# Date 2008-01-16 Time 05:28:26 PST -0800 (1200490106.23 s)
#phil __OFF__

Command line arguments: "../747.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21681
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 747

-------------------------------------------------------------------------------
  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: (70.6012, 45.9914, 88.5498, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.96359
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922704

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1485
                             d_min =   1.9636

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: (70.6012, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1485 1.96359
Completeness in resolution range: 0.925363
Completeness with d_max=infinity: 0.922704

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1489 -  4.2031 [2220/2246]  1997   223  10.0%
  bin  2:  4.2031 -  3.3480 [2141/2161]  1930   211   9.9%
  bin  3:  3.3480 -  2.9283 [2101/2120]  1892   209   9.9%
  bin  4:  2.9283 -  2.6621 [2102/2132]  1881   221  10.5%
  bin  5:  2.6621 -  2.4722 [2075/2094]  1871   204   9.8%
  bin  6:  2.4722 -  2.3270 [2072/2097]  1864   208  10.0%
  bin  7:  2.3270 -  2.2108 [2046/2074]  1842   204  10.0%
  bin  8:  2.2108 -  2.1148 [2065/2101]  1854   211  10.2%
  bin  9:  2.1148 -  2.0336 [2005/2078]  1817   188   9.4%
  bin 10:  2.0336 -  1.9636 [ 762/2066]   682    80  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/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:
        1.69 -     2.33: 28
        2.33 -     2.97: 1772
        2.97 -     3.62: 4565
        3.62 -     4.26: 9115
        4.26 -     4.90: 12711
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.688 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.700 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.800 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.828 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28186 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_747/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/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 = 70.60125 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4687   r_free= 0.4719   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.285639                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.3810 0.3606      6.6019      6.5331|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.4054 0.4115      6.8171      6.8043|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.4300 0.4128      6.6645      6.6481|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.4702 0.4948      6.5296      6.5353|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.5038 0.4823      6.3575      6.3952|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.4979 0.5371      6.2634      6.2075|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.4985 0.5149      6.2328      6.1821|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.5262 0.5337      6.1718       6.159|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.5066 0.5221      6.1194      6.2103|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.5219 0.5512      6.0739      6.0869|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.5146 0.4843      6.0237      6.0244|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.5174 0.5275      5.9351      5.9405|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.5080 0.4920      5.8908      5.7863|
| 14:  2.0126 -  1.9636 0.23    298   34 0.5362 0.5174       5.857      5.8743|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.6887  1438   158  0.74  30.75   0.81     0.78      61669.23|
|  2:  4.6887 -  3.7400  1391   158  0.71  34.54   0.89     0.81     107153.60|
|  3:  3.7400 -  3.2727  1368   149  0.57  46.33   0.92     0.75     120598.15|
|  4:  3.2727 -  2.9759  1351   153  0.45  55.81   0.89     0.63     115037.03|
|  5:  2.9759 -  2.7640  1351   149  0.37  61.70   0.86     0.54      87716.43|
|  6:  2.7640 -  2.6019  1340   146  0.34  64.65   0.89     0.48      76508.40|
|  7:  2.6019 -  2.4722  1332   155  0.33  65.22   0.91     0.46      67865.25|
|  8:  2.4722 -  2.3650  1325   151  0.31  67.05   0.89     0.46      62589.40|
|  9:  2.3650 -  2.2742  1313   140  0.31  66.57   0.91     0.46      57724.83|
| 10:  2.2742 -  2.1960  1354   147  0.32  66.35   0.91     0.47      50797.19|
| 11:  2.1960 -  2.1275  1318   147  0.29  68.04   0.94     0.45      50458.82|
| 12:  2.1275 -  2.0669  1306   141  0.29  68.22   0.91     0.47      44598.00|
| 13:  2.0669 -  2.0126  1145   131  0.29  68.04   0.94     0.49      39055.93|
| 14:  2.0126 -  1.9636   298    34  0.41  59.59   0.94     0.58      28362.73|
|alpha:            min =        0.45 max =            0.81 mean =         0.56|
|beta:             min =    28362.73 max =       120598.15 mean =     72318.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.33|
|phase err.(test): min =        0.00 max =           89.82 mean =        58.82|
|-----------------------------------------------------------------------------|

============================== 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 = 18.368593             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.831   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.021245              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.983   (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 |  1.688 -  2.009:       11 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.009 -  2.330:       17 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.330 -  2.651:       67 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.651 -  2.973:     1705 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.973 -  3.294:     1910 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.294 -  3.615:     2655 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.615 -  3.936:     4710 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.936 -  4.258:     4405 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.258 -  4.579:     5777 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.579 -  4.900:     6934 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.178 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.688 |       0.400 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4687   r_free= 0.4719   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.285639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4580   r_free= 0.4661   ksol= 0.33   Bsol= 50.00   scale= 0.930   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,1.41,4.21,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.278651                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.458159             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.732   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.358703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.602   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4580      final r-factor (work) = 0.3485          |
| start r-factor (free) = 0.4661      final r-factor (free) = 0.3903          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.5233 = 14.46 * 0.50 * 6.2726 + 1.00 * 0.1781                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.6762 = 14.46 * 0.50 * 6.1590 + 1.00 * 0.1524                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3485      final r-factor (work) = 0.3170          |
| start r-factor (free) = 0.3903      final r-factor (free) = 0.4067          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3745 = 1.36 * 1.00 * 6.1590 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2234 = 1.36 * 1.00 * 6.0372 + 1.00 * 0.0207                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.02   19.12    None  None   None       |
|    all(noH): 2823   0      0.00    93.02   19.12    None  None   None       |
|    Sol.    : 438    0      0.00    93.02   40.06    None  None   None       |
|    Mac.    : 2385   0      0.00    74.27   15.27    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 -   9.302:  808   |   5:    46.510 -  55.812:   91        |
|      1:     9.302 -  18.604:  893   |   6:    55.812 -  65.113:   47        |
|      2:    18.604 -  27.906:  530   |   7:    65.113 -  74.415:   32        |
|      3:    27.906 -  37.208:  244   |   8:    74.415 -  83.717:   12        |
|      4:    37.208 -  46.510:  158   |   9:    83.717 -  93.019:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3170 r_free = 0.4067             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3169 r_free = 0.4080             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3169   r_free= 0.4080   ksol= 0.33   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.99,1.41,4.21,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.046264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3156   r_free= 0.4054   ksol= 0.35   Bsol= 75.05   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.44,1.95,-0.00,0.00,0.00); trace/3= -0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.046736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.059736              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.081  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460483              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.505  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3156      final r-factor (work) = 0.2617          |
| start r-factor (free) = 0.4054      final r-factor (free) = 0.3397          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4452 = 6.06 * 0.50 * 6.0375 + 1.00 * 0.1524                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2029 = 6.06 * 0.50 * 5.9849 + 1.00 * 0.0694                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2617      final r-factor (work) = 0.2508          |
| start r-factor (free) = 0.3397      final r-factor (free) = 0.3253          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7763 = 0.46 * 1.00 * 5.9849 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7437 = 0.46 * 1.00 * 5.8784 + 1.00 * 0.0368                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.19  18.75    None  None   None       |
|    all(noH): 2823   0      0.00    106.19  18.75    None  None   None       |
|    Sol.    : 438    0      1.59    91.66   40.28    None  None   None       |
|    Mac.    : 2385   0      0.00    106.19  14.80    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 -  10.619:  995   |   5:    53.096 -  63.715:   59        |
|      1:    10.619 -  21.238:  972   |   6:    63.715 -  74.334:   31        |
|      2:    21.238 -  31.858:  403   |   7:    74.334 -  84.953:   14        |
|      3:    31.858 -  42.477:  219   |   8:    84.953 -  95.572:    5        |
|      4:    42.477 -  53.096:  124   |   9:    95.572 - 106.192:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2508 r_free = 0.3253             target_work(ml) = 5.862         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2506 r_free = 0.3251             target_work(ml) = 5.861         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2506   r_free= 0.3251   ksol= 0.35   Bsol= 75.05   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,-0.44,1.95,-0.00,0.00,0.00); trace/3= -0.04                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.861366                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2510   r_free= 0.3253   ksol= 0.35   Bsol= 73.86   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.98,1.09,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.861821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.171262              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.524485              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.668   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2510      final r-factor (work) = 0.1880          |
| start r-factor (free) = 0.3253      final r-factor (free) = 0.2438          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2089 = 6.17 * 0.50 * 5.8787 + 1.00 * 0.0694                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.8316 = 6.17 * 0.50 * 5.7524 + 1.00 * 0.0818                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1880      final r-factor (work) = 0.1843          |
| start r-factor (free) = 0.2438      final r-factor (free) = 0.2410          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0322 = 0.52 * 1.00 * 5.7524 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2143 = 0.52 * 1.00 * 5.5795 + 1.00 * 0.2880                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.94  18.81    None  None   None       |
|    all(noH): 2823   0      0.00    104.94  18.81    None  None   None       |
|    Sol.    : 438    0      3.48    91.71   40.54    None  None   None       |
|    Mac.    : 2385   0      0.00    104.94  14.82    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 -  10.494:  972   |   5:    52.469 -  62.963:   63        |
|      1:    10.494 -  20.988: 1003   |   6:    62.963 -  73.457:   30        |
|      2:    20.988 -  31.481:  387   |   7:    73.457 -  83.950:   16        |
|      3:    31.481 -  41.975:  219   |   8:    83.950 -  94.444:    5        |
|      4:    41.975 -  52.469:  127   |   9:    94.444 - 104.938:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1843 r_free = 0.2410             target_work(ml) = 5.574         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1838 r_free = 0.2406             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1838   r_free= 0.2406   ksol= 0.35   Bsol= 73.86   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-0.98,1.09,-0.00,0.00,0.00); trace/3= -0.52                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.571959                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1834   r_free= 0.2396   ksol= 0.33   Bsol= 60.67   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.18,-0.06,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.570600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.261274              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.409  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663056              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 86.711   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2396      final r-factor (free) = 0.2255          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1840 = 3.26 * 0.50 * 5.5820 + 1.00 * 0.0818                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0692 = 3.26 * 0.50 * 5.5249 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1648      final r-factor (work) = 0.1425          |
| start r-factor (free) = 0.2255      final r-factor (free) = 0.1966          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6823 = 0.66 * 1.00 * 5.5249 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6134 = 0.66 * 1.00 * 5.4329 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.71   18.22    None  None   None       |
|    all(noH): 2823   0      0.00    93.71   18.22    None  None   None       |
|    Sol.    : 438    0      6.18    93.71   44.16    None  None   None       |
|    Mac.    : 2385   0      0.00    80.33   13.46    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 -   9.371:  826   |   5:    46.855 -  56.226:   92        |
|      1:     9.371 -  18.742: 1216   |   6:    56.226 -  65.597:   84        |
|      2:    18.742 -  28.113:  301   |   7:    65.597 -  74.968:   45        |
|      3:    28.113 -  37.484:  126   |   8:    74.968 -  84.339:   14        |
|      4:    37.484 -  46.855:  116   |   9:    84.339 -  93.710:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1425 r_free = 0.1966             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1423 r_free = 0.1967             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1423   r_free= 0.1967   ksol= 0.33   Bsol= 60.67   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.27,-2.18,-0.06,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.361835                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1426   r_free= 0.1968   ksol= 0.33   Bsol= 67.77   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.60,-0.38,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.361449                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.290507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.520  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.662512              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.671  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1426      final r-factor (work) = 0.1297          |
| start r-factor (free) = 0.1968      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2829 = 2.29 * 0.50 * 5.4337 + 1.00 * 0.0600                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1538 = 2.29 * 0.50 * 5.3234 + 1.00 * 0.0572                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1297      final r-factor (work) = 0.1267          |
| start r-factor (free) = 0.1795      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5382 = 0.66 * 1.00 * 5.3234 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8662 = 0.66 * 1.00 * 5.2627 + 1.00 * 0.3796                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.78   18.04    None  None   None       |
|    all(noH): 2823   0      0.00    93.78   18.04    None  None   None       |
|    Sol.    : 438    0      6.00    93.78   44.21    None  None   None       |
|    Mac.    : 2385   0      0.00    81.40   13.23    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 -   9.378:  888   |   5:    46.892 -  56.271:   94        |
|      1:     9.378 -  18.757: 1185   |   6:    56.271 -  65.649:   82        |
|      2:    18.757 -  28.135:  275   |   7:    65.649 -  75.027:   48        |
|      3:    28.135 -  37.514:  120   |   8:    75.027 -  84.406:   13        |
|      4:    37.514 -  46.892:  114   |   9:    84.406 -  93.784:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1267 r_free = 0.1763             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1266 r_free = 0.1763             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1763   ksol= 0.33   Bsol= 67.77   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.60,-0.38,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252903                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.0942 0.1282      5.3644      5.5766|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.0858 0.1234      5.4647      5.7315|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.1190 0.1732      5.5669      5.8912|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.1475 0.1963      5.5837      5.7313|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.1567 0.1973      5.4649      5.6934|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.1460 0.2230      5.3339      5.5804|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.1460 0.1797      5.2933      5.4259|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.1435 0.1972      5.2082      5.4661|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.1411 0.1979      5.1567      5.4163|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.1296 0.1765      5.0367      5.2442|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.1301 0.2051      5.0449      5.4146|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.1331 0.1991      4.9663      5.2106|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.1172 0.1654       4.824      5.0059|
| 14:  2.0126 -  1.9636 0.23    298   34 0.1059 0.1674      4.7082      4.9805|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.6887  1438   158  0.94   9.10   0.97     0.94       7185.57|
|  2:  4.6887 -  3.7400  1391   158  0.95   8.54   1.02     1.01       9959.06|
|  3:  3.7400 -  3.2727  1368   149  0.92  13.22   1.04     1.04      12556.37|
|  4:  3.2727 -  2.9759  1351   153  0.89  16.92   1.02     1.00      13431.41|
|  5:  2.9759 -  2.7640  1351   149  0.88  18.56   1.00     0.98      10964.43|
|  6:  2.7640 -  2.6019  1340   146  0.87  19.05   0.98     0.95       9024.11|
|  7:  2.6019 -  2.4722  1332   155  0.88  18.75   1.00     0.97       8326.08|
|  8:  2.4722 -  2.3650  1325   151  0.88  18.24   0.99     0.96       6793.98|
|  9:  2.3650 -  2.2742  1313   140  0.88  18.44   1.00     0.95       6312.83|
| 10:  2.2742 -  2.1960  1354   147  0.89  17.61   1.00     0.97       5147.54|
| 11:  2.1960 -  2.1275  1318   147  0.88  18.30   0.99     0.93       5331.28|
| 12:  2.1275 -  2.0669  1306   141  0.89  17.87   1.00     1.00       4682.87|
| 13:  2.0669 -  2.0126  1145   131  0.88  18.15   0.99     0.96       3743.25|
| 14:  2.0126 -  1.9636   298    34  0.93  13.08   0.99     0.97       2752.91|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2752.91 max =        13431.41 mean =      7941.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.21|
|phase err.(test): min =        0.00 max =           88.54 mean =        15.67|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1763   ksol= 0.33   Bsol= 67.77   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.60,-0.38,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252903                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1266   r_free= 0.1763   ksol= 0.33   Bsol= 67.77   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.48,-2.60,-0.38,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.252903                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1489 -  4.6887 0.99   1438  158 0.0942 0.1282      5.3644      5.5766|
|  2:  4.6887 -  3.7400 0.99   1391  158 0.0858 0.1234      5.4647      5.7315|
|  3:  3.7400 -  3.2727 0.99   1368  149 0.1190 0.1732      5.5669      5.8912|
|  4:  3.2727 -  2.9759 0.99   1351  153 0.1475 0.1963      5.5837      5.7313|
|  5:  2.9759 -  2.7640 0.99   1351  149 0.1567 0.1973      5.4649      5.6934|
|  6:  2.7640 -  2.6019 0.99   1340  146 0.1460 0.2230      5.3339      5.5804|
|  7:  2.6019 -  2.4722 0.99   1332  155 0.1460 0.1797      5.2933      5.4259|
|  8:  2.4722 -  2.3650 0.98   1325  151 0.1435 0.1972      5.2082      5.4661|
|  9:  2.3650 -  2.2742 0.98   1313  140 0.1411 0.1979      5.1567      5.4163|
| 10:  2.2742 -  2.1960 1.00   1354  147 0.1296 0.1765      5.0367      5.2442|
| 11:  2.1960 -  2.1275 0.98   1318  147 0.1301 0.2051      5.0449      5.4146|
| 12:  2.1275 -  2.0669 0.98   1306  141 0.1331 0.1991      4.9663      5.2106|
| 13:  2.0669 -  2.0126 0.87   1145  131 0.1172 0.1654       4.824      5.0059|
| 14:  2.0126 -  1.9636 0.23    298   34 0.1059 0.1674      4.7082      4.9805|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1489 -  4.6887  1438   158  0.94   9.10   0.97     0.94       7185.57|
|  2:  4.6887 -  3.7400  1391   158  0.95   8.54   1.02     1.01       9959.06|
|  3:  3.7400 -  3.2727  1368   149  0.92  13.22   1.04     1.04      12556.37|
|  4:  3.2727 -  2.9759  1351   153  0.89  16.92   1.02     1.00      13431.41|
|  5:  2.9759 -  2.7640  1351   149  0.88  18.56   1.00     0.98      10964.43|
|  6:  2.7640 -  2.6019  1340   146  0.87  19.05   0.98     0.95       9024.11|
|  7:  2.6019 -  2.4722  1332   155  0.88  18.75   1.00     0.97       8326.08|
|  8:  2.4722 -  2.3650  1325   151  0.88  18.24   0.99     0.96       6793.98|
|  9:  2.3650 -  2.2742  1313   140  0.88  18.44   1.00     0.95       6312.83|
| 10:  2.2742 -  2.1960  1354   147  0.89  17.61   1.00     0.97       5147.54|
| 11:  2.1960 -  2.1275  1318   147  0.88  18.30   0.99     0.93       5331.28|
| 12:  2.1275 -  2.0669  1306   141  0.89  17.87   1.00     1.00       4682.87|
| 13:  2.0669 -  2.0126  1145   131  0.88  18.15   0.99     0.96       3743.25|
| 14:  2.0126 -  1.9636   298    34  0.93  13.08   0.99     0.97       2752.91|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2752.91 max =        13431.41 mean =      7941.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        16.21|
|phase err.(test): min =        0.00 max =           88.54 mean =        15.67|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.915)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.79   18.04    None  None   None       |
|    all(noH): 2823   0      0.00    93.79   18.04    None  None   None       |
|    Sol.    : 438    0      6.00    93.79   44.21    None  None   None       |
|    Mac.    : 2385   0      0.00    81.40   13.24    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:     0.003 -   9.381:  888   |   5:    46.895 -  56.274:   94        |
|      1:     9.381 -  18.760: 1185   |   6:    56.274 -  65.652:   82        |
|      2:    18.760 -  28.138:  275   |   7:    65.652 -  75.030:   48        |
|      3:    28.138 -  37.517:  120   |   8:    75.030 -  84.409:   13        |
|      4:    37.517 -  46.895:  114   |   9:    84.409 -  93.787:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.670 - 5.430
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 339
   mapped sites are within: 0.714 - 5.430

peak=    5.572 closest distance to " CG  PRO A  54 " =    1.451
peak=    5.522 closest distance to " O   HOH Z 142 " =    2.165
peak=    5.392 closest distance to " O   HOH Z 222 " =    1.355
peak=    5.375 closest distance to " O   HOH Z 417 " =    2.692
peak=    5.368 closest distance to " O   HOH Z  63 " =    1.770
peak=    5.311 closest distance to " O   HOH Z 287 " =    2.055
peak=    5.283 closest distance to " NE2 GLN A  11 " =    1.230
peak=    5.189 closest distance to " O   HOH Z 278 " =    1.384
peak=    5.128 closest distance to " CG  PRO A  90 " =    1.425
peak=    5.072 closest distance to " O   HOH Z   7 " =    1.831
peak=    4.802 closest distance to " O   HOH Z 427 " =    2.487
peak=    4.789 closest distance to " O   HOH Z 423 " =    2.065
peak=    4.746 closest distance to " O   HOH Z 371 " =    2.074
peak=    4.735 closest distance to " O   HOH Z 419 " =    2.142
peak=    4.734 closest distance to " O   HOH Z 126 " =    2.135
peak=    4.680 closest distance to " CB  ASN A 148 " =    1.416
peak=    4.640 closest distance to " O   HOH Z  65 " =    1.177
peak=    4.580 closest distance to " CB  GLN A 223 " =    1.539
peak=    4.569 closest distance to " O   HOH Z 380 " =    1.901
peak=    4.543 closest distance to " CZ3 TRP A 266 " =    1.176
peak=    4.499 closest distance to " O   HOH Z   9 " =    2.082
peak=    4.471 closest distance to " O   HOH Z  69 " =    1.525
peak=    4.431 closest distance to " CB  SER A  63 " =    1.297
peak=    4.373 closest distance to " O   HOH Z 414 " =    1.458
peak=    4.303 closest distance to " CB  SER A 216 " =    1.069
peak=    4.274 closest distance to " CG  PRO A 198 " =    1.280
peak=    4.270 closest distance to " CA  ARG A 195 " =    1.353
peak=    4.260 closest distance to " O   HOH Z 127 " =    0.987
peak=    4.236 closest distance to " O   HOH Z 103 " =    0.894
peak=    4.232 closest distance to " O   HOH Z 232 " =    2.287
peak=    4.232 closest distance to " NH2 ARG A  56 " =    2.069
peak=    4.231 closest distance to " O   HOH Z  66 " =    1.021
peak=    4.206 closest distance to " CB  PRO A  54 " =    1.128
peak=    4.192 closest distance to " O   HOH Z 316 " =    3.153
peak=    4.181 closest distance to " O   HOH Z 425 " =    1.582
peak=    4.177 closest distance to " CG  LEU A 167 " =    1.257
peak=    4.163 closest distance to " CA  VAL A 125 " =    1.164
peak=    4.156 closest distance to " O   HOH Z  78 " =    1.627
peak=    4.147 closest distance to " O   HOH Z 375 " =    1.151
peak=    4.142 closest distance to " CG  LYS A  76 " =    1.803
peak=    4.100 closest distance to " O   PRO A 198 " =    1.384
peak=    4.097 closest distance to " O   HOH Z 145 " =    1.580
peak=    4.082 closest distance to " CA  TYR A  30 " =    1.127
peak=    4.069 closest distance to " O   HOH Z 298 " =    2.104
peak=    4.060 closest distance to " CG  PRO A 243 " =    1.067
peak=    4.044 closest distance to " O   TYR A 116 " =    1.336
peak=    4.044 closest distance to " O   HOH Z 105 " =    1.013
peak=    4.033 closest distance to " O   HOH Z  49 " =    1.279
peak=    4.027 closest distance to " CA  ALA A  51 " =    1.043
peak=    4.024 closest distance to " CG  TRP A 179 " =    2.248
peak=    4.017 closest distance to " N   TYR A  15 " =    1.183
peak=    4.005 closest distance to " OE1 GLN A  77 " =    1.375
peak=    3.966 closest distance to " O   HOH Z 403 " =    1.674
peak=    3.962 closest distance to " NH1AARG A 145 " =    1.233
peak=    3.961 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.950 closest distance to " CB  ARG A 275 " =    0.982
peak=    3.944 closest distance to " O   HOH Z  11 " =    1.020
peak=    3.941 closest distance to " NZ  LYS A 117 " =    2.803
peak=    3.939 closest distance to " CG2 THR A 221 " =    1.163
peak=    3.917 closest distance to " CG  GLN A  58 " =    1.112
peak=    3.914 closest distance to " CB  PRO A  90 " =    1.094
peak=    3.908 closest distance to " O   HOH Z 422 " =    0.993
peak=    3.892 closest distance to " CE  LYS A 119 " =    1.238
peak=    3.887 closest distance to " O   HOH Z 295 " =    1.182
peak=    3.884 closest distance to " N   GLN A 278 " =    1.121
peak=    3.879 closest distance to " O   HOH Z 357 " =    2.075
peak=    3.869 closest distance to " CE3 TRP A 150 " =    1.159
peak=    3.867 closest distance to " O   HOH Z 359 " =    1.463
peak=    3.840 closest distance to " O   HOH Z 126 " =    1.504
peak=    3.833 closest distance to " CB  GLU A 277 " =    3.638
peak=    3.832 closest distance to " O   HOH Z  97 " =    1.286
peak=    3.831 closest distance to " O   HOH Z  61 " =    1.660
peak=    3.827 closest distance to " O   HOH Z 411 " =    3.799
peak=    3.823 closest distance to " CB  SER A  62 " =    0.851
peak=    3.817 closest distance to " CG2 VAL A 257 " =    0.880
peak=    3.813 closest distance to " O   HOH Z 298 " =    4.298
peak=    3.804 closest distance to " O   HOH Z  26 " =    1.373
peak=    3.802 closest distance to " CB  ALA A 114 " =    0.841
peak=    3.798 closest distance to " NH2AARG A 190 " =    2.029
peak=    3.797 closest distance to " O   HOH Z 437 " =    1.625
peak=    3.797 closest distance to " ND2 ASN A  60 " =    3.040
peak=    3.794 closest distance to " CB  ASN A 142 " =    0.917
peak=    3.794 closest distance to " CE  LYS A  76 " =    0.890
peak=    3.766 closest distance to " O   HOH Z 218 " =    1.817
peak=    3.764 closest distance to " CB  ASP A 124 " =    0.832
peak=    3.764 closest distance to " CZ  PHE A 218 " =    1.151
peak=    3.760 closest distance to " O   HOH Z 392 " =    1.254
peak=    3.759 closest distance to " NZ  LYS A 119 " =    2.362
peak=    3.751 closest distance to " CB  ARG A  79 " =    1.004
peak=    3.739 closest distance to " O   HOH Z 211 " =    1.276
peak=    3.733 closest distance to " NE2 HIS A 207 " =    1.102
peak=    3.721 closest distance to " O   HOH Z 368 " =    3.689
peak=    3.720 closest distance to " ND2BASN A 224 " =    0.890
peak=    3.702 closest distance to " CB  LEU A 300 " =    0.924
peak=    3.691 closest distance to " CA  ARG A 156 " =    1.064
peak=    3.684 closest distance to " CA  MET A 105 " =    0.925
peak=    3.681 closest distance to " CG AARG A 275 " =    1.346
peak=    3.680 closest distance to " CG  PRO A 213 " =    1.326
peak=    3.680 closest distance to " O   HOH Z 225 " =    1.767
peak=    3.665 closest distance to " O   HOH Z 362 " =    2.202
peak=    3.663 closest distance to " O   HOH Z  39 " =    0.971
peak=    3.649 closest distance to " O   HOH Z   1 " =    1.786
peak=    3.648 closest distance to " O   HOH Z 193 " =    1.729
peak=    3.645 closest distance to " O  BHOH Z  74 " =    1.137
peak=    3.639 closest distance to " O   HOH Z 361 " =    1.384
peak=    3.636 closest distance to " O   HOH Z 215 " =    1.689
peak=    3.631 closest distance to " O   HOH Z 216 " =    3.934
peak=    3.630 closest distance to " CB  SER A 212 " =    1.313
peak=    3.626 closest distance to " CA  ASN A 127 " =    1.163
peak=    3.618 closest distance to " ND2 ASN A 249 " =    0.854
peak=    3.618 closest distance to " N   ASN A 127 " =    1.413
peak=    3.617 closest distance to " CB  ALA A  43 " =    0.840
peak=    3.616 closest distance to " O   HOH Z 273 " =    1.237
peak=    3.609 closest distance to " O   HOH Z  88 " =    3.903
peak=    3.606 closest distance to " CB  ARG A 190 " =    1.704
peak=    3.599 closest distance to " O   HOH Z 180 " =    2.249
peak=    3.599 closest distance to " CB  TYR A 169 " =    0.783
peak=    3.594 closest distance to " CB  ASN A  39 " =    0.862
peak=    3.591 closest distance to " CB  ASN A 187 " =    0.960
peak=    3.587 closest distance to " O   HOH Z 365 " =    2.693
peak=    3.581 closest distance to " O   HOH Z 327 " =    1.672
peak=    3.580 closest distance to " O   HOH Z 153 " =    3.689
peak=    3.580 closest distance to " CG  GLN A  89 " =    1.513
peak=    3.574 closest distance to " ND2 ASN A 187 " =    1.814
peak=    3.570 closest distance to " CB  TRP A 179 " =    1.493
peak=    3.570 closest distance to " CB  GLU A 128 " =    0.973
peak=    3.569 closest distance to " O   HOH Z  91 " =    2.428
peak=    3.569 closest distance to " CA  ALA A 160 " =    1.088
peak=    3.565 closest distance to " CG2 ILE A 120 " =    1.038
peak=    3.562 closest distance to " O   HOH Z 201 " =    1.630
peak=    3.560 closest distance to " O   HOH Z 272 " =    1.839
peak=    3.558 closest distance to " OE2 GLU A  53 " =    1.957
peak=    3.556 closest distance to " CD  ARG A 259 " =    1.764
peak=    3.555 closest distance to " CB  VAL A 265 " =    1.295
peak=    3.540 closest distance to " O   HOH Z  90 " =    2.066
peak=    3.540 closest distance to " CB  TRP A 266 " =    1.015
peak=    3.539 closest distance to " O   HOH Z 406 " =    1.615
peak=    3.533 closest distance to " N   VAL A 296 " =    1.779
peak=    3.531 closest distance to " O   HOH Z  59 " =    1.829
peak=    3.528 closest distance to " O   HOH Z 240 " =    2.178
peak=    3.527 closest distance to " O   HOH Z 431 " =    1.085
peak=    3.519 closest distance to " N   CYS A 260 " =    0.861
peak=    3.515 closest distance to " CB  LYS A 117 " =    1.194
peak=    3.515 closest distance to " O   HOH Z  92 " =    1.272
peak=    3.513 closest distance to " CD  ARG A  66 " =    2.044
peak=    3.513 closest distance to " O   HOH Z 130 " =    1.994
peak=    3.504 closest distance to " CB  GLU A 152 " =    1.193
peak=    3.502 closest distance to " O   HOH Z   3 " =    2.121
peak=    3.501 closest distance to " ND1 HIS A  86 " =    1.795
peak=    3.501 closest distance to " O   HOH Z 245 " =    0.934
peak=    3.498 closest distance to " O   HOH Z 368 " =    1.823
peak=    3.497 closest distance to " CB  SER A 210 " =    0.900
peak=    3.497 closest distance to " O   HOH Z 394 " =    1.863
peak=    3.497 closest distance to " O   HOH Z 214 " =    2.579
peak=    3.491 closest distance to " O   HOH Z 385 " =    0.714
peak=    3.488 closest distance to " O   HOH Z 280 " =    1.598
peak=    3.487 closest distance to " CG2 ILE A  20 " =    1.571
peak=    3.486 closest distance to " CZ3 TRP A 274 " =    1.437
peak=    3.481 closest distance to " O   HOH Z 422 " =    2.420
peak=    3.479 closest distance to " CD2 TRP A 179 " =    1.225
peak=    3.472 closest distance to " O   HOH Z   1 " =    1.729
peak=    3.469 closest distance to " O   HOH Z 258 " =    2.039
peak=    3.468 closest distance to " O   ASN A 209 " =    1.585
peak=    3.464 closest distance to " O   HOH Z 286 " =    2.272
peak=    3.458 closest distance to " O   THR A 294 " =    0.979
peak=    3.458 closest distance to " CD1 ILE A 199 " =    1.205
peak=    3.457 closest distance to " CA  PHE A 283 " =    1.255
peak=    3.455 closest distance to " CB  VAL A 202 " =    1.628
peak=    3.454 closest distance to " O   HOH Z 132 " =    0.931
peak=    3.453 closest distance to " NH2 ARG A  56 " =    1.050
peak=    3.452 closest distance to " N   SER A  97 " =    0.889
peak=    3.448 closest distance to " O   HOH Z  24 " =    1.834
peak=    3.440 closest distance to " NZ  LYS A 166 " =    0.894
peak=    3.439 closest distance to " O   HOH Z 393 " =    1.339
peak=    3.439 closest distance to " O   HOH Z  76 " =    1.219
peak=    3.436 closest distance to " CZ  PHE A  38 " =    1.206
peak=    3.435 closest distance to " O   HOH Z 156 " =    2.647
peak=    3.431 closest distance to " CA  TYR A 116 " =    1.402
peak=    3.429 closest distance to " O   HOH Z 207 " =    0.802
peak=    3.428 closest distance to " O   HOH Z  40 " =    2.121
peak=    3.425 closest distance to " O   HOH Z   7 " =    3.288
peak=    3.422 closest distance to " O   THR A 220 " =    1.685
peak=    3.418 closest distance to " CB  SER A   3 " =    1.491
peak=    3.415 closest distance to " O   HOH Z  68 " =    1.942
peak=    3.413 closest distance to " NE AARG A 275 " =    1.549
peak=    3.405 closest distance to " O   HOH Z 285 " =    2.378
peak=    3.403 closest distance to " OG  SER A  26 " =    1.481
peak=    3.401 closest distance to " CA  ASP A 124 " =    0.854
peak=    3.401 closest distance to " NZ BLYS A 290 " =    0.946
peak=    3.396 closest distance to " O   HOH Z 104 " =    1.649
peak=    3.396 closest distance to " O   HOH Z 130 " =    3.621
peak=    3.393 closest distance to " CB  MET A  40 " =    0.804
peak=    3.392 closest distance to " CB  ALA A   1 " =    4.390
peak=    3.392 closest distance to " OE1 GLN A 240 " =    1.546
peak=    3.385 closest distance to " CB  SER A  99 " =    0.915
peak=    3.381 closest distance to " O   GLN A 240 " =    1.649
peak=    3.371 closest distance to " CB  GLN A  88 " =    1.369
peak=    3.370 closest distance to " CA  SER A  87 " =    1.073
peak=    3.370 closest distance to " O   HOH Z 383 " =    2.582
peak=    3.367 closest distance to " CB  TRP A 274 " =    1.101
peak=    3.367 closest distance to " N   ALA A 165 " =    1.316
peak=    3.365 closest distance to " O   HOH Z 112 " =    1.083
peak=    3.365 closest distance to " O   HOH Z 157 " =    1.728
peak=    3.360 closest distance to " CA  ALA A 129 " =    1.175
peak=    3.358 closest distance to " O   HOH Z 122 " =    2.270
peak=    3.354 closest distance to " O   MET A 105 " =    1.676
peak=    3.352 closest distance to " O   HOH Z  20 " =    1.578
peak=    3.348 closest distance to " CB  GLN A  89 " =    1.249
peak=    3.347 closest distance to " O   HOH Z 116 " =    3.149
peak=    3.347 closest distance to " O   HOH Z 258 " =    1.029
peak=    3.345 closest distance to " CD  ARG A  66 " =    2.312
peak=    3.345 closest distance to " CB  ASN A 215 " =    1.140
peak=    3.342 closest distance to " O   HOH Z 345 " =    1.988
peak=    3.342 closest distance to " CB  MET A  47 " =    1.109
peak=    3.342 closest distance to " CA  ALA A 233 " =    1.492
peak=    3.339 closest distance to " CB  TYR A  30 " =    1.406
peak=    3.338 closest distance to " CD  ARG A 195 " =    3.557
peak=    3.336 closest distance to " CA  ASP A 162 " =    0.936
peak=    3.335 closest distance to " O   HOH Z  77 " =    1.284
peak=    3.331 closest distance to " O   HOH Z  60 " =    1.486
peak=    3.330 closest distance to " O   HOH Z  88 " =    3.177
peak=    3.330 closest distance to " CG  ARG A 159 " =    0.729
peak=    3.320 closest distance to " O   ASN A  74 " =    1.486
peak=    3.318 closest distance to " O   ILE A  20 " =    2.094
peak=    3.313 closest distance to " CE3 TRP A  85 " =    0.980
peak=    3.310 closest distance to " CA  GLY A 267 " =    1.286
peak=    3.309 closest distance to " O   HOH Z 374 " =    1.117
peak=    3.309 closest distance to " NZ  LYS A 117 " =    1.464
peak=    3.308 closest distance to " CA  TRP A  92 " =    1.123
peak=    3.300 closest distance to " O   HOH Z 183 " =    1.461
peak=    3.300 closest distance to " O   HOH Z 425 " =    2.011
peak=    3.299 closest distance to " CG1 ILE A 120 " =    1.446
peak=    3.299 closest distance to " O   HOH Z 172 " =    4.916
peak=    3.299 closest distance to " CD1 LEU A 300 " =    1.042
peak=    3.293 closest distance to " OG BSER A  99 " =    2.224
peak=    3.287 closest distance to " O   HOH Z  53 " =    2.307
peak=    3.285 closest distance to " O   GLY A 302 " =    2.348
peak=    3.284 closest distance to " CB  GLU A 236 " =    1.457
peak=    3.283 closest distance to " O   HOH Z 328 " =    1.568
peak=    3.282 closest distance to " N   ARG A 156 " =    1.227
peak=    3.279 closest distance to " CA  THR A 264 " =    0.798
peak=    3.279 closest distance to " CB  GLN A 183 " =    1.206
peak=    3.278 closest distance to " O   HOH Z 410 " =    1.507
peak=    3.272 closest distance to " N   GLU A   2 " =    1.418
peak=    3.270 closest distance to " O   HOH Z 394 " =    3.896
peak=    3.269 closest distance to " O   HOH Z 181 " =    2.332
peak=    3.266 closest distance to " CE  MET A  93 " =    1.442
peak=    3.266 closest distance to " NE1 TRP A 274 " =    0.911
peak=    3.265 closest distance to " N   TYR A 116 " =    1.525
peak=    3.265 closest distance to " CA  SER A  95 " =    0.982
peak=    3.260 closest distance to " O   HOH Z 119 " =    1.647
peak=    3.257 closest distance to " O   TRP A  70 " =    1.455
peak=    3.257 closest distance to " CB  ASN A 110 " =    1.071
peak=    3.254 closest distance to " CB  ARG A 219 " =    0.865
peak=    3.254 closest distance to " OE2 GLU A  53 " =    1.456
peak=    3.254 closest distance to " CA  ILE A 234 " =    1.097
peak=    3.247 closest distance to " O   HOH Z   2 " =    1.813
peak=    3.245 closest distance to " CA  ALA A 180 " =    1.320
peak=    3.243 closest distance to " O   HOH Z 287 " =    2.106
peak=    3.243 closest distance to " CB  ASP A 200 " =    0.934
peak=    3.240 closest distance to " CB  ARG A 138 " =    1.013
peak=    3.239 closest distance to " O   HOH Z  58 " =    1.812
peak=    3.239 closest distance to " O   HOH Z 172 " =    2.146
peak=    3.239 closest distance to " CB  ASP A 191 " =    1.286
peak=    3.235 closest distance to " O   GLN A  55 " =    1.813
peak=    3.234 closest distance to " O   HOH Z 119 " =    4.261
peak=    3.232 closest distance to " C   GLN A  73 " =    1.053
peak=    3.232 closest distance to " CB  SER A 276 " =    1.138
peak=    3.231 closest distance to " CA  ILE A 263 " =    1.056
peak=    3.230 closest distance to " O   HOH Z 234 " =    3.650
peak=    3.228 closest distance to " CA  ILE A 106 " =    0.800
peak=    3.228 closest distance to " NH1BARG A 145 " =    1.344
peak=    3.226 closest distance to " O   HOH Z 371 " =    3.254
peak=    3.222 closest distance to " O   HOH Z  10 " =    1.640
peak=    3.221 closest distance to " O   HOH Z 244 " =    1.557
peak=    3.220 closest distance to " N   ASP A 162 " =    1.003
peak=    3.218 closest distance to " CB  THR A  31 " =    1.668
peak=    3.214 closest distance to " CB  ASN A 285 " =    1.013
peak=    3.213 closest distance to " O   HOH Z 171 " =    2.450
peak=    3.213 closest distance to " O   HOH Z  70 " =    0.808
peak=    3.206 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.205 closest distance to " O   ASP A 200 " =    1.385
peak=    3.205 closest distance to " CB  ALA A  10 " =    0.909
peak=    3.203 closest distance to " O   HOH Z 329 " =    4.168
peak=    3.202 closest distance to " CB  ALA A 160 " =    1.385
peak=    3.197 closest distance to " O   ASN A 142 " =    1.023
peak=    3.195 closest distance to " O   HOH Z 104 " =    1.925
peak=    3.195 closest distance to " O   HOH Z 120 " =    3.757
peak=    3.194 closest distance to " CA  ASN A  74 " =    1.287
peak=    3.194 closest distance to " CB  PRO A 163 " =    4.207
peak=    3.191 closest distance to " CB  SER A  97 " =    0.830
peak=    3.190 closest distance to " O   HOH Z 265 " =    2.129
peak=    3.183 closest distance to " O   HOH Z 296 " =    1.053
peak=    3.169 closest distance to " O   HOH Z 293 " =    1.411
peak=    3.167 closest distance to " O   HOH Z 112 " =    1.237
peak=    3.166 closest distance to " NE2 GLN A  58 " =    4.571
peak=    3.165 closest distance to " CG2 ILE A 239 " =    0.860
peak=    3.163 closest distance to " CB  PHE A 130 " =    0.974
peak=    3.160 closest distance to " O   HOH Z 344 " =    3.089
peak=    3.157 closest distance to " OG BSER A 164 " =    2.353
peak=    3.156 closest distance to " NH2AARG A 190 " =    1.962
peak=    3.155 closest distance to " CB  GLU A  46 " =    1.076
peak=    3.148 closest distance to " CB  ARG A 102 " =    0.859
peak=    3.146 closest distance to " O   HOH Z   6 " =    1.619
peak=    3.140 closest distance to " CA  ASN A 217 " =    1.154
peak=    3.137 closest distance to " CA  GLY A 136 " =    0.974
peak=    3.135 closest distance to " CB  ASN A 176 " =    1.013
peak=    3.134 closest distance to " O   HOH Z 353 " =    1.839
peak=    3.131 closest distance to " O   HOH Z 346 " =    1.677
peak=    3.130 closest distance to " O   HOH Z 285 " =    2.056
peak=    3.127 closest distance to " O   HOH Z 438 " =    2.393
peak=    3.124 closest distance to " CD  LYS A 119 " =    1.738
peak=    3.121 closest distance to " O   HOH Z 310 " =    2.416
peak=    3.117 closest distance to " N   THR A  42 " =    1.398
peak=    3.111 closest distance to " O   HOH Z 153 " =    4.154
peak=    3.106 closest distance to " CD1 ILE A  33 " =    1.759
peak=    3.104 closest distance to " N   VAL A  72 " =    1.696
peak=    3.100 closest distance to " O   HOH Z 380 " =    4.904
peak=    3.098 closest distance to " O   HOH Z 147 " =    1.389
peak=    3.095 closest distance to " N   VAL A 125 " =    1.522
peak=    3.093 closest distance to " O   HOH Z 116 " =    1.039
peak=    3.093 closest distance to " O   HOH Z 188 " =    2.817
peak=    3.091 closest distance to " NH2 ARG A  66 " =    5.430
peak=    3.090 closest distance to " CA  GLY A  35 " =    0.898
peak=    3.087 closest distance to " CA  GLN A  94 " =    0.722
peak=    3.085 closest distance to " CG1 VAL A 257 " =    1.435
peak=    3.084 closest distance to " CG2 VAL A 232 " =    1.036
peak=    3.082 closest distance to " O   HOH Z 251 " =    1.379
peak=    3.062 closest distance to " CB  GLU A 175 " =    0.856
peak=    3.059 closest distance to " O   HOH Z 219 " =    1.982
peak=    3.055 closest distance to " CB  PHE A  16 " =    0.957
peak=    3.049 closest distance to " CA  ARG A 102 " =    1.178
peak=    3.048 closest distance to " CG2 THR A 294 " =    1.443
peak=    3.048 closest distance to " OH  TYR A 116 " =    1.840
peak=    3.039 closest distance to " CG  LYS A 119 " =    1.036
peak=    3.036 closest distance to " CB  TYR A  30 " =    1.345

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.635 - 5.398
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.708 - 5.398

peak=   -4.820 closest distance to " CZ2 TRP A  92 " =    2.843
peak=   -4.713 closest distance to " CD  ARG A  14 " =    3.256
peak=   -4.437 closest distance to " O   ALA A  10 " =    1.625
peak=   -4.421 closest distance to " O   PRO A 198 " =    1.176
peak=   -4.343 closest distance to " O   HOH Z  60 " =    1.525
peak=   -4.217 closest distance to " O   HOH Z 231 " =    0.880
peak=   -4.195 closest distance to " CB  PRO A 243 " =    2.593
peak=   -4.180 closest distance to " CG1BVAL A  41 " =    2.783
peak=   -4.136 closest distance to " O   SER A  22 " =    2.748
peak=   -4.107 closest distance to " CD  ARG A 156 " =    2.082
peak=   -4.104 closest distance to " OG BSER A 134 " =    1.586
peak=   -4.057 closest distance to " CB  ALA A  43 " =    2.523
peak=   -4.053 closest distance to " CD2 TYR A 293 " =    1.918
peak=   -4.051 closest distance to " O   HOH Z  28 " =    1.288
peak=   -4.035 closest distance to " CA  GLY A  98 " =    1.907
peak=   -4.035 closest distance to " O   SER A 135 " =    1.443
peak=   -4.006 closest distance to " O   HOH Z 298 " =    2.353
peak=   -3.983 closest distance to " CB  ALA A   9 " =    2.384
peak=   -3.983 closest distance to " O   HOH Z 131 " =    3.915
peak=   -3.977 closest distance to " CB  ASP A  27 " =    2.485
peak=   -3.957 closest distance to " O   HOH Z 377 " =    1.950
peak=   -3.937 closest distance to " O   GLU A 152 " =    1.410
peak=   -3.899 closest distance to " O   HOH Z 216 " =    1.420
peak=   -3.884 closest distance to " O   HOH Z  32 " =    1.919
peak=   -3.876 closest distance to " O   HOH Z  52 " =    1.490
peak=   -3.869 closest distance to " CZ3 TRP A 179 " =    1.266
peak=   -3.859 closest distance to " O   HOH Z  69 " =    1.418
peak=   -3.848 closest distance to " O   HOH Z 275 " =    1.750
peak=   -3.830 closest distance to " NE2 GLN A  55 " =    1.220
peak=   -3.820 closest distance to " CG  GLN A  55 " =    1.308
peak=   -3.812 closest distance to " CD1 LEU A 101 " =    2.259
peak=   -3.810 closest distance to " O   HOH Z  39 " =    0.970
peak=   -3.805 closest distance to " O   HOH Z 105 " =    2.160
peak=   -3.804 closest distance to " CG  MET A 105 " =    0.998
peak=   -3.799 closest distance to " OG  SER A  97 " =    2.150
peak=   -3.797 closest distance to " CE BMET A  47 " =    1.391
peak=   -3.794 closest distance to " O   HOH Z  24 " =    0.976
peak=   -3.786 closest distance to " O   HOH Z 100 " =    1.092
peak=   -3.761 closest distance to " N   THR A 157 " =    1.536
peak=   -3.719 closest distance to " NE2 GLN A 194 " =    1.943
peak=   -3.705 closest distance to " CD  LYS A 166 " =    2.608
peak=   -3.696 closest distance to " CA  GLY A 133 " =    1.967
peak=   -3.689 closest distance to " O   HOH Z 185 " =    2.104
peak=   -3.687 closest distance to " O   HOH Z 276 " =    1.297
peak=   -3.677 closest distance to " O   HOH Z 231 " =    2.084
peak=   -3.675 closest distance to " O   HOH Z 313 " =    1.546
peak=   -3.672 closest distance to " O   HOH Z  71 " =    1.220
peak=   -3.670 closest distance to " CD2 TYR A 116 " =    2.155
peak=   -3.653 closest distance to " O   HOH Z 389 " =    2.299
peak=   -3.647 closest distance to " O   HOH Z 385 " =    1.563
peak=   -3.641 closest distance to " CA  HIS A 207 " =    1.077
peak=   -3.636 closest distance to " O   LYS A  76 " =    1.898
peak=   -3.633 closest distance to " C   HIS A 108 " =    1.214
peak=   -3.632 closest distance to " O   VAL A  67 " =    2.704
peak=   -3.619 closest distance to " O   HOH Z 111 " =    1.696
peak=   -3.617 closest distance to " OG  SER A 245 " =    1.563
peak=   -3.616 closest distance to " CD2 PHE A  61 " =    2.084
peak=   -3.616 closest distance to " O   HOH Z 147 " =    2.058
peak=   -3.609 closest distance to " CG  GLN A 223 " =    2.457
peak=   -3.608 closest distance to " O   HOH Z 166 " =    1.654
peak=   -3.598 closest distance to " CG  GLN A  88 " =    0.841
peak=   -3.588 closest distance to " O   HOH Z 407 " =    3.158
peak=   -3.575 closest distance to " O   HOH Z  11 " =    1.669
peak=   -3.571 closest distance to " O   HOH Z 368 " =    1.428
peak=   -3.569 closest distance to " CD  GLU A 277 " =    1.249
peak=   -3.568 closest distance to " CA  GLY A 241 " =    2.244
peak=   -3.563 closest distance to " O   HOH Z 123 " =    2.460
peak=   -3.555 closest distance to " CZ  PHE A  59 " =    1.640
peak=   -3.551 closest distance to " CG  ASN A  39 " =    1.726
peak=   -3.534 closest distance to " CG1 VAL A 250 " =    2.660
peak=   -3.521 closest distance to " OE1 GLU A 277 " =    2.120
peak=   -3.517 closest distance to " CG1 VAL A 112 " =    2.687
peak=   -3.497 closest distance to " CB  ASN A  39 " =    2.293
peak=   -3.495 closest distance to " OD1 ASP A 191 " =    1.895
peak=   -3.462 closest distance to " CG1 VAL A 125 " =    2.312
peak=   -3.454 closest distance to " CB  TYR A  68 " =    1.158
peak=   -3.454 closest distance to " NZ  LYS A 119 " =    0.708
peak=   -3.450 closest distance to " CD1 TYR A 247 " =    2.829
peak=   -3.449 closest distance to " O   HOH Z 389 " =    1.268
peak=   -3.449 closest distance to " CZ2 TRP A 274 " =    1.048
peak=   -3.442 closest distance to " N   ASP A 270 " =    1.415
peak=   -3.441 closest distance to " NH2 ARG A  79 " =    2.341
peak=   -3.437 closest distance to " O   HOH Z 181 " =    2.331
peak=   -3.435 closest distance to " N   ARG A 159 " =    1.935
peak=   -3.429 closest distance to " O   HOH Z 351 " =    1.721
peak=   -3.428 closest distance to " O   HOH Z 163 " =    1.783
peak=   -3.419 closest distance to " O   ASP A  27 " =    1.586
peak=   -3.415 closest distance to " CG2 ILE A  20 " =    2.749
peak=   -3.410 closest distance to " CB  ALA A 291 " =    2.227
peak=   -3.409 closest distance to " O   HOH Z 165 " =    1.708
peak=   -3.406 closest distance to " NE1 TRP A 179 " =    1.367
peak=   -3.404 closest distance to " ND2 ASN A  60 " =    4.039
peak=   -3.403 closest distance to " O   HOH Z 266 " =    5.398
peak=   -3.401 closest distance to " O   HOH Z  64 " =    1.054
peak=   -3.395 closest distance to " CG2 THR A 178 " =    2.163
peak=   -3.393 closest distance to " OG  SER A  87 " =    1.613
peak=   -3.390 closest distance to " CE  LYS A  76 " =    2.982
peak=   -3.382 closest distance to " CA  GLY A 203 " =    2.414
peak=   -3.375 closest distance to " OH  TYR A 172 " =    1.791
peak=   -3.375 closest distance to " O   HOH Z 414 " =    1.322
peak=   -3.372 closest distance to " O   ILE A  49 " =    1.615
peak=   -3.371 closest distance to " O   PRO A 163 " =    1.679
peak=   -3.367 closest distance to " O   HOH Z  73 " =    2.191
peak=   -3.366 closest distance to " CE2 TYR A  30 " =    2.467
peak=   -3.366 closest distance to " CZ  TYR A 169 " =    1.863
peak=   -3.365 closest distance to " CB  PRO A  54 " =    2.285
peak=   -3.362 closest distance to " N   ALA A  43 " =    2.604
peak=   -3.358 closest distance to " CD  PRO A 213 " =    2.133
peak=   -3.357 closest distance to " CZ  PHE A  38 " =    2.513
peak=   -3.350 closest distance to " O   HOH Z 428 " =    2.622
peak=   -3.347 closest distance to " CB  ALA A 227 " =    2.350
peak=   -3.346 closest distance to " CD2 PHE A  16 " =    2.521
peak=   -3.338 closest distance to " CG1 VAL A 265 " =    2.521
peak=   -3.337 closest distance to " CG  TRP A 266 " =    1.709
peak=   -3.335 closest distance to " O   HOH Z 364 " =    2.374
peak=   -3.333 closest distance to " CE  MET A 105 " =    2.643
peak=   -3.331 closest distance to " O   HOH Z  77 " =    1.840
peak=   -3.329 closest distance to " O   ARG A 145 " =    1.266
peak=   -3.328 closest distance to " O   HOH Z 128 " =    2.553
peak=   -3.327 closest distance to " O   HOH Z 108 " =    1.201
peak=   -3.319 closest distance to " CG  GLN A  58 " =    1.128
peak=   -3.317 closest distance to " ND2 ASN A 249 " =    2.108
peak=   -3.314 closest distance to " O   ARG A  56 " =    4.407
peak=   -3.311 closest distance to " O   HOH Z 198 " =    1.396
peak=   -3.310 closest distance to " O   HOH Z  68 " =    1.328
peak=   -3.307 closest distance to " O   HOH Z  26 " =    0.825
peak=   -3.305 closest distance to " SG BCYS A 201 " =    2.158
peak=   -3.304 closest distance to " O   HOH Z 412 " =    4.328
peak=   -3.291 closest distance to " O   HOH Z 286 " =    1.472
peak=   -3.290 closest distance to " O   HOH Z 348 " =    2.035
peak=   -3.284 closest distance to " CG  LEU A  83 " =    2.245
peak=   -3.283 closest distance to " O   HOH Z  60 " =    1.336
peak=   -3.273 closest distance to " CA  ASN A 110 " =    0.938
peak=   -3.272 closest distance to " O   HOH Z 278 " =    1.341
peak=   -3.270 closest distance to " NH2 ARG A 219 " =    1.849
peak=   -3.261 closest distance to " CB  ASP A 132 " =    2.472
peak=   -3.261 closest distance to " O   HOH Z 425 " =    0.887
peak=   -3.258 closest distance to " O   GLN A 240 " =    3.106
peak=   -3.257 closest distance to " O   HOH Z 105 " =    1.492
peak=   -3.256 closest distance to " O   ASP A 162 " =    2.163
peak=   -3.253 closest distance to " OD2 ASP A 171 " =    1.561
peak=   -3.252 closest distance to " OD1 ASN A 148 " =    1.425
peak=   -3.245 closest distance to " O   HOH Z 290 " =    0.952
peak=   -3.244 closest distance to " CG1 VAL A 197 " =    2.374
peak=   -3.244 closest distance to " NH2AARG A 275 " =    5.279
peak=   -3.242 closest distance to " N   ASN A 127 " =    1.451
peak=   -3.241 closest distance to " CD2 HIS A 207 " =    1.607
peak=   -3.241 closest distance to " O   HOH Z 384 " =    3.124
peak=   -3.235 closest distance to " CB  SER A  63 " =    3.348
peak=   -3.234 closest distance to " CD  ARG A  79 " =    1.097
peak=   -3.233 closest distance to " CG  ARG A 269 " =    2.314
peak=   -3.230 closest distance to " CE3 TRP A 274 " =    2.363
peak=   -3.228 closest distance to " CB  ASP A 171 " =    2.200
peak=   -3.227 closest distance to " NE2 GLN A 223 " =    1.596
peak=   -3.226 closest distance to " O   HOH Z  28 " =    2.149
peak=   -3.216 closest distance to " O   HOH Z 277 " =    1.707
peak=   -3.215 closest distance to " O   HOH Z  37 " =    1.656
peak=   -3.211 closest distance to " O   HOH Z 421 " =    3.041
peak=   -3.205 closest distance to " ND2 ASN A 285 " =    2.079
peak=   -3.201 closest distance to " CA  ASP A 298 " =    1.187
peak=   -3.200 closest distance to " O   HOH Z 359 " =    3.078
peak=   -3.197 closest distance to " CB  ALA A 291 " =    1.978
peak=   -3.196 closest distance to " CZ  ARG A 259 " =    0.947
peak=   -3.189 closest distance to " O   HOH Z 238 " =    1.067
peak=   -3.186 closest distance to " CE1 TYR A 247 " =    2.709
peak=   -3.183 closest distance to " N   GLN A  58 " =    1.948
peak=   -3.180 closest distance to " CB  ASP A 132 " =    2.528
peak=   -3.177 closest distance to " OG  SER A  63 " =    1.410
peak=   -3.177 closest distance to " O   HOH Z  49 " =    1.164
peak=   -3.176 closest distance to " CE3 TRP A 150 " =    2.297
peak=   -3.169 closest distance to " O   HOH Z  22 " =    2.977
peak=   -3.167 closest distance to " OE1 GLN A  88 " =    1.105
peak=   -3.164 closest distance to " CB  TRP A  85 " =    2.316
peak=   -3.161 closest distance to " O   HOH Z 140 " =    1.070
peak=   -3.160 closest distance to " CB  SER A 210 " =    1.123
peak=   -3.157 closest distance to " CG BMET A  47 " =    3.090
peak=   -3.157 closest distance to " ND2 ASN A  45 " =    2.398
peak=   -3.155 closest distance to " O   HOH Z 102 " =    1.547
peak=   -3.155 closest distance to " CB  ALA A 100 " =    2.228
peak=   -3.153 closest distance to " O   PRO A 243 " =    2.496
peak=   -3.150 closest distance to " NZ  LYS A 166 " =    1.216
peak=   -3.146 closest distance to " CG  ARG A 259 " =    2.411
peak=   -3.134 closest distance to " CB  GLN A  11 " =    1.567
peak=   -3.133 closest distance to " CZ  PHE A 130 " =    1.039
peak=   -3.129 closest distance to " CA  GLY A 133 " =    2.202
peak=   -3.127 closest distance to " CB  ALA A 131 " =    1.900
peak=   -3.126 closest distance to " CZ3 TRP A 266 " =    1.245
peak=   -3.125 closest distance to " O   HOH Z 337 " =    1.457
peak=   -3.124 closest distance to " O   HOH Z 377 " =    1.375
peak=   -3.121 closest distance to " O   HOH Z 165 " =    2.361
peak=   -3.120 closest distance to " O   HOH Z 181 " =    1.471
peak=   -3.116 closest distance to " C   VAL A 257 " =    1.332
peak=   -3.110 closest distance to " OD2 ASP A  50 " =    2.399
peak=   -3.108 closest distance to " O   HOH Z 134 " =    4.038
peak=   -3.108 closest distance to " CG2 ILE A 151 " =    2.604
peak=   -3.102 closest distance to " CB  ALA A 291 " =    1.754
peak=   -3.101 closest distance to " O   HOH Z  51 " =    0.732
peak=   -3.099 closest distance to " O   HOH Z 438 " =    1.495
peak=   -3.096 closest distance to " O   TRP A  70 " =    1.431
peak=   -3.083 closest distance to " OD1 ASP A 171 " =    1.659
peak=   -3.081 closest distance to " OE1 GLN A 183 " =    1.686
peak=   -3.078 closest distance to " CG2 THR A 221 " =    2.244
peak=   -3.077 closest distance to " CB  HIS A  81 " =    1.076
peak=   -3.077 closest distance to " CZ  PHE A 225 " =    1.509
peak=   -3.071 closest distance to " O   HOH Z 281 " =    2.680
peak=   -3.067 closest distance to " CD1 ILE A 199 " =    2.514
peak=   -3.061 closest distance to " O   HOH Z 268 " =    2.922
peak=   -3.058 closest distance to " O   HOH Z 211 " =    0.974
peak=   -3.052 closest distance to " CG1 VAL A  78 " =    2.667
peak=   -3.043 closest distance to " OE1 GLU A  44 " =    1.048
peak=   -3.003 closest distance to " O   HOH Z 136 " =    1.777

================= 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    :  0.4687 0.4719   6.285639e+00   6.273776e+00
   1_bss:  0.4580 0.4661   6.278651e+00   6.266443e+00
   1_xyz:  0.3485 0.3903   6.087550e+00   6.155450e+00
   1_adp:  0.3170 0.4067   6.046204e+00   6.172774e+00
   1_occ:  0.3169 0.4080   6.046264e+00   6.173635e+00
   2_bss:  0.3156 0.4054   6.046736e+00   6.173276e+00
   2_xyz:  0.2617 0.3397   5.889112e+00   6.057673e+00
   2_adp:  0.2508 0.3253   5.861530e+00   6.028511e+00
   2_occ:  0.2506 0.3251   5.861366e+00   6.028690e+00
   3_bss:  0.2510 0.3253   5.861821e+00   6.028569e+00
   3_xyz:  0.1880 0.2438   5.590823e+00   5.787763e+00
   3_adp:  0.1843 0.2410   5.574310e+00   5.777173e+00
   3_occ:  0.1838 0.2406   5.571959e+00   5.774134e+00
   4_bss:  0.1834 0.2396   5.570600e+00   5.772775e+00
   4_xyz:  0.1648 0.2255   5.494399e+00   5.718880e+00
   4_adp:  0.1425 0.1966   5.361838e+00   5.592235e+00
   4_occ:  0.1423 0.1967   5.361835e+00   5.592882e+00
   5_bss:  0.1426 0.1968   5.361449e+00   5.592500e+00
   5_xyz:  0.1297 0.1795   5.272754e+00   5.507351e+00
   5_adp:  0.1267 0.1763   5.253002e+00   5.490566e+00
   5_occ:  0.1266 0.1763   5.252903e+00   5.490445e+00
   5_bss:  0.1266 0.1763   5.252903e+00   5.490445e+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:  0.335  50.001  -2.990   1.406   4.207   0.000   0.000   0.000
   1_xyz:  0.335  50.001  -2.990   1.406   4.207   0.000   0.000   0.000
   1_adp:  0.335  50.001  -2.990   1.406   4.207   0.000   0.000   0.000
   1_occ:  0.335  50.001  -2.990   1.406   4.207   0.000   0.000   0.000
   2_bss:  0.351  75.053  -1.627  -0.442   1.947  -0.000   0.000   0.000
   2_xyz:  0.351  75.053  -1.627  -0.442   1.947  -0.000   0.000   0.000
   2_adp:  0.351  75.053  -1.627  -0.442   1.947  -0.000   0.000   0.000
   2_occ:  0.351  75.053  -1.627  -0.442   1.947  -0.000   0.000   0.000
   3_bss:  0.345  73.856  -1.655  -0.977   1.086  -0.000   0.000   0.000
   3_xyz:  0.345  73.856  -1.655  -0.977   1.086  -0.000   0.000   0.000
   3_adp:  0.345  73.856  -1.655  -0.977   1.086  -0.000   0.000   0.000
   3_occ:  0.345  73.856  -1.655  -0.977   1.086  -0.000   0.000   0.000
   4_bss:  0.327  60.674  -2.274  -2.180  -0.057  -0.000  -0.000  -0.000
   4_xyz:  0.327  60.674  -2.274  -2.180  -0.057  -0.000  -0.000  -0.000
   4_adp:  0.327  60.674  -2.274  -2.180  -0.057  -0.000  -0.000  -0.000
   4_occ:  0.327  60.674  -2.274  -2.180  -0.057  -0.000  -0.000  -0.000
   5_bss:  0.328  67.766  -2.472  -2.601  -0.375  -0.000  -0.000  -0.000
   5_xyz:  0.328  67.766  -2.472  -2.601  -0.375  -0.000  -0.000  -0.000
   5_adp:  0.328  67.766  -2.472  -2.601  -0.375  -0.000  -0.000  -0.000
   5_occ:  0.328  67.766  -2.472  -2.601  -0.375  -0.000  -0.000  -0.000
   5_bss:  0.328  67.769  -2.475  -2.604  -0.378  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.383 0.4138  0.5627    72324.254
   1_bss:  57.184 0.4283  0.6054    70104.809
   1_xyz:  43.657 0.5984  0.8179    44607.390
   1_adp:  45.092 0.5800  0.8015    47207.986
   1_occ:  45.224 0.5782  0.7982    47343.339
   2_bss:  44.884 0.5825  0.7816    47066.160
   2_xyz:  36.152 0.6862  0.8953    31397.445
   2_adp:  34.093 0.7108  0.9126    28940.487
   2_occ:  34.103 0.7107  0.9122    28953.747
   3_bss:  34.058 0.7111  0.8975    28907.857
   3_xyz:  24.279 0.8177  0.9916    15388.825
   3_adp:  23.920 0.8215  1.0036    15013.491
   3_occ:  23.825 0.8225  1.0040    14903.058
   4_bss:  23.733 0.8232  0.9707    14820.615
   4_xyz:  21.879 0.8425  0.9735    12918.482
   4_adp:  18.795 0.8725  0.9757     9977.689
   4_occ:  18.800 0.8724  0.9755     9990.681
   5_bss:  18.780 0.8726  0.9650     9979.729
   5_xyz:  16.704 0.8916  0.9769     8231.140
   5_adp:  16.161 0.8969  0.9727     7948.349
   5_occ:  16.158 0.8969  0.9727     7942.450
   5_bss:  16.158 0.8969  0.9727     7942.450
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.7814e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.7814e-01
   1_xyz:   1.639  0.013  0.111 16.456  0.007  4.099   1.5241e-01
   1_adp:   1.639  0.013  0.111 16.456  0.007  4.099   1.5241e-01
   1_occ:   1.639  0.013  0.111 16.456  0.007  4.099   1.5241e-01
   2_bss:   1.639  0.013  0.111 16.456  0.007  4.099   1.5241e-01
   2_xyz:   1.119  0.007  0.083 14.878  0.005  4.106   6.9444e-02
   2_adp:   1.119  0.007  0.083 14.878  0.005  4.106   6.9444e-02
   2_occ:   1.119  0.007  0.083 14.878  0.005  4.106   6.9444e-02
   3_bss:   1.119  0.007  0.083 14.878  0.005  4.106   6.9444e-02
   3_xyz:   1.175  0.010  0.082 15.169  0.005  4.120   8.1805e-02
   3_adp:   1.175  0.010  0.082 15.169  0.005  4.120   8.1805e-02
   3_occ:   1.175  0.010  0.082 15.169  0.005  4.120   8.1805e-02
   4_bss:   1.175  0.010  0.082 15.169  0.005  4.120   8.1805e-02
   4_xyz:   1.003  0.007  0.074 14.878  0.004  4.112   6.0005e-02
   4_adp:   1.003  0.007  0.074 14.878  0.004  4.112   6.0005e-02
   4_occ:   1.003  0.007  0.074 14.878  0.004  4.112   6.0005e-02
   5_bss:   1.003  0.007  0.074 14.878  0.004  4.112   6.0005e-02
   5_xyz:   0.976  0.007  0.073 14.638  0.004  4.117   5.7155e-02
   5_adp:   0.976  0.007  0.073 14.638  0.004  4.117   5.7155e-02
   5_occ:   0.976  0.007  0.073 14.638  0.004  4.117   5.7155e-02
   5_bss:   0.976  0.007  0.073 14.638  0.004  4.117   5.7155e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.688   2.4215e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.688   2.4215e-01
   1_xyz:   9.162  0.092  0.379 82.133  0.049  2.023   1.1833e-01
   1_adp:   9.162  0.092  0.379 82.133  0.049  2.023   1.1833e-01
   1_occ:   9.162  0.092  0.379 82.133  0.049  2.023   1.1833e-01
   2_bss:   9.162  0.092  0.379 82.133  0.049  2.023   1.1833e-01
   2_xyz:   8.478  0.037  0.286 83.185  0.045  2.309   5.4538e-02
   2_adp:   8.478  0.037  0.286 83.185  0.045  2.309   5.4538e-02
   2_occ:   8.478  0.037  0.286 83.185  0.045  2.309   5.4538e-02
   3_bss:   8.478  0.037  0.286 83.185  0.045  2.309   5.4538e-02
   3_xyz:   9.992  0.057  0.267 86.546  0.031  2.251   1.0119e-01
   3_adp:   9.992  0.057  0.267 86.546  0.031  2.251   1.0119e-01
   3_occ:   9.992  0.057  0.267 86.546  0.031  2.251   1.0119e-01
   4_bss:   9.992  0.057  0.267 86.546  0.031  2.251   1.0119e-01
   4_xyz:   6.535  0.032  0.253 82.252  0.039  2.380   5.6080e-02
   4_adp:   6.535  0.032  0.253 82.252  0.039  2.380   5.6080e-02
   4_occ:   6.535  0.032  0.253 82.252  0.039  2.380   5.6080e-02
   5_bss:   6.535  0.032  0.253 82.252  0.039  2.380   5.6080e-02
   5_xyz:   7.516  0.040  0.218 82.200  0.037  2.367   3.9438e-02
   5_adp:   7.516  0.040  0.218 82.200  0.037  2.367   3.9438e-02
   5_occ:   7.516  0.040  0.218 82.200  0.037  2.367   3.9438e-02
   5_bss:   7.516  0.040  0.218 82.200  0.037  2.367   3.9438e-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:  93.02   0.00  19.12  74.27   0.00  15.27  93.02   0.00  40.06
   1_occ:  93.02   0.00  19.12  74.27   0.00  15.27  93.02   0.00  40.06
   2_bss:  93.02   0.00  19.12  74.27   0.00  15.27  93.02   0.00  40.06
   2_xyz:  93.02   0.00  19.12  74.27   0.00  15.27  93.02   0.00  40.06
   2_adp: 106.19   0.00  18.75 106.19   0.00  14.80  91.66   1.59  40.28
   2_occ: 106.19   0.00  18.75 106.19   0.00  14.80  91.66   1.59  40.28
   3_bss: 106.19   0.00  18.75 106.19   0.00  14.80  91.66   1.59  40.28
   3_xyz: 106.19   0.00  18.75 106.19   0.00  14.80  91.66   1.59  40.28
   3_adp: 104.94   0.00  18.81 104.94   0.00  14.82  91.71   3.48  40.54
   3_occ: 104.94   0.00  18.81 104.94   0.00  14.82  91.71   3.48  40.54
   4_bss: 104.94   0.00  18.81 104.94   0.00  14.82  91.71   3.48  40.54
   4_xyz: 104.94   0.00  18.81 104.94   0.00  14.82  91.71   3.48  40.54
   4_adp:  93.71   0.00  18.22  80.33   0.00  13.46  93.71   6.18  44.16
   4_occ:  93.71   0.00  18.22  80.33   0.00  13.46  93.71   6.18  44.16
   5_bss:  93.71   0.00  18.22  80.33   0.00  13.46  93.71   6.18  44.16
   5_xyz:  93.71   0.00  18.22  80.33   0.00  13.46  93.71   6.18  44.16
   5_adp:  93.78   0.00  18.04  81.40   0.00  13.23  93.78   6.00  44.21
   5_occ:  93.78   0.00  18.04  81.40   0.00  13.23  93.78   6.00  44.21
   5_bss:  93.79   0.00  18.04  81.40   0.00  13.24  93.79   6.00  44.21
------------------------------------------------------------------------
 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:    1.822    0.009    0.446
   1_adp:    1.822    0.009    0.446
   1_occ:    1.822    0.009    0.446
   2_bss:    1.822    0.009    0.446
   2_xyz:    1.510    0.019    0.537
   2_adp:    1.510    0.019    0.537
   2_occ:    1.510    0.019    0.537
   3_bss:    1.510    0.019    0.537
   3_xyz:    1.445    0.033    0.734
   3_adp:    1.445    0.033    0.734
   3_occ:    1.445    0.033    0.734
   4_bss:    1.445    0.033    0.734
   4_xyz:    1.628    0.054    0.754
   4_adp:    1.628    0.054    0.754
   4_occ:    1.628    0.054    0.754
   5_bss:    1.628    0.054    0.754
   5_xyz:    1.715    0.080    0.794
   5_adp:    1.715    0.080    0.794
   5_occ:    1.715    0.080    0.794
   5_bss:    1.715    0.080    0.794
------------------------------------------------------------------------

CPU time actual refinement: 337.62


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/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_747/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_747/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.47 
  Macro-tasks:
    bulk solvent and scale       = 43.79  
    individual site refinement   = 133.61 
    weights calculation          = 30.23  
    collect and process          = 6.62   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.36 
  Micro-tasks:
    mask                            = 2.38   
    f_calc                          = 105.44 
    alpha_beta                      = 8.73   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 112.96 
    fmodel                         = 7.42   
    r_factors                      = 0.30   
    phase_errors                   = 10.46  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 249.10 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.851 micro seconds
Total CPU time: 5.85 minutes
from_scatterers_fft:    631 calls, 105.21 s
gradients_fft:          576 calls, 100.42 s

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

# Date 2008-01-16 Time 05:34:17 PST -0800 (1200490457.57 s)
Start R-work = 0.4687, R-free = 0.4719 (no bulk solvent and anisotropic scale)
Final R-work = 0.1496, R-free = 0.1952 (no bulk solvent and anisotropic scale)

Start R-work = 0.4580, R-free = 0.4661
Final R-work = 0.1266, R-free = 0.1763