+00
   5_xyz:  0.1082 0.1579   5.133420e+00   5.390732e+00
   5_adp:  0.1083 0.1580   5.133185e+00   5.390821e+00
   5_occ:  0.1082 0.1581   5.133379e+00   5.391247e+00
   5_bss:  0.1081 0.1580   5.133514e+00   5.391298e+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:  0.318  42.596   0.137  -2.943  -0.450  -0.000  -0.000  -0.000
   1_xyz:  0.318  42.596   0.137  -2.943  -0.450  -0.000  -0.000  -0.000
   1_adp:  0.318  42.596   0.137  -2.943  -0.450  -0.000  -0.000  -0.000
   1_occ:  0.318  42.596   0.137  -2.943  -0.450  -0.000  -0.000  -0.000
   2_bss:  0.330  50.534  -1.923  -3.039  -1.676  -0.000  -0.000  -0.000
   2_xyz:  0.330  50.534  -1.923  -3.039  -1.676  -0.000  -0.000  -0.000
   2_adp:  0.330  50.534  -1.923  -3.039  -1.676  -0.000  -0.000  -0.000
   2_occ:  0.330  50.534  -1.923  -3.039  -1.676  -0.000  -0.000  -0.000
   3_bss:  0.324  50.534  -2.183  -2.703  -1.693  -0.000  -0.000  -0.000
   3_xyz:  0.324  50.534  -2.183  -2.703  -1.693  -0.000  -0.000  -0.000
   3_adp:  0.324  50.534  -2.183  -2.703  -1.693  -0.000  -0.000  -0.000
   3_occ:  0.324  50.534  -2.183  -2.703  -1.693  -0.000  -0.000  -0.000
   4_bss:  0.324  50.534  -2.179  -2.475  -1.602  -0.000  -0.000  -0.000
   4_xyz:  0.324  50.534  -2.179  -2.475  -1.602  -0.000  -0.000  -0.000
   4_adp:  0.324  50.534  -2.179  -2.475  -1.602  -0.000  -0.000  -0.000
   4_occ:  0.324  50.534  -2.179  -2.475  -1.602  -0.000  -0.000  -0.000
   5_bss:  0.324  50.534  -2.057  -2.266  -1.458  -0.000  -0.000  -0.000
   5_xyz:  0.324  50.534  -2.057  -2.266  -1.458  -0.000  -0.000  -0.000
   5_adp:  0.324  50.534  -2.057  -2.266  -1.458  -0.000  -0.000  -0.000
   5_occ:  0.324  50.534  -2.057  -2.266  -1.458  -0.000  -0.000  -0.000
   5_bss:  0.324  50.523  -1.860  -2.039  -1.247  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  31.543 0.7439  0.9198    26947.521
   1_bss:  30.267 0.7561  0.9048    23999.077
   1_xyz:  17.648 0.8853  1.0020     9397.128
   1_adp:  18.148 0.8803  0.9991     9698.036
   1_occ:  18.126 0.8804  0.9991     9642.452
   2_bss:  17.948 0.8820  0.9606     9499.371
   2_xyz:  14.264 0.9128  0.9769     6613.729
   2_adp:  13.840 0.9162  0.9765     6279.246
   2_occ:  13.837 0.9163  0.9764     6274.333
   3_bss:  13.817 0.9164  0.9761     6238.806
   3_xyz:  13.591 0.9183  0.9760     6121.884
   3_adp:  13.438 0.9196  0.9729     6052.315
   3_occ:  13.443 0.9196  0.9728     6053.582
   4_bss:  13.443 0.9196  0.9765     6051.826
   4_xyz:  13.596 0.9185  0.9753     6151.535
   4_adp:  13.814 0.9168  0.9689     6258.952
   4_occ:  13.820 0.9167  0.9688     6263.804
   5_bss:  13.825 0.9167  0.9743     6264.921
   5_xyz:  13.932 0.9159  0.9735     6341.482
   5_adp:  13.944 0.9157  0.9674     6340.248
   5_occ:  13.951 0.9157  0.9673     6345.483
   5_bss:  13.955 0.9156  0.9742     6347.073
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6156e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6156e-01
   1_xyz:   1.014  0.007  0.067 14.712  0.004  4.114   5.9211e-02
   1_adp:   1.014  0.007  0.067 14.712  0.004  4.114   5.9211e-02
   1_occ:   1.014  0.007  0.067 14.712  0.004  4.114   5.9211e-02
   2_bss:   1.014  0.007  0.067 14.712  0.004  4.114   5.9211e-02
   2_xyz:   1.067  0.009  0.080 14.729  0.005  4.124   6.8764e-02
   2_adp:   1.067  0.009  0.080 14.729  0.005  4.124   6.8764e-02
   2_occ:   1.067  0.009  0.080 14.729  0.005  4.124   6.8764e-02
   3_bss:   1.067  0.009  0.080 14.729  0.005  4.124   6.8764e-02
   3_xyz:   1.112  0.010  0.084 14.988  0.005  4.127   7.4314e-02
   3_adp:   1.112  0.010  0.084 14.988  0.005  4.127   7.4314e-02
   3_occ:   1.112  0.010  0.084 14.988  0.005  4.127   7.4314e-02
   4_bss:   1.112  0.010  0.084 14.988  0.005  4.127   7.4314e-02
   4_xyz:   0.979  0.007  0.074 14.591  0.004  4.126   5.8057e-02
   4_adp:   0.979  0.007  0.074 14.591  0.004  4.126   5.8057e-02
   4_occ:   0.979  0.007  0.074 14.591  0.004  4.126   5.8057e-02
   5_bss:   0.979  0.007  0.074 14.591  0.004  4.126   5.8057e-02
   5_xyz:   0.985  0.007  0.075 14.568  0.004  4.127   5.8001e-02
   5_adp:   0.985  0.007  0.075 14.568  0.004  4.127   5.8001e-02
   5_occ:   0.985  0.007  0.075 14.568  0.004  4.127   5.8001e-02
   5_bss:   0.985  0.007  0.075 14.568  0.004  4.127   5.8001e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4132e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4132e-01
   1_xyz:   8.693  0.036  0.282 84.070  0.036  2.327   8.0159e-02
   1_adp:   8.693  0.036  0.282 84.070  0.036  2.327   8.0159e-02
   1_occ:   8.693  0.036  0.282 84.070  0.036  2.327   8.0159e-02
   2_bss:   8.693  0.036  0.282 84.070  0.036  2.327   8.0159e-02
   2_xyz:   7.146  0.044  0.249 83.682  0.039  2.298   7.6383e-02
   2_adp:   7.146  0.044  0.249 83.682  0.039  2.298   7.6383e-02
   2_occ:   7.146  0.044  0.249 83.682  0.039  2.298   7.6383e-02
   3_bss:   7.146  0.044  0.249 83.682  0.039  2.298   7.6383e-02
   3_xyz:   7.208  0.046  0.275 82.843  0.042  2.277   6.2706e-02
   3_adp:   7.208  0.046  0.275 82.843  0.042  2.277   6.2706e-02
   3_occ:   7.208  0.046  0.275 82.843  0.042  2.277   6.2706e-02
   4_bss:   7.208  0.046  0.275 82.843  0.042  2.277   6.2706e-02
   4_xyz:   7.324  0.041  0.226 83.629  0.038  2.354   4.0198e-02
   4_adp:   7.324  0.041  0.226 83.629  0.038  2.354   4.0198e-02
   4_occ:   7.324  0.041  0.226 83.629  0.038  2.354   4.0198e-02
   5_bss:   7.324  0.041  0.226 83.629  0.038  2.354   4.0198e-02
   5_xyz:   7.338  0.039  0.228 83.255  0.037  2.325   3.8517e-02
   5_adp:   7.338  0.039  0.228 83.255  0.037  2.325   3.8517e-02
   5_occ:   7.338  0.039  0.228 83.255  0.037  2.325   3.8517e-02
   5_bss:   7.338  0.039  0.228 83.255  0.037  2.325   3.8517e-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:  82.46   0.00  16.48  82.46   0.00  12.64  62.81   5.35  37.33
   1_occ:  82.46   0.00  16.48  82.46   0.00  12.64  62.81   5.35  37.33
   2_bss:  82.46   0.00  16.48  82.46   0.00  12.64  62.81   5.35  37.33
   2_xyz:  82.46   0.00  16.48  82.46   0.00  12.64  62.81   5.35  37.33
   2_adp:  78.67   1.39  17.05  78.67   1.39  13.01  71.24   2.06  39.04
   2_occ:  78.67   1.39  17.05  78.67   1.39  13.01  71.24   2.06  39.04
   3_bss:  78.67   1.39  17.05  78.67   1.39  13.01  71.24   2.06  39.04
   3_xyz:  78.67   1.39  17.05  78.67   1.39  13.01  71.24   2.06  39.04
   3_adp:  78.85   1.75  16.88  78.85   1.75  12.91  71.49   2.43  38.48
   3_occ:  78.85   1.75  16.88  78.85   1.75  12.91  71.49   2.43  38.48
   4_bss:  78.85   1.75  16.88  78.85   1.75  12.91  71.49   2.43  38.48
   4_xyz:  78.85   1.75  16.88  78.85   1.75  12.91  71.49   2.43  38.48
   4_adp:  89.13   0.48  17.07  89.13   0.48  12.93  77.49   3.15  39.62
   4_occ:  89.13   0.48  17.07  89.13   0.48  12.93  77.49   3.15  39.62
   5_bss:  89.13   0.48  17.07  89.13   0.48  12.93  77.49   3.15  39.62
   5_xyz:  89.13   0.48  17.07  89.13   0.48  12.93  77.49   3.15  39.62
   5_adp:  89.72   0.37  16.90  89.72   0.37  12.76  77.69   4.79  39.44
   5_occ:  89.72   0.37  16.90  89.72   0.37  12.76  77.69   4.79  39.44
   5_bss:  89.71   0.36  16.89  89.71   0.36  12.75  77.68   4.78  39.43
------------------------------------------------------------------------
 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:    1.247    0.008    0.273
   1_adp:    1.247    0.008    0.273
   1_occ:    1.247    0.008    0.273
   2_bss:    1.247    0.008    0.273
   2_xyz:    0.790    0.032    0.330
   2_adp:    0.790    0.032    0.330
   2_occ:    0.790    0.032    0.330
   3_bss:    0.790    0.032    0.330
   3_xyz:    0.823    0.028    0.344
   3_adp:    0.823    0.028    0.344
   3_occ:    0.823    0.028    0.344
   4_bss:    0.823    0.028    0.344
   4_xyz:    0.875    0.031    0.349
   4_adp:    0.875    0.031    0.349
   4_occ:    0.875    0.031    0.349
   5_bss:    0.875    0.031    0.349
   5_xyz:    0.989    0.030    0.354
   5_adp:    0.989    0.030    0.354
   5_occ:    0.989    0.030    0.354
   5_bss:    0.989    0.030    0.354
------------------------------------------------------------------------

CPU time actual refinement: 317.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/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_1026/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1026/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 317.60 
  Macro-tasks:
    bulk solvent and scale       = 38.25  
    individual site refinement   = 125.36 
    weights calculation          = 28.33  
    collect and process          = 6.44   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 198.48 
  Micro-tasks:
    mask                            = 1.15   
    f_calc                          = 101.12 
    alpha_beta                      = 8.32   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.37 
    fmodel                         = 6.22   
    r_factors                      = 0.21   
    phase_errors                   = 10.91  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 238.71 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.558 micro seconds
Total CPU time: 5.52 minutes
from_scatterers_fft:    652 calls, 100.82 s
gradients_fft:          597 calls,  96.34 s

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

# Date 2008-01-16 Time 06:14:45 PST -0800 (1200492885.33 s)
Start R-work = 0.3017, R-free = 0.3068 (no bulk solvent and anisotropic scale)
Final R-work = 0.1315, R-free = 0.1766 (no bulk solvent and anisotropic scale)

Start R-work = 0.2869, R-free = 0.2935
Final R-work = 0.1081, R-free = 0.1580