# Date 2008-01-16 Time 04:50:24 PST -0800 (1200487824.46 s)
#phil __OFF__

Command line arguments: "../487.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14614
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 487

-------------------------------------------------------------------------------
  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: (69.8988, 45.7567, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.95284
Completeness in resolution range: 0.955608
Completeness with d_max=infinity: 0.952726

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8986
                             d_min =   1.9528

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: (69.8988, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8986 1.95284
Completeness in resolution range: 0.955608
Completeness with d_max=infinity: 0.952726

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8990 -  4.1792 [2154/2179]  1939   215  10.0%
  bin  2:  4.1792 -  3.3293 [2053/2073]  1848   205  10.0%
  bin  3:  3.3293 -  2.9121 [2059/2078]  1850   209  10.2%
  bin  4:  2.9121 -  2.6474 [2011/2041]  1813   198   9.8%
  bin  5:  2.6474 -  2.4586 [2020/2039]  1822   198   9.8%
  bin  6:  2.4586 -  2.3142 [2001/2026]  1794   207  10.3%
  bin  7:  2.3142 -  2.1987 [1978/2006]  1781   197  10.0%
  bin  8:  2.1987 -  2.1032 [1997/2033]  1800   197   9.9%
  bin  9:  2.1032 -  2.0225 [1961/2003]  1762   199  10.1%
  bin 10:  2.0225 -  1.9528 [1355/2021]  1221   134   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 36
        2.32 -     2.97: 1802
        2.97 -     3.61: 4673
        3.61 -     4.26: 9356
        4.26 -     4.90: 12996
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.677 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.677 3.040 -x+1/2,-y+1,z-1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28858 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_487/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/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 = 69.89875 45.75675 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4397   r_free= 0.4343   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.257541                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6616 0.99   1398  155 0.3710 0.3812      6.5592      6.5752|
|  2:  4.6616 -  3.7190 0.99   1345  152 0.3851 0.3503      6.7859      6.7118|
|  3:  3.7190 -  3.2545 0.99   1319  141 0.4157 0.3962      6.6749      6.7269|
|  4:  3.2545 -  2.9594 0.99   1314  152 0.4230 0.4207      6.5113      6.4757|
|  5:  2.9594 -  2.7487 0.99   1307  147 0.4686 0.4513      6.3462       6.359|
|  6:  2.7487 -  2.5876 0.99   1302  136 0.4573 0.4937      6.2519      6.1972|
|  7:  2.5876 -  2.4586 0.99   1287  142 0.4625 0.4828      6.2138      6.1897|
|  8:  2.4586 -  2.3520 0.98   1271  145 0.4844 0.4535      6.1551      6.1443|
|  9:  2.3520 -  2.2618 0.98   1265  148 0.4764 0.4915      6.1011      6.1602|
| 10:  2.2618 -  2.1840 1.00   1303  145 0.4721 0.4882      6.0724      6.0722|
| 11:  2.1840 -  2.1159 0.98   1271  136 0.4731 0.4608      6.0031       6.025|
| 12:  2.1159 -  2.0555 0.98   1256  140 0.4552 0.4241      5.9449      5.9673|
| 13:  2.0555 -  2.0016 0.99   1281  139 0.4824 0.4555      5.8468      5.7747|
| 14:  2.0016 -  1.9528 0.54    711   81 0.5132 0.4362      5.8964      5.7631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6616  1398   155  0.69  35.54   0.83     0.75      77213.75|
|  2:  4.6616 -  3.7190  1345   152  0.71  34.46   0.91     0.83     102726.64|
|  3:  3.7190 -  3.2545  1319   141  0.63  41.42   0.94     0.82     105570.77|
|  4:  3.2545 -  2.9594  1314   152  0.55  47.84   0.96     0.74      95433.09|
|  5:  2.9594 -  2.7487  1307   147  0.47  54.45   0.91     0.66      74910.70|
|  6:  2.7487 -  2.5876  1302   136  0.45  56.03   0.91     0.62      65895.01|
|  7:  2.5876 -  2.4586  1287   142  0.43  57.35   0.95     0.61      59336.90|
|  8:  2.4586 -  2.3520  1271   145  0.42  58.43   0.95     0.61      55020.81|
|  9:  2.3520 -  2.2618  1265   148  0.43  57.67   0.94     0.62      49508.54|
| 10:  2.2618 -  2.1840  1303   145  0.45  56.23   0.97     0.65      42633.79|
| 11:  2.1840 -  2.1159  1271   136  0.45  55.87   1.00     0.69      39350.89|
| 12:  2.1159 -  2.0555  1256   140  0.49  53.38   1.03     0.73      33702.11|
| 13:  2.0555 -  2.0016  1281   139  0.48  53.51   0.98     0.76      27708.01|
| 14:  2.0016 -  1.9528   711    81  0.57  46.69   1.01     0.81      20086.48|
|alpha:            min =        0.61 max =            0.83 mean =         0.71|
|beta:             min =    20086.48 max =       105570.77 mean =     62453.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.58|
|phase err.(test): min =        0.00 max =           89.98 mean =        50.58|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.032951              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.898   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.890336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.663   (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 |  1.677 -  1.999:       17 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.999 -  2.321:       19 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.321 -  2.644:       90 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.644 -  2.966:     1712 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.966 -  3.288:     1969 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.288 -  3.611:     2704 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.611 -  3.933:     4828 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.933 -  4.255:     4528 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.255 -  4.578:     5934 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     7062 |
|-----------------------------------------------------------------------------|
|-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 |        0.187 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.106    4.900  1.677 |       0.583 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4397   r_free= 0.4343   ksol= 0.00   Bsol= 0.00   scale= 0.919    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.257541                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4275   r_free= 0.4225   ksol= 0.36   Bsol= 34.76   scale= 0.931   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,3.07,-1.11,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.248044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.937967              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.758   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.045285              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.711   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4275      final r-factor (work) = 0.3617          |
| start r-factor (free) = 0.4225      final r-factor (free) = 0.3895          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8602 = 6.94 * 0.50 * 6.2476 + 1.00 * 0.1872                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4547 = 6.94 * 0.50 * 6.1569 + 1.00 * 0.0966                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3617      final r-factor (work) = 0.3328          |
| start r-factor (free) = 0.3895      final r-factor (free) = 0.3992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4419 = 1.05 * 1.00 * 6.1569 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3920 = 1.05 * 1.00 * 6.0904 + 1.00 * 0.0258                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.94  18.21    None  None   None       |
|    all(noH): 2823   0      0.00    107.94  18.21    None  None   None       |
|    Sol.    : 438    0      0.00    107.94  33.82    None  None   None       |
|    Mac.    : 2385   0      0.00    96.53   15.34    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 -  10.794:  973   |   5:    53.968 -  64.761:   30        |
|      1:    10.794 -  21.587:  974   |   6:    64.761 -  75.555:   21        |
|      2:    21.587 -  32.381:  480   |   7:    75.555 -  86.348:    2        |
|      3:    32.381 -  43.174:  233   |   8:    86.348 -  97.142:    3        |
|      4:    43.174 -  53.968:  104   |   9:    97.142 - 107.935:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3328 r_free = 0.3992             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3325 r_free = 0.3994             target_work(ml) = 6.094         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3325   r_free= 0.3994   ksol= 0.36   Bsol= 34.76   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.41,3.07,-1.11,0.00,-0.00,-0.00); trace/3= -0.48                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.093656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3330   r_free= 0.3994   ksol= 0.36   Bsol= 49.29   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,1.45,-0.51,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.096565                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.385188             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.473  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3330      final r-factor (work) = 0.2695          |
| start r-factor (free) = 0.3994      final r-factor (free) = 0.3377          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8297 = 12.39 * 0.50 * 6.0933 + 1.00 * 0.0966                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.3374 = 12.39 * 0.50 * 6.0105 + 1.00 * 0.1170                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2695      final r-factor (work) = 0.2464          |
| start r-factor (free) = 0.3377      final r-factor (free) = 0.3256          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2161 = 0.70 * 1.00 * 6.0105 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1177 = 0.70 * 1.00 * 5.8767 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.63  18.00    None  None   None       |
|    all(noH): 2823   0      0.00    104.63  18.00    None  None   None       |
|    Sol.    : 438    0      0.00    104.63  37.88    None  None   None       |
|    Mac.    : 2385   0      0.00    92.85   14.34    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 -  10.463: 1038   |   5:    52.317 -  62.780:   61        |
|      1:    10.463 -  20.927:  954   |   6:    62.780 -  73.244:   20        |
|      2:    20.927 -  31.390:  387   |   7:    73.244 -  83.707:    6        |
|      3:    31.390 -  41.854:  211   |   8:    83.707 -  94.170:    4        |
|      4:    41.854 -  52.317:  140   |   9:    94.170 - 104.634:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2464 r_free = 0.3256             target_work(ml) = 5.859         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2462 r_free = 0.3253             target_work(ml) = 5.858         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2462   r_free= 0.3253   ksol= 0.36   Bsol= 49.29   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.72,1.45,-0.51,0.00,-0.00,-0.00); trace/3= -0.26                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.858156                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2453   r_free= 0.3218   ksol= 0.35   Bsol= 57.29   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.38,-0.25,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.851590                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.730395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263892              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.266  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2453      final r-factor (work) = 0.2032          |
| start r-factor (free) = 0.3218      final r-factor (free) = 0.2661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0761 = 3.73 * 0.50 * 5.8756 + 1.00 * 0.1170                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8366 = 3.73 * 0.50 * 5.7763 + 1.00 * 0.0626                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2032      final r-factor (work) = 0.1915          |
| start r-factor (free) = 0.2661      final r-factor (free) = 0.2464          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5377 = 0.26 * 1.00 * 5.7763 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5001 = 0.26 * 1.00 * 5.6481 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.75   17.32    None  None   None       |
|    all(noH): 2823   0      0.00    94.75   17.32    None  None   None       |
|    Sol.    : 438    0      5.44    94.75   39.08    None  None   None       |
|    Mac.    : 2385   0      0.00    90.84   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.475:  929   |   5:    47.376 -  56.851:   96        |
|      1:     9.475 -  18.951: 1111   |   6:    56.851 -  66.327:   45        |
|      2:    18.951 -  28.426:  308   |   7:    66.327 -  75.802:    9        |
|      3:    28.426 -  37.901:  172   |   8:    75.802 -  85.277:    2        |
|      4:    37.901 -  47.376:  148   |   9:    85.277 -  94.752:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1915 r_free = 0.2464             target_work(ml) = 5.614         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1911 r_free = 0.2455             target_work(ml) = 5.613         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1911   r_free= 0.2455   ksol= 0.35   Bsol= 57.29   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.38,-0.25,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.612622                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1906   r_free= 0.2440   ksol= 0.32   Bsol= 43.58   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.61,-0.78,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.610078                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.132876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.961   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213247              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.435  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1906      final r-factor (work) = 0.1544          |
| start r-factor (free) = 0.2440      final r-factor (free) = 0.2028          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0866 = 2.13 * 0.50 * 5.6491 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9343 = 2.13 * 0.50 * 5.5151 + 1.00 * 0.0528                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1544      final r-factor (work) = 0.1466          |
| start r-factor (free) = 0.2028      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1852 = 0.21 * 1.00 * 5.5151 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1590 = 0.21 * 1.00 * 5.3928 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.50   17.18    None  None   None       |
|    all(noH): 2823   0      0.00    87.50   17.18    None  None   None       |
|    Sol.    : 438    0      5.47    87.50   40.53    None  None   None       |
|    Mac.    : 2385   0      0.00    85.99   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.751:  753   |   5:    43.752 -  52.503:  106        |
|      1:     8.751 -  17.501: 1284   |   6:    52.503 -  61.253:   74        |
|      2:    17.501 -  26.251:  289   |   7:    61.253 -  70.004:   39        |
|      3:    26.251 -  35.002:  146   |   8:    70.004 -  78.754:    7        |
|      4:    35.002 -  43.752:  121   |   9:    78.754 -  87.504:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1466 r_free = 0.1959             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1465 r_free = 0.1956             target_work(ml) = 5.374         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1465   r_free= 0.1956   ksol= 0.32   Bsol= 43.58   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-1.61,-0.78,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.373603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1468   r_free= 0.1952   ksol= 0.32   Bsol= 43.58   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.27,-1.08,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.373302                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.323869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.270861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.184  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3206 = 2.32 * 0.50 * 5.3943 + 1.00 * 0.0528                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2234 = 2.32 * 0.50 * 5.3102 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1264      final r-factor (work) = 0.1223          |
| start r-factor (free) = 0.1722      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4471 = 0.27 * 1.00 * 5.3102 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4237 = 0.27 * 1.00 * 5.2258 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.86    88.64   17.06    None  None   None       |
|    all(noH): 2823   0      0.86    88.64   17.06    None  None   None       |
|    Sol.    : 438    0      5.62    87.96   41.10    None  None   None       |
|    Mac.    : 2385   0      0.86    88.64   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.858 -   9.636:  984   |   5:    44.748 -  53.525:   85        |
|      1:     9.636 -  18.414: 1144   |   6:    53.525 -  62.303:   80        |
|      2:    18.414 -  27.192:  237   |   7:    62.303 -  71.081:   35        |
|      3:    27.192 -  35.970:  130   |   8:    71.081 -  79.859:   14        |
|      4:    35.970 -  44.748:  109   |   9:    79.859 -  88.637:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1223 r_free = 0.1681             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1222 r_free = 0.1680             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1680   ksol= 0.32   Bsol= 43.58   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.25,-2.27,-1.08,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211196                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6616 0.99   1398  155 0.1038 0.1346      5.4135      5.5983|
|  2:  4.6616 -  3.7190 0.99   1345  152 0.0906 0.1205      5.5031      5.7249|
|  3:  3.7190 -  3.2545 0.99   1319  141 0.1161 0.1485      5.5587      5.8618|
|  4:  3.2545 -  2.9594 0.99   1314  152 0.1351 0.1890      5.5464      5.7093|
|  5:  2.9594 -  2.7487 0.99   1307  147 0.1489 0.1896      5.4121      5.6332|
|  6:  2.7487 -  2.5876 0.99   1302  136 0.1317 0.1772      5.2654      5.4314|
|  7:  2.5876 -  2.4586 0.99   1287  142 0.1376 0.1780      5.2199      5.4341|
|  8:  2.4586 -  2.3520 0.98   1271  145 0.1338 0.1896       5.149      5.3888|
|  9:  2.3520 -  2.2618 0.98   1265  148 0.1303 0.1828       5.097      5.3236|
| 10:  2.2618 -  2.1840 1.00   1303  145 0.1223 0.1855      5.0194      5.2446|
| 11:  2.1840 -  2.1159 0.98   1271  136 0.1257 0.1938      5.0118      5.3329|
| 12:  2.1159 -  2.0555 0.98   1256  140 0.1218 0.1837       4.945      5.2474|
| 13:  2.0555 -  2.0016 0.99   1281  139 0.1226 0.1889      4.8247      5.1147|
| 14:  2.0016 -  1.9528 0.54    711   81 0.1102 0.1514      4.7013      4.8607|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6616  1398   155  0.93   9.71   0.99     0.96       7676.36|
|  2:  4.6616 -  3.7190  1345   152  0.95   8.71   1.03     1.02      10370.31|
|  3:  3.7190 -  3.2545  1319   141  0.92  13.08   1.04     1.03      12542.14|
|  4:  3.2545 -  2.9594  1314   152  0.91  15.24   1.02     1.00      12358.42|
|  5:  2.9594 -  2.7487  1307   147  0.89  16.94   1.01     0.98       9330.57|
|  6:  2.7487 -  2.5876  1302   136  0.89  17.28   0.99     0.97       7742.62|
|  7:  2.5876 -  2.4586  1287   142  0.89  16.85   1.01     0.98       6855.58|
|  8:  2.4586 -  2.3520  1271   145  0.89  16.83   1.00     0.99       6048.04|
|  9:  2.3520 -  2.2618  1265   148  0.90  16.31   1.02     0.98       5486.76|
| 10:  2.2618 -  2.1840  1303   145  0.89  17.17   1.01     0.97       4992.35|
| 11:  2.1840 -  2.1159  1271   136  0.89  17.67   1.01     0.97       4936.40|
| 12:  2.1159 -  2.0555  1256   140  0.90  16.58   1.03     1.01       4497.05|
| 13:  2.0555 -  2.0016  1281   139  0.89  17.13   1.02     1.01       3542.95|
| 14:  2.0016 -  1.9528   711    81  0.92  14.13   1.01     0.98       2651.26|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2651.26 max =        12542.14 mean =      7262.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.23|
|phase err.(test): min =        0.00 max =           89.76 mean =        14.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1680   ksol= 0.32   Bsol= 43.55   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.24,-1.05,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1222   r_free= 0.1680   ksol= 0.32   Bsol= 43.55   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.22,-2.24,-1.05,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211196                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8990 -  4.6616 0.99   1398  155 0.1038 0.1346      5.4135      5.5983|
|  2:  4.6616 -  3.7190 0.99   1345  152 0.0906 0.1205      5.5031      5.7249|
|  3:  3.7190 -  3.2545 0.99   1319  141 0.1161 0.1485      5.5587      5.8618|
|  4:  3.2545 -  2.9594 0.99   1314  152 0.1351 0.1890      5.5464      5.7093|
|  5:  2.9594 -  2.7487 0.99   1307  147 0.1489 0.1896      5.4121      5.6332|
|  6:  2.7487 -  2.5876 0.99   1302  136 0.1317 0.1772      5.2654      5.4314|
|  7:  2.5876 -  2.4586 0.99   1287  142 0.1376 0.1780      5.2199      5.4341|
|  8:  2.4586 -  2.3520 0.98   1271  145 0.1338 0.1896       5.149      5.3888|
|  9:  2.3520 -  2.2618 0.98   1265  148 0.1303 0.1828       5.097      5.3236|
| 10:  2.2618 -  2.1840 1.00   1303  145 0.1223 0.1855      5.0194      5.2446|
| 11:  2.1840 -  2.1159 0.98   1271  136 0.1257 0.1938      5.0118      5.3329|
| 12:  2.1159 -  2.0555 0.98   1256  140 0.1218 0.1837       4.945      5.2474|
| 13:  2.0555 -  2.0016 0.99   1281  139 0.1226 0.1889      4.8247      5.1147|
| 14:  2.0016 -  1.9528 0.54    711   81 0.1102 0.1514      4.7013      4.8607|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8990 -  4.6616  1398   155  0.93   9.71   0.99     0.96       7676.36|
|  2:  4.6616 -  3.7190  1345   152  0.95   8.71   1.03     1.02      10370.31|
|  3:  3.7190 -  3.2545  1319   141  0.92  13.08   1.04     1.03      12542.14|
|  4:  3.2545 -  2.9594  1314   152  0.91  15.24   1.02     1.00      12358.42|
|  5:  2.9594 -  2.7487  1307   147  0.89  16.94   1.01     0.98       9330.57|
|  6:  2.7487 -  2.5876  1302   136  0.89  17.28   0.99     0.97       7742.62|
|  7:  2.5876 -  2.4586  1287   142  0.89  16.85   1.01     0.98       6855.58|
|  8:  2.4586 -  2.3520  1271   145  0.89  16.83   1.00     0.99       6048.04|
|  9:  2.3520 -  2.2618  1265   148  0.90  16.31   1.02     0.98       5486.76|
| 10:  2.2618 -  2.1840  1303   145  0.89  17.17   1.01     0.97       4992.35|
| 11:  2.1840 -  2.1159  1271   136  0.89  17.67   1.01     0.97       4936.40|
| 12:  2.1159 -  2.0555  1256   140  0.90  16.58   1.03     1.01       4497.05|
| 13:  2.0555 -  2.0016  1281   139  0.89  17.13   1.02     1.01       3542.95|
| 14:  2.0016 -  1.9528   711    81  0.92  14.13   1.01     0.98       2651.26|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2651.26 max =        12542.14 mean =      7262.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.23|
|phase err.(test): min =        0.00 max =           89.76 mean =        14.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.411)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    88.61   17.03    None  None   None       |
|    all(noH): 2823   0      0.83    88.61   17.03    None  None   None       |
|    Sol.    : 438    0      5.59    87.93   41.07    None  None   None       |
|    Mac.    : 2385   0      0.83    88.61   12.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.829 -   9.607:  984   |   5:    44.718 -  53.496:   85        |
|      1:     9.607 -  18.385: 1144   |   6:    53.496 -  62.274:   80        |
|      2:    18.385 -  27.163:  237   |   7:    62.274 -  71.052:   35        |
|      3:    27.163 -  35.941:  130   |   8:    71.052 -  79.830:   14        |
|      4:    35.941 -  44.718:  109   |   9:    79.830 -  88.608:    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)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 4.179
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 302
   mapped sites are within: 0.782 - 4.179

peak=    7.125 closest distance to " O   HOH Z 385 " =    1.858
peak=    6.879 closest distance to " O   HOH Z 390 " =    1.136
peak=    6.639 closest distance to " O   HOH Z 431 " =    1.930
peak=    6.347 closest distance to " O   HOH Z  65 " =    1.713
peak=    6.281 closest distance to " NE2 GLN A  11 " =    1.368
peak=    6.245 closest distance to " O   HOH Z 289 " =    1.393
peak=    5.978 closest distance to " O   HOH Z   7 " =    1.895
peak=    5.895 closest distance to " O   HOH Z 222 " =    1.423
peak=    5.837 closest distance to " O   HOH Z 427 " =    1.454
peak=    5.668 closest distance to " O   HOH Z 214 " =    1.884
peak=    5.313 closest distance to " O   HOH Z 142 " =    1.912
peak=    5.311 closest distance to " O   HOH Z 403 " =    1.607
peak=    5.257 closest distance to " O   HOH Z 417 " =    2.261
peak=    5.210 closest distance to " O   HOH Z 287 " =    1.968
peak=    5.199 closest distance to " O   HOH Z 130 " =    1.006
peak=    5.168 closest distance to " NH2 ARG A  56 " =    1.978
peak=    5.104 closest distance to " O   HOH Z  78 " =    1.723
peak=    5.031 closest distance to " O   HOH Z  29 " =    1.304
peak=    5.014 closest distance to " O   HOH Z 424 " =    1.310
peak=    5.004 closest distance to " CB  ARG A 275 " =    1.015
peak=    5.002 closest distance to " O   HOH Z 145 " =    1.728
peak=    4.950 closest distance to " CB  PRO A  54 " =    1.067
peak=    4.900 closest distance to " O   HOH Z 124 " =    1.531
peak=    4.898 closest distance to " O   HOH Z  63 " =    1.910
peak=    4.809 closest distance to " O   PRO A 198 " =    1.321
peak=    4.809 closest distance to " O   ASP A 286 " =    2.486
peak=    4.791 closest distance to " CG  PRO A  54 " =    1.286
peak=    4.769 closest distance to " O   HOH Z  49 " =    1.349
peak=    4.769 closest distance to " O   HOH Z 402 " =    1.614
peak=    4.764 closest distance to " CB  SER A   3 " =    1.300
peak=    4.736 closest distance to " O   HOH Z 427 " =    1.730
peak=    4.653 closest distance to " O   HOH Z 158 " =    1.440
peak=    4.642 closest distance to " O   HOH Z 232 " =    2.243
peak=    4.640 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.635 closest distance to " O   HOH Z 399 " =    0.866
peak=    4.630 closest distance to " O   HOH Z  28 " =    1.441
peak=    4.624 closest distance to " O   HOH Z 139 " =    1.507
peak=    4.617 closest distance to " O   HOH Z 193 " =    1.762
peak=    4.572 closest distance to " O   HOH Z 415 " =    1.220
peak=    4.556 closest distance to " O   HOH Z  63 " =    1.964
peak=    4.548 closest distance to " O   HOH Z 363 " =    1.089
peak=    4.536 closest distance to " OG BSER A 216 " =    1.072
peak=    4.528 closest distance to " O   HOH Z 293 " =    1.391
peak=    4.477 closest distance to " O   HOH Z 236 " =    1.516
peak=    4.466 closest distance to " CA  TYR A  30 " =    1.054
peak=    4.455 closest distance to " CB  GLN A 223 " =    1.439
peak=    4.422 closest distance to " O   HOH Z 380 " =    1.881
peak=    4.383 closest distance to " O   HOH Z 298 " =    1.968
peak=    4.380 closest distance to " O   HOH Z 112 " =    1.357
peak=    4.333 closest distance to " O   HOH Z 368 " =    3.638
peak=    4.317 closest distance to " O   HOH Z 414 " =    1.456
peak=    4.309 closest distance to " O   HOH Z  61 " =    1.522
peak=    4.272 closest distance to " O   HOH Z 369 " =    1.876
peak=    4.247 closest distance to " O   HOH Z 423 " =    1.867
peak=    4.220 closest distance to " O   HOH Z 416 " =    1.300
peak=    4.219 closest distance to " O   HOH Z 272 " =    1.881
peak=    4.217 closest distance to " O   HOH Z 358 " =    1.288
peak=    4.211 closest distance to " O   HOH Z 389 " =    1.402
peak=    4.195 closest distance to " CB  GLU A 128 " =    0.992
peak=    4.175 closest distance to " O   HOH Z 156 " =    3.326
peak=    4.171 closest distance to " O   HOH Z 217 " =    2.611
peak=    4.165 closest distance to " O   HOH Z 316 " =    2.954
peak=    4.156 closest distance to " O   HOH Z 245 " =    1.283
peak=    4.127 closest distance to " CB  ASN A 148 " =    1.372
peak=    4.121 closest distance to " O   HOH Z 392 " =    1.476
peak=    4.116 closest distance to " CB  GLN A 183 " =    1.100
peak=    4.110 closest distance to " O   HOH Z 371 " =    1.945
peak=    4.087 closest distance to " O   HOH Z 425 " =    1.505
peak=    4.064 closest distance to " O   HOH Z  91 " =    2.365
peak=    4.063 closest distance to " O   HOH Z 209 " =    2.305
peak=    4.044 closest distance to " O   HOH Z 302 " =    1.472
peak=    4.042 closest distance to " O   HOH Z 365 " =    2.654
peak=    4.036 closest distance to " O   HOH Z 244 " =    1.530
peak=    4.027 closest distance to " CB  TRP A 179 " =    1.339
peak=    3.996 closest distance to " O   HOH Z 352 " =    1.579
peak=    3.994 closest distance to " CD  ARG A  66 " =    2.397
peak=    3.994 closest distance to " O   HOH Z   2 " =    1.962
peak=    3.991 closest distance to " O   HOH Z 327 " =    1.840
peak=    3.984 closest distance to " O   HOH Z 412 " =    1.632
peak=    3.978 closest distance to " N   GLN A 278 " =    1.056
peak=    3.956 closest distance to " CG  PRO A 198 " =    1.301
peak=    3.948 closest distance to " O   HOH Z 166 " =    1.572
peak=    3.943 closest distance to " O   HOH Z 119 " =    1.451
peak=    3.941 closest distance to " O   HOH Z 413 " =    1.558
peak=    3.941 closest distance to " O   HOH Z 394 " =    1.816
peak=    3.917 closest distance to " NZ  LYS A 117 " =    1.207
peak=    3.897 closest distance to " NE1 TRP A 274 " =    1.053
peak=    3.888 closest distance to " N   ALA A   1 " =    1.325
peak=    3.886 closest distance to " NE2 GLN A  58 " =    3.736
peak=    3.883 closest distance to " O   HOH Z  88 " =    2.824
peak=    3.861 closest distance to " CB  SER A  63 " =    1.286
peak=    3.859 closest distance to " CG  PRO A  90 " =    1.224
peak=    3.853 closest distance to " O   HOH Z 250 " =    1.519
peak=    3.852 closest distance to " OG BSER A  99 " =    2.275
peak=    3.829 closest distance to " O   HOH Z 211 " =    1.247
peak=    3.826 closest distance to " CB  SER A 276 " =    1.160
peak=    3.821 closest distance to " CG1BVAL A 121 " =    2.226
peak=    3.813 closest distance to " N   GLU A   2 " =    1.283
peak=    3.798 closest distance to " NH1AARG A 145 " =    1.143
peak=    3.795 closest distance to " OD2 ASP A 286 " =    2.461
peak=    3.794 closest distance to " O   HOH Z 261 " =    1.807
peak=    3.788 closest distance to " O   HOH Z  65 " =    1.488
peak=    3.787 closest distance to " CB  TRP A 266 " =    1.068
peak=    3.779 closest distance to " OG BSER A 258 " =    0.965
peak=    3.761 closest distance to " CA  ALA A 299 " =    0.967
peak=    3.759 closest distance to " O   HOH Z   6 " =    2.077
peak=    3.755 closest distance to " O   HOH Z 258 " =    2.075
peak=    3.748 closest distance to " NE2 GLN A 278 " =    3.623
peak=    3.738 closest distance to " O   HOH Z 234 " =    3.665
peak=    3.736 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.716 closest distance to " CG2 THR A 221 " =    1.241
peak=    3.714 closest distance to " O   HOH Z 193 " =    1.909
peak=    3.713 closest distance to " O   HOH Z 215 " =    1.496
peak=    3.711 closest distance to " O   HOH Z 426 " =    1.129
peak=    3.710 closest distance to " N   ALA A   1 " =    2.403
peak=    3.702 closest distance to " NZ BLYS A 290 " =    0.925
peak=    3.696 closest distance to " O   HOH Z 329 " =    3.425
peak=    3.681 closest distance to " O   HOH Z 311 " =    1.572
peak=    3.681 closest distance to " O   HOH Z 422 " =    2.558
peak=    3.677 closest distance to " O   HOH Z   9 " =    1.116
peak=    3.671 closest distance to " CG  LEU A 167 " =    1.274
peak=    3.660 closest distance to " O   HOH Z 213 " =    1.601
peak=    3.654 closest distance to " CB  ALA A   1 " =    0.978
peak=    3.653 closest distance to " CG  TRP A 179 " =    2.142
peak=    3.645 closest distance to " OG BSER A 212 " =    2.710
peak=    3.638 closest distance to " O   HOH Z  44 " =    2.731
peak=    3.634 closest distance to " CB  LEU A 300 " =    0.926
peak=    3.620 closest distance to " N   SER A 210 " =    1.129
peak=    3.613 closest distance to " O   HOH Z 405 " =    1.489
peak=    3.611 closest distance to " CB  GLU A 152 " =    1.162
peak=    3.611 closest distance to " CE  MET A  93 " =    1.450
peak=    3.606 closest distance to " O   HOH Z 434 " =    1.391
peak=    3.605 closest distance to " O   HOH Z 147 " =    1.345
peak=    3.598 closest distance to " O   HOH Z  44 " =    1.684
peak=    3.575 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.573 closest distance to " CA  ASN A 215 " =    1.139
peak=    3.572 closest distance to " O   HOH Z 151 " =    1.736
peak=    3.557 closest distance to " CB  LYS A 290 " =    1.490
peak=    3.546 closest distance to " CG2AVAL A 121 " =    2.551
peak=    3.541 closest distance to " O   HOH Z 385 " =    3.321
peak=    3.533 closest distance to " CB  ARG A 190 " =    1.773
peak=    3.529 closest distance to " O   HOH Z  30 " =    1.866
peak=    3.528 closest distance to " O   HOH Z  50 " =    1.888
peak=    3.526 closest distance to " O   HOH Z 115 " =    1.535
peak=    3.525 closest distance to " CD  ARG A 138 " =    0.782
peak=    3.521 closest distance to " OD1 ASP A 286 " =    1.185
peak=    3.521 closest distance to " O   HOH Z 359 " =    1.459
peak=    3.520 closest distance to " O   HOH Z  28 " =    2.037
peak=    3.515 closest distance to " CD  LYS A 166 " =    1.600
peak=    3.506 closest distance to " O   HOH Z 345 " =    2.021
peak=    3.506 closest distance to " O   HOH Z 390 " =    2.475
peak=    3.505 closest distance to " OD1 ASN A  45 " =    1.219
peak=    3.502 closest distance to " O   HOH Z 222 " =    2.077
peak=    3.501 closest distance to " CA  LEU A 282 " =    1.094
peak=    3.494 closest distance to " O   HOH Z  47 " =    1.548
peak=    3.494 closest distance to " CA  PHE A 283 " =    1.271
peak=    3.493 closest distance to " O   HOH Z  57 " =    1.782
peak=    3.485 closest distance to " CB  ASN A 187 " =    1.008
peak=    3.480 closest distance to " CD1 ILE A 263 " =    1.294
peak=    3.477 closest distance to " O   ALA A 165 " =    1.271
peak=    3.472 closest distance to " CB  LYS A 117 " =    1.141
peak=    3.470 closest distance to " CB  VAL A 265 " =    1.284
peak=    3.469 closest distance to " O   HOH Z 422 " =    0.853
peak=    3.465 closest distance to " CA  ILE A 234 " =    1.012
peak=    3.463 closest distance to " CB  MET A 105 " =    1.286
peak=    3.459 closest distance to " CG  GLN A  11 " =    2.081
peak=    3.458 closest distance to " O   HOH Z  40 " =    2.057
peak=    3.452 closest distance to " O   ASN A 301 " =    2.148
peak=    3.452 closest distance to " O   HOH Z 384 " =    1.364
peak=    3.442 closest distance to " O   HOH Z 189 " =    2.074
peak=    3.441 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.430 closest distance to " O   HOH Z  59 " =    1.484
peak=    3.424 closest distance to " CB  ASP A 124 " =    0.978
peak=    3.423 closest distance to " CA  ARG A 195 " =    1.470
peak=    3.419 closest distance to " CB  GLU A 277 " =    1.050
peak=    3.418 closest distance to " OG  SER A  62 " =    3.012
peak=    3.411 closest distance to " O   HOH Z 225 " =    1.381
peak=    3.401 closest distance to " O   HOH Z 368 " =    1.939
peak=    3.396 closest distance to " O   HOH Z  32 " =    2.043
peak=    3.392 closest distance to " O   HOH Z 393 " =    1.401
peak=    3.392 closest distance to " ND2 ASN A 187 " =    1.604
peak=    3.387 closest distance to " O   HOH Z 106 " =    2.505
peak=    3.387 closest distance to " NE AARG A 275 " =    1.476
peak=    3.381 closest distance to " O   HOH Z  97 " =    1.909
peak=    3.378 closest distance to " CB  ALA A 114 " =    1.182
peak=    3.375 closest distance to " OG  SER A  22 " =    2.684
peak=    3.372 closest distance to " O   HOH Z 152 " =    2.125
peak=    3.372 closest distance to " O   HOH Z   7 " =    3.280
peak=    3.367 closest distance to " O   HOH Z 425 " =    2.220
peak=    3.361 closest distance to " CA  GLU A 152 " =    1.123
peak=    3.355 closest distance to " O   HOH Z 130 " =    2.428
peak=    3.354 closest distance to " O   HOH Z 435 " =    2.015
peak=    3.352 closest distance to " CD2 TRP A 179 " =    1.457
peak=    3.351 closest distance to " CG  LYS A 166 " =    1.373
peak=    3.350 closest distance to " O   ASN A  74 " =    1.527
peak=    3.349 closest distance to " O   GLY A 302 " =    2.326
peak=    3.345 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.340 closest distance to " NZ  LYS A 119 " =    1.350
peak=    3.339 closest distance to " O   HOH Z 419 " =    1.861
peak=    3.337 closest distance to " O   HOH Z 431 " =    1.188
peak=    3.327 closest distance to " CG2 THR A 220 " =    0.975
peak=    3.315 closest distance to " O   HOH Z 153 " =    3.661
peak=    3.315 closest distance to " O   HOH Z 423 " =    2.012
peak=    3.313 closest distance to " CB  GLU A 236 " =    1.388
peak=    3.312 closest distance to " CG1 ILE A 120 " =    1.432
peak=    3.302 closest distance to " O   HOH Z 119 " =    4.179
peak=    3.301 closest distance to " O   HOH Z 158 " =    3.000
peak=    3.295 closest distance to " CB  TYR A 116 " =    1.130
peak=    3.294 closest distance to " O   HOH Z 216 " =    1.446
peak=    3.293 closest distance to " CB  MET A 105 " =    1.063
peak=    3.291 closest distance to " O   HOH Z 311 " =    2.322
peak=    3.290 closest distance to " CE3 TRP A 150 " =    1.108
peak=    3.287 closest distance to " CG1 VAL A 202 " =    1.946
peak=    3.287 closest distance to " CZ  ARG A  14 " =    1.422
peak=    3.283 closest distance to " O   HOH Z  10 " =    1.722
peak=    3.282 closest distance to " CZ3 TRP A 274 " =    2.084
peak=    3.278 closest distance to " CA  ALA A  21 " =    1.169
peak=    3.275 closest distance to " OG1 THR A 246 " =    1.387
peak=    3.274 closest distance to " O   HOH Z  61 " =    1.657
peak=    3.274 closest distance to " O   HOH Z 313 " =    1.812
peak=    3.274 closest distance to " NZ  LYS A 119 " =    2.725
peak=    3.272 closest distance to " O   HOH Z 128 " =    2.102
peak=    3.269 closest distance to " N   ARG A 156 " =    1.349
peak=    3.266 closest distance to " CB  ASP A 298 " =    1.211
peak=    3.265 closest distance to " CA  ASN A 127 " =    0.998
peak=    3.265 closest distance to " CG1 ILE A  33 " =    1.252
peak=    3.263 closest distance to " O   HOH Z 340 " =    1.811
peak=    3.262 closest distance to " O   HOH Z 291 " =    1.458
peak=    3.260 closest distance to " O   HOH Z 156 " =    2.663
peak=    3.257 closest distance to " CB  ARG A 156 " =    0.980
peak=    3.257 closest distance to " O   HOH Z 288 " =    1.906
peak=    3.255 closest distance to " N   ASN A 127 " =    1.342
peak=    3.254 closest distance to " O   HOH Z  55 " =    1.753
peak=    3.248 closest distance to " OD1 ASN A  69 " =    2.519
peak=    3.244 closest distance to " O   HOH Z 227 " =    1.751
peak=    3.244 closest distance to " CB  SER A 212 " =    1.156
peak=    3.241 closest distance to " ND1 HIS A  81 " =    1.397
peak=    3.240 closest distance to " O   HOH Z 175 " =    1.930
peak=    3.237 closest distance to " O   HOH Z 116 " =    2.544
peak=    3.236 closest distance to " O   HOH Z 207 " =    2.258
peak=    3.235 closest distance to " O   HOH Z 424 " =    2.937
peak=    3.235 closest distance to " O   HOH Z  57 " =    1.230
peak=    3.231 closest distance to " O   HOH Z 104 " =    1.417
peak=    3.231 closest distance to " O   HOH Z 344 " =    3.101
peak=    3.230 closest distance to " O   HOH Z  17 " =    2.050
peak=    3.230 closest distance to " O   HOH Z   9 " =    2.074
peak=    3.228 closest distance to " CG2BVAL A  41 " =    1.013
peak=    3.224 closest distance to " CB  GLU A 277 " =    3.517
peak=    3.222 closest distance to " CB  MET A  40 " =    0.960
peak=    3.215 closest distance to " O   HOH Z  73 " =    1.608
peak=    3.211 closest distance to " CA  MET A 105 " =    0.782
peak=    3.211 closest distance to " OG BSER A 164 " =    2.061
peak=    3.207 closest distance to " O   HOH Z 258 " =    1.571
peak=    3.204 closest distance to " CG  ARG A 159 " =    0.815
peak=    3.200 closest distance to " O   HOH Z 155 " =    1.832
peak=    3.197 closest distance to " O   HOH Z 135 " =    1.951
peak=    3.195 closest distance to " CA  GLY A 136 " =    0.948
peak=    3.191 closest distance to " O   HOH Z  93 " =    1.817
peak=    3.190 closest distance to " O   HOH Z 214 " =    2.750
peak=    3.190 closest distance to " NH2AARG A 190 " =    1.445
peak=    3.188 closest distance to " N   SER A  97 " =    0.936
peak=    3.184 closest distance to " CB  ASP A 200 " =    0.963
peak=    3.182 closest distance to " O   HOH Z 263 " =    2.511
peak=    3.179 closest distance to " NH2 ARG A 219 " =    1.664
peak=    3.178 closest distance to " O   THR A 220 " =    1.660
peak=    3.177 closest distance to " CD  PRO A 243 " =    1.525
peak=    3.175 closest distance to " O   HOH Z 172 " =    2.203
peak=    3.174 closest distance to " O   HOH Z 423 " =    1.405
peak=    3.172 closest distance to " CB  ARG A  79 " =    1.173
peak=    3.171 closest distance to " CG  GLN A 240 " =    3.518
peak=    3.171 closest distance to " CG  LYS A 119 " =    1.038
peak=    3.170 closest distance to " CE3 TRP A 274 " =    1.329
peak=    3.170 closest distance to " CA  ALA A 233 " =    0.918
peak=    3.168 closest distance to " O   HOH Z 282 " =    1.553
peak=    3.164 closest distance to " O   ALA A   1 " =    1.689
peak=    3.161 closest distance to " OE2 GLU A  53 " =    2.022
peak=    3.158 closest distance to " O   HOH Z 189 " =    2.768
peak=    3.157 closest distance to " CD1 ILE A  33 " =    1.703
peak=    3.155 closest distance to " O   GLY A 147 " =    1.482
peak=    3.155 closest distance to " O   HOH Z  58 " =    1.563
peak=    3.149 closest distance to " OG1 THR A 221 " =    1.329
peak=    3.148 closest distance to " O   HOH Z 409 " =    2.148
peak=    3.144 closest distance to " CB  THR A  31 " =    1.525
peak=    3.132 closest distance to " O   HOH Z 255 " =    1.570
peak=    3.131 closest distance to " O   HOH Z 389 " =    2.676
peak=    3.122 closest distance to " CA  ALA A 158 " =    1.115
peak=    3.121 closest distance to " CB  PHE A 225 " =    1.382
peak=    3.116 closest distance to " CB  ASP A 140 " =    0.798
peak=    3.111 closest distance to " O   HOH Z 422 " =    2.381
peak=    3.108 closest distance to " CA  ASN A 217 " =    1.205
peak=    3.104 closest distance to " CE AMET A  47 " =    1.323
peak=    3.095 closest distance to " O   HOH Z 410 " =    1.756
peak=    3.093 closest distance to " CA  ALA A  51 " =    1.031
peak=    3.092 closest distance to " O   HOH Z 362 " =    1.653
peak=    3.087 closest distance to " CB  ARG A 138 " =    0.811
peak=    3.079 closest distance to " O   HOH Z 438 " =    2.445
peak=    3.069 closest distance to " O   HOH Z 326 " =    1.720
peak=    3.059 closest distance to " O   HOH Z 357 " =    1.631
peak=    3.057 closest distance to " CA  LEU A 101 " =    1.903
peak=    3.037 closest distance to " O   HOH Z 334 " =    1.789
peak=    3.019 closest distance to " O   HOH Z 406 " =    1.687

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.675 - 5.382
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.711 - 5.382

peak=   -4.574 closest distance to " O   HOH Z  60 " =    1.907
peak=   -4.545 closest distance to " O   HOH Z 409 " =    3.231
peak=   -4.476 closest distance to " O   HOH Z 385 " =    1.091
peak=   -4.392 closest distance to " CB  PRO A 243 " =    2.523
peak=   -4.242 closest distance to " CA  GLY A  98 " =    1.764
peak=   -4.227 closest distance to " O   PRO A 198 " =    1.169
peak=   -4.224 closest distance to " CB  ALA A 248 " =    2.004
peak=   -4.203 closest distance to " O   SER A  22 " =    2.589
peak=   -4.150 closest distance to " CD  ARG A  14 " =    3.159
peak=   -4.129 closest distance to " O   HOH Z 298 " =    0.966
peak=   -4.085 closest distance to " O   HOH Z 197 " =    3.263
peak=   -4.051 closest distance to " O   HOH Z 290 " =    1.024
peak=   -4.015 closest distance to " CD1 LEU A 255 " =    3.006
peak=   -3.994 closest distance to " O   HOH Z 185 " =    1.905
peak=   -3.923 closest distance to " N   THR A 157 " =    1.492
peak=   -3.896 closest distance to " CG  ASP A 231 " =    0.868
peak=   -3.883 closest distance to " N   ALA A   1 " =    0.908
peak=   -3.874 closest distance to " CZ  PHE A  59 " =    1.405
peak=   -3.871 closest distance to " O   HOH Z 438 " =    0.796
peak=   -3.850 closest distance to " O   HOH Z  88 " =    1.848
peak=   -3.844 closest distance to " O   HOH Z 195 " =    1.821
peak=   -3.821 closest distance to " CD  ARG A 156 " =    1.946
peak=   -3.774 closest distance to " OE1 GLU A 277 " =    2.179
peak=   -3.770 closest distance to " O   HOH Z  56 " =    1.905
peak=   -3.747 closest distance to " O   MET A  40 " =    2.809
peak=   -3.737 closest distance to " O   HOH Z  52 " =    1.030
peak=   -3.728 closest distance to " O   HOH Z  24 " =    1.127
peak=   -3.708 closest distance to " O   HOH Z 313 " =    1.223
peak=   -3.700 closest distance to " N   GLN A  58 " =    1.178
peak=   -3.698 closest distance to " NH2 ARG A 219 " =    1.831
peak=   -3.694 closest distance to " CD  GLN A  58 " =    0.944
peak=   -3.694 closest distance to " OD2 ASP A 171 " =    1.849
peak=   -3.693 closest distance to " CZ2 TRP A 274 " =    0.966
peak=   -3.674 closest distance to " OG BSER A 134 " =    1.457
peak=   -3.673 closest distance to " O   SER A 135 " =    1.613
peak=   -3.671 closest distance to " O   HOH Z  28 " =    1.782
peak=   -3.662 closest distance to " O   HOH Z 166 " =    1.317
peak=   -3.658 closest distance to " CG  MET A 105 " =    0.957
peak=   -3.648 closest distance to " O   HOH Z 415 " =    1.017
peak=   -3.640 closest distance to " O   ILE A  49 " =    1.667
peak=   -3.628 closest distance to " O   SER A  95 " =    1.156
peak=   -3.624 closest distance to " CB  ALA A 291 " =    2.170
peak=   -3.615 closest distance to " ND2 ASN A 209 " =    1.848
peak=   -3.615 closest distance to " O   HOH Z   1 " =    3.809
peak=   -3.615 closest distance to " O   HOH Z 122 " =    2.394
peak=   -3.612 closest distance to " O   HOH Z 416 " =    0.871
peak=   -3.612 closest distance to " CD2 TYR A 293 " =    1.747
peak=   -3.607 closest distance to " N   HIS A 115 " =    2.071
peak=   -3.590 closest distance to " O   HOH Z 372 " =    2.585
peak=   -3.589 closest distance to " OG  SER A  97 " =    2.130
peak=   -3.581 closest distance to " O   THR A 235 " =    1.406
peak=   -3.565 closest distance to " CD2 PHE A 130 " =    2.934
peak=   -3.561 closest distance to " NE2 GLN A  55 " =    0.811
peak=   -3.555 closest distance to " O   ARG A 145 " =    1.381
peak=   -3.545 closest distance to " CB  TYR A  15 " =    2.095
peak=   -3.541 closest distance to " CD1 TRP A 179 " =    1.179
peak=   -3.535 closest distance to " OD2 ASP A  27 " =    1.584
peak=   -3.532 closest distance to " O   HOH Z  13 " =    1.643
peak=   -3.526 closest distance to " O   ASN A 301 " =    1.407
peak=   -3.521 closest distance to " O   TRP A  70 " =    1.428
peak=   -3.520 closest distance to " CA  GLY A 302 " =    3.136
peak=   -3.519 closest distance to " O   HOH Z  90 " =    2.471
peak=   -3.519 closest distance to " O   HOH Z 429 " =    2.030
peak=   -3.518 closest distance to " CD  GLN A 223 " =    1.116
peak=   -3.514 closest distance to " CE3 TRP A 179 " =    1.155
peak=   -3.511 closest distance to " ND2 ASN A 249 " =    2.436
peak=   -3.510 closest distance to " O   HOH Z 425 " =    0.875
peak=   -3.506 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.503 closest distance to " O   HOH Z 393 " =    2.913
peak=   -3.491 closest distance to " CE3 TRP A  70 " =    2.120
peak=   -3.488 closest distance to " CD2 LEU A 237 " =    2.453
peak=   -3.488 closest distance to " CE2 TYR A 116 " =    2.975
peak=   -3.482 closest distance to " C   HIS A 108 " =    1.281
peak=   -3.480 closest distance to " O   HOH Z  43 " =    1.720
peak=   -3.473 closest distance to " O   HOH Z 359 " =    1.468
peak=   -3.472 closest distance to " OG  SER A 245 " =    1.122
peak=   -3.471 closest distance to " CG  ARG A 219 " =    2.375
peak=   -3.466 closest distance to " O   ALA A   1 " =    1.238
peak=   -3.463 closest distance to " C   ILE A 239 " =    1.957
peak=   -3.453 closest distance to " OG  SER A  87 " =    1.253
peak=   -3.449 closest distance to " O   HOH Z 388 " =    2.241
peak=   -3.435 closest distance to " O   HOH Z 352 " =    1.732
peak=   -3.433 closest distance to " O   HOH Z 231 " =    0.991
peak=   -3.433 closest distance to " CA  GLY A 241 " =    2.156
peak=   -3.432 closest distance to " O   ALA A 180 " =    1.107
peak=   -3.432 closest distance to " O   HOH Z 211 " =    1.311
peak=   -3.428 closest distance to " OD2 ASP A 191 " =    1.587
peak=   -3.423 closest distance to " CA  ASP A  27 " =    2.230
peak=   -3.420 closest distance to " O   HOH Z 316 " =    1.926
peak=   -3.414 closest distance to " O   SER A 216 " =    1.821
peak=   -3.414 closest distance to " O   ALA A  51 " =    1.356
peak=   -3.398 closest distance to " OG BSER A 210 " =    2.039
peak=   -3.396 closest distance to " O   HOH Z 236 " =    2.129
peak=   -3.396 closest distance to " N   ARG A 159 " =    1.717
peak=   -3.394 closest distance to " CG  GLU A 152 " =    1.937
peak=   -3.393 closest distance to " O   HOH Z 218 " =    3.638
peak=   -3.389 closest distance to " N   ALA A 248 " =    1.563
peak=   -3.386 closest distance to " ND2 ASN A 187 " =    1.311
peak=   -3.375 closest distance to " O   HOH Z  77 " =    1.746
peak=   -3.372 closest distance to " O   HOH Z 198 " =    1.938
peak=   -3.371 closest distance to " CB  ALA A  10 " =    2.288
peak=   -3.371 closest distance to " OG ASER A 216 " =    1.216
peak=   -3.357 closest distance to " O   GLY A  80 " =    2.554
peak=   -3.353 closest distance to " CE  LYS A  76 " =    3.063
peak=   -3.351 closest distance to " CG2 ILE A  20 " =    2.841
peak=   -3.349 closest distance to " OD1 ASN A 170 " =    2.393
peak=   -3.347 closest distance to " O   VAL A  67 " =    2.686
peak=   -3.335 closest distance to " NH2AARG A 275 " =    5.382
peak=   -3.326 closest distance to " O   HOH Z 426 " =    1.603
peak=   -3.324 closest distance to " O   HOH Z 377 " =    0.865
peak=   -3.321 closest distance to " CG  PHE A 283 " =    2.542
peak=   -3.321 closest distance to " CA  GLY A 203 " =    2.257
peak=   -3.318 closest distance to " N   GLN A  58 " =    1.800
peak=   -3.315 closest distance to " CB  PHE A 192 " =    1.642
peak=   -3.309 closest distance to " O   HOH Z   2 " =    0.870
peak=   -3.307 closest distance to " O   HOH Z   1 " =    1.129
peak=   -3.306 closest distance to " CZ  TYR A 169 " =    1.997
peak=   -3.304 closest distance to " O   PRO A 198 " =    1.037
peak=   -3.301 closest distance to " CE3 TRP A 274 " =    2.500
peak=   -3.300 closest distance to " CD2 TYR A  30 " =    2.678
peak=   -3.293 closest distance to " CG  GLN A  58 " =    1.270
peak=   -3.293 closest distance to " OG ASER A 134 " =    1.193
peak=   -3.291 closest distance to " CD1 LEU A 101 " =    2.243
peak=   -3.286 closest distance to " O   HOH Z 266 " =    4.416
peak=   -3.286 closest distance to " O   ALA A  34 " =    2.440
peak=   -3.282 closest distance to " OG BSER A  99 " =    1.382
peak=   -3.282 closest distance to " CA  TRP A  70 " =    2.375
peak=   -3.277 closest distance to " CE  MET A 105 " =    2.470
peak=   -3.271 closest distance to " O   PHE A 218 " =    1.430
peak=   -3.268 closest distance to " CD  LYS A 166 " =    2.395
peak=   -3.266 closest distance to " O   HOH Z  93 " =    1.713
peak=   -3.261 closest distance to " O   HOH Z  63 " =    2.858
peak=   -3.259 closest distance to " O   HOH Z 131 " =    4.226
peak=   -3.255 closest distance to " CG  GLN A  88 " =    0.830
peak=   -3.253 closest distance to " O   HOH Z 140 " =    1.550
peak=   -3.251 closest distance to " O   HOH Z 111 " =    2.257
peak=   -3.250 closest distance to " O   HOH Z 288 " =    1.337
peak=   -3.248 closest distance to " O   HOH Z  76 " =    1.117
peak=   -3.244 closest distance to " OG  SER A   3 " =    1.220
peak=   -3.241 closest distance to " CB  ALA A   7 " =    1.869
peak=   -3.237 closest distance to " C   GLY A  13 " =    1.035
peak=   -3.236 closest distance to " O   HOH Z 364 " =    1.171
peak=   -3.232 closest distance to " O   HOH Z 390 " =    1.120
peak=   -3.231 closest distance to " O   ILE A 120 " =    1.961
peak=   -3.226 closest distance to " O   HOH Z 422 " =    0.718
peak=   -3.225 closest distance to " O   HOH Z 251 " =    1.208
peak=   -3.224 closest distance to " O   PRO A 243 " =    2.394
peak=   -3.223 closest distance to " N   PRO A 163 " =    1.614
peak=   -3.223 closest distance to " CA  ALA A  34 " =    2.376
peak=   -3.223 closest distance to " O   HOH Z 125 " =    3.363
peak=   -3.220 closest distance to " OE1 GLN A 223 " =    2.297
peak=   -3.213 closest distance to " CE3 TRP A 123 " =    1.698
peak=   -3.213 closest distance to " O   HOH Z 231 " =    1.613
peak=   -3.212 closest distance to " OG  SER A  63 " =    1.231
peak=   -3.212 closest distance to " CB  ALA A  43 " =    2.081
peak=   -3.203 closest distance to " CD1 LEU A   5 " =    2.268
peak=   -3.193 closest distance to " OG  SER A  87 " =    1.743
peak=   -3.192 closest distance to " O   HOH Z 414 " =    1.637
peak=   -3.188 closest distance to " O   ASP A 162 " =    2.239
peak=   -3.186 closest distance to " O   HOH Z 437 " =    0.711
peak=   -3.186 closest distance to " O   HOH Z 351 " =    1.542
peak=   -3.186 closest distance to " O   HOH Z 352 " =    1.506
peak=   -3.183 closest distance to " CB  ASP A 132 " =    2.413
peak=   -3.180 closest distance to " OD1 ASN A 176 " =    1.533
peak=   -3.177 closest distance to " OXT GLY A 302 " =    3.005
peak=   -3.177 closest distance to " O   HOH Z  64 " =    1.083
peak=   -3.175 closest distance to " O   HOH Z 368 " =    2.531
peak=   -3.174 closest distance to " CB  ALA A 100 " =    1.824
peak=   -3.160 closest distance to " O   HOH Z 132 " =    1.168
peak=   -3.159 closest distance to " CD2 TYR A 116 " =    1.972
peak=   -3.151 closest distance to " O   HOH Z  49 " =    1.637
peak=   -3.151 closest distance to " O   HOH Z  37 " =    1.451
peak=   -3.147 closest distance to " C   ASN A 285 " =    2.069
peak=   -3.143 closest distance to " CB  SER A  62 " =    2.424
peak=   -3.141 closest distance to " O   HOH Z  14 " =    1.561
peak=   -3.138 closest distance to " O   HOH Z 217 " =    1.894
peak=   -3.137 closest distance to " CG1 VAL A 230 " =    1.884
peak=   -3.137 closest distance to " O   HOH Z 412 " =    5.120
peak=   -3.132 closest distance to " N   VAL A  72 " =    1.786
peak=   -3.123 closest distance to " CE  LYS A 166 " =    1.115
peak=   -3.123 closest distance to " OG  SER A 206 " =    1.869
peak=   -3.122 closest distance to " OD2 ASP A 171 " =    1.386
peak=   -3.118 closest distance to " CG  GLU A   2 " =    2.043
peak=   -3.100 closest distance to " ND2 ASN A  60 " =    1.320
peak=   -3.093 closest distance to " OH  TYR A 247 " =    1.492
peak=   -3.087 closest distance to " CD2 TRP A 150 " =    0.920
peak=   -3.079 closest distance to " OD1 ASN A 148 " =    1.710
peak=   -3.076 closest distance to " O   HOH Z 137 " =    1.376
peak=   -3.071 closest distance to " O   HOH Z 292 " =    1.793
peak=   -3.068 closest distance to " O   GLU A 152 " =    1.470
peak=   -3.066 closest distance to " O   HOH Z  51 " =    1.623
peak=   -3.043 closest distance to " CG2 THR A 178 " =    1.963
peak=   -3.037 closest distance to " CG  ARG A 259 " =    2.792
peak=   -3.027 closest distance to " CD2 LEU A 237 " =    2.642
peak=   -3.022 closest distance to " CB  LYS A 289 " =    2.930
peak=   -3.010 closest distance to " CB  ALA A 114 " =    2.205

================= 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    :  0.4397 0.4343   6.257541e+00   6.246100e+00
   1_bss:  0.4275 0.4225   6.248044e+00   6.229462e+00
   1_xyz:  0.3617 0.3895   6.138425e+00   6.187025e+00
   1_adp:  0.3328 0.3992   6.094360e+00   6.193793e+00
   1_occ:  0.3325 0.3994   6.093656e+00   6.193655e+00
   2_bss:  0.3330 0.3994   6.096565e+00   6.195224e+00
   2_xyz:  0.2695 0.3377   5.915714e+00   6.057112e+00
   2_adp:  0.2464 0.3256   5.858670e+00   6.030798e+00
   2_occ:  0.2462 0.3253   5.858156e+00   6.030792e+00
   3_bss:  0.2453 0.3218   5.851590e+00   6.024193e+00
   3_xyz:  0.2032 0.2661   5.673211e+00   5.872342e+00
   3_adp:  0.1915 0.2464   5.614328e+00   5.808972e+00
   3_occ:  0.1911 0.2455   5.612622e+00   5.806828e+00
   4_bss:  0.1906 0.2440   5.610078e+00   5.803338e+00
   4_xyz:  0.1544 0.2028   5.416010e+00   5.631015e+00
   4_adp:  0.1466 0.1959   5.374201e+00   5.595863e+00
   4_occ:  0.1465 0.1956   5.373603e+00   5.595357e+00
   5_bss:  0.1468 0.1952   5.373302e+00   5.593420e+00
   5_xyz:  0.1264 0.1722   5.240457e+00   5.471238e+00
   5_adp:  0.1223 0.1681   5.211553e+00   5.444481e+00
   5_occ:  0.1222 0.1680   5.211196e+00   5.444067e+00
   5_bss:  0.1222 0.1680   5.211196e+00   5.444067e+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:  0.357  34.763  -3.412   3.073  -1.113   0.000  -0.000  -0.000
   1_xyz:  0.357  34.763  -3.412   3.073  -1.113   0.000  -0.000  -0.000
   1_adp:  0.357  34.763  -3.412   3.073  -1.113   0.000  -0.000  -0.000
   1_occ:  0.357  34.763  -3.412   3.073  -1.113   0.000  -0.000  -0.000
   2_bss:  0.355  49.292  -1.723   1.452  -0.505   0.000  -0.000  -0.000
   2_xyz:  0.355  49.292  -1.723   1.452  -0.505   0.000  -0.000  -0.000
   2_adp:  0.355  49.292  -1.723   1.452  -0.505   0.000  -0.000  -0.000
   2_occ:  0.355  49.292  -1.723   1.452  -0.505   0.000  -0.000  -0.000
   3_bss:  0.346  57.292  -1.240  -0.383  -0.255  -0.000  -0.000  -0.000
   3_xyz:  0.346  57.292  -1.240  -0.383  -0.255  -0.000  -0.000  -0.000
   3_adp:  0.346  57.292  -1.240  -0.383  -0.255  -0.000  -0.000  -0.000
   3_occ:  0.346  57.292  -1.240  -0.383  -0.255  -0.000  -0.000  -0.000
   4_bss:  0.325  43.579  -2.014  -1.605  -0.776  -0.000  -0.000  -0.000
   4_xyz:  0.325  43.579  -2.014  -1.605  -0.776  -0.000  -0.000  -0.000
   4_adp:  0.325  43.579  -2.014  -1.605  -0.776  -0.000  -0.000  -0.000
   4_occ:  0.325  43.579  -2.014  -1.605  -0.776  -0.000  -0.000  -0.000
   5_bss:  0.325  43.579  -2.251  -2.270  -1.078  -0.000  -0.000  -0.000
   5_xyz:  0.325  43.579  -2.251  -2.270  -1.078  -0.000  -0.000  -0.000
   5_adp:  0.325  43.579  -2.251  -2.270  -1.078  -0.000  -0.000  -0.000
   5_occ:  0.325  43.579  -2.251  -2.270  -1.078  -0.000  -0.000  -0.000
   5_bss:  0.325  43.550  -2.221  -2.241  -1.049  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.583 0.5155  0.7057    62456.993
   1_bss:  49.660 0.5257  0.7059    58697.831
   1_xyz:  45.204 0.5799  0.7636    48545.674
   1_adp:  45.759 0.5728  0.7562    49802.353
   1_occ:  45.771 0.5727  0.7556    49868.352
   2_bss:  45.650 0.5743  0.7670    49928.564
   2_xyz:  36.086 0.6885  0.9099    32021.070
   2_adp:  34.098 0.7118  0.9226    29537.119
   2_occ:  34.113 0.7116  0.9219    29508.983
   3_bss:  33.684 0.7161  0.9159    28712.244
   3_xyz:  26.789 0.7922  0.9804    18617.751
   3_adp:  24.327 0.8188  0.9920    15848.217
   3_occ:  24.249 0.8196  0.9921    15733.870
   4_bss:  24.155 0.8203  0.9619    15537.355
   4_xyz:  19.511 0.8660  0.9935    10639.924
   4_adp:  18.542 0.8757  0.9957     9900.366
   4_occ:  18.526 0.8758  0.9955     9874.639
   5_bss:  18.479 0.8762  0.9815     9822.984
   5_xyz:  15.829 0.8994  0.9913     7593.426
   5_adp:  15.195 0.9051  0.9891     7272.527
   5_occ:  15.187 0.9052  0.9891     7262.840
   5_bss:  15.187 0.9052  0.9891     7262.840
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.106   1.8719e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.106   1.8719e-01
   1_xyz:   1.351  0.010  0.090 14.989  0.005  4.102   9.6551e-02
   1_adp:   1.351  0.010  0.090 14.989  0.005  4.102   9.6551e-02
   1_occ:   1.351  0.010  0.090 14.989  0.005  4.102   9.6551e-02
   2_bss:   1.351  0.010  0.090 14.989  0.005  4.102   9.6551e-02
   2_xyz:   1.425  0.011  0.102 15.505  0.006  4.101   1.1698e-01
   2_adp:   1.425  0.011  0.102 15.505  0.006  4.101   1.1698e-01
   2_occ:   1.425  0.011  0.102 15.505  0.006  4.101   1.1698e-01
   3_bss:   1.425  0.011  0.102 15.505  0.006  4.101   1.1698e-01
   3_xyz:   0.970  0.007  0.070 14.254  0.004  4.107   6.2610e-02
   3_adp:   0.970  0.007  0.070 14.254  0.004  4.107   6.2610e-02
   3_occ:   0.970  0.007  0.070 14.254  0.004  4.107   6.2610e-02
   4_bss:   0.970  0.007  0.070 14.254  0.004  4.107   6.2610e-02
   4_xyz:   0.920  0.005  0.068 14.217  0.003  4.109   5.2787e-02
   4_adp:   0.920  0.005  0.068 14.217  0.003  4.109   5.2787e-02
   4_occ:   0.920  0.005  0.068 14.217  0.003  4.109   5.2787e-02
   5_bss:   0.920  0.005  0.068 14.217  0.003  4.109   5.2787e-02
   5_xyz:   0.933  0.005  0.067 14.378  0.004  4.107   5.3244e-02
   5_adp:   0.933  0.005  0.067 14.378  0.004  4.107   5.3244e-02
   5_occ:   0.933  0.005  0.067 14.378  0.004  4.107   5.3244e-02
   5_bss:   0.933  0.005  0.067 14.378  0.004  4.107   5.3244e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.677   2.3818e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.677   2.3818e-01
   1_xyz:   8.917  0.097  0.369 83.547  0.041  2.136   8.3791e-02
   1_adp:   8.917  0.097  0.369 83.547  0.041  2.136   8.3791e-02
   1_occ:   8.917  0.097  0.369 83.547  0.041  2.136   8.3791e-02
   2_bss:   8.917  0.097  0.369 83.547  0.041  2.136   8.3791e-02
   2_xyz:   8.839  0.049  0.306 76.348  0.043  1.995   1.0171e-01
   2_adp:   8.839  0.049  0.306 76.348  0.043  1.995   1.0171e-01
   2_occ:   8.839  0.049  0.306 76.348  0.043  1.995   1.0171e-01
   3_bss:   8.839  0.049  0.306 76.348  0.043  1.995   1.0171e-01
   3_xyz:   6.470  0.062  0.225 78.617  0.018  2.332   1.1954e-01
   3_adp:   6.470  0.062  0.225 78.617  0.018  2.332   1.1954e-01
   3_occ:   6.470  0.062  0.225 78.617  0.018  2.332   1.1954e-01
   4_bss:   6.470  0.062  0.225 78.617  0.018  2.332   1.1954e-01
   4_xyz:   7.669  0.038  0.221 76.967  0.035  2.326   3.4221e-02
   4_adp:   7.669  0.038  0.221 76.967  0.035  2.326   3.4221e-02
   4_occ:   7.669  0.038  0.221 76.967  0.035  2.326   3.4221e-02
   5_bss:   7.669  0.038  0.221 76.967  0.035  2.326   3.4221e-02
   5_xyz:   7.012  0.037  0.189 83.001  0.033  2.338   3.7235e-02
   5_adp:   7.012  0.037  0.189 83.001  0.033  2.338   3.7235e-02
   5_occ:   7.012  0.037  0.189 83.001  0.033  2.338   3.7235e-02
   5_bss:   7.012  0.037  0.189 83.001  0.033  2.338   3.7235e-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: 107.94   0.00  18.21  96.53   0.00  15.34 107.94   0.00  33.82
   1_occ: 107.94   0.00  18.21  96.53   0.00  15.34 107.94   0.00  33.82
   2_bss: 107.94   0.00  18.21  96.53   0.00  15.34 107.94   0.00  33.82
   2_xyz: 107.94   0.00  18.21  96.53   0.00  15.34 107.94   0.00  33.82
   2_adp: 104.63   0.00  18.00  92.85   0.00  14.34 104.63   0.00  37.88
   2_occ: 104.63   0.00  18.00  92.85   0.00  14.34 104.63   0.00  37.88
   3_bss: 104.63   0.00  18.00  92.85   0.00  14.34 104.63   0.00  37.88
   3_xyz: 104.63   0.00  18.00  92.85   0.00  14.34 104.63   0.00  37.88
   3_adp:  94.75   0.00  17.32  90.84   0.00  13.32  94.75   5.44  39.08
   3_occ:  94.75   0.00  17.32  90.84   0.00  13.32  94.75   5.44  39.08
   4_bss:  94.75   0.00  17.32  90.84   0.00  13.32  94.75   5.44  39.08
   4_xyz:  94.75   0.00  17.32  90.84   0.00  13.32  94.75   5.44  39.08
   4_adp:  87.50   0.00  17.18  85.99   0.00  12.90  87.50   5.47  40.53
   4_occ:  87.50   0.00  17.18  85.99   0.00  12.90  87.50   5.47  40.53
   5_bss:  87.50   0.00  17.18  85.99   0.00  12.90  87.50   5.47  40.53
   5_xyz:  87.50   0.00  17.18  85.99   0.00  12.90  87.50   5.47  40.53
   5_adp:  88.64   0.86  17.06  88.64   0.86  12.64  87.96   5.62  41.10
   5_occ:  88.64   0.86  17.06  88.64   0.86  12.64  87.96   5.62  41.10
   5_bss:  88.61   0.83  17.03  88.61   0.83  12.61  87.93   5.59  41.07
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.565    0.017    0.255
   1_adp:    1.565    0.017    0.255
   1_occ:    1.565    0.017    0.255
   2_bss:    1.565    0.017    0.255
   2_xyz:    1.572    0.016    0.579
   2_adp:    1.572    0.016    0.579
   2_occ:    1.572    0.016    0.579
   3_bss:    1.572    0.016    0.579
   3_xyz:    1.652    0.055    0.648
   3_adp:    1.652    0.055    0.648
   3_occ:    1.652    0.055    0.648
   4_bss:    1.652    0.055    0.648
   4_xyz:    1.682    0.058    0.728
   4_adp:    1.682    0.058    0.728
   4_occ:    1.682    0.058    0.728
   5_bss:    1.682    0.058    0.728
   5_xyz:    1.679    0.071    0.775
   5_adp:    1.679    0.071    0.775
   5_occ:    1.679    0.071    0.775
   5_bss:    1.679    0.071    0.775
------------------------------------------------------------------------

CPU time actual refinement: 349.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/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_487/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_487/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.83 
  Macro-tasks:
    bulk solvent and scale       = 39.57  
    individual site refinement   = 153.67 
    weights calculation          = 29.77  
    collect and process          = 6.55   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 229.65 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 112.51 
    alpha_beta                      = 8.47   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.75 
    fmodel                         = 6.68   
    r_factors                      = 0.20   
    phase_errors                   = 10.62  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 265.98 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.836 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    670 calls, 112.15 s
gradients_fft:          615 calls, 109.15 s

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

# Date 2008-01-16 Time 04:56:27 PST -0800 (1200488187.93 s)
Start R-work = 0.4397, R-free = 0.4343 (no bulk solvent and anisotropic scale)
Final R-work = 0.1455, R-free = 0.1865 (no bulk solvent and anisotropic scale)

Start R-work = 0.4275, R-free = 0.4225
Final R-work = 0.1222, R-free = 0.1680