# Date 2008-01-16 Time 05:52:55 PST -0800 (1200491575.24 s)
#phil __OFF__

Command line arguments: "../916.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17410
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 916

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 47.1647, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98117
Completeness in resolution range: 0.954676
Completeness with d_max=infinity: 0.951754

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0608
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0608 1.98117
Completeness in resolution range: 0.954676
Completeness with d_max=infinity: 0.951754

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0612 -  4.2395 [2153/2181]  1941   212   9.8%
  bin  2:  4.2395 -  3.3775 [2061/2077]  1852   209  10.1%
  bin  3:  3.3775 -  2.9543 [2048/2067]  1843   205  10.0%
  bin  4:  2.9543 -  2.6858 [2033/2063]  1833   200   9.8%
  bin  5:  2.6858 -  2.4942 [2018/2037]  1818   200   9.9%
  bin  6:  2.4942 -  2.3477 [2006/2042]  1798   208  10.4%
  bin  7:  2.3477 -  2.2306 [1972/2005]  1775   197  10.0%
  bin  8:  2.2306 -  2.1337 [1996/2030]  1798   198   9.9%
  bin  9:  2.1337 -  2.0518 [1977/2005]  1780   197  10.0%
  bin 10:  2.0518 -  1.9812 [1325/2012]  1192   133  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/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: 15
        2.42 -     3.04: 2191
        3.04 -     3.66: 4663
        3.66 -     4.28: 9002
        4.28 -     4.90: 12347
  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 "  1.983 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.158 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28213 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_916/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 47.16465 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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2903   r_free= 0.2919   ksol= 0.00   Bsol= 0.00   scale= 0.984    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.938832                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7287 0.99   1390  155 0.2679 0.2675      6.3028      6.2597|
|  2:  4.7287 -  3.7727 0.99   1361  147 0.2151 0.2169      6.2739      6.2522|
|  3:  3.7727 -  3.3016 0.99   1315  151 0.2445 0.2348      6.1829      6.2618|
|  4:  3.3016 -  3.0023 0.99   1317  148 0.2606 0.2749      6.0888      6.0884|
|  5:  3.0023 -  2.7886 0.99   1310  142 0.2812 0.2766      5.9596      5.9973|
|  6:  2.7886 -  2.6251 0.99   1286  146 0.3086 0.3004      5.9238      5.9018|
|  7:  2.6251 -  2.4942 0.99   1308  137 0.3080 0.2600      5.9193      5.8144|
|  8:  2.4942 -  2.3861 0.98   1275  151 0.3299 0.3440      5.8667      5.9176|
|  9:  2.3861 -  2.2946 0.98   1276  144 0.3232 0.3281      5.8313      5.8227|
| 10:  2.2946 -  2.2156 0.98   1288  132 0.3319 0.3890      5.8155      5.9319|
| 11:  2.2156 -  2.1466 1.00   1277  146 0.3408 0.3652      5.7764      5.8553|
| 12:  2.1466 -  2.0854 0.97   1263  140 0.3470 0.3506      5.7376      5.7712|
| 13:  2.0854 -  2.0306 0.98   1271  140 0.3438 0.3272      5.6411      5.5377|
| 14:  2.0306 -  1.9812 0.54    693   80 0.3474 0.3553      5.6002      5.5992|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7287  1390   155  0.81  24.18   0.87     0.82      37093.93|
|  2:  4.7287 -  3.7727  1361   147  0.86  19.71   0.99     0.92      35710.81|
|  3:  3.7727 -  3.3016  1315   151  0.84  22.77   1.00     0.97      33559.61|
|  4:  3.3016 -  3.0023  1317   148  0.82  24.73   1.01     0.96      29698.13|
|  5:  3.0023 -  2.7886  1310   142  0.77  28.84   1.00     0.94      25095.62|
|  6:  2.7886 -  2.6251  1286   146  0.77  29.10   1.03     0.95      21192.13|
|  7:  2.6251 -  2.4942  1308   137  0.78  28.12   1.01     0.96      18943.73|
|  8:  2.4942 -  2.3861  1275   151  0.75  31.11   1.02     0.96      19092.67|
|  9:  2.3861 -  2.2946  1276   144  0.74  32.00   1.05     0.94      18959.40|
| 10:  2.2946 -  2.2156  1288   132  0.71  34.56   1.06     0.94      19920.97|
| 11:  2.2156 -  2.1466  1277   146  0.71  34.66   1.07     0.95      18526.72|
| 12:  2.1466 -  2.0854  1263   140  0.71  34.65   1.06     0.99      17315.88|
| 13:  2.0854 -  2.0306  1271   140  0.71  34.67   1.04     0.97      14037.01|
| 14:  2.0306 -  1.9812   693    80  0.73  33.27   1.06     0.92      11229.64|
|alpha:            min =        0.82 max =            0.99 mean =         0.94|
|beta:             min =    11229.64 max =        37093.93 mean =     23463.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.77|
|phase err.(work): min =        0.00 max =           89.93 mean =        29.22|
|phase err.(test): min =        0.00 max =           89.86 mean =        28.91|
|-----------------------------------------------------------------------------|

============================== 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 = 2.332827              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.088   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559056              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.291   (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:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      186 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2005 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1839 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2824 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4641 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4361 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5606 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6741 |
|-----------------------------------------------------------------------------|
|-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 = 11.988)------------------------------------------|
|    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 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2903   r_free= 0.2919   ksol= 0.00   Bsol= 0.00   scale= 0.984    |
|                                                                             |
| 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:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.938832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2767   r_free= 0.2786   ksol= 0.30   Bsol= 50.00   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-1.83,-0.55,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.916381                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.047304              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.271   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.277501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.109   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2767      final r-factor (work) = 0.1730          |
| start r-factor (free) = 0.2786      final r-factor (free) = 0.1915          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2327 = 2.05 * 0.50 * 5.9308 + 1.00 * 0.1616                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8370 = 2.05 * 0.50 * 5.6485 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1730      final r-factor (work) = 0.1615          |
| start r-factor (free) = 0.1915      final r-factor (free) = 0.1948          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5740 = 0.28 * 1.00 * 5.6485 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5657 = 0.28 * 1.00 * 5.4281 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.36   16.46    None  None   None       |
|    all(noH): 2823   0      0.00    84.36   16.46    None  None   None       |
|    Sol.    : 438    0      6.11    62.92   37.21    None  None   None       |
|    Mac.    : 2385   0      0.00    84.36   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 -   8.436:  560   |   5:    42.180 -  50.616:  103        |
|      1:     8.436 -  16.872: 1467   |   6:    50.616 -  59.052:   66        |
|      2:    16.872 -  25.308:  328   |   7:    59.052 -  67.488:   10        |
|      3:    25.308 -  33.744:  159   |   8:    67.488 -  75.924:    0        |
|      4:    33.744 -  42.180:  129   |   9:    75.924 -  84.360:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1615 r_free = 0.1948             target_work(ml) = 5.435         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1610 r_free = 0.1948             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1610   r_free= 0.1948   ksol= 0.30   Bsol= 50.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-1.83,-0.55,-0.00,-0.00,-0.00); trace/3= -1.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.433001                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1606   r_free= 0.1933   ksol= 0.33   Bsol= 53.86   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.49,-1.68,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.433059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.969713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398305              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.914   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1606      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1933      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1322 = 2.97 * 0.50 * 5.4397 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9415 = 2.97 * 0.50 * 5.3054 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1447 = 0.40 * 1.00 * 5.3054 + 1.00 * 0.0316                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0649 = 0.40 * 1.00 * 5.1634 + 1.00 * 0.0083                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    81.09   16.99    None  None   None       |
|    all(noH): 2823   0      1.74    81.09   16.99    None  None   None       |
|    Sol.    : 438    0      3.41    68.88   38.95    None  None   None       |
|    Mac.    : 2385   0      1.74    81.09   12.96    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:     1.737 -   9.672:  910   |   5:    41.411 -  49.346:  111        |
|      1:     9.672 -  17.607: 1150   |   6:    49.346 -  57.281:   79        |
|      2:    17.607 -  25.541:  269   |   7:    57.281 -  65.216:   48        |
|      3:    25.541 -  33.476:  133   |   8:    65.216 -  73.151:   11        |
|      4:    33.476 -  41.411:  110   |   9:    73.151 -  81.086:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1553             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1551             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1551   ksol= 0.33   Bsol= 53.86   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.54,-2.49,-1.68,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152876                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1548   ksol= 0.33   Bsol= 53.86   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.30,-1.61,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.154057                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.704832              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.754  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.222  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1548      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4657 = 1.70 * 0.50 * 5.1641 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4386 = 1.70 * 0.50 * 5.1440 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4016 = 0.27 * 1.00 * 5.1440 + 1.00 * 0.0083                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3999 = 0.27 * 1.00 * 5.1387 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    82.66   16.78    None  None   None       |
|    all(noH): 2823   0      1.42    82.66   16.78    None  None   None       |
|    Sol.    : 438    0      2.20    69.57   38.29    None  None   None       |
|    Mac.    : 2385   0      1.42    82.66   12.83    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:     1.422 -   9.546:  904   |   5:    42.043 -  50.167:  105        |
|      1:     9.546 -  17.670: 1174   |   6:    50.167 -  58.291:   71        |
|      2:    17.670 -  25.794:  265   |   7:    58.291 -  66.416:   35        |
|      3:    25.794 -  33.919:  136   |   8:    66.416 -  74.540:    6        |
|      4:    33.919 -  42.043:  122   |   9:    74.540 -  82.664:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1543             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1542             target_work(ml) = 5.139         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1542   ksol= 0.33   Bsol= 53.86   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.40,-2.30,-1.61,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138602                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1542   ksol= 0.33   Bsol= 53.86   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.17,-1.55,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.762949              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.241  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287738              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1528 = 2.76 * 0.50 * 5.1387 + 1.00 * 0.0538                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1420 = 2.76 * 0.50 * 5.1202 + 1.00 * 0.0687                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1069          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4812 = 0.29 * 1.00 * 5.1202 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4799 = 0.29 * 1.00 * 5.1154 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    82.83   16.64    None  None   None       |
|    all(noH): 2823   0      1.18    82.83   16.64    None  None   None       |
|    Sol.    : 438    0      3.42    69.67   38.14    None  None   None       |
|    Mac.    : 2385   0      1.18    82.83   12.69    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:     1.184 -   9.349:  891   |   5:    42.010 -  50.175:  104        |
|      1:     9.349 -  17.515: 1184   |   6:    50.175 -  58.340:   73        |
|      2:    17.515 -  25.680:  271   |   7:    58.340 -  66.505:   33        |
|      3:    25.680 -  33.845:  133   |   8:    66.505 -  74.670:    5        |
|      4:    33.845 -  42.010:  124   |   9:    74.670 -  82.835:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1069 r_free = 0.1545             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1547             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1547   ksol= 0.33   Bsol= 53.86   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,-2.17,-1.55,-0.00,-0.00,-0.00); trace/3= -2.02                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115804                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1547   ksol= 0.33   Bsol= 53.86   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.01,-1.38,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.115884                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.462040              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.209  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.171053              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.545  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8086 = 1.46 * 0.50 * 5.1160 + 1.00 * 0.0687                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8028 = 1.46 * 0.50 * 5.1308 + 1.00 * 0.0521                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1557      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8856 = 0.17 * 1.00 * 5.1308 + 1.00 * 0.0080                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8866 = 0.17 * 1.00 * 5.1396 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.26    82.33   16.43    None  None   None       |
|    all(noH): 2823   0      1.26    82.33   16.43    None  None   None       |
|    Sol.    : 438    0      5.16    69.39   37.48    None  None   None       |
|    Mac.    : 2385   0      1.26    82.33   12.57    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:     1.257 -   9.365:  917   |   5:    41.793 -  49.901:  100        |
|      1:     9.365 -  17.472: 1170   |   6:    49.901 -  58.008:   73        |
|      2:    17.472 -  25.579:  266   |   7:    58.008 -  66.115:   25        |
|      3:    25.579 -  33.686:  134   |   8:    66.115 -  74.222:    6        |
|      4:    33.686 -  41.793:  127   |   9:    74.222 -  82.329:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1554             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1554             target_work(ml) = 5.138         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1554   ksol= 0.33   Bsol= 53.86   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.01,-1.38,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138476                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7287 0.99   1390  155 0.1005 0.1261      5.3822      5.5055|
|  2:  4.7287 -  3.7727 0.99   1361  147 0.0871 0.1073      5.4393      5.6108|
|  3:  3.7727 -  3.3016 0.99   1315  151 0.1048 0.1508      5.4604       5.858|
|  4:  3.3016 -  3.0023 0.99   1317  148 0.1193 0.1484      5.4478      5.5585|
|  5:  3.0023 -  2.7886 0.99   1310  142 0.1308 0.1778       5.321      5.5574|
|  6:  2.7886 -  2.6251 0.99   1286  146 0.1209 0.1808       5.199       5.439|
|  7:  2.6251 -  2.4942 0.99   1308  137 0.1226 0.1614      5.1549       5.356|
|  8:  2.4942 -  2.3861 0.98   1275  151 0.1137 0.1727      5.0446      5.3112|
|  9:  2.3861 -  2.2946 0.98   1276  144 0.1165 0.1795      5.0227      5.3046|
| 10:  2.2946 -  2.2156 0.98   1288  132 0.1115 0.1702      4.9454      5.2033|
| 11:  2.2156 -  2.1466 1.00   1277  146 0.1147 0.1729      4.9348      5.2684|
| 12:  2.1466 -  2.0854 0.97   1263  140 0.1066 0.1596      4.8536      5.0818|
| 13:  2.0854 -  2.0306 0.98   1271  140 0.1153 0.1727      4.7844      5.0666|
| 14:  2.0306 -  1.9812 0.54    693   80 0.1054 0.1641      4.6602       4.892|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7287  1390   155  0.94   8.88   0.98     0.95       6793.63|
|  2:  4.7287 -  3.7727  1361   147  0.95   7.71   1.01     0.99       8583.62|
|  3:  3.7727 -  3.3016  1315   151  0.94  11.14   1.02     1.01      10070.19|
|  4:  3.3016 -  3.0023  1317   148  0.92  13.66   1.00     0.98      10319.51|
|  5:  3.0023 -  2.7886  1310   142  0.90  15.87   0.99     0.96       8191.14|
|  6:  2.7886 -  2.6251  1286   146  0.90  15.68   0.98     0.96       6891.14|
|  7:  2.6251 -  2.4942  1308   137  0.91  15.07   0.99     0.96       5965.37|
|  8:  2.4942 -  2.3861  1275   151  0.91  14.88   0.99     0.97       5121.56|
|  9:  2.3861 -  2.2946  1276   144  0.91  14.99   1.00     0.97       4820.87|
| 10:  2.2946 -  2.2156  1288   132  0.91  15.13   0.99     0.95       4150.85|
| 11:  2.2156 -  2.1466  1277   146  0.90  15.90   0.99     0.96       4248.15|
| 12:  2.1466 -  2.0854  1263   140  0.92  14.38   1.00     0.98       3787.58|
| 13:  2.0854 -  2.0306  1271   140  0.90  16.33   0.99     0.99       3294.54|
| 14:  2.0306 -  1.9812   693    80  0.92  14.44   0.97     0.94       2489.07|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2489.07 max =        10319.51 mean =      6211.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.30|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1554   ksol= 0.33   Bsol= 53.81   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.93,-1.29,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.06 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1554   ksol= 0.33   Bsol= 53.81   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.11,-1.93,-1.29,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.138505                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0612 -  4.7287 0.99   1390  155 0.1005 0.1261      5.3824      5.5057|
|  2:  4.7287 -  3.7727 0.99   1361  147 0.0871 0.1073      5.4393      5.6107|
|  3:  3.7727 -  3.3016 0.99   1315  151 0.1048 0.1508      5.4603      5.8578|
|  4:  3.3016 -  3.0023 0.99   1317  148 0.1193 0.1484      5.4478      5.5585|
|  5:  3.0023 -  2.7886 0.99   1310  142 0.1308 0.1778      5.3211      5.5575|
|  6:  2.7886 -  2.6251 0.99   1286  146 0.1210 0.1807       5.199      5.4388|
|  7:  2.6251 -  2.4942 0.99   1308  137 0.1226 0.1614      5.1548      5.3559|
|  8:  2.4942 -  2.3861 0.98   1275  151 0.1137 0.1727      5.0446      5.3112|
|  9:  2.3861 -  2.2946 0.98   1276  144 0.1165 0.1795      5.0227      5.3045|
| 10:  2.2946 -  2.2156 0.98   1288  132 0.1115 0.1702      4.9455      5.2035|
| 11:  2.2156 -  2.1466 1.00   1277  146 0.1147 0.1730      4.9349      5.2686|
| 12:  2.1466 -  2.0854 0.97   1263  140 0.1066 0.1596      4.8538       5.082|
| 13:  2.0854 -  2.0306 0.98   1271  140 0.1154 0.1727      4.7845      5.0667|
| 14:  2.0306 -  1.9812 0.54    693   80 0.1054 0.1641      4.6602      4.8919|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0612 -  4.7287  1390   155  0.94   8.89   0.98     0.95       6795.69|
|  2:  4.7287 -  3.7727  1361   147  0.95   7.71   1.01     0.99       8583.71|
|  3:  3.7727 -  3.3016  1315   151  0.94  11.14   1.02     1.01      10067.09|
|  4:  3.3016 -  3.0023  1317   148  0.92  13.66   1.00     0.98      10319.90|
|  5:  3.0023 -  2.7886  1310   142  0.90  15.87   0.99     0.96       8190.73|
|  6:  2.7886 -  2.6251  1286   146  0.90  15.68   0.98     0.96       6891.21|
|  7:  2.6251 -  2.4942  1308   137  0.91  15.07   0.99     0.96       5964.27|
|  8:  2.4942 -  2.3861  1275   151  0.91  14.88   0.99     0.98       5121.28|
|  9:  2.3861 -  2.2946  1276   144  0.91  14.99   1.00     0.97       4820.03|
| 10:  2.2946 -  2.2156  1288   132  0.91  15.13   0.99     0.95       4151.31|
| 11:  2.2156 -  2.1466  1277   146  0.90  15.91   1.00     0.96       4248.81|
| 12:  2.1466 -  2.0854  1263   140  0.92  14.38   1.00     0.99       3789.02|
| 13:  2.0854 -  2.0306  1271   140  0.90  16.33   0.99     0.99       3294.99|
| 14:  2.0306 -  1.9812   693    80  0.92  14.44   0.98     0.94       2489.09|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2489.09 max =        10319.90 mean =      6211.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.30|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.988)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    82.29   16.39    None  None   None       |
|    all(noH): 2823   0      1.21    82.29   16.39    None  None   None       |
|    Sol.    : 438    0      5.11    69.35   37.44    None  None   None       |
|    Mac.    : 2385   0      1.21    82.29   12.52    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:     1.213 -   9.320:  917   |   5:    41.749 -  49.856:  100        |
|      1:     9.320 -  17.428: 1170   |   6:    49.856 -  57.964:   73        |
|      2:    17.428 -  25.535:  266   |   7:    57.964 -  66.071:   25        |
|      3:    25.535 -  33.642:  134   |   8:    66.071 -  74.178:    6        |
|      4:    33.642 -  41.749:  127   |   9:    74.178 -  82.285:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 311         
Filter by distance & map next to the model:
   mapped sites are within: 0.613 - 4.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 311
   mapped sites are within: 0.715 - 4.626

peak=    5.908 closest distance to " NH2 ARG A  56 " =    2.257
peak=    5.845 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.540 closest distance to " CG  PRO A  54 " =    1.290
peak=    5.291 closest distance to " O   HOH Z 126 " =    1.872
peak=    5.252 closest distance to " CB  SER A  63 " =    1.216
peak=    5.155 closest distance to " CB  ARG A 275 " =    0.893
peak=    4.964 closest distance to " CB  PRO A  54 " =    0.937
peak=    4.926 closest distance to " O   HOH Z 232 " =    2.263
peak=    4.899 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.729 closest distance to " O   HOH Z 298 " =    1.937
peak=    4.719 closest distance to " C   PRO A 198 " =    1.535
peak=    4.660 closest distance to " CG  PRO A  90 " =    1.163
peak=    4.622 closest distance to " O   HOH Z 236 " =    1.940
peak=    4.609 closest distance to " CB  LEU A 228 " =    1.046
peak=    4.572 closest distance to " CB  GLU A 128 " =    1.055
peak=    4.542 closest distance to " CA  TYR A  30 " =    0.927
peak=    4.534 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.504 closest distance to " CB  TYR A 169 " =    0.761
peak=    4.503 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.478 closest distance to " CG  PRO A 243 " =    1.094
peak=    4.471 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.420 closest distance to " CB  ASN A 148 " =    1.460
peak=    4.351 closest distance to " O   HOH Z 234 " =    3.796
peak=    4.289 closest distance to " OD1 ASN A  69 " =    2.550
peak=    4.276 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.273 closest distance to " O   HOH Z 369 " =    2.051
peak=    4.256 closest distance to " O   HOH Z  78 " =    1.630
peak=    4.252 closest distance to " ND2 ASN A 187 " =    1.520
peak=    4.246 closest distance to " O   HOH Z 193 " =    1.916
peak=    4.228 closest distance to " CB  ASN A 187 " =    1.084
peak=    4.218 closest distance to " O   HOH Z  15 " =    2.160
peak=    4.165 closest distance to " CB  SER A   3 " =    1.360
peak=    4.142 closest distance to " CD1 LEU A 300 " =    1.212
peak=    4.142 closest distance to " CA  PRO A  54 " =    1.331
peak=    4.138 closest distance to " O   HOH Z 142 " =    1.608
peak=    4.092 closest distance to " CB  ARG A 190 " =    1.682
peak=    4.073 closest distance to " NH2 ARG A 156 " =    1.185
peak=    4.067 closest distance to " CA  ALA A  21 " =    1.203
peak=    4.061 closest distance to " CZ  PHE A 218 " =    1.067
peak=    4.054 closest distance to " O   HOH Z 427 " =    3.039
peak=    3.990 closest distance to " CB  TRP A 266 " =    0.931
peak=    3.990 closest distance to " CB  VAL A 265 " =    1.234
peak=    3.988 closest distance to " O   HOH Z 368 " =    1.983
peak=    3.986 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.976 closest distance to " O   HOH Z 303 " =    2.039
peak=    3.937 closest distance to " O   HOH Z 158 " =    2.979
peak=    3.936 closest distance to " CG2 VAL A 257 " =    0.975
peak=    3.926 closest distance to " CB  ARG A  79 " =    1.355
peak=    3.921 closest distance to " CA  THR A 264 " =    0.867
peak=    3.911 closest distance to " CA  THR A 221 " =    0.961
peak=    3.894 closest distance to " O   HOH Z  21 " =    1.748
peak=    3.894 closest distance to " O   HOH Z 316 " =    3.125
peak=    3.886 closest distance to " O   HOH Z 261 " =    2.063
peak=    3.879 closest distance to " O   HOH Z 403 " =    1.697
peak=    3.872 closest distance to " O   HOH Z  40 " =    1.759
peak=    3.866 closest distance to " NH1AARG A 145 " =    1.145
peak=    3.863 closest distance to " CA  ASN A 215 " =    1.167
peak=    3.862 closest distance to " CB  SER A 216 " =    0.789
peak=    3.853 closest distance to " CB  GLU A 277 " =    3.609
peak=    3.847 closest distance to " OD2 ASP A 286 " =    2.910
peak=    3.846 closest distance to " O   HOH Z 344 " =    3.152
peak=    3.835 closest distance to " O   HOH Z 272 " =    1.846
peak=    3.828 closest distance to " ND2 ASN A 110 " =    1.791
peak=    3.821 closest distance to " CB  TYR A 169 " =    0.757
peak=    3.813 closest distance to " O   HOH Z 250 " =    1.452
peak=    3.812 closest distance to " O   HOH Z  66 " =    2.207
peak=    3.811 closest distance to " CG1 ILE A  33 " =    1.287
peak=    3.794 closest distance to " CD  ARG A 269 " =    0.957
peak=    3.792 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.792 closest distance to " O   HOH Z 346 " =    1.687
peak=    3.787 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.786 closest distance to " O   HOH Z 389 " =    1.940
peak=    3.776 closest distance to " O   HOH Z 135 " =    1.631
peak=    3.767 closest distance to " O   HOH Z 209 " =    2.242
peak=    3.763 closest distance to " O   HOH Z 352 " =    1.894
peak=    3.763 closest distance to " O   HOH Z 189 " =    2.420
peak=    3.729 closest distance to " CB  ASP A 140 " =    0.829
peak=    3.720 closest distance to " O   HOH Z 214 " =    2.034
peak=    3.716 closest distance to " CB  ASN A  39 " =    0.881
peak=    3.712 closest distance to " O   HOH Z 132 " =    2.578
peak=    3.712 closest distance to " NZ  LYS A 117 " =    3.225
peak=    3.707 closest distance to " CA  ALA A  51 " =    0.892
peak=    3.691 closest distance to " CB  TRP A 179 " =    1.330
peak=    3.690 closest distance to " O   HOH Z 423 " =    1.877
peak=    3.684 closest distance to " CB  LEU A 143 " =    1.102
peak=    3.684 closest distance to " O   HOH Z  43 " =    1.851
peak=    3.679 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.679 closest distance to " CA  MET A  40 " =    1.113
peak=    3.674 closest distance to " CG2 ILE A 120 " =    1.115
peak=    3.673 closest distance to " O   TRP A 274 " =    1.871
peak=    3.667 closest distance to " O   MET A 105 " =    1.796
peak=    3.667 closest distance to " CG2 THR A 221 " =    1.000
peak=    3.664 closest distance to " O   HOH Z 368 " =    3.619
peak=    3.664 closest distance to " O   HOH Z 108 " =    2.582
peak=    3.656 closest distance to " CA  ARG A 195 " =    1.205
peak=    3.653 closest distance to " O   HOH Z 147 " =    1.746
peak=    3.651 closest distance to " O   HOH Z 213 " =    1.716
peak=    3.648 closest distance to " CD1 ILE A 106 " =    0.863
peak=    3.647 closest distance to " CG1BVAL A  72 " =    1.625
peak=    3.641 closest distance to " CA  ARG A  36 " =    1.136
peak=    3.641 closest distance to " CA  SER A  87 " =    0.998
peak=    3.638 closest distance to " O   SER A  87 " =    2.229
peak=    3.635 closest distance to " CB  SER A 212 " =    1.150
peak=    3.634 closest distance to " O   HOH Z 197 " =    3.029
peak=    3.624 closest distance to " O   HOH Z 295 " =    1.460
peak=    3.621 closest distance to " O   HOH Z  44 " =    1.762
peak=    3.615 closest distance to " CZ  PHE A 192 " =    0.955
peak=    3.613 closest distance to " CB  ILE A 120 " =    1.200
peak=    3.611 closest distance to " N   ARG A 156 " =    1.381
peak=    3.606 closest distance to " NH2BARG A 145 " =    2.106
peak=    3.605 closest distance to " O   HOH Z  88 " =    3.423
peak=    3.603 closest distance to " O   HOH Z  97 " =    1.976
peak=    3.599 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.597 closest distance to " O   HOH Z  54 " =    1.655
peak=    3.591 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.589 closest distance to " CB  ALA A 291 " =    1.282
peak=    3.585 closest distance to " O   HOH Z 280 " =    2.991
peak=    3.581 closest distance to " CD2 LEU A 297 " =    0.869
peak=    3.578 closest distance to " ND1 HIS A  81 " =    1.669
peak=    3.577 closest distance to " O   HOH Z 426 " =    1.566
peak=    3.571 closest distance to " CD  ARG A  66 " =    2.479
peak=    3.565 closest distance to " CG2BVAL A  41 " =    0.855
peak=    3.564 closest distance to " O   HOH Z 193 " =    1.681
peak=    3.561 closest distance to " CD  LYS A 166 " =    1.272
peak=    3.552 closest distance to " CA  ASP A 140 " =    1.166
peak=    3.544 closest distance to " O   HOH Z 245 " =    1.353
peak=    3.543 closest distance to " CG  LEU A 167 " =    1.213
peak=    3.540 closest distance to " O   HOH Z   1 " =    2.136
peak=    3.532 closest distance to " O   HOH Z 193 " =    2.060
peak=    3.495 closest distance to " O   HOH Z 411 " =    3.740
peak=    3.491 closest distance to " O   HOH Z 305 " =    3.698
peak=    3.488 closest distance to " O   HOH Z  93 " =    2.710
peak=    3.485 closest distance to " CB  MET A  47 " =    0.994
peak=    3.482 closest distance to " CA  ILE A  33 " =    1.503
peak=    3.480 closest distance to " CB  MET A  40 " =    0.847
peak=    3.479 closest distance to " CA  ASP A 191 " =    0.727
peak=    3.479 closest distance to " O   HOH Z 133 " =    1.613
peak=    3.479 closest distance to " O   HOH Z 291 " =    1.550
peak=    3.477 closest distance to " CD1 LEU A  96 " =    0.742
peak=    3.473 closest distance to " O   HOH Z 406 " =    1.650
peak=    3.471 closest distance to " O   HOH Z 402 " =    1.453
peak=    3.466 closest distance to " CB  ARG A  79 " =    0.891
peak=    3.463 closest distance to " O   HOH Z  92 " =    2.484
peak=    3.463 closest distance to " CB  PRO A 198 " =    0.984
peak=    3.458 closest distance to " O   HOH Z  63 " =    2.102
peak=    3.453 closest distance to " O   HOH Z 273 " =    2.669
peak=    3.451 closest distance to " O   HOH Z 134 " =    1.344
peak=    3.449 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.444 closest distance to " N   ASN A  39 " =    1.277
peak=    3.443 closest distance to " O   HOH Z 425 " =    1.947
peak=    3.442 closest distance to " CB  GLU A  46 " =    1.013
peak=    3.442 closest distance to " O   HOH Z 327 " =    2.198
peak=    3.442 closest distance to " CB  ALA A 242 " =    0.916
peak=    3.436 closest distance to " CZ2 TRP A 179 " =    1.727
peak=    3.435 closest distance to " O   HOH Z 172 " =    3.574
peak=    3.434 closest distance to " CB  ASN A 142 " =    1.011
peak=    3.431 closest distance to " CD BLYS A 290 " =    1.071
peak=    3.426 closest distance to " CB  SER A 141 " =    0.978
peak=    3.426 closest distance to " OD1 ASN A 217 " =    1.710
peak=    3.425 closest distance to " O   HOH Z 281 " =    4.626
peak=    3.424 closest distance to " O   HOH Z 371 " =    3.247
peak=    3.422 closest distance to " OE1 GLU A   2 " =    2.216
peak=    3.414 closest distance to " CB  ALA A 248 " =    0.942
peak=    3.407 closest distance to " CG1 VAL A 153 " =    0.901
peak=    3.406 closest distance to " O   HOH Z  66 " =    2.155
peak=    3.406 closest distance to " O   HOH Z 185 " =    1.762
peak=    3.403 closest distance to " O   HOH Z 133 " =    2.438
peak=    3.403 closest distance to " O   THR A 251 " =    1.181
peak=    3.390 closest distance to " CB  ARG A 139 " =    0.891
peak=    3.389 closest distance to " CD2 LEU A 255 " =    1.437
peak=    3.385 closest distance to " ND1 HIS A  86 " =    1.686
peak=    3.383 closest distance to " CE1 TYR A 186 " =    1.317
peak=    3.380 closest distance to " CA  ASN A 176 " =    1.194
peak=    3.363 closest distance to " O   HOH Z 234 " =    1.792
peak=    3.362 closest distance to " CD2 TRP A 179 " =    1.328
peak=    3.362 closest distance to " N   VAL A 126 " =    1.396
peak=    3.361 closest distance to " O   HOH Z 128 " =    2.185
peak=    3.360 closest distance to " CB  GLN A 103 " =    0.816
peak=    3.359 closest distance to " CA  VAL A  41 " =    0.850
peak=    3.358 closest distance to " O   HOH Z 247 " =    1.377
peak=    3.356 closest distance to " O   HOH Z  49 " =    2.315
peak=    3.353 closest distance to " O   HOH Z 329 " =    3.680
peak=    3.353 closest distance to " O   HOH Z 411 " =    1.805
peak=    3.352 closest distance to " N   SER A 135 " =    1.301
peak=    3.351 closest distance to " CA  THR A 221 " =    1.440
peak=    3.349 closest distance to " O   HOH Z  54 " =    2.402
peak=    3.347 closest distance to " CA  ALA A 291 " =    0.932
peak=    3.341 closest distance to " CG  GLU A 277 " =    2.185
peak=    3.338 closest distance to " O   HOH Z 345 " =    3.418
peak=    3.338 closest distance to " CZ  PHE A 208 " =    1.164
peak=    3.335 closest distance to " CG  MET A 113 " =    1.307
peak=    3.335 closest distance to " O   HOH Z  61 " =    1.524
peak=    3.335 closest distance to " O   HOH Z 258 " =    1.791
peak=    3.334 closest distance to " O   HOH Z 148 " =    3.285
peak=    3.328 closest distance to " CG1 ILE A 151 " =    1.028
peak=    3.315 closest distance to " CA  ASP A 162 " =    1.098
peak=    3.311 closest distance to " CA  ALA A 233 " =    1.471
peak=    3.311 closest distance to " O   ALA A 165 " =    1.458
peak=    3.310 closest distance to " O   HOH Z 337 " =    3.773
peak=    3.301 closest distance to " O   HOH Z 383 " =    1.898
peak=    3.299 closest distance to " O   HOH Z 209 " =    2.482
peak=    3.299 closest distance to " CB  PHE A  16 " =    1.038
peak=    3.294 closest distance to " CB  TYR A 116 " =    0.878
peak=    3.290 closest distance to " NZ  LYS A 166 " =    2.979
peak=    3.290 closest distance to " O   HOH Z 219 " =    1.895
peak=    3.283 closest distance to " CB  HIS A 108 " =    0.837
peak=    3.282 closest distance to " CA  ALA A 248 " =    1.199
peak=    3.280 closest distance to " CG  LYS A  76 " =    0.974
peak=    3.275 closest distance to " NZ  LYS A  76 " =    1.151
peak=    3.274 closest distance to " CA  ALA A 158 " =    1.084
peak=    3.271 closest distance to " N   ASN A 127 " =    1.237
peak=    3.271 closest distance to " CG2 VAL A  78 " =    0.962
peak=    3.266 closest distance to " CD  ARG A  66 " =    2.475
peak=    3.258 closest distance to " OG BSER A 164 " =    2.496
peak=    3.256 closest distance to " CB  ALA A 114 " =    1.129
peak=    3.256 closest distance to " OG1 THR A 246 " =    3.197
peak=    3.255 closest distance to " O   ALA A   1 " =    1.495
peak=    3.252 closest distance to " O   HOH Z   9 " =    2.125
peak=    3.251 closest distance to " CA  GLN A 223 " =    0.929
peak=    3.249 closest distance to " O   HOH Z 374 " =    2.669
peak=    3.249 closest distance to " CA  GLY A 267 " =    1.104
peak=    3.242 closest distance to " CB  ASN A 215 " =    1.119
peak=    3.242 closest distance to " CG2 VAL A 197 " =    1.116
peak=    3.241 closest distance to " O   HOH Z  59 " =    2.140
peak=    3.240 closest distance to " O   HOH Z 263 " =    1.718
peak=    3.236 closest distance to " NH1 ARG A 138 " =    1.148
peak=    3.236 closest distance to " CB  LYS A 193 " =    0.931
peak=    3.236 closest distance to " O   HOH Z 353 " =    2.719
peak=    3.234 closest distance to " OG  SER A  97 " =    3.616
peak=    3.221 closest distance to " CD  LYS A 119 " =    1.304
peak=    3.220 closest distance to " O   HOH Z  88 " =    1.823
peak=    3.219 closest distance to " CG2 THR A 220 " =    0.805
peak=    3.218 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.216 closest distance to " CA  ALA A  84 " =    1.316
peak=    3.215 closest distance to " CA  GLY A  80 " =    0.715
peak=    3.213 closest distance to " C   TYR A 214 " =    1.453
peak=    3.208 closest distance to " N   GLN A 278 " =    0.970
peak=    3.207 closest distance to " O   HOH Z   4 " =    1.877
peak=    3.206 closest distance to " O   HOH Z  88 " =    2.960
peak=    3.205 closest distance to " CG  GLN A  11 " =    1.296
peak=    3.205 closest distance to " CD  ARG A 219 " =    1.020
peak=    3.204 closest distance to " O   HOH Z 173 " =    1.934
peak=    3.203 closest distance to " CA  ALA A 154 " =    0.918
peak=    3.203 closest distance to " OG  SER A  22 " =    2.732
peak=    3.202 closest distance to " O   HOH Z 391 " =    2.931
peak=    3.202 closest distance to " CG  MET A 185 " =    1.081
peak=    3.202 closest distance to " O   HOH Z 359 " =    3.881
peak=    3.198 closest distance to " OD1 ASP A 231 " =    1.872
peak=    3.197 closest distance to " N   GLY A  98 " =    1.121
peak=    3.195 closest distance to " CB  ALA A 248 " =    1.328
peak=    3.193 closest distance to " O   HOH Z 435 " =    1.926
peak=    3.191 closest distance to " CG BARG A 102 " =    1.847
peak=    3.188 closest distance to " O   HOH Z 183 " =    1.442
peak=    3.188 closest distance to " NZ ALYS A 290 " =    1.160
peak=    3.187 closest distance to " O   HOH Z 425 " =    1.285
peak=    3.186 closest distance to " CA  ASN A 217 " =    1.309
peak=    3.185 closest distance to " CB  ALA A  34 " =    1.069
peak=    3.180 closest distance to " O   HOH Z 421 " =    1.650
peak=    3.179 closest distance to " CZ3 TRP A 123 " =    1.244
peak=    3.169 closest distance to " CB  THR A 157 " =    1.106
peak=    3.168 closest distance to " OG  SER A 206 " =    1.309
peak=    3.168 closest distance to " O   HOH Z  49 " =    2.637
peak=    3.165 closest distance to " CG2 ILE A  20 " =    1.274
peak=    3.164 closest distance to " O   HOH Z  20 " =    1.589
peak=    3.159 closest distance to " CG  MET A 185 " =    1.158
peak=    3.155 closest distance to " O   HOH Z 271 " =    2.375
peak=    3.154 closest distance to " O   HOH Z 334 " =    1.500
peak=    3.154 closest distance to " CB  LEU A 255 " =    0.850
peak=    3.154 closest distance to " O   ALA A 158 " =    1.264
peak=    3.151 closest distance to " O   HOH Z 227 " =    1.629
peak=    3.145 closest distance to " OD1BASN A 224 " =    2.312
peak=    3.144 closest distance to " O   HOH Z 294 " =    1.546
peak=    3.143 closest distance to " O   HOH Z 250 " =    1.511
peak=    3.138 closest distance to " CD1AILE A 234 " =    0.992
peak=    3.137 closest distance to " CD2 HIS A  81 " =    1.188
peak=    3.135 closest distance to " NH2AARG A 190 " =    1.277
peak=    3.134 closest distance to " O   HOH Z 144 " =    1.799
peak=    3.134 closest distance to " OG1 THR A 294 " =    1.648
peak=    3.133 closest distance to " CB  GLN A 278 " =    0.853
peak=    3.133 closest distance to " O  BHOH Z 338 " =    2.316
peak=    3.131 closest distance to " O   HOH Z 166 " =    3.698
peak=    3.128 closest distance to " O  BHOH Z  74 " =    1.379
peak=    3.128 closest distance to " N   ASN A 252 " =    1.349
peak=    3.127 closest distance to " O   HOH Z 437 " =    1.476
peak=    3.127 closest distance to " O   HOH Z 409 " =    3.163
peak=    3.118 closest distance to " O   HOH Z 279 " =    2.205
peak=    3.118 closest distance to " CB  GLU A 152 " =    1.453
peak=    3.116 closest distance to " CA  ILE A 234 " =    0.865
peak=    3.114 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.110 closest distance to " O   HOH Z 417 " =    1.990
peak=    3.103 closest distance to " CA  ALA A  43 " =    1.152
peak=    3.101 closest distance to " O   HOH Z 116 " =    1.776
peak=    3.101 closest distance to " O   HOH Z  68 " =    1.532
peak=    3.101 closest distance to " O   HOH Z 419 " =    1.900
peak=    3.096 closest distance to " O   HOH Z 403 " =    1.340
peak=    3.092 closest distance to " O   HOH Z 171 " =    1.983
peak=    3.083 closest distance to " N   TYR A  15 " =    0.752
peak=    3.080 closest distance to " O   HOH Z 261 " =    2.091
peak=    3.071 closest distance to " OH  TYR A  30 " =    1.118
peak=    3.064 closest distance to " OD1 ASP A 238 " =    0.981
peak=    3.042 closest distance to " O   HOH Z 302 " =    1.991
peak=    3.038 closest distance to " CA  MET A 105 " =    0.976
peak=    3.036 closest distance to " CB  TRP A 179 " =    1.440
peak=    3.019 closest distance to " O   HOH Z 389 " =    1.803

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 5.372
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 192
   mapped sites are within: 0.731 - 5.372

peak=   -4.546 closest distance to " O   HOH Z 290 " =    1.124
peak=   -4.543 closest distance to " CB  PRO A 243 " =    2.629
peak=   -4.458 closest distance to " O   HOH Z 266 " =    4.765
peak=   -4.306 closest distance to " O   ILE A 109 " =    2.617
peak=   -4.292 closest distance to " CD  ARG A 156 " =    2.008
peak=   -4.223 closest distance to " O   VAL A  67 " =    2.681
peak=   -4.170 closest distance to " O   HOH Z 372 " =    2.429
peak=   -4.112 closest distance to " CG  GLN A 223 " =    1.797
peak=   -4.108 closest distance to " ND2 ASN A  45 " =    1.337
peak=   -4.053 closest distance to " O   PRO A 198 " =    1.231
peak=   -3.984 closest distance to " CE2 TYR A  30 " =    2.819
peak=   -3.976 closest distance to " O   HOH Z 118 " =    3.248
peak=   -3.958 closest distance to " CG  ASP A 231 " =    0.798
peak=   -3.943 closest distance to " CZ3 TRP A 179 " =    1.165
peak=   -3.941 closest distance to " C   HIS A 108 " =    1.080
peak=   -3.934 closest distance to " SG  CYS A 254 " =    3.333
peak=   -3.927 closest distance to " N   ALA A  43 " =    2.480
peak=   -3.922 closest distance to " O   HOH Z  10 " =    1.575
peak=   -3.914 closest distance to " O   HOH Z 377 " =    2.008
peak=   -3.894 closest distance to " O   HOH Z 126 " =    1.870
peak=   -3.882 closest distance to " O   HOH Z 185 " =    2.367
peak=   -3.874 closest distance to " O   HOH Z  52 " =    1.401
peak=   -3.862 closest distance to " NH2AARG A 275 " =    5.372
peak=   -3.852 closest distance to " O   HOH Z 353 " =    2.155
peak=   -3.833 closest distance to " O   HOH Z 198 " =    2.172
peak=   -3.830 closest distance to " OG  SER A  97 " =    2.182
peak=   -3.814 closest distance to " CD  GLN A  58 " =    0.989
peak=   -3.755 closest distance to " O   HOH Z 351 " =    1.444
peak=   -3.743 closest distance to " O   HOH Z 196 " =    2.059
peak=   -3.738 closest distance to " O   HOH Z  43 " =    1.580
peak=   -3.732 closest distance to " CD1 LEU A 228 " =    2.347
peak=   -3.726 closest distance to " O   HOH Z 389 " =    1.811
peak=   -3.720 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.705 closest distance to " CG1 VAL A 112 " =    2.836
peak=   -3.701 closest distance to " O   HOH Z 231 " =    2.197
peak=   -3.673 closest distance to " OG BSER A 134 " =    1.204
peak=   -3.656 closest distance to " CG2 ILE A 263 " =    2.342
peak=   -3.650 closest distance to " CZ  TYR A 169 " =    1.714
peak=   -3.641 closest distance to " O   PRO A 163 " =    2.129
peak=   -3.638 closest distance to " CD1 PHE A  59 " =    1.799
peak=   -3.636 closest distance to " O   HOH Z 311 " =    3.640
peak=   -3.627 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.600 closest distance to " CD2 LEU A 300 " =    2.869
peak=   -3.595 closest distance to " N   SER A 212 " =    1.890
peak=   -3.586 closest distance to " CB  CYS A 201 " =    2.671
peak=   -3.582 closest distance to " CG1 VAL A 112 " =    2.941
peak=   -3.579 closest distance to " CB  ASN A  39 " =    2.172
peak=   -3.575 closest distance to " O   HOH Z 407 " =    3.216
peak=   -3.572 closest distance to " OG  SER A  62 " =    1.593
peak=   -3.570 closest distance to " OXT GLY A 302 " =    2.817
peak=   -3.569 closest distance to " CB  ALA A 291 " =    2.294
peak=   -3.564 closest distance to " O   HOH Z 435 " =    2.753
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.468
peak=   -3.555 closest distance to " CB  ALA A  43 " =    2.510
peak=   -3.547 closest distance to " CG1 VAL A 250 " =    2.683
peak=   -3.541 closest distance to " CE2 PHE A 218 " =    2.477
peak=   -3.539 closest distance to " O   VAL A  67 " =    2.645
peak=   -3.535 closest distance to " CG  ARG A 269 " =    2.416
peak=   -3.534 closest distance to " SG ACYS A 201 " =    2.001
peak=   -3.527 closest distance to " O   HOH Z  73 " =    2.358
peak=   -3.523 closest distance to " NH1 ARG A 195 " =    2.566
peak=   -3.521 closest distance to " CG  PHE A 283 " =    2.755
peak=   -3.515 closest distance to " C   ASN A 285 " =    2.511
peak=   -3.503 closest distance to " CD2 TYR A 293 " =    2.050
peak=   -3.494 closest distance to " CA  ASP A 298 " =    1.105
peak=   -3.492 closest distance to " OD1 ASN A 148 " =    1.618
peak=   -3.486 closest distance to " CG1 VAL A 112 " =    2.630
peak=   -3.485 closest distance to " O   HOH Z 394 " =    1.492
peak=   -3.484 closest distance to " O   HOH Z  13 " =    1.486
peak=   -3.482 closest distance to " O   GLY A 211 " =    1.408
peak=   -3.481 closest distance to " O   HOH Z  38 " =    1.471
peak=   -3.473 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.473 closest distance to " CD2 PHE A 192 " =    2.091
peak=   -3.471 closest distance to " OG BSER A 134 " =    1.788
peak=   -3.471 closest distance to " CG  ARG A  66 " =    2.389
peak=   -3.467 closest distance to " O   HOH Z 292 " =    4.506
peak=   -3.448 closest distance to " N   ALA A 226 " =    2.113
peak=   -3.440 closest distance to " CA  GLY A 203 " =    2.335
peak=   -3.440 closest distance to " CB  ALA A 291 " =    2.246
peak=   -3.439 closest distance to " O   HOH Z  60 " =    2.543
peak=   -3.438 closest distance to " O   HOH Z 211 " =    1.680
peak=   -3.436 closest distance to " O   HOH Z 313 " =    2.023
peak=   -3.434 closest distance to " CD  ARG A 195 " =    5.172
peak=   -3.432 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.428 closest distance to " CZ  PHE A  59 " =    1.644
peak=   -3.424 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.420 closest distance to " NH2 ARG A  79 " =    1.944
peak=   -3.418 closest distance to " CG  GLU A  53 " =    1.378
peak=   -3.415 closest distance to " O   HOH Z 198 " =    1.324
peak=   -3.410 closest distance to " N   GLN A  58 " =    1.767
peak=   -3.409 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.398 closest distance to " CG  TRP A 266 " =    1.872
peak=   -3.391 closest distance to " C   LEU A 143 " =    1.118
peak=   -3.387 closest distance to " O   HOH Z 111 " =    2.096
peak=   -3.374 closest distance to " CB  ASP A 286 " =    2.145
peak=   -3.373 closest distance to " CD  GLU A 236 " =    1.000
peak=   -3.367 closest distance to " O   HOH Z 222 " =    1.277
peak=   -3.362 closest distance to " O   GLY A 196 " =    1.112
peak=   -3.360 closest distance to " CB  PRO A 163 " =    2.591
peak=   -3.355 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.354 closest distance to " CD1 ILE A 239 " =    2.068
peak=   -3.354 closest distance to " CE  MET A 105 " =    2.029
peak=   -3.342 closest distance to " NH2 ARG A 159 " =    2.366
peak=   -3.338 closest distance to " OE1 GLN A  88 " =    1.191
peak=   -3.338 closest distance to " N   MET A 105 " =    2.870
peak=   -3.337 closest distance to " CE3 TRP A 150 " =    2.029
peak=   -3.331 closest distance to " CA  GLY A 241 " =    3.112
peak=   -3.324 closest distance to " ND2 ASN A 249 " =    2.125
peak=   -3.323 closest distance to " O   HOH Z  76 " =    1.892
peak=   -3.317 closest distance to " OD2 ASP A 171 " =    1.855
peak=   -3.316 closest distance to " CD2 PHE A  61 " =    2.465
peak=   -3.310 closest distance to " CE  MET A  93 " =    1.214
peak=   -3.309 closest distance to " NH2 ARG A  79 " =    1.594
peak=   -3.305 closest distance to " CB  ALA A 248 " =    2.015
peak=   -3.303 closest distance to " N   THR A 235 " =    1.286
peak=   -3.300 closest distance to " C   SER A 206 " =    1.534
peak=   -3.298 closest distance to " CG1 VAL A 197 " =    2.260
peak=   -3.296 closest distance to " OG BSER A 210 " =    2.185
peak=   -3.294 closest distance to " OD1 ASP A 191 " =    1.610
peak=   -3.291 closest distance to " CD1 LEU A 297 " =    2.454
peak=   -3.290 closest distance to " O   HOH Z 298 " =    2.548
peak=   -3.287 closest distance to " O   VAL A 189 " =    2.577
peak=   -3.278 closest distance to " NE2 GLN A 103 " =    1.722
peak=   -3.276 closest distance to " O   HOH Z 252 " =    3.939
peak=   -3.276 closest distance to " O   HOH Z 348 " =    2.282
peak=   -3.267 closest distance to " NH2 ARG A  66 " =    1.958
peak=   -3.267 closest distance to " O   HOH Z 393 " =    1.422
peak=   -3.266 closest distance to " OH  TYR A 247 " =    2.109
peak=   -3.266 closest distance to " C   MET A 188 " =    1.561
peak=   -3.258 closest distance to " O   HOH Z  93 " =    1.933
peak=   -3.255 closest distance to " CB  TRP A  85 " =    2.426
peak=   -3.255 closest distance to " CD  GLN A  88 " =    0.777
peak=   -3.249 closest distance to " O   HOH Z 275 " =    1.550
peak=   -3.242 closest distance to " O   HOH Z  47 " =    1.548
peak=   -3.239 closest distance to " NE1 TRP A 266 " =    2.279
peak=   -3.232 closest distance to " O   HOH Z 417 " =    2.507
peak=   -3.229 closest distance to " O   HOH Z  51 " =    1.419
peak=   -3.226 closest distance to " CE BMET A  47 " =    2.101
peak=   -3.224 closest distance to " O   HOH Z 166 " =    1.531
peak=   -3.224 closest distance to " CD2 LEU A 237 " =    2.863
peak=   -3.223 closest distance to " O   ALA A  10 " =    1.681
peak=   -3.217 closest distance to " O   HOH Z 281 " =    2.648
peak=   -3.215 closest distance to " O   HOH Z  37 " =    1.858
peak=   -3.208 closest distance to " O   HOH Z 174 " =    3.128
peak=   -3.206 closest distance to " O   HOH Z 166 " =    1.838
peak=   -3.201 closest distance to " O   ALA A  34 " =    2.589
peak=   -3.200 closest distance to " O   HOH Z 298 " =    1.209
peak=   -3.195 closest distance to " N   ALA A 248 " =    1.606
peak=   -3.194 closest distance to " O   LEU A 167 " =    1.421
peak=   -3.193 closest distance to " O   HOH Z 252 " =    4.265
peak=   -3.192 closest distance to " CG  GLU A 152 " =    0.841
peak=   -3.184 closest distance to " O   HOH Z 317 " =    1.630
peak=   -3.183 closest distance to " O   HOH Z 436 " =    1.416
peak=   -3.180 closest distance to " O   HOH Z 210 " =    1.002
peak=   -3.176 closest distance to " OD2 ASP A  50 " =    2.321
peak=   -3.173 closest distance to " CD2 LEU A 300 " =    2.889
peak=   -3.172 closest distance to " CA  GLY A  98 " =    1.987
peak=   -3.172 closest distance to " OD1 ASN A 187 " =    1.583
peak=   -3.171 closest distance to " O   HOH Z 377 " =    1.400
peak=   -3.171 closest distance to " O   HOH Z 377 " =    0.731
peak=   -3.171 closest distance to " NE2 GLN A  58 " =    1.095
peak=   -3.168 closest distance to " O   HOH Z 177 " =    1.668
peak=   -3.166 closest distance to " O   HOH Z 241 " =    1.345
peak=   -3.160 closest distance to " CZ  ARG A  66 " =    0.792
peak=   -3.149 closest distance to " CB  CYS A 254 " =    2.422
peak=   -3.148 closest distance to " CD  GLN A  11 " =    0.906
peak=   -3.148 closest distance to " O   ALA A 161 " =    1.623
peak=   -3.147 closest distance to " O   HOH Z 322 " =    1.519
peak=   -3.146 closest distance to " N   PHE A  59 " =    2.185
peak=   -3.145 closest distance to " NE2 GLN A  88 " =    1.862
peak=   -3.143 closest distance to " O   HOH Z 128 " =    2.533
peak=   -3.138 closest distance to " O   HOH Z 426 " =    1.632
peak=   -3.132 closest distance to " O   HOH Z 377 " =    0.870
peak=   -3.131 closest distance to " O   HOH Z  19 " =    2.354
peak=   -3.123 closest distance to " CB  ALA A 248 " =    2.436
peak=   -3.123 closest distance to " O   GLN A 240 " =    2.110
peak=   -3.113 closest distance to " O   TRP A  70 " =    1.549
peak=   -3.108 closest distance to " OD1 ASP A 171 " =    1.550
peak=   -3.106 closest distance to " CG2 THR A 221 " =    2.223
peak=   -3.101 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.097 closest distance to " CG  PRO A 163 " =    2.532
peak=   -3.084 closest distance to " O   HOH Z 234 " =    4.240
peak=   -3.068 closest distance to " O   HOH Z 357 " =    2.020
peak=   -3.067 closest distance to " O   VAL A 125 " =    2.369
peak=   -3.057 closest distance to " O   HOH Z 414 " =    1.584
peak=   -3.050 closest distance to " CD1 ILE A 199 " =    2.541
peak=   -3.033 closest distance to " O   HOH Z 184 " =    1.806
peak=   -3.029 closest distance to " CA  GLY A 241 " =    2.774
peak=   -3.025 closest distance to " CG1 VAL A  67 " =    3.039
peak=   -3.008 closest distance to " CD1 LEU A 255 " =    2.744

================= 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    :  0.2903 0.2919   5.938832e+00   5.945322e+00
   1_bss:  0.2767 0.2786   5.916381e+00   5.912518e+00
   1_xyz:  0.1730 0.1915   5.481660e+00   5.576795e+00
   1_adp:  0.1615 0.1948   5.435274e+00   5.595573e+00
   1_occ:  0.1610 0.1948   5.433001e+00   5.593583e+00
   2_bss:  0.1606 0.1933   5.433059e+00   5.590938e+00
   2_xyz:  0.1222 0.1581   5.194954e+00   5.399492e+00
   2_adp:  0.1150 0.1553   5.153168e+00   5.378563e+00
   2_occ:  0.1149 0.1551   5.152876e+00   5.378461e+00
   3_bss:  0.1152 0.1548   5.154057e+00   5.378194e+00
   3_xyz:  0.1119 0.1542   5.141066e+00   5.373958e+00
   3_adp:  0.1114 0.1543   5.138579e+00   5.372872e+00
   3_occ:  0.1114 0.1542   5.138602e+00   5.373229e+00
   4_bss:  0.1113 0.1542   5.138644e+00   5.373252e+00
   4_xyz:  0.1071 0.1545   5.116713e+00   5.367878e+00
   4_adp:  0.1069 0.1545   5.115503e+00   5.367228e+00
   4_occ:  0.1069 0.1547   5.115804e+00   5.367881e+00
   5_bss:  0.1068 0.1547   5.115884e+00   5.367933e+00
   5_xyz:  0.1103 0.1557   5.137919e+00   5.380545e+00
   5_adp:  0.1108 0.1554   5.138418e+00   5.378283e+00
   5_occ:  0.1108 0.1554   5.138476e+00   5.378463e+00
   5_bss:  0.1108 0.1554   5.138505e+00   5.378474e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  50.000  -1.548  -1.826  -0.546  -0.000  -0.000  -0.000
   1_xyz:  0.300  50.000  -1.548  -1.826  -0.546  -0.000  -0.000  -0.000
   1_adp:  0.300  50.000  -1.548  -1.826  -0.546  -0.000  -0.000  -0.000
   1_occ:  0.300  50.000  -1.548  -1.826  -0.546  -0.000  -0.000  -0.000
   2_bss:  0.326  53.857  -2.539  -2.491  -1.682  -0.000  -0.000  -0.000
   2_xyz:  0.326  53.857  -2.539  -2.491  -1.682  -0.000  -0.000  -0.000
   2_adp:  0.326  53.857  -2.539  -2.491  -1.682  -0.000  -0.000  -0.000
   2_occ:  0.326  53.857  -2.539  -2.491  -1.682  -0.000  -0.000  -0.000
   3_bss:  0.326  53.857  -2.397  -2.296  -1.613  -0.000  -0.000  -0.000
   3_xyz:  0.326  53.857  -2.397  -2.296  -1.613  -0.000  -0.000  -0.000
   3_adp:  0.326  53.857  -2.397  -2.296  -1.613  -0.000  -0.000  -0.000
   3_occ:  0.326  53.857  -2.397  -2.296  -1.613  -0.000  -0.000  -0.000
   4_bss:  0.326  53.857  -2.333  -2.175  -1.550  -0.000  -0.000  -0.000
   4_xyz:  0.326  53.857  -2.333  -2.175  -1.550  -0.000  -0.000  -0.000
   4_adp:  0.326  53.857  -2.333  -2.175  -1.550  -0.000  -0.000  -0.000
   4_occ:  0.326  53.857  -2.333  -2.175  -1.550  -0.000  -0.000  -0.000
   5_bss:  0.326  53.857  -2.169  -2.014  -1.382  -0.000  -0.000  -0.000
   5_xyz:  0.326  53.857  -2.169  -2.014  -1.382  -0.000  -0.000  -0.000
   5_adp:  0.326  53.857  -2.169  -2.014  -1.382  -0.000  -0.000  -0.000
   5_occ:  0.326  53.857  -2.169  -2.014  -1.382  -0.000  -0.000  -0.000
   5_bss:  0.326  53.812  -2.106  -1.929  -1.290  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  29.186 0.7703  0.9423    23462.583
   1_bss:  27.828 0.7828  0.9181    20436.446
   1_xyz:  17.718 0.8848  0.9910     9404.531
   1_adp:  18.308 0.8789  0.9852     9744.118
   1_occ:  18.280 0.8791  0.9853     9688.847
   2_bss:  18.201 0.8797  0.9535     9595.210
   2_xyz:  14.311 0.9124  0.9722     6559.344
   2_adp:  13.892 0.9158  0.9710     6251.180
   2_occ:  13.898 0.9157  0.9708     6250.628
   3_bss:  13.905 0.9157  0.9749     6250.927
   3_xyz:  13.682 0.9177  0.9749     6133.412
   3_adp:  13.646 0.9181  0.9706     6132.782
   3_occ:  13.650 0.9180  0.9705     6136.066
   4_bss:  13.652 0.9180  0.9733     6136.576
   4_xyz:  13.597 0.9183  0.9737     6089.547
   4_adp:  13.572 0.9185  0.9692     6080.272
   4_occ:  13.585 0.9184  0.9690     6088.874
   5_bss:  13.587 0.9184  0.9747     6089.936
   5_xyz:  13.778 0.9171  0.9736     6225.820
   5_adp:  13.727 0.9174  0.9707     6209.796
   5_occ:  13.733 0.9174  0.9706     6211.536
   5_bss:  13.734 0.9174  0.9718     6211.533
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6162e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6162e-01
   1_xyz:   0.963  0.006  0.063 14.855  0.004  4.113   5.4949e-02
   1_adp:   0.963  0.006  0.063 14.855  0.004  4.113   5.4949e-02
   1_occ:   0.963  0.006  0.063 14.855  0.004  4.113   5.4949e-02
   2_bss:   0.963  0.006  0.063 14.855  0.004  4.113   5.4949e-02
   2_xyz:   1.033  0.008  0.077 14.602  0.004  4.122   6.3734e-02
   2_adp:   1.033  0.008  0.077 14.602  0.004  4.122   6.3734e-02
   2_occ:   1.033  0.008  0.077 14.602  0.004  4.122   6.3734e-02
   3_bss:   1.033  0.008  0.077 14.602  0.004  4.122   6.3734e-02
   3_xyz:   0.939  0.007  0.072 14.524  0.004  4.123   5.3801e-02
   3_adp:   0.939  0.007  0.072 14.524  0.004  4.123   5.3801e-02
   3_occ:   0.939  0.007  0.072 14.524  0.004  4.123   5.3801e-02
   4_bss:   0.939  0.007  0.072 14.524  0.004  4.123   5.3801e-02
   4_xyz:   1.069  0.009  0.081 14.800  0.004  4.126   6.8658e-02
   4_adp:   1.069  0.009  0.081 14.800  0.004  4.126   6.8658e-02
   4_occ:   1.069  0.009  0.081 14.800  0.004  4.126   6.8658e-02
   5_bss:   1.069  0.009  0.081 14.800  0.004  4.126   6.8658e-02
   5_xyz:   0.924  0.006  0.071 14.457  0.004  4.125   5.2120e-02
   5_adp:   0.924  0.006  0.071 14.457  0.004  4.125   5.2120e-02
   5_occ:   0.924  0.006  0.071 14.457  0.004  4.125   5.2120e-02
   5_bss:   0.924  0.006  0.071 14.457  0.004  4.125   5.2120e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4146e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4146e-01
   1_xyz:   7.324  0.041  0.224 84.333  0.031  2.314   5.6381e-02
   1_adp:   7.324  0.041  0.224 84.333  0.031  2.314   5.6381e-02
   1_occ:   7.324  0.041  0.224 84.333  0.031  2.314   5.6381e-02
   2_bss:   7.324  0.041  0.224 84.333  0.031  2.314   5.6381e-02
   2_xyz:   6.924  0.055  0.226 84.341  0.038  2.311   9.5397e-02
   2_adp:   6.924  0.055  0.226 84.341  0.038  2.311   9.5397e-02
   2_occ:   6.924  0.055  0.226 84.341  0.038  2.311   9.5397e-02
   3_bss:   6.924  0.055  0.226 84.341  0.038  2.311   9.5397e-02
   3_xyz:   7.010  0.039  0.228 82.807  0.036  2.372   3.5953e-02
   3_adp:   7.010  0.039  0.228 82.807  0.036  2.372   3.5953e-02
   3_occ:   7.010  0.039  0.228 82.807  0.036  2.372   3.5953e-02
   4_bss:   7.010  0.039  0.228 82.807  0.036  2.372   3.5953e-02
   4_xyz:   7.252  0.046  0.257 83.087  0.038  2.275   6.0435e-02
   4_adp:   7.252  0.046  0.257 83.087  0.038  2.275   6.0435e-02
   4_occ:   7.252  0.046  0.257 83.087  0.038  2.275   6.0435e-02
   5_bss:   7.252  0.046  0.257 83.087  0.038  2.275   6.0435e-02
   5_xyz:   7.013  0.039  0.223 83.154  0.034  2.381   3.1662e-02
   5_adp:   7.013  0.039  0.223 83.154  0.034  2.381   3.1662e-02
   5_occ:   7.013  0.039  0.223 83.154  0.034  2.381   3.1662e-02
   5_bss:   7.013  0.039  0.223 83.154  0.034  2.381   3.1662e-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:  84.36   0.00  16.46  84.36   0.00  12.64  62.92   6.11  37.21
   1_occ:  84.36   0.00  16.46  84.36   0.00  12.64  62.92   6.11  37.21
   2_bss:  84.36   0.00  16.46  84.36   0.00  12.64  62.92   6.11  37.21
   2_xyz:  84.36   0.00  16.46  84.36   0.00  12.64  62.92   6.11  37.21
   2_adp:  81.09   1.74  16.99  81.09   1.74  12.96  68.88   3.41  38.95
   2_occ:  81.09   1.74  16.99  81.09   1.74  12.96  68.88   3.41  38.95
   3_bss:  81.09   1.74  16.99  81.09   1.74  12.96  68.88   3.41  38.95
   3_xyz:  81.09   1.74  16.99  81.09   1.74  12.96  68.88   3.41  38.95
   3_adp:  82.66   1.42  16.78  82.66   1.42  12.83  69.57   2.20  38.29
   3_occ:  82.66   1.42  16.78  82.66   1.42  12.83  69.57   2.20  38.29
   4_bss:  82.66   1.42  16.78  82.66   1.42  12.83  69.57   2.20  38.29
   4_xyz:  82.66   1.42  16.78  82.66   1.42  12.83  69.57   2.20  38.29
   4_adp:  82.83   1.18  16.64  82.83   1.18  12.69  69.67   3.42  38.14
   4_occ:  82.83   1.18  16.64  82.83   1.18  12.69  69.67   3.42  38.14
   5_bss:  82.83   1.18  16.64  82.83   1.18  12.69  69.67   3.42  38.14
   5_xyz:  82.83   1.18  16.64  82.83   1.18  12.69  69.67   3.42  38.14
   5_adp:  82.33   1.26  16.43  82.33   1.26  12.57  69.39   5.16  37.48
   5_occ:  82.33   1.26  16.43  82.33   1.26  12.57  69.39   5.16  37.48
   5_bss:  82.29   1.21  16.39  82.29   1.21  12.52  69.35   5.11  37.44
------------------------------------------------------------------------
 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:    1.318    0.013    0.219
   1_adp:    1.318    0.013    0.219
   1_occ:    1.318    0.013    0.219
   2_bss:    1.318    0.013    0.219
   2_xyz:    0.702    0.025    0.306
   2_adp:    0.702    0.025    0.306
   2_occ:    0.702    0.025    0.306
   3_bss:    0.702    0.025    0.306
   3_xyz:    0.852    0.044    0.319
   3_adp:    0.852    0.044    0.319
   3_occ:    0.852    0.044    0.319
   4_bss:    0.852    0.044    0.319
   4_xyz:    0.810    0.032    0.333
   4_adp:    0.810    0.032    0.333
   4_occ:    0.810    0.032    0.333
   5_bss:    0.810    0.032    0.333
   5_xyz:    0.876    0.029    0.334
   5_adp:    0.876    0.029    0.334
   5_occ:    0.876    0.029    0.334
   5_bss:    0.876    0.029    0.334
------------------------------------------------------------------------

CPU time actual refinement: 328.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/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_916/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_916/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.49 
  Macro-tasks:
    bulk solvent and scale       = 38.04  
    individual site refinement   = 135.49 
    weights calculation          = 28.83  
    collect and process          = 6.63   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 209.10 
  Micro-tasks:
    mask                            = 1.17   
    f_calc                          = 105.26 
    alpha_beta                      = 7.78   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 114.29 
    fmodel                         = 6.83   
    r_factors                      = 0.19   
    phase_errors                   = 11.29  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 248.21 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    664 calls, 104.82 s
gradients_fft:          609 calls, 100.64 s

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

# Date 2008-01-16 Time 05:58:36 PST -0800 (1200491916.34 s)
Start R-work = 0.2903, R-free = 0.2919 (no bulk solvent and anisotropic scale)
Final R-work = 0.1342, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.2767, R-free = 0.2786
Final R-work = 0.1108, R-free = 0.1554