# Date 2008-01-16 Time 04:08:22 PST -0800 (1200485302.22 s)
#phil __OFF__

Command line arguments: "../191.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13349
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 191

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.1647, 85.9581, 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: (68.845, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7647 1.96068
Completeness in resolution range: 0.94977
Completeness with d_max=infinity: 0.946832

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7647
                             d_min =   1.9607

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7647 1.96068
Completeness in resolution range: 0.94977
Completeness with d_max=infinity: 0.946832

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7652 -  4.1949 [2179/2207]  1958   221  10.1%
  bin  2:  4.1949 -  3.3423 [2066/2089]  1862   204   9.9%
  bin  3:  3.3423 -  2.9236 [2061/2083]  1854   207  10.0%
  bin  4:  2.9236 -  2.6579 [2033/2052]  1832   201   9.9%
  bin  5:  2.6579 -  2.4684 [2025/2054]  1814   211  10.4%
  bin  6:  2.4684 -  2.3234 [2005/2047]  1810   195   9.7%
  bin  7:  2.3234 -  2.2075 [2000/2036]  1803   197   9.8%
  bin  8:  2.2075 -  2.1117 [2000/2038]  1799   201  10.1%
  bin  9:  2.1117 -  2.0306 [1987/2018]  1789   198  10.0%
  bin 10:  2.0306 -  1.9607 [1233/2001]  1109   124  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.36 -     2.07: 13
        2.07 -     2.77: 553
        2.77 -     3.48: 4576
        3.48 -     4.19: 9459
        4.19 -     4.90: 14018
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.357 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.602 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.621 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.628 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.801 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28614 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_191/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/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 = 68.845 47.16465 85.95805 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: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3292   r_free= 0.3275   ksol= 0.00   Bsol= 0.00   scale= 0.977    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.058777                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7652 -  4.6785 0.99   1404  157 0.2889 0.2966      6.3633      6.4158|
|  2:  4.6785 -  3.7333 0.99   1362  151 0.2596 0.2397      6.4403        6.42|
|  3:  3.7333 -  3.2672 0.99   1329  149 0.2786 0.2643      6.3316      6.3981|
|  4:  3.2672 -  2.9711 0.99   1313  138 0.2985 0.3303      6.2221      6.2581|
|  5:  2.9711 -  2.7596 0.99   1307  148 0.3309 0.2975      6.1049      6.0599|
|  6:  2.7596 -  2.5979 0.98   1303  149 0.3509 0.3782       6.055      5.9632|
|  7:  2.5979 -  2.4684 0.99   1302  152 0.3498 0.3078      6.0229      5.9245|
|  8:  2.4684 -  2.3614 0.99   1308  131 0.3594 0.3653      5.9747      5.9793|
|  9:  2.3614 -  2.2708 0.98   1291  148 0.3792 0.3957      5.9439      6.0055|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.3658 0.3675      5.9201      5.8942|
| 11:  2.1927 -  2.1244 0.98   1280  147 0.3844 0.4052      5.8714      5.9212|
| 12:  2.1244 -  2.0638 0.99   1288  138 0.3904 0.3849       5.826      5.8417|
| 13:  2.0638 -  2.0096 0.97   1269  138 0.3862 0.3830      5.7507      5.6806|
| 14:  2.0096 -  1.9607 0.47    596   71 0.4240 0.3955      5.7786      5.6116|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7652 -  4.6785  1404   157  0.77  27.93   0.87     0.78      46870.26|
|  2:  4.6785 -  3.7333  1362   151  0.83  23.21   0.99     0.91      49794.04|
|  3:  3.7333 -  3.2672  1329   149  0.80  26.24   1.00     0.96      47054.60|
|  4:  3.2672 -  2.9711  1313   138  0.77  29.11   1.00     0.95      40438.41|
|  5:  2.9711 -  2.7596  1307   148  0.72  33.33   0.99     0.93      33278.39|
|  6:  2.7596 -  2.5979  1303   149  0.71  34.34   0.99     0.92      28707.92|
|  7:  2.5979 -  2.4684  1302   152  0.73  33.03   1.00     0.94      25746.18|
|  8:  2.4684 -  2.3614  1308   131  0.71  34.74   1.02     0.94      24560.33|
|  9:  2.3614 -  2.2708  1291   148  0.69  36.71   1.02     0.93      24290.56|
| 10:  2.2708 -  2.1927  1278   142  0.67  37.87   1.05     0.92      23291.52|
| 11:  2.1927 -  2.1244  1280   147  0.67  38.73   1.03     0.93      22423.25|
| 12:  2.1244 -  2.0638  1288   138  0.66  39.59   1.05     0.94      20608.66|
| 13:  2.0638 -  2.0096  1269   138  0.64  40.66   1.05     0.91      18603.85|
| 14:  2.0096 -  1.9607   596    71  0.64  41.29   1.01     0.81      15788.67|
|alpha:            min =        0.78 max =            0.96 mean =         0.92|
|beta:             min =    15788.67 max =        49794.04 mean =     30924.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           90.00 mean =        33.65|
|phase err.(test): min =        0.00 max =           89.90 mean =        33.55|
|-----------------------------------------------------------------------------|

============================== 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 = 4.153778              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.420   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.685718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.275   (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 |  1.357 -  1.711:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.711 -  2.065:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.065 -  2.420:       24 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.420 -  2.774:      529 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.774 -  3.128:     2204 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.128 -  3.483:     2372 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.483 -  3.837:     4517 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.837 -  4.191:     4942 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.191 -  4.546:     6329 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.546 -  4.900:     7689 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.357 |       0.544 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    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: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3292   r_free= 0.3275   ksol= 0.00   Bsol= 0.00   scale= 0.977    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.058777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3165   r_free= 0.3137   ksol= 0.31   Bsol= 30.86   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,-1.89,-1.36,-0.00,-0.00,-0.00); trace/3= -0.94                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.036975                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.810443              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.254   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362808              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.002   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3165      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3137      final r-factor (free) = 0.2053          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7173 = 3.81 * 0.50 * 6.0526 + 1.00 * 0.1858                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0284 = 3.81 * 0.50 * 5.7523 + 1.00 * 0.0690                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1685          |
| start r-factor (free) = 0.2053      final r-factor (free) = 0.2118          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0931 = 0.36 * 1.00 * 5.7523 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9940 = 0.36 * 1.00 * 5.4715 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.66   17.24    None  None   None       |
|    all(noH): 2823   0      0.00    78.66   17.24    None  None   None       |
|    Sol.    : 438    0      7.46    71.42   38.74    None  None   None       |
|    Mac.    : 2385   0      0.00    78.66   13.29    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 -   7.866:  522   |   5:    39.331 -  47.197:  129        |
|      1:     7.866 -  15.732: 1326   |   6:    47.197 -  55.064:   77        |
|      2:    15.732 -  23.599:  416   |   7:    55.064 -  62.930:   64        |
|      3:    23.599 -  31.465:  142   |   8:    62.930 -  70.796:   13        |
|      4:    31.465 -  39.331:  130   |   9:    70.796 -  78.662:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1685 r_free = 0.2118             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1683 r_free = 0.2117             target_work(ml) = 5.482         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1683   r_free= 0.2117   ksol= 0.31   Bsol= 30.86   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.45,-1.89,-1.36,-0.00,-0.00,-0.00); trace/3= -0.94                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.482045                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1646   r_free= 0.2078   ksol= 0.32   Bsol= 39.16   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.36,-1.71,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.468195                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.607022              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.032   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.163104              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.894  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1646      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.2078      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9479 = 3.61 * 0.50 * 5.4776 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6982 = 3.61 * 0.50 * 5.3431 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1223      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8803 = 0.16 * 1.00 * 5.3431 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8531 = 0.16 * 1.00 * 5.1878 + 1.00 * 0.0069                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.79    79.23   16.80    None  None   None       |
|    all(noH): 2823   0      1.79    79.23   16.80    None  None   None       |
|    Sol.    : 438    0      6.44    67.63   37.54    None  None   None       |
|    Mac.    : 2385   0      1.79    79.23   12.99    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:     1.785 -   9.530:  855   |   5:    40.508 -  48.252:  110        |
|      1:     9.530 -  17.274: 1186   |   6:    48.252 -  55.996:   86        |
|      2:    17.274 -  25.019:  282   |   7:    55.996 -  63.741:   27        |
|      3:    25.019 -  32.763:  135   |   8:    63.741 -  71.485:   11        |
|      4:    32.763 -  40.508:  128   |   9:    71.485 -  79.230:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1590             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1587             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1587   ksol= 0.32   Bsol= 39.16   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.41,-2.36,-1.71,-0.00,-0.00,-0.00); trace/3= -2.16                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.166324                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1576   ksol= 0.32   Bsol= 40.84   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.25,-1.54,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162797                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.622670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.084  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.965  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8633 = 2.62 * 0.50 * 5.1869 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7975 = 2.62 * 0.50 * 5.1349 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1094      final r-factor (work) = 0.1078          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1527          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9567 = 0.38 * 1.00 * 5.1349 + 1.00 * 0.0069                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9488 = 0.38 * 1.00 * 5.1120 + 1.00 * 0.0078                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.81    80.84   16.83    None  None   None       |
|    all(noH): 2823   0      1.81    80.84   16.83    None  None   None       |
|    Sol.    : 438    0      6.21    69.38   38.26    None  None   None       |
|    Mac.    : 2385   0      1.81    80.84   12.89    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:     1.814 -   9.717:  939   |   5:    41.328 -  49.231:  119        |
|      1:     9.717 -  17.620: 1122   |   6:    49.231 -  57.134:   93        |
|      2:    17.620 -  25.523:  269   |   7:    57.134 -  65.036:   20        |
|      3:    25.523 -  33.425:  136   |   8:    65.036 -  72.939:   13        |
|      4:    33.425 -  41.328:  109   |   9:    72.939 -  80.842:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1078 r_free = 0.1527             target_work(ml) = 5.113         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1078 r_free = 0.1526             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1078   r_free= 0.1526   ksol= 0.32   Bsol= 40.84   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.94,-2.25,-1.54,-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: 5.112367                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1077   r_free= 0.1526   ksol= 0.32   Bsol= 42.09   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-2.11,-1.37,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.112291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.672367              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 156.065  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.586755              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.885  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8944 = 2.67 * 0.50 * 5.1120 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8868 = 2.67 * 0.50 * 5.1057 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1054          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0035 = 0.59 * 1.00 * 5.1057 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0022 = 0.59 * 1.00 * 5.1023 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    83.51   16.77    None  None   None       |
|    all(noH): 2823   0      1.21    83.51   16.77    None  None   None       |
|    Sol.    : 438    0      5.90    72.64   38.64    None  None   None       |
|    Mac.    : 2385   0      1.21    83.51   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.213 -   9.443:  915   |   5:    42.363 -  50.593:  113        |
|      1:     9.443 -  17.673: 1170   |   6:    50.593 -  58.823:   83        |
|      2:    17.673 -  25.903:  258   |   7:    58.823 -  67.053:   28        |
|      3:    25.903 -  34.133:  127   |   8:    67.053 -  75.283:    8        |
|      4:    34.133 -  42.363:  116   |   9:    75.283 -  83.513:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1054 r_free = 0.1531             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1054 r_free = 0.1531             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1531   ksol= 0.32   Bsol= 42.09   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-2.11,-1.37,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.105328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1053   r_free= 0.1531   ksol= 0.32   Bsol= 42.97   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-1.91,-1.16,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.105371                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.037858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 166.448  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.101165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.647  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1053      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2642 = 2.04 * 0.50 * 5.1030 + 1.00 * 0.0647                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2641 = 2.04 * 0.50 * 5.1105 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1064      final r-factor (work) = 0.1064          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6359 = 1.10 * 1.00 * 5.1105 + 1.00 * 0.0084                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6389 = 1.10 * 1.00 * 5.1129 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.78    84.12   16.65    None  None   None       |
|    all(noH): 2823   0      0.78    84.12   16.65    None  None   None       |
|    Sol.    : 438    0      5.61    73.59   38.71    None  None   None       |
|    Mac.    : 2385   0      0.78    84.12   12.60    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:     0.776 -   9.111:  873   |   5:    42.450 -  50.785:  114        |
|      1:     9.111 -  17.446: 1205   |   6:    50.785 -  59.120:   81        |
|      2:    17.446 -  25.780:  265   |   7:    59.120 -  67.454:   31        |
|      3:    25.780 -  34.115:  126   |   8:    67.454 -  75.789:    7        |
|      4:    34.115 -  42.450:  116   |   9:    75.789 -  84.124:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1064 r_free = 0.1549             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1063 r_free = 0.1549             target_work(ml) = 5.116         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1549   ksol= 0.32   Bsol= 42.97   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.82,-1.91,-1.16,-0.00,-0.00,-0.00); trace/3= -1.96                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.116229                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7652 -  4.6785 0.99   1404  157 0.0972 0.1268      5.3686      5.5495|
|  2:  4.6785 -  3.7333 0.99   1362  151 0.0822 0.1092      5.4116      5.6101|
|  3:  3.7333 -  3.2672 0.99   1329  149 0.1015 0.1508       5.439      5.8291|
|  4:  3.2672 -  2.9711 0.99   1313  138 0.1135 0.1475      5.4047      5.5577|
|  5:  2.9711 -  2.7596 0.99   1307  148 0.1231 0.1664      5.2788      5.5009|
|  6:  2.7596 -  2.5979 0.98   1303  149 0.1189 0.1992      5.1841      5.4656|
|  7:  2.5979 -  2.4684 0.99   1302  152 0.1139 0.1511      5.1136      5.3172|
|  8:  2.4684 -  2.3614 0.99   1308  131 0.1088 0.1608       5.042      5.2641|
|  9:  2.3614 -  2.2708 0.98   1291  148 0.1114 0.1884      4.9877      5.3251|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1057 0.1596      4.9277      5.1402|
| 11:  2.1927 -  2.1244 0.98   1280  147 0.1054 0.1747      4.8857      5.2167|
| 12:  2.1244 -  2.0638 0.99   1288  138 0.1055 0.1688       4.831      5.1683|
| 13:  2.0638 -  2.0096 0.97   1269  138 0.1060 0.1671      4.7679       5.003|
| 14:  2.0096 -  1.9607 0.47    596   71 0.1055 0.1798      4.6907      4.9513|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7652 -  4.6785  1404   157  0.94   9.07   0.98     0.95       6966.07|
|  2:  4.6785 -  3.7333  1362   151  0.95   7.89   1.02     1.01       8762.41|
|  3:  3.7333 -  3.2672  1329   149  0.94  10.91   1.03     1.02       9875.37|
|  4:  3.2672 -  2.9711  1313   138  0.93  13.00   1.01     1.00       9731.37|
|  5:  2.9711 -  2.7596  1307   148  0.90  15.44   1.00     0.97       7870.22|
|  6:  2.7596 -  2.5979  1303   149  0.90  16.10   0.98     0.95       6749.19|
|  7:  2.5979 -  2.4684  1302   152  0.91  14.84   0.98     0.95       5759.12|
|  8:  2.4684 -  2.3614  1308   131  0.91  14.71   1.00     0.97       5234.55|
|  9:  2.3614 -  2.2708  1291   148  0.91  15.33   1.00     0.96       4709.61|
| 10:  2.2708 -  2.1927  1278   142  0.90  15.32   0.99     0.96       4260.93|
| 11:  2.1927 -  2.1244  1280   147  0.91  15.31   0.99     0.96       4050.32|
| 12:  2.1244 -  2.0638  1288   138  0.91  14.94   1.00     1.00       3679.97|
| 13:  2.0638 -  2.0096  1269   138  0.91  15.60   1.00     0.98       3306.73|
| 14:  2.0096 -  1.9607   596    71  0.90  15.75   0.97     0.93       2737.41|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2737.41 max =         9875.37 mean =      6144.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.74|
|phase err.(test): min =        0.00 max =           89.40 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1549   ksol= 0.32   Bsol= 43.67   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.69,-0.95,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116249                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1063   r_free= 0.1549   ksol= 0.32   Bsol= 43.67   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.69,-0.95,-0.00,-0.00,-0.00); trace/3= -1.76                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116249                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7652 -  4.6785 0.99   1404  157 0.0973 0.1270      5.3694      5.5506|
|  2:  4.6785 -  3.7333 0.99   1362  151 0.0822 0.1091      5.4123        5.61|
|  3:  3.7333 -  3.2672 0.99   1329  149 0.1015 0.1508       5.439      5.8291|
|  4:  3.2672 -  2.9711 0.99   1313  138 0.1134 0.1474      5.4044      5.5574|
|  5:  2.9711 -  2.7596 0.99   1307  148 0.1230 0.1664      5.2786      5.5007|
|  6:  2.7596 -  2.5979 0.98   1303  149 0.1189 0.1991       5.184      5.4651|
|  7:  2.5979 -  2.4684 0.99   1302  152 0.1139 0.1511      5.1134      5.3171|
|  8:  2.4684 -  2.3614 0.99   1308  131 0.1088 0.1607      5.0417      5.2635|
|  9:  2.3614 -  2.2708 0.98   1291  148 0.1114 0.1885      4.9878      5.3253|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1056 0.1596      4.9278      5.1401|
| 11:  2.1927 -  2.1244 0.98   1280  147 0.1054 0.1748      4.8858      5.2168|
| 12:  2.1244 -  2.0638 0.99   1288  138 0.1055 0.1689      4.8308      5.1685|
| 13:  2.0638 -  2.0096 0.97   1269  138 0.1060 0.1671      4.7678      5.0027|
| 14:  2.0096 -  1.9607 0.47    596   71 0.1055 0.1798      4.6906      4.9512|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7652 -  4.6785  1404   157  0.94   9.08   0.98     0.95       6974.69|
|  2:  4.6785 -  3.7333  1362   151  0.95   7.89   1.02     1.01       8769.50|
|  3:  3.7333 -  3.2672  1329   149  0.94  10.92   1.03     1.03       9875.25|
|  4:  3.2672 -  2.9711  1313   138  0.93  13.00   1.02     1.01       9726.01|
|  5:  2.9711 -  2.7596  1307   148  0.90  15.44   1.01     0.98       7866.80|
|  6:  2.7596 -  2.5979  1303   149  0.90  16.09   0.98     0.95       6745.60|
|  7:  2.5979 -  2.4684  1302   152  0.91  14.82   0.99     0.96       5754.24|
|  8:  2.4684 -  2.3614  1308   131  0.91  14.71   1.00     0.98       5230.31|
|  9:  2.3614 -  2.2708  1291   148  0.91  15.33   1.01     0.97       4707.35|
| 10:  2.2708 -  2.1927  1278   142  0.90  15.33   1.00     0.97       4261.23|
| 11:  2.1927 -  2.1244  1280   147  0.91  15.32   1.00     0.97       4049.93|
| 12:  2.1244 -  2.0638  1288   138  0.91  14.94   1.01     1.00       3679.51|
| 13:  2.0638 -  2.0096  1269   138  0.91  15.60   1.01     0.99       3306.28|
| 14:  2.0096 -  1.9607   596    71  0.90  15.75   0.98     0.94       2737.27|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2737.27 max =         9875.25 mean =      6143.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.74|
|phase err.(test): min =        0.00 max =           89.46 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.611)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.75    84.10   16.63    None  None   None       |
|    all(noH): 2823   0      0.75    84.10   16.63    None  None   None       |
|    Sol.    : 438    0      5.58    73.56   38.69    None  None   None       |
|    Mac.    : 2385   0      0.75    84.10   12.58    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:     0.750 -   9.085:  873   |   5:    42.424 -  50.759:  114        |
|      1:     9.085 -  17.419: 1205   |   6:    50.759 -  59.093:   81        |
|      2:    17.419 -  25.754:  265   |   7:    59.093 -  67.428:   31        |
|      3:    25.754 -  34.089:  126   |   8:    67.428 -  75.763:    7        |
|      4:    34.089 -  42.424:  116   |   9:    75.763 -  84.098:    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)= 273         
Filter by distance & map next to the model:
   mapped sites are within: 0.693 - 4.293
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 271 from: 273
   mapped sites are within: 0.724 - 4.293

peak=    5.724 closest distance to " CB  ARG A 275 " =    0.968
peak=    5.491 closest distance to " NH2 ARG A  56 " =    2.223
peak=    5.417 closest distance to " O   HOH Z 142 " =    1.684
peak=    5.239 closest distance to " CG  PRO A  54 " =    1.237
peak=    5.130 closest distance to " O   HOH Z 126 " =    1.910
peak=    4.940 closest distance to " CB  GLN A 223 " =    1.434
peak=    4.858 closest distance to " NE2 GLN A  11 " =    1.064
peak=    4.840 closest distance to " CB  SER A  63 " =    1.121
peak=    4.806 closest distance to " C   PRO A 198 " =    1.438
peak=    4.769 closest distance to " CG  PRO A 213 " =    1.282
peak=    4.707 closest distance to " CB  GLN A 183 " =    1.289
peak=    4.704 closest distance to " O   HOH Z 272 " =    1.834
peak=    4.694 closest distance to " CA  TYR A  30 " =    0.921
peak=    4.579 closest distance to " O   HOH Z 232 " =    2.379
peak=    4.566 closest distance to " O   HOH Z 209 " =    2.235
peak=    4.564 closest distance to " CB  GLU A 152 " =    1.178
peak=    4.532 closest distance to " O   HOH Z 287 " =    2.103
peak=    4.517 closest distance to " CG  PRO A  90 " =    1.154
peak=    4.462 closest distance to " O   HOH Z 203 " =    1.790
peak=    4.416 closest distance to " CB  PRO A  54 " =    0.966
peak=    4.380 closest distance to " O   HOH Z  97 " =    2.468
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.765
peak=    4.329 closest distance to " O   HOH Z  78 " =    1.670
peak=    4.327 closest distance to " CB  ASN A 148 " =    1.479
peak=    4.318 closest distance to " O   HOH Z 402 " =    1.412
peak=    4.287 closest distance to " O   HOH Z 193 " =    1.785
peak=    4.287 closest distance to " CB  ARG A 190 " =    1.731
peak=    4.286 closest distance to " CD2 TRP A 179 " =    1.393
peak=    4.286 closest distance to " O   HOH Z 234 " =    3.596
peak=    4.278 closest distance to " O   HOH Z 427 " =    2.887
peak=    4.275 closest distance to " CB  ARG A  79 " =    1.327
peak=    4.259 closest distance to " ND2 ASN A 187 " =    1.443
peak=    4.254 closest distance to " O   HOH Z 250 " =    1.487
peak=    4.244 closest distance to " O   HOH Z 392 " =    2.747
peak=    4.242 closest distance to " CG  PRO A 243 " =    1.081
peak=    4.235 closest distance to " CG  PRO A 198 " =    1.235
peak=    4.227 closest distance to " O   HOH Z  54 " =    1.739
peak=    4.206 closest distance to " O   SER A  87 " =    2.209
peak=    4.192 closest distance to " O   HOH Z  44 " =    1.892
peak=    4.174 closest distance to " O   HOH Z 369 " =    2.113
peak=    4.151 closest distance to " O   HOH Z 346 " =    1.659
peak=    4.149 closest distance to " O   HOH Z 327 " =    1.660
peak=    4.145 closest distance to " O   HOH Z 316 " =    3.039
peak=    4.121 closest distance to " CB  VAL A 265 " =    1.213
peak=    4.116 closest distance to " O   HOH Z 128 " =    1.892
peak=    4.103 closest distance to " O   HOH Z  59 " =    2.089
peak=    4.101 closest distance to " O   HOH Z  15 " =    2.242
peak=    4.073 closest distance to " O   HOH Z  97 " =    1.911
peak=    4.049 closest distance to " O   HOH Z 389 " =    1.881
peak=    4.048 closest distance to " O   HOH Z  43 " =    1.961
peak=    4.039 closest distance to " NZ  LYS A 117 " =    3.174
peak=    4.030 closest distance to " CG1 ILE A  33 " =    1.240
peak=    4.027 closest distance to " O   HOH Z 303 " =    2.057
peak=    3.975 closest distance to " CA  ARG A  36 " =    0.984
peak=    3.974 closest distance to " O   HOH Z 344 " =    3.056
peak=    3.970 closest distance to " O   HOH Z 128 " =    2.187
peak=    3.959 closest distance to " CG  ARG A  66 " =    2.564
peak=    3.943 closest distance to " CB  TYR A 169 " =    0.817
peak=    3.921 closest distance to " NH2BARG A 145 " =    2.072
peak=    3.920 closest distance to " CD2 LEU A 297 " =    0.921
peak=    3.909 closest distance to " O   HOH Z 368 " =    2.068
peak=    3.905 closest distance to " CB  SER A   3 " =    1.220
peak=    3.883 closest distance to " O   HOH Z 132 " =    2.542
peak=    3.870 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.869 closest distance to " CG2 ILE A 120 " =    1.143
peak=    3.854 closest distance to " O   HOH Z 144 " =    2.128
peak=    3.854 closest distance to " CA  ALA A  21 " =    1.120
peak=    3.841 closest distance to " O   HOH Z  40 " =    1.797
peak=    3.839 closest distance to " O   HOH Z 423 " =    1.969
peak=    3.836 closest distance to " CB  GLU A 128 " =    1.095
peak=    3.835 closest distance to " OE1 GLU A   2 " =    2.248
peak=    3.829 closest distance to " O   HOH Z 158 " =    2.974
peak=    3.822 closest distance to " CB  SER A  26 " =    1.659
peak=    3.819 closest distance to " CB  VAL A 202 " =    1.560
peak=    3.812 closest distance to " O   HOH Z 416 " =    2.637
peak=    3.780 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.777 closest distance to " O   HOH Z 403 " =    1.736
peak=    3.770 closest distance to " CB  GLU A 277 " =    3.512
peak=    3.765 closest distance to " O   HOH Z 291 " =    1.531
peak=    3.761 closest distance to " O   HOH Z 227 " =    1.597
peak=    3.752 closest distance to " CB  LEU A 228 " =    1.136
peak=    3.746 closest distance to " O   HOH Z  68 " =    2.109
peak=    3.746 closest distance to " O   HOH Z 265 " =    2.256
peak=    3.732 closest distance to " O   HOH Z 173 " =    2.006
peak=    3.724 closest distance to " N   ASN A  39 " =    1.236
peak=    3.721 closest distance to " CA  ALA A  84 " =    1.232
peak=    3.715 closest distance to " O   HOH Z 406 " =    1.481
peak=    3.714 closest distance to " CB  TRP A 266 " =    1.014
peak=    3.709 closest distance to " OD2 ASP A 286 " =    2.767
peak=    3.706 closest distance to " CA  ASN A 215 " =    1.096
peak=    3.705 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.703 closest distance to " CG2 ILE A  20 " =    1.384
peak=    3.696 closest distance to " O   HOH Z 417 " =    3.220
peak=    3.692 closest distance to " CG1BVAL A  72 " =    1.545
peak=    3.679 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.676 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.670 closest distance to " CZ  PHE A 218 " =    1.058
peak=    3.652 closest distance to " O   HOH Z 245 " =    1.327
peak=    3.646 closest distance to " CA  ASN A 176 " =    1.142
peak=    3.636 closest distance to " O   HOH Z 147 " =    1.750
peak=    3.633 closest distance to " O   HOH Z 172 " =    3.849
peak=    3.632 closest distance to " CB  TRP A 179 " =    1.172
peak=    3.630 closest distance to " O   HOH Z 425 " =    2.020
peak=    3.622 closest distance to " O   HOH Z 187 " =    2.254
peak=    3.616 closest distance to " CG2 VAL A 257 " =    0.846
peak=    3.606 closest distance to " C   ILE A 106 " =    1.905
peak=    3.602 closest distance to " O   HOH Z  19 " =    1.983
peak=    3.600 closest distance to " CA  MET A  40 " =    1.062
peak=    3.591 closest distance to " CG  GLN A  77 " =    2.259
peak=    3.582 closest distance to " O   HOH Z 371 " =    3.337
peak=    3.568 closest distance to " CE  LYS A  76 " =    0.783
peak=    3.565 closest distance to " O   HOH Z 193 " =    2.081
peak=    3.565 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.562 closest distance to " O   HOH Z 109 " =    2.313
peak=    3.561 closest distance to " O   HOH Z 337 " =    3.510
peak=    3.559 closest distance to " NH1AARG A 145 " =    1.247
peak=    3.553 closest distance to " O   HOH Z 189 " =    2.032
peak=    3.550 closest distance to " O   HOH Z 180 " =    2.270
peak=    3.533 closest distance to " CG  LYS A  76 " =    0.992
peak=    3.533 closest distance to " N   ARG A 156 " =    1.331
peak=    3.526 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.522 closest distance to " CA  ARG A 195 " =    1.294
peak=    3.515 closest distance to " CA  ASP A 140 " =    1.090
peak=    3.514 closest distance to " O   HOH Z  21 " =    1.812
peak=    3.513 closest distance to " O   HOH Z 357 " =    1.916
peak=    3.512 closest distance to " O   HOH Z 411 " =    3.812
peak=    3.510 closest distance to " N   TYR A 116 " =    1.554
peak=    3.509 closest distance to " CB  THR A  31 " =    1.675
peak=    3.508 closest distance to " O   HOH Z  35 " =    2.458
peak=    3.502 closest distance to " O   HOH Z  61 " =    1.508
peak=    3.501 closest distance to " O   HOH Z   1 " =    1.967
peak=    3.500 closest distance to " CB  ALA A 291 " =    1.249
peak=    3.500 closest distance to " CB  TYR A 169 " =    0.967
peak=    3.499 closest distance to " CA  LYS A 117 " =    1.239
peak=    3.488 closest distance to " CD1 ILE A 106 " =    0.914
peak=    3.486 closest distance to " O   HOH Z 421 " =    1.589
peak=    3.478 closest distance to " O   HOH Z 336 " =    1.672
peak=    3.471 closest distance to " CG2BVAL A  41 " =    0.824
peak=    3.469 closest distance to " O   HOH Z 365 " =    2.809
peak=    3.463 closest distance to " OG BSER A 164 " =    2.258
peak=    3.463 closest distance to " CB  ALA A 248 " =    1.356
peak=    3.458 closest distance to " O   HOH Z 279 " =    2.175
peak=    3.457 closest distance to " O   HOH Z 361 " =    3.672
peak=    3.456 closest distance to " O   HOH Z 132 " =    2.457
peak=    3.455 closest distance to " O   HOH Z  88 " =    2.901
peak=    3.452 closest distance to " O  BHOH Z 338 " =    2.362
peak=    3.447 closest distance to " O   HOH Z 214 " =    2.209
peak=    3.446 closest distance to " O   HOH Z 185 " =    1.739
peak=    3.444 closest distance to " CB  ASP A 140 " =    1.002
peak=    3.443 closest distance to " O   HOH Z 380 " =    1.960
peak=    3.435 closest distance to " CB  GLU A  46 " =    1.000
peak=    3.426 closest distance to " O   ALA A   1 " =    1.667
peak=    3.424 closest distance to " O   HOH Z 426 " =    1.473
peak=    3.424 closest distance to " O   HOH Z 273 " =    2.730
peak=    3.422 closest distance to " O   HOH Z 359 " =    1.473
peak=    3.421 closest distance to " CA  MET A 105 " =    1.021
peak=    3.421 closest distance to " CB  GLN A  89 " =    1.378
peak=    3.420 closest distance to " CB  ILE A 120 " =    1.305
peak=    3.416 closest distance to " CG AARG A 275 " =    1.098
peak=    3.412 closest distance to " O   HOH Z  71 " =    2.202
peak=    3.408 closest distance to " O   HOH Z 299 " =    4.293
peak=    3.388 closest distance to " CE  LYS A 119 " =    1.085
peak=    3.380 closest distance to " O   HOH Z 126 " =    1.528
peak=    3.378 closest distance to " CB  GLN A  88 " =    1.121
peak=    3.374 closest distance to " O   HOH Z 261 " =    1.594
peak=    3.373 closest distance to " CA  ALA A 291 " =    0.833
peak=    3.372 closest distance to " CZ2 TRP A 179 " =    1.688
peak=    3.371 closest distance to " O   HOH Z 345 " =    2.930
peak=    3.370 closest distance to " CD2 HIS A  81 " =    1.108
peak=    3.348 closest distance to " CA  THR A 221 " =    1.019
peak=    3.346 closest distance to " O   HOH Z  80 " =    1.659
peak=    3.343 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.335 closest distance to " O   HOH Z 305 " =    3.564
peak=    3.331 closest distance to " CD  LYS A 166 " =    1.271
peak=    3.329 closest distance to " ND2 ASN A 110 " =    1.670
peak=    3.323 closest distance to " CG2 THR A 294 " =    1.628
peak=    3.323 closest distance to " O   HOH Z  47 " =    1.547
peak=    3.322 closest distance to " CA  SER A 146 " =    1.806
peak=    3.319 closest distance to " O   HOH Z  89 " =    2.158
peak=    3.317 closest distance to " CB  ALA A 114 " =    1.114
peak=    3.317 closest distance to " O   HOH Z  66 " =    2.151
peak=    3.315 closest distance to " CG  MET A 185 " =    1.119
peak=    3.313 closest distance to " CB  ASN A 215 " =    1.128
peak=    3.311 closest distance to " O   HOH Z  10 " =    1.783
peak=    3.307 closest distance to " CA  ALA A 248 " =    1.225
peak=    3.303 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.302 closest distance to " N   PHE A 130 " =    1.304
peak=    3.299 closest distance to " CA  ALA A  43 " =    1.238
peak=    3.296 closest distance to " CB  ARG A 139 " =    0.900
peak=    3.294 closest distance to " OG  SER A  62 " =    2.776
peak=    3.291 closest distance to " CB  SER A 212 " =    1.064
peak=    3.291 closest distance to " O   ALA A 165 " =    1.429
peak=    3.285 closest distance to " O   HOH Z  85 " =    1.334
peak=    3.280 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.280 closest distance to " O   HOH Z 267 " =    2.019
peak=    3.278 closest distance to " CD  LYS A  76 " =    1.997
peak=    3.276 closest distance to " O   HOH Z 250 " =    1.546
peak=    3.272 closest distance to " CG  ARG A  66 " =    0.923
peak=    3.269 closest distance to " O   HOH Z 380 " =    1.988
peak=    3.268 closest distance to " OE2 GLU A  53 " =    2.033
peak=    3.265 closest distance to " O   HOH Z 253 " =    2.404
peak=    3.264 closest distance to " NE2 GLN A  77 " =    3.131
peak=    3.264 closest distance to " O   TRP A 274 " =    1.932
peak=    3.260 closest distance to " O   HOH Z 329 " =    3.910
peak=    3.248 closest distance to " CA  ARG A 159 " =    1.314
peak=    3.241 closest distance to " CA  ASP A 162 " =    1.131
peak=    3.233 closest distance to " O   HOH Z 298 " =    2.333
peak=    3.229 closest distance to " CB  SER A 141 " =    1.093
peak=    3.229 closest distance to " O   HOH Z 342 " =    0.899
peak=    3.225 closest distance to " CG2 VAL A 197 " =    1.108
peak=    3.224 closest distance to " O   HOH Z 171 " =    1.775
peak=    3.223 closest distance to " O   HOH Z  49 " =    2.081
peak=    3.223 closest distance to " CD BLYS A 290 " =    1.186
peak=    3.221 closest distance to " CB  TYR A 116 " =    0.799
peak=    3.220 closest distance to " O   HOH Z 367 " =    3.657
peak=    3.216 closest distance to " OH  TYR A 116 " =    1.029
peak=    3.213 closest distance to " NH2 ARG A 219 " =    1.888
peak=    3.213 closest distance to " CB  GLN A 205 " =    1.156
peak=    3.211 closest distance to " O   HOH Z 286 " =    2.179
peak=    3.203 closest distance to " NZ  LYS A 119 " =    1.494
peak=    3.202 closest distance to " O   HOH Z 393 " =    3.254
peak=    3.199 closest distance to " C   TYR A 214 " =    1.453
peak=    3.197 closest distance to " CG  GLN A  11 " =    1.533
peak=    3.195 closest distance to " O   HOH Z 108 " =    2.570
peak=    3.194 closest distance to " O   HOH Z 257 " =    2.207
peak=    3.193 closest distance to " CB  GLN A 278 " =    0.887
peak=    3.192 closest distance to " CG2 VAL A 202 " =    1.141
peak=    3.180 closest distance to " CB  LYS A 290 " =    1.039
peak=    3.180 closest distance to " O   HOH Z 368 " =    2.734
peak=    3.179 closest distance to " O   HOH Z  88 " =    2.511
peak=    3.179 closest distance to " CB  ALA A  34 " =    1.108
peak=    3.177 closest distance to " CG1 ILE A 120 " =    1.100
peak=    3.175 closest distance to " O   HOH Z 313 " =    1.879
peak=    3.175 closest distance to " O   HOH Z 325 " =    2.469
peak=    3.162 closest distance to " CG  LYS A 119 " =    1.134
peak=    3.160 closest distance to " CD  LYS A 119 " =    1.314
peak=    3.156 closest distance to " CA  ALA A  51 " =    0.906
peak=    3.156 closest distance to " O   HOH Z 345 " =    1.507
peak=    3.152 closest distance to " CD1 LEU A 300 " =    1.309
peak=    3.151 closest distance to " CD1AILE A 234 " =    0.949
peak=    3.144 closest distance to " O   HOH Z 251 " =    1.592
peak=    3.143 closest distance to " CA  ALA A 233 " =    1.128
peak=    3.142 closest distance to " O   HOH Z 411 " =    1.610
peak=    3.137 closest distance to " CB  SER A  62 " =    0.960
peak=    3.134 closest distance to " O   HOH Z 433 " =    1.938
peak=    3.134 closest distance to " O   HOH Z 353 " =    2.674
peak=    3.133 closest distance to " CG  MET A 113 " =    1.031
peak=    3.129 closest distance to " O   HOH Z 334 " =    1.303
peak=    3.128 closest distance to " N   ASP A 162 " =    1.156
peak=    3.125 closest distance to " CB  MET A  47 " =    1.167
peak=    3.125 closest distance to " CA  THR A 264 " =    0.875
peak=    3.120 closest distance to " CB  GLN A 103 " =    0.826
peak=    3.116 closest distance to " O   HOH Z 112 " =    2.608
peak=    3.112 closest distance to " O   HOH Z 425 " =    1.265
peak=    3.109 closest distance to " CA  GLY A  80 " =    0.734
peak=    3.101 closest distance to " CD2 TYR A  30 " =    0.986
peak=    3.094 closest distance to " O   HOH Z 409 " =    3.205
peak=    3.092 closest distance to " CG1 VAL A 153 " =    0.964
peak=    3.092 closest distance to " CZ  PHE A  38 " =    1.305
peak=    3.090 closest distance to " O   THR A 220 " =    1.277
peak=    3.082 closest distance to " O   HOH Z 184 " =    1.991
peak=    3.079 closest distance to " O   HOH Z 406 " =    2.869
peak=    3.075 closest distance to " NE AARG A 190 " =    2.079
peak=    3.061 closest distance to " O   HOH Z 148 " =    3.249
peak=    3.061 closest distance to " O   HOH Z 124 " =    1.208
peak=    3.058 closest distance to " O   HOH Z  47 " =    1.664
peak=    3.052 closest distance to " O   HOH Z 403 " =    1.296
peak=    3.050 closest distance to " O   HOH Z 302 " =    1.998
peak=    3.050 closest distance to " CB  THR A 279 " =    1.662
peak=    3.049 closest distance to " CD  ARG A  66 " =    2.686
peak=    3.036 closest distance to " NH1 ARG A 138 " =    1.234

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.691 - 5.857
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.841 - 5.857

peak=   -4.929 closest distance to " O   HOH Z 266 " =    4.859
peak=   -4.611 closest distance to " C   HIS A 108 " =    1.080
peak=   -4.507 closest distance to " CB  PRO A 243 " =    2.635
peak=   -4.396 closest distance to " CD  ARG A 156 " =    2.126
peak=   -4.389 closest distance to " O   VAL A  67 " =    2.713
peak=   -4.387 closest distance to " CG  GLN A  58 " =    1.163
peak=   -4.323 closest distance to " OG BSER A 134 " =    1.282
peak=   -4.248 closest distance to " O   HOH Z 377 " =    2.118
peak=   -4.202 closest distance to " SG  CYS A 254 " =    3.327
peak=   -4.196 closest distance to " N   ALA A 248 " =    1.748
peak=   -4.194 closest distance to " CA  VAL A  67 " =    2.775
peak=   -4.169 closest distance to " CZ  TYR A 169 " =    1.808
peak=   -4.116 closest distance to " O   HOH Z 198 " =    1.919
peak=   -4.094 closest distance to " CG  GLN A 223 " =    2.068
peak=   -4.092 closest distance to " O   HOH Z 290 " =    1.065
peak=   -4.053 closest distance to " O   HOH Z  13 " =    1.595
peak=   -4.045 closest distance to " CG1 VAL A 112 " =    2.770
peak=   -4.039 closest distance to " OXT GLY A 302 " =    2.800
peak=   -4.004 closest distance to " CD1 LEU A 101 " =    2.362
peak=   -3.962 closest distance to " O   HOH Z 231 " =    2.371
peak=   -3.904 closest distance to " ND2 ASN A  45 " =    1.075
peak=   -3.897 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.886 closest distance to " CE2 TYR A  30 " =    2.772
peak=   -3.858 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.855 closest distance to " N   GLN A  58 " =    1.704
peak=   -3.848 closest distance to " O   HOH Z 353 " =    2.205
peak=   -3.833 closest distance to " CB  ALA A 161 " =    2.515
peak=   -3.820 closest distance to " O   HOH Z 372 " =    2.180
peak=   -3.817 closest distance to " OD2 ASP A 171 " =    2.330
peak=   -3.813 closest distance to " CB  ASN A  39 " =    2.300
peak=   -3.808 closest distance to " CB  PHE A 192 " =    1.983
peak=   -3.808 closest distance to " CG2 ILE A 263 " =    2.195
peak=   -3.806 closest distance to " O   PHE A 218 " =    1.571
peak=   -3.801 closest distance to " O   HOH Z 351 " =    1.452
peak=   -3.801 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.785 closest distance to " O   HOH Z 114 " =    3.226
peak=   -3.780 closest distance to " ND2 ASN A  45 " =    1.818
peak=   -3.762 closest distance to " O   HOH Z 126 " =    1.874
peak=   -3.760 closest distance to " CB  ALA A 291 " =    2.342
peak=   -3.737 closest distance to " OD2 ASP A 191 " =    1.424
peak=   -3.735 closest distance to " OG  SER A   3 " =    1.730
peak=   -3.730 closest distance to " CZ3 TRP A 179 " =    1.253
peak=   -3.714 closest distance to " O   PRO A 163 " =    2.062
peak=   -3.708 closest distance to " N   ALA A  43 " =    2.643
peak=   -3.699 closest distance to " O   ALA A 161 " =    1.633
peak=   -3.694 closest distance to " OG  SER A  97 " =    2.137
peak=   -3.689 closest distance to " O   HOH Z 165 " =    2.036
peak=   -3.680 closest distance to " O   HOH Z 185 " =    2.379
peak=   -3.678 closest distance to " O   SER A 210 " =    1.958
peak=   -3.674 closest distance to " O   HOH Z 407 " =    2.668
peak=   -3.670 closest distance to " CD1 LEU A  25 " =    2.491
peak=   -3.669 closest distance to " CA  ASP A 298 " =    1.063
peak=   -3.639 closest distance to " N   ALA A 248 " =    2.211
peak=   -3.639 closest distance to " O   HOH Z  88 " =    4.373
peak=   -3.620 closest distance to " CB  ASP A 132 " =    2.276
peak=   -3.595 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.587 closest distance to " O   HOH Z  63 " =    1.499
peak=   -3.573 closest distance to " O   SER A  95 " =    1.505
peak=   -3.572 closest distance to " O   HOH Z 196 " =    2.004
peak=   -3.571 closest distance to " O   HOH Z 102 " =    1.617
peak=   -3.571 closest distance to " O   HOH Z 389 " =    1.719
peak=   -3.569 closest distance to " CB  PHE A 208 " =    2.261
peak=   -3.551 closest distance to " CG1 VAL A  78 " =    2.939
peak=   -3.550 closest distance to " O   HOH Z 362 " =    5.857
peak=   -3.548 closest distance to " O   VAL A 174 " =    2.103
peak=   -3.529 closest distance to " O   HOH Z 243 " =    1.961
peak=   -3.522 closest distance to " O   HOH Z 166 " =    1.935
peak=   -3.516 closest distance to " CB  ALA A 248 " =    2.061
peak=   -3.516 closest distance to " NE2 GLN A  88 " =    1.760
peak=   -3.513 closest distance to " O   PRO A 198 " =    1.274
peak=   -3.503 closest distance to " CG  PHE A 283 " =    2.601
peak=   -3.499 closest distance to " ND2 ASN A  39 " =    1.217
peak=   -3.493 closest distance to " CD2 LEU A 237 " =    2.478
peak=   -3.488 closest distance to " CB  ALA A 248 " =    2.233
peak=   -3.488 closest distance to " O   HOH Z 211 " =    1.749
peak=   -3.486 closest distance to " OG BSER A 134 " =    1.746
peak=   -3.485 closest distance to " O   HOH Z 166 " =    1.555
peak=   -3.484 closest distance to " CZ  PHE A  59 " =    1.531
peak=   -3.481 closest distance to " O   HOH Z 313 " =    1.975
peak=   -3.481 closest distance to " O   HOH Z  44 " =    2.213
peak=   -3.463 closest distance to " N   THR A  52 " =    1.691
peak=   -3.451 closest distance to " O   HOH Z  11 " =    2.061
peak=   -3.446 closest distance to " O   SER A 135 " =    1.514
peak=   -3.445 closest distance to " CD1 LEU A 255 " =    2.715
peak=   -3.445 closest distance to " O   HOH Z  10 " =    1.422
peak=   -3.426 closest distance to " O   HOH Z 385 " =    2.084
peak=   -3.426 closest distance to " O   HOH Z 395 " =    5.175
peak=   -3.422 closest distance to " O   GLN A  89 " =    1.541
peak=   -3.421 closest distance to " N   ASP A 286 " =    2.288
peak=   -3.420 closest distance to " C   ILE A 234 " =    1.389
peak=   -3.418 closest distance to " CG  GLU A   2 " =    1.926
peak=   -3.413 closest distance to " CA  GLY A 203 " =    2.312
peak=   -3.409 closest distance to " OD1 ASN A 148 " =    1.553
peak=   -3.404 closest distance to " C   LEU A 143 " =    1.008
peak=   -3.404 closest distance to " CD2 TYR A 293 " =    1.948
peak=   -3.394 closest distance to " OD1 ASN A  39 " =    2.165
peak=   -3.393 closest distance to " O   HOH Z 309 " =    2.564
peak=   -3.389 closest distance to " O   HOH Z 427 " =    1.427
peak=   -3.387 closest distance to " O   LEU A 167 " =    1.487
peak=   -3.386 closest distance to " NH2AARG A 275 " =    4.989
peak=   -3.386 closest distance to " OD2 ASP A  50 " =    1.408
peak=   -3.381 closest distance to " CG  GLU A  53 " =    1.492
peak=   -3.377 closest distance to " O   HOH Z 422 " =    1.547
peak=   -3.374 closest distance to " O   HOH Z 394 " =    1.521
peak=   -3.373 closest distance to " CB  ALA A 291 " =    2.278
peak=   -3.370 closest distance to " CG1 VAL A 230 " =    1.978
peak=   -3.366 closest distance to " OD1 ASP A 191 " =    1.567
peak=   -3.364 closest distance to " O   ALA A 292 " =    2.043
peak=   -3.352 closest distance to " OE1 GLN A 183 " =    1.429
peak=   -3.345 closest distance to " CD1 LEU A 228 " =    2.030
peak=   -3.344 closest distance to " CA  GLY A 133 " =    1.881
peak=   -3.338 closest distance to " CZ  ARG A  66 " =    1.112
peak=   -3.337 closest distance to " O   HOH Z 134 " =    2.953
peak=   -3.334 closest distance to " CB  GLN A  11 " =    1.812
peak=   -3.332 closest distance to " CG  ASP A 231 " =    0.841
peak=   -3.328 closest distance to " O   HOH Z 377 " =    1.473
peak=   -3.327 closest distance to " CB  ASP A 286 " =    2.154
peak=   -3.320 closest distance to " OD2 ASP A  50 " =    2.314
peak=   -3.305 closest distance to " CD2 TYR A 247 " =    2.436
peak=   -3.301 closest distance to " CG1 VAL A 125 " =    2.323
peak=   -3.298 closest distance to " CD2 LEU A 300 " =    2.915
peak=   -3.297 closest distance to " O   HOH Z 198 " =    1.484
peak=   -3.295 closest distance to " O   ALA A  51 " =    1.262
peak=   -3.290 closest distance to " O   GLU A 152 " =    1.417
peak=   -3.285 closest distance to " OD1 ASP A 171 " =    1.528
peak=   -3.285 closest distance to " O   HOH Z 197 " =    5.060
peak=   -3.283 closest distance to " O   HOH Z 139 " =    3.098
peak=   -3.283 closest distance to " CB  PRO A 163 " =    2.471
peak=   -3.280 closest distance to " C   MET A 188 " =    1.523
peak=   -3.278 closest distance to " O   ILE A 106 " =    1.902
peak=   -3.275 closest distance to " CG1AVAL A  41 " =    2.682
peak=   -3.271 closest distance to " NH1 ARG A 195 " =    2.609
peak=   -3.270 closest distance to " O  BHOH Z 338 " =    1.374
peak=   -3.270 closest distance to " OD1 ASP A 191 " =    1.688
peak=   -3.270 closest distance to " O   HOH Z  15 " =    1.530
peak=   -3.269 closest distance to " OD1 ASN A 301 " =    1.992
peak=   -3.269 closest distance to " O   HOH Z 351 " =    1.418
peak=   -3.268 closest distance to " O   HOH Z  38 " =    1.650
peak=   -3.267 closest distance to " OG ASER A 134 " =    1.275
peak=   -3.261 closest distance to " C   GLN A 205 " =    1.842
peak=   -3.258 closest distance to " O   MET A  40 " =    2.742
peak=   -3.254 closest distance to " O   ALA A  34 " =    2.195
peak=   -3.252 closest distance to " CG  GLU A 152 " =    1.028
peak=   -3.252 closest distance to " O   HOH Z 263 " =    2.912
peak=   -3.250 closest distance to " O   VAL A 189 " =    1.769
peak=   -3.248 closest distance to " CG2 VAL A 189 " =    2.157
peak=   -3.247 closest distance to " O   HOH Z 234 " =    3.946
peak=   -3.247 closest distance to " OE1 GLN A  88 " =    1.146
peak=   -3.242 closest distance to " OG  SER A  62 " =    1.584
peak=   -3.235 closest distance to " C   ASP A 231 " =    2.571
peak=   -3.233 closest distance to " O   HOH Z 183 " =    1.562
peak=   -3.232 closest distance to " O   HOH Z 281 " =    2.623
peak=   -3.231 closest distance to " N   ALA A 226 " =    1.968
peak=   -3.228 closest distance to " O   HOH Z 111 " =    3.758
peak=   -3.226 closest distance to " CG  GLU A 277 " =    1.204
peak=   -3.223 closest distance to " O   HOH Z 421 " =    3.257
peak=   -3.222 closest distance to " CZ  PHE A 130 " =    0.927
peak=   -3.222 closest distance to " O   SER A 146 " =    1.090
peak=   -3.221 closest distance to " CB  ASP A 132 " =    2.403
peak=   -3.219 closest distance to " CB  TRP A  85 " =    2.594
peak=   -3.215 closest distance to " N   PHE A  59 " =    2.194
peak=   -3.214 closest distance to " CD2 PHE A 225 " =    1.243
peak=   -3.213 closest distance to " CD2 LEU A 300 " =    2.830
peak=   -3.213 closest distance to " O   HOH Z 250 " =    1.390
peak=   -3.209 closest distance to " NE2 GLN A 194 " =    1.729
peak=   -3.209 closest distance to " NH2 ARG A  79 " =    2.020
peak=   -3.208 closest distance to " O   HOH Z 174 " =    4.190
peak=   -3.206 closest distance to " O   HOH Z  71 " =    1.831
peak=   -3.204 closest distance to " N   MET A 105 " =    2.622
peak=   -3.199 closest distance to " O   HOH Z 200 " =    4.876
peak=   -3.197 closest distance to " O   ALA A  10 " =    1.754
peak=   -3.197 closest distance to " N   HIS A 115 " =    2.004
peak=   -3.196 closest distance to " O   HOH Z 283 " =    2.149
peak=   -3.195 closest distance to " O   HOH Z  11 " =    1.768
peak=   -3.187 closest distance to " O   HOH Z  43 " =    1.706
peak=   -3.186 closest distance to " O   ASN A  45 " =    1.871
peak=   -3.185 closest distance to " CA  GLY A 241 " =    3.077
peak=   -3.184 closest distance to " NH2 ARG A  66 " =    5.180
peak=   -3.179 closest distance to " O   SER A  26 " =    1.195
peak=   -3.170 closest distance to " O   HOH Z  37 " =    1.759
peak=   -3.169 closest distance to " O   HOH Z 417 " =    2.413
peak=   -3.168 closest distance to " ND2 ASN A  69 " =    1.575
peak=   -3.164 closest distance to " OXT GLY A 302 " =    3.234
peak=   -3.163 closest distance to " OE2 GLU A 152 " =    1.341
peak=   -3.161 closest distance to " O   HOH Z 414 " =    1.444
peak=   -3.156 closest distance to " O   HOH Z  47 " =    1.643
peak=   -3.146 closest distance to " CE3 TRP A 150 " =    2.206
peak=   -3.141 closest distance to " NE2 GLN A  88 " =    1.123
peak=   -3.139 closest distance to " O   ALA A 160 " =    1.514
peak=   -3.130 closest distance to " O   HOH Z  24 " =    1.603
peak=   -3.127 closest distance to " O   HOH Z 193 " =    1.618
peak=   -3.120 closest distance to " CA  GLY A 241 " =    2.308
peak=   -3.115 closest distance to " CZ3 TRP A 274 " =    2.406
peak=   -3.112 closest distance to " CZ2 TRP A 274 " =    1.068
peak=   -3.112 closest distance to " CB  VAL A  78 " =    1.744
peak=   -3.111 closest distance to " O   HOH Z 339 " =    1.776
peak=   -3.109 closest distance to " O   HOH Z 326 " =    1.697
peak=   -3.107 closest distance to " O   HOH Z 191 " =    5.800
peak=   -3.100 closest distance to " O   ALA A   1 " =    1.760
peak=   -3.100 closest distance to " O   HOH Z 362 " =    4.376
peak=   -3.093 closest distance to " C   ALA A 158 " =    1.305
peak=   -3.091 closest distance to " O   HOH Z 361 " =    3.455
peak=   -3.090 closest distance to " O   HOH Z 210 " =    1.091
peak=   -3.089 closest distance to " O   GLY A 111 " =    1.196
peak=   -3.088 closest distance to " O   HOH Z 265 " =    2.165
peak=   -3.083 closest distance to " CG  PHE A 283 " =    2.626
peak=   -3.081 closest distance to " ND2 ASN A  60 " =    1.413
peak=   -3.079 closest distance to " O   HOH Z 405 " =    2.492
peak=   -3.074 closest distance to " O   HOH Z 377 " =    1.882
peak=   -3.063 closest distance to " CE  MET A 105 " =    2.222
peak=   -3.031 closest distance to " CG  ARG A 269 " =    2.189

================= 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    :  0.3292 0.3275   6.058777e+00   6.047742e+00
   1_bss:  0.3165 0.3137   6.036975e+00   6.024365e+00
   1_xyz:  0.1858 0.2053   5.540168e+00   5.635942e+00
   1_adp:  0.1685 0.2118   5.482678e+00   5.664147e+00
   1_occ:  0.1683 0.2117   5.482045e+00   5.664140e+00
   2_bss:  0.1646 0.2078   5.468195e+00   5.650360e+00
   2_xyz:  0.1223 0.1646   5.208865e+00   5.426964e+00
   2_adp:  0.1171 0.1590   5.167300e+00   5.385785e+00
   2_occ:  0.1169 0.1587   5.166324e+00   5.384934e+00
   3_bss:  0.1169 0.1576   5.162797e+00   5.377694e+00
   3_xyz:  0.1094 0.1526   5.120068e+00   5.354097e+00
   3_adp:  0.1078 0.1527   5.112664e+00   5.354043e+00
   3_occ:  0.1078 0.1526   5.112367e+00   5.353877e+00
   4_bss:  0.1077 0.1526   5.112291e+00   5.353697e+00
   4_xyz:  0.1059 0.1526   5.105724e+00   5.354658e+00
   4_adp:  0.1054 0.1531   5.105357e+00   5.358056e+00
   4_occ:  0.1054 0.1531   5.105328e+00   5.358231e+00
   5_bss:  0.1053 0.1531   5.105371e+00   5.358202e+00
   5_xyz:  0.1064 0.1542   5.114412e+00   5.365755e+00
   5_adp:  0.1064 0.1549   5.116169e+00   5.370005e+00
   5_occ:  0.1063 0.1549   5.116229e+00   5.370219e+00
   5_bss:  0.1063 0.1549   5.116249e+00   5.370192e+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:  0.315  30.856   0.445  -1.891  -1.361  -0.000  -0.000  -0.000
   1_xyz:  0.315  30.856   0.445  -1.891  -1.361  -0.000  -0.000  -0.000
   1_adp:  0.315  30.856   0.445  -1.891  -1.361  -0.000  -0.000  -0.000
   1_occ:  0.315  30.856   0.445  -1.891  -1.361  -0.000  -0.000  -0.000
   2_bss:  0.317  39.164  -2.410  -2.360  -1.710  -0.000  -0.000  -0.000
   2_xyz:  0.317  39.164  -2.410  -2.360  -1.710  -0.000  -0.000  -0.000
   2_adp:  0.317  39.164  -2.410  -2.360  -1.710  -0.000  -0.000  -0.000
   2_occ:  0.317  39.164  -2.410  -2.360  -1.710  -0.000  -0.000  -0.000
   3_bss:  0.320  40.841  -2.943  -2.249  -1.541  -0.000  -0.000  -0.000
   3_xyz:  0.320  40.841  -2.943  -2.249  -1.541  -0.000  -0.000  -0.000
   3_adp:  0.320  40.841  -2.943  -2.249  -1.541  -0.000  -0.000  -0.000
   3_occ:  0.320  40.841  -2.943  -2.249  -1.541  -0.000  -0.000  -0.000
   4_bss:  0.322  42.091  -2.962  -2.107  -1.372  -0.000  -0.000  -0.000
   4_xyz:  0.322  42.091  -2.962  -2.107  -1.372  -0.000  -0.000  -0.000
   4_adp:  0.322  42.091  -2.962  -2.107  -1.372  -0.000  -0.000  -0.000
   4_occ:  0.322  42.091  -2.962  -2.107  -1.372  -0.000  -0.000  -0.000
   5_bss:  0.323  42.971  -2.823  -1.910  -1.159  -0.000  -0.000  -0.000
   5_xyz:  0.323  42.971  -2.823  -1.910  -1.159  -0.000  -0.000  -0.000
   5_adp:  0.323  42.971  -2.823  -1.910  -1.159  -0.000  -0.000  -0.000
   5_occ:  0.323  42.971  -2.823  -1.910  -1.159  -0.000  -0.000  -0.000
   5_bss:  0.323  43.669  -2.643  -1.693  -0.952  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.640 0.7205  0.9159    30921.823
   1_bss:  32.458 0.7324  0.9055    27802.151
   1_xyz:  19.449 0.8679  1.0101    10741.309
   1_adp:  20.216 0.8599  1.0048    11296.594
   1_occ:  20.234 0.8597  1.0045    11306.545
   2_bss:  19.814 0.8636  0.9633    10872.252
   2_xyz:  15.065 0.9057  0.9848     6854.684
   2_adp:  14.221 0.9129  0.9842     6434.929
   2_occ:  14.209 0.9129  0.9840     6412.893
   3_bss:  14.095 0.9137  0.9809     6281.590
   3_xyz:  13.503 0.9187  0.9837     5959.797
   3_adp:  13.478 0.9190  0.9798     5953.280
   3_occ:  13.472 0.9190  0.9797     5947.215
   4_bss:  13.471 0.9190  0.9831     5946.131
   4_xyz:  13.459 0.9193  0.9815     5973.077
   4_adp:  13.512 0.9189  0.9751     6006.345
   4_occ:  13.514 0.9189  0.9751     6005.998
   5_bss:  13.515 0.9189  0.9815     6005.889
   5_xyz:  13.610 0.9183  0.9817     6096.561
   5_adp:  13.697 0.9176  0.9753     6140.656
   5_occ:  13.699 0.9176  0.9753     6143.160
   5_bss:  13.700 0.9176  0.9815     6142.551
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.8581e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.8581e-01
   1_xyz:   1.092  0.008  0.072 15.117  0.005  4.108   6.8951e-02
   1_adp:   1.092  0.008  0.072 15.117  0.005  4.108   6.8951e-02
   1_occ:   1.092  0.008  0.072 15.117  0.005  4.108   6.8951e-02
   2_bss:   1.092  0.008  0.072 15.117  0.005  4.108   6.8951e-02
   2_xyz:   1.055  0.007  0.074 14.810  0.004  4.113   6.1769e-02
   2_adp:   1.055  0.007  0.074 14.810  0.004  4.113   6.1769e-02
   2_occ:   1.055  0.007  0.074 14.810  0.004  4.113   6.1769e-02
   3_bss:   1.055  0.007  0.074 14.810  0.004  4.113   6.1769e-02
   3_xyz:   1.052  0.007  0.076 14.870  0.004  4.112   6.3861e-02
   3_adp:   1.052  0.007  0.076 14.870  0.004  4.112   6.3861e-02
   3_occ:   1.052  0.007  0.076 14.870  0.004  4.112   6.3861e-02
   4_bss:   1.052  0.007  0.076 14.870  0.004  4.112   6.3861e-02
   4_xyz:   1.057  0.008  0.079 14.819  0.005  4.112   6.4658e-02
   4_adp:   1.057  0.008  0.079 14.819  0.005  4.112   6.4658e-02
   4_occ:   1.057  0.008  0.079 14.819  0.005  4.112   6.4658e-02
   5_bss:   1.057  0.008  0.079 14.819  0.005  4.112   6.4658e-02
   5_xyz:   0.983  0.006  0.074 14.601  0.004  4.112   5.6891e-02
   5_adp:   0.983  0.006  0.074 14.601  0.004  4.112   5.6891e-02
   5_occ:   0.983  0.006  0.074 14.601  0.004  4.112   5.6891e-02
   5_bss:   0.983  0.006  0.074 14.601  0.004  4.112   5.6891e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.357   2.4016e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.357   2.4016e-01
   1_xyz:   7.147  0.056  0.258 84.403  0.037  2.192   7.0303e-02
   1_adp:   7.147  0.056  0.258 84.403  0.037  2.192   7.0303e-02
   1_occ:   7.147  0.056  0.258 84.403  0.037  2.192   7.0303e-02
   2_bss:   7.147  0.056  0.258 84.403  0.037  2.192   7.0303e-02
   2_xyz:   7.585  0.045  0.220 82.860  0.040  2.291   4.5437e-02
   2_adp:   7.585  0.045  0.220 82.860  0.040  2.291   4.5437e-02
   2_occ:   7.585  0.045  0.220 82.860  0.040  2.291   4.5437e-02
   3_bss:   7.585  0.045  0.220 82.860  0.040  2.291   4.5437e-02
   3_xyz:   7.502  0.046  0.235 82.564  0.041  2.335   4.8450e-02
   3_adp:   7.502  0.046  0.235 82.564  0.041  2.335   4.8450e-02
   3_occ:   7.502  0.046  0.235 82.564  0.041  2.335   4.8450e-02
   4_bss:   7.502  0.046  0.235 82.564  0.041  2.335   4.8450e-02
   4_xyz:   7.319  0.049  0.258 82.592  0.043  2.308   4.9845e-02
   4_adp:   7.319  0.049  0.258 82.592  0.043  2.308   4.9845e-02
   4_occ:   7.319  0.049  0.258 82.592  0.043  2.308   4.9845e-02
   5_bss:   7.319  0.049  0.258 82.592  0.043  2.308   4.9845e-02
   5_xyz:   6.897  0.046  0.236 83.424  0.040  2.357   3.8716e-02
   5_adp:   6.897  0.046  0.236 83.424  0.040  2.357   3.8716e-02
   5_occ:   6.897  0.046  0.236 83.424  0.040  2.357   3.8716e-02
   5_bss:   6.897  0.046  0.236 83.424  0.040  2.357   3.8716e-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:  78.66   0.00  17.24  78.66   0.00  13.29  71.42   7.46  38.74
   1_occ:  78.66   0.00  17.24  78.66   0.00  13.29  71.42   7.46  38.74
   2_bss:  78.66   0.00  17.24  78.66   0.00  13.29  71.42   7.46  38.74
   2_xyz:  78.66   0.00  17.24  78.66   0.00  13.29  71.42   7.46  38.74
   2_adp:  79.23   1.79  16.80  79.23   1.79  12.99  67.63   6.44  37.54
   2_occ:  79.23   1.79  16.80  79.23   1.79  12.99  67.63   6.44  37.54
   3_bss:  79.23   1.79  16.80  79.23   1.79  12.99  67.63   6.44  37.54
   3_xyz:  79.23   1.79  16.80  79.23   1.79  12.99  67.63   6.44  37.54
   3_adp:  80.84   1.81  16.83  80.84   1.81  12.89  69.38   6.21  38.26
   3_occ:  80.84   1.81  16.83  80.84   1.81  12.89  69.38   6.21  38.26
   4_bss:  80.84   1.81  16.83  80.84   1.81  12.89  69.38   6.21  38.26
   4_xyz:  80.84   1.81  16.83  80.84   1.81  12.89  69.38   6.21  38.26
   4_adp:  83.51   1.21  16.77  83.51   1.21  12.75  72.64   5.90  38.64
   4_occ:  83.51   1.21  16.77  83.51   1.21  12.75  72.64   5.90  38.64
   5_bss:  83.51   1.21  16.77  83.51   1.21  12.75  72.64   5.90  38.64
   5_xyz:  83.51   1.21  16.77  83.51   1.21  12.75  72.64   5.90  38.64
   5_adp:  84.12   0.78  16.65  84.12   0.78  12.60  73.59   5.61  38.71
   5_occ:  84.12   0.78  16.65  84.12   0.78  12.60  73.59   5.61  38.71
   5_bss:  84.10   0.75  16.63  84.10   0.75  12.58  73.56   5.58  38.69
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.445    0.014    0.309
   1_adp:    1.445    0.014    0.309
   1_occ:    1.445    0.014    0.309
   2_bss:    1.445    0.014    0.309
   2_xyz:    1.044    0.032    0.381
   2_adp:    1.044    0.032    0.381
   2_occ:    1.044    0.032    0.381
   3_bss:    1.044    0.032    0.381
   3_xyz:    1.060    0.042    0.400
   3_adp:    1.060    0.042    0.400
   3_occ:    1.060    0.042    0.400
   4_bss:    1.060    0.042    0.400
   4_xyz:    1.187    0.064    0.412
   4_adp:    1.187    0.064    0.412
   4_occ:    1.187    0.064    0.412
   5_bss:    1.187    0.064    0.412
   5_xyz:    1.301    0.057    0.415
   5_adp:    1.301    0.057    0.415
   5_occ:    1.301    0.057    0.415
   5_bss:    1.301    0.057    0.415
------------------------------------------------------------------------

CPU time actual refinement: 333.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/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_191/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_191/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.74 
  Macro-tasks:
    bulk solvent and scale       = 36.24  
    individual site refinement   = 139.83 
    weights calculation          = 30.15  
    collect and process          = 6.71   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.04 
  Micro-tasks:
    mask                            = 1.20   
    f_calc                          = 107.75 
    alpha_beta                      = 8.29   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.16 
    fmodel                         = 6.54   
    r_factors                      = 0.15   
    phase_errors                   = 11.20  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 253.75 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.700 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    655 calls, 107.37 s
gradients_fft:          600 calls, 103.33 s

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

# Date 2008-01-16 Time 04:14:09 PST -0800 (1200485649.45 s)
Start R-work = 0.3292, R-free = 0.3275 (no bulk solvent and anisotropic scale)
Final R-work = 0.1307, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.3165, R-free = 0.3137
Final R-work = 0.1063, R-free = 0.1549