# Date 2008-01-16 Time 04:35:27 PST -0800 (1200486927.05 s)
#phil __OFF__

Command line arguments: "../377.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23277
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 377

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.9622
Completeness in resolution range: 0.969321
Completeness with d_max=infinity: 0.966308

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9622

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: (69.5475, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.9622
Completeness in resolution range: 0.969321
Completeness with d_max=infinity: 0.966308

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.1985 [2119/2143]  1906   213  10.1%
  bin  2:  4.1985 -  3.3451 [2038/2058]  1835   203  10.0%
  bin  3:  3.3451 -  2.9259 [2013/2032]  1813   200   9.9%
  bin  4:  2.9259 -  2.6601 [2000/2030]  1800   200  10.0%
  bin  5:  2.6601 -  2.4703 [1987/2006]  1787   200  10.1%
  bin  6:  2.4703 -  2.3253 [1959/1984]  1760   199  10.2%
  bin  7:  2.3253 -  2.2092 [1955/1983]  1762   193   9.9%
  bin  8:  2.2092 -  2.1133 [1968/2004]  1772   196  10.0%
  bin  9:  2.1133 -  2.0322 [1944/1986]  1751   193   9.9%
  bin 10:  2.0322 -  1.9622 [1606/1983]  1444   162  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 31
        2.29 -     2.94: 1674
        2.94 -     3.59: 4623
        3.59 -     4.25: 9397
        4.25 -     4.90: 13155
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.636 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.801 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.801 3.040 -x+1/2,-y+1,z-1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.814 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28875 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_377/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/model_refine_001.geo

CPU time processing inputs: 9.33


============================ 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 = 69.5475 45.9914 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4251   r_free= 0.4228   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.232267                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.6828 0.99   1382  153 0.3474 0.3463      6.5068       6.498|
|  2:  4.6828 -  3.7364 0.99   1324  149 0.3589 0.3237      6.7205      6.6484|
|  3:  3.7364 -  3.2698 0.99   1297  142 0.3922 0.3745      6.6352      6.6925|
|  4:  3.2698 -  2.9735 0.99   1291  145 0.4016 0.4161      6.4699      6.4689|
|  5:  2.9735 -  2.7618 0.99   1279  143 0.4511 0.4150      6.3233      6.3095|
|  6:  2.7618 -  2.5999 0.99   1299  140 0.4503 0.4833      6.2455        6.19|
|  7:  2.5999 -  2.4703 0.99   1269  144 0.4527 0.4712      6.1917      6.1672|
|  8:  2.4703 -  2.3632 0.98   1259  138 0.4755 0.4693      6.1606      6.1593|
|  9:  2.3632 -  2.2726 0.98   1261  143 0.4657 0.4787      6.0896      6.1155|
| 10:  2.2726 -  2.1944 1.00   1266  143 0.4642 0.4993      6.0709      6.1045|
| 11:  2.1944 -  2.1260 0.97   1261  135 0.4663 0.4852      5.9998      6.0476|
| 12:  2.1260 -  2.0654 0.98   1239  141 0.4632 0.4477       5.954      5.9388|
| 13:  2.0654 -  2.0112 0.99   1287  141 0.4729 0.4617      5.8599      5.8206|
| 14:  2.0112 -  1.9622 0.73    916  102 0.5073 0.4579      5.8546      5.7538|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.6828  1382   153  0.73  31.94   0.84     0.77      63464.02|
|  2:  4.6828 -  3.7364  1324   149  0.75  30.79   0.94     0.87      85674.37|
|  3:  3.7364 -  3.2698  1297   142  0.67  37.82   0.96     0.86      91566.04|
|  4:  3.2698 -  2.9735  1291   145  0.60  44.01   0.97     0.79      84803.35|
|  5:  2.9735 -  2.7618  1279   143  0.51  51.02   0.93     0.71      68328.40|
|  6:  2.7618 -  2.5999  1299   140  0.50  51.92   0.93     0.68      59919.74|
|  7:  2.5999 -  2.4703  1269   144  0.47  54.04   0.96     0.66      55348.32|
|  8:  2.4703 -  2.3632  1259   138  0.45  55.98   0.97     0.65      52451.27|
|  9:  2.3632 -  2.2726  1261   143  0.45  55.97   0.94     0.65      48100.17|
| 10:  2.2726 -  2.1944  1266   143  0.46  55.62   0.99     0.65      42564.63|
| 11:  2.1944 -  2.1260  1261   135  0.45  55.76   1.00     0.69      39400.12|
| 12:  2.1260 -  2.0654  1239   141  0.48  53.86   1.02     0.72      34141.26|
| 13:  2.0654 -  2.0112  1287   141  0.48  53.82   0.99     0.73      28370.63|
| 14:  2.0112 -  1.9622   916   102  0.52  50.55   1.00     0.72      21494.50|
|alpha:            min =        0.65 max =            0.87 mean =         0.73|
|beta:             min =    21494.50 max =        91566.04 mean =     56359.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.97 mean =        48.56|
|phase err.(test): min =        0.00 max =           89.83 mean =        48.74|
|-----------------------------------------------------------------------------|

============================== 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 = 10.061427             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.384   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.644874              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.882   (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 |  1.636 -  1.962:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.962 -  2.289:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.289 -  2.615:       67 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.615 -  2.942:     1607 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.942 -  3.268:     1964 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.268 -  3.594:     2659 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.594 -  3.921:     4804 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.921 -  4.247:     4593 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.574:     5982 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.574 -  4.900:     7173 |
|-----------------------------------------------------------------------------|
|-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 |        0.178 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.636 |       0.443 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    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 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4251   r_free= 0.4228   ksol= 0.00   Bsol= 0.00   scale= 0.933    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.232267                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4135   r_free= 0.4095   ksol= 0.34   Bsol= 22.80   scale= 0.952   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,2.92,-0.88,0.00,-0.00,-0.00); trace/3= -0.19                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.221497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.292356              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.242   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.899478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.729   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4135      final r-factor (work) = 0.2844          |
| start r-factor (free) = 0.4095      final r-factor (free) = 0.3161          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.9643 = 8.29 * 0.50 * 6.2194 + 1.00 * 0.1777                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.1846 = 8.29 * 0.50 * 6.0444 + 1.00 * 0.1235                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2844      final r-factor (work) = 0.2581          |
| start r-factor (free) = 0.3161      final r-factor (free) = 0.3320          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4429 = 0.90 * 1.00 * 6.0444 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2989 = 0.90 * 1.00 * 5.8741 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.58   18.01    None  None   None       |
|    all(noH): 2823   0      0.00    97.58   18.01    None  None   None       |
|    Sol.    : 438    0      3.42    97.58   38.99    None  None   None       |
|    Mac.    : 2385   0      0.00    78.40   14.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.758:  923   |   5:    48.791 -  58.549:  105        |
|      1:     9.758 -  19.516: 1016   |   6:    58.549 -  68.307:   38        |
|      2:    19.516 -  29.274:  387   |   7:    68.307 -  78.065:   15        |
|      3:    29.274 -  39.033:  211   |   8:    78.065 -  87.823:    1        |
|      4:    39.033 -  48.791:  126   |   9:    87.823 -  97.581:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2581 r_free = 0.3320             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2577 r_free = 0.3325             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2577   r_free= 0.3325   ksol= 0.34   Bsol= 22.80   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.62,2.92,-0.88,0.00,-0.00,-0.00); trace/3= -0.19                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.891656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2561   r_free= 0.3301   ksol= 0.33   Bsol= 38.74   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-0.11,-0.90,-0.00,-0.00,-0.00); trace/3= -1.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.884324                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.953471              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.856   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248008              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2561      final r-factor (work) = 0.1891          |
| start r-factor (free) = 0.3301      final r-factor (free) = 0.2404          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6047 = 5.95 * 0.50 * 5.8726 + 1.00 * 0.1235                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2380 = 5.95 * 0.50 * 5.7670 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1891      final r-factor (work) = 0.1670          |
| start r-factor (free) = 0.2404      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4453 = 0.25 * 1.00 * 5.7670 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3812 = 0.25 * 1.00 * 5.5367 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    91.54   17.17    None  None   None       |
|    all(noH): 2823   0      1.07    91.54   17.17    None  None   None       |
|    Sol.    : 438    0      5.95    91.54   39.20    None  None   None       |
|    Mac.    : 2385   0      1.07    80.20   13.12    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:     1.073 -  10.120: 1007   |   5:    46.306 -  55.352:  107        |
|      1:    10.120 -  19.166: 1087   |   6:    55.352 -  64.398:   51        |
|      2:    19.166 -  28.213:  268   |   7:    64.398 -  73.445:   14        |
|      3:    28.213 -  37.259:  152   |   8:    73.445 -  82.491:    2        |
|      4:    37.259 -  46.306:  134   |   9:    82.491 -  91.538:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1670 r_free = 0.2149             target_work(ml) = 5.487         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1668 r_free = 0.2147             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1668   r_free= 0.2147   ksol= 0.33   Bsol= 38.74   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.13,-0.11,-0.90,-0.00,-0.00,-0.00); trace/3= -1.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.485721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1664   r_free= 0.2129   ksol= 0.33   Bsol= 40.74   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.59,-1.02,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.478175                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.885645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.660  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343729              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.226  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1664      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.2129      final r-factor (free) = 0.1830          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2905 = 1.89 * 0.50 * 5.5357 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1296 = 1.89 * 0.50 * 5.3889 + 1.00 * 0.0488                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1301          |
| start r-factor (free) = 0.1830      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8604 = 0.34 * 1.00 * 5.3889 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8239 = 0.34 * 1.00 * 5.2811 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.73    89.68   17.22    None  None   None       |
|    all(noH): 2823   0      0.73    89.68   17.22    None  None   None       |
|    Sol.    : 438    0      5.67    89.68   40.93    None  None   None       |
|    Mac.    : 2385   0      0.73    84.73   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.731 -   9.626:  946   |   5:    45.206 -  54.102:  115        |
|      1:     9.626 -  18.521: 1162   |   6:    54.102 -  62.997:   68        |
|      2:    18.521 -  27.416:  244   |   7:    62.997 -  71.892:   32        |
|      3:    27.416 -  36.311:  126   |   8:    71.892 -  80.787:    7        |
|      4:    36.311 -  45.206:  121   |   9:    80.787 -  89.682:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1301 r_free = 0.1785             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1300 r_free = 0.1784             target_work(ml) = 5.265         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1784   ksol= 0.33   Bsol= 40.74   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.32,-1.59,-1.02,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.264703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1784   ksol= 0.32   Bsol= 39.62   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.29,-1.28,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.264532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.077539              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.315  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.412990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.145  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1784      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5368 = 2.08 * 0.50 * 5.2831 + 1.00 * 0.0488                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4738 = 2.08 * 0.50 * 5.2171 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1632 = 0.41 * 1.00 * 5.2171 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1397 = 0.41 * 1.00 * 5.1599 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.42    89.77   17.11    None  None   None       |
|    all(noH): 2823   0      0.42    89.77   17.11    None  None   None       |
|    Sol.    : 438    0      6.06    89.77   40.83    None  None   None       |
|    Mac.    : 2385   0      0.42    89.44   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.416 -   9.351:  887   |   5:    45.092 -  54.027:  105        |
|      1:     9.351 -  18.286: 1228   |   6:    54.027 -  62.962:   71        |
|      2:    18.286 -  27.221:  249   |   7:    62.962 -  71.897:   35        |
|      3:    27.221 -  36.156:  126   |   8:    71.897 -  80.832:   10        |
|      4:    36.156 -  45.092:  109   |   9:    80.832 -  89.767:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1603             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1602             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1602   ksol= 0.32   Bsol= 39.62   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-2.29,-1.28,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150312                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1602   ksol= 0.32   Bsol= 40.87   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.32,-1.23,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.149951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.583528              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.178  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.401711              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.843  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1136      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1398 = 1.58 * 0.50 * 5.1597 + 1.00 * 0.0545                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1213 = 1.58 * 0.50 * 5.1444 + 1.00 * 0.0481                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0753 = 0.40 * 1.00 * 5.1444 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0724 = 0.40 * 1.00 * 5.1372 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    90.02   16.97    None  None   None       |
|    all(noH): 2823   0      0.55    90.02   16.97    None  None   None       |
|    Sol.    : 438    0      6.09    89.61   40.58    None  None   None       |
|    Mac.    : 2385   0      0.55    90.02   12.63    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:     0.545 -   9.493:  959   |   5:    45.284 -  54.232:  104        |
|      1:     9.493 -  18.441: 1176   |   6:    54.232 -  63.180:   67        |
|      2:    18.441 -  27.389:  230   |   7:    63.180 -  72.128:   33        |
|      3:    27.389 -  36.337:  133   |   8:    72.128 -  81.076:   11        |
|      4:    36.337 -  45.284:  107   |   9:    81.076 -  90.023:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1581             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1582             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1582   ksol= 0.32   Bsol= 40.87   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-2.32,-1.23,-0.00,-0.00,-0.00); trace/3= -2.03                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136704                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.6828 0.99   1382  153 0.0993 0.1242      5.3716      5.5216|
|  2:  4.6828 -  3.7364 0.99   1324  149 0.0848 0.1131      5.4366      5.6376|
|  3:  3.7364 -  3.2698 0.99   1297  142 0.1078 0.1500      5.4931      5.8487|
|  4:  3.2698 -  2.9735 0.99   1291  145 0.1235 0.1638      5.4542       5.609|
|  5:  2.9735 -  2.7618 0.99   1279  143 0.1327 0.1773       5.333      5.5276|
|  6:  2.7618 -  2.5999 0.99   1299  140 0.1176 0.1773      5.1973      5.4214|
|  7:  2.5999 -  2.4703 0.99   1269  144 0.1278 0.1582      5.1578      5.3631|
|  8:  2.4703 -  2.3632 0.98   1259  138 0.1169 0.1734      5.0623      5.3292|
|  9:  2.3632 -  2.2726 0.98   1261  143 0.1140 0.1644      5.0131      5.2368|
| 10:  2.2726 -  2.1944 1.00   1266  143 0.1104 0.1766      4.9508      5.2274|
| 11:  2.1944 -  2.1260 0.97   1261  135 0.1120 0.1781      4.9332      5.2635|
| 12:  2.1260 -  2.0654 0.98   1239  141 0.1134 0.1716      4.8834      5.1945|
| 13:  2.0654 -  2.0112 0.99   1287  141 0.1124 0.1831      4.7872      5.0851|
| 14:  2.0112 -  1.9622 0.73    916  102 0.1003 0.1652      4.6506      4.8972|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.6828  1382   153  0.94   8.89   0.99     0.96       6707.95|
|  2:  4.6828 -  3.7364  1324   149  0.95   7.82   1.03     1.02       8920.49|
|  3:  3.7364 -  3.2698  1297   142  0.93  11.26   1.04     1.03      10507.72|
|  4:  3.2698 -  2.9735  1291   145  0.92  13.67   1.02     1.00      10154.93|
|  5:  2.9735 -  2.7618  1279   143  0.90  15.46   1.01     0.98       8211.62|
|  6:  2.7618 -  2.5999  1299   140  0.90  15.46   0.99     0.96       6846.35|
|  7:  2.5999 -  2.4703  1269   144  0.90  15.88   0.99     0.96       6064.24|
|  8:  2.4703 -  2.3632  1259   138  0.91  14.68   1.00     0.98       5074.30|
|  9:  2.3632 -  2.2726  1261   143  0.92  14.65   1.01     0.98       4785.43|
| 10:  2.2726 -  2.1944  1266   143  0.91  15.18   1.01     0.98       4300.86|
| 11:  2.1944 -  2.1260  1261   135  0.90  16.15   1.00     0.97       4308.45|
| 12:  2.1260 -  2.0654  1239   141  0.91  15.34   1.02     1.01       3982.22|
| 13:  2.0654 -  2.0112  1287   141  0.90  15.77   1.01     0.99       3284.50|
| 14:  2.0112 -  1.9622   916   102  0.93  13.65   1.00     0.97       2495.28|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2495.28 max =        10507.72 mean =      6220.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.75 mean =        13.43|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1582   ksol= 0.32   Bsol= 41.46   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.25,-1.11,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136628                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1582   ksol= 0.32   Bsol= 41.46   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,-2.25,-1.11,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.136628                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.6828 0.99   1382  153 0.0994 0.1244      5.3723      5.5226|
|  2:  4.6828 -  3.7364 0.99   1324  149 0.0848 0.1131      5.4373      5.6381|
|  3:  3.7364 -  3.2698 0.99   1297  142 0.1078 0.1500      5.4936      5.8492|
|  4:  3.2698 -  2.9735 0.99   1291  145 0.1235 0.1638      5.4542       5.609|
|  5:  2.9735 -  2.7618 0.99   1279  143 0.1327 0.1772      5.3327      5.5269|
|  6:  2.7618 -  2.5999 0.99   1299  140 0.1175 0.1771      5.1968      5.4207|
|  7:  2.5999 -  2.4703 0.99   1269  144 0.1278 0.1582      5.1575      5.3631|
|  8:  2.4703 -  2.3632 0.98   1259  138 0.1169 0.1733      5.0621      5.3284|
|  9:  2.3632 -  2.2726 0.98   1261  143 0.1140 0.1643       5.013      5.2367|
| 10:  2.2726 -  2.1944 1.00   1266  143 0.1104 0.1767      4.9507       5.228|
| 11:  2.1944 -  2.1260 0.97   1261  135 0.1119 0.1780      4.9332      5.2634|
| 12:  2.1260 -  2.0654 0.98   1239  141 0.1133 0.1717       4.883      5.1944|
| 13:  2.0654 -  2.0112 0.99   1287  141 0.1124 0.1829      4.7868      5.0842|
| 14:  2.0112 -  1.9622 0.73    916  102 0.1003 0.1650      4.6497       4.896|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.6828  1382   153  0.94   8.90   0.99     0.96       6718.62|
|  2:  4.6828 -  3.7364  1324   149  0.95   7.83   1.03     1.02       8933.20|
|  3:  3.7364 -  3.2698  1297   142  0.93  11.27   1.04     1.03      10519.12|
|  4:  3.2698 -  2.9735  1291   145  0.92  13.67   1.02     1.00      10154.47|
|  5:  2.9735 -  2.7618  1279   143  0.90  15.46   1.01     0.98       8203.59|
|  6:  2.7618 -  2.5999  1299   140  0.90  15.46   0.99     0.97       6839.19|
|  7:  2.5999 -  2.4703  1269   144  0.90  15.87   1.00     0.97       6058.23|
|  8:  2.4703 -  2.3632  1259   138  0.91  14.68   1.00     0.99       5070.17|
|  9:  2.3632 -  2.2726  1261   143  0.92  14.65   1.02     0.99       4785.36|
| 10:  2.2726 -  2.1944  1266   143  0.91  15.18   1.01     0.98       4300.45|
| 11:  2.1944 -  2.1260  1261   135  0.90  16.15   1.01     0.97       4309.87|
| 12:  2.1260 -  2.0654  1239   141  0.91  15.34   1.02     1.01       3979.79|
| 13:  2.0654 -  2.0112  1287   141  0.90  15.75   1.02     1.00       3279.83|
| 14:  2.0112 -  1.9622   916   102  0.93  13.63   1.00     0.97       2488.75|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2488.75 max =        10519.12 mean =      6219.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.76 mean =        13.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.418)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.53    90.01   16.95    None  None   None       |
|    all(noH): 2823   0      0.53    90.01   16.95    None  None   None       |
|    Sol.    : 438    0      6.07    89.59   40.56    None  None   None       |
|    Mac.    : 2385   0      0.53    90.01   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.528 -   9.476:  959   |   5:    45.267 -  54.215:  104        |
|      1:     9.476 -  18.423: 1176   |   6:    54.215 -  63.163:   67        |
|      2:    18.423 -  27.371:  230   |   7:    63.163 -  72.110:   33        |
|      3:    27.371 -  36.319:  133   |   8:    72.110 -  81.058:   11        |
|      4:    36.319 -  45.267:  107   |   9:    81.058 -  90.006:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 303         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 4.312
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 303
   mapped sites are within: 0.707 - 4.312

peak=    6.651 closest distance to " NE2 GLN A  11 " =    1.299
peak=    6.046 closest distance to " O   HOH Z 144 " =    1.850
peak=    5.795 closest distance to " O   HOH Z 126 " =    2.138
peak=    5.619 closest distance to " CG  PRO A  54 " =    1.339
peak=    5.584 closest distance to " O   HOH Z 236 " =    1.542
peak=    5.307 closest distance to " O   HOH Z  65 " =    1.006
peak=    5.256 closest distance to " NH2 ARG A  56 " =    2.041
peak=    5.241 closest distance to " O   HOH Z 427 " =    2.113
peak=    5.190 closest distance to " CG  PRO A 213 " =    1.299
peak=    5.186 closest distance to " CB  ARG A 275 " =    0.950
peak=    5.128 closest distance to " O   HOH Z 287 " =    1.863
peak=    5.110 closest distance to " O   HOH Z 417 " =    1.586
peak=    5.072 closest distance to " O   HOH Z 423 " =    1.621
peak=    4.970 closest distance to " O   HOH Z 112 " =    1.418
peak=    4.853 closest distance to " CG  PRO A  90 " =    1.170
peak=    4.836 closest distance to " O   HOH Z 232 " =    2.254
peak=    4.814 closest distance to " CG2 VAL A 257 " =    0.899
peak=    4.790 closest distance to " O   HOH Z 375 " =    1.106
peak=    4.773 closest distance to " O   HOH Z 380 " =    1.705
peak=    4.759 closest distance to " CB  PRO A  54 " =    1.004
peak=    4.699 closest distance to " O   HOH Z  78 " =    1.622
peak=    4.636 closest distance to " CB  SER A  63 " =    1.254
peak=    4.634 closest distance to " O   HOH Z 427 " =    1.110
peak=    4.634 closest distance to " CB  GLN A 223 " =    1.527
peak=    4.621 closest distance to " O   HOH Z  63 " =    1.666
peak=    4.584 closest distance to " CB  GLU A 128 " =    1.027
peak=    4.568 closest distance to " O   HOH Z 124 " =    1.448
peak=    4.563 closest distance to " O   HOH Z 193 " =    1.777
peak=    4.536 closest distance to " O   HOH Z 298 " =    1.874
peak=    4.510 closest distance to " CB  ASN A 148 " =    1.351
peak=    4.485 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.481 closest distance to " CB  SER A   3 " =    1.261
peak=    4.459 closest distance to " CG  TRP A 179 " =    2.259
peak=    4.441 closest distance to " O   HOH Z 272 " =    1.822
peak=    4.362 closest distance to " CG  ARG A  66 " =    2.409
peak=    4.358 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.331 closest distance to " O   HOH Z  44 " =    1.850
peak=    4.298 closest distance to " OG BSER A 164 " =    2.309
peak=    4.292 closest distance to " O   HOH Z 419 " =    2.334
peak=    4.291 closest distance to " O   HOH Z 316 " =    2.971
peak=    4.291 closest distance to " CB  GLN A 183 " =    1.189
peak=    4.269 closest distance to " O   HOH Z 368 " =    3.598
peak=    4.237 closest distance to " O   HOH Z   9 " =    2.051
peak=    4.226 closest distance to " O   HOH Z 371 " =    1.934
peak=    4.219 closest distance to " O   HOH Z 371 " =    2.182
peak=    4.195 closest distance to " NZ  LYS A 117 " =    2.925
peak=    4.129 closest distance to " CG  PRO A 280 " =    0.782
peak=    4.105 closest distance to " O   HOH Z   9 " =    1.133
peak=    4.101 closest distance to " O   SER A  87 " =    2.247
peak=    4.081 closest distance to " O   HOH Z 209 " =    2.235
peak=    4.074 closest distance to " O   HOH Z 403 " =    1.349
peak=    4.049 closest distance to " O   HOH Z   1 " =    1.582
peak=    4.029 closest distance to " O   HOH Z 425 " =    1.383
peak=    4.016 closest distance to " CB  ARG A  79 " =    1.302
peak=    4.014 closest distance to " O   HOH Z 234 " =    3.575
peak=    3.997 closest distance to " O   HOH Z 352 " =    1.648
peak=    3.984 closest distance to " O   HOH Z 425 " =    1.946
peak=    3.967 closest distance to " CB  GLU A 152 " =    1.263
peak=    3.964 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.959 closest distance to " O   HOH Z 365 " =    2.683
peak=    3.953 closest distance to " CB  VAL A 265 " =    1.304
peak=    3.952 closest distance to " ND2 ASN A 187 " =    1.529
peak=    3.951 closest distance to " O   HOH Z 128 " =    1.992
peak=    3.947 closest distance to " CB  ASN A 187 " =    1.448
peak=    3.940 closest distance to " O   HOH Z 394 " =    1.598
peak=    3.924 closest distance to " CG  PRO A 243 " =    1.132
peak=    3.920 closest distance to " OG BSER A  99 " =    2.294
peak=    3.919 closest distance to " O   HOH Z   2 " =    1.800
peak=    3.913 closest distance to " O   HOH Z 250 " =    1.516
peak=    3.889 closest distance to " CB  ARG A 139 " =    1.006
peak=    3.885 closest distance to " O   HOH Z   1 " =    1.707
peak=    3.860 closest distance to " CG  GLN A  11 " =    2.040
peak=    3.857 closest distance to " CA  ALA A 299 " =    0.929
peak=    3.853 closest distance to " NH1BARG A 145 " =    1.310
peak=    3.844 closest distance to " CB  TYR A 169 " =    0.712
peak=    3.839 closest distance to " O   HOH Z 389 " =    1.704
peak=    3.828 closest distance to " CA  ASN A 215 " =    1.031
peak=    3.815 closest distance to " N   GLU A   2 " =    1.329
peak=    3.808 closest distance to " O   HOH Z 344 " =    3.125
peak=    3.800 closest distance to " NH1AARG A 145 " =    1.155
peak=    3.799 closest distance to " O   HOH Z 245 " =    1.274
peak=    3.798 closest distance to " O   HOH Z 261 " =    2.103
peak=    3.796 closest distance to " O   HOH Z   7 " =    1.310
peak=    3.792 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.781 closest distance to " N   GLN A 278 " =    1.127
peak=    3.776 closest distance to " OD1 ASN A  69 " =    2.445
peak=    3.759 closest distance to " O   HOH Z  61 " =    1.730
peak=    3.759 closest distance to " CB  SER A 216 " =    0.776
peak=    3.758 closest distance to " CB  ILE A 120 " =    1.291
peak=    3.730 closest distance to " O   HOH Z 405 " =    1.391
peak=    3.725 closest distance to " CB  TRP A 179 " =    1.317
peak=    3.714 closest distance to " O   HOH Z 327 " =    1.704
peak=    3.707 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.703 closest distance to " CH2 TRP A  92 " =    2.108
peak=    3.700 closest distance to " O   HOH Z 214 " =    2.250
peak=    3.699 closest distance to " CD  ARG A 159 " =    0.788
peak=    3.697 closest distance to " O   HOH Z 132 " =    2.194
peak=    3.687 closest distance to " O   HOH Z 286 " =    2.297
peak=    3.671 closest distance to " O   HOH Z 139 " =    1.157
peak=    3.670 closest distance to " CD BLYS A 290 " =    1.096
peak=    3.669 closest distance to " O   HOH Z 146 " =    1.726
peak=    3.666 closest distance to " O   HOH Z 371 " =    2.992
peak=    3.665 closest distance to " CG2 THR A 221 " =    1.237
peak=    3.664 closest distance to " NE2 GLN A  73 " =    3.543
peak=    3.661 closest distance to " CE  LYS A  76 " =    0.851
peak=    3.643 closest distance to " OD1BASN A 224 " =    2.160
peak=    3.642 closest distance to " O   HOH Z 368 " =    1.883
peak=    3.635 closest distance to " O   HOH Z  59 " =    2.091
peak=    3.631 closest distance to " O   HOH Z 158 " =    2.654
peak=    3.628 closest distance to " C   PRO A 198 " =    1.491
peak=    3.619 closest distance to " CB  ARG A 190 " =    1.684
peak=    3.618 closest distance to " O   HOH Z 386 " =    2.993
peak=    3.610 closest distance to " O   HOH Z 289 " =    1.601
peak=    3.609 closest distance to " O   HOH Z  97 " =    1.923
peak=    3.607 closest distance to " OG  SER A  62 " =    2.940
peak=    3.603 closest distance to " O   HOH Z 151 " =    1.541
peak=    3.595 closest distance to " CG2 ILE A 120 " =    1.143
peak=    3.594 closest distance to " O   HOH Z 119 " =    4.312
peak=    3.594 closest distance to " O   HOH Z 189 " =    1.844
peak=    3.589 closest distance to " O   HOH Z 426 " =    1.887
peak=    3.585 closest distance to " O   HOH Z 227 " =    1.921
peak=    3.583 closest distance to " CB  LEU A 228 " =    1.046
peak=    3.582 closest distance to " CB  SER A  26 " =    1.663
peak=    3.581 closest distance to " O   HOH Z  93 " =    2.014
peak=    3.579 closest distance to " O   HOH Z 222 " =    2.276
peak=    3.577 closest distance to " N   ALA A   1 " =    2.809
peak=    3.577 closest distance to " N   HIS A  86 " =    1.842
peak=    3.572 closest distance to " O   HOH Z 392 " =    1.165
peak=    3.564 closest distance to " O   HOH Z 362 " =    2.067
peak=    3.560 closest distance to " O   HOH Z  21 " =    1.751
peak=    3.559 closest distance to " O   HOH Z 378 " =    0.934
peak=    3.555 closest distance to " CB  ASN A  39 " =    0.791
peak=    3.550 closest distance to " N   ALA A   1 " =    1.040
peak=    3.549 closest distance to " O   HOH Z 166 " =    1.456
peak=    3.545 closest distance to " O   HOH Z  44 " =    3.031
peak=    3.545 closest distance to " CG1 ILE A 151 " =    0.960
peak=    3.537 closest distance to " O  BHOH Z  74 " =    1.395
peak=    3.537 closest distance to " O   HOH Z  10 " =    1.729
peak=    3.529 closest distance to " CE1 TYR A 186 " =    1.314
peak=    3.524 closest distance to " O   HOH Z  66 " =    2.168
peak=    3.522 closest distance to " CG AARG A 275 " =    1.047
peak=    3.521 closest distance to " NZ  LYS A 119 " =    2.702
peak=    3.520 closest distance to " O   ALA A   1 " =    1.416
peak=    3.511 closest distance to " O   HOH Z  32 " =    1.980
peak=    3.507 closest distance to " CG2BVAL A  41 " =    0.733
peak=    3.504 closest distance to " CD  ARG A 138 " =    0.707
peak=    3.503 closest distance to " CB  ALA A  34 " =    1.177
peak=    3.500 closest distance to " O   HOH Z 244 " =    1.746
peak=    3.495 closest distance to " O   HOH Z 272 " =    2.074
peak=    3.494 closest distance to " O   HOH Z 291 " =    1.514
peak=    3.492 closest distance to " CB  THR A 157 " =    1.093
peak=    3.491 closest distance to " CB  SER A 276 " =    1.201
peak=    3.482 closest distance to " CD2 LEU A 297 " =    1.031
peak=    3.478 closest distance to " O   HOH Z  88 " =    2.742
peak=    3.474 closest distance to " CE AMET A  47 " =    1.247
peak=    3.472 closest distance to " CA  PHE A 283 " =    1.388
peak=    3.469 closest distance to " O   HOH Z 302 " =    1.415
peak=    3.468 closest distance to " N   ARG A 156 " =    1.329
peak=    3.463 closest distance to " O   HOH Z  59 " =    1.367
peak=    3.461 closest distance to " CA  THR A 264 " =    0.783
peak=    3.458 closest distance to " O   HOH Z 414 " =    1.244
peak=    3.457 closest distance to " O   HOH Z 207 " =    2.090
peak=    3.452 closest distance to " CG  GLU A 277 " =    2.051
peak=    3.451 closest distance to " O   HOH Z 145 " =    2.377
peak=    3.449 closest distance to " CB  TRP A 266 " =    1.055
peak=    3.449 closest distance to " CB  LYS A 117 " =    1.191
peak=    3.448 closest distance to " O   HOH Z 313 " =    1.680
peak=    3.447 closest distance to " CB  ALA A  21 " =    1.862
peak=    3.442 closest distance to " O   HOH Z 171 " =    2.836
peak=    3.442 closest distance to " O   HOH Z 257 " =    2.130
peak=    3.436 closest distance to " O   HOH Z 213 " =    1.561
peak=    3.434 closest distance to " CZ  PHE A 218 " =    1.040
peak=    3.433 closest distance to " O   HOH Z   6 " =    2.156
peak=    3.429 closest distance to " CA  ALA A  21 " =    1.126
peak=    3.424 closest distance to " O   HOH Z 298 " =    2.619
peak=    3.421 closest distance to " O   HOH Z 126 " =    1.403
peak=    3.419 closest distance to " O   HOH Z 128 " =    2.045
peak=    3.419 closest distance to " O   HOH Z 175 " =    2.101
peak=    3.417 closest distance to " CA  ASN A 127 " =    0.939
peak=    3.417 closest distance to " O   HOH Z 109 " =    2.562
peak=    3.415 closest distance to " NE2 GLN A  58 " =    3.668
peak=    3.413 closest distance to " O   HOH Z 423 " =    1.887
peak=    3.410 closest distance to " CB  VAL A 202 " =    1.615
peak=    3.408 closest distance to " CA  ILE A 234 " =    1.007
peak=    3.406 closest distance to " CB  TYR A 116 " =    0.917
peak=    3.404 closest distance to " O   HOH Z 284 " =    1.435
peak=    3.403 closest distance to " CB  THR A  31 " =    1.666
peak=    3.402 closest distance to " O   HOH Z  92 " =    1.155
peak=    3.396 closest distance to " O   HOH Z 305 " =    3.479
peak=    3.395 closest distance to " N   ASN A 127 " =    1.351
peak=    3.393 closest distance to " NE2 GLN A 278 " =    3.418
peak=    3.383 closest distance to " O   HOH Z 173 " =    2.022
peak=    3.383 closest distance to " O   HOH Z  40 " =    2.220
peak=    3.376 closest distance to " NE AARG A 275 " =    1.361
peak=    3.374 closest distance to " CB  SER A  62 " =    1.204
peak=    3.370 closest distance to " O   HOH Z 130 " =    2.286
peak=    3.369 closest distance to " O   HOH Z 128 " =    2.037
peak=    3.361 closest distance to " NZ  LYS A 117 " =    1.256
peak=    3.359 closest distance to " O   HOH Z 419 " =    1.578
peak=    3.358 closest distance to " CE  LYS A 119 " =    1.216
peak=    3.357 closest distance to " O   HOH Z 189 " =    2.064
peak=    3.349 closest distance to " O   HOH Z 437 " =    1.889
peak=    3.346 closest distance to " CG  LEU A 167 " =    1.206
peak=    3.335 closest distance to " CB  LEU A 143 " =    1.107
peak=    3.334 closest distance to " O   HOH Z  17 " =    1.938
peak=    3.334 closest distance to " O   HOH Z 422 " =    2.592
peak=    3.332 closest distance to " O   HOH Z 357 " =    1.872
peak=    3.330 closest distance to " O   HOH Z  64 " =    2.462
peak=    3.329 closest distance to " OD2 ASP A 286 " =    2.576
peak=    3.329 closest distance to " O   HOH Z 432 " =    1.942
peak=    3.325 closest distance to " O   HOH Z 290 " =    1.076
peak=    3.324 closest distance to " N   PHE A 130 " =    1.203
peak=    3.322 closest distance to " O   HOH Z 281 " =    1.767
peak=    3.311 closest distance to " CA  GLY A 241 " =    3.699
peak=    3.311 closest distance to " O   HOH Z 329 " =    3.516
peak=    3.308 closest distance to " O   HOH Z 359 " =    1.342
peak=    3.304 closest distance to " O   HOH Z  88 " =    2.580
peak=    3.302 closest distance to " CG  GLN A  77 " =    2.325
peak=    3.301 closest distance to " O   HOH Z 106 " =    2.647
peak=    3.301 closest distance to " CB  LEU A 300 " =    0.960
peak=    3.300 closest distance to " CA  MET A 105 " =    0.835
peak=    3.298 closest distance to " O   HOH Z 193 " =    1.643
peak=    3.293 closest distance to " O   HOH Z  39 " =    1.083
peak=    3.291 closest distance to " CD  PRO A 243 " =    1.606
peak=    3.285 closest distance to " O   HOH Z 193 " =    1.971
peak=    3.283 closest distance to " O   HOH Z  71 " =    1.943
peak=    3.282 closest distance to " CD2 TRP A 179 " =    1.309
peak=    3.281 closest distance to " O   HOH Z 423 " =    1.620
peak=    3.276 closest distance to " NH2AARG A 190 " =    1.717
peak=    3.274 closest distance to " O   HOH Z 125 " =    2.338
peak=    3.272 closest distance to " CB  GLN A  88 " =    1.233
peak=    3.259 closest distance to " O  BHOH Z 338 " =    2.378
peak=    3.257 closest distance to " O   HOH Z  80 " =    1.927
peak=    3.255 closest distance to " O   HOH Z 334 " =    1.493
peak=    3.254 closest distance to " CB  LYS A 290 " =    1.380
peak=    3.247 closest distance to " O   HOH Z 172 " =    2.746
peak=    3.247 closest distance to " O   HOH Z 211 " =    2.675
peak=    3.241 closest distance to " NZ  LYS A  76 " =    1.549
peak=    3.237 closest distance to " O   HOH Z 116 " =    2.690
peak=    3.232 closest distance to " O   HOH Z 409 " =    2.329
peak=    3.229 closest distance to " CA  ALA A 158 " =    1.102
peak=    3.228 closest distance to " O   PRO A 198 " =    1.224
peak=    3.227 closest distance to " O   HOH Z  50 " =    1.538
peak=    3.226 closest distance to " O   HOH Z 283 " =    2.309
peak=    3.223 closest distance to " NH1 ARG A  14 " =    0.992
peak=    3.213 closest distance to " O   HOH Z 135 " =    1.603
peak=    3.213 closest distance to " OH  TYR A 116 " =    1.014
peak=    3.212 closest distance to " NH2BARG A 145 " =    2.066
peak=    3.210 closest distance to " O   HOH Z 345 " =    3.298
peak=    3.210 closest distance to " CA  SER A  32 " =    1.613
peak=    3.210 closest distance to " O   HOH Z 247 " =    1.157
peak=    3.204 closest distance to " O   HOH Z 291 " =    1.987
peak=    3.204 closest distance to " CB  PRO A 243 " =    1.160
peak=    3.199 closest distance to " CA  ARG A 102 " =    1.132
peak=    3.199 closest distance to " CB  ALA A 114 " =    1.082
peak=    3.196 closest distance to " O   HOH Z 153 " =    3.695
peak=    3.193 closest distance to " O   GLN A 278 " =    1.453
peak=    3.190 closest distance to " O   HOH Z  11 " =    1.008
peak=    3.187 closest distance to " N   TYR A  15 " =    1.015
peak=    3.186 closest distance to " O   HOH Z 273 " =    2.888
peak=    3.186 closest distance to " CG1BVAL A  72 " =    1.298
peak=    3.182 closest distance to " O   HOH Z 108 " =    1.201
peak=    3.181 closest distance to " CG1BVAL A  72 " =    1.250
peak=    3.180 closest distance to " CB  ARG A 138 " =    0.819
peak=    3.179 closest distance to " CB  ASN A 215 " =    1.042
peak=    3.177 closest distance to " O   HOH Z  24 " =    1.745
peak=    3.171 closest distance to " O   HOH Z 112 " =    2.338
peak=    3.170 closest distance to " O   HOH Z 108 " =    2.217
peak=    3.167 closest distance to " O   HOH Z 433 " =    1.737
peak=    3.158 closest distance to " O   HOH Z 213 " =    1.898
peak=    3.157 closest distance to " N   ASN A  39 " =    1.109
peak=    3.156 closest distance to " N   CYS A 260 " =    0.749
peak=    3.152 closest distance to " N   ALA A   1 " =    2.178
peak=    3.151 closest distance to " O   HOH Z 183 " =    1.426
peak=    3.148 closest distance to " O   HOH Z 207 " =    1.574
peak=    3.147 closest distance to " O   HOH Z 336 " =    1.862
peak=    3.144 closest distance to " O   HOH Z 266 " =    3.105
peak=    3.141 closest distance to " O   HOH Z 434 " =    1.144
peak=    3.139 closest distance to " CE1 HIS A 108 " =    1.351
peak=    3.134 closest distance to " CA  MET A  40 " =    1.047
peak=    3.134 closest distance to " CB  GLU A 152 " =    1.318
peak=    3.133 closest distance to " CA  ALA A  84 " =    1.280
peak=    3.129 closest distance to " CG2 ILE A 106 " =    0.861
peak=    3.127 closest distance to " O   HOH Z 383 " =    1.853
peak=    3.126 closest distance to " CG2 THR A 294 " =    1.639
peak=    3.125 closest distance to " O   HOH Z 271 " =    2.071
peak=    3.122 closest distance to " O   HOH Z   3 " =    2.362
peak=    3.099 closest distance to " CB  ALA A 114 " =    1.439
peak=    3.096 closest distance to " O   GLY A 147 " =    1.430
peak=    3.082 closest distance to " O   HOH Z 218 " =    1.926
peak=    3.077 closest distance to " O   HOH Z 130 " =    3.346
peak=    3.076 closest distance to " O   HOH Z 390 " =    2.368
peak=    3.069 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.064 closest distance to " O   HOH Z 365 " =    1.642
peak=    3.062 closest distance to " CB  MET A 188 " =    1.617
peak=    3.061 closest distance to " O   HOH Z 217 " =    1.598
peak=    3.055 closest distance to " O   ASN A 209 " =    1.388
peak=    3.050 closest distance to " NH2BARG A 190 " =    1.497
peak=    3.044 closest distance to " O   HOH Z 412 " =    1.963
peak=    3.034 closest distance to " CB  VAL A 126 " =    1.153
peak=    3.034 closest distance to " N   SER A 134 " =    1.381

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.765 - 5.751
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.765 - 5.751

peak=   -4.542 closest distance to " C   HIS A 108 " =    1.151
peak=   -4.385 closest distance to " CD1 LEU A 255 " =    2.860
peak=   -4.347 closest distance to " CD  ARG A 156 " =    1.992
peak=   -4.274 closest distance to " O   HOH Z 290 " =    1.026
peak=   -4.257 closest distance to " O   PRO A 198 " =    1.267
peak=   -4.213 closest distance to " CD  ARG A  14 " =    3.272
peak=   -4.109 closest distance to " CZ  PHE A  59 " =    1.401
peak=   -4.058 closest distance to " CA  GLY A  98 " =    1.733
peak=   -4.030 closest distance to " O   HOH Z 266 " =    4.592
peak=   -3.994 closest distance to " O   HOH Z  65 " =    0.887
peak=   -3.990 closest distance to " CG  PHE A 283 " =    2.565
peak=   -3.982 closest distance to " N   GLN A  58 " =    1.697
peak=   -3.978 closest distance to " CB  PRO A 243 " =    2.571
peak=   -3.959 closest distance to " O   PRO A 243 " =    2.544
peak=   -3.959 closest distance to " OD2 ASP A 191 " =    1.408
peak=   -3.955 closest distance to " O   HOH Z 438 " =    0.958
peak=   -3.939 closest distance to " O   HOH Z 407 " =    3.052
peak=   -3.933 closest distance to " O   HOH Z 372 " =    2.578
peak=   -3.924 closest distance to " O   HOH Z 198 " =    1.863
peak=   -3.891 closest distance to " CB  ALA A 291 " =    2.146
peak=   -3.884 closest distance to " O   HOH Z  52 " =    1.331
peak=   -3.883 closest distance to " O   HOH Z 185 " =    2.001
peak=   -3.883 closest distance to " O   HOH Z 377 " =    1.780
peak=   -3.875 closest distance to " O   HOH Z 351 " =    1.551
peak=   -3.875 closest distance to " CG  GLN A 223 " =    1.586
peak=   -3.849 closest distance to " OG BSER A 134 " =    1.363
peak=   -3.848 closest distance to " CG1 VAL A 112 " =    2.982
peak=   -3.836 closest distance to " O   SER A 135 " =    1.502
peak=   -3.833 closest distance to " ND2 ASN A  45 " =    1.003
peak=   -3.832 closest distance to " O   HOH Z 231 " =    2.060
peak=   -3.814 closest distance to " O   VAL A  67 " =    2.907
peak=   -3.805 closest distance to " CB  ALA A 248 " =    2.049
peak=   -3.779 closest distance to " O   SER A  22 " =    2.480
peak=   -3.775 closest distance to " CB  ASN A  39 " =    2.311
peak=   -3.771 closest distance to " O   ARG A 145 " =    1.520
peak=   -3.771 closest distance to " CB  ILE A  33 " =    2.843
peak=   -3.765 closest distance to " OD1 ASP A 191 " =    1.493
peak=   -3.763 closest distance to " OG  SER A   3 " =    1.607
peak=   -3.744 closest distance to " O   HOH Z  60 " =    1.834
peak=   -3.741 closest distance to " CG  PRO A 243 " =    1.529
peak=   -3.732 closest distance to " O   VAL A  67 " =    2.618
peak=   -3.717 closest distance to " O   HOH Z  13 " =    1.476
peak=   -3.695 closest distance to " O   SER A  95 " =    1.387
peak=   -3.694 closest distance to " O   ALA A 161 " =    1.592
peak=   -3.690 closest distance to " CB  TYR A  15 " =    2.126
peak=   -3.685 closest distance to " CA  GLY A 133 " =    1.956
peak=   -3.679 closest distance to " O   HOH Z 313 " =    1.797
peak=   -3.664 closest distance to " O   HOH Z 211 " =    1.549
peak=   -3.664 closest distance to " CG  GLN A  58 " =    1.110
peak=   -3.664 closest distance to " O   HOH Z 126 " =    1.884
peak=   -3.657 closest distance to " CZ2 TRP A 274 " =    1.008
peak=   -3.646 closest distance to " CG  MET A 105 " =    0.918
peak=   -3.635 closest distance to " O   HOH Z 388 " =    2.171
peak=   -3.626 closest distance to " O   HOH Z 389 " =    1.902
peak=   -3.624 closest distance to " O   HOH Z 131 " =    4.059
peak=   -3.614 closest distance to " O   HOH Z 166 " =    1.292
peak=   -3.613 closest distance to " O   HOH Z  43 " =    1.851
peak=   -3.609 closest distance to " CD1 LEU A 101 " =    2.219
peak=   -3.609 closest distance to " O   HOH Z 427 " =    1.826
peak=   -3.603 closest distance to " C   ALA A 158 " =    1.375
peak=   -3.584 closest distance to " CE  MET A 105 " =    2.208
peak=   -3.580 closest distance to " CE3 TRP A 123 " =    1.365
peak=   -3.571 closest distance to " CB  ALA A   7 " =    1.946
peak=   -3.555 closest distance to " OD1 ASP A 191 " =    1.915
peak=   -3.555 closest distance to " CD2 TYR A 293 " =    1.855
peak=   -3.536 closest distance to " O   ASP A 162 " =    2.148
peak=   -3.535 closest distance to " O   HOH Z  90 " =    2.337
peak=   -3.528 closest distance to " O   PHE A 218 " =    1.377
peak=   -3.524 closest distance to " N   THR A 157 " =    1.465
peak=   -3.510 closest distance to " O   HOH Z 250 " =    1.357
peak=   -3.508 closest distance to " O   HOH Z  37 " =    1.613
peak=   -3.504 closest distance to " CZ3 TRP A 179 " =    1.291
peak=   -3.501 closest distance to " NH1AARG A 275 " =    1.831
peak=   -3.501 closest distance to " OE1 GLN A  88 " =    1.087
peak=   -3.498 closest distance to " O   VAL A 189 " =    2.421
peak=   -3.497 closest distance to " O   HOH Z 298 " =    2.463
peak=   -3.489 closest distance to " O   HOH Z 377 " =    0.955
peak=   -3.482 closest distance to " O   HOH Z  24 " =    1.211
peak=   -3.478 closest distance to " N   ASN A 127 " =    1.483
peak=   -3.476 closest distance to " O   HOH Z 213 " =    1.330
peak=   -3.469 closest distance to " NH2 ARG A  79 " =    2.051
peak=   -3.466 closest distance to " N   ALA A 248 " =    1.519
peak=   -3.465 closest distance to " OG  SER A  87 " =    1.354
peak=   -3.461 closest distance to " CA  GLY A  57 " =    2.070
peak=   -3.458 closest distance to " O   HOH Z 263 " =    2.860
peak=   -3.458 closest distance to " OE1 GLU A 277 " =    2.127
peak=   -3.452 closest distance to " O   HOH Z  11 " =    1.866
peak=   -3.451 closest distance to " CB  PHE A 192 " =    1.783
peak=   -3.435 closest distance to " ND2 ASN A 252 " =    1.736
peak=   -3.429 closest distance to " CZ  TYR A 169 " =    1.700
peak=   -3.427 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.426 closest distance to " O   HOH Z 412 " =    5.751
peak=   -3.422 closest distance to " N   GLN A 122 " =    1.420
peak=   -3.421 closest distance to " NE2 GLN A 278 " =    1.651
peak=   -3.418 closest distance to " OG  SER A  87 " =    1.827
peak=   -3.417 closest distance to " CA  GLY A 203 " =    2.231
peak=   -3.406 closest distance to " CB  CYS A 254 " =    2.220
peak=   -3.403 closest distance to " O   HOH Z 352 " =    1.667
peak=   -3.401 closest distance to " OD1 ASN A 148 " =    1.608
peak=   -3.401 closest distance to " CG2 THR A 178 " =    2.083
peak=   -3.400 closest distance to " CD2 LEU A 237 " =    2.687
peak=   -3.394 closest distance to " O   PRO A 198 " =    1.221
peak=   -3.382 closest distance to " O   HOH Z 152 " =    4.816
peak=   -3.376 closest distance to " ND2 ASN A  45 " =    1.754
peak=   -3.366 closest distance to " NE2 GLN A 194 " =    2.706
peak=   -3.364 closest distance to " N   ALA A  43 " =    2.367
peak=   -3.363 closest distance to " O   HOH Z  63 " =    2.319
peak=   -3.361 closest distance to " O   HOH Z  93 " =    2.043
peak=   -3.357 closest distance to " C   LEU A 143 " =    1.044
peak=   -3.350 closest distance to " O   HOH Z 384 " =    3.004
peak=   -3.349 closest distance to " O   HOH Z 298 " =    1.212
peak=   -3.346 closest distance to " ND2 ASN A  39 " =    1.476
peak=   -3.340 closest distance to " O   HOH Z 385 " =    1.796
peak=   -3.337 closest distance to " CE2 PHE A 218 " =    2.351
peak=   -3.333 closest distance to " N   GLN A  77 " =    1.562
peak=   -3.328 closest distance to " CD2 PHE A 225 " =    1.137
peak=   -3.325 closest distance to " O   HOH Z 140 " =    1.658
peak=   -3.323 closest distance to " OE2 GLU A 152 " =    1.064
peak=   -3.315 closest distance to " O   HOH Z 435 " =    2.928
peak=   -3.313 closest distance to " O   ALA A  34 " =    2.551
peak=   -3.310 closest distance to " OG  SER A 245 " =    1.275
peak=   -3.310 closest distance to " O   ALA A   7 " =    1.569
peak=   -3.309 closest distance to " O   HOH Z 348 " =    1.808
peak=   -3.307 closest distance to " CE3 TRP A 274 " =    2.318
peak=   -3.306 closest distance to " O   PRO A 163 " =    1.184
peak=   -3.305 closest distance to " O   SER A 146 " =    1.011
peak=   -3.302 closest distance to " OE1 GLN A 183 " =    1.416
peak=   -3.294 closest distance to " CD  GLU A 236 " =    1.029
peak=   -3.293 closest distance to " O   ALA A 180 " =    1.087
peak=   -3.290 closest distance to " ND2 ASN A 187 " =    1.461
peak=   -3.290 closest distance to " OD1 ASP A 200 " =    1.334
peak=   -3.287 closest distance to " O   HOH Z  60 " =    2.202
peak=   -3.286 closest distance to " O   HOH Z 148 " =    1.853
peak=   -3.286 closest distance to " O   HOH Z 266 " =    4.304
peak=   -3.285 closest distance to " O   HOH Z 415 " =    1.533
peak=   -3.281 closest distance to " C   ASN A 285 " =    2.191
peak=   -3.278 closest distance to " O   VAL A 197 " =    1.530
peak=   -3.278 closest distance to " CE  MET A  93 " =    1.117
peak=   -3.276 closest distance to " NH2 ARG A 219 " =    1.727
peak=   -3.271 closest distance to " O   ALA A  51 " =    1.287
peak=   -3.263 closest distance to " CD2 LEU A 237 " =    2.370
peak=   -3.263 closest distance to " O   HOH Z 102 " =    1.609
peak=   -3.262 closest distance to " OD2 ASP A 171 " =    2.065
peak=   -3.261 closest distance to " CD1 PHE A  59 " =    1.974
peak=   -3.256 closest distance to " CB  ALA A  43 " =    2.228
peak=   -3.254 closest distance to " N   VAL A  72 " =    1.525
peak=   -3.252 closest distance to " ND2 ASN A  69 " =    1.543
peak=   -3.251 closest distance to " C   ALA A 114 " =    2.117
peak=   -3.243 closest distance to " O   HOH Z 348 " =    2.222
peak=   -3.239 closest distance to " O   HOH Z 191 " =    5.599
peak=   -3.237 closest distance to " CE  LYS A  76 " =    2.860
peak=   -3.237 closest distance to " CD  GLU A 277 " =    1.166
peak=   -3.230 closest distance to " CB  ALA A 114 " =    2.495
peak=   -3.229 closest distance to " CB  ALA A 131 " =    1.915
peak=   -3.228 closest distance to " O   HOH Z 234 " =    3.691
peak=   -3.227 closest distance to " OG  SER A 206 " =    1.773
peak=   -3.225 closest distance to " O   PRO A 163 " =    1.800
peak=   -3.223 closest distance to " OG BSER A 134 " =    1.562
peak=   -3.218 closest distance to " O   THR A 220 " =    1.726
peak=   -3.217 closest distance to " CE2 TYR A  30 " =    2.680
peak=   -3.216 closest distance to " O   MET A  40 " =    2.697
peak=   -3.214 closest distance to " O   GLN A 183 " =    1.298
peak=   -3.214 closest distance to " CD  LYS A 289 " =    2.418
peak=   -3.210 closest distance to " O   HOH Z 134 " =    2.998
peak=   -3.210 closest distance to " NE  ARG A  36 " =    1.865
peak=   -3.209 closest distance to " O   VAL A 174 " =    2.089
peak=   -3.206 closest distance to " CD1 LEU A 228 " =    2.034
peak=   -3.202 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.200 closest distance to " OD2 ASP A  50 " =    1.578
peak=   -3.198 closest distance to " CB  ASP A  27 " =    2.318
peak=   -3.193 closest distance to " N   ALA A 295 " =    1.412
peak=   -3.190 closest distance to " CG1 VAL A 230 " =    1.973
peak=   -3.187 closest distance to " O   HOH Z 236 " =    1.974
peak=   -3.183 closest distance to " O   GLY A  80 " =    2.294
peak=   -3.179 closest distance to " CG2 ILE A 151 " =    2.543
peak=   -3.177 closest distance to " O   HOH Z 423 " =    2.484
peak=   -3.171 closest distance to " CB  ALA A 291 " =    2.369
peak=   -3.171 closest distance to " O   HOH Z  51 " =    1.017
peak=   -3.163 closest distance to " O   ILE A  49 " =    1.639
peak=   -3.163 closest distance to " O   HOH Z 432 " =    3.671
peak=   -3.160 closest distance to " CG1 VAL A 197 " =    2.107
peak=   -3.157 closest distance to " O   ASP A 270 " =    1.718
peak=   -3.146 closest distance to " O   HOH Z  39 " =    1.414
peak=   -3.140 closest distance to " O   HOH Z  28 " =    1.987
peak=   -3.138 closest distance to " CE1 PHE A  59 " =    2.020
peak=   -3.135 closest distance to " ND2 ASN A 285 " =    2.032
peak=   -3.134 closest distance to " CG2 VAL A 296 " =    1.964
peak=   -3.132 closest distance to " O   HOH Z 256 " =    1.314
peak=   -3.122 closest distance to " OE1 GLN A 223 " =    2.007
peak=   -3.120 closest distance to " N   ALA A   1 " =    1.610
peak=   -3.113 closest distance to " O   HOH Z 359 " =    3.397
peak=   -3.106 closest distance to " NH1 ARG A  56 " =    2.420
peak=   -3.106 closest distance to " O   HOH Z 326 " =    1.568
peak=   -3.106 closest distance to " CD  GLN A  88 " =    0.820
peak=   -3.105 closest distance to " CZ  ARG A 259 " =    0.848
peak=   -3.091 closest distance to " O   GLN A 240 " =    1.971
peak=   -3.091 closest distance to " O   ARG A  66 " =    1.147
peak=   -3.088 closest distance to " O   ASN A 127 " =    1.750
peak=   -3.066 closest distance to " C   MET A 188 " =    1.564
peak=   -3.064 closest distance to " O   HOH Z 134 " =    3.431
peak=   -3.064 closest distance to " O   HOH Z 318 " =    1.750
peak=   -3.061 closest distance to " CD1 TRP A 179 " =    1.162
peak=   -3.051 closest distance to " O   HOH Z 288 " =    1.500

================= 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    :  0.4251 0.4228   6.232267e+00   6.221998e+00
   1_bss:  0.4135 0.4095   6.221497e+00   6.201532e+00
   1_xyz:  0.2844 0.3161   5.938952e+00   6.014292e+00
   1_adp:  0.2581 0.3320   5.891861e+00   6.048529e+00
   1_occ:  0.2577 0.3325   5.891656e+00   6.048735e+00
   2_bss:  0.2561 0.3301   5.884324e+00   6.041217e+00
   2_xyz:  0.1891 0.2404   5.593881e+00   5.778984e+00
   2_adp:  0.1670 0.2149   5.486804e+00   5.689239e+00
   2_occ:  0.1668 0.2147   5.485721e+00   5.687864e+00
   3_bss:  0.1664 0.2129   5.478175e+00   5.678398e+00
   3_xyz:  0.1372 0.1830   5.306479e+00   5.525908e+00
   3_adp:  0.1301 0.1785   5.264973e+00   5.495451e+00
   3_occ:  0.1300 0.1784   5.264703e+00   5.495096e+00
   4_bss:  0.1301 0.1784   5.264532e+00   5.494912e+00
   4_xyz:  0.1165 0.1636   5.169894e+00   5.411010e+00
   4_adp:  0.1137 0.1603   5.150669e+00   5.394017e+00
   4_occ:  0.1136 0.1602   5.150312e+00   5.393472e+00
   5_bss:  0.1136 0.1602   5.149951e+00   5.393121e+00
   5_xyz:  0.1122 0.1588   5.139332e+00   5.382923e+00
   5_adp:  0.1118 0.1581   5.136844e+00   5.381306e+00
   5_occ:  0.1118 0.1582   5.136704e+00   5.381149e+00
   5_bss:  0.1117 0.1582   5.136628e+00   5.381053e+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:  0.340  22.799  -2.617   2.916  -0.884   0.000  -0.000  -0.000
   1_xyz:  0.340  22.799  -2.617   2.916  -0.884   0.000  -0.000  -0.000
   1_adp:  0.340  22.799  -2.617   2.916  -0.884   0.000  -0.000  -0.000
   1_occ:  0.340  22.799  -2.617   2.916  -0.884   0.000  -0.000  -0.000
   2_bss:  0.328  38.745  -2.129  -0.115  -0.897  -0.000  -0.000  -0.000
   2_xyz:  0.328  38.745  -2.129  -0.115  -0.897  -0.000  -0.000  -0.000
   2_adp:  0.328  38.745  -2.129  -0.115  -0.897  -0.000  -0.000  -0.000
   2_occ:  0.328  38.745  -2.129  -0.115  -0.897  -0.000  -0.000  -0.000
   3_bss:  0.326  40.737  -2.323  -1.589  -1.017  -0.000  -0.000  -0.000
   3_xyz:  0.326  40.737  -2.323  -1.589  -1.017  -0.000  -0.000  -0.000
   3_adp:  0.326  40.737  -2.323  -1.589  -1.017  -0.000  -0.000  -0.000
   3_occ:  0.326  40.737  -2.323  -1.589  -1.017  -0.000  -0.000  -0.000
   4_bss:  0.318  39.617  -2.576  -2.294  -1.285  -0.000  -0.000  -0.000
   4_xyz:  0.318  39.617  -2.576  -2.294  -1.285  -0.000  -0.000  -0.000
   4_adp:  0.318  39.617  -2.576  -2.294  -1.285  -0.000  -0.000  -0.000
   4_occ:  0.318  39.617  -2.576  -2.294  -1.285  -0.000  -0.000  -0.000
   5_bss:  0.317  40.866  -2.531  -2.319  -1.233  -0.000  -0.000  -0.000
   5_xyz:  0.317  40.866  -2.531  -2.319  -1.233  -0.000  -0.000  -0.000
   5_adp:  0.317  40.866  -2.531  -2.319  -1.233  -0.000  -0.000  -0.000
   5_occ:  0.317  40.866  -2.531  -2.319  -1.233  -0.000  -0.000  -0.000
   5_bss:  0.318  41.460  -2.393  -2.249  -1.106  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.580 0.5400  0.7268    56360.418
   1_bss:  47.235 0.5549  0.7394    52037.069
   1_xyz:  32.698 0.7292  0.9282    27651.248
   1_adp:  34.807 0.7037  0.8982    30414.030
   1_occ:  34.858 0.7031  0.8969    30477.550
   2_bss:  34.241 0.7098  0.8816    29480.237
   2_xyz:  23.839 0.8228  0.9879    14659.718
   2_adp:  20.701 0.8554  1.0080    11913.465
   2_occ:  20.673 0.8556  1.0079    11868.413
   3_bss:  20.395 0.8579  0.9881    11513.785
   3_xyz:  16.958 0.8895  1.0015     8367.432
   3_adp:  16.141 0.8973  0.9989     7953.533
   3_occ:  16.133 0.8973  0.9987     7936.342
   4_bss:  16.117 0.8974  0.9838     7934.376
   4_xyz:  14.447 0.9110  0.9921     6623.288
   4_adp:  14.048 0.9146  0.9904     6422.724
   4_occ:  14.036 0.9146  0.9903     6411.496
   5_bss:  14.025 0.9147  0.9914     6406.473
   5_xyz:  13.812 0.9165  0.9902     6250.402
   5_adp:  13.761 0.9170  0.9856     6223.674
   5_occ:  13.760 0.9170  0.9855     6220.085
   5_bss:  13.758 0.9170  0.9891     6220.060
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7765e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7765e-01
   1_xyz:   1.512  0.013  0.101 15.307  0.007  4.102   1.2346e-01
   1_adp:   1.512  0.013  0.101 15.307  0.007  4.102   1.2346e-01
   1_occ:   1.512  0.013  0.101 15.307  0.007  4.102   1.2346e-01
   2_bss:   1.512  0.013  0.101 15.307  0.007  4.102   1.2346e-01
   2_xyz:   1.156  0.007  0.082 14.663  0.004  4.106   7.1238e-02
   2_adp:   1.156  0.007  0.082 14.663  0.004  4.106   7.1238e-02
   2_occ:   1.156  0.007  0.082 14.663  0.004  4.106   7.1238e-02
   3_bss:   1.156  0.007  0.082 14.663  0.004  4.106   7.1238e-02
   3_xyz:   0.885  0.005  0.062 14.331  0.003  4.108   4.8843e-02
   3_adp:   0.885  0.005  0.062 14.331  0.003  4.108   4.8843e-02
   3_occ:   0.885  0.005  0.062 14.331  0.003  4.108   4.8843e-02
   4_bss:   0.885  0.005  0.062 14.331  0.003  4.108   4.8843e-02
   4_xyz:   0.960  0.005  0.070 14.480  0.004  4.111   5.4473e-02
   4_adp:   0.960  0.005  0.070 14.480  0.004  4.111   5.4473e-02
   4_occ:   0.960  0.005  0.070 14.480  0.004  4.111   5.4473e-02
   5_bss:   0.960  0.005  0.070 14.480  0.004  4.111   5.4473e-02
   5_xyz:   0.875  0.005  0.065 14.272  0.004  4.107   4.8124e-02
   5_adp:   0.875  0.005  0.065 14.272  0.004  4.107   4.8124e-02
   5_occ:   0.875  0.005  0.065 14.272  0.004  4.107   4.8124e-02
   5_bss:   0.875  0.005  0.065 14.272  0.004  4.107   4.8124e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.636   2.3755e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.636   2.3755e-01
   1_xyz:   8.828  0.067  0.423 83.337  0.043  2.090   9.8233e-02
   1_adp:   8.828  0.067  0.423 83.337  0.043  2.090   9.8233e-02
   1_occ:   8.828  0.067  0.423 83.337  0.043  2.090   9.8233e-02
   2_bss:   8.828  0.067  0.423 83.337  0.043  2.090   9.8233e-02
   2_xyz:   7.248  0.045  0.267 80.862  0.025  2.295   6.5897e-02
   2_adp:   7.248  0.045  0.267 80.862  0.025  2.295   6.5897e-02
   2_occ:   7.248  0.045  0.267 80.862  0.025  2.295   6.5897e-02
   3_bss:   7.248  0.045  0.267 80.862  0.025  2.295   6.5897e-02
   3_xyz:   6.581  0.049  0.192 81.252  0.029  2.360   3.2964e-02
   3_adp:   6.581  0.049  0.192 81.252  0.029  2.360   3.2964e-02
   3_occ:   6.581  0.049  0.192 81.252  0.029  2.360   3.2964e-02
   4_bss:   6.581  0.049  0.192 81.252  0.029  2.360   3.2964e-02
   4_xyz:   6.582  0.035  0.211 83.804  0.037  2.317   3.8361e-02
   4_adp:   6.582  0.035  0.211 83.804  0.037  2.317   3.8361e-02
   4_occ:   6.582  0.035  0.211 83.804  0.037  2.317   3.8361e-02
   5_bss:   6.582  0.035  0.211 83.804  0.037  2.317   3.8361e-02
   5_xyz:   6.602  0.038  0.206 84.163  0.035  2.336   3.0869e-02
   5_adp:   6.602  0.038  0.206 84.163  0.035  2.336   3.0869e-02
   5_occ:   6.602  0.038  0.206 84.163  0.035  2.336   3.0869e-02
   5_bss:   6.602  0.038  0.206 84.163  0.035  2.336   3.0869e-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:  97.58   0.00  18.01  78.40   0.00  14.15  97.58   3.42  38.99
   1_occ:  97.58   0.00  18.01  78.40   0.00  14.15  97.58   3.42  38.99
   2_bss:  97.58   0.00  18.01  78.40   0.00  14.15  97.58   3.42  38.99
   2_xyz:  97.58   0.00  18.01  78.40   0.00  14.15  97.58   3.42  38.99
   2_adp:  91.54   1.07  17.17  80.20   1.07  13.12  91.54   5.95  39.20
   2_occ:  91.54   1.07  17.17  80.20   1.07  13.12  91.54   5.95  39.20
   3_bss:  91.54   1.07  17.17  80.20   1.07  13.12  91.54   5.95  39.20
   3_xyz:  91.54   1.07  17.17  80.20   1.07  13.12  91.54   5.95  39.20
   3_adp:  89.68   0.73  17.22  84.73   0.73  12.87  89.68   5.67  40.93
   3_occ:  89.68   0.73  17.22  84.73   0.73  12.87  89.68   5.67  40.93
   4_bss:  89.68   0.73  17.22  84.73   0.73  12.87  89.68   5.67  40.93
   4_xyz:  89.68   0.73  17.22  84.73   0.73  12.87  89.68   5.67  40.93
   4_adp:  89.77   0.42  17.11  89.44   0.42  12.76  89.77   6.06  40.83
   4_occ:  89.77   0.42  17.11  89.44   0.42  12.76  89.77   6.06  40.83
   5_bss:  89.77   0.42  17.11  89.44   0.42  12.76  89.77   6.06  40.83
   5_xyz:  89.77   0.42  17.11  89.44   0.42  12.76  89.77   6.06  40.83
   5_adp:  90.02   0.55  16.97  90.02   0.55  12.63  89.61   6.09  40.58
   5_occ:  90.02   0.55  16.97  90.02   0.55  12.63  89.61   6.09  40.58
   5_bss:  90.01   0.53  16.95  90.01   0.53  12.61  89.59   6.07  40.56
------------------------------------------------------------------------
 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:    1.733    0.017    0.412
   1_adp:    1.733    0.017    0.412
   1_occ:    1.733    0.017    0.412
   2_bss:    1.733    0.017    0.412
   2_xyz:    1.339    0.035    0.565
   2_adp:    1.339    0.035    0.565
   2_occ:    1.339    0.035    0.565
   3_bss:    1.339    0.035    0.565
   3_xyz:    1.225    0.054    0.625
   3_adp:    1.225    0.054    0.625
   3_occ:    1.225    0.054    0.625
   4_bss:    1.225    0.054    0.625
   4_xyz:    1.293    0.076    0.662
   4_adp:    1.293    0.076    0.662
   4_occ:    1.293    0.076    0.662
   5_bss:    1.293    0.076    0.662
   5_xyz:    1.357    0.048    0.671
   5_adp:    1.357    0.048    0.671
   5_occ:    1.357    0.048    0.671
   5_bss:    1.357    0.048    0.671
------------------------------------------------------------------------

CPU time actual refinement: 331.11


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/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_377/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_377/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.97 
  Macro-tasks:
    bulk solvent and scale       = 43.37  
    individual site refinement   = 132.96 
    weights calculation          = 29.26  
    collect and process          = 6.46   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 212.14 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 102.83 
    alpha_beta                      = 8.28   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.89 
    fmodel                         = 7.22   
    r_factors                      = 0.21   
    phase_errors                   = 10.55  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 246.16 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.724 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    634 calls, 102.56 s
gradients_fft:          579 calls, 100.78 s

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

# Date 2008-01-16 Time 04:41:09 PST -0800 (1200487269.97 s)
Start R-work = 0.4251, R-free = 0.4228 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1768 (no bulk solvent and anisotropic scale)

Start R-work = 0.4135, R-free = 0.4095
Final R-work = 0.1117, R-free = 0.1582