# Date 2008-01-16 Time 05:04:55 PST -0800 (1200488695.28 s)
#phil __OFF__

Command line arguments: "../583.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9596
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 583

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.8686, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.923879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9212
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.8686, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9212 1.95155
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.923879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9216 -  4.1766 [2222/2251]  1999   223  10.0%
  bin  2:  4.1766 -  3.3272 [2122/2145]  1912   210   9.9%
  bin  3:  3.3272 -  2.9102 [2092/2117]  1882   210  10.0%
  bin  4:  2.9102 -  2.6457 [2083/2109]  1878   205   9.8%
  bin  5:  2.6457 -  2.4570 [2091/2125]  1881   210  10.0%
  bin  6:  2.4570 -  2.3127 [2043/2071]  1842   201   9.8%
  bin  7:  2.3127 -  2.1972 [2041/2077]  1834   207  10.1%
  bin  8:  2.1972 -  2.1019 [2042/2084]  1833   209  10.2%
  bin  9:  2.1019 -  2.0211 [1991/2073]  1793   198   9.9%
  bin 10:  2.0211 -  1.9516 [ 862/2088]   776    86  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/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:
        1.39 -     2.09: 22
        2.09 -     2.80: 748
        2.80 -     3.50: 4477
        3.50 -     4.20: 9389
        4.20 -     4.90: 13901
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.393 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.539 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.539 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.626 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.654 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28532 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_583/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/model_refine_001.geo

CPU time processing inputs: 9.12


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.8686 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4646   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277537                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.3712 0.3811      6.5633       6.581|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.4042 0.4008      6.8099      6.7704|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.4297 0.4130      6.6528      6.7233|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.4462 0.4251      6.4963      6.4655|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.4844 0.4475      6.3594       6.302|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.4958 0.4574       6.264      6.1602|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.4937 0.4508      6.2418      6.2031|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.5144 0.5705      6.1442      6.1894|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.5386 0.5122      6.1455      6.1294|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.5051 0.5350      6.0885      6.1215|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.5298 0.5491      6.0261      6.0287|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.5039 0.5436      5.9391      5.9784|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.5260 0.4882      5.8776       5.859|
| 14:  2.0002 -  1.9516 0.28    380   37 0.5631 0.4539      5.8272      5.6631|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.68  35.99   0.83     0.71      76211.81|
|  2:  4.6588 -  3.7166  1382   148  0.70  35.27   0.91     0.80     103037.18|
|  3:  3.7166 -  3.2524  1360   152  0.61  42.88   0.92     0.80     107322.45|
|  4:  3.2524 -  2.9575  1339   153  0.54  48.74   0.92     0.75      93164.63|
|  5:  2.9575 -  2.7470  1355   149  0.49  52.75   0.88     0.69      73745.48|
|  6:  2.7470 -  2.5859  1328   149  0.45  55.64   0.90     0.64      63059.46|
|  7:  2.5859 -  2.4570  1344   144  0.43  57.42   0.92     0.58      59321.99|
|  8:  2.4570 -  2.3504  1306   147  0.34  64.51   0.89     0.52      60177.95|
|  9:  2.3504 -  2.2603  1325   140  0.30  67.65   0.92     0.45      57532.93|
| 10:  2.2603 -  2.1825  1316   153  0.26  70.78   0.96     0.39      55739.55|
| 11:  2.1825 -  2.1145  1296   140  0.21  74.42   0.93     0.32      52263.12|
| 12:  2.1145 -  2.0542  1305   152  0.18  76.50   0.95     0.30      49694.72|
| 13:  2.0542 -  2.0002  1150   132  0.21  74.39   0.94     0.34      41050.64|
| 14:  2.0002 -  1.9516   380    37  0.30  67.81   0.89     0.47      31826.26|
|alpha:            min =        0.30 max =            0.80 mean =         0.57|
|beta:             min =    31826.26 max =       107322.45 mean =     68440.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.94|
|phase err.(test): min =        0.00 max =           90.00 mean =        58.08|
|-----------------------------------------------------------------------------|

============================== 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 = 11.959804             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.991   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.060788              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.032   (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 |  1.393 -  1.744:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.744 -  2.095:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.095 -  2.445:       32 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.445 -  2.796:      716 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.796 -  3.147:     2094 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.147 -  3.497:     2383 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.497 -  3.848:     4595 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.848 -  4.199:     4794 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.199 -  4.549:     6299 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.549 -  4.900:     7602 |
|-----------------------------------------------------------------------------|
|-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 |        0.199 |
| 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  1.393 |       0.729 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4646   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.898    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277537                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4537   r_free= 0.4474   ksol= 0.30   Bsol= 20.00   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,3.55,1.99,0.00,0.00,0.00); trace/3= 0.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.269966                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.878890              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.724   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.319087              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.823   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4537      final r-factor (work) = 0.3635          |
| start r-factor (free) = 0.4474      final r-factor (free) = 0.3922          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.1619 = 9.88 * 0.50 * 6.2686 + 1.00 * 0.1987                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5528 = 9.88 * 0.50 * 6.1581 + 1.00 * 0.1351                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3635      final r-factor (work) = 0.3300          |
| start r-factor (free) = 0.3922      final r-factor (free) = 0.4010          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1292 = 1.32 * 1.00 * 6.1581 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0135 = 1.32 * 1.00 * 6.0575 + 1.00 * 0.0231                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.09  19.72    None  None   None       |
|    all(noH): 2823   0      0.00    100.09  19.72    None  None   None       |
|    Sol.    : 438    0      0.69    100.09  38.51    None  None   None       |
|    Mac.    : 2385   0      0.00    93.24   16.27    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 -  10.010:  896   |   5:    50.047 -  60.057:   74        |
|      1:    10.010 -  20.019:  863   |   6:    60.057 -  70.066:   48        |
|      2:    20.019 -  30.029:  484   |   7:    70.066 -  80.076:   20        |
|      3:    30.029 -  40.038:  277   |   8:    80.076 -  90.085:   14        |
|      4:    40.038 -  50.047:  144   |   9:    90.085 - 100.095:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3300 r_free = 0.4010             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3297 r_free = 0.4013             target_work(ml) = 6.065         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3297   r_free= 0.4013   ksol= 0.30   Bsol= 20.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.21,3.55,1.99,0.00,0.00,0.00); trace/3= 0.78                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.064557                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3276   r_free= 0.3985   ksol= 0.32   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,1.79,0.38,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.063610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.808996              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.690   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.622387              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.550  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3276      final r-factor (work) = 0.2614          |
| start r-factor (free) = 0.3985      final r-factor (free) = 0.3304          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.7837 = 7.81 * 0.50 * 6.0568 + 1.00 * 0.1351                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4454 = 7.81 * 0.50 * 5.9828 + 1.00 * 0.0856                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2614      final r-factor (work) = 0.2440          |
| start r-factor (free) = 0.3304      final r-factor (free) = 0.3155          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7457 = 0.62 * 1.00 * 5.9828 + 1.00 * 0.0221                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6565 = 0.62 * 1.00 * 5.8541 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.28   18.81    None  None   None       |
|    all(noH): 2823   0      0.00    98.28   18.81    None  None   None       |
|    Sol.    : 438    0      4.27    98.28   39.29    None  None   None       |
|    Mac.    : 2385   0      0.00    93.76   15.05    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 -   9.828:  948   |   5:    49.140 -  58.968:   86        |
|      1:     9.828 -  19.656:  928   |   6:    58.968 -  68.796:   42        |
|      2:    19.656 -  29.484:  405   |   7:    68.796 -  78.624:   19        |
|      3:    29.484 -  39.312:  238   |   8:    78.624 -  88.452:   14        |
|      4:    39.312 -  49.140:  138   |   9:    88.452 -  98.280:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2440 r_free = 0.3155             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2438 r_free = 0.3152             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2438   r_free= 0.3152   ksol= 0.32   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.94,1.79,0.38,0.00,0.00,0.00); trace/3= 0.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.832609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2436   r_free= 0.3144   ksol= 0.32   Bsol= 50.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,0.54,-0.59,0.00,-0.00,-0.00); trace/3= -0.61                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.831077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.652127              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.513   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 19.363282             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.896  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2436      final r-factor (work) = 0.1830          |
| start r-factor (free) = 0.3144      final r-factor (free) = 0.2350          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6295 = 5.65 * 0.50 * 5.8540 + 1.00 * 0.0856                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2579 = 5.65 * 0.50 * 5.7280 + 1.00 * 0.0703                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1830      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2350      final r-factor (free) = 0.2172          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 110.9252 = 19.36 * 1.00 * 5.7280 + 1.00 * 0.0130                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 106.5494 = 19.36 * 1.00 * 5.5018 + 1.00 * 0.0161                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.10  19.15    None  None   None       |
|    all(noH): 2823   0      0.00    110.10  19.15    None  None   None       |
|    Sol.    : 438    0      6.73    106.79  47.38    None  None   None       |
|    Mac.    : 2385   0      0.00    110.10  13.96    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 -  11.011: 1234   |   5:    55.052 -  66.063:   94        |
|      1:    11.011 -  22.021:  905   |   6:    66.063 -  77.073:   49        |
|      2:    22.021 -  33.031:  239   |   7:    77.073 -  88.084:   37        |
|      3:    33.031 -  44.042:  124   |   8:    88.084 -  99.094:   19        |
|      4:    44.042 -  55.052:  117   |   9:    99.094 - 110.105:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1592 r_free = 0.2172             target_work(ml) = 5.458         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1592 r_free = 0.2172             target_work(ml) = 5.458         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1592   r_free= 0.2172   ksol= 0.32   Bsol= 50.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,0.54,-0.59,0.00,-0.00,-0.00); trace/3= -0.61                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.457643                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1591   r_free= 0.2170   ksol= 0.33   Bsol= 60.15   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-0.56,-1.40,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.458328                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.241301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.778  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259603              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.022  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1591      final r-factor (work) = 0.1399          |
| start r-factor (free) = 0.2170      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2422 = 2.24 * 0.50 * 5.5074 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1114 = 2.24 * 0.50 * 5.4059 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1399      final r-factor (work) = 0.1369          |
| start r-factor (free) = 0.1943      final r-factor (free) = 0.1887          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4195 = 0.26 * 1.00 * 5.4059 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4092 = 0.26 * 1.00 * 5.3375 + 1.00 * 0.0236                               |
|-----------------------------------------------------------------------------|
| number of iterations = 3       |    number of function evaluations = 3      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.94  19.15    None  None   None       |
|    all(noH): 2823   0      0.00    109.94  19.15    None  None   None       |
|    Sol.    : 438    0      6.20    106.22  47.12    None  None   None       |
|    Mac.    : 2385   0      0.00    109.94  14.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.994: 1246   |   5:    54.972 -  65.966:   92        |
|      1:    10.994 -  21.989:  906   |   6:    65.966 -  76.961:   52        |
|      2:    21.989 -  32.983:  227   |   7:    76.961 -  87.955:   36        |
|      3:    32.983 -  43.978:  125   |   8:    87.955 -  98.950:   18        |
|      4:    43.978 -  54.972:  116   |   9:    98.950 - 109.944:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1369 r_free = 0.1887             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1368 r_free = 0.1885             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1368   r_free= 0.1885   ksol= 0.33   Bsol= 60.15   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-0.56,-1.40,-0.00,-0.00,-0.00); trace/3= -1.42                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.320523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1886   ksol= 0.32   Bsol= 57.13   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.19,-1.72,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.323268                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.699004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.819  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.105369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.140   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1886      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9260 = 3.70 * 0.50 * 5.3381 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8402 = 3.70 * 0.50 * 5.2819 + 1.00 * 0.0714                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1221          |
| start r-factor (free) = 0.1771      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6149 = 0.11 * 1.00 * 5.2819 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.5600 = 0.11 * 1.00 * 5.2455 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.71    96.54   17.27    None  None   None       |
|    all(noH): 2823   0      2.71    96.54   17.27    None  None   None       |
|    Sol.    : 438    0      5.70    85.81   39.91    None  None   None       |
|    Mac.    : 2385   0      2.71    96.54   13.11    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:     2.706 -  12.089: 1453   |   5:    49.621 -  59.004:   60        |
|      1:    12.089 -  21.472:  806   |   6:    59.004 -  68.387:   38        |
|      2:    21.472 -  30.855:  179   |   7:    68.387 -  77.769:   19        |
|      3:    30.855 -  40.238:  132   |   8:    77.769 -  87.152:   17        |
|      4:    40.238 -  49.621:  115   |   9:    87.152 -  96.535:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1221 r_free = 0.1653             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1652             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1652   ksol= 0.32   Bsol= 57.13   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.19,-1.72,-0.00,-0.00,-0.00); trace/3= -1.83                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.208763                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.0946 0.1278      5.3511      5.5522|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.0871 0.1123      5.4546      5.6768|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.1139 0.1646      5.5254      5.9112|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.1385 0.1621      5.5255      5.6602|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.1444 0.1856      5.3841      5.5394|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.1399 0.2016      5.2866      5.4809|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.1370 0.1857      5.2398      5.4534|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.1377 0.1883      5.1573      5.3701|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.1320 0.1768       5.086      5.2827|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.1266 0.1831      5.0316      5.2792|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.1244 0.1839      4.9679      5.2462|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.1245 0.1822      4.9024      5.1257|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.1254 0.1744      4.8309      5.0371|
| 14:  2.0002 -  1.9516 0.28    380   37 0.1288 0.2027      4.7534      5.0131|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.94   9.24   0.98     0.96       7131.97|
|  2:  4.6588 -  3.7166  1382   148  0.95   8.38   1.02     1.01       9455.06|
|  3:  3.7166 -  3.2524  1360   152  0.92  12.52   1.03     1.02      11419.74|
|  4:  3.2524 -  2.9575  1339   153  0.91  15.25   1.02     1.00      11602.52|
|  5:  2.9575 -  2.7470  1355   149  0.89  17.43   1.01     0.98       9245.81|
|  6:  2.7470 -  2.5859  1328   149  0.89  17.12   0.99     0.97       7822.02|
|  7:  2.5859 -  2.4570  1344   144  0.89  16.92   1.00     0.97       7087.11|
|  8:  2.4570 -  2.3504  1306   147  0.89  17.72   1.01     0.98       6358.95|
|  9:  2.3504 -  2.2603  1325   140  0.89  17.18   1.01     0.99       5472.65|
| 10:  2.2603 -  2.1825  1316   153  0.90  16.27   1.01     0.97       4846.58|
| 11:  2.1825 -  2.1145  1296   140  0.89  16.98   1.02     0.99       4512.10|
| 12:  2.1145 -  2.0542  1305   152  0.91  15.95   1.01     1.00       3977.19|
| 13:  2.0542 -  2.0002  1150   132  0.89  17.18   1.01     1.01       3468.39|
| 14:  2.0002 -  1.9516   380    37  0.88  17.57   0.99     0.96       2978.00|
|alpha:            min =        0.96 max =            1.02 mean =         0.99|
|beta:             min =     2978.00 max =        11602.52 mean =      7088.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.31 mean =        14.57|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1651   ksol= 0.33   Bsol= 49.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.46,-1.83,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.208539                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1216   r_free= 0.1651   ksol= 0.33   Bsol= 49.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-1.46,-1.83,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.208539                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9216 -  4.6588 0.99   1444  163 0.0944 0.1276      5.3498      5.5466|
|  2:  4.6588 -  3.7166 0.99   1382  148 0.0863 0.1109      5.4472      5.6679|
|  3:  3.7166 -  3.2524 0.99   1360  152 0.1137 0.1641      5.5212      5.9099|
|  4:  3.2524 -  2.9575 0.98   1339  153 0.1385 0.1617      5.5252      5.6594|
|  5:  2.9575 -  2.7470 0.99   1355  149 0.1446 0.1858      5.3851      5.5398|
|  6:  2.7470 -  2.5859 0.99   1328  149 0.1400 0.2019      5.2876      5.4826|
|  7:  2.5859 -  2.4570 0.98   1344  144 0.1373 0.1856       5.241      5.4529|
|  8:  2.4570 -  2.3504 0.98   1306  147 0.1377 0.1888      5.1588      5.3733|
|  9:  2.3504 -  2.2603 0.99   1325  140 0.1319 0.1771      5.0872      5.2848|
| 10:  2.2603 -  2.1825 0.99   1316  153 0.1267 0.1833      5.0329      5.2812|
| 11:  2.1825 -  2.1145 0.97   1296  140 0.1246 0.1840      4.9688      5.2463|
| 12:  2.1145 -  2.0542 0.98   1305  152 0.1247 0.1826      4.9041      5.1278|
| 13:  2.0542 -  2.0002 0.87   1150  132 0.1253 0.1744      4.8318      5.0365|
| 14:  2.0002 -  1.9516 0.28    380   37 0.1288 0.2027      4.7538      5.0139|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9216 -  4.6588  1444   163  0.94   9.20   0.98     0.96       7113.83|
|  2:  4.6588 -  3.7166  1382   148  0.95   8.35   1.02     1.01       9331.96|
|  3:  3.7166 -  3.2524  1360   152  0.93  12.41   1.02     1.02      11261.66|
|  4:  3.2524 -  2.9575  1339   153  0.91  15.21   1.01     0.99      11581.76|
|  5:  2.9575 -  2.7470  1355   149  0.89  17.41   1.00     0.97       9240.59|
|  6:  2.7470 -  2.5859  1328   149  0.89  17.12   0.98     0.96       7831.01|
|  7:  2.5859 -  2.4570  1344   144  0.89  16.93   0.99     0.96       7104.28|
|  8:  2.4570 -  2.3504  1306   147  0.89  17.77   1.00     0.97       6386.27|
|  9:  2.3504 -  2.2603  1325   140  0.89  17.22   1.00     0.98       5499.53|
| 10:  2.2603 -  2.1825  1316   153  0.90  16.30   0.99     0.95       4862.95|
| 11:  2.1825 -  2.1145  1296   140  0.89  17.00   1.00     0.97       4525.63|
| 12:  2.1145 -  2.0542  1305   152  0.91  15.97   1.00     0.99       3990.79|
| 13:  2.0542 -  2.0002  1150   132  0.89  17.19   1.00     1.00       3473.88|
| 14:  2.0002 -  1.9516   380    37  0.88  17.57   0.98     0.95       2975.24|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2975.24 max =        11581.76 mean =      7072.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.20|
|phase err.(test): min =        0.00 max =           89.54 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.720)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.61    96.44   17.17    None  None   None       |
|    all(noH): 2823   0      2.61    96.44   17.17    None  None   None       |
|    Sol.    : 438    0      5.60    85.71   39.81    None  None   None       |
|    Mac.    : 2385   0      2.61    96.44   13.01    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:     2.608 -  11.991: 1453   |   5:    49.522 -  58.905:   60        |
|      1:    11.991 -  21.374:  806   |   6:    58.905 -  68.288:   38        |
|      2:    21.374 -  30.756:  179   |   7:    68.288 -  77.671:   19        |
|      3:    30.756 -  40.139:  132   |   8:    77.671 -  87.054:   17        |
|      4:    40.139 -  49.522:  115   |   9:    87.054 -  96.437:    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)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.442 - 5.914
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 315 from: 321
   mapped sites are within: 0.718 - 5.914

peak=    6.342 closest distance to " O   HOH Z 352 " =    1.348
peak=    5.700 closest distance to " CB  SER A  63 " =    1.168
peak=    5.676 closest distance to " O   HOH Z 138 " =    1.084
peak=    5.464 closest distance to " O   HOH Z 210 " =    1.317
peak=    5.435 closest distance to " O   HOH Z 113 " =    2.283
peak=    5.326 closest distance to " O   HOH Z 124 " =    1.548
peak=    5.199 closest distance to " O   HOH Z 402 " =    1.655
peak=    5.186 closest distance to " O   HOH Z  11 " =    1.386
peak=    5.068 closest distance to " CG  PRO A  54 " =    1.183
peak=    5.012 closest distance to " O   HOH Z 134 " =    1.989
peak=    4.976 closest distance to " CA  TYR A  30 " =    1.084
peak=    4.935 closest distance to " O   HOH Z  80 " =    1.865
peak=    4.894 closest distance to " O   HOH Z 132 " =    1.473
peak=    4.851 closest distance to " O   HOH Z 142 " =    1.508
peak=    4.834 closest distance to " O   PRO A 198 " =    1.580
peak=    4.728 closest distance to " O   HOH Z  97 " =    1.889
peak=    4.713 closest distance to " O   HOH Z  15 " =    2.192
peak=    4.698 closest distance to " O   HOH Z 389 " =    2.024
peak=    4.675 closest distance to " O   HOH Z 209 " =    2.259
peak=    4.637 closest distance to " O   HOH Z 133 " =    1.736
peak=    4.550 closest distance to " O   HOH Z 214 " =    1.128
peak=    4.547 closest distance to " O   HOH Z 211 " =    1.387
peak=    4.517 closest distance to " O   SER A  87 " =    2.073
peak=    4.499 closest distance to " O   HOH Z  43 " =    1.637
peak=    4.484 closest distance to " CB  SER A   3 " =    1.449
peak=    4.434 closest distance to " O   HOH Z 234 " =    3.866
peak=    4.408 closest distance to " O   HOH Z 411 " =    3.482
peak=    4.379 closest distance to " O   HOH Z  40 " =    1.807
peak=    4.338 closest distance to " O   HOH Z 127 " =    1.169
peak=    4.326 closest distance to " O   HOH Z 371 " =    3.342
peak=    4.310 closest distance to " O   HOH Z 108 " =    1.505
peak=    4.308 closest distance to " CB  GLN A 223 " =    1.516
peak=    4.304 closest distance to " O   HOH Z 316 " =    2.817
peak=    4.290 closest distance to " NH2 ARG A 156 " =    1.280
peak=    4.284 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.270 closest distance to " CB  GLN A 183 " =    1.219
peak=    4.255 closest distance to " O   HOH Z 126 " =    1.746
peak=    4.249 closest distance to " O   HOH Z 272 " =    2.013
peak=    4.247 closest distance to " O   HOH Z 193 " =    1.914
peak=    4.242 closest distance to " O   HOH Z 154 " =    1.550
peak=    4.210 closest distance to " O   HOH Z 278 " =    1.029
peak=    4.205 closest distance to " O   HOH Z 403 " =    1.797
peak=    4.187 closest distance to " CD  LYS A 166 " =    1.456
peak=    4.183 closest distance to " OE1 GLN A  11 " =    1.945
peak=    4.180 closest distance to " O   HOH Z 422 " =    0.750
peak=    4.157 closest distance to " O   HOH Z 247 " =    1.423
peak=    4.149 closest distance to " O   HOH Z 189 " =    1.843
peak=    4.148 closest distance to " CB  SER A 141 " =    0.988
peak=    4.143 closest distance to " CD  PRO A  54 " =    0.985
peak=    4.143 closest distance to " O   HOH Z 130 " =    1.300
peak=    4.131 closest distance to " CB  VAL A 202 " =    1.527
peak=    4.128 closest distance to " O   HOH Z 236 " =    1.963
peak=    4.121 closest distance to " NZ  LYS A 117 " =    0.939
peak=    4.111 closest distance to " N   ASN A  39 " =    1.273
peak=    4.063 closest distance to " CG  GLN A  77 " =    0.835
peak=    4.039 closest distance to " O   HOH Z 433 " =    1.558
peak=    4.035 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.021 closest distance to " CB  GLU A 152 " =    1.142
peak=    4.020 closest distance to " O   HOH Z 326 " =    1.610
peak=    4.012 closest distance to " O   HOH Z   6 " =    2.002
peak=    4.011 closest distance to " CG1 ILE A  33 " =    1.199
peak=    4.007 closest distance to " O   HOH Z 260 " =    1.394
peak=    4.006 closest distance to " O   HOH Z  97 " =    2.364
peak=    4.003 closest distance to " ND2 ASN A 187 " =    1.624
peak=    3.999 closest distance to " O   HOH Z 163 " =    1.655
peak=    3.996 closest distance to " O   HOH Z 406 " =    1.492
peak=    3.994 closest distance to " CB  ASN A 285 " =    0.925
peak=    3.988 closest distance to " O   HOH Z 334 " =    1.548
peak=    3.986 closest distance to " O   HOH Z  63 " =    2.323
peak=    3.977 closest distance to " O   HOH Z  39 " =    1.513
peak=    3.970 closest distance to " O   HOH Z  35 " =    2.261
peak=    3.959 closest distance to " CB  ARG A  79 " =    1.481
peak=    3.951 closest distance to " CA  ALA A  21 " =    1.235
peak=    3.947 closest distance to " O   HOH Z 369 " =    1.952
peak=    3.941 closest distance to " CG AARG A 275 " =    0.943
peak=    3.916 closest distance to " O   HOH Z 386 " =    2.251
peak=    3.901 closest distance to " O   HOH Z 108 " =    2.179
peak=    3.900 closest distance to " O   HOH Z 357 " =    1.945
peak=    3.893 closest distance to " O   HOH Z 147 " =    1.658
peak=    3.892 closest distance to " O   HOH Z 232 " =    2.406
peak=    3.875 closest distance to " OD1 ASP A 238 " =    0.849
peak=    3.872 closest distance to " O   HOH Z 196 " =    1.125
peak=    3.871 closest distance to " O   HOH Z 130 " =    2.629
peak=    3.863 closest distance to " O   HOH Z  67 " =    1.989
peak=    3.862 closest distance to " CB  GLU A 277 " =    3.619
peak=    3.857 closest distance to " CB  ARG A 139 " =    1.222
peak=    3.851 closest distance to " CB  TYR A 169 " =    0.879
peak=    3.851 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.850 closest distance to " O   HOH Z 394 " =    1.680
peak=    3.846 closest distance to " O   HOH Z 313 " =    1.817
peak=    3.845 closest distance to " O   HOH Z 427 " =    3.061
peak=    3.843 closest distance to " CB  SER A  62 " =    0.894
peak=    3.827 closest distance to " O   HOH Z 106 " =    1.508
peak=    3.813 closest distance to " CG AARG A 275 " =    1.195
peak=    3.810 closest distance to " O   HOH Z 132 " =    2.594
peak=    3.809 closest distance to " CB  GLU A 128 " =    1.146
peak=    3.808 closest distance to " O   HOH Z  44 " =    1.939
peak=    3.805 closest distance to " O   HOH Z 118 " =    1.346
peak=    3.803 closest distance to " O   HOH Z 221 " =    1.437
peak=    3.791 closest distance to " O   HOH Z 291 " =    1.578
peak=    3.787 closest distance to " CA  ASP A 191 " =    0.885
peak=    3.768 closest distance to " O   HOH Z 365 " =    2.077
peak=    3.756 closest distance to " NH2AARG A 190 " =    1.324
peak=    3.751 closest distance to " O   HOH Z 199 " =    1.072
peak=    3.750 closest distance to " O   SER A  26 " =    1.643
peak=    3.736 closest distance to " CB  ALA A 100 " =    1.282
peak=    3.727 closest distance to " O   ALA A 165 " =    1.196
peak=    3.722 closest distance to " O   HOH Z 358 " =    2.077
peak=    3.721 closest distance to " NH2BARG A 145 " =    1.913
peak=    3.717 closest distance to " O   HOH Z  54 " =    1.631
peak=    3.710 closest distance to " O   HOH Z 133 " =    1.870
peak=    3.707 closest distance to " O   HOH Z 280 " =    2.354
peak=    3.702 closest distance to " NH2AARG A 145 " =    2.178
peak=    3.686 closest distance to " O   HOH Z 369 " =    1.488
peak=    3.685 closest distance to " O   HOH Z  20 " =    1.618
peak=    3.684 closest distance to " CA  ILE A 106 " =    0.791
peak=    3.679 closest distance to " CG2 THR A 221 " =    1.108
peak=    3.679 closest distance to " O   HOH Z 279 " =    1.995
peak=    3.674 closest distance to " CA  ASN A 176 " =    1.779
peak=    3.673 closest distance to " O   HOH Z 344 " =    2.795
peak=    3.664 closest distance to " O   HOH Z 227 " =    1.692
peak=    3.663 closest distance to " CB  ASN A 148 " =    1.858
peak=    3.663 closest distance to " O   HOH Z 287 " =    1.811
peak=    3.654 closest distance to " O   HOH Z 408 " =    1.607
peak=    3.647 closest distance to " CB  ARG A 190 " =    1.777
peak=    3.646 closest distance to " O   HOH Z 374 " =    2.564
peak=    3.644 closest distance to " O   HOH Z 197 " =    2.014
peak=    3.642 closest distance to " O   HOH Z 362 " =    3.308
peak=    3.639 closest distance to " CG1 VAL A 153 " =    1.125
peak=    3.635 closest distance to " CB  PRO A 198 " =    1.087
peak=    3.630 closest distance to " NE2 GLN A  11 " =    1.100
peak=    3.628 closest distance to " CB  TRP A 179 " =    1.258
peak=    3.627 closest distance to " CG  PRO A 198 " =    1.337
peak=    3.626 closest distance to " CG1BVAL A  72 " =    1.684
peak=    3.626 closest distance to " OD2 ASP A 286 " =    2.653
peak=    3.622 closest distance to " O   HOH Z 402 " =    2.677
peak=    3.619 closest distance to " O   HOH Z 163 " =    2.025
peak=    3.613 closest distance to " O   HOH Z 279 " =    1.182
peak=    3.612 closest distance to " CG  ARG A  66 " =    0.949
peak=    3.608 closest distance to " O   HOH Z 227 " =    1.915
peak=    3.604 closest distance to " OG  SER A  62 " =    3.095
peak=    3.599 closest distance to " O   HOH Z 145 " =    1.873
peak=    3.598 closest distance to " O   HOH Z 109 " =    3.091
peak=    3.596 closest distance to " ND1 HIS A  81 " =    1.362
peak=    3.595 closest distance to " O   HOH Z 166 " =    1.267
peak=    3.595 closest distance to " O   HOH Z 109 " =    2.363
peak=    3.594 closest distance to " O   HOH Z  88 " =    3.388
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.782
peak=    3.582 closest distance to " O   HOH Z  61 " =    1.527
peak=    3.572 closest distance to " CA  ASP A 162 " =    1.138
peak=    3.566 closest distance to " CB  ASN A 187 " =    1.250
peak=    3.565 closest distance to " CA  GLN A 223 " =    0.825
peak=    3.560 closest distance to " O   HOH Z  78 " =    1.696
peak=    3.558 closest distance to " CG  PRO A 243 " =    1.224
peak=    3.558 closest distance to " O   GLY A 211 " =    1.443
peak=    3.548 closest distance to " O   HOH Z 345 " =    1.856
peak=    3.546 closest distance to " CB  ASN A 148 " =    1.248
peak=    3.540 closest distance to " O   HOH Z 438 " =    2.449
peak=    3.534 closest distance to " CB  LEU A 228 " =    1.199
peak=    3.532 closest distance to " O   HOH Z 250 " =    1.746
peak=    3.531 closest distance to " O   HOH Z 130 " =    2.456
peak=    3.528 closest distance to " O   GLY A  91 " =    1.324
peak=    3.519 closest distance to " O   HOH Z 117 " =    1.170
peak=    3.519 closest distance to " O   HOH Z 298 " =    1.900
peak=    3.518 closest distance to " CA  THR A 221 " =    0.942
peak=    3.515 closest distance to " O   HOH Z 207 " =    2.448
peak=    3.510 closest distance to " CD  ARG A 195 " =    1.057
peak=    3.506 closest distance to " C   SER A  32 " =    1.083
peak=    3.495 closest distance to " CA  GLY A 196 " =    1.063
peak=    3.492 closest distance to " O   HOH Z  66 " =    2.177
peak=    3.485 closest distance to " O   HOH Z 261 " =    2.043
peak=    3.484 closest distance to " O   HOH Z 327 " =    1.719
peak=    3.479 closest distance to " CD  LYS A 119 " =    1.686
peak=    3.478 closest distance to " O   HOH Z 150 " =    1.587
peak=    3.476 closest distance to " O   HOH Z 255 " =    1.748
peak=    3.474 closest distance to " CB  GLN A  73 " =    0.974
peak=    3.472 closest distance to " NE AARG A 275 " =    1.275
peak=    3.469 closest distance to " O   HOH Z 173 " =    2.120
peak=    3.469 closest distance to " NE1 TRP A 274 " =    0.884
peak=    3.454 closest distance to " O   HOH Z 155 " =    2.947
peak=    3.451 closest distance to " CB  GLN A  88 " =    1.151
peak=    3.442 closest distance to " O   HOH Z  71 " =    1.318
peak=    3.442 closest distance to " O   HOH Z 128 " =    2.166
peak=    3.437 closest distance to " O   HOH Z  51 " =    1.511
peak=    3.433 closest distance to " O   HOH Z 428 " =    1.319
peak=    3.430 closest distance to " CB  ASN A  39 " =    0.807
peak=    3.423 closest distance to " CG1BVAL A  72 " =    3.246
peak=    3.420 closest distance to " CA  ARG A 195 " =    1.116
peak=    3.418 closest distance to " O   HOH Z 248 " =    1.575
peak=    3.417 closest distance to " OD1 ASN A  69 " =    2.461
peak=    3.413 closest distance to " O   HOH Z 423 " =    1.942
peak=    3.408 closest distance to " OE1 GLN A  58 " =    5.914
peak=    3.407 closest distance to " O   HOH Z 437 " =    1.651
peak=    3.407 closest distance to " O   HOH Z 387 " =    2.328
peak=    3.403 closest distance to " O   HOH Z 404 " =    1.589
peak=    3.402 closest distance to " CA  GLU A 152 " =    0.909
peak=    3.397 closest distance to " CB  GLN A  58 " =    0.815
peak=    3.390 closest distance to " CG2 THR A 251 " =    1.066
peak=    3.389 closest distance to " CD  ARG A 269 " =    1.161
peak=    3.389 closest distance to " O   GLY A  23 " =    2.366
peak=    3.386 closest distance to " O   HOH Z 346 " =    1.503
peak=    3.382 closest distance to " CG  GLN A  58 " =    2.177
peak=    3.376 closest distance to " O   HOH Z 102 " =    1.259
peak=    3.373 closest distance to " NH1AARG A 145 " =    0.945
peak=    3.373 closest distance to " OH  TYR A  30 " =    1.239
peak=    3.370 closest distance to " O   HOH Z  30 " =    1.463
peak=    3.367 closest distance to " O   ARG A 102 " =    2.280
peak=    3.367 closest distance to " O   HOH Z 403 " =    1.586
peak=    3.366 closest distance to " O   HOH Z 345 " =    2.534
peak=    3.364 closest distance to " O  BHOH Z 338 " =    2.261
peak=    3.364 closest distance to " SD  MET A 185 " =    1.065
peak=    3.363 closest distance to " O   HOH Z  47 " =    1.372
peak=    3.355 closest distance to " CD2 HIS A  81 " =    1.424
peak=    3.353 closest distance to " CB  TRP A 179 " =    1.697
peak=    3.353 closest distance to " O   HOH Z 409 " =    3.337
peak=    3.347 closest distance to " CH2 TRP A 274 " =    1.879
peak=    3.342 closest distance to " CB  GLN A 194 " =    0.814
peak=    3.338 closest distance to " O   MET A 105 " =    1.875
peak=    3.331 closest distance to " OG1 THR A 294 " =    2.428
peak=    3.325 closest distance to " CB  GLU A 277 " =    0.777
peak=    3.322 closest distance to " O   HOH Z 284 " =    2.777
peak=    3.319 closest distance to " O   HOH Z 395 " =    1.521
peak=    3.312 closest distance to " O   HOH Z 250 " =    1.537
peak=    3.310 closest distance to " CA  ARG A  66 " =    1.264
peak=    3.310 closest distance to " O   HOH Z 426 " =    1.519
peak=    3.310 closest distance to " CE  LYS A 119 " =    1.083
peak=    3.301 closest distance to " O   HOH Z 106 " =    2.215
peak=    3.297 closest distance to " O   HOH Z  29 " =    1.514
peak=    3.297 closest distance to " O   HOH Z 434 " =    1.513
peak=    3.296 closest distance to " NH2AARG A 275 " =    3.572
peak=    3.292 closest distance to " CA  LEU A 282 " =    1.183
peak=    3.290 closest distance to " O   HOH Z 104 " =    3.326
peak=    3.289 closest distance to " O   HOH Z  66 " =    1.533
peak=    3.281 closest distance to " NZ  LYS A 117 " =    3.064
peak=    3.279 closest distance to " NZ  LYS A  76 " =    1.822
peak=    3.273 closest distance to " NZ  LYS A  76 " =    1.240
peak=    3.271 closest distance to " CA  VAL A 126 " =    0.862
peak=    3.270 closest distance to " CG  PRO A  90 " =    1.185
peak=    3.270 closest distance to " OG BSER A 164 " =    2.497
peak=    3.269 closest distance to " O   HOH Z 343 " =    2.361
peak=    3.267 closest distance to " O   ALA A 158 " =    1.199
peak=    3.266 closest distance to " O   HOH Z  63 " =    2.088
peak=    3.264 closest distance to " O   HOH Z 368 " =    2.433
peak=    3.263 closest distance to " CB  ILE A 199 " =    1.179
peak=    3.258 closest distance to " OG  SER A 245 " =    1.495
peak=    3.254 closest distance to " NZ  LYS A 119 " =    1.445
peak=    3.252 closest distance to " CA  ARG A  36 " =    1.023
peak=    3.251 closest distance to " CG  GLN A  11 " =    1.156
peak=    3.249 closest distance to " O   HOH Z 417 " =    3.075
peak=    3.249 closest distance to " O   THR A 264 " =    1.479
peak=    3.245 closest distance to " CB  ALA A  71 " =    1.200
peak=    3.243 closest distance to " O   HOH Z 298 " =    5.041
peak=    3.242 closest distance to " CA  VAL A  41 " =    0.816
peak=    3.242 closest distance to " CD2 TRP A 179 " =    1.299
peak=    3.241 closest distance to " CG1 VAL A 174 " =    1.221
peak=    3.238 closest distance to " O   HOH Z 435 " =    1.661
peak=    3.237 closest distance to " CB  ALA A 291 " =    1.284
peak=    3.233 closest distance to " OG BSER A 210 " =    1.248
peak=    3.228 closest distance to " O   HOH Z 144 " =    1.864
peak=    3.223 closest distance to " O   HOH Z 126 " =    2.041
peak=    3.221 closest distance to " N   ARG A 156 " =    1.408
peak=    3.218 closest distance to " O   HOH Z 126 " =    1.760
peak=    3.218 closest distance to " CD1 LEU A 300 " =    1.281
peak=    3.217 closest distance to " CB  PHE A  16 " =    1.261
peak=    3.217 closest distance to " CB  MET A 105 " =    1.175
peak=    3.216 closest distance to " O   HOH Z 383 " =    1.898
peak=    3.214 closest distance to " O   HOH Z 281 " =    4.115
peak=    3.211 closest distance to " OD1 ASN A  60 " =    1.199
peak=    3.210 closest distance to " CB  ALA A 244 " =    0.902
peak=    3.210 closest distance to " CB  ALA A 256 " =    1.106
peak=    3.207 closest distance to " O   HOH Z 299 " =    1.585
peak=    3.207 closest distance to " O   HOH Z 156 " =    2.573
peak=    3.204 closest distance to " O   HOH Z 382 " =    1.345
peak=    3.198 closest distance to " CB  TRP A 123 " =    1.203
peak=    3.193 closest distance to " O   HOH Z 162 " =    1.753
peak=    3.190 closest distance to " O   HOH Z 421 " =    1.592
peak=    3.188 closest distance to " O   HOH Z 261 " =    2.237
peak=    3.182 closest distance to " O   HOH Z  78 " =    2.055
peak=    3.181 closest distance to " CA  PRO A  90 " =    1.003
peak=    3.179 closest distance to " O   HOH Z 265 " =    2.304
peak=    3.179 closest distance to " O   HOH Z 425 " =    1.497
peak=    3.171 closest distance to " CG1 VAL A 202 " =    1.997
peak=    3.171 closest distance to " O   HOH Z  98 " =    2.027
peak=    3.168 closest distance to " O   HOH Z  59 " =    1.834
peak=    3.163 closest distance to " NH1BARG A 145 " =    1.279
peak=    3.162 closest distance to " O   THR A 251 " =    1.390
peak=    3.136 closest distance to " CB  MET A  47 " =    1.199
peak=    3.131 closest distance to " O   HOH Z  76 " =    1.538
peak=    3.129 closest distance to " CG2 ILE A 120 " =    1.149
peak=    3.126 closest distance to " CB  ASN A 127 " =    0.953
peak=    3.125 closest distance to " O   HOH Z 303 " =    2.229
peak=    3.124 closest distance to " O   SER A 164 " =    1.347
peak=    3.122 closest distance to " OD1 ASP A 253 " =    1.913
peak=    3.119 closest distance to " O   HOH Z  88 " =    1.559
peak=    3.118 closest distance to " O   HOH Z 427 " =    2.785
peak=    3.114 closest distance to " O   HOH Z  22 " =    2.212
peak=    3.113 closest distance to " OG1 THR A 294 " =    4.092
peak=    3.097 closest distance to " CA  THR A  52 " =    1.150
peak=    3.097 closest distance to " O   HOH Z 273 " =    2.535
peak=    3.096 closest distance to " CG  MET A 113 " =    1.499
peak=    3.096 closest distance to " O   HOH Z 110 " =    1.684
peak=    3.087 closest distance to " CD1 LEU A 228 " =    1.746
peak=    3.087 closest distance to " CG  MET A 185 " =    1.254
peak=    3.083 closest distance to " O   HOH Z 420 " =    2.040
peak=    3.083 closest distance to " O   HOH Z 214 " =    2.090
peak=    3.073 closest distance to " O   HOH Z 293 " =    1.866
peak=    3.070 closest distance to " CA  ALA A 158 " =    1.137
peak=    3.070 closest distance to " N   PHE A 130 " =    1.384
peak=    3.062 closest distance to " O   HOH Z 130 " =    3.107
peak=    3.052 closest distance to " CB  PRO A  54 " =    1.229
peak=    3.045 closest distance to " CB  PHE A 283 " =    0.718
peak=    3.036 closest distance to " CB  THR A  31 " =    1.823
peak=    3.033 closest distance to " CB  ALA A   1 " =    1.117
peak=    3.029 closest distance to " CA  GLY A  80 " =    0.882
peak=    3.023 closest distance to " CD2 LEU A 297 " =    0.751

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.393 - 5.130
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 213
   mapped sites are within: 0.700 - 5.130

peak=   -5.203 closest distance to " O   HOH Z 290 " =    0.733
peak=   -4.861 closest distance to " O   HOH Z 221 " =    1.057
peak=   -4.660 closest distance to " O   HOH Z 377 " =    0.808
peak=   -4.310 closest distance to " O   HOH Z 166 " =    1.972
peak=   -4.292 closest distance to " O   HOH Z 266 " =    4.225
peak=   -4.276 closest distance to " NH2 ARG A  79 " =    1.856
peak=   -4.267 closest distance to " OXT GLY A 302 " =    2.749
peak=   -4.169 closest distance to " O   HOH Z 396 " =    1.740
peak=   -4.135 closest distance to " N   ALA A  43 " =    2.748
peak=   -4.130 closest distance to " CD  GLN A  88 " =    0.833
peak=   -4.116 closest distance to " CB  LEU A 167 " =    2.111
peak=   -4.086 closest distance to " O   HOH Z 350 " =    0.832
peak=   -4.080 closest distance to " OG  SER A  97 " =    2.229
peak=   -4.073 closest distance to " O   HOH Z 423 " =    2.458
peak=   -4.061 closest distance to " O   HOH Z 292 " =    4.482
peak=   -4.031 closest distance to " O   VAL A  67 " =    2.747
peak=   -4.019 closest distance to " O   HOH Z  13 " =    1.532
peak=   -4.016 closest distance to " CA  SER A 276 " =    1.426
peak=   -4.003 closest distance to " CA  VAL A  67 " =    2.930
peak=   -3.966 closest distance to " NH2 ARG A  66 " =    1.347
peak=   -3.966 closest distance to " O   HOH Z 138 " =    0.754
peak=   -3.961 closest distance to " CA  SER A 164 " =    1.970
peak=   -3.954 closest distance to " CG  GLN A  58 " =    1.300
peak=   -3.946 closest distance to " OG ASER A 134 " =    1.413
peak=   -3.944 closest distance to " O   HOH Z 234 " =    4.326
peak=   -3.903 closest distance to " O   HOH Z  52 " =    2.091
peak=   -3.903 closest distance to " O   TRP A  92 " =    1.887
peak=   -3.855 closest distance to " O   SER A 146 " =    0.823
peak=   -3.848 closest distance to " CD1 LEU A 101 " =    2.606
peak=   -3.847 closest distance to " CE  MET A 105 " =    1.946
peak=   -3.822 closest distance to " CE2 TYR A  30 " =    2.750
peak=   -3.813 closest distance to " O   HOH Z  71 " =    1.230
peak=   -3.807 closest distance to " O   HOH Z 377 " =    2.060
peak=   -3.767 closest distance to " O   HOH Z  17 " =    1.033
peak=   -3.756 closest distance to " O   HOH Z  93 " =    1.136
peak=   -3.749 closest distance to " CH2 TRP A 179 " =    1.188
peak=   -3.731 closest distance to " N   GLN A  58 " =    1.807
peak=   -3.725 closest distance to " C   HIS A 108 " =    1.126
peak=   -3.722 closest distance to " O   HOH Z 388 " =    2.112
peak=   -3.714 closest distance to " O   HOH Z  20 " =    1.394
peak=   -3.710 closest distance to " CB  ALA A 291 " =    2.430
peak=   -3.681 closest distance to " O   HOH Z 151 " =    1.655
peak=   -3.679 closest distance to " CG  ASP A 231 " =    0.770
peak=   -3.672 closest distance to " C   THR A 279 " =    1.152
peak=   -3.650 closest distance to " OD1 ASP A 191 " =    1.689
peak=   -3.639 closest distance to " CD  GLN A 223 " =    0.848
peak=   -3.638 closest distance to " C   SER A 206 " =    1.578
peak=   -3.636 closest distance to " OG  SER A 273 " =    2.134
peak=   -3.630 closest distance to " O   ASN A 187 " =    1.587
peak=   -3.623 closest distance to " O   HOH Z 313 " =    1.218
peak=   -3.622 closest distance to " O   HOH Z 352 " =    0.700
peak=   -3.615 closest distance to " CA  ASN A 148 " =    1.676
peak=   -3.606 closest distance to " SG  CYS A 254 " =    3.192
peak=   -3.602 closest distance to " O   HOH Z  11 " =    1.556
peak=   -3.598 closest distance to " O   HOH Z  29 " =    0.808
peak=   -3.597 closest distance to " O   HOH Z 165 " =    2.088
peak=   -3.596 closest distance to " CD1 TRP A 179 " =    1.152
peak=   -3.591 closest distance to " OD1 ASN A 176 " =    1.049
peak=   -3.590 closest distance to " O   HOH Z 407 " =    3.480
peak=   -3.588 closest distance to " O   HOH Z 423 " =    0.999
peak=   -3.580 closest distance to " O   HOH Z 412 " =    4.810
peak=   -3.577 closest distance to " CE  MET A  93 " =    1.353
peak=   -3.566 closest distance to " C   ALA A 158 " =    1.277
peak=   -3.564 closest distance to " CD1 PHE A  59 " =    2.001
peak=   -3.548 closest distance to " CG2 THR A 221 " =    2.412
peak=   -3.539 closest distance to " CD  ARG A 156 " =    1.907
peak=   -3.532 closest distance to " O   PRO A 198 " =    1.253
peak=   -3.530 closest distance to " O   GLY A 196 " =    1.012
peak=   -3.505 closest distance to " O   HOH Z 418 " =    1.230
peak=   -3.502 closest distance to " CD2 LEU A 237 " =    2.684
peak=   -3.502 closest distance to " CB  PRO A 163 " =    2.849
peak=   -3.498 closest distance to " O   HOH Z 118 " =    3.289
peak=   -3.497 closest distance to " ND2 ASN A  60 " =    1.469
peak=   -3.494 closest distance to " O   HOH Z  78 " =    1.657
peak=   -3.483 closest distance to " CG2 THR A   4 " =    1.829
peak=   -3.480 closest distance to " O   GLN A  11 " =    1.235
peak=   -3.479 closest distance to " O   HOH Z 422 " =    1.471
peak=   -3.472 closest distance to " CD1 TYR A 247 " =    2.294
peak=   -3.469 closest distance to " OG  SER A  32 " =    1.243
peak=   -3.467 closest distance to " CB  ALA A 244 " =    2.219
peak=   -3.449 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.448 closest distance to " CD  GLN A  58 " =    1.328
peak=   -3.448 closest distance to " O   VAL A 125 " =    2.042
peak=   -3.444 closest distance to " CB  ARG A 219 " =    2.257
peak=   -3.443 closest distance to " CG  ASP A  50 " =    2.303
peak=   -3.440 closest distance to " CG  GLU A 152 " =    0.847
peak=   -3.436 closest distance to " CD  GLN A  58 " =    0.864
peak=   -3.426 closest distance to " CB  LEU A 167 " =    2.260
peak=   -3.420 closest distance to " O   HOH Z  10 " =    1.445
peak=   -3.419 closest distance to " OG  SER A  62 " =    1.279
peak=   -3.417 closest distance to " O  BHOH Z 338 " =    1.577
peak=   -3.408 closest distance to " CD2 PHE A  59 " =    2.339
peak=   -3.408 closest distance to " O   ALA A   1 " =    1.908
peak=   -3.407 closest distance to " O   HOH Z 210 " =    2.576
peak=   -3.402 closest distance to " O   HOH Z 100 " =    0.741
peak=   -3.401 closest distance to " O   HOH Z 222 " =    1.068
peak=   -3.396 closest distance to " O   HOH Z 424 " =    2.944
peak=   -3.396 closest distance to " O   ALA A 161 " =    1.627
peak=   -3.395 closest distance to " CZ  TYR A 169 " =    1.902
peak=   -3.390 closest distance to " OD1 ASN A 110 " =    1.144
peak=   -3.389 closest distance to " O   HOH Z 140 " =    0.805
peak=   -3.387 closest distance to " N   GLY A 262 " =    1.879
peak=   -3.386 closest distance to " N   LEU A 255 " =    2.668
peak=   -3.380 closest distance to " CB  ALA A 161 " =    2.505
peak=   -3.379 closest distance to " CD  ARG A 139 " =    1.623
peak=   -3.376 closest distance to " N   ARG A 275 " =    1.752
peak=   -3.367 closest distance to " C   ASN A 285 " =    2.459
peak=   -3.366 closest distance to " N   MET A 188 " =    1.951
peak=   -3.358 closest distance to " O   PHE A 218 " =    1.393
peak=   -3.354 closest distance to " CG2 VAL A 189 " =    2.136
peak=   -3.349 closest distance to " NH1 ARG A 195 " =    2.522
peak=   -3.348 closest distance to " N   SER A 210 " =    1.365
peak=   -3.345 closest distance to " O   HOH Z 166 " =    2.114
peak=   -3.343 closest distance to " O   HOH Z 150 " =    1.365
peak=   -3.339 closest distance to " CB  PHE A 208 " =    2.346
peak=   -3.337 closest distance to " O   HOH Z  37 " =    1.436
peak=   -3.334 closest distance to " CG  GLU A  53 " =    1.393
peak=   -3.331 closest distance to " OG  SER A   3 " =    1.440
peak=   -3.331 closest distance to " CB  ALA A 131 " =    2.263
peak=   -3.330 closest distance to " O   HOH Z  97 " =    1.458
peak=   -3.324 closest distance to " ND2 ASN A 187 " =    1.609
peak=   -3.314 closest distance to " O   SER A 210 " =    1.782
peak=   -3.305 closest distance to " O   HOH Z 117 " =    0.938
peak=   -3.302 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.299 closest distance to " OG BSER A 210 " =    1.201
peak=   -3.299 closest distance to " CA  GLY A 241 " =    2.277
peak=   -3.287 closest distance to " O   VAL A 174 " =    2.040
peak=   -3.286 closest distance to " O   HOH Z 395 " =    1.208
peak=   -3.286 closest distance to " CG  LEU A  83 " =    1.939
peak=   -3.282 closest distance to " O   HOH Z 205 " =    0.852
peak=   -3.280 closest distance to " O   ASP A 191 " =    1.325
peak=   -3.273 closest distance to " CD2 HIS A 115 " =    1.087
peak=   -3.268 closest distance to " CE3 TRP A 150 " =    1.858
peak=   -3.267 closest distance to " OG1 THR A 178 " =    1.088
peak=   -3.265 closest distance to " O   HOH Z 378 " =    1.197
peak=   -3.265 closest distance to " O   HOH Z 138 " =    0.946
peak=   -3.264 closest distance to " NH2 ARG A  66 " =    4.961
peak=   -3.263 closest distance to " CZ  ARG A  66 " =    1.209
peak=   -3.260 closest distance to " O   MET A 113 " =    1.252
peak=   -3.258 closest distance to " O   HOH Z  65 " =    0.890
peak=   -3.254 closest distance to " CD2 LEU A 300 " =    2.767
peak=   -3.252 closest distance to " CB  ASN A  39 " =    2.319
peak=   -3.246 closest distance to " O   HOH Z 384 " =    1.918
peak=   -3.243 closest distance to " ND2 ASN A  60 " =    1.578
peak=   -3.235 closest distance to " OG BSER A 134 " =    1.482
peak=   -3.228 closest distance to " O   HOH Z  39 " =    1.460
peak=   -3.224 closest distance to " O   HOH Z 198 " =    0.931
peak=   -3.224 closest distance to " O   HOH Z  19 " =    2.186
peak=   -3.224 closest distance to " O   HOH Z 145 " =    1.937
peak=   -3.219 closest distance to " CD1 LEU A  25 " =    2.426
peak=   -3.219 closest distance to " OG1 THR A  82 " =    1.258
peak=   -3.218 closest distance to " ND2 ASN A  39 " =    1.204
peak=   -3.215 closest distance to " CD  ARG A 195 " =    5.130
peak=   -3.213 closest distance to " CG  ARG A 269 " =    2.239
peak=   -3.212 closest distance to " OG  SER A  63 " =    1.267
peak=   -3.210 closest distance to " CB  SER A 146 " =    2.183
peak=   -3.209 closest distance to " CD2 TRP A 274 " =    0.928
peak=   -3.209 closest distance to " O   HOH Z 213 " =    1.249
peak=   -3.206 closest distance to " O   HOH Z 281 " =    2.913
peak=   -3.205 closest distance to " ND2 ASN A  45 " =    1.005
peak=   -3.205 closest distance to " CA  VAL A 197 " =    0.918
peak=   -3.199 closest distance to " O   THR A  52 " =    2.009
peak=   -3.193 closest distance to " C   LEU A 143 " =    1.130
peak=   -3.187 closest distance to " O   HOH Z 292 " =    2.889
peak=   -3.187 closest distance to " OD2 ASP A 171 " =    1.680
peak=   -3.185 closest distance to " O   GLY A 118 " =    2.224
peak=   -3.184 closest distance to " O   HOH Z 236 " =    2.008
peak=   -3.182 closest distance to " O   HOH Z 119 " =    1.978
peak=   -3.181 closest distance to " CB  TYR A  15 " =    2.316
peak=   -3.173 closest distance to " NE2 GLN A 103 " =    1.546
peak=   -3.173 closest distance to " CD  GLN A  58 " =    1.243
peak=   -3.171 closest distance to " O   VAL A 197 " =    1.108
peak=   -3.169 closest distance to " NH2 ARG A 159 " =    2.431
peak=   -3.169 closest distance to " ND2 ASN A 252 " =    1.656
peak=   -3.168 closest distance to " CG1AVAL A  41 " =    2.607
peak=   -3.158 closest distance to " OE2 GLU A 277 " =    3.000
peak=   -3.156 closest distance to " O   ALA A 256 " =    1.496
peak=   -3.155 closest distance to " CD  GLN A  88 " =    2.207
peak=   -3.150 closest distance to " CG  ASP A 132 " =    2.257
peak=   -3.150 closest distance to " CD2 PHE A  61 " =    1.886
peak=   -3.149 closest distance to " O   LEU A 167 " =    1.676
peak=   -3.146 closest distance to " O   HOH Z 185 " =    2.386
peak=   -3.145 closest distance to " OD2 ASP A 171 " =    2.378
peak=   -3.142 closest distance to " OG  SER A  87 " =    1.523
peak=   -3.134 closest distance to " O   HOH Z 385 " =    3.676
peak=   -3.131 closest distance to " CE2 TRP A 274 " =    1.209
peak=   -3.129 closest distance to " CD  GLN A  73 " =    0.866
peak=   -3.129 closest distance to " OE2 GLU A   2 " =    1.401
peak=   -3.128 closest distance to " O   HOH Z  38 " =    1.330
peak=   -3.112 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.104 closest distance to " O   HOH Z 417 " =    2.509
peak=   -3.103 closest distance to " N   GLY A 133 " =    1.738
peak=   -3.096 closest distance to " C   SER A 271 " =    1.247
peak=   -3.096 closest distance to " CA  GLY A 203 " =    2.296
peak=   -3.085 closest distance to " CG  GLU A 152 " =    2.463
peak=   -3.079 closest distance to " O   HOH Z 212 " =    1.159
peak=   -3.074 closest distance to " O   HOH Z 283 " =    1.717
peak=   -3.069 closest distance to " O   ASN A  69 " =    1.209
peak=   -3.066 closest distance to " CZ  PHE A 130 " =    2.353
peak=   -3.065 closest distance to " O   HOH Z  47 " =    1.236
peak=   -3.062 closest distance to " O   HOH Z 422 " =    1.638
peak=   -3.055 closest distance to " CZ  ARG A 259 " =    0.705
peak=   -3.049 closest distance to " O   ALA A  34 " =    2.555
peak=   -3.039 closest distance to " O   HOH Z 427 " =    1.532

================= 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    :  0.4646 0.4575   6.277537e+00   6.266556e+00
   1_bss:  0.4537 0.4474   6.269966e+00   6.251425e+00
   1_xyz:  0.3635 0.3922   6.111711e+00   6.162517e+00
   1_adp:  0.3300 0.4010   6.065152e+00   6.180026e+00
   1_occ:  0.3297 0.4013   6.064557e+00   6.179707e+00
   2_bss:  0.3276 0.3985   6.063610e+00   6.179210e+00
   2_xyz:  0.2614 0.3304   5.878939e+00   6.047789e+00
   2_adp:  0.2440 0.3155   5.833497e+00   6.012420e+00
   2_occ:  0.2438 0.3152   5.832609e+00   6.011261e+00
   3_bss:  0.2436 0.3144   5.831077e+00   6.009544e+00
   3_xyz:  0.1830 0.2350   5.564975e+00   5.764392e+00
   3_adp:  0.1592 0.2172   5.457776e+00   5.677321e+00
   3_occ:  0.1592 0.2172   5.457643e+00   5.677435e+00
   4_bss:  0.1591 0.2170   5.458328e+00   5.678328e+00
   4_xyz:  0.1399 0.1943   5.343739e+00   5.575256e+00
   4_adp:  0.1369 0.1887   5.320954e+00   5.546731e+00
   4_occ:  0.1368 0.1885   5.320523e+00   5.546690e+00
   5_bss:  0.1372 0.1886   5.323268e+00   5.547594e+00
   5_xyz:  0.1244 0.1771   5.247874e+00   5.489665e+00
   5_adp:  0.1221 0.1653   5.209957e+00   5.430284e+00
   5_occ:  0.1217 0.1652   5.208763e+00   5.430135e+00
   5_bss:  0.1216 0.1651   5.208539e+00   5.429647e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000  -3.212   3.552   1.991   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -3.212   3.552   1.991   0.000   0.000   0.000
   1_adp:  0.300  20.000  -3.212   3.552   1.991   0.000   0.000   0.000
   1_occ:  0.300  20.000  -3.212   3.552   1.991   0.000   0.000   0.000
   2_bss:  0.322  50.000  -1.938   1.786   0.376   0.000   0.000   0.000
   2_xyz:  0.322  50.000  -1.938   1.786   0.376   0.000   0.000   0.000
   2_adp:  0.322  50.000  -1.938   1.786   0.376   0.000   0.000   0.000
   2_occ:  0.322  50.000  -1.938   1.786   0.376   0.000   0.000   0.000
   3_bss:  0.321  50.000  -1.767   0.539  -0.591   0.000  -0.000  -0.000
   3_xyz:  0.321  50.000  -1.767   0.539  -0.591   0.000  -0.000  -0.000
   3_adp:  0.321  50.000  -1.767   0.539  -0.591   0.000  -0.000  -0.000
   3_occ:  0.321  50.000  -1.767   0.539  -0.591   0.000  -0.000  -0.000
   4_bss:  0.325  60.153  -2.306  -0.561  -1.403  -0.000  -0.000  -0.000
   4_xyz:  0.325  60.153  -2.306  -0.561  -1.403  -0.000  -0.000  -0.000
   4_adp:  0.325  60.153  -2.306  -0.561  -1.403  -0.000  -0.000  -0.000
   4_occ:  0.325  60.153  -2.306  -0.561  -1.403  -0.000  -0.000  -0.000
   5_bss:  0.324  57.127  -2.562  -1.194  -1.720  -0.000  -0.000  -0.000
   5_xyz:  0.324  57.127  -2.562  -1.194  -1.720  -0.000  -0.000  -0.000
   5_adp:  0.324  57.127  -2.562  -1.194  -1.720  -0.000  -0.000  -0.000
   5_occ:  0.324  57.127  -2.562  -1.194  -1.720  -0.000  -0.000  -0.000
   5_bss:  0.325  49.884  -2.662  -1.462  -1.832  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.953 0.4191  0.5650    68440.186
   1_bss:  56.289 0.4388  0.6063    64178.281
   1_xyz:  44.321 0.5894  0.8040    44067.027
   1_adp:  45.872 0.5698  0.7922    46555.604
   1_occ:  45.877 0.5697  0.7903    46505.591
   2_bss:  45.601 0.5731  0.7802    46149.615
   2_xyz:  35.597 0.6926  0.9195    29942.218
   2_adp:  33.229 0.7208  0.9307    27121.937
   2_occ:  33.194 0.7212  0.9305    27056.533
   3_bss:  33.019 0.7231  0.9102    26824.322
   3_xyz:  23.619 0.8245  0.9958    14449.682
   3_adp:  21.181 0.8493  0.9955    12081.618
   3_occ:  21.182 0.8493  0.9952    12077.528
   4_bss:  21.161 0.8495  0.9678    12094.447
   4_xyz:  18.493 0.8751  0.9838     9502.597
   4_adp:  17.765 0.8821  0.9942     9002.157
   4_occ:  17.763 0.8821  0.9941     9003.910
   5_bss:  17.770 0.8821  0.9802     9030.393
   5_xyz:  16.523 0.8933  0.9851     7993.825
   5_adp:  15.155 0.9054  0.9869     7087.987
   5_occ:  15.141 0.9055  0.9871     7088.082
   5_bss:  15.134 0.9055  0.9782     7072.345
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9874e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9874e-01
   1_xyz:   1.588  0.012  0.093 16.117  0.006  4.106   1.3506e-01
   1_adp:   1.588  0.012  0.093 16.117  0.006  4.106   1.3506e-01
   1_occ:   1.588  0.012  0.093 16.117  0.006  4.106   1.3506e-01
   2_bss:   1.588  0.012  0.093 16.117  0.006  4.106   1.3506e-01
   2_xyz:   1.290  0.009  0.080 14.639  0.005  4.108   8.5633e-02
   2_adp:   1.290  0.009  0.080 14.639  0.005  4.108   8.5633e-02
   2_occ:   1.290  0.009  0.080 14.639  0.005  4.108   8.5633e-02
   3_bss:   1.290  0.009  0.080 14.639  0.005  4.108   8.5633e-02
   3_xyz:   1.097  0.008  0.070 14.624  0.005  4.120   7.0311e-02
   3_adp:   1.097  0.008  0.070 14.624  0.005  4.120   7.0311e-02
   3_occ:   1.097  0.008  0.070 14.624  0.005  4.120   7.0311e-02
   4_bss:   1.097  0.008  0.070 14.624  0.005  4.120   7.0311e-02
   4_xyz:   0.954  0.005  0.066 14.263  0.003  4.110   5.3245e-02
   4_adp:   0.954  0.005  0.066 14.263  0.003  4.110   5.3245e-02
   4_occ:   0.954  0.005  0.066 14.263  0.003  4.110   5.3245e-02
   5_bss:   0.954  0.005  0.066 14.263  0.003  4.110   5.3245e-02
   5_xyz:   1.142  0.009  0.078 14.812  0.004  4.114   7.1415e-02
   5_adp:   1.142  0.009  0.078 14.812  0.004  4.114   7.1415e-02
   5_occ:   1.142  0.009  0.078 14.812  0.004  4.114   7.1415e-02
   5_bss:   1.142  0.009  0.078 14.812  0.004  4.114   7.1415e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.393   2.4155e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.393   2.4155e-01
   1_xyz:  10.438  0.082  0.458 89.556  0.025  2.020   1.0665e-01
   1_adp:  10.438  0.082  0.458 89.556  0.025  2.020   1.0665e-01
   1_occ:  10.438  0.082  0.458 89.556  0.025  2.020   1.0665e-01
   2_bss:  10.438  0.082  0.458 89.556  0.025  2.020   1.0665e-01
   2_xyz:   7.504  0.048  0.271 87.716  0.030  2.257   1.0494e-01
   2_adp:   7.504  0.048  0.271 87.716  0.030  2.257   1.0494e-01
   2_occ:   7.504  0.048  0.271 87.716  0.030  2.257   1.0494e-01
   3_bss:   7.504  0.048  0.271 87.716  0.030  2.257   1.0494e-01
   3_xyz:   8.045  0.063  0.227 78.031  0.048  2.256   8.1724e-02
   3_adp:   8.045  0.063  0.227 78.031  0.048  2.256   8.1724e-02
   3_occ:   8.045  0.063  0.227 78.031  0.048  2.256   8.1724e-02
   4_bss:   8.045  0.063  0.227 78.031  0.048  2.256   8.1724e-02
   4_xyz:   6.713  0.039  0.239 80.021  0.031  2.377   3.1370e-02
   4_adp:   6.713  0.039  0.239 80.021  0.031  2.377   3.1370e-02
   4_occ:   6.713  0.039  0.239 80.021  0.031  2.377   3.1370e-02
   5_bss:   6.713  0.039  0.239 80.021  0.031  2.377   3.1370e-02
   5_xyz:   7.836  0.057  0.252 81.526  0.030  2.310   5.4402e-02
   5_adp:   7.836  0.057  0.252 81.526  0.030  2.310   5.4402e-02
   5_occ:   7.836  0.057  0.252 81.526  0.030  2.310   5.4402e-02
   5_bss:   7.836  0.057  0.252 81.526  0.030  2.310   5.4402e-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: 100.09   0.00  19.72  93.24   0.00  16.27 100.09   0.69  38.51
   1_occ: 100.09   0.00  19.72  93.24   0.00  16.27 100.09   0.69  38.51
   2_bss: 100.09   0.00  19.72  93.24   0.00  16.27 100.09   0.69  38.51
   2_xyz: 100.09   0.00  19.72  93.24   0.00  16.27 100.09   0.69  38.51
   2_adp:  98.28   0.00  18.81  93.76   0.00  15.05  98.28   4.27  39.29
   2_occ:  98.28   0.00  18.81  93.76   0.00  15.05  98.28   4.27  39.29
   3_bss:  98.28   0.00  18.81  93.76   0.00  15.05  98.28   4.27  39.29
   3_xyz:  98.28   0.00  18.81  93.76   0.00  15.05  98.28   4.27  39.29
   3_adp: 110.10   0.00  19.15 110.10   0.00  13.96 106.79   6.73  47.38
   3_occ: 110.10   0.00  19.15 110.10   0.00  13.96 106.79   6.73  47.38
   4_bss: 110.10   0.00  19.15 110.10   0.00  13.96 106.79   6.73  47.38
   4_xyz: 110.10   0.00  19.15 110.10   0.00  13.96 106.79   6.73  47.38
   4_adp: 109.94   0.00  19.15 109.94   0.00  14.02 106.22   6.20  47.12
   4_occ: 109.94   0.00  19.15 109.94   0.00  14.02 106.22   6.20  47.12
   5_bss: 109.94   0.00  19.15 109.94   0.00  14.02 106.22   6.20  47.12
   5_xyz: 109.94   0.00  19.15 109.94   0.00  14.02 106.22   6.20  47.12
   5_adp:  96.54   2.71  17.27  96.54   2.71  13.11  85.81   5.70  39.91
   5_occ:  96.54   2.71  17.27  96.54   2.71  13.11  85.81   5.70  39.91
   5_bss:  96.44   2.61  17.17  96.44   2.61  13.01  85.71   5.60  39.81
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.297    0.020    0.362
   1_adp:    2.297    0.020    0.362
   1_occ:    2.297    0.020    0.362
   2_bss:    2.297    0.020    0.362
   2_xyz:    1.583    0.040    0.537
   2_adp:    1.583    0.040    0.537
   2_occ:    1.583    0.040    0.537
   3_bss:    1.583    0.040    0.537
   3_xyz:    1.575    0.061    0.732
   3_adp:    1.575    0.061    0.732
   3_occ:    1.575    0.061    0.732
   4_bss:    1.575    0.061    0.732
   4_xyz:    1.591    0.053    0.762
   4_adp:    1.591    0.053    0.762
   4_occ:    1.591    0.053    0.762
   5_bss:    1.591    0.053    0.762
   5_xyz:    1.607    0.103    0.800
   5_adp:    1.607    0.103    0.800
   5_occ:    1.607    0.103    0.800
   5_bss:    1.607    0.103    0.800
------------------------------------------------------------------------

CPU time actual refinement: 342.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/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_583/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_583/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.65 
  Macro-tasks:
    bulk solvent and scale       = 44.91  
    individual site refinement   = 135.66 
    weights calculation          = 29.69  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 216.97 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 109.16 
    alpha_beta                      = 8.30   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.03 
    fmodel                         = 7.39   
    r_factors                      = 0.22   
    phase_errors                   = 10.41  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 255.35 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.926 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    634 calls, 108.75 s
gradients_fft:          579 calls, 103.48 s

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

# Date 2008-01-16 Time 05:10:51 PST -0800 (1200489051.17 s)
Start R-work = 0.4646, R-free = 0.4575 (no bulk solvent and anisotropic scale)
Final R-work = 0.1457, R-free = 0.1875 (no bulk solvent and anisotropic scale)

Start R-work = 0.4537, R-free = 0.4474
Final R-work = 0.1216, R-free = 0.1651