# Date 2008-01-16 Time 04:47:45 PST -0800 (1200487665.35 s)
#phil __OFF__

Command line arguments: "../462.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 350
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 462

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.8686, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.931346
Completeness with d_max=infinity: 0.928565

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9515

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.931346
Completeness with d_max=infinity: 0.928565

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1766 [2210/2239]  1988   222  10.0%
  bin  2:  4.1766 -  3.3272 [2113/2136]  1904   209   9.9%
  bin  3:  3.3272 -  2.9102 [2080/2105]  1872   208  10.0%
  bin  4:  2.9102 -  2.6457 [2072/2098]  1868   204   9.8%
  bin  5:  2.6457 -  2.4570 [2078/2112]  1865   213  10.3%
  bin  6:  2.4570 -  2.3127 [2042/2070]  1846   196   9.6%
  bin  7:  2.3127 -  2.1972 [2031/2067]  1823   208  10.2%
  bin  8:  2.1972 -  2.1018 [2031/2073]  1823   208  10.2%
  bin  9:  2.1018 -  2.0211 [1977/2057]  1786   191   9.7%
  bin 10:  2.0211 -  1.9515 [ 955/2076]   855   100  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.36 -     2.07: 26
        2.07 -     2.78: 601
        2.78 -     3.48: 4532
        3.48 -     4.19: 9434
        4.19 -     4.90: 14028
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.361 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.444 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.517 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.574 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.589 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28616 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_462/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/model_refine_001.geo

CPU time processing inputs: 9.16


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.8686 84.23025 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: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4737   r_free= 0.4652   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.282580                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1438  162 0.3791 0.3904      6.5729      6.5965|
|  2:  4.6588 -  3.7166 0.99   1377  147 0.4122 0.4045      6.8184       6.789|
|  3:  3.7166 -  3.2524 0.99   1346  152 0.4422 0.4250      6.6678       6.737|
|  4:  3.2524 -  2.9575 0.98   1341  152 0.4522 0.4292      6.5045      6.4735|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.4960 0.4618      6.3673      6.3114|
|  6:  2.7469 -  2.5859 0.99   1321  148 0.5050 0.4750      6.2689      6.1667|
|  7:  2.5859 -  2.4570 0.98   1332  146 0.5064 0.4494      6.2493      6.2111|
|  8:  2.4570 -  2.3504 0.98   1303  142 0.5229 0.5700      6.1611      6.1955|
|  9:  2.3504 -  2.2603 0.99   1331  143 0.5449 0.5282       6.141      6.1285|
| 10:  2.2603 -  2.1825 0.99   1320  147 0.5184 0.5477      6.0943      6.1331|
| 11:  2.1825 -  2.1145 0.97   1277  145 0.5389 0.5331       6.034      6.0181|
| 12:  2.1145 -  2.0542 0.98   1296  147 0.5118 0.5547      5.9496      5.9931|
| 13:  2.0542 -  2.0002 0.88   1167  133 0.5303 0.5093      5.8722      5.8713|
| 14:  2.0002 -  1.9515 0.33    439   46 0.5554 0.4559      5.8276       5.647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6588  1438   162  0.66  37.31   0.83     0.70      80492.57|
|  2:  4.6588 -  3.7166  1377   147  0.69  36.32   0.91     0.79     108567.24|
|  3:  3.7166 -  3.2524  1346   152  0.60  44.10   0.92     0.79     112757.04|
|  4:  3.2524 -  2.9575  1341   152  0.53  49.66   0.92     0.74      96905.55|
|  5:  2.9575 -  2.7469  1342   149  0.47  54.13   0.88     0.68      76282.95|
|  6:  2.7469 -  2.5859  1321   148  0.44  56.50   0.89     0.63      64560.52|
|  7:  2.5859 -  2.4570  1332   146  0.41  59.35   0.91     0.55      61297.97|
|  8:  2.4570 -  2.3504  1303   142  0.32  66.11   0.89     0.48      62651.88|
|  9:  2.3504 -  2.2603  1331   143  0.26  70.67   0.91     0.40      60154.08|
| 10:  2.2603 -  2.1825  1320   147  0.23  72.92   0.95     0.35      57703.22|
| 11:  2.1825 -  2.1145  1277   145  0.18  76.31   0.93     0.29      52827.19|
| 12:  2.1145 -  2.0542  1296   147  0.17  77.03   0.95     0.28      49972.83|
| 13:  2.0542 -  2.0002  1167   133  0.18  76.96   0.94     0.29      41863.09|
| 14:  2.0002 -  1.9515   439    46  0.21  74.02   0.91     0.34      34572.72|
|alpha:            min =        0.28 max =            0.79 mean =         0.54|
|beta:             min =    34572.72 max =       112757.04 mean =     70924.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.67|
|phase err.(test): min =        0.00 max =           89.99 mean =        59.65|
|-----------------------------------------------------------------------------|

============================== 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 = 15.550623             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.128   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.284837              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.088   (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 |  1.361 -  1.715:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.715 -  2.068:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.068 -  2.422:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.422 -  2.776:      568 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.776 -  3.130:     2181 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.130 -  3.484:     2351 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.484 -  3.838:     4517 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.838 -  4.192:     4917 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.192 -  4.546:     6323 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.546 -  4.900:     7705 |
|-----------------------------------------------------------------------------|
|-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 |        0.205 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.361 |       0.821 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    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: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4737   r_free= 0.4652   ksol= 0.00   Bsol= 0.00   scale= 0.895    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.282580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4641   r_free= 0.4558   ksol= 0.30   Bsol= 20.00   scale= 0.933   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,3.22,1.73,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.276480                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.743944             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.874   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.412959              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.816   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4641      final r-factor (work) = 0.3551          |
| start r-factor (free) = 0.4558      final r-factor (free) = 0.3843          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.1887 = 12.74 * 0.50 * 6.2750 + 1.00 * 0.2045                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3853 = 12.74 * 0.50 * 6.1562 + 1.00 * 0.1581                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3551      final r-factor (work) = 0.3205          |
| start r-factor (free) = 0.3843      final r-factor (free) = 0.3917          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7046 = 1.41 * 1.00 * 6.1562 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5391 = 1.41 * 1.00 * 6.0283 + 1.00 * 0.0214                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.63  19.81    None  None   None       |
|    all(noH): 2823   0      0.00    101.63  19.81    None  None   None       |
|    Sol.    : 438    0      0.78    101.63  40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    97.84   16.09    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 -  10.163:  931   |   5:    50.815 -  60.978:   78        |
|      1:    10.163 -  20.326:  855   |   6:    60.978 -  71.140:   43        |
|      2:    20.326 -  30.489:  459   |   7:    71.140 -  81.303:   32        |
|      3:    30.489 -  40.652:  265   |   8:    81.303 -  91.466:   11        |
|      4:    40.652 -  50.815:  147   |   9:    91.466 - 101.629:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3205 r_free = 0.3917             target_work(ml) = 6.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3201 r_free = 0.3924             target_work(ml) = 6.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3201   r_free= 0.3924   ksol= 0.30   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,3.22,1.73,0.00,0.00,0.00); trace/3= 0.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.037302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3173   r_free= 0.3899   ksol= 0.32   Bsol= 47.72   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,1.39,0.02,0.00,0.00,0.00); trace/3= -0.19                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.035311                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.717969              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.337   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.704614              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.308  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3173      final r-factor (work) = 0.2505          |
| start r-factor (free) = 0.3899      final r-factor (free) = 0.3134          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4005 = 6.72 * 0.50 * 6.0264 + 1.00 * 0.1581                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0776 = 6.72 * 0.50 * 5.9529 + 1.00 * 0.0817                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2505      final r-factor (work) = 0.2292          |
| start r-factor (free) = 0.3134      final r-factor (free) = 0.2982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2158 = 0.70 * 1.00 * 5.9529 + 1.00 * 0.0213                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1028 = 0.70 * 1.00 * 5.8008 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.09  18.85    None  None   None       |
|    all(noH): 2823   0      0.00    101.09  18.85    None  None   None       |
|    Sol.    : 438    0      4.59    101.09  41.34    None  None   None       |
|    Mac.    : 2385   0      0.00    100.36  14.72    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 -  10.109: 1003   |   5:    50.547 -  60.656:   82        |
|      1:    10.109 -  20.219:  950   |   6:    60.656 -  70.766:   52        |
|      2:    20.219 -  30.328:  369   |   7:    70.766 -  80.875:   22        |
|      3:    30.328 -  40.438:  195   |   8:    80.875 -  90.984:    9        |
|      4:    40.438 -  50.547:  132   |   9:    90.984 - 101.094:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2292 r_free = 0.2982             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2291 r_free = 0.2980             target_work(ml) = 5.776         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2291   r_free= 0.2980   ksol= 0.32   Bsol= 47.72   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.99,1.39,0.02,0.00,0.00,0.00); trace/3= -0.19                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.775745                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2290   r_free= 0.2972   ksol= 0.32   Bsol= 48.79   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,0.33,-0.70,0.00,-0.00,-0.00); trace/3= -0.78                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.774041                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.120343              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.393718              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.220  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.1686          |
| start r-factor (free) = 0.2972      final r-factor (free) = 0.2196          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7335 = 7.12 * 0.50 * 5.8008 + 1.00 * 0.0817                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.2330 = 7.12 * 0.50 * 5.6609 + 1.00 * 0.0791                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1686      final r-factor (work) = 0.1500          |
| start r-factor (free) = 0.2196      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2430 = 0.39 * 1.00 * 5.6609 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1533 = 0.39 * 1.00 * 5.4435 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.57  17.98    None  None   None       |
|    all(noH): 2823   0      0.00    100.57  17.98    None  None   None       |
|    Sol.    : 438    0      5.89    100.57  42.84    None  None   None       |
|    Mac.    : 2385   0      0.00    92.13   13.42    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 -  10.057: 1048   |   5:    50.285 -  60.343:   87        |
|      1:    10.057 -  20.114: 1074   |   6:    60.343 -  70.400:   55        |
|      2:    20.114 -  30.171:  249   |   7:    70.400 -  80.457:   19        |
|      3:    30.171 -  40.228:  130   |   8:    80.457 -  90.514:   13        |
|      4:    40.228 -  50.285:  143   |   9:    90.514 - 100.571:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1500 r_free = 0.1980             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1499 r_free = 0.1979             target_work(ml) = 5.386         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1499   r_free= 0.1979   ksol= 0.32   Bsol= 48.79   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.97,0.33,-0.70,0.00,-0.00,-0.00); trace/3= -0.78                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.385890                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1972   ksol= 0.32   Bsol= 48.79   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.97,-1.61,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.388415                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.121140              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.158  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.514927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.354  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1496      final r-factor (work) = 0.1268          |
| start r-factor (free) = 0.1972      final r-factor (free) = 0.1741          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.3110 = 4.12 * 0.50 * 5.4509 + 1.00 * 0.0791                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0373 = 4.12 * 0.50 * 5.3210 + 1.00 * 0.0731                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1268      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1741      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7500 = 0.51 * 1.00 * 5.3210 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7028 = 0.51 * 1.00 * 5.2295 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    97.86   17.68    None  None   None       |
|    all(noH): 2823   0      0.99    97.86   17.68    None  None   None       |
|    Sol.    : 438    0      6.08    91.98   43.06    None  None   None       |
|    Mac.    : 2385   0      0.99    97.86   13.02    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:     0.986 -  10.674: 1199   |   5:    49.424 -  59.112:   95        |
|      1:    10.674 -  20.361:  991   |   6:    59.112 -  68.799:   56        |
|      2:    20.361 -  30.049:  210   |   7:    68.799 -  78.487:   31        |
|      3:    30.049 -  39.736:  101   |   8:    78.487 -  88.174:   12        |
|      4:    39.736 -  49.424:  120   |   9:    88.174 -  97.862:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1703             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1702             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1702   ksol= 0.32   Bsol= 48.79   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.61,-0.97,-1.61,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1701   ksol= 0.32   Bsol= 50.91   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.30,-1.74,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.217132                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.484288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.127443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.084  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5707 = 2.48 * 0.50 * 5.2310 + 1.00 * 0.0731                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5233 = 2.48 * 0.50 * 5.2013 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1166          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1620          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6728 = 0.13 * 1.00 * 5.2013 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6689 = 0.13 * 1.00 * 5.1898 + 1.00 * 0.0075                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.96    93.49   16.86    None  None   None       |
|    all(noH): 2823   0      1.96    93.49   16.86    None  None   None       |
|    Sol.    : 438    0      5.31    88.06   39.45    None  None   None       |
|    Mac.    : 2385   0      1.96    93.49   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:     1.963 -  11.115: 1310   |   5:    47.725 -  56.878:   72        |
|      1:    11.115 -  20.268:  923   |   6:    56.878 -  66.030:   46        |
|      2:    20.268 -  29.420:  191   |   7:    66.030 -  75.183:   28        |
|      3:    29.420 -  38.573:  120   |   8:    75.183 -  84.336:   11        |
|      4:    38.573 -  47.725:  117   |   9:    84.336 -  93.488:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1166 r_free = 0.1620             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1620             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1620   ksol= 0.32   Bsol= 50.91   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.30,-1.74,-0.00,-0.00,-0.00); trace/3= -1.90                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180475                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1438  162 0.0974 0.1272       5.371      5.5422|
|  2:  4.6588 -  3.7166 0.99   1377  147 0.0866 0.1102      5.4409      5.6467|
|  3:  3.7166 -  3.2524 0.99   1346  152 0.1099 0.1591      5.4991      5.8672|
|  4:  3.2524 -  2.9575 0.98   1341  152 0.1310 0.1596      5.4953      5.6666|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.1370 0.1888      5.3588      5.5251|
|  6:  2.7469 -  2.5859 0.99   1321  148 0.1321 0.1988      5.2617      5.4756|
|  7:  2.5859 -  2.4570 0.98   1332  146 0.1268 0.1729      5.1933      5.4194|
|  8:  2.4570 -  2.3504 0.98   1303  142 0.1278 0.1764      5.1305      5.3178|
|  9:  2.3504 -  2.2603 0.99   1331  143 0.1238 0.1910      5.0588      5.3169|
| 10:  2.2603 -  2.1825 0.99   1320  147 0.1207 0.1727      5.0043      5.2309|
| 11:  2.1825 -  2.1145 0.97   1277  145 0.1165 0.1817      4.9341      5.2262|
| 12:  2.1145 -  2.0542 0.98   1296  147 0.1181 0.1687      4.8644      5.0919|
| 13:  2.0542 -  2.0002 0.88   1167  133 0.1144 0.1790      4.7838      5.0821|
| 14:  2.0002 -  1.9515 0.33    439   46 0.1216 0.1782      4.7239      4.9205|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6588  1438   162  0.94   8.98   0.98     0.96       7053.39|
|  2:  4.6588 -  3.7166  1377   147  0.95   8.03   1.02     1.00       9053.13|
|  3:  3.7166 -  3.2524  1346   152  0.93  11.91   1.02     1.02      10912.11|
|  4:  3.2524 -  2.9575  1341   152  0.91  14.80   1.01     0.99      11217.02|
|  5:  2.9575 -  2.7469  1342   149  0.89  16.87   1.00     0.97       8957.90|
|  6:  2.7469 -  2.5859  1321   148  0.89  16.85   0.98     0.95       7669.62|
|  7:  2.5859 -  2.4570  1332   146  0.90  16.13   0.99     0.95       6619.02|
|  8:  2.4570 -  2.3504  1303   142  0.90  16.82   1.00     0.97       6153.34|
|  9:  2.3504 -  2.2603  1331   143  0.90  16.56   1.00     0.98       5301.58|
| 10:  2.2603 -  2.1825  1320   147  0.90  15.83   0.99     0.94       4616.71|
| 11:  2.1825 -  2.1145  1277   145  0.90  16.07   1.00     0.97       4235.05|
| 12:  2.1145 -  2.0542  1296   147  0.91  15.15   1.00     0.98       3667.18|
| 13:  2.0542 -  2.0002  1167   133  0.90  16.07   1.00     1.00       3272.69|
| 14:  2.0002 -  1.9515   439    46  0.89  16.75   0.98     0.94       2822.96|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2822.96 max =        11217.02 mean =      6789.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.31 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1620   ksol= 0.33   Bsol= 50.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.26,-1.61,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180673                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1620   ksol= 0.33   Bsol= 50.84   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.26,-1.61,-0.00,-0.00,-0.00); trace/3= -1.81                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180673                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1438  162 0.0975 0.1277      5.3733      5.5438|
|  2:  4.6588 -  3.7166 0.99   1377  147 0.0865 0.1101      5.4409      5.6458|
|  3:  3.7166 -  3.2524 0.99   1346  152 0.1099 0.1590      5.4987      5.8672|
|  4:  3.2524 -  2.9575 0.98   1341  152 0.1310 0.1596      5.4953      5.6666|
|  5:  2.9575 -  2.7469 0.99   1342  149 0.1370 0.1887      5.3586      5.5248|
|  6:  2.7469 -  2.5859 0.99   1321  148 0.1320 0.1987      5.2615      5.4752|
|  7:  2.5859 -  2.4570 0.98   1332  146 0.1268 0.1730      5.1932      5.4194|
|  8:  2.4570 -  2.3504 0.98   1303  142 0.1278 0.1764      5.1305       5.318|
|  9:  2.3504 -  2.2603 0.99   1331  143 0.1237 0.1910      5.0588       5.317|
| 10:  2.2603 -  2.1825 0.99   1320  147 0.1207 0.1727      5.0045      5.2314|
| 11:  2.1825 -  2.1145 0.97   1277  145 0.1165 0.1816      4.9342      5.2261|
| 12:  2.1145 -  2.0542 0.98   1296  147 0.1181 0.1689      4.8647      5.0928|
| 13:  2.0542 -  2.0002 0.88   1167  133 0.1144 0.1790       4.784      5.0817|
| 14:  2.0002 -  1.9515 0.33    439   46 0.1217 0.1782      4.7242      4.9201|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9216 -  4.6588  1438   162  0.94   9.01   0.98     0.96       7102.30|
|  2:  4.6588 -  3.7166  1377   147  0.95   8.04   1.02     1.00       9066.24|
|  3:  3.7166 -  3.2524  1346   152  0.93  11.90   1.02     1.02      10896.37|
|  4:  3.2524 -  2.9575  1341   152  0.91  14.80   1.01     0.99      11215.67|
|  5:  2.9575 -  2.7469  1342   149  0.89  16.86   1.00     0.97       8950.25|
|  6:  2.7469 -  2.5859  1321   148  0.89  16.84   0.98     0.95       7664.20|
|  7:  2.5859 -  2.4570  1332   146  0.90  16.13   0.99     0.95       6617.17|
|  8:  2.4570 -  2.3504  1303   142  0.90  16.82   1.00     0.97       6153.82|
|  9:  2.3504 -  2.2603  1331   143  0.90  16.56   1.01     0.98       5305.69|
| 10:  2.2603 -  2.1825  1320   147  0.90  15.83   0.99     0.94       4618.33|
| 11:  2.1825 -  2.1145  1277   145  0.90  16.07   1.01     0.98       4237.37|
| 12:  2.1145 -  2.0542  1296   147  0.91  15.16   1.00     0.99       3670.22|
| 13:  2.0542 -  2.0002  1167   133  0.90  16.07   1.00     1.00       3274.25|
| 14:  2.0002 -  1.9515   439    46  0.89  16.76   0.98     0.94       2821.99|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2821.99 max =        11215.67 mean =      6792.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.31 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.650)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.89    93.42   16.79    None  None   None       |
|    all(noH): 2823   0      1.89    93.42   16.79    None  None   None       |
|    Sol.    : 438    0      5.24    87.99   39.38    None  None   None       |
|    Mac.    : 2385   0      1.89    93.42   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.892 -  11.045: 1310   |   5:    47.655 -  56.807:   72        |
|      1:    11.045 -  20.197:  923   |   6:    56.807 -  65.960:   46        |
|      2:    20.197 -  29.350:  191   |   7:    65.960 -  75.112:   28        |
|      3:    29.350 -  38.502:  120   |   8:    75.112 -  84.265:   11        |
|      4:    38.502 -  47.655:  117   |   9:    84.265 -  93.417:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.509 - 5.023
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.724 - 5.023

peak=    9.648 closest distance to " CB  SER A 216 " =    1.155
peak=    5.733 closest distance to " O   HOH Z 113 " =    2.340
peak=    5.546 closest distance to " CB  SER A  63 " =    1.112
peak=    5.448 closest distance to " O   HOH Z 132 " =    1.699
peak=    5.416 closest distance to " O   HOH Z 142 " =    1.590
peak=    5.298 closest distance to " O   HOH Z 124 " =    1.520
peak=    5.039 closest distance to " CG  PRO A  54 " =    1.263
peak=    4.887 closest distance to " O   HOH Z 402 " =    1.533
peak=    4.871 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.787 closest distance to " O   HOH Z  15 " =    2.063
peak=    4.771 closest distance to " C   PRO A 198 " =    1.580
peak=    4.702 closest distance to " O   HOH Z 234 " =    3.743
peak=    4.701 closest distance to " CB  GLN A 223 " =    1.423
peak=    4.596 closest distance to " CA  TYR A  30 " =    1.018
peak=    4.567 closest distance to " O   HOH Z  80 " =    1.733
peak=    4.551 closest distance to " CG  PRO A  90 " =    1.189
peak=    4.534 closest distance to " O   HOH Z  11 " =    1.358
peak=    4.530 closest distance to " O   HOH Z 154 " =    1.580
peak=    4.505 closest distance to " O   HOH Z 134 " =    1.909
peak=    4.503 closest distance to " CB  ARG A 275 " =    0.858
peak=    4.463 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.460 closest distance to " CG  PRO A 198 " =    1.242
peak=    4.449 closest distance to " CB  SER A   3 " =    1.339
peak=    4.432 closest distance to " O   HOH Z 199 " =    1.073
peak=    4.429 closest distance to " NH2BARG A 145 " =    1.947
peak=    4.403 closest distance to " O   HOH Z 316 " =    2.922
peak=    4.366 closest distance to " CB  ARG A  79 " =    1.347
peak=    4.361 closest distance to " O   HOH Z 334 " =    1.516
peak=    4.359 closest distance to " O   HOH Z 108 " =    1.451
peak=    4.358 closest distance to " O   HOH Z 389 " =    1.989
peak=    4.348 closest distance to " O   SER A  87 " =    2.115
peak=    4.328 closest distance to " O   HOH Z  97 " =    1.914
peak=    4.326 closest distance to " O   HOH Z 298 " =    1.916
peak=    4.313 closest distance to " CG1 ILE A  33 " =    1.249
peak=    4.302 closest distance to " O   HOH Z 133 " =    1.672
peak=    4.302 closest distance to " CB  GLN A 183 " =    1.271
peak=    4.292 closest distance to " O   HOH Z 193 " =    1.830
peak=    4.286 closest distance to " O   HOH Z 189 " =    1.841
peak=    4.261 closest distance to " CB  GLU A 152 " =    1.081
peak=    4.242 closest distance to " O   HOH Z  63 " =    2.094
peak=    4.226 closest distance to " O   HOH Z 209 " =    2.390
peak=    4.206 closest distance to " O   HOH Z  59 " =    2.317
peak=    4.204 closest distance to " O   HOH Z 326 " =    1.559
peak=    4.183 closest distance to " O   HOH Z 313 " =    1.835
peak=    4.169 closest distance to " O   HOH Z  20 " =    1.551
peak=    4.162 closest distance to " O   HOH Z  39 " =    1.394
peak=    4.161 closest distance to " O   HOH Z 278 " =    0.980
peak=    4.154 closest distance to " O   HOH Z 426 " =    1.481
peak=    4.152 closest distance to " O   HOH Z  97 " =    2.478
peak=    4.125 closest distance to " O   HOH Z  44 " =    2.003
peak=    4.118 closest distance to " O   HOH Z 203 " =    1.818
peak=    4.109 closest distance to " O   HOH Z 247 " =    1.390
peak=    4.106 closest distance to " O   HOH Z 126 " =    1.661
peak=    4.102 closest distance to " O   HOH Z 163 " =    2.051
peak=    4.094 closest distance to " O   HOH Z 260 " =    1.378
peak=    4.049 closest distance to " O   HOH Z 147 " =    1.789
peak=    4.025 closest distance to " O   HOH Z  40 " =    1.632
peak=    4.021 closest distance to " OD2 ASP A 286 " =    2.701
peak=    4.014 closest distance to " NE2 GLN A  11 " =    1.071
peak=    4.008 closest distance to " O   HOH Z  67 " =    1.971
peak=    4.007 closest distance to " N   ASN A  39 " =    1.240
peak=    3.995 closest distance to " CA  ALA A  21 " =    1.232
peak=    3.986 closest distance to " O   HOH Z 232 " =    2.373
peak=    3.985 closest distance to " O   HOH Z   6 " =    2.041
peak=    3.979 closest distance to " O   HOH Z 368 " =    1.949
peak=    3.976 closest distance to " O   HOH Z 279 " =    2.014
peak=    3.974 closest distance to " CG  PRO A 243 " =    1.172
peak=    3.962 closest distance to " CB  PRO A  54 " =    0.771
peak=    3.957 closest distance to " O   HOH Z 145 " =    1.942
peak=    3.949 closest distance to " CB  GLU A 277 " =    3.537
peak=    3.949 closest distance to " CD  LYS A 166 " =    1.383
peak=    3.945 closest distance to " NZ  LYS A 117 " =    3.047
peak=    3.945 closest distance to " CB  ARG A 139 " =    0.972
peak=    3.945 closest distance to " O   HOH Z 403 " =    1.826
peak=    3.943 closest distance to " O   HOH Z 369 " =    2.061
peak=    3.942 closest distance to " O   HOH Z 411 " =    3.160
peak=    3.935 closest distance to " CB  GLU A 128 " =    1.158
peak=    3.933 closest distance to " CB  ARG A 190 " =    1.671
peak=    3.929 closest distance to " O   HOH Z 163 " =    1.604
peak=    3.923 closest distance to " O   HOH Z  43 " =    1.477
peak=    3.918 closest distance to " CB  SER A 141 " =    1.007
peak=    3.914 closest distance to " OE1 GLN A  11 " =    1.871
peak=    3.906 closest distance to " O   HOH Z 227 " =    1.640
peak=    3.903 closest distance to " O   HOH Z 357 " =    1.859
peak=    3.902 closest distance to " O   HOH Z 406 " =    1.624
peak=    3.900 closest distance to " NH2 ARG A 156 " =    1.135
peak=    3.900 closest distance to " O   HOH Z 128 " =    2.115
peak=    3.899 closest distance to " O   HOH Z 371 " =    3.204
peak=    3.891 closest distance to " CG  ARG A  66 " =    2.799
peak=    3.888 closest distance to " CA  ASP A 191 " =    0.866
peak=    3.872 closest distance to " O   HOH Z 196 " =    1.198
peak=    3.871 closest distance to " ND2 ASN A 187 " =    1.780
peak=    3.870 closest distance to " CB  TRP A 179 " =    1.128
peak=    3.863 closest distance to " CG AARG A 275 " =    0.907
peak=    3.856 closest distance to " CB  PRO A 198 " =    1.072
peak=    3.852 closest distance to " CB  ASN A 148 " =    1.745
peak=    3.843 closest distance to " CD  ARG A 195 " =    0.936
peak=    3.835 closest distance to " O   HOH Z 227 " =    1.797
peak=    3.827 closest distance to " O   HOH Z 345 " =    1.845
peak=    3.824 closest distance to " O   HOH Z 408 " =    1.576
peak=    3.819 closest distance to " CB  TYR A 169 " =    0.844
peak=    3.814 closest distance to " O   HOH Z 402 " =    2.729
peak=    3.811 closest distance to " NZ  LYS A 117 " =    1.093
peak=    3.804 closest distance to " CG1BVAL A  72 " =    1.653
peak=    3.801 closest distance to " CA  THR A 221 " =    0.932
peak=    3.792 closest distance to " O   HOH Z 345 " =    2.540
peak=    3.787 closest distance to " CB  VAL A 202 " =    1.532
peak=    3.773 closest distance to " O   HOH Z 236 " =    1.957
peak=    3.760 closest distance to " O   HOH Z 118 " =    1.163
peak=    3.758 closest distance to " O   HOH Z 386 " =    2.241
peak=    3.750 closest distance to " CG  ARG A  66 " =    1.095
peak=    3.745 closest distance to " O   HOH Z 210 " =    1.136
peak=    3.738 closest distance to " O   HOH Z  35 " =    2.268
peak=    3.735 closest distance to " O   HOH Z 374 " =    2.522
peak=    3.718 closest distance to " O   HOH Z  59 " =    1.886
peak=    3.713 closest distance to " O   HOH Z 358 " =    2.083
peak=    3.708 closest distance to " CD  ARG A 269 " =    1.120
peak=    3.707 closest distance to " O   HOH Z 315 " =    1.892
peak=    3.705 closest distance to " CB  ASN A 148 " =    1.343
peak=    3.703 closest distance to " CB  LEU A 228 " =    1.215
peak=    3.702 closest distance to " CG AARG A 275 " =    1.261
peak=    3.699 closest distance to " O   HOH Z 207 " =    2.344
peak=    3.698 closest distance to " CD  PRO A  54 " =    1.077
peak=    3.685 closest distance to " O   HOH Z  54 " =    1.614
peak=    3.679 closest distance to " O   HOH Z 344 " =    2.865
peak=    3.673 closest distance to " O   HOH Z 427 " =    2.984
peak=    3.663 closest distance to " CA  ARG A  36 " =    1.007
peak=    3.663 closest distance to " O   HOH Z 126 " =    1.836
peak=    3.643 closest distance to " O   GLY A  23 " =    2.310
peak=    3.640 closest distance to " O   HOH Z 128 " =    2.212
peak=    3.639 closest distance to " NZ  LYS A 119 " =    1.572
peak=    3.635 closest distance to " O   HOH Z 183 " =    1.651
peak=    3.630 closest distance to " O   HOH Z 156 " =    2.624
peak=    3.630 closest distance to " CG2 VAL A 197 " =    1.071
peak=    3.628 closest distance to " NZ  LYS A  76 " =    1.158
peak=    3.628 closest distance to " O   HOH Z 245 " =    1.400
peak=    3.627 closest distance to " O   HOH Z 132 " =    2.657
peak=    3.626 closest distance to " O   HOH Z  30 " =    1.386
peak=    3.620 closest distance to " NH2AARG A 145 " =    2.143
peak=    3.610 closest distance to " O   HOH Z 336 " =    1.610
peak=    3.606 closest distance to " O   HOH Z 173 " =    2.103
peak=    3.596 closest distance to " O   HOH Z 362 " =    3.334
peak=    3.592 closest distance to " NH2AARG A 190 " =    1.208
peak=    3.578 closest distance to " OG BSER A 164 " =    2.554
peak=    3.577 closest distance to " CA  GLU A 152 " =    0.868
peak=    3.575 closest distance to " O   HOH Z 150 " =    1.571
peak=    3.575 closest distance to " OD1 ASN A  60 " =    1.267
peak=    3.574 closest distance to " O   HOH Z 255 " =    1.662
peak=    3.564 closest distance to " O   HOH Z  88 " =    3.342
peak=    3.563 closest distance to " O   HOH Z 280 " =    2.559
peak=    3.557 closest distance to " O   HOH Z 303 " =    1.978
peak=    3.550 closest distance to " O   HOH Z 427 " =    2.649
peak=    3.549 closest distance to " CB  SER A  62 " =    0.887
peak=    3.539 closest distance to " O   GLY A 211 " =    1.363
peak=    3.525 closest distance to " O   HOH Z  49 " =    1.829
peak=    3.524 closest distance to " O   HOH Z 108 " =    2.204
peak=    3.524 closest distance to " O   SER A  26 " =    1.659
peak=    3.510 closest distance to " CD2 LEU A 297 " =    0.936
peak=    3.499 closest distance to " O   HOH Z  78 " =    1.712
peak=    3.496 closest distance to " O   HOH Z 423 " =    2.033
peak=    3.494 closest distance to " CB  ASN A  39 " =    0.853
peak=    3.494 closest distance to " O   HOH Z 166 " =    1.275
peak=    3.487 closest distance to " O   HOH Z 194 " =    2.065
peak=    3.485 closest distance to " CB  GLN A  58 " =    0.798
peak=    3.481 closest distance to " O   HOH Z  61 " =    1.470
peak=    3.480 closest distance to " CB  ALA A 100 " =    1.238
peak=    3.478 closest distance to " OG BSER A 210 " =    1.218
peak=    3.472 closest distance to " CA  ARG A  66 " =    1.072
peak=    3.472 closest distance to " OG1 THR A 294 " =    2.406
peak=    3.467 closest distance to " O   HOH Z 276 " =    1.297
peak=    3.467 closest distance to " O   HOH Z 214 " =    0.963
peak=    3.466 closest distance to " O   HOH Z 291 " =    1.614
peak=    3.465 closest distance to " O   HOH Z 327 " =    1.855
peak=    3.465 closest distance to " O   GLY A  91 " =    1.327
peak=    3.452 closest distance to " O   HOH Z 438 " =    2.399
peak=    3.448 closest distance to " CA  ASP A 140 " =    1.161
peak=    3.444 closest distance to " O   HOH Z 383 " =    1.897
peak=    3.442 closest distance to " O   MET A 105 " =    1.868
peak=    3.441 closest distance to " CG2 THR A 221 " =    1.135
peak=    3.436 closest distance to " CA  SER A  87 " =    0.907
peak=    3.434 closest distance to " CB  PRO A  90 " =    2.054
peak=    3.433 closest distance to " O   HOH Z 261 " =    2.030
peak=    3.433 closest distance to " CG1 VAL A 153 " =    1.123
peak=    3.433 closest distance to " NE1 TRP A 274 " =    0.903
peak=    3.432 closest distance to " CB  ALA A  71 " =    1.178
peak=    3.430 closest distance to " CE  LYS A 119 " =    1.087
peak=    3.428 closest distance to " O   HOH Z 287 " =    1.743
peak=    3.427 closest distance to " O   HOH Z  10 " =    1.767
peak=    3.426 closest distance to " CA  ASN A 215 " =    1.076
peak=    3.424 closest distance to " CG2 THR A 220 " =    0.829
peak=    3.415 closest distance to " CA  ALA A 248 " =    1.290
peak=    3.414 closest distance to " CA  ILE A 263 " =    0.975
peak=    3.414 closest distance to " CZ2 TRP A 179 " =    1.813
peak=    3.413 closest distance to " O   ALA A 165 " =    1.236
peak=    3.410 closest distance to " CD  GLN A 194 " =    1.634
peak=    3.402 closest distance to " O   HOH Z  66 " =    2.213
peak=    3.401 closest distance to " NH1AARG A 145 " =    1.171
peak=    3.394 closest distance to " O   HOH Z 299 " =    2.205
peak=    3.394 closest distance to " O   HOH Z 387 " =    2.250
peak=    3.387 closest distance to " O   HOH Z 261 " =    1.997
peak=    3.381 closest distance to " CD2 HIS A  81 " =    1.291
peak=    3.373 closest distance to " O   HOH Z  32 " =    1.550
peak=    3.370 closest distance to " CB  THR A  52 " =    1.231
peak=    3.369 closest distance to " C   SER A  32 " =    1.063
peak=    3.368 closest distance to " ND2 ASN A 209 " =    3.651
peak=    3.367 closest distance to " CD2 PHE A 225 " =    1.181
peak=    3.366 closest distance to " CB  SER A 273 " =    0.818
peak=    3.366 closest distance to " CZ2 TRP A 274 " =    1.776
peak=    3.365 closest distance to " O   GLY A  57 " =    2.446
peak=    3.361 closest distance to " CA  ASP A 124 " =    0.724
peak=    3.359 closest distance to " CA  ALA A  84 " =    1.162
peak=    3.345 closest distance to " O   HOH Z 433 " =    1.476
peak=    3.344 closest distance to " CA  ASN A 176 " =    1.175
peak=    3.343 closest distance to " O   HOH Z 127 " =    1.006
peak=    3.340 closest distance to " O   HOH Z 346 " =    1.510
peak=    3.340 closest distance to " CG2AVAL A 121 " =    2.100
peak=    3.333 closest distance to " CD BLYS A 290 " =    1.259
peak=    3.327 closest distance to " O   HOH Z 434 " =    1.567
peak=    3.324 closest distance to " CA  ASP A 162 " =    1.106
peak=    3.318 closest distance to " CD  LYS A 119 " =    1.630
peak=    3.317 closest distance to " CD AARG A 102 " =    2.343
peak=    3.317 closest distance to " CA  ALA A  51 " =    0.872
peak=    3.317 closest distance to " O   HOH Z  63 " =    2.118
peak=    3.317 closest distance to " CA  ARG A 195 " =    1.261
peak=    3.316 closest distance to " O   HOH Z 421 " =    1.721
peak=    3.312 closest distance to " O   HOH Z  71 " =    1.321
peak=    3.310 closest distance to " CB  ASN A 187 " =    1.152
peak=    3.310 closest distance to " CD2 TRP A 179 " =    1.339
peak=    3.308 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.306 closest distance to " CB  ASN A 285 " =    0.970
peak=    3.299 closest distance to " CG2BVAL A  41 " =    0.883
peak=    3.298 closest distance to " CB  ALA A 291 " =    1.103
peak=    3.296 closest distance to " O   HOH Z 250 " =    1.852
peak=    3.295 closest distance to " CB  GLN A 194 " =    0.832
peak=    3.294 closest distance to " O   HOH Z 132 " =    1.769
peak=    3.293 closest distance to " O   TRP A 274 " =    1.833
peak=    3.291 closest distance to " O   HOH Z 394 " =    1.597
peak=    3.289 closest distance to " O   HOH Z 284 " =    2.901
peak=    3.284 closest distance to " CB  GLN A 278 " =    0.757
peak=    3.277 closest distance to " OD1 ASN A  69 " =    2.442
peak=    3.276 closest distance to " CB  VAL A 265 " =    1.161
peak=    3.270 closest distance to " OH  TYR A  30 " =    1.122
peak=    3.269 closest distance to " CG  GLN A  58 " =    2.313
peak=    3.264 closest distance to " O   HOH Z 250 " =    1.418
peak=    3.263 closest distance to " O   HOH Z 106 " =    1.605
peak=    3.259 closest distance to " CA  GLY A  80 " =    1.133
peak=    3.258 closest distance to " CG1 ILE A 120 " =    1.002
peak=    3.257 closest distance to " O   HOH Z 282 " =    2.057
peak=    3.253 closest distance to " OD2 ASP A 298 " =    4.072
peak=    3.252 closest distance to " OD1 ASP A 238 " =    1.017
peak=    3.251 closest distance to " O   HOH Z 171 " =    2.770
peak=    3.250 closest distance to " O   HOH Z  51 " =    1.481
peak=    3.250 closest distance to " O   HOH Z 162 " =    1.752
peak=    3.249 closest distance to " CB  TYR A 247 " =    1.022
peak=    3.246 closest distance to " O   HOH Z  47 " =    1.450
peak=    3.244 closest distance to " O   HOH Z 155 " =    2.750
peak=    3.244 closest distance to " O   HOH Z 197 " =    2.306
peak=    3.236 closest distance to " CB  ASN A 127 " =    1.049
peak=    3.236 closest distance to " OG  SER A  62 " =    3.025
peak=    3.233 closest distance to " CB  PHE A  16 " =    1.199
peak=    3.232 closest distance to " O   HOH Z 273 " =    2.616
peak=    3.228 closest distance to " CD  ARG A 159 " =    0.804
peak=    3.228 closest distance to " CZ AARG A 102 " =    1.736
peak=    3.224 closest distance to " CA  ASN A  74 " =    1.100
peak=    3.224 closest distance to " CB  GLN A 103 " =    0.792
peak=    3.223 closest distance to " O   HOH Z  40 " =    1.883
peak=    3.223 closest distance to " O   HOH Z  61 " =    1.480
peak=    3.210 closest distance to " CD1 LEU A 300 " =    1.229
peak=    3.207 closest distance to " CG  GLN A  11 " =    1.217
peak=    3.204 closest distance to " OG  SER A  28 " =    1.545
peak=    3.204 closest distance to " O   HOH Z 155 " =    1.484
peak=    3.203 closest distance to " CG1BVAL A  72 " =    3.287
peak=    3.203 closest distance to " N   PHE A 130 " =    1.367
peak=    3.201 closest distance to " CA  VAL A 126 " =    0.831
peak=    3.200 closest distance to " OG BSER A 258 " =    3.309
peak=    3.200 closest distance to " O   THR A 264 " =    1.478
peak=    3.200 closest distance to " CA  VAL A  41 " =    0.813
peak=    3.198 closest distance to " O   HOH Z 368 " =    2.473
peak=    3.196 closest distance to " CG  GLU A 277 " =    2.220
peak=    3.190 closest distance to " O   HOH Z 419 " =    2.577
peak=    3.178 closest distance to " O   HOH Z 104 " =    3.416
peak=    3.177 closest distance to " NH1 ARG A 269 " =    0.775
peak=    3.150 closest distance to " O   HOH Z 414 " =    1.644
peak=    3.145 closest distance to " CD1 LEU A  96 " =    0.749
peak=    3.141 closest distance to " O   HOH Z 214 " =    2.331
peak=    3.141 closest distance to " CB  TRP A 150 " =    1.655
peak=    3.140 closest distance to " O   ALA A 158 " =    1.178
peak=    3.138 closest distance to " CA  GLN A 223 " =    0.751
peak=    3.135 closest distance to " N   ALA A  84 " =    1.315
peak=    3.133 closest distance to " CG2 ILE A  20 " =    1.405
peak=    3.132 closest distance to " CB  PRO A 163 " =    3.912
peak=    3.130 closest distance to " O   HOH Z 175 " =    3.586
peak=    3.129 closest distance to " O   HOH Z 419 " =    1.620
peak=    3.128 closest distance to " O   HOH Z 409 " =    3.441
peak=    3.123 closest distance to " CA  ALA A 158 " =    1.091
peak=    3.111 closest distance to " CB  ALA A 244 " =    0.944
peak=    3.109 closest distance to " CG2 ILE A 120 " =    1.200
peak=    3.108 closest distance to " O   HOH Z 128 " =    1.710
peak=    3.103 closest distance to " O   HOH Z 148 " =    3.080
peak=    3.103 closest distance to " O   HOH Z 109 " =    2.229
peak=    3.095 closest distance to " NE AARG A 275 " =    1.278
peak=    3.095 closest distance to " CB  ALA A 256 " =    1.088
peak=    3.086 closest distance to " O   HOH Z 298 " =    5.023
peak=    3.039 closest distance to " CA  LYS A 117 " =    1.244
peak=    3.036 closest distance to " O   HOH Z 112 " =    3.214
peak=    3.035 closest distance to " O   THR A 251 " =    1.321

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.469 - 5.126
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 215
   mapped sites are within: 0.744 - 5.126

peak=   -4.603 closest distance to " O   HOH Z 266 " =    4.144
peak=   -4.456 closest distance to " C   HIS A 108 " =    1.101
peak=   -4.383 closest distance to " CD1 LEU A 101 " =    2.554
peak=   -4.380 closest distance to " O   HOH Z 290 " =    0.853
peak=   -4.379 closest distance to " OXT GLY A 302 " =    2.798
peak=   -4.375 closest distance to " CA  SER A 164 " =    1.978
peak=   -4.088 closest distance to " O   VAL A  67 " =    2.690
peak=   -4.079 closest distance to " O   PRO A 198 " =    1.297
peak=   -4.020 closest distance to " O   HOH Z 292 " =    4.543
peak=   -3.999 closest distance to " CD  ARG A 156 " =    1.960
peak=   -3.994 closest distance to " C   THR A 279 " =    1.180
peak=   -3.970 closest distance to " O   HOH Z 423 " =    2.339
peak=   -3.970 closest distance to " O   VAL A  67 " =    2.657
peak=   -3.956 closest distance to " O   HOH Z  13 " =    1.577
peak=   -3.956 closest distance to " CD  GLN A  58 " =    0.885
peak=   -3.927 closest distance to " N   SER A 276 " =    1.407
peak=   -3.924 closest distance to " O   TRP A  92 " =    1.893
peak=   -3.908 closest distance to " ND2 ASN A 187 " =    1.464
peak=   -3.889 closest distance to " CE2 TYR A  30 " =    2.691
peak=   -3.878 closest distance to " O   HOH Z 377 " =    0.886
peak=   -3.846 closest distance to " CH2 TRP A 179 " =    1.246
peak=   -3.846 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.845 closest distance to " O   HOH Z 313 " =    1.042
peak=   -3.843 closest distance to " CZ  TYR A 169 " =    1.897
peak=   -3.840 closest distance to " OG  SER A  97 " =    2.135
peak=   -3.813 closest distance to " O   HOH Z  52 " =    1.862
peak=   -3.800 closest distance to " OG BSER A 134 " =    1.737
peak=   -3.800 closest distance to " OG ASER A 134 " =    1.402
peak=   -3.765 closest distance to " CD2 LEU A 300 " =    2.855
peak=   -3.764 closest distance to " CB  ALA A 244 " =    2.030
peak=   -3.752 closest distance to " C   ASP A 191 " =    1.297
peak=   -3.743 closest distance to " O   HOH Z 234 " =    4.220
peak=   -3.736 closest distance to " CG  GLN A  58 " =    1.254
peak=   -3.728 closest distance to " CB  PHE A 208 " =    2.293
peak=   -3.723 closest distance to " CB  ARG A 219 " =    2.358
peak=   -3.719 closest distance to " ND2 ASN A 209 " =    1.821
peak=   -3.712 closest distance to " CB  ALA A 291 " =    2.345
peak=   -3.709 closest distance to " O   HOH Z 165 " =    2.004
peak=   -3.702 closest distance to " O   HOH Z  11 " =    1.583
peak=   -3.701 closest distance to " O   GLY A 196 " =    1.007
peak=   -3.696 closest distance to " CB  LEU A 167 " =    2.122
peak=   -3.690 closest distance to " O   HOH Z 396 " =    1.721
peak=   -3.679 closest distance to " O   HOH Z 377 " =    1.850
peak=   -3.676 closest distance to " CE  MET A  93 " =    1.117
peak=   -3.674 closest distance to " ND2 ASN A  45 " =    0.962
peak=   -3.673 closest distance to " OG1 THR A   4 " =    1.855
peak=   -3.649 closest distance to " O   HOH Z 407 " =    3.358
peak=   -3.628 closest distance to " N   ALA A 248 " =    1.745
peak=   -3.603 closest distance to " CE  MET A 105 " =    1.797
peak=   -3.569 closest distance to " OD1 ASP A 191 " =    1.616
peak=   -3.568 closest distance to " C   ALA A 158 " =    1.169
peak=   -3.564 closest distance to " CD2 LEU A 237 " =    2.298
peak=   -3.561 closest distance to " NH2 ARG A  66 " =    1.696
peak=   -3.556 closest distance to " CD  GLN A  88 " =    0.744
peak=   -3.553 closest distance to " O   HOH Z 222 " =    1.217
peak=   -3.553 closest distance to " CB  CYS A 254 " =    2.665
peak=   -3.551 closest distance to " N   ALA A  43 " =    2.646
peak=   -3.548 closest distance to " NH2 ARG A  79 " =    1.941
peak=   -3.540 closest distance to " O   ALA A 161 " =    1.688
peak=   -3.539 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.535 closest distance to " OD2 ASP A 171 " =    2.226
peak=   -3.529 closest distance to " N   GLN A  58 " =    1.741
peak=   -3.526 closest distance to " CD  ARG A 195 " =    5.126
peak=   -3.520 closest distance to " CB  PRO A 163 " =    2.851
peak=   -3.519 closest distance to " C   LEU A 143 " =    1.232
peak=   -3.518 closest distance to " O   ASN A 187 " =    1.471
peak=   -3.517 closest distance to " CD1 TYR A 247 " =    2.304
peak=   -3.515 closest distance to " O   SER A 146 " =    0.871
peak=   -3.515 closest distance to " OG  SER A  62 " =    1.250
peak=   -3.515 closest distance to " O   HOH Z 118 " =    3.213
peak=   -3.513 closest distance to " O   HOH Z  17 " =    1.236
peak=   -3.510 closest distance to " O   HOH Z 151 " =    1.556
peak=   -3.510 closest distance to " O   PHE A 218 " =    1.461
peak=   -3.508 closest distance to " O   HOH Z  10 " =    1.449
peak=   -3.500 closest distance to " O   HOH Z 100 " =    0.767
peak=   -3.483 closest distance to " C   ALA A 242 " =    1.867
peak=   -3.482 closest distance to " CG  GLU A  53 " =    1.456
peak=   -3.481 closest distance to " O   HOH Z 196 " =    2.011
peak=   -3.476 closest distance to " CG  LEU A  83 " =    1.962
peak=   -3.473 closest distance to " O   HOH Z 311 " =    3.493
peak=   -3.462 closest distance to " O   HOH Z 424 " =    2.972
peak=   -3.460 closest distance to " CB  ALA A 161 " =    2.520
peak=   -3.458 closest distance to " C   SER A 206 " =    1.665
peak=   -3.449 closest distance to " O   HOH Z 422 " =    0.931
peak=   -3.445 closest distance to " ND2 ASN A  69 " =    1.421
peak=   -3.440 closest distance to " O   HOH Z  93 " =    1.227
peak=   -3.439 closest distance to " CD1 LEU A 228 " =    2.252
peak=   -3.435 closest distance to " O   ALA A 256 " =    1.466
peak=   -3.427 closest distance to " O   HOH Z  63 " =    0.956
peak=   -3.427 closest distance to " O   ALA A 161 " =    2.654
peak=   -3.413 closest distance to " OG ASER A 216 " =    1.033
peak=   -3.412 closest distance to " CD  ARG A  14 " =    3.217
peak=   -3.407 closest distance to " O   ALA A   1 " =    1.932
peak=   -3.397 closest distance to " O   HOH Z 250 " =    1.403
peak=   -3.393 closest distance to " NH2 ARG A  66 " =    4.803
peak=   -3.391 closest distance to " CA  GLY A 133 " =    1.760
peak=   -3.390 closest distance to " O   SER A  26 " =    1.184
peak=   -3.390 closest distance to " O   HOH Z  71 " =    1.489
peak=   -3.387 closest distance to " CD  ARG A 139 " =    1.487
peak=   -3.382 closest distance to " OG BSER A 134 " =    1.442
peak=   -3.378 closest distance to " CA  ASN A 148 " =    1.667
peak=   -3.371 closest distance to " O   HOH Z  78 " =    1.719
peak=   -3.367 closest distance to " O   HOH Z 185 " =    2.377
peak=   -3.366 closest distance to " OD1 ASN A  39 " =    2.267
peak=   -3.360 closest distance to " O   HOH Z  15 " =    1.600
peak=   -3.357 closest distance to " O   SER A 210 " =    1.751
peak=   -3.356 closest distance to " O   VAL A 174 " =    2.030
peak=   -3.356 closest distance to " CB  LYS A 193 " =    2.372
peak=   -3.355 closest distance to " CG  ASP A  50 " =    2.415
peak=   -3.354 closest distance to " CB  SER A 258 " =    1.936
peak=   -3.353 closest distance to " CD1 PHE A 130 " =    2.230
peak=   -3.352 closest distance to " N   ALA A 226 " =    1.925
peak=   -3.344 closest distance to " CD2 LEU A 237 " =    2.577
peak=   -3.339 closest distance to " CB  ASN A  39 " =    2.275
peak=   -3.335 closest distance to " O   HOH Z  38 " =    1.427
peak=   -3.332 closest distance to " CA  TRP A 274 " =    1.480
peak=   -3.331 closest distance to " O   HOH Z 418 " =    1.288
peak=   -3.327 closest distance to " O   HOH Z  39 " =    1.507
peak=   -3.323 closest distance to " N   MET A 188 " =    1.880
peak=   -3.323 closest distance to " O   HOH Z 360 " =    2.486
peak=   -3.323 closest distance to " O   HOH Z   6 " =    1.880
peak=   -3.322 closest distance to " ND2 ASN A  45 " =    1.058
peak=   -3.322 closest distance to " O   HOH Z 414 " =    1.452
peak=   -3.319 closest distance to " CZ3 TRP A 274 " =    1.029
peak=   -3.314 closest distance to " O   HOH Z  68 " =    2.842
peak=   -3.308 closest distance to " O   HOH Z 196 " =    2.250
peak=   -3.305 closest distance to " O   HOH Z 299 " =    1.971
peak=   -3.302 closest distance to " CG  GLU A 152 " =    0.912
peak=   -3.298 closest distance to " CB  ALA A 291 " =    2.044
peak=   -3.290 closest distance to " NE2 GLN A 103 " =    1.639
peak=   -3.289 closest distance to " CD1 LEU A  25 " =    2.455
peak=   -3.289 closest distance to " O   HOH Z 221 " =    1.127
peak=   -3.284 closest distance to " O   HOH Z  43 " =    1.640
peak=   -3.283 closest distance to " O   HOH Z 150 " =    1.466
peak=   -3.282 closest distance to " N   VAL A 189 " =    1.791
peak=   -3.281 closest distance to " O   PRO A 198 " =    1.223
peak=   -3.281 closest distance to " CE1 TYR A 169 " =    2.305
peak=   -3.280 closest distance to " N   GLY A  98 " =    2.190
peak=   -3.279 closest distance to " OG  SER A  32 " =    1.214
peak=   -3.272 closest distance to " O   HOH Z 388 " =    2.155
peak=   -3.266 closest distance to " ND2 ASN A  60 " =    1.430
peak=   -3.264 closest distance to " O   GLN A  11 " =    1.359
peak=   -3.260 closest distance to " ND2 ASN A  39 " =    1.159
peak=   -3.260 closest distance to " CB  PRO A 243 " =    2.626
peak=   -3.258 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.256 closest distance to " OG  SER A  63 " =    1.335
peak=   -3.255 closest distance to " O   LEU A 167 " =    1.585
peak=   -3.253 closest distance to " CD1 TRP A 179 " =    1.201
peak=   -3.251 closest distance to " CZ2 TRP A  92 " =    2.668
peak=   -3.250 closest distance to " O   HOH Z 412 " =    4.564
peak=   -3.250 closest distance to " O   HOH Z 283 " =    1.714
peak=   -3.249 closest distance to " O   SER A 273 " =    1.387
peak=   -3.242 closest distance to " CE3 TRP A 150 " =    1.953
peak=   -3.241 closest distance to " CG1AVAL A  41 " =    2.581
peak=   -3.240 closest distance to " O   HOH Z 417 " =    2.489
peak=   -3.240 closest distance to " O   HOH Z 405 " =    2.297
peak=   -3.239 closest distance to " O   HOH Z  16 " =    2.414
peak=   -3.235 closest distance to " CG  ASP A 132 " =    2.237
peak=   -3.232 closest distance to " CD2 LEU A 237 " =    2.733
peak=   -3.232 closest distance to " O   THR A  52 " =    1.708
peak=   -3.223 closest distance to " CA  VAL A 197 " =    0.958
peak=   -3.220 closest distance to " O   ALA A 160 " =    1.491
peak=   -3.218 closest distance to " O   HOH Z  39 " =    1.206
peak=   -3.216 closest distance to " O   HOH Z 380 " =    4.652
peak=   -3.214 closest distance to " N   SER A 210 " =    1.444
peak=   -3.213 closest distance to " CD  PRO A 198 " =    1.228
peak=   -3.211 closest distance to " O   HOH Z 427 " =    1.237
peak=   -3.208 closest distance to " C   GLY A  80 " =    2.317
peak=   -3.202 closest distance to " CB  ALA A 248 " =    1.967
peak=   -3.201 closest distance to " CA  ASP A 298 " =    1.118
peak=   -3.201 closest distance to " O   HOH Z 116 " =    1.072
peak=   -3.200 closest distance to " OD1 ASN A 176 " =    1.088
peak=   -3.200 closest distance to " CA  ALA A  34 " =    2.366
peak=   -3.198 closest distance to " O   HOH Z 280 " =    2.236
peak=   -3.192 closest distance to " CZ  TYR A  68 " =    1.041
peak=   -3.181 closest distance to " CD  GLN A  58 " =    1.150
peak=   -3.164 closest distance to " CG  GLU A 277 " =    1.186
peak=   -3.163 closest distance to " O   HOH Z 163 " =    4.988
peak=   -3.160 closest distance to " O   HOH Z 392 " =    1.611
peak=   -3.154 closest distance to " CD1 LEU A 167 " =    2.147
peak=   -3.152 closest distance to " O   SER A 135 " =    1.617
peak=   -3.150 closest distance to " O   VAL A 125 " =    2.063
peak=   -3.148 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.145 closest distance to " CG1 VAL A 153 " =    2.321
peak=   -3.144 closest distance to " O   ALA A  51 " =    1.554
peak=   -3.143 closest distance to " O   HOH Z 111 " =    2.553
peak=   -3.133 closest distance to " OE2 GLU A   2 " =    1.479
peak=   -3.131 closest distance to " O   HOH Z  76 " =    2.049
peak=   -3.127 closest distance to " CG  LYS A 119 " =    2.904
peak=   -3.126 closest distance to " NE2 GLN A  88 " =    1.951
peak=   -3.121 closest distance to " O   HOH Z  47 " =    1.432
peak=   -3.117 closest distance to " O   TYR A  15 " =    1.614
peak=   -3.110 closest distance to " O   HOH Z 158 " =    2.059
peak=   -3.109 closest distance to " C   LEU A 101 " =    1.008
peak=   -3.095 closest distance to " O   HOH Z  97 " =    1.501
peak=   -3.092 closest distance to " NZ  LYS A 117 " =    1.633
peak=   -3.087 closest distance to " O   HOH Z 145 " =    1.900
peak=   -3.085 closest distance to " CG  ARG A 269 " =    2.213
peak=   -3.084 closest distance to " OG1 THR A 178 " =    1.163
peak=   -3.079 closest distance to " O   ALA A  34 " =    2.520
peak=   -3.072 closest distance to " O   HOH Z 431 " =    2.664
peak=   -3.071 closest distance to " CG1 VAL A  78 " =    2.607
peak=   -3.070 closest distance to " O   HOH Z 111 " =    3.323
peak=   -3.063 closest distance to " CZ  PHE A  16 " =    2.255
peak=   -3.053 closest distance to " CB  TRP A  85 " =    2.476
peak=   -3.050 closest distance to " O   ALA A  10 " =    1.651
peak=   -3.042 closest distance to " C   LEU A 143 " =    1.914
peak=   -3.013 closest distance to " CZ  ARG A  66 " =    1.507

================= 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    :  0.4737 0.4652   6.282580e+00   6.271804e+00
   1_bss:  0.4641 0.4558   6.276480e+00   6.257952e+00
   1_xyz:  0.3551 0.3843   6.087100e+00   6.140017e+00
   1_adp:  0.3205 0.3917   6.037750e+00   6.161547e+00
   1_occ:  0.3201 0.3924   6.037302e+00   6.161208e+00
   2_bss:  0.3173 0.3899   6.035311e+00   6.160058e+00
   2_xyz:  0.2505 0.3134   5.835338e+00   6.008000e+00
   2_adp:  0.2292 0.2982   5.776431e+00   5.963330e+00
   2_occ:  0.2291 0.2980   5.775745e+00   5.962601e+00
   3_bss:  0.2290 0.2972   5.774041e+00   5.959475e+00
   3_xyz:  0.1686 0.2196   5.493529e+00   5.707449e+00
   3_adp:  0.1500 0.1980   5.386224e+00   5.598651e+00
   3_occ:  0.1499 0.1979   5.385890e+00   5.598718e+00
   4_bss:  0.1496 0.1972   5.388415e+00   5.600005e+00
   4_xyz:  0.1268 0.1741   5.247485e+00   5.475632e+00
   4_adp:  0.1210 0.1703   5.214976e+00   5.447578e+00
   4_occ:  0.1209 0.1702   5.214676e+00   5.447759e+00
   5_bss:  0.1213 0.1701   5.217132e+00   5.449290e+00
   5_xyz:  0.1158 0.1652   5.185165e+00   5.422859e+00
   5_adp:  0.1166 0.1620   5.181052e+00   5.409724e+00
   5_occ:  0.1164 0.1620   5.180475e+00   5.410347e+00
   5_bss:  0.1164 0.1620   5.180673e+00   5.410442e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000  -2.858   3.216   1.729   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -2.858   3.216   1.729   0.000   0.000   0.000
   1_adp:  0.300  20.000  -2.858   3.216   1.729   0.000   0.000   0.000
   1_occ:  0.300  20.000  -2.858   3.216   1.729   0.000   0.000   0.000
   2_bss:  0.323  47.718  -1.989   1.393   0.018   0.000   0.000   0.000
   2_xyz:  0.323  47.718  -1.989   1.393   0.018   0.000   0.000   0.000
   2_adp:  0.323  47.718  -1.989   1.393   0.018   0.000   0.000   0.000
   2_occ:  0.323  47.718  -1.989   1.393   0.018   0.000   0.000   0.000
   3_bss:  0.323  48.792  -1.974   0.335  -0.700   0.000  -0.000  -0.000
   3_xyz:  0.323  48.792  -1.974   0.335  -0.700   0.000  -0.000  -0.000
   3_adp:  0.323  48.792  -1.974   0.335  -0.700   0.000  -0.000  -0.000
   3_occ:  0.323  48.792  -1.974   0.335  -0.700   0.000  -0.000  -0.000
   4_bss:  0.321  48.792  -2.615  -0.968  -1.613  -0.000  -0.000  -0.000
   4_xyz:  0.321  48.792  -2.615  -0.968  -1.613  -0.000  -0.000  -0.000
   4_adp:  0.321  48.792  -2.615  -0.968  -1.613  -0.000  -0.000  -0.000
   4_occ:  0.321  48.792  -2.615  -0.968  -1.613  -0.000  -0.000  -0.000
   5_bss:  0.325  50.906  -2.660  -1.303  -1.742  -0.000  -0.000  -0.000
   5_xyz:  0.325  50.906  -2.660  -1.303  -1.742  -0.000  -0.000  -0.000
   5_adp:  0.325  50.906  -2.660  -1.303  -1.742  -0.000  -0.000  -0.000
   5_occ:  0.325  50.906  -2.660  -1.303  -1.742  -0.000  -0.000  -0.000
   5_bss:  0.329  50.836  -2.548  -1.255  -1.612  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.669 0.3969  0.5365    70921.478
   1_bss:  57.816 0.4193  0.5808    66532.533
   1_xyz:  42.404 0.6130  0.8322    40822.504
   1_adp:  44.108 0.5915  0.8164    43434.883
   1_occ:  44.128 0.5912  0.8150    43451.312
   2_bss:  43.897 0.5940  0.7983    43171.446
   2_xyz:  33.281 0.7192  0.9355    26528.624
   2_adp:  30.775 0.7482  0.9434    23596.427
   2_occ:  30.754 0.7484  0.9432    23553.617
   3_bss:  30.619 0.7498  0.9253    23332.348
   3_xyz:  21.942 0.8413  1.0003    12651.386
   3_adp:  18.994 0.8708  1.0103    10189.980
   3_occ:  18.994 0.8709  1.0103    10198.624
   4_bss:  19.020 0.8707  0.9769    10251.091
   4_xyz:  16.221 0.8958  0.9876     7726.583
   4_adp:  15.521 0.9023  0.9838     7307.751
   4_occ:  15.519 0.9024  0.9838     7308.707
   5_bss:  15.535 0.9023  0.9781     7354.900
   5_xyz:  14.884 0.9079  0.9789     6931.257
   5_adp:  14.550 0.9109  0.9752     6784.175
   5_occ:  14.551 0.9109  0.9752     6789.423
   5_bss:  14.554 0.9109  0.9762     6792.940
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.0450e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.0450e-01
   1_xyz:   1.678  0.013  0.100 16.547  0.007  4.105   1.5812e-01
   1_adp:   1.678  0.013  0.100 16.547  0.007  4.105   1.5812e-01
   1_occ:   1.678  0.013  0.100 16.547  0.007  4.105   1.5812e-01
   2_bss:   1.678  0.013  0.100 16.547  0.007  4.105   1.5812e-01
   2_xyz:   1.250  0.009  0.082 14.709  0.005  4.108   8.1741e-02
   2_adp:   1.250  0.009  0.082 14.709  0.005  4.108   8.1741e-02
   2_occ:   1.250  0.009  0.082 14.709  0.005  4.108   8.1741e-02
   3_bss:   1.250  0.009  0.082 14.709  0.005  4.108   8.1741e-02
   3_xyz:   1.196  0.009  0.074 14.925  0.005  4.117   7.9064e-02
   3_adp:   1.196  0.009  0.074 14.925  0.005  4.117   7.9064e-02
   3_occ:   1.196  0.009  0.074 14.925  0.005  4.117   7.9064e-02
   4_bss:   1.196  0.009  0.074 14.925  0.005  4.117   7.9064e-02
   4_xyz:   1.144  0.008  0.077 14.907  0.005  4.109   7.3061e-02
   4_adp:   1.144  0.008  0.077 14.907  0.005  4.109   7.3061e-02
   4_occ:   1.144  0.008  0.077 14.907  0.005  4.109   7.3061e-02
   5_bss:   1.144  0.008  0.077 14.907  0.005  4.109   7.3061e-02
   5_xyz:   1.044  0.007  0.072 14.725  0.004  4.112   6.2488e-02
   5_adp:   1.044  0.007  0.072 14.725  0.004  4.112   6.2488e-02
   5_occ:   1.044  0.007  0.072 14.725  0.004  4.112   6.2488e-02
   5_bss:   1.044  0.007  0.072 14.725  0.004  4.112   6.2488e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.361   2.4144e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.361   2.4144e-01
   1_xyz:  10.431  0.091  0.435 89.041  0.042  2.008   1.1855e-01
   1_adp:  10.431  0.091  0.435 89.041  0.042  2.008   1.1855e-01
   1_occ:  10.431  0.091  0.435 89.041  0.042  2.008   1.1855e-01
   2_bss:  10.431  0.091  0.435 89.041  0.042  2.008   1.1855e-01
   2_xyz:   8.120  0.063  0.264 85.309  0.036  2.252   7.4589e-02
   2_adp:   8.120  0.063  0.264 85.309  0.036  2.252   7.4589e-02
   2_occ:   8.120  0.063  0.264 85.309  0.036  2.252   7.4589e-02
   3_bss:   8.120  0.063  0.264 85.309  0.036  2.252   7.4589e-02
   3_xyz:   8.166  0.076  0.242 80.402  0.031  2.247   6.3348e-02
   3_adp:   8.166  0.076  0.242 80.402  0.031  2.247   6.3348e-02
   3_occ:   8.166  0.076  0.242 80.402  0.031  2.247   6.3348e-02
   4_bss:   8.166  0.076  0.242 80.402  0.031  2.247   6.3348e-02
   4_xyz:   7.785  0.055  0.270 81.957  0.035  2.277   6.6107e-02
   4_adp:   7.785  0.055  0.270 81.957  0.035  2.277   6.6107e-02
   4_occ:   7.785  0.055  0.270 81.957  0.035  2.277   6.6107e-02
   5_bss:   7.785  0.055  0.270 81.957  0.035  2.277   6.6107e-02
   5_xyz:   7.323  0.039  0.238 81.035  0.036  2.345   5.5699e-02
   5_adp:   7.323  0.039  0.238 81.035  0.036  2.345   5.5699e-02
   5_occ:   7.323  0.039  0.238 81.035  0.036  2.345   5.5699e-02
   5_bss:   7.323  0.039  0.238 81.035  0.036  2.345   5.5699e-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: 101.63   0.00  19.81  97.84   0.00  16.09 101.63   0.78  40.06
   1_occ: 101.63   0.00  19.81  97.84   0.00  16.09 101.63   0.78  40.06
   2_bss: 101.63   0.00  19.81  97.84   0.00  16.09 101.63   0.78  40.06
   2_xyz: 101.63   0.00  19.81  97.84   0.00  16.09 101.63   0.78  40.06
   2_adp: 101.09   0.00  18.85 100.36   0.00  14.72 101.09   4.59  41.34
   2_occ: 101.09   0.00  18.85 100.36   0.00  14.72 101.09   4.59  41.34
   3_bss: 101.09   0.00  18.85 100.36   0.00  14.72 101.09   4.59  41.34
   3_xyz: 101.09   0.00  18.85 100.36   0.00  14.72 101.09   4.59  41.34
   3_adp: 100.57   0.00  17.98  92.13   0.00  13.42 100.57   5.89  42.84
   3_occ: 100.57   0.00  17.98  92.13   0.00  13.42 100.57   5.89  42.84
   4_bss: 100.57   0.00  17.98  92.13   0.00  13.42 100.57   5.89  42.84
   4_xyz: 100.57   0.00  17.98  92.13   0.00  13.42 100.57   5.89  42.84
   4_adp:  97.86   0.99  17.68  97.86   0.99  13.02  91.98   6.08  43.06
   4_occ:  97.86   0.99  17.68  97.86   0.99  13.02  91.98   6.08  43.06
   5_bss:  97.86   0.99  17.68  97.86   0.99  13.02  91.98   6.08  43.06
   5_xyz:  97.86   0.99  17.68  97.86   0.99  13.02  91.98   6.08  43.06
   5_adp:  93.49   1.96  16.86  93.49   1.96  12.71  88.06   5.31  39.45
   5_occ:  93.49   1.96  16.86  93.49   1.96  12.71  88.06   5.31  39.45
   5_bss:  93.42   1.89  16.79  93.42   1.89  12.64  87.99   5.24  39.38
------------------------------------------------------------------------
 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:    2.473    0.030    0.456
   1_adp:    2.473    0.030    0.456
   1_occ:    2.473    0.030    0.456
   2_bss:    2.473    0.030    0.456
   2_xyz:    1.820    0.064    0.594
   2_adp:    1.820    0.064    0.594
   2_occ:    1.820    0.064    0.594
   3_bss:    1.820    0.064    0.594
   3_xyz:    1.888    0.113    0.760
   3_adp:    1.888    0.113    0.760
   3_occ:    1.888    0.113    0.760
   4_bss:    1.888    0.113    0.760
   4_xyz:    1.937    0.124    0.806
   4_adp:    1.937    0.124    0.806
   4_occ:    1.937    0.124    0.806
   5_bss:    1.937    0.124    0.806
   5_xyz:    2.014    0.110    0.829
   5_adp:    2.014    0.110    0.829
   5_occ:    2.014    0.110    0.829
   5_bss:    2.014    0.110    0.829
------------------------------------------------------------------------

CPU time actual refinement: 334.85


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/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_462/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_462/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.70 
  Macro-tasks:
    bulk solvent and scale       = 43.71  
    individual site refinement   = 131.86 
    weights calculation          = 29.10  
    collect and process          = 6.48   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 211.26 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 106.15 
    alpha_beta                      = 8.47   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 113.44 
    fmodel                         = 7.05   
    r_factors                      = 0.15   
    phase_errors                   = 10.54  
    foms                           = 0.16   
    TOTAL for micro-tasks          = 249.60 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.833 micro seconds
Total CPU time: 5.81 minutes
from_scatterers_fft:    628 calls, 105.84 s
gradients_fft:          573 calls, 101.06 s

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

# Date 2008-01-16 Time 04:53:32 PST -0800 (1200488012.90 s)
Start R-work = 0.4737, R-free = 0.4652 (no bulk solvent and anisotropic scale)
Final R-work = 0.1399, R-free = 0.1830 (no bulk solvent and anisotropic scale)

Start R-work = 0.4641, R-free = 0.4558
Final R-work = 0.1164, R-free = 0.1620