# Date 2008-01-16 Time 04:10:31 PST -0800 (1200485431.47 s)
#phil __OFF__

Command line arguments: "../211.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26507
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 211

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 47.6339, 85.0941, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.96062
Completeness in resolution range: 0.949309
Completeness with d_max=infinity: 0.94642

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8759
                             d_min =   1.9606

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.96062
Completeness in resolution range: 0.949309
Completeness with d_max=infinity: 0.94642

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8763 -  4.1954 [2170/2199]  1953   217  10.0%
  bin  2:  4.1954 -  3.3424 [2079/2102]  1873   206   9.9%
  bin  3:  3.3424 -  2.9236 [2063/2088]  1851   212  10.3%
  bin  4:  2.9236 -  2.6579 [2025/2041]  1830   195   9.6%
  bin  5:  2.6579 -  2.4683 [2004/2048]  1794   210  10.5%
  bin  6:  2.4683 -  2.3234 [2025/2053]  1835   190   9.4%
  bin  7:  2.3234 -  2.2074 [2002/2038]  1795   207  10.3%
  bin  8:  2.2074 -  2.1116 [1978/2020]  1786   192   9.7%
  bin  9:  2.1116 -  2.0305 [1987/2033]  1786   201  10.1%
  bin 10:  2.0305 -  1.9606 [1256/2013]  1127   129  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 15
        1.99 -     2.72: 206
        2.72 -     3.44: 4652
        3.44 -     4.17: 9455
        4.17 -     4.90: 14332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.261 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.516 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.601 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.634 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.668 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28655 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_211/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.63395 85.09415 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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4428   r_free= 0.4407   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.245050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.3519 0.3634      6.5095      6.5666|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.3708 0.3652      6.7269      6.7158|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.3946 0.3855      6.6019      6.6679|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.4194 0.4091      6.4503      6.4176|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.4491 0.4182      6.3252      6.2923|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.4732 0.4661      6.2372       6.132|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.4791 0.4525       6.235      6.1615|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.4936 0.5069      6.1636      6.1641|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.5170 0.5127      6.1058      6.1694|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.4981 0.5443      6.1012      6.1291|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.5136 0.5307        6.02      6.0379|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.5056 0.4962      5.9523      5.9903|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.5160 0.5276      5.8793       5.875|
| 14:  2.0095 -  1.9606 0.50    635   76 0.5166 0.4752      5.8363      5.7018|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.70  34.29   0.84     0.71      68567.57|
|  2:  4.6794 -  3.7335  1350   151  0.73  32.66   0.94     0.83      90938.64|
|  3:  3.7335 -  3.2673  1331   146  0.66  38.58   0.95     0.86      93003.13|
|  4:  3.2673 -  2.9711  1324   139  0.60  43.79   0.95     0.82      78990.77|
|  5:  2.9711 -  2.7596  1306   148  0.56  47.10   0.92     0.78      62726.81|
|  6:  2.7596 -  2.5978  1303   147  0.52  50.61   0.92     0.72      54509.04|
|  7:  2.5978 -  2.4683  1282   151  0.51  51.64   0.92     0.68      52828.01|
|  8:  2.4683 -  2.3613  1310   133  0.43  57.81   0.94     0.60      52906.17|
|  9:  2.3613 -  2.2708  1298   149  0.37  62.29   0.92     0.56      52670.77|
| 10:  2.2708 -  2.1927  1278   142  0.34  64.59   0.97     0.49      50384.29|
| 11:  2.1927 -  2.1243  1281   149  0.32  66.50   0.93     0.49      48053.22|
| 12:  2.1243 -  2.0637  1273   141  0.31  67.13   0.97     0.49      44230.64|
| 13:  2.0637 -  2.0095  1254   129  0.31  67.02   0.95     0.49      37873.63|
| 14:  2.0095 -  1.9606   635    76  0.32  65.93   0.94     0.45      30390.74|
|alpha:            min =        0.45 max =            0.86 mean =         0.65|
|beta:             min =    30390.74 max =        93003.13 mean =     59833.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.80|
|phase err.(test): min =        0.00 max =           89.95 mean =        52.90|
|-----------------------------------------------------------------------------|

============================== 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 = 8.419477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.788   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.971951              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.197   (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 |  1.261 -  1.625:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.625 -  1.989:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.989 -  2.353:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.353 -  2.717:      173 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.717 -  3.081:     2320 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.081 -  3.445:     2332 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.445 -  3.808:     4173 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.808 -  4.172:     5282 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.172 -  4.536:     6413 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.536 -  4.900:     7919 |
|-----------------------------------------------------------------------------|
|-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 |        0.201 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.261 |       0.771 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    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 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4428   r_free= 0.4407   ksol= 0.00   Bsol= 0.00   scale= 0.920    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.245050                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4309   ksol= 0.32   Bsol= 22.06   scale= 0.954   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,1.94,0.31,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.236502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.341350              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.497   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.001628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.899   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4352      final r-factor (work) = 0.2921          |
| start r-factor (free) = 0.4309      final r-factor (free) = 0.3149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1007 = 7.34 * 0.50 * 6.2386 + 1.00 * 0.2009                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.4214 = 7.34 * 0.50 * 6.0744 + 1.00 * 0.1242                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2921      final r-factor (work) = 0.2638          |
| start r-factor (free) = 0.3149      final r-factor (free) = 0.3260          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0904 = 1.00 * 1.00 * 6.0744 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8993 = 1.00 * 1.00 * 5.8716 + 1.00 * 0.0182                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.97   18.38    None  None   None       |
|    all(noH): 2823   0      0.00    80.97   18.38    None  None   None       |
|    Sol.    : 438    0      3.62    80.97   39.43    None  None   None       |
|    Mac.    : 2385   0      0.00    66.30   14.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.097:  698   |   5:    40.487 -  48.584:  118        |
|      1:     8.097 -  16.195:  945   |   6:    48.584 -  56.682:   88        |
|      2:    16.195 -  24.292:  472   |   7:    56.682 -  64.779:   52        |
|      3:    24.292 -  32.390:  247   |   8:    64.779 -  72.876:   13        |
|      4:    32.390 -  40.487:  186   |   9:    72.876 -  80.974:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2638 r_free = 0.3260             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2635 r_free = 0.3266             target_work(ml) = 5.883         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2635   r_free= 0.3266   ksol= 0.32   Bsol= 22.06   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,1.94,0.31,0.00,0.00,0.00); trace/3= 0.49                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.883198                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2604   r_free= 0.3228   ksol= 0.32   Bsol= 40.09   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.00,-1.02,0.00,-0.00,-0.00); trace/3= -1.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.876193                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.715537              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.638   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332401              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.152  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2604      final r-factor (work) = 0.1933          |
| start r-factor (free) = 0.3228      final r-factor (free) = 0.2439          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0336 = 3.72 * 0.50 * 5.8723 + 1.00 * 0.1242                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7648 = 3.72 * 0.50 * 5.7596 + 1.00 * 0.0647                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1933      final r-factor (work) = 0.1783          |
| start r-factor (free) = 0.2439      final r-factor (free) = 0.2260          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9327 = 0.33 * 1.00 * 5.7596 + 1.00 * 0.0182                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8630 = 0.33 * 1.00 * 5.5763 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.14    80.75   17.64    None  None   None       |
|    all(noH): 2823   0      1.14    80.75   17.64    None  None   None       |
|    Sol.    : 438    0      4.05    80.75   39.39    None  None   None       |
|    Mac.    : 2385   0      1.14    75.78   13.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.138 -   9.099:  819   |   5:    40.942 -  48.902:   94        |
|      1:     9.099 -  17.059: 1089   |   6:    48.902 -  56.863:   88        |
|      2:    17.059 -  25.020:  360   |   7:    56.863 -  64.824:   51        |
|      3:    25.020 -  32.981:  158   |   8:    64.824 -  72.785:   16        |
|      4:    32.981 -  40.942:  137   |   9:    72.785 -  80.746:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1783 r_free = 0.2260             target_work(ml) = 5.543         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1780 r_free = 0.2261             target_work(ml) = 5.542         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1780   r_free= 0.2261   ksol= 0.32   Bsol= 40.09   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.33,0.00,-1.02,0.00,-0.00,-0.00); trace/3= -1.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.542346                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1783   r_free= 0.2252   ksol= 0.32   Bsol= 40.09   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.76,-1.34,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.542033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.957032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.861  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.353  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1783      final r-factor (work) = 0.1371          |
| start r-factor (free) = 0.2252      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3114 = 2.96 * 0.50 * 5.5777 + 1.00 * 0.0647                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0874 = 2.96 * 0.50 * 5.4293 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1371      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2628 = 0.60 * 1.00 * 5.4293 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1740 = 0.60 * 1.00 * 5.2803 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.53    91.14   17.71    None  None   None       |
|    all(noH): 2823   0      1.53    91.14   17.71    None  None   None       |
|    Sol.    : 438    0      3.78    90.26   41.95    None  None   None       |
|    Mac.    : 2385   0      1.53    91.14   13.26    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:     1.526 -  10.487: 1118   |   5:    46.331 -  55.292:  103        |
|      1:    10.487 -  19.448: 1012   |   6:    55.292 -  64.252:   77        |
|      2:    19.448 -  28.409:  224   |   7:    64.252 -  73.213:   27        |
|      3:    28.409 -  37.370:  117   |   8:    73.213 -  82.174:   17        |
|      4:    37.370 -  46.331:  123   |   9:    82.174 -  91.135:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1279 r_free = 0.1751             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1278 r_free = 0.1751             target_work(ml) = 5.258         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1751   ksol= 0.32   Bsol= 40.09   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.67,-0.76,-1.34,-0.00,-0.00,-0.00); trace/3= -1.59                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.257656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1747   ksol= 0.32   Bsol= 40.09   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.38,-1.60,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.258905                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.242047              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.813  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219230              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.666  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1747      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9836 = 2.24 * 0.50 * 5.2840 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9115 = 2.24 * 0.50 * 5.2198 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1170      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1542 = 0.22 * 1.00 * 5.2198 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1443 = 0.22 * 1.00 * 5.1822 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    90.97   17.01    None  None   None       |
|    all(noH): 2823   0      1.63    90.97   17.01    None  None   None       |
|    Sol.    : 438    0      1.63    80.67   39.46    None  None   None       |
|    Mac.    : 2385   0      2.10    90.97   12.88    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:     1.635 -  10.569: 1172   |   5:    46.303 -  55.237:   97        |
|      1:    10.569 -  19.502: 1010   |   6:    55.237 -  64.171:   57        |
|      2:    19.502 -  28.436:  195   |   7:    64.171 -  73.105:   20        |
|      3:    28.436 -  37.370:  132   |   8:    73.105 -  82.038:    7        |
|      4:    37.370 -  46.303:  129   |   9:    82.038 -  90.972:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1620             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1159 r_free = 0.1618             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1159   r_free= 0.1618   ksol= 0.32   Bsol= 40.09   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.98,-1.38,-1.60,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1158   r_free= 0.1619   ksol= 0.32   Bsol= 41.92   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.45,-1.49,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171771                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.115521              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.195  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.657957              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.041  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1321 = 3.12 * 0.50 * 5.1819 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0916 = 3.12 * 0.50 * 5.1489 + 1.00 * 0.0709                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3959 = 0.66 * 1.00 * 5.1489 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3833 = 0.66 * 1.00 * 5.1286 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    95.28   16.93    None  None   None       |
|    all(noH): 2823   0      1.06    95.28   16.93    None  None   None       |
|    Sol.    : 438    0      2.53    83.14   39.69    None  None   None       |
|    Mac.    : 2385   0      1.06    95.28   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.063 -  10.485: 1192   |   5:    48.174 -  57.596:   99        |
|      1:    10.485 -  19.907: 1010   |   6:    57.596 -  67.018:   46        |
|      2:    19.907 -  29.329:  195   |   7:    67.018 -  76.440:   12        |
|      3:    29.329 -  38.752:  125   |   8:    76.440 -  85.862:    7        |
|      4:    38.752 -  48.174:  134   |   9:    85.862 -  95.285:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1585             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1585             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1585   ksol= 0.32   Bsol= 41.92   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-1.45,-1.49,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131047                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.0968 0.1305      5.3702      5.5626|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.0818 0.1085      5.4093      5.6086|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.1014 0.1512      5.4375      5.8179|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.1192 0.1614      5.4315      5.6351|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.1273 0.1660      5.3083      5.4859|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.1239 0.2005       5.211      5.4756|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.1148 0.1555      5.1255      5.3368|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1154 0.1785      5.0699      5.3408|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.1140 0.1801      5.0112      5.3031|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1093 0.1774      4.9705      5.2158|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.1110 0.1814      4.9135      5.2266|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.1067 0.1671      4.8383      5.1106|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.1085 0.1734      4.7679      5.0397|
| 14:  2.0095 -  1.9606 0.50    635   76 0.1015 0.1774      4.6613      4.9186|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.94   9.15   0.98     0.96       7140.72|
|  2:  4.6794 -  3.7335  1350   151  0.95   7.96   1.02     1.01       8805.02|
|  3:  3.7335 -  3.2673  1331   146  0.94  11.06   1.03     1.02       9942.46|
|  4:  3.2673 -  2.9711  1324   139  0.92  13.73   1.02     1.01      10168.97|
|  5:  2.9711 -  2.7596  1306   148  0.90  15.79   1.00     0.97       8181.89|
|  6:  2.7596 -  2.5978  1303   147  0.90  16.21   0.98     0.94       6992.17|
|  7:  2.5978 -  2.4683  1282   151  0.91  14.91   0.99     0.96       5897.21|
|  8:  2.4683 -  2.3613  1310   133  0.91  15.15   1.01     0.98       5459.36|
|  9:  2.3613 -  2.2708  1298   149  0.90  15.82   1.00     0.96       4901.61|
| 10:  2.2708 -  2.1927  1278   142  0.90  15.73   1.00     0.96       4639.50|
| 11:  2.1927 -  2.1243  1281   149  0.90  16.25   1.00     0.97       4334.63|
| 12:  2.1243 -  2.0637  1273   141  0.91  14.94   1.00     0.98       3697.09|
| 13:  2.0637 -  2.0095  1254   129  0.90  15.88   1.00     1.00       3255.50|
| 14:  2.0095 -  1.9606   635    76  0.91  14.79   0.98     0.94       2586.04|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2586.04 max =        10168.97 mean =      6318.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.01|
|phase err.(test): min =        0.00 max =           89.19 mean =        13.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1586   ksol= 0.32   Bsol= 44.91   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.36,-1.30,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1084   r_free= 0.1586   ksol= 0.32   Bsol= 44.91   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.74,-1.36,-1.30,-0.00,-0.00,-0.00); trace/3= -1.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.130993                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.6794 0.99   1405  158 0.0969 0.1309      5.3716      5.5649|
|  2:  4.6794 -  3.7335 0.99   1350  151 0.0821 0.1087       5.412       5.611|
|  3:  3.7335 -  3.2673 0.99   1331  146 0.1015 0.1513      5.4391      5.8193|
|  4:  3.2673 -  2.9711 0.99   1324  139 0.1191 0.1614      5.4311      5.6348|
|  5:  2.9711 -  2.7596 0.98   1306  148 0.1272 0.1659      5.3071      5.4849|
|  6:  2.7596 -  2.5978 0.99   1303  147 0.1238 0.2002      5.2099      5.4737|
|  7:  2.5978 -  2.4683 0.98   1282  151 0.1148 0.1557      5.1246      5.3364|
|  8:  2.4683 -  2.3613 0.99   1310  133 0.1153 0.1782      5.0691      5.3394|
|  9:  2.3613 -  2.2708 0.99   1298  149 0.1139 0.1803      5.0106      5.3035|
| 10:  2.2708 -  2.1927 0.98   1278  142 0.1092 0.1775      4.9703      5.2158|
| 11:  2.1927 -  2.1243 0.97   1281  149 0.1110 0.1811      4.9131      5.2259|
| 12:  2.1243 -  2.0637 0.99   1273  141 0.1066 0.1672      4.8379      5.1109|
| 13:  2.0637 -  2.0095 0.94   1254  129 0.1086 0.1731      4.7676       5.039|
| 14:  2.0095 -  1.9606 0.50    635   76 0.1014 0.1774      4.6606      4.9177|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.6794  1405   158  0.94   9.16   0.98     0.96       7167.73|
|  2:  4.6794 -  3.7335  1350   151  0.95   7.98   1.02     1.01       8849.20|
|  3:  3.7335 -  3.2673  1331   146  0.93  11.09   1.03     1.02       9984.97|
|  4:  3.2673 -  2.9711  1324   139  0.92  13.73   1.02     1.01      10170.31|
|  5:  2.9711 -  2.7596  1306   148  0.90  15.78   1.00     0.98       8164.25|
|  6:  2.7596 -  2.5978  1303   147  0.90  16.19   0.98     0.95       6976.87|
|  7:  2.5978 -  2.4683  1282   151  0.91  14.90   0.99     0.96       5885.03|
|  8:  2.4683 -  2.3613  1310   133  0.91  15.14   1.01     0.99       5450.28|
|  9:  2.3613 -  2.2708  1298   149  0.90  15.81   1.01     0.97       4897.44|
| 10:  2.2708 -  2.1927  1278   142  0.90  15.73   1.00     0.97       4637.20|
| 11:  2.1927 -  2.1243  1281   149  0.90  16.25   1.01     0.98       4331.54|
| 12:  2.1243 -  2.0637  1273   141  0.91  14.93   1.01     0.98       3693.97|
| 13:  2.0637 -  2.0095  1254   129  0.90  15.87   1.01     1.01       3250.17|
| 14:  2.0095 -  1.9606   635    76  0.91  14.78   0.99     0.95       2579.15|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2579.15 max =        10170.31 mean =      6322.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.01|
|phase err.(test): min =        0.00 max =           88.32 mean =        13.57|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.594)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    95.25   16.89    None  None   None       |
|    all(noH): 2823   0      1.03    95.25   16.89    None  None   None       |
|    Sol.    : 438    0      2.50    83.10   39.65    None  None   None       |
|    Mac.    : 2385   0      1.03    95.25   12.71    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:     1.026 -  10.448: 1192   |   5:    48.137 -  57.559:   99        |
|      1:    10.448 -  19.870: 1010   |   6:    57.559 -  66.981:   46        |
|      2:    19.870 -  29.292:  195   |   7:    66.981 -  76.403:   12        |
|      3:    29.292 -  38.715:  125   |   8:    76.403 -  85.826:    7        |
|      4:    38.715 -  48.137:  134   |   9:    85.826 -  95.248:    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)= 282         
Filter by distance & map next to the model:
   mapped sites are within: 0.419 - 4.291
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 282
   mapped sites are within: 0.755 - 4.291

peak=    8.376 closest distance to " OG BSER A 216 " =    1.147
peak=    5.756 closest distance to " O   HOH Z 102 " =    1.376
peak=    5.666 closest distance to " NH2 ARG A  56 " =    2.306
peak=    5.440 closest distance to " CB  ARG A 275 " =    0.954
peak=    5.033 closest distance to " O   HOH Z 124 " =    1.457
peak=    5.020 closest distance to " CB  GLN A 223 " =    1.394
peak=    5.016 closest distance to " CB  SER A  63 " =    1.097
peak=    4.941 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.936 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.927 closest distance to " O   HOH Z 193 " =    1.796
peak=    4.842 closest distance to " O   HOH Z 298 " =    1.904
peak=    4.841 closest distance to " CA  TYR A  30 " =    0.930
peak=    4.790 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.782 closest distance to " O   HOH Z 142 " =    1.653
peak=    4.674 closest distance to " CG  PRO A  54 " =    1.145
peak=    4.640 closest distance to " O   HOH Z  52 " =    1.009
peak=    4.629 closest distance to " O   HOH Z 234 " =    3.666
peak=    4.580 closest distance to " O   SER A  87 " =    2.247
peak=    4.554 closest distance to " O   HOH Z 126 " =    1.801
peak=    4.530 closest distance to " O   HOH Z  97 " =    1.894
peak=    4.496 closest distance to " O   HOH Z  44 " =    2.134
peak=    4.486 closest distance to " C   PRO A 198 " =    1.492
peak=    4.467 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.417 closest distance to " O   HOH Z 209 " =    2.250
peak=    4.403 closest distance to " NE2 GLN A  11 " =    1.005
peak=    4.365 closest distance to " O   HOH Z 402 " =    1.442
peak=    4.356 closest distance to " O   HOH Z  97 " =    2.442
peak=    4.351 closest distance to " O   HOH Z 403 " =    1.981
peak=    4.343 closest distance to " CB  ARG A  79 " =    1.444
peak=    4.330 closest distance to " NZ  LYS A 117 " =    3.039
peak=    4.325 closest distance to " O   HOH Z 327 " =    1.813
peak=    4.323 closest distance to " O   HOH Z  15 " =    2.072
peak=    4.316 closest distance to " CB  GLU A 152 " =    1.176
peak=    4.286 closest distance to " O   HOH Z  80 " =    1.691
peak=    4.252 closest distance to " CD  ARG A 269 " =    1.022
peak=    4.234 closest distance to " O   HOH Z 203 " =    1.797
peak=    4.188 closest distance to " CB  SER A   3 " =    1.213
peak=    4.183 closest distance to " NH2BARG A 145 " =    2.137
peak=    4.177 closest distance to " O   HOH Z 132 " =    1.076
peak=    4.170 closest distance to " O   HOH Z 130 " =    2.811
peak=    4.157 closest distance to " CB  GLU A 277 " =    3.516
peak=    4.151 closest distance to " O   HOH Z  59 " =    2.270
peak=    4.150 closest distance to " O   HOH Z  78 " =    1.708
peak=    4.145 closest distance to " O   HOH Z 426 " =    1.471
peak=    4.138 closest distance to " CB  TYR A 169 " =    0.815
peak=    4.130 closest distance to " O   HOH Z 134 " =    1.515
peak=    4.119 closest distance to " O   HOH Z 279 " =    2.075
peak=    4.088 closest distance to " O   HOH Z  85 " =    1.518
peak=    4.086 closest distance to " CA  ALA A  21 " =    1.220
peak=    4.080 closest distance to " CG  ARG A  66 " =    1.042
peak=    4.079 closest distance to " O   HOH Z  63 " =    1.886
peak=    4.076 closest distance to " O   HOH Z 345 " =    1.804
peak=    4.074 closest distance to " O   HOH Z 368 " =    2.011
peak=    4.073 closest distance to " O   HOH Z 389 " =    1.887
peak=    4.061 closest distance to " O   HOH Z 227 " =    1.698
peak=    4.054 closest distance to " CD2 TRP A 179 " =    1.436
peak=    4.054 closest distance to " O   HOH Z 406 " =    1.586
peak=    4.046 closest distance to " O   HOH Z 369 " =    2.515
peak=    4.042 closest distance to " CB  ASN A 148 " =    1.443
peak=    4.029 closest distance to " CG2 ILE A  20 " =    1.380
peak=    4.005 closest distance to " CG1 ILE A  33 " =    1.232
peak=    4.004 closest distance to " O   HOH Z 287 " =    1.924
peak=    3.996 closest distance to " O   HOH Z 346 " =    1.536
peak=    3.995 closest distance to " O   HOH Z 303 " =    2.052
peak=    3.978 closest distance to " CB  ARG A 190 " =    1.660
peak=    3.966 closest distance to " O   HOH Z 316 " =    2.861
peak=    3.952 closest distance to " O   HOH Z  21 " =    1.888
peak=    3.930 closest distance to " CA  ASN A 176 " =    1.101
peak=    3.916 closest distance to " N   ASN A  39 " =    1.301
peak=    3.912 closest distance to " O   HOH Z 128 " =    2.272
peak=    3.905 closest distance to " CA  ALA A  84 " =    1.192
peak=    3.904 closest distance to " O  BHOH Z  74 " =    1.267
peak=    3.899 closest distance to " O   HOH Z 345 " =    2.539
peak=    3.889 closest distance to " O   HOH Z 365 " =    2.747
peak=    3.881 closest distance to " O   HOH Z  54 " =    1.717
peak=    3.879 closest distance to " CA  ARG A 195 " =    1.244
peak=    3.876 closest distance to " O   HOH Z 425 " =    2.020
peak=    3.874 closest distance to " O   HOH Z 423 " =    1.988
peak=    3.857 closest distance to " O   HOH Z  40 " =    1.837
peak=    3.852 closest distance to " CB  GLU A 128 " =    1.205
peak=    3.847 closest distance to " O   HOH Z 421 " =    1.769
peak=    3.846 closest distance to " O   HOH Z  49 " =    2.224
peak=    3.843 closest distance to " O   HOH Z   6 " =    2.300
peak=    3.835 closest distance to " O   HOH Z 154 " =    1.384
peak=    3.833 closest distance to " O   HOH Z 408 " =    1.632
peak=    3.828 closest distance to " CE  LYS A 119 " =    1.145
peak=    3.826 closest distance to " CB  TRP A 179 " =    1.143
peak=    3.820 closest distance to " CG  PRO A 243 " =    1.182
peak=    3.794 closest distance to " O   HOH Z 128 " =    1.864
peak=    3.793 closest distance to " O   HOH Z  43 " =    2.142
peak=    3.792 closest distance to " O   HOH Z 284 " =    2.840
peak=    3.786 closest distance to " CB  ARG A 139 " =    0.887
peak=    3.786 closest distance to " O   HOH Z 344 " =    2.821
peak=    3.785 closest distance to " ND2 ASN A 187 " =    1.509
peak=    3.768 closest distance to " NH2AARG A 145 " =    2.218
peak=    3.763 closest distance to " O   HOH Z 163 " =    1.449
peak=    3.758 closest distance to " O   HOH Z 416 " =    2.767
peak=    3.756 closest distance to " OD2 ASP A 286 " =    2.806
peak=    3.744 closest distance to " O   HOH Z 392 " =    2.573
peak=    3.738 closest distance to " CB  SER A  26 " =    1.650
peak=    3.736 closest distance to " CA  LYS A 117 " =    1.284
peak=    3.732 closest distance to " O   HOH Z 144 " =    2.115
peak=    3.725 closest distance to " O   HOH Z 245 " =    1.384
peak=    3.713 closest distance to " CB  PRO A  54 " =    0.826
peak=    3.712 closest distance to " O   HOH Z 147 " =    1.808
peak=    3.701 closest distance to " OG1 THR A 294 " =    2.302
peak=    3.686 closest distance to " O   HOH Z 250 " =    1.664
peak=    3.684 closest distance to " O   HOH Z 163 " =    2.078
peak=    3.681 closest distance to " CG2 ILE A 120 " =    1.228
peak=    3.680 closest distance to " CD  GLN A 194 " =    1.523
peak=    3.679 closest distance to " CA  THR A 221 " =    0.957
peak=    3.647 closest distance to " OG  SER A  62 " =    2.834
peak=    3.644 closest distance to " O   HOH Z 419 " =    1.571
peak=    3.643 closest distance to " O   HOH Z 427 " =    2.972
peak=    3.634 closest distance to " OD2 ASP A 298 " =    3.923
peak=    3.626 closest distance to " O   HOH Z  35 " =    2.357
peak=    3.618 closest distance to " NZ  LYS A 119 " =    1.693
peak=    3.615 closest distance to " CB  ALA A 248 " =    1.400
peak=    3.614 closest distance to " O   HOH Z 383 " =    2.087
peak=    3.611 closest distance to " CB  ASN A  39 " =    0.809
peak=    3.609 closest distance to " O   HOH Z 132 " =    2.598
peak=    3.604 closest distance to " O   HOH Z  68 " =    1.788
peak=    3.599 closest distance to " CA  ARG A  36 " =    1.042
peak=    3.594 closest distance to " CB  LEU A 228 " =    1.104
peak=    3.591 closest distance to " O   HOH Z 326 " =    1.503
peak=    3.588 closest distance to " O   HOH Z 250 " =    1.425
peak=    3.588 closest distance to " O   HOH Z 108 " =    2.569
peak=    3.586 closest distance to " O   HOH Z 427 " =    2.710
peak=    3.582 closest distance to " CG AARG A 275 " =    1.193
peak=    3.581 closest distance to " CB  TRP A 266 " =    1.051
peak=    3.580 closest distance to " O   HOH Z 189 " =    1.779
peak=    3.580 closest distance to " OG BSER A 212 " =    2.586
peak=    3.572 closest distance to " O   HOH Z 132 " =    2.080
peak=    3.562 closest distance to " O   HOH Z 337 " =    3.595
peak=    3.562 closest distance to " CG2BVAL A  41 " =    0.816
peak=    3.560 closest distance to " O   HOH Z 214 " =    2.309
peak=    3.560 closest distance to " OG BSER A 164 " =    2.456
peak=    3.559 closest distance to " O   ALA A 165 " =    1.339
peak=    3.559 closest distance to " O   HOH Z 313 " =    1.706
peak=    3.558 closest distance to " O   HOH Z 261 " =    1.618
peak=    3.554 closest distance to " O   HOH Z 411 " =    3.505
peak=    3.544 closest distance to " CA  ALA A  51 " =    0.873
peak=    3.539 closest distance to " O   HOH Z  47 " =    1.508
peak=    3.537 closest distance to " OD1 ASN A  69 " =    2.662
peak=    3.535 closest distance to " CA  ARG A  66 " =    1.202
peak=    3.528 closest distance to " O   HOH Z 334 " =    1.363
peak=    3.512 closest distance to " CA  ASN A 215 " =    1.075
peak=    3.503 closest distance to " O   HOH Z 173 " =    2.094
peak=    3.501 closest distance to " CB  THR A  31 " =    1.751
peak=    3.482 closest distance to " O   HOH Z 299 " =    2.353
peak=    3.480 closest distance to " O   HOH Z 357 " =    1.730
peak=    3.474 closest distance to " O   HOH Z 374 " =    2.566
peak=    3.470 closest distance to " O   HOH Z  66 " =    2.134
peak=    3.466 closest distance to " O   HOH Z 123 " =    2.147
peak=    3.461 closest distance to " CD1 LEU A  96 " =    0.812
peak=    3.461 closest distance to " O   HOH Z 158 " =    2.928
peak=    3.458 closest distance to " CG  GLN A  58 " =    2.404
peak=    3.455 closest distance to " C   ALA A   1 " =    1.570
peak=    3.451 closest distance to " NH1AARG A 145 " =    1.227
peak=    3.443 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.440 closest distance to " O   HOH Z 423 " =    3.439
peak=    3.436 closest distance to " O   HOH Z 130 " =    2.392
peak=    3.435 closest distance to " CG1BVAL A  72 " =    1.610
peak=    3.431 closest distance to " CB  SER A  62 " =    0.793
peak=    3.427 closest distance to " CD  LYS A 166 " =    1.294
peak=    3.422 closest distance to " O   HOH Z 425 " =    1.309
peak=    3.416 closest distance to " OD1 ASP A 253 " =    1.885
peak=    3.415 closest distance to " O   HOH Z 265 " =    2.312
peak=    3.412 closest distance to " O   HOH Z 185 " =    1.704
peak=    3.410 closest distance to " O   HOH Z  61 " =    1.586
peak=    3.403 closest distance to " CA  ASP A 162 " =    1.173
peak=    3.402 closest distance to " C   ILE A 106 " =    1.859
peak=    3.382 closest distance to " CA  ASP A 140 " =    1.090
peak=    3.373 closest distance to " O   HOH Z 401 " =    0.994
peak=    3.372 closest distance to " O   HOH Z 371 " =    3.185
peak=    3.361 closest distance to " O   HOH Z 305 " =    3.619
peak=    3.360 closest distance to " O   HOH Z 257 " =    2.282
peak=    3.351 closest distance to " CD  PRO A  54 " =    1.119
peak=    3.348 closest distance to " O   HOH Z 361 " =    3.075
peak=    3.346 closest distance to " O   HOH Z 273 " =    2.753
peak=    3.346 closest distance to " O   HOH Z 299 " =    4.291
peak=    3.344 closest distance to " O   HOH Z 336 " =    1.779
peak=    3.341 closest distance to " CB  VAL A 202 " =    1.514
peak=    3.335 closest distance to " O   HOH Z  30 " =    2.058
peak=    3.332 closest distance to " CA  ALA A 291 " =    0.875
peak=    3.328 closest distance to " O   HOH Z 417 " =    3.120
peak=    3.327 closest distance to " O   HOH Z 404 " =    2.183
peak=    3.326 closest distance to " O   HOH Z  63 " =    2.191
peak=    3.325 closest distance to " CB  SER A 141 " =    1.022
peak=    3.324 closest distance to " O   HOH Z  88 " =    3.194
peak=    3.316 closest distance to " CD BLYS A 290 " =    1.186
peak=    3.315 closest distance to " CB  ASP A 140 " =    1.041
peak=    3.313 closest distance to " O   HOH Z 380 " =    1.824
peak=    3.313 closest distance to " O   HOH Z 428 " =    3.665
peak=    3.307 closest distance to " O   HOH Z  89 " =    2.251
peak=    3.294 closest distance to " CG2 VAL A 197 " =    1.108
peak=    3.292 closest distance to " O   HOH Z  49 " =    2.449
peak=    3.291 closest distance to " O   HOH Z   1 " =    2.292
peak=    3.291 closest distance to " O   HOH Z 155 " =    3.075
peak=    3.287 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.287 closest distance to " CD  ARG A 195 " =    0.841
peak=    3.283 closest distance to " O   HOH Z 422 " =    2.641
peak=    3.282 closest distance to " CA  MET A  40 " =    1.058
peak=    3.282 closest distance to " CD  GLN A 240 " =    1.431
peak=    3.273 closest distance to " O   HOH Z 359 " =    1.425
peak=    3.272 closest distance to " N   ASP A 162 " =    1.282
peak=    3.265 closest distance to " O   HOH Z 234 " =    1.778
peak=    3.264 closest distance to " CG  PRO A 198 " =    1.412
peak=    3.263 closest distance to " N   CYS A 260 " =    0.886
peak=    3.258 closest distance to " CG2 THR A 294 " =    1.596
peak=    3.257 closest distance to " O   HOH Z 148 " =    3.117
peak=    3.251 closest distance to " CB  GLN A 278 " =    0.809
peak=    3.246 closest distance to " CB  ILE A 120 " =    1.265
peak=    3.242 closest distance to " OE1 GLN A  11 " =    1.909
peak=    3.231 closest distance to " O   HOH Z  19 " =    1.862
peak=    3.229 closest distance to " O   HOH Z 435 " =    1.828
peak=    3.226 closest distance to " CB  PRO A 163 " =    3.951
peak=    3.225 closest distance to " CB  ASP A 191 " =    1.301
peak=    3.223 closest distance to " O   HOH Z 217 " =    2.144
peak=    3.221 closest distance to " CG  GLN A  77 " =    1.980
peak=    3.219 closest distance to " CZ2 TRP A 179 " =    1.752
peak=    3.218 closest distance to " O   HOH Z 171 " =    1.820
peak=    3.217 closest distance to " CD1AILE A 234 " =    0.981
peak=    3.216 closest distance to " CD2 LEU A 297 " =    0.825
peak=    3.213 closest distance to " CG  PRO A  90 " =    1.210
peak=    3.208 closest distance to " O   HOH Z 247 " =    1.291
peak=    3.207 closest distance to " CZ  PHE A  38 " =    1.416
peak=    3.207 closest distance to " O   HOH Z 194 " =    1.896
peak=    3.206 closest distance to " O   HOH Z  59 " =    1.630
peak=    3.206 closest distance to " O   HOH Z 438 " =    2.155
peak=    3.204 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.204 closest distance to " O   HOH Z 193 " =    2.202
peak=    3.204 closest distance to " CB  ALA A 100 " =    1.140
peak=    3.204 closest distance to " O   HOH Z 336 " =    1.673
peak=    3.199 closest distance to " O   HOH Z 286 " =    2.109
peak=    3.195 closest distance to " CA  ALA A 160 " =    0.851
peak=    3.194 closest distance to " NH1AARG A 275 " =    3.154
peak=    3.190 closest distance to " O   HOH Z  10 " =    1.761
peak=    3.190 closest distance to " NH2 ARG A  79 " =    1.324
peak=    3.183 closest distance to " O   HOH Z 358 " =    2.116
peak=    3.181 closest distance to " O   HOH Z 280 " =    2.543
peak=    3.181 closest distance to " CD  LYS A 119 " =    1.681
peak=    3.178 closest distance to " N   TRP A 150 " =    1.404
peak=    3.175 closest distance to " CA  SER A 146 " =    1.880
peak=    3.173 closest distance to " CB  ALA A  71 " =    1.259
peak=    3.171 closest distance to " CB  ALA A   9 " =    1.535
peak=    3.171 closest distance to " O   HOH Z  85 " =    2.062
peak=    3.165 closest distance to " CD1 LEU A 300 " =    1.197
peak=    3.163 closest distance to " O   HOH Z  47 " =    1.365
peak=    3.163 closest distance to " O   HOH Z 353 " =    2.796
peak=    3.159 closest distance to " O   HOH Z  94 " =    2.058
peak=    3.159 closest distance to " O   HOH Z 281 " =    4.205
peak=    3.156 closest distance to " CB  ASN A 215 " =    1.124
peak=    3.151 closest distance to " CB  ALA A 131 " =    1.405
peak=    3.147 closest distance to " O   HOH Z 341 " =    1.818
peak=    3.142 closest distance to " CB  ALA A 291 " =    1.237
peak=    3.140 closest distance to " CD1 LEU A 228 " =    1.636
peak=    3.136 closest distance to " O   HOH Z  19 " =    1.374
peak=    3.136 closest distance to " CB  PRO A  90 " =    1.938
peak=    3.130 closest distance to " CD  ARG A  79 " =    2.080
peak=    3.128 closest distance to " CB  ALA A 295 " =    1.224
peak=    3.128 closest distance to " O   HOH Z 227 " =    1.846
peak=    3.126 closest distance to " O   HOH Z  46 " =    1.387
peak=    3.125 closest distance to " O   HOH Z 394 " =    1.636
peak=    3.123 closest distance to " OH  TYR A 116 " =    1.050
peak=    3.117 closest distance to " O   HOH Z 367 " =    3.466
peak=    3.115 closest distance to " NZ  LYS A  76 " =    1.823
peak=    3.105 closest distance to " CB  LYS A 289 " =    1.037
peak=    3.102 closest distance to " CG1 VAL A 202 " =    2.019
peak=    3.101 closest distance to " O   HOH Z 414 " =    1.582
peak=    3.100 closest distance to " CG  MET A 185 " =    1.028
peak=    3.097 closest distance to " CB  TYR A 116 " =    0.881
peak=    3.084 closest distance to " CB  MET A  47 " =    1.171
peak=    3.077 closest distance to " O   HOH Z 145 " =    1.931
peak=    3.073 closest distance to " CZ2 TRP A 274 " =    1.577
peak=    3.068 closest distance to " CA  VAL A 126 " =    1.183
peak=    3.046 closest distance to " CA  GLY A  80 " =    0.890
peak=    3.034 closest distance to " O   HOH Z 298 " =    2.049
peak=    3.019 closest distance to " CD  ARG A 139 " =    1.755
peak=    3.004 closest distance to " O   HOH Z 214 " =    1.574

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.832 - 5.879
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 211
   mapped sites are within: 0.832 - 5.879

peak=   -5.110 closest distance to " O   HOH Z 266 " =    4.336
peak=   -4.699 closest distance to " CD  ARG A 156 " =    2.098
peak=   -4.592 closest distance to " CG  MET A  93 " =    2.434
peak=   -4.506 closest distance to " C   HIS A 108 " =    1.129
peak=   -4.450 closest distance to " O   VAL A  67 " =    2.716
peak=   -4.298 closest distance to " OXT GLY A 302 " =    2.884
peak=   -4.280 closest distance to " N   ALA A 248 " =    1.761
peak=   -4.252 closest distance to " O   HOH Z  13 " =    1.712
peak=   -4.217 closest distance to " O   HOH Z 165 " =    1.920
peak=   -4.215 closest distance to " SG  CYS A 254 " =    3.228
peak=   -4.150 closest distance to " O   VAL A  67 " =    2.669
peak=   -4.142 closest distance to " CB  ALA A 291 " =    2.307
peak=   -4.117 closest distance to " CB  ALA A 161 " =    2.547
peak=   -4.036 closest distance to " OG BSER A 134 " =    1.355
peak=   -4.029 closest distance to " O   HOH Z 372 " =    2.261
peak=   -4.018 closest distance to " CD  GLN A  58 " =    1.196
peak=   -4.006 closest distance to " O   PRO A 163 " =    2.059
peak=   -3.997 closest distance to " O   TRP A  92 " =    1.913
peak=   -3.968 closest distance to " O   HOH Z  52 " =    0.953
peak=   -3.936 closest distance to " O   PHE A 218 " =    1.557
peak=   -3.903 closest distance to " O   HOH Z 377 " =    2.108
peak=   -3.873 closest distance to " OE1 GLN A 223 " =    2.233
peak=   -3.868 closest distance to " O   HOH Z 353 " =    2.177
peak=   -3.857 closest distance to " O   SER A 210 " =    1.806
peak=   -3.851 closest distance to " CG1AVAL A  41 " =    2.671
peak=   -3.828 closest distance to " O   PRO A 198 " =    1.354
peak=   -3.825 closest distance to " CG  ASP A 132 " =    2.313
peak=   -3.810 closest distance to " ND2 ASN A  45 " =    1.009
peak=   -3.805 closest distance to " CZ  TYR A 169 " =    1.873
peak=   -3.794 closest distance to " CG1 VAL A 112 " =    2.722
peak=   -3.788 closest distance to " O   HOH Z 114 " =    3.465
peak=   -3.786 closest distance to " CD2 TYR A  30 " =    2.761
peak=   -3.786 closest distance to " CB  PHE A 192 " =    1.942
peak=   -3.784 closest distance to " O   HOH Z 198 " =    2.045
peak=   -3.759 closest distance to " O   HOH Z  52 " =    1.436
peak=   -3.739 closest distance to " O   HOH Z  88 " =    4.479
peak=   -3.726 closest distance to " CD1 PHE A  59 " =    1.970
peak=   -3.725 closest distance to " O   HOH Z 234 " =    4.051
peak=   -3.712 closest distance to " CD2 LEU A 300 " =    2.761
peak=   -3.697 closest distance to " O   HOH Z  71 " =    1.556
peak=   -3.695 closest distance to " CD1 PHE A 130 " =    2.272
peak=   -3.690 closest distance to " CD1 LEU A 228 " =    2.122
peak=   -3.680 closest distance to " CD2 LEU A 237 " =    2.489
peak=   -3.674 closest distance to " O   ALA A 160 " =    1.591
peak=   -3.673 closest distance to " O   HOH Z 290 " =    0.986
peak=   -3.666 closest distance to " C   GLY A  80 " =    2.435
peak=   -3.654 closest distance to " NH2 ARG A  79 " =    2.015
peak=   -3.648 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.644 closest distance to " CD  ARG A 139 " =    1.581
peak=   -3.642 closest distance to " N   GLN A  58 " =    1.738
peak=   -3.637 closest distance to " NH1 ARG A 195 " =    2.559
peak=   -3.634 closest distance to " CB  PRO A 243 " =    2.627
peak=   -3.630 closest distance to " OG  SER A  97 " =    2.077
peak=   -3.614 closest distance to " CG  GLU A  53 " =    1.429
peak=   -3.612 closest distance to " N   ASP A 200 " =    1.599
peak=   -3.609 closest distance to " C   THR A 279 " =    1.184
peak=   -3.606 closest distance to " OD2 ASP A 171 " =    2.323
peak=   -3.604 closest distance to " N   ALA A 248 " =    2.239
peak=   -3.589 closest distance to " NH2 ARG A  66 " =    5.083
peak=   -3.589 closest distance to " O   HOH Z 126 " =    1.816
peak=   -3.583 closest distance to " O   ARG A  56 " =    1.653
peak=   -3.583 closest distance to " O   HOH Z 407 " =    2.863
peak=   -3.582 closest distance to " O   HOH Z 422 " =    1.020
peak=   -3.580 closest distance to " CB  ASN A  39 " =    2.312
peak=   -3.579 closest distance to " CD1 LEU A  25 " =    2.526
peak=   -3.578 closest distance to " ND2 ASN A  39 " =    1.173
peak=   -3.577 closest distance to " OD1 ASN A  39 " =    2.190
peak=   -3.562 closest distance to " OD2 ASP A 191 " =    1.400
peak=   -3.554 closest distance to " CH2 TRP A 179 " =    1.324
peak=   -3.545 closest distance to " CA  TYR A  68 " =    2.924
peak=   -3.538 closest distance to " O   SER A 273 " =    1.375
peak=   -3.530 closest distance to " O   VAL A 174 " =    2.093
peak=   -3.523 closest distance to " N   SER A 276 " =    1.358
peak=   -3.519 closest distance to " ND2 ASN A  69 " =    1.549
peak=   -3.510 closest distance to " O   ASN A 187 " =    1.440
peak=   -3.496 closest distance to " CG  GLU A   2 " =    1.787
peak=   -3.495 closest distance to " O   HOH Z 166 " =    1.717
peak=   -3.491 closest distance to " O   ALA A 256 " =    1.486
peak=   -3.484 closest distance to " O   HOH Z 174 " =    4.052
peak=   -3.481 closest distance to " CD  ARG A 195 " =    5.124
peak=   -3.480 closest distance to " N   GLY A 133 " =    1.860
peak=   -3.475 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.475 closest distance to " O   HOH Z  41 " =    2.244
peak=   -3.467 closest distance to " CD  GLN A  58 " =    1.019
peak=   -3.458 closest distance to " O   HOH Z 311 " =    3.483
peak=   -3.440 closest distance to " O   HOH Z 377 " =    1.590
peak=   -3.438 closest distance to " O   MET A  40 " =    2.746
peak=   -3.437 closest distance to " CA  VAL A 125 " =    2.334
peak=   -3.430 closest distance to " CD  LYS A 289 " =    2.408
peak=   -3.430 closest distance to " O   HOH Z 251 " =    1.470
peak=   -3.429 closest distance to " O   SER A 135 " =    1.630
peak=   -3.427 closest distance to " O   ALA A  34 " =    2.321
peak=   -3.426 closest distance to " OG ASER A 134 " =    1.209
peak=   -3.424 closest distance to " CB  ASP A 286 " =    1.931
peak=   -3.421 closest distance to " O   ALA A   1 " =    1.834
peak=   -3.414 closest distance to " NE2 GLN A  88 " =    1.747
peak=   -3.399 closest distance to " O   HOH Z  11 " =    1.808
peak=   -3.392 closest distance to " CB  ALA A 248 " =    1.947
peak=   -3.389 closest distance to " OG BSER A 134 " =    1.640
peak=   -3.386 closest distance to " O   ALA A 161 " =    1.502
peak=   -3.384 closest distance to " C   GLY A  91 " =    1.349
peak=   -3.382 closest distance to " CD2 LEU A 237 " =    2.138
peak=   -3.377 closest distance to " N   THR A 235 " =    1.319
peak=   -3.376 closest distance to " CB  PHE A 208 " =    2.268
peak=   -3.370 closest distance to " N   GLN A 122 " =    1.518
peak=   -3.369 closest distance to " O   HOH Z 250 " =    1.423
peak=   -3.369 closest distance to " O   HOH Z 196 " =    1.826
peak=   -3.367 closest distance to " O   ASN A  45 " =    1.769
peak=   -3.361 closest distance to " OG BSER A 210 " =    2.181
peak=   -3.360 closest distance to " OG  SER A  62 " =    1.313
peak=   -3.359 closest distance to " O  BHOH Z 338 " =    1.508
peak=   -3.351 closest distance to " CD1 LEU A  83 " =    2.319
peak=   -3.350 closest distance to " O   HOH Z  11 " =    1.896
peak=   -3.350 closest distance to " ND2 ASN A 187 " =    1.409
peak=   -3.349 closest distance to " O   HOH Z 427 " =    1.466
peak=   -3.348 closest distance to " O   HOH Z 252 " =    3.204
peak=   -3.347 closest distance to " C   ALA A 158 " =    1.201
peak=   -3.347 closest distance to " O   HOH Z 401 " =    0.924
peak=   -3.346 closest distance to " O   HOH Z   6 " =    1.839
peak=   -3.345 closest distance to " O   HOH Z  15 " =    1.543
peak=   -3.344 closest distance to " O   HOH Z  37 " =    1.634
peak=   -3.336 closest distance to " O   HOH Z 280 " =    2.308
peak=   -3.336 closest distance to " CG  LYS A 119 " =    2.838
peak=   -3.322 closest distance to " CG2 THR A 178 " =    2.191
peak=   -3.321 closest distance to " O   HOH Z   5 " =    1.554
peak=   -3.319 closest distance to " CD  GLN A  58 " =    1.038
peak=   -3.318 closest distance to " CG2 ILE A 263 " =    2.117
peak=   -3.318 closest distance to " O   ALA A  51 " =    1.454
peak=   -3.316 closest distance to " CG  GLU A 152 " =    1.104
peak=   -3.315 closest distance to " N   SER A  12 " =    1.393
peak=   -3.314 closest distance to " N   VAL A 189 " =    1.588
peak=   -3.307 closest distance to " O   PRO A 198 " =    1.273
peak=   -3.306 closest distance to " CD  GLN A  88 " =    0.989
peak=   -3.304 closest distance to " O   HOH Z 361 " =    3.511
peak=   -3.304 closest distance to " OD1 ASN A 148 " =    1.624
peak=   -3.300 closest distance to " CG  PRO A 163 " =    2.575
peak=   -3.290 closest distance to " O   HOH Z 414 " =    1.362
peak=   -3.290 closest distance to " O   HOH Z  77 " =    2.092
peak=   -3.287 closest distance to " O   SER A   3 " =    1.055
peak=   -3.282 closest distance to " OG  SER A  63 " =    1.337
peak=   -3.274 closest distance to " O   VAL A 189 " =    2.598
peak=   -3.273 closest distance to " O   HOH Z 109 " =    5.879
peak=   -3.270 closest distance to " NE2 GLN A 103 " =    1.653
peak=   -3.267 closest distance to " NH1 ARG A  66 " =    0.931
peak=   -3.265 closest distance to " OD1 ASP A 171 " =    1.581
peak=   -3.260 closest distance to " O   HOH Z 435 " =    2.642
peak=   -3.260 closest distance to " O   HOH Z 171 " =    1.984
peak=   -3.255 closest distance to " CE1 TYR A 247 " =    2.558
peak=   -3.251 closest distance to " O   HOH Z 123 " =    2.173
peak=   -3.250 closest distance to " CB  PRO A 163 " =    2.653
peak=   -3.249 closest distance to " O   HOH Z  17 " =    1.312
peak=   -3.243 closest distance to " OD2 ASP A  50 " =    1.366
peak=   -3.241 closest distance to " C   LEU A 143 " =    1.031
peak=   -3.241 closest distance to " O   HOH Z 191 " =    5.735
peak=   -3.238 closest distance to " O   HOH Z 360 " =    2.604
peak=   -3.237 closest distance to " O   HOH Z 364 " =    5.279
peak=   -3.234 closest distance to " O   GLY A  75 " =    1.625
peak=   -3.233 closest distance to " O   HOH Z 263 " =    2.813
peak=   -3.233 closest distance to " N   ALA A 226 " =    1.945
peak=   -3.231 closest distance to " O   HOH Z 431 " =    2.020
peak=   -3.227 closest distance to " OD1 ASP A 191 " =    1.568
peak=   -3.227 closest distance to " O   HOH Z 283 " =    1.753
peak=   -3.220 closest distance to " CB  ALA A  43 " =    2.271
peak=   -3.219 closest distance to " O   HOH Z 384 " =    3.256
peak=   -3.219 closest distance to " CG  ASP A 231 " =    0.832
peak=   -3.218 closest distance to " O   HOH Z 326 " =    1.705
peak=   -3.217 closest distance to " CD2 TYR A 293 " =    1.946
peak=   -3.213 closest distance to " O   HOH Z 369 " =    2.246
peak=   -3.211 closest distance to " O   HOH Z 388 " =    2.083
peak=   -3.208 closest distance to " CB  ALA A   1 " =    1.886
peak=   -3.204 closest distance to " CE1 TYR A 169 " =    2.222
peak=   -3.196 closest distance to " CB  SER A 258 " =    1.970
peak=   -3.194 closest distance to " O   HOH Z  90 " =    2.721
peak=   -3.189 closest distance to " NH2 ARG A  66 " =    1.852
peak=   -3.189 closest distance to " O   HOH Z 397 " =    1.179
peak=   -3.188 closest distance to " CB  ALA A 248 " =    2.241
peak=   -3.187 closest distance to " CA  GLY A 203 " =    2.164
peak=   -3.187 closest distance to " O   HOH Z 193 " =    1.613
peak=   -3.185 closest distance to " CE  LYS A 166 " =    2.964
peak=   -3.185 closest distance to " O   HOH Z  61 " =    1.657
peak=   -3.167 closest distance to " O   GLY A 196 " =    0.995
peak=   -3.166 closest distance to " OD1 ASN A 187 " =    1.785
peak=   -3.159 closest distance to " O   MET A 188 " =    1.841
peak=   -3.159 closest distance to " CG2 VAL A 189 " =    2.217
peak=   -3.157 closest distance to " N   ALA A  43 " =    2.513
peak=   -3.149 closest distance to " O   THR A 182 " =    1.254
peak=   -3.148 closest distance to " O   HOH Z 174 " =    2.226
peak=   -3.142 closest distance to " O   HOH Z 385 " =    1.977
peak=   -3.138 closest distance to " O   HOH Z 411 " =    3.530
peak=   -3.136 closest distance to " OE1 GLN A  77 " =    1.700
peak=   -3.135 closest distance to " O   GLU A 152 " =    1.575
peak=   -3.133 closest distance to " O   ALA A  10 " =    1.792
peak=   -3.133 closest distance to " O   HOH Z 357 " =    1.762
peak=   -3.132 closest distance to " O   ASP A 171 " =    2.003
peak=   -3.131 closest distance to " O   HOH Z 414 " =    1.760
peak=   -3.130 closest distance to " O   HOH Z 385 " =    3.447
peak=   -3.127 closest distance to " O   HOH Z 185 " =    2.260
peak=   -3.113 closest distance to " O   HOH Z 418 " =    1.455
peak=   -3.112 closest distance to " O   HOH Z 396 " =    1.703
peak=   -3.107 closest distance to " CG  ASP A  50 " =    2.408
peak=   -3.103 closest distance to " OE2 GLU A   2 " =    1.594
peak=   -3.103 closest distance to " O   HOH Z 154 " =    1.583
peak=   -3.103 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.101 closest distance to " CD2 TYR A 247 " =    2.314
peak=   -3.090 closest distance to " CD2 LEU A 300 " =    2.646
peak=   -3.082 closest distance to " CD2 HIS A 115 " =    1.036
peak=   -3.079 closest distance to " NH1 ARG A  66 " =    5.315
peak=   -3.067 closest distance to " OG  SER A  26 " =    1.318
peak=   -3.046 closest distance to " O   HOH Z 175 " =    1.173
peak=   -3.023 closest distance to " O   HOH Z 422 " =    1.586
peak=   -3.008 closest distance to " CA  GLY A 133 " =    2.021

================= 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    :  0.4428 0.4407   6.245050e+00   6.240484e+00
   1_bss:  0.4352 0.4309   6.236502e+00   6.226029e+00
   1_xyz:  0.2921 0.3149   5.939867e+00   5.997427e+00
   1_adp:  0.2638 0.3260   5.883598e+00   6.024888e+00
   1_occ:  0.2635 0.3266   5.883198e+00   6.025127e+00
   2_bss:  0.2604 0.3228   5.876193e+00   6.021330e+00
   2_xyz:  0.1933 0.2439   5.609976e+00   5.794658e+00
   2_adp:  0.1783 0.2260   5.542680e+00   5.725915e+00
   2_occ:  0.1780 0.2261   5.542346e+00   5.725628e+00
   3_bss:  0.1783 0.2252   5.542033e+00   5.721922e+00
   3_xyz:  0.1371 0.1817   5.312002e+00   5.522936e+00
   3_adp:  0.1279 0.1751   5.257769e+00   5.479341e+00
   3_occ:  0.1278 0.1751   5.257656e+00   5.479282e+00
   4_bss:  0.1284 0.1747   5.258905e+00   5.477752e+00
   4_xyz:  0.1170 0.1647   5.185729e+00   5.419492e+00
   4_adp:  0.1160 0.1620   5.172414e+00   5.403170e+00
   4_occ:  0.1159 0.1618   5.171702e+00   5.402873e+00
   5_bss:  0.1158 0.1619   5.171771e+00   5.403017e+00
   5_xyz:  0.1095 0.1578   5.133659e+00   5.379852e+00
   5_adp:  0.1085 0.1585   5.131026e+00   5.382833e+00
   5_occ:  0.1085 0.1585   5.131047e+00   5.383149e+00
   5_bss:  0.1084 0.1586   5.130993e+00   5.383171e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.315  22.064  -0.797   1.945   0.315   0.000   0.000   0.000
   1_xyz:  0.315  22.064  -0.797   1.945   0.315   0.000   0.000   0.000
   1_adp:  0.315  22.064  -0.797   1.945   0.315   0.000   0.000   0.000
   1_occ:  0.315  22.064  -0.797   1.945   0.315   0.000   0.000   0.000
   2_bss:  0.316  40.089  -2.326   0.003  -1.017   0.000  -0.000  -0.000
   2_xyz:  0.316  40.089  -2.326   0.003  -1.017   0.000  -0.000  -0.000
   2_adp:  0.316  40.089  -2.326   0.003  -1.017   0.000  -0.000  -0.000
   2_occ:  0.316  40.089  -2.326   0.003  -1.017   0.000  -0.000  -0.000
   3_bss:  0.316  40.089  -2.673  -0.762  -1.338  -0.000  -0.000  -0.000
   3_xyz:  0.316  40.089  -2.673  -0.762  -1.338  -0.000  -0.000  -0.000
   3_adp:  0.316  40.089  -2.673  -0.762  -1.338  -0.000  -0.000  -0.000
   3_occ:  0.316  40.089  -2.673  -0.762  -1.338  -0.000  -0.000  -0.000
   4_bss:  0.316  40.089  -2.979  -1.376  -1.596  -0.000  -0.000  -0.000
   4_xyz:  0.316  40.089  -2.979  -1.376  -1.596  -0.000  -0.000  -0.000
   4_adp:  0.316  40.089  -2.979  -1.376  -1.596  -0.000  -0.000  -0.000
   4_occ:  0.316  40.089  -2.979  -1.376  -1.596  -0.000  -0.000  -0.000
   5_bss:  0.320  41.920  -2.916  -1.452  -1.487  -0.000  -0.000  -0.000
   5_xyz:  0.320  41.920  -2.916  -1.452  -1.487  -0.000  -0.000  -0.000
   5_adp:  0.320  41.920  -2.916  -1.452  -1.487  -0.000  -0.000  -0.000
   5_occ:  0.320  41.920  -2.916  -1.452  -1.487  -0.000  -0.000  -0.000
   5_bss:  0.324  44.908  -2.741  -1.360  -1.301  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.813 0.4853  0.6498    59824.072
   1_bss:  51.634 0.4984  0.6803    56109.188
   1_xyz:  32.623 0.7291  0.9483    26392.468
   1_adp:  34.209 0.7101  0.9298    28442.814
   1_occ:  34.251 0.7097  0.9289    28501.088
   2_bss:  33.880 0.7135  0.8836    27831.533
   2_xyz:  24.625 0.8141  0.9732    15361.920
   2_adp:  22.083 0.8412  0.9848    13104.311
   2_occ:  22.082 0.8412  0.9847    13100.632
   3_bss:  21.997 0.8419  0.9685    12961.959
   3_xyz:  17.197 0.8871  0.9957     8347.799
   3_adp:  16.166 0.8967  0.9930     7712.827
   3_occ:  16.168 0.8967  0.9928     7708.522
   4_bss:  16.113 0.8971  0.9788     7666.936
   4_xyz:  14.874 0.9076  0.9830     6769.677
   4_adp:  14.466 0.9113  0.9800     6617.663
   4_occ:  14.453 0.9114  0.9799     6607.899
   5_bss:  14.456 0.9114  0.9814     6613.234
   5_xyz:  13.930 0.9155  0.9836     6280.304
   5_adp:  13.962 0.9154  0.9779     6318.048
   5_occ:  13.966 0.9154  0.9779     6317.379
   5_bss:  13.965 0.9154  0.9822     6320.671
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   2.0090e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   2.0090e-01
   1_xyz:   1.493  0.012  0.089 15.685  0.006  4.108   1.2424e-01
   1_adp:   1.493  0.012  0.089 15.685  0.006  4.108   1.2424e-01
   1_occ:   1.493  0.012  0.089 15.685  0.006  4.108   1.2424e-01
   2_bss:   1.493  0.012  0.089 15.685  0.006  4.108   1.2424e-01
   2_xyz:   1.094  0.007  0.071 14.640  0.005  4.122   6.4737e-02
   2_adp:   1.094  0.007  0.071 14.640  0.005  4.122   6.4737e-02
   2_occ:   1.094  0.007  0.071 14.640  0.005  4.122   6.4737e-02
   3_bss:   1.094  0.007  0.071 14.640  0.005  4.122   6.4737e-02
   3_xyz:   1.021  0.007  0.068 14.726  0.004  4.114   6.0058e-02
   3_adp:   1.021  0.007  0.068 14.726  0.004  4.114   6.0058e-02
   3_occ:   1.021  0.007  0.068 14.726  0.004  4.114   6.0058e-02
   4_bss:   1.021  0.007  0.068 14.726  0.004  4.114   6.0058e-02
   4_xyz:   1.013  0.007  0.072 14.776  0.004  4.107   5.9895e-02
   4_adp:   1.013  0.007  0.072 14.776  0.004  4.107   5.9895e-02
   4_occ:   1.013  0.007  0.072 14.776  0.004  4.107   5.9895e-02
   5_bss:   1.013  0.007  0.072 14.776  0.004  4.107   5.9895e-02
   5_xyz:   1.127  0.008  0.079 14.947  0.005  4.108   7.0935e-02
   5_adp:   1.127  0.008  0.079 14.947  0.005  4.108   7.0935e-02
   5_occ:   1.127  0.008  0.079 14.947  0.005  4.108   7.0935e-02
   5_bss:   1.127  0.008  0.079 14.947  0.005  4.108   7.0935e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.261   2.4103e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.261   2.4103e-01
   1_xyz:   8.709  0.060  0.394 87.086  0.032  2.050   1.7515e-01
   1_adp:   8.709  0.060  0.394 87.086  0.032  2.050   1.7515e-01
   1_occ:   8.709  0.060  0.394 87.086  0.032  2.050   1.7515e-01
   2_bss:   8.709  0.060  0.394 87.086  0.032  2.050   1.7515e-01
   2_xyz:   8.407  0.044  0.233 81.557  0.048  2.290   6.2804e-02
   2_adp:   8.407  0.044  0.233 81.557  0.048  2.290   6.2804e-02
   2_occ:   8.407  0.044  0.233 81.557  0.048  2.290   6.2804e-02
   3_bss:   8.407  0.044  0.233 81.557  0.048  2.290   6.2804e-02
   3_xyz:   7.361  0.048  0.237 78.603  0.038  2.250   4.9422e-02
   3_adp:   7.361  0.048  0.237 78.603  0.038  2.250   4.9422e-02
   3_occ:   7.361  0.048  0.237 78.603  0.038  2.250   4.9422e-02
   4_bss:   7.361  0.048  0.237 78.603  0.038  2.250   4.9422e-02
   4_xyz:   7.043  0.041  0.234 83.849  0.039  2.338   6.1660e-02
   4_adp:   7.043  0.041  0.234 83.849  0.039  2.338   6.1660e-02
   4_occ:   7.043  0.041  0.234 83.849  0.039  2.338   6.1660e-02
   5_bss:   7.043  0.041  0.234 83.849  0.039  2.338   6.1660e-02
   5_xyz:   8.035  0.048  0.260 82.047  0.042  2.267   5.4090e-02
   5_adp:   8.035  0.048  0.260 82.047  0.042  2.267   5.4090e-02
   5_occ:   8.035  0.048  0.260 82.047  0.042  2.267   5.4090e-02
   5_bss:   8.035  0.048  0.260 82.047  0.042  2.267   5.4090e-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:  80.97   0.00  18.38  66.30   0.00  14.52  80.97   3.62  39.43
   1_occ:  80.97   0.00  18.38  66.30   0.00  14.52  80.97   3.62  39.43
   2_bss:  80.97   0.00  18.38  66.30   0.00  14.52  80.97   3.62  39.43
   2_xyz:  80.97   0.00  18.38  66.30   0.00  14.52  80.97   3.62  39.43
   2_adp:  80.75   1.14  17.64  75.78   1.14  13.64  80.75   4.05  39.39
   2_occ:  80.75   1.14  17.64  75.78   1.14  13.64  80.75   4.05  39.39
   3_bss:  80.75   1.14  17.64  75.78   1.14  13.64  80.75   4.05  39.39
   3_xyz:  80.75   1.14  17.64  75.78   1.14  13.64  80.75   4.05  39.39
   3_adp:  91.14   1.53  17.71  91.14   1.53  13.26  90.26   3.78  41.95
   3_occ:  91.14   1.53  17.71  91.14   1.53  13.26  90.26   3.78  41.95
   4_bss:  91.14   1.53  17.71  91.14   1.53  13.26  90.26   3.78  41.95
   4_xyz:  91.14   1.53  17.71  91.14   1.53  13.26  90.26   3.78  41.95
   4_adp:  90.97   1.63  17.01  90.97   2.10  12.88  80.67   1.63  39.46
   4_occ:  90.97   1.63  17.01  90.97   2.10  12.88  80.67   1.63  39.46
   5_bss:  90.97   1.63  17.01  90.97   2.10  12.88  80.67   1.63  39.46
   5_xyz:  90.97   1.63  17.01  90.97   2.10  12.88  80.67   1.63  39.46
   5_adp:  95.28   1.06  16.93  95.28   1.06  12.75  83.14   2.53  39.69
   5_occ:  95.28   1.06  16.93  95.28   1.06  12.75  83.14   2.53  39.69
   5_bss:  95.25   1.03  16.89  95.25   1.03  12.71  83.10   2.50  39.65
------------------------------------------------------------------------
 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:    2.900    0.028    0.405
   1_adp:    2.900    0.028    0.405
   1_occ:    2.900    0.028    0.405
   2_bss:    2.900    0.028    0.405
   2_xyz:    2.264    0.008    0.515
   2_adp:    2.264    0.008    0.515
   2_occ:    2.264    0.008    0.515
   3_bss:    2.264    0.008    0.515
   3_xyz:    2.134    0.047    0.624
   3_adp:    2.134    0.047    0.624
   3_occ:    2.134    0.047    0.624
   4_bss:    2.134    0.047    0.624
   4_xyz:    1.933    0.059    0.658
   4_adp:    1.933    0.059    0.658
   4_occ:    1.933    0.059    0.658
   5_bss:    1.933    0.059    0.658
   5_xyz:    1.547    0.086    0.676
   5_adp:    1.547    0.086    0.676
   5_occ:    1.547    0.086    0.676
   5_bss:    1.547    0.086    0.676
------------------------------------------------------------------------

CPU time actual refinement: 338.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/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_211/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_211/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.07 
  Macro-tasks:
    bulk solvent and scale       = 43.90  
    individual site refinement   = 136.35 
    weights calculation          = 30.06  
    collect and process          = 6.62   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 217.05 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 107.12 
    alpha_beta                      = 8.34   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 114.59 
    fmodel                         = 7.35   
    r_factors                      = 0.26   
    phase_errors                   = 10.73  
    foms                           = 0.33   
    TOTAL for micro-tasks          = 251.73 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.833 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    628 calls, 106.78 s
gradients_fft:          573 calls, 101.61 s

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

# Date 2008-01-16 Time 04:16:23 PST -0800 (1200485783.13 s)
Start R-work = 0.4428, R-free = 0.4407 (no bulk solvent and anisotropic scale)
Final R-work = 0.1329, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.4352, R-free = 0.4309
Final R-work = 0.1084, R-free = 0.1586