# Date 2008-01-16 Time 03:40:26 PST -0800 (1200483626.32 s)
#phil __OFF__

Command line arguments: "../7.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26344
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 7

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 45.7567, 87.2539, 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: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.756 1.95047
Completeness in resolution range: 0.952309
Completeness with d_max=infinity: 0.949401

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7560
                             d_min =   1.9505

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 45.7567, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.756 1.95047
Completeness in resolution range: 0.952309
Completeness with d_max=infinity: 0.949401

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7564 -  4.1735 [2167/2191]  1948   219  10.1%
  bin  2:  4.1735 -  3.3251 [2069/2089]  1862   207  10.0%
  bin  3:  3.3251 -  2.9084 [2055/2074]  1855   200   9.7%
  bin  4:  2.9084 -  2.6441 [2007/2037]  1799   208  10.4%
  bin  5:  2.6441 -  2.4556 [2037/2056]  1834   203  10.0%
  bin  6:  2.4556 -  2.3114 [1998/2023]  1799   199  10.0%
  bin  7:  2.3114 -  2.1960 [2002/2030]  1807   195   9.7%
  bin  8:  2.1960 -  2.1007 [1988/2024]  1780   208  10.5%
  bin  9:  2.1007 -  2.0200 [1981/2023]  1792   189   9.5%
  bin 10:  2.0200 -  1.9505 [1285/2023]  1154   131  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 35
        2.05 -     2.76: 508
        2.76 -     3.47: 4711
        3.47 -     4.19: 9609
        4.19 -     4.90: 14194
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.336 3.040 -x+1/2,-y+1,z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.338 3.120 -x+1,y-1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.420 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.477 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.501 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 29052 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_7/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 45.75675 87.2539 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 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4849   r_free= 0.4801   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293633                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6548 0.99   1406  154 0.3968 0.3929      6.6045      6.6017|
|  2:  4.6548 -  3.7140 0.99   1351  152 0.4241 0.4142      6.8249      6.8353|
|  3:  3.7140 -  3.2503 0.99   1309  148 0.4679 0.4611       6.722      6.7434|
|  4:  3.2503 -  2.9557 0.99   1337  140 0.4785 0.4882      6.5575      6.5678|
|  5:  2.9557 -  2.7453 0.99   1287  153 0.5196 0.4576      6.3809      6.3975|
|  6:  2.7453 -  2.5844 0.99   1311  139 0.5170 0.5375      6.2915      6.2055|
|  7:  2.5844 -  2.4556 0.99   1297  151 0.5258 0.4997       6.245      6.1635|
|  8:  2.4556 -  2.3491 0.98   1284  136 0.5360 0.5628      6.1953      6.2127|
|  9:  2.3491 -  2.2590 0.98   1279  145 0.5194 0.5405      6.1124      6.2047|
| 10:  2.2590 -  2.1813 1.00   1296  142 0.5290 0.5158      6.1118      6.0896|
| 11:  2.1813 -  2.1133 0.98   1268  146 0.5151 0.5455       6.033      6.0533|
| 12:  2.1133 -  2.0531 0.98   1277  137 0.5059 0.4793      5.9567      6.0225|
| 13:  2.0531 -  1.9991 0.96   1246  136 0.5194 0.5072      5.8942      5.8177|
| 14:  1.9991 -  1.9505 0.53    682   80 0.5266 0.5199      5.9083      5.7995|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6548  1406   154  0.66  37.32   0.81     0.73      85256.63|
|  2:  4.6548 -  3.7140  1351   152  0.63  41.09   0.90     0.74     135678.00|
|  3:  3.7140 -  3.2503  1309   148  0.49  52.31   0.91     0.67     146952.64|
|  4:  3.2503 -  2.9557  1337   140  0.38  61.17   0.91     0.56     135512.03|
|  5:  2.9557 -  2.7453  1287   153  0.34  64.00   0.88     0.52      94091.23|
|  6:  2.7453 -  2.5844  1311   139  0.35  63.62   0.88     0.51      76608.05|
|  7:  2.5844 -  2.4556  1297   151  0.34  64.29   0.92     0.49      66326.62|
|  8:  2.4556 -  2.3491  1284   136  0.31  67.09   0.90     0.45      63030.72|
|  9:  2.3491 -  2.2590  1279   145  0.28  68.78   0.92     0.42      59325.23|
| 10:  2.2590 -  2.1813  1296   142  0.30  67.70   0.94     0.45      52080.07|
| 11:  2.1813 -  2.1133  1268   146  0.30  67.77   0.96     0.48      50949.00|
| 12:  2.1133 -  2.0531  1277   137  0.30  67.32   0.98     0.49      44727.75|
| 13:  2.0531 -  1.9991  1246   136  0.28  68.96   0.97     0.46      39281.11|
| 14:  1.9991 -  1.9505   682    80  0.31  66.81   1.00     0.43      30914.63|
|alpha:            min =        0.42 max =            0.74 mean =         0.53|
|beta:             min =    30914.63 max =       146952.64 mean =     79428.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.84|
|phase err.(test): min =        0.00 max =           89.90 mean =        60.84|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.620606             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.077   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.444757              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.821   (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 |  1.336 -  1.693:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.693 -  2.049:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.049 -  2.405:       52 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.405 -  2.762:      456 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.762 -  3.118:     2310 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.118 -  3.475:     2401 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.475 -  3.831:     4530 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.831 -  4.187:     5079 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.187 -  4.544:     6391 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.544 -  4.900:     7803 |
|-----------------------------------------------------------------------------|
|-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 |        0.238 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.104    4.900  1.336 |       1.358 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    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 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4849   r_free= 0.4801   ksol= 0.00   Bsol= 0.00   scale= 0.892    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.293633                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4768   r_free= 0.4748   ksol= 0.34   Bsol= 20.00   scale= 0.921   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,1.34,-0.31,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.289970                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.610610             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 88.754   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.555935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.427   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4768      final r-factor (work) = 0.4073          |
| start r-factor (free) = 0.4748      final r-factor (free) = 0.4466          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.7375 = 11.61 * 0.50 * 6.2873 + 1.00 * 0.2380                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.2526 = 11.61 * 0.50 * 6.2222 + 1.00 * 0.1308                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4073      final r-factor (work) = 0.3729          |
| start r-factor (free) = 0.4466      final r-factor (free) = 0.4558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6875 = 1.56 * 1.00 * 6.2222 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6169 = 1.56 * 1.00 * 6.1651 + 1.00 * 0.0244                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.62   19.07    None  None   None       |
|    all(noH): 2823   0      0.00    78.62   19.07    None  None   None       |
|    Sol.    : 438    0      0.00    78.62   32.75    None  None   None       |
|    Mac.    : 2385   0      0.00    75.66   16.56    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 -   7.862:  628   |   5:    39.309 -  47.170:  139        |
|      1:     7.862 -  15.723:  738   |   6:    47.170 -  55.032:   72        |
|      2:    15.723 -  23.585:  569   |   7:    55.032 -  62.894:   37        |
|      3:    23.585 -  31.447:  388   |   8:    62.894 -  70.755:   13        |
|      4:    31.447 -  39.309:  233   |   9:    70.755 -  78.617:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3729 r_free = 0.4558             target_work(ml) = 6.171         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3724 r_free = 0.4565             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3724   r_free= 0.4565   ksol= 0.34   Bsol= 20.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.72,1.34,-0.31,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.171540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3726   r_free= 0.4529   ksol= 0.35   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.34,0.84,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.170965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.256919             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.945   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.870172              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.730  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3726      final r-factor (work) = 0.3235          |
| start r-factor (free) = 0.4529      final r-factor (free) = 0.4057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.0129 = 13.26 * 0.50 * 6.1677 + 1.00 * 0.1308                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.7027 = 13.26 * 0.50 * 6.1252 + 1.00 * 0.1018                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3235      final r-factor (work) = 0.3093          |
| start r-factor (free) = 0.4057      final r-factor (free) = 0.3970          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3563 = 0.87 * 1.00 * 6.1252 + 1.00 * 0.0263                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2813 = 0.87 * 1.00 * 6.0512 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.39   18.12    None  None   None       |
|    all(noH): 2823   0      0.00    85.39   18.12    None  None   None       |
|    Sol.    : 438    0      0.00    75.56   32.84    None  None   None       |
|    Mac.    : 2385   0      0.00    85.39   15.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.539:  743   |   5:    42.695 -  51.234:   99        |
|      1:     8.539 -  17.078:  870   |   6:    51.234 -  59.773:   41        |
|      2:    17.078 -  25.617:  531   |   7:    59.773 -  68.312:   31        |
|      3:    25.617 -  34.156:  327   |   8:    68.312 -  76.851:    5        |
|      4:    34.156 -  42.695:  174   |   9:    76.851 -  85.390:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3093 r_free = 0.3970             target_work(ml) = 6.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3091 r_free = 0.3974             target_work(ml) = 6.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3091   r_free= 0.3974   ksol= 0.35   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.34,0.84,0.00,0.00,0.00); trace/3= 0.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.041791                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3099   r_free= 0.3965   ksol= 0.34   Bsol= 57.80   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.27,1.32,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.041356                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.016770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.015  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.044035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3099      final r-factor (work) = 0.2592          |
| start r-factor (free) = 0.3965      final r-factor (free) = 0.3393          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3896 = 9.02 * 0.50 * 6.0527 + 1.00 * 0.1018                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0421 = 9.02 * 0.50 * 5.9800 + 1.00 * 0.0820                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2592      final r-factor (work) = 0.2381          |
| start r-factor (free) = 0.3393      final r-factor (free) = 0.3256          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2718 = 1.04 * 1.00 * 5.9800 + 1.00 * 0.0285                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1386 = 1.04 * 1.00 * 5.8532 + 1.00 * 0.0276                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.16   18.35    None  None   None       |
|    all(noH): 2823   0      0.00    95.16   18.35    None  None   None       |
|    Sol.    : 438    0      1.49    93.12   39.77    None  None   None       |
|    Mac.    : 2385   0      0.00    95.16   14.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.516:  986   |   5:    47.578 -  57.094:   81        |
|      1:     9.516 -  19.031:  863   |   6:    57.094 -  66.610:   56        |
|      2:    19.031 -  28.547:  423   |   7:    66.610 -  76.125:   32        |
|      3:    28.547 -  38.063:  218   |   8:    76.125 -  85.641:   10        |
|      4:    38.063 -  47.578:  148   |   9:    85.641 -  95.157:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2381 r_free = 0.3256             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2379 r_free = 0.3249             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2379   r_free= 0.3249   ksol= 0.34   Bsol= 57.80   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.34,1.27,1.32,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.832943                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2379   r_free= 0.3243   ksol= 0.34   Bsol= 57.80   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.17,1.01,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.831561                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.477258              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.928361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.739   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2379      final r-factor (work) = 0.2004          |
| start r-factor (free) = 0.3243      final r-factor (free) = 0.2674          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2579 = 3.48 * 0.50 * 5.8528 + 1.00 * 0.0820                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0860 = 3.48 * 0.50 * 5.7694 + 1.00 * 0.0551                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2004      final r-factor (work) = 0.1852          |
| start r-factor (free) = 0.2674      final r-factor (free) = 0.2518          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.9118 = 2.93 * 1.00 * 5.7694 + 1.00 * 0.0169                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.5167 = 2.93 * 1.00 * 5.6337 + 1.00 * 0.0191                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.71  18.81    None  None   None       |
|    all(noH): 2823   0      0.00    110.71  18.81    None  None   None       |
|    Sol.    : 438    0      4.17    105.75  47.66    None  None   None       |
|    Mac.    : 2385   0      0.00    110.71  13.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.071: 1349   |   5:    55.354 -  66.425:  110        |
|      1:    11.071 -  22.142:  773   |   6:    66.425 -  77.496:   65        |
|      2:    22.142 -  33.213:  231   |   7:    77.496 -  88.567:   33        |
|      3:    33.213 -  44.283:  144   |   8:    88.567 -  99.638:    7        |
|      4:    44.283 -  55.354:  104   |   9:    99.638 - 110.708:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1852 r_free = 0.2518             target_work(ml) = 5.602         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1850 r_free = 0.2512             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1850   r_free= 0.2512   ksol= 0.34   Bsol= 57.80   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.17,1.01,0.00,0.00,0.00); trace/3= 0.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.601014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1852   r_free= 0.2506   ksol= 0.33   Bsol= 57.80   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,-0.29,1.12,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.599080                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.249501              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.932  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.324625              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.323  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1852      final r-factor (work) = 0.1595          |
| start r-factor (free) = 0.2506      final r-factor (free) = 0.2193          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3915 = 2.25 * 0.50 * 5.6336 + 1.00 * 0.0551                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2766 = 2.25 * 0.50 * 5.5352 + 1.00 * 0.0509                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1595      final r-factor (work) = 0.1519          |
| start r-factor (free) = 0.2193      final r-factor (free) = 0.2025          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8156 = 0.32 * 1.00 * 5.5352 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7781 = 0.32 * 1.00 * 5.4416 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.51  17.09    None  None   None       |
|    all(noH): 2823   0      0.00    105.51  17.09    None  None   None       |
|    Sol.    : 438    0      3.82    100.43  44.35    None  None   None       |
|    Mac.    : 2385   0      0.00    105.51  12.08    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 -  10.551: 1425   |   5:    52.755 -  63.306:   94        |
|      1:    10.551 -  21.102:  778   |   6:    63.306 -  73.857:   61        |
|      2:    21.102 -  31.653:  196   |   7:    73.857 -  84.408:   24        |
|      3:    31.653 -  42.204:  141   |   8:    84.408 -  94.959:    6        |
|      4:    42.204 -  52.755:   91   |   9:    94.959 - 105.510:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1519 r_free = 0.2025             target_work(ml) = 5.402         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1517 r_free = 0.2020             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2020   ksol= 0.33   Bsol= 57.80   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,-0.29,1.12,-0.00,0.00,0.00); trace/3= -0.06                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.400511                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6548 0.99   1406  154 0.1094 0.1452      5.4799      5.6989|
|  2:  4.6548 -  3.7140 0.99   1351  152 0.1070 0.1459      5.6337      5.8896|
|  3:  3.7140 -  3.2503 0.99   1309  148 0.1408 0.1779      5.7242      5.9991|
|  4:  3.2503 -  2.9557 0.99   1337  140 0.1629 0.2235      5.7076      5.9103|
|  5:  2.9557 -  2.7453 0.99   1287  153 0.1818 0.2152      5.5973      5.7535|
|  6:  2.7453 -  2.5844 0.99   1311  139 0.1726 0.2479      5.4704      5.6764|
|  7:  2.5844 -  2.4556 0.99   1297  151 0.1747 0.2172      5.4351      5.5801|
|  8:  2.4556 -  2.3491 0.98   1284  136 0.1703 0.2293      5.3729      5.6093|
|  9:  2.3491 -  2.2590 0.98   1279  145 0.1697 0.2196      5.2947      5.5416|
| 10:  2.2590 -  2.1813 1.00   1296  142 0.1570 0.2137      5.2158      5.3697|
| 11:  2.1813 -  2.1133 0.98   1268  146 0.1548 0.2389      5.1914      5.5093|
| 12:  2.1133 -  2.0531 0.98   1277  137 0.1679 0.2196      5.1569      5.4671|
| 13:  2.0531 -  1.9991 0.96   1246  136 0.1640 0.2252      5.0664      5.2067|
| 14:  1.9991 -  1.9505 0.53    682   80 0.1599 0.2559      5.0366       5.294|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6548  1406   154  0.92  11.15   0.98     0.96       9483.68|
|  2:  4.6548 -  3.7140  1351   152  0.93  10.70   1.04     1.03      13210.07|
|  3:  3.7140 -  3.2503  1309   148  0.90  16.02   1.07     1.06      17439.42|
|  4:  3.2503 -  2.9557  1337   140  0.88  18.63   1.04     1.01      16986.46|
|  5:  2.9557 -  2.7453  1287   153  0.85  21.16   1.04     0.99      13948.81|
|  6:  2.7453 -  2.5844  1311   139  0.85  21.84   1.00     0.96      11695.28|
|  7:  2.5844 -  2.4556  1297   151  0.85  22.02   1.03     0.97      10721.78|
|  8:  2.4556 -  2.3491  1284   136  0.85  21.53   1.03     0.99       9735.23|
|  9:  2.3491 -  2.2590  1279   145  0.86  20.51   1.02     0.97       7960.82|
| 10:  2.2590 -  2.1813  1296   142  0.85  21.31   1.03     0.99       7157.83|
| 11:  2.1813 -  2.1133  1268   146  0.85  21.35   1.04     1.00       7350.24|
| 12:  2.1133 -  2.0531  1277   137  0.85  22.16   1.05     1.03       6842.82|
| 13:  2.0531 -  1.9991  1246   136  0.84  22.71   1.03     0.98       5792.21|
| 14:  1.9991 -  1.9505   682    80  0.87  19.96   1.02     0.98       4929.91|
|alpha:            min =        0.96 max =            1.06 mean =         0.99|
|beta:             min =     4929.91 max =        17439.42 mean =     10465.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.86 mean =        19.24|
|phase err.(test): min =        0.00 max =           89.96 mean =        18.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2015   ksol= 0.31   Bsol= 43.52   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,-0.78,0.85,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.399613                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2015   ksol= 0.31   Bsol= 43.52   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.33,-0.78,0.85,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.399613                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7564 -  4.6548 0.99   1406  154 0.1100 0.1404      5.4726      5.6839|
|  2:  4.6548 -  3.7140 0.99   1351  152 0.1059 0.1451      5.6267      5.8811|
|  3:  3.7140 -  3.2503 0.99   1309  148 0.1406 0.1776      5.7217      5.9929|
|  4:  3.2503 -  2.9557 0.99   1337  140 0.1627 0.2238      5.7062      5.9129|
|  5:  2.9557 -  2.7453 0.99   1287  153 0.1819 0.2156      5.5981      5.7538|
|  6:  2.7453 -  2.5844 0.99   1311  139 0.1725 0.2487      5.4716      5.6791|
|  7:  2.5844 -  2.4556 0.99   1297  151 0.1746 0.2179      5.4363      5.5812|
|  8:  2.4556 -  2.3491 0.98   1284  136 0.1704 0.2302      5.3739      5.6129|
|  9:  2.3491 -  2.2590 0.98   1279  145 0.1697 0.2196      5.2952      5.5401|
| 10:  2.2590 -  2.1813 1.00   1296  142 0.1570 0.2135      5.2164      5.3709|
| 11:  2.1813 -  2.1133 0.98   1268  146 0.1546 0.2396      5.1921      5.5127|
| 12:  2.1133 -  2.0531 0.98   1277  137 0.1680 0.2198      5.1572      5.4677|
| 13:  2.0531 -  1.9991 0.96   1246  136 0.1643 0.2241      5.0669      5.2042|
| 14:  1.9991 -  1.9505 0.53    682   80 0.1602 0.2566      5.0374      5.2956|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7564 -  4.6548  1406   154  0.93  10.97   0.98     0.96       9074.36|
|  2:  4.6548 -  3.7140  1351   152  0.94  10.50   1.04     1.03      12883.76|
|  3:  3.7140 -  3.2503  1309   148  0.90  15.94   1.06     1.05      17271.75|
|  4:  3.2503 -  2.9557  1337   140  0.88  18.61   1.04     1.00      16918.13|
|  5:  2.9557 -  2.7453  1287   153  0.85  21.20   1.02     0.98      13979.50|
|  6:  2.7453 -  2.5844  1311   139  0.85  21.89   0.98     0.95      11757.48|
|  7:  2.5844 -  2.4556  1297   151  0.84  22.06   1.01     0.96      10778.79|
|  8:  2.4556 -  2.3491  1284   136  0.85  21.56   1.01     0.98       9773.70|
|  9:  2.3491 -  2.2590  1279   145  0.86  20.53   1.01     0.96       7986.73|
| 10:  2.2590 -  2.1813  1296   142  0.85  21.33   1.02     0.97       7165.74|
| 11:  2.1813 -  2.1133  1268   146  0.85  21.39   1.02     0.98       7380.47|
| 12:  2.1133 -  2.0531  1277   137  0.85  22.18   1.02     1.00       6850.58|
| 13:  2.0531 -  1.9991  1246   136  0.84  22.72   1.00     0.96       5798.81|
| 14:  1.9991 -  1.9505   682    80  0.87  19.94   1.00     0.96       4927.10|
|alpha:            min =        0.95 max =            1.05 mean =         0.98|
|beta:             min =     4927.10 max =        17271.75 mean =     10409.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.86 mean =        19.22|
|phase err.(test): min =        0.00 max =           89.91 mean =        18.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.286)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.51  17.09    None  None   None       |
|    all(noH): 2823   0      0.00    105.51  17.09    None  None   None       |
|    Sol.    : 438    0      3.83    100.43  44.35    None  None   None       |
|    Mac.    : 2385   0      0.00    105.51  12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.554: 1425   |   5:    52.758 -  63.309:   94        |
|      1:    10.554 -  21.105:  778   |   6:    63.309 -  73.860:   61        |
|      2:    21.105 -  31.656:  196   |   7:    73.860 -  84.411:   24        |
|      3:    31.656 -  42.207:  141   |   8:    84.411 -  94.962:    6        |
|      4:    42.207 -  52.758:   91   |   9:    94.962 - 105.513:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 358         
Filter by distance & map next to the model:
   mapped sites are within: 0.676 - 5.719
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 356 from: 358
   mapped sites are within: 0.714 - 5.719

peak=    7.381 closest distance to " OD1 ASP A  27 " =    1.192
peak=    7.247 closest distance to " O   HOH Z 403 " =    1.324
peak=    7.154 closest distance to " N   ARG A 275 " =    0.916
peak=    6.875 closest distance to " O   HOH Z 390 " =    1.248
peak=    6.036 closest distance to " O   HOH Z 130 " =    1.381
peak=    5.989 closest distance to " O   HOH Z 245 " =    1.617
peak=    5.908 closest distance to " CG2 ILE A 120 " =    1.256
peak=    5.848 closest distance to " O   HOH Z 103 " =    1.111
peak=    5.651 closest distance to " O   ARG A 275 " =    0.810
peak=    5.642 closest distance to " O   HOH Z 431 " =    2.005
peak=    5.626 closest distance to " O   HOH Z 227 " =    1.897
peak=    5.582 closest distance to " O   PRO A 198 " =    1.449
peak=    5.563 closest distance to " O   HOH Z  81 " =    1.071
peak=    5.469 closest distance to " O   HOH Z 385 " =    2.306
peak=    5.450 closest distance to " OD1 ASP A 286 " =    1.148
peak=    5.282 closest distance to " O   HOH Z 422 " =    1.593
peak=    5.268 closest distance to " O   HOH Z 244 " =    1.637
peak=    5.236 closest distance to " O   HOH Z 415 " =    1.219
peak=    5.235 closest distance to " CB  ARG A 275 " =    1.363
peak=    5.152 closest distance to " CG  PRO A  90 " =    1.331
peak=    5.100 closest distance to " O   HOH Z 427 " =    1.580
peak=    5.037 closest distance to " O   HOH Z 120 " =    1.395
peak=    4.965 closest distance to " O   HOH Z  69 " =    1.737
peak=    4.906 closest distance to " O   HOH Z 418 " =    1.496
peak=    4.895 closest distance to " O   HOH Z  84 " =    2.633
peak=    4.881 closest distance to " O   HOH Z 222 " =    1.470
peak=    4.863 closest distance to " N   GLU A 277 " =    0.763
peak=    4.860 closest distance to " O   HOH Z  77 " =    1.263
peak=    4.792 closest distance to " NE2 GLN A 103 " =    0.980
peak=    4.765 closest distance to " O   HOH Z  49 " =    1.562
peak=    4.760 closest distance to " O   HOH Z 416 " =    1.586
peak=    4.745 closest distance to " O   HOH Z  39 " =    1.709
peak=    4.673 closest distance to " NE1 TRP A 274 " =    1.265
peak=    4.670 closest distance to " NE2 GLN A  11 " =    1.290
peak=    4.653 closest distance to " NZ  LYS A 289 " =    1.177
peak=    4.644 closest distance to " O   HOH Z  53 " =    1.224
peak=    4.637 closest distance to " O   HOH Z 255 " =    0.968
peak=    4.628 closest distance to " O   HOH Z 105 " =    1.237
peak=    4.618 closest distance to " O   HOH Z  63 " =    1.709
peak=    4.588 closest distance to " O   HOH Z  83 " =    1.175
peak=    4.575 closest distance to " O   HOH Z 109 " =    2.627
peak=    4.571 closest distance to " O   HOH Z 293 " =    1.598
peak=    4.522 closest distance to " O   HOH Z  46 " =    1.368
peak=    4.520 closest distance to " O   HOH Z   7 " =    1.454
peak=    4.520 closest distance to " O   HOH Z 427 " =    1.456
peak=    4.502 closest distance to " O   HOH Z 124 " =    1.707
peak=    4.494 closest distance to " CB  SER A 216 " =    1.059
peak=    4.494 closest distance to " O   HOH Z 119 " =    1.480
peak=    4.477 closest distance to " O   HOH Z 142 " =    1.733
peak=    4.466 closest distance to " O   HOH Z 287 " =    1.990
peak=    4.462 closest distance to " O   HOH Z  61 " =    1.285
peak=    4.429 closest distance to " O   HOH Z  65 " =    2.043
peak=    4.427 closest distance to " OD1 ASN A  45 " =    1.243
peak=    4.424 closest distance to " O   HOH Z 363 " =    2.911
peak=    4.402 closest distance to " N   GLN A 278 " =    0.922
peak=    4.383 closest distance to " CB  ALA A 114 " =    1.096
peak=    4.366 closest distance to " CE2 PHE A  16 " =    0.917
peak=    4.366 closest distance to " O   HOH Z  63 " =    2.119
peak=    4.361 closest distance to " CD  GLN A  77 " =    1.378
peak=    4.276 closest distance to " N   PHE A  59 " =    0.758
peak=    4.266 closest distance to " O   HOH Z  30 " =    2.029
peak=    4.258 closest distance to " CB  ARG A  79 " =    0.932
peak=    4.255 closest distance to " O   HOH Z 425 " =    1.251
peak=    4.251 closest distance to " NH2 ARG A 269 " =    0.945
peak=    4.219 closest distance to " O   HOH Z   9 " =    1.664
peak=    4.216 closest distance to " O   HOH Z  29 " =    2.351
peak=    4.201 closest distance to " O   HOH Z 365 " =    2.496
peak=    4.199 closest distance to " O   HOH Z 112 " =    1.392
peak=    4.199 closest distance to " O   HOH Z  92 " =    1.632
peak=    4.188 closest distance to " CD AARG A 275 " =    1.366
peak=    4.167 closest distance to " O   HOH Z 113 " =    2.133
peak=    4.149 closest distance to " O   HOH Z  41 " =    0.886
peak=    4.133 closest distance to " C   SER A 276 " =    0.912
peak=    4.130 closest distance to " O   ASP A 286 " =    2.316
peak=    4.097 closest distance to " O   HOH Z 330 " =    1.201
peak=    4.097 closest distance to " O   HOH Z 132 " =    1.498
peak=    4.077 closest distance to " CB  GLN A 278 " =    0.925
peak=    4.070 closest distance to " OE1 GLN A  55 " =    2.072
peak=    4.066 closest distance to " O  BHOH Z  74 " =    1.132
peak=    4.063 closest distance to " O   ASN A 285 " =    0.890
peak=    4.063 closest distance to " O   HOH Z 236 " =    1.657
peak=    4.055 closest distance to " CZ3 TRP A 266 " =    1.074
peak=    4.053 closest distance to " NZ  LYS A 119 " =    1.767
peak=    4.037 closest distance to " C   GLN A  73 " =    1.132
peak=    4.037 closest distance to " O   HOH Z 358 " =    1.308
peak=    4.033 closest distance to " OE2 GLU A  53 " =    2.056
peak=    4.027 closest distance to " CB  ASN A  74 " =    1.235
peak=    4.023 closest distance to " NZ  LYS A 117 " =    3.117
peak=    4.016 closest distance to " O   HOH Z 232 " =    2.347
peak=    4.013 closest distance to " O   HOH Z 209 " =    1.200
peak=    3.992 closest distance to " N   GLU A   2 " =    1.399
peak=    3.977 closest distance to " CG  PRO A 213 " =    1.308
peak=    3.977 closest distance to " CD1AILE A 234 " =    1.204
peak=    3.976 closest distance to " O   HOH Z  97 " =    1.270
peak=    3.975 closest distance to " N   ARG A 156 " =    1.234
peak=    3.961 closest distance to " CB  SER A   3 " =    1.145
peak=    3.958 closest distance to " O   HOH Z 259 " =    2.144
peak=    3.938 closest distance to " O   HOH Z 291 " =    1.459
peak=    3.934 closest distance to " O   HOH Z  61 " =    1.829
peak=    3.917 closest distance to " CG  LYS A 119 " =    1.093
peak=    3.915 closest distance to " O   ASN A 142 " =    1.192
peak=    3.915 closest distance to " CE1 PHE A  38 " =    0.835
peak=    3.909 closest distance to " O   HOH Z 406 " =    1.688
peak=    3.885 closest distance to " NZ  LYS A 119 " =    2.220
peak=    3.878 closest distance to " NE1 TRP A 266 " =    1.830
peak=    3.865 closest distance to " CB  VAL A 202 " =    1.685
peak=    3.861 closest distance to " O   HOH Z 130 " =    2.146
peak=    3.843 closest distance to " O   HOH Z  51 " =    1.738
peak=    3.836 closest distance to " CA  ALA A  84 " =    0.775
peak=    3.833 closest distance to " O   HOH Z 276 " =    1.519
peak=    3.830 closest distance to " O   HOH Z 248 " =    1.964
peak=    3.825 closest distance to " O   HOH Z 145 " =    1.834
peak=    3.820 closest distance to " O   HOH Z 400 " =    0.815
peak=    3.818 closest distance to " O   HOH Z 363 " =    1.231
peak=    3.816 closest distance to " O   HOH Z 287 " =    1.597
peak=    3.813 closest distance to " CD1 ILE A  49 " =    2.417
peak=    3.809 closest distance to " O   HOH Z  57 " =    2.114
peak=    3.807 closest distance to " O   HOH Z 361 " =    3.596
peak=    3.796 closest distance to " O   HOH Z 369 " =    1.437
peak=    3.793 closest distance to " CB  ARG A 156 " =    1.114
peak=    3.784 closest distance to " O   HOH Z 201 " =    1.522
peak=    3.781 closest distance to " CB  PHE A 130 " =    1.079
peak=    3.779 closest distance to " O   HOH Z 250 " =    1.098
peak=    3.778 closest distance to " CB  ASN A 148 " =    1.259
peak=    3.777 closest distance to " CE  LYS A 119 " =    1.280
peak=    3.776 closest distance to " O   HOH Z 347 " =    1.093
peak=    3.773 closest distance to " CG2AVAL A  72 " =    0.739
peak=    3.773 closest distance to " CG  PRO A  54 " =    1.393
peak=    3.761 closest distance to " O   HOH Z 392 " =    1.689
peak=    3.761 closest distance to " CA  ALA A   7 " =    1.049
peak=    3.755 closest distance to " O   HOH Z 423 " =    1.998
peak=    3.747 closest distance to " O   HOH Z  32 " =    2.022
peak=    3.747 closest distance to " CA  PRO A 280 " =    1.347
peak=    3.746 closest distance to " O   GLN A  55 " =    0.950
peak=    3.744 closest distance to " O   HOH Z 289 " =    1.325
peak=    3.730 closest distance to " O   HOH Z 197 " =    2.011
peak=    3.729 closest distance to " O   GLN A 240 " =    1.654
peak=    3.726 closest distance to " CD  ARG A 139 " =    1.318
peak=    3.719 closest distance to " O   HOH Z  44 " =    2.885
peak=    3.714 closest distance to " C   VAL A  72 " =    1.049
peak=    3.707 closest distance to " CB  LYS A 290 " =    0.895
peak=    3.702 closest distance to " ND1 HIS A  81 " =    1.120
peak=    3.701 closest distance to " CE AMET A  47 " =    1.307
peak=    3.697 closest distance to " CB  THR A  31 " =    1.710
peak=    3.697 closest distance to " O   HOH Z  89 " =    2.001
peak=    3.695 closest distance to " O   HOH Z 344 " =    1.527
peak=    3.694 closest distance to " O   HOH Z 424 " =    1.132
peak=    3.689 closest distance to " O   HOH Z   1 " =    3.308
peak=    3.687 closest distance to " O   HOH Z  67 " =    1.712
peak=    3.687 closest distance to " N   GLY A 287 " =    0.880
peak=    3.677 closest distance to " O   HOH Z  40 " =    1.574
peak=    3.674 closest distance to " CB  LEU A  83 " =    0.859
peak=    3.651 closest distance to " CB  PRO A 243 " =    1.044
peak=    3.650 closest distance to " O   HOH Z 284 " =    1.550
peak=    3.650 closest distance to " O   HOH Z 128 " =    1.964
peak=    3.649 closest distance to " O   HOH Z 371 " =    2.624
peak=    3.644 closest distance to " O   HOH Z 106 " =    2.830
peak=    3.643 closest distance to " O   HOH Z  53 " =    1.871
peak=    3.638 closest distance to " O   HOH Z 434 " =    1.470
peak=    3.635 closest distance to " CG2 THR A  29 " =    0.998
peak=    3.634 closest distance to " O   HOH Z 177 " =    1.181
peak=    3.630 closest distance to " CB  PRO A  54 " =    1.209
peak=    3.630 closest distance to " CG2 VAL A 268 " =    0.971
peak=    3.626 closest distance to " O   HOH Z 368 " =    1.771
peak=    3.620 closest distance to " CG2 THR A 279 " =    1.051
peak=    3.611 closest distance to " CB  GLN A 223 " =    1.581
peak=    3.606 closest distance to " CG2 ILE A  20 " =    1.307
peak=    3.584 closest distance to " O   HOH Z  65 " =    1.506
peak=    3.584 closest distance to " CG  PRO A 243 " =    1.363
peak=    3.581 closest distance to " CG1 VAL A 265 " =    0.843
peak=    3.581 closest distance to " O   HOH Z 222 " =    2.233
peak=    3.572 closest distance to " CD1 PHE A 208 " =    0.941
peak=    3.566 closest distance to " OD1 ASN A 148 " =    2.046
peak=    3.565 closest distance to " O   HOH Z 426 " =    1.253
peak=    3.564 closest distance to " CB  ASN A 187 " =    0.971
peak=    3.559 closest distance to " CG  GLN A  58 " =    1.094
peak=    3.558 closest distance to " CB  SER A 273 " =    0.928
peak=    3.558 closest distance to " CG  GLN A  73 " =    1.139
peak=    3.557 closest distance to " CB  SER A 210 " =    0.962
peak=    3.556 closest distance to " CG2 ILE A 234 " =    0.897
peak=    3.551 closest distance to " O   HOH Z 211 " =    1.233
peak=    3.550 closest distance to " O   SER A 273 " =    0.781
peak=    3.547 closest distance to " O   HOH Z 419 " =    2.166
peak=    3.546 closest distance to " ND2 ASN A 209 " =    1.345
peak=    3.543 closest distance to " O   HOH Z 117 " =    2.378
peak=    3.541 closest distance to " CA  ARG A  36 " =    1.078
peak=    3.538 closest distance to " O   HOH Z 258 " =    1.304
peak=    3.532 closest distance to " N   TYR A  15 " =    1.264
peak=    3.532 closest distance to " CA  ALA A 129 " =    1.102
peak=    3.527 closest distance to " O   HOH Z 402 " =    1.360
peak=    3.516 closest distance to " O   HOH Z  28 " =    1.327
peak=    3.515 closest distance to " CZ  PHE A  59 " =    1.075
peak=    3.512 closest distance to " NH2 ARG A  36 " =    1.355
peak=    3.510 closest distance to " O   HOH Z 378 " =    1.107
peak=    3.502 closest distance to " CG  GLU A 277 " =    1.085
peak=    3.501 closest distance to " O   HOH Z 405 " =    1.814
peak=    3.497 closest distance to " O   HOH Z 422 " =    1.876
peak=    3.497 closest distance to " CB  LEU A 300 " =    1.042
peak=    3.497 closest distance to " O   HOH Z 409 " =    3.178
peak=    3.496 closest distance to " O   HOH Z   3 " =    2.111
peak=    3.493 closest distance to " N   ALA A   1 " =    2.916
peak=    3.485 closest distance to " CB  ALA A 291 " =    1.236
peak=    3.485 closest distance to " NE2 GLN A  58 " =    5.719
peak=    3.483 closest distance to " O   HOH Z 352 " =    1.427
peak=    3.482 closest distance to " N   TRP A  85 " =    1.070
peak=    3.481 closest distance to " O   THR A  82 " =    1.211
peak=    3.481 closest distance to " CG2 THR A 220 " =    1.089
peak=    3.463 closest distance to " NZ BLYS A 290 " =    1.134
peak=    3.462 closest distance to " OG ASER A 258 " =    2.964
peak=    3.461 closest distance to " O   HOH Z 205 " =    1.173
peak=    3.460 closest distance to " CA  TYR A  30 " =    1.096
peak=    3.459 closest distance to " O   HOH Z 173 " =    2.489
peak=    3.458 closest distance to " CD2 LEU A 297 " =    0.951
peak=    3.455 closest distance to " O   HOH Z 216 " =    3.527
peak=    3.453 closest distance to " O   HOH Z 198 " =    1.292
peak=    3.451 closest distance to " O   HOH Z 423 " =    1.662
peak=    3.450 closest distance to " NH2BARG A 102 " =    0.924
peak=    3.446 closest distance to " CD1 PHE A 130 " =    0.858
peak=    3.425 closest distance to " O   HOH Z 116 " =    1.202
peak=    3.423 closest distance to " O   HOH Z 143 " =    1.413
peak=    3.419 closest distance to " O   HOH Z 249 " =    1.612
peak=    3.417 closest distance to " O   HOH Z 137 " =    1.395
peak=    3.415 closest distance to " CG2 THR A 178 " =    1.047
peak=    3.406 closest distance to " CA  ALA A 299 " =    0.899
peak=    3.406 closest distance to " O   HOH Z 153 " =    3.258
peak=    3.403 closest distance to " O   HOH Z  47 " =    1.770
peak=    3.402 closest distance to " CA  GLU A 152 " =    1.166
peak=    3.397 closest distance to " CB  LYS A  48 " =    0.911
peak=    3.394 closest distance to " O   HOH Z 352 " =    1.409
peak=    3.392 closest distance to " O   HOH Z 296 " =    1.437
peak=    3.386 closest distance to " O   HOH Z 172 " =    1.620
peak=    3.385 closest distance to " CZ3 TRP A 274 " =    1.248
peak=    3.382 closest distance to " CG2 ILE A 151 " =    1.043
peak=    3.380 closest distance to " CB  SER A  63 " =    1.311
peak=    3.375 closest distance to " O   HOH Z  89 " =    1.756
peak=    3.372 closest distance to " CA  ASN A 284 " =    0.902
peak=    3.370 closest distance to " O   HOH Z 185 " =    1.652
peak=    3.365 closest distance to " O   HOH Z 272 " =    1.835
peak=    3.355 closest distance to " CA  ILE A 234 " =    1.229
peak=    3.352 closest distance to " O   HOH Z 303 " =    2.226
peak=    3.349 closest distance to " CG  GLN A  89 " =    1.586
peak=    3.347 closest distance to " O   HOH Z 128 " =    1.468
peak=    3.345 closest distance to " N   PHE A  61 " =    0.966
peak=    3.343 closest distance to " O   HOH Z 389 " =    1.533
peak=    3.343 closest distance to " O   HOH Z 421 " =    2.085
peak=    3.342 closest distance to " CB  SER A  62 " =    1.319
peak=    3.341 closest distance to " O   HOH Z 193 " =    1.264
peak=    3.333 closest distance to " OD1 ASN A 170 " =    1.706
peak=    3.332 closest distance to " O   HOH Z 170 " =    1.229
peak=    3.322 closest distance to " NH1AARG A 102 " =    1.093
peak=    3.319 closest distance to " CB  SER A  99 " =    0.987
peak=    3.318 closest distance to " CG2 VAL A 232 " =    1.658
peak=    3.314 closest distance to " OD1 ASN A  45 " =    2.945
peak=    3.314 closest distance to " O   HOH Z 334 " =    2.192
peak=    3.313 closest distance to " O   HOH Z 298 " =    1.633
peak=    3.311 closest distance to " OG  SER A 146 " =    0.948
peak=    3.309 closest distance to " O   HOH Z  99 " =    1.989
peak=    3.308 closest distance to " O   HOH Z 388 " =    2.055
peak=    3.303 closest distance to " CB  ASN A  39 " =    0.982
peak=    3.302 closest distance to " OE1 GLN A 223 " =    2.045
peak=    3.300 closest distance to " O   HOH Z 139 " =    1.073
peak=    3.292 closest distance to " O   HOH Z 215 " =    1.872
peak=    3.292 closest distance to " CG  LYS A  76 " =    1.739
peak=    3.290 closest distance to " O   HOH Z 125 " =    1.544
peak=    3.289 closest distance to " CH2 TRP A 150 " =    1.177
peak=    3.289 closest distance to " N   ALA A 165 " =    1.362
peak=    3.287 closest distance to " CB  MET A  47 " =    0.917
peak=    3.286 closest distance to " OG1 THR A 279 " =    1.203
peak=    3.286 closest distance to " O   HOH Z 147 " =    1.300
peak=    3.283 closest distance to " O   HOH Z 216 " =    4.111
peak=    3.275 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.264 closest distance to " CG  PRO A 198 " =    1.310
peak=    3.262 closest distance to " O   HOH Z 402 " =    1.195
peak=    3.262 closest distance to " CA  ARG A  24 " =    0.880
peak=    3.260 closest distance to " O   HOH Z  68 " =    1.621
peak=    3.259 closest distance to " O   HOH Z  66 " =    1.111
peak=    3.259 closest distance to " O   HOH Z 223 " =    1.065
peak=    3.256 closest distance to " CG1 VAL A 202 " =    1.798
peak=    3.254 closest distance to " NE2 GLN A 278 " =    1.952
peak=    3.245 closest distance to " O   HOH Z 162 " =    2.346
peak=    3.244 closest distance to " OG BSER A  12 " =    1.115
peak=    3.243 closest distance to " CG2 ILE A 239 " =    0.893
peak=    3.242 closest distance to " NH2BARG A 145 " =    1.583
peak=    3.239 closest distance to " N   ASN A  60 " =    1.098
peak=    3.236 closest distance to " CB  ARG A 138 " =    0.909
peak=    3.234 closest distance to " CA  MET A 113 " =    1.153
peak=    3.234 closest distance to " O   HOH Z 287 " =    2.105
peak=    3.234 closest distance to " O   HOH Z 199 " =    1.190
peak=    3.233 closest distance to " OG1 THR A 246 " =    1.080
peak=    3.232 closest distance to " O   HOH Z 334 " =    1.694
peak=    3.229 closest distance to " OG  SER A 276 " =    0.961
peak=    3.226 closest distance to " O   HOH Z 298 " =    4.508
peak=    3.226 closest distance to " O   HOH Z 362 " =    1.598
peak=    3.226 closest distance to " O   HOH Z 365 " =    1.529
peak=    3.226 closest distance to " O   HOH Z 393 " =    1.496
peak=    3.225 closest distance to " O   HOH Z 166 " =    2.534
peak=    3.221 closest distance to " O   HOH Z 389 " =    1.377
peak=    3.219 closest distance to " OD1 ASP A 238 " =    0.987
peak=    3.217 closest distance to " CG  GLN A 205 " =    1.216
peak=    3.216 closest distance to " OG BSER A 164 " =    2.036
peak=    3.215 closest distance to " O   HOH Z 295 " =    1.157
peak=    3.214 closest distance to " NZ  LYS A 117 " =    1.054
peak=    3.212 closest distance to " O   HOH Z 272 " =    2.010
peak=    3.212 closest distance to " O  BHOH Z 338 " =    2.229
peak=    3.211 closest distance to " O   HOH Z 222 " =    1.704
peak=    3.210 closest distance to " O   HOH Z 156 " =    3.028
peak=    3.210 closest distance to " O   HOH Z  30 " =    1.486
peak=    3.208 closest distance to " CA  ARG A 159 " =    1.254
peak=    3.206 closest distance to " CG1AVAL A  41 " =    1.070
peak=    3.201 closest distance to " CB  GLU A 128 " =    0.931
peak=    3.200 closest distance to " O   HOH Z 119 " =    4.233
peak=    3.200 closest distance to " CG2 VAL A 202 " =    1.424
peak=    3.199 closest distance to " O   VAL A 250 " =    1.155
peak=    3.199 closest distance to " O   HOH Z  59 " =    1.625
peak=    3.197 closest distance to " CB  ASP A 272 " =    1.193
peak=    3.192 closest distance to " O   HOH Z 380 " =    2.403
peak=    3.192 closest distance to " O   HOH Z 424 " =    2.671
peak=    3.190 closest distance to " CG2 ILE A  49 " =    1.269
peak=    3.189 closest distance to " CA  LEU A 282 " =    1.108
peak=    3.189 closest distance to " O   HOH Z  22 " =    1.663
peak=    3.188 closest distance to " O   HOH Z 150 " =    1.253
peak=    3.188 closest distance to " O   HOH Z 419 " =    1.863
peak=    3.185 closest distance to " O   ALA A 242 " =    0.879
peak=    3.185 closest distance to " O   HOH Z  88 " =    2.170
peak=    3.184 closest distance to " O   HOH Z 413 " =    2.271
peak=    3.182 closest distance to " N   TRP A 274 " =    0.837
peak=    3.181 closest distance to " NH1 ARG A  14 " =    0.989
peak=    3.180 closest distance to " N   ASN A 148 " =    1.055
peak=    3.176 closest distance to " O   HOH Z   6 " =    1.952
peak=    3.173 closest distance to " CA  GLY A  57 " =    0.974
peak=    3.169 closest distance to " O   ARG A  14 " =    0.993
peak=    3.169 closest distance to " NH2 ARG A  56 " =    1.075
peak=    3.157 closest distance to " O   HOH Z 153 " =    1.567
peak=    3.154 closest distance to " CA  ALA A 129 " =    1.698
peak=    3.152 closest distance to " O   HOH Z 357 " =    1.987
peak=    3.150 closest distance to " O   HOH Z 323 " =    1.639
peak=    3.148 closest distance to " O   HOH Z  58 " =    1.729
peak=    3.138 closest distance to " O   HOH Z 425 " =    1.836
peak=    3.133 closest distance to " O   HOH Z  49 " =    2.157
peak=    3.129 closest distance to " O   HOH Z 155 " =    2.236
peak=    3.126 closest distance to " CB  TYR A 116 " =    1.433
peak=    3.125 closest distance to " CA  ILE A  20 " =    0.890
peak=    3.124 closest distance to " CB  ALA A 160 " =    1.609
peak=    3.122 closest distance to " O   ALA A 158 " =    1.170
peak=    3.120 closest distance to " O   GLY A 302 " =    1.560
peak=    3.118 closest distance to " O   ASP A 124 " =    1.177
peak=    3.115 closest distance to " CB  SER A 276 " =    1.252
peak=    3.112 closest distance to " O   HOH Z 163 " =    2.099
peak=    3.107 closest distance to " O   THR A 157 " =    1.497
peak=    3.107 closest distance to " N   THR A 264 " =    1.462
peak=    3.094 closest distance to " CB  PHE A 204 " =    0.714
peak=    3.090 closest distance to " O   HOH Z   1 " =    1.588
peak=    3.049 closest distance to " CB  VAL A 265 " =    1.292
peak=    3.027 closest distance to " O   HOH Z  55 " =    1.460
peak=    3.027 closest distance to " O   HOH Z  24 " =    1.545
peak=    3.021 closest distance to " O   HOH Z 201 " =    2.556

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.434 - 5.191
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 211
   mapped sites are within: 0.701 - 5.191

peak=   -5.627 closest distance to " N   GLU A 277 " =    1.060
peak=   -4.711 closest distance to " O   HOH Z  24 " =    0.826
peak=   -4.673 closest distance to " O   PRO A 198 " =    0.926
peak=   -4.614 closest distance to " O   HOH Z  77 " =    2.020
peak=   -4.584 closest distance to " O   HOH Z  69 " =    1.530
peak=   -4.277 closest distance to " CA  GLN A  55 " =    1.274
peak=   -4.274 closest distance to " OG  SER A  97 " =    2.286
peak=   -4.270 closest distance to " O   HOH Z 244 " =    0.791
peak=   -4.259 closest distance to " ND2 ASN A 209 " =    1.637
peak=   -4.227 closest distance to " ND2 ASN A 285 " =    1.882
peak=   -4.211 closest distance to " O   SER A 135 " =    1.571
peak=   -4.190 closest distance to " NE1 TRP A 179 " =    1.140
peak=   -4.118 closest distance to " OG  SER A  63 " =    1.351
peak=   -4.109 closest distance to " ND2 ASN A  39 " =    1.402
peak=   -4.098 closest distance to " C   PHE A  59 " =    0.928
peak=   -4.094 closest distance to " CB  ASN A 285 " =    1.716
peak=   -4.074 closest distance to " O   HOH Z 415 " =    1.024
peak=   -4.048 closest distance to " O   HOH Z  41 " =    0.734
peak=   -4.013 closest distance to " O   HOH Z 147 " =    0.850
peak=   -4.012 closest distance to " CG BLYS A 290 " =    0.938
peak=   -4.004 closest distance to " CE BLYS A 290 " =    1.991
peak=   -3.939 closest distance to " O   HOH Z 177 " =    0.792
peak=   -3.936 closest distance to " CE2 TYR A  30 " =    2.675
peak=   -3.927 closest distance to " CZ2 TRP A 274 " =    1.088
peak=   -3.915 closest distance to " O   HOH Z  81 " =    0.921
peak=   -3.910 closest distance to " O   HOH Z 385 " =    1.281
peak=   -3.903 closest distance to " CG2 ILE A 120 " =    0.816
peak=   -3.890 closest distance to " OE1 GLU A 277 " =    1.943
peak=   -3.865 closest distance to " O   HOH Z 416 " =    1.030
peak=   -3.862 closest distance to " OG  SER A  32 " =    0.817
peak=   -3.854 closest distance to " O   HOH Z 255 " =    0.967
peak=   -3.841 closest distance to " CZ  PHE A 225 " =    1.953
peak=   -3.838 closest distance to " O   HOH Z  61 " =    1.143
peak=   -3.824 closest distance to " O   GLY A 196 " =    0.887
peak=   -3.806 closest distance to " CD1 ILE A  33 " =    2.139
peak=   -3.785 closest distance to " CG2 ILE A 120 " =    1.218
peak=   -3.784 closest distance to " O   HOH Z 413 " =    4.234
peak=   -3.776 closest distance to " O   HOH Z  52 " =    0.970
peak=   -3.744 closest distance to " CG  LEU A  83 " =    2.160
peak=   -3.724 closest distance to " CD1 PHE A  59 " =    0.993
peak=   -3.712 closest distance to " O   HOH Z 394 " =    1.319
peak=   -3.707 closest distance to " O   HOH Z 129 " =    3.428
peak=   -3.705 closest distance to " O   HIS A 108 " =    1.126
peak=   -3.693 closest distance to " O   HOH Z  52 " =    1.404
peak=   -3.686 closest distance to " CD  ARG A  14 " =    3.043
peak=   -3.682 closest distance to " N   ASN A 127 " =    1.156
peak=   -3.680 closest distance to " OD2 ASP A 253 " =    0.795
peak=   -3.678 closest distance to " CG2 ILE A  20 " =    2.700
peak=   -3.667 closest distance to " O   LYS A 193 " =    1.249
peak=   -3.667 closest distance to " O   GLY A 136 " =    1.456
peak=   -3.662 closest distance to " O   HOH Z  51 " =    0.838
peak=   -3.657 closest distance to " O   GLU A 152 " =    1.136
peak=   -3.656 closest distance to " CB  PHE A  59 " =    1.886
peak=   -3.645 closest distance to " O   ILE A  49 " =    1.496
peak=   -3.644 closest distance to " CG1BVAL A  41 " =    2.934
peak=   -3.644 closest distance to " CE3 TRP A 274 " =    2.225
peak=   -3.642 closest distance to " CB  ASN A  45 " =    1.909
peak=   -3.633 closest distance to " C   VAL A  72 " =    0.823
peak=   -3.631 closest distance to " CG  PRO A 243 " =    1.937
peak=   -3.630 closest distance to " O   HOH Z 375 " =    2.020
peak=   -3.622 closest distance to " O   HOH Z 276 " =    1.540
peak=   -3.612 closest distance to " O   HOH Z 347 " =    0.701
peak=   -3.607 closest distance to " OG  SER A  87 " =    2.264
peak=   -3.604 closest distance to " OD1 ASP A  50 " =    0.881
peak=   -3.599 closest distance to " O   HOH Z  53 " =    1.231
peak=   -3.591 closest distance to " NE2 GLN A  55 " =    0.934
peak=   -3.590 closest distance to " CB  ALA A  84 " =    2.163
peak=   -3.583 closest distance to " O   HOH Z 426 " =    1.524
peak=   -3.581 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.579 closest distance to " O   HOH Z  89 " =    2.625
peak=   -3.571 closest distance to " O   HOH Z 174 " =    1.382
peak=   -3.562 closest distance to " N   GLN A  11 " =    1.058
peak=   -3.553 closest distance to " CG1BVAL A  72 " =    2.167
peak=   -3.539 closest distance to " O   PHE A 218 " =    1.412
peak=   -3.504 closest distance to " CG  ASP A 140 " =    1.101
peak=   -3.494 closest distance to " CD1 TRP A 274 " =    1.010
peak=   -3.491 closest distance to " O   HOH Z 315 " =    1.398
peak=   -3.489 closest distance to " CG1 VAL A 126 " =    2.335
peak=   -3.478 closest distance to " O   ARG A 275 " =    0.702
peak=   -3.469 closest distance to " ND2 ASN A 285 " =    1.511
peak=   -3.467 closest distance to " CD2 HIS A  81 " =    1.309
peak=   -3.453 closest distance to " O   HOH Z 165 " =    2.377
peak=   -3.452 closest distance to " CB  ALA A 114 " =    2.298
peak=   -3.451 closest distance to " CD1 ILE A  49 " =    1.848
peak=   -3.446 closest distance to " O   HOH Z  37 " =    1.149
peak=   -3.438 closest distance to " O   HOH Z 412 " =    2.537
peak=   -3.437 closest distance to " O   HOH Z  88 " =    1.484
peak=   -3.424 closest distance to " O   ALA A 226 " =    1.233
peak=   -3.421 closest distance to " O   HOH Z 323 " =    2.006
peak=   -3.419 closest distance to " O   HOH Z 168 " =    2.756
peak=   -3.418 closest distance to " O   SER A  22 " =    2.425
peak=   -3.413 closest distance to " O   HOH Z 100 " =    0.961
peak=   -3.406 closest distance to " O   HOH Z 105 " =    1.076
peak=   -3.405 closest distance to " OD2 ASP A 140 " =    1.107
peak=   -3.403 closest distance to " O   HOH Z 339 " =    1.565
peak=   -3.402 closest distance to " O   HOH Z 357 " =    2.005
peak=   -3.396 closest distance to " CB  PHE A 208 " =    2.121
peak=   -3.390 closest distance to " O   HOH Z 371 " =    2.213
peak=   -3.386 closest distance to " O   ALA A  51 " =    0.991
peak=   -3.386 closest distance to " O   HOH Z 437 " =    2.978
peak=   -3.386 closest distance to " O   HOH Z 296 " =    1.227
peak=   -3.384 closest distance to " C   GLN A  55 " =    1.459
peak=   -3.381 closest distance to " OD2 ASP A 171 " =    1.536
peak=   -3.378 closest distance to " O   HOH Z 398 " =    0.998
peak=   -3.372 closest distance to " CB  CYS A 201 " =    1.768
peak=   -3.365 closest distance to " CG  GLN A  88 " =    1.170
peak=   -3.357 closest distance to " O   HOH Z 412 " =    2.764
peak=   -3.356 closest distance to " CD1 TYR A 214 " =    1.609
peak=   -3.353 closest distance to " O   HOH Z  60 " =    1.931
peak=   -3.346 closest distance to " O   HOH Z 286 " =    1.464
peak=   -3.342 closest distance to " CA  GLY A 133 " =    1.953
peak=   -3.340 closest distance to " O   HOH Z 201 " =    1.855
peak=   -3.336 closest distance to " O   HOH Z 425 " =    0.873
peak=   -3.332 closest distance to " O   HOH Z 316 " =    1.990
peak=   -3.330 closest distance to " O   HOH Z 308 " =    1.711
peak=   -3.330 closest distance to " OG BSER A 134 " =    1.723
peak=   -3.328 closest distance to " N   ALA A   1 " =    1.165
peak=   -3.324 closest distance to " O   HOH Z 198 " =    1.107
peak=   -3.320 closest distance to " O   HOH Z 414 " =    1.308
peak=   -3.319 closest distance to " CE2 TRP A 274 " =    1.200
peak=   -3.319 closest distance to " CB  ALA A  43 " =    2.406
peak=   -3.317 closest distance to " CD  GLN A 223 " =    1.751
peak=   -3.316 closest distance to " O   HOH Z 100 " =    1.292
peak=   -3.316 closest distance to " NH1 ARG A 195 " =    1.092
peak=   -3.312 closest distance to " O   TRP A  70 " =    1.550
peak=   -3.312 closest distance to " O   HOH Z 298 " =    2.414
peak=   -3.308 closest distance to " O   ARG A  24 " =    2.095
peak=   -3.306 closest distance to " OG  SER A 245 " =    2.093
peak=   -3.306 closest distance to " OG  SER A 276 " =    0.915
peak=   -3.301 closest distance to " ND2 ASN A  69 " =    0.938
peak=   -3.298 closest distance to " CB  ASP A 132 " =    2.758
peak=   -3.297 closest distance to " O   HOH Z 265 " =    2.406
peak=   -3.295 closest distance to " OG  SER A 273 " =    2.124
peak=   -3.292 closest distance to " O   HOH Z  40 " =    1.222
peak=   -3.285 closest distance to " NE2 GLN A 122 " =    1.027
peak=   -3.281 closest distance to " O   HOH Z 266 " =    4.815
peak=   -3.278 closest distance to " OH  TYR A  30 " =    0.888
peak=   -3.278 closest distance to " CE  LYS A 289 " =    1.044
peak=   -3.277 closest distance to " O   LEU A 222 " =    1.643
peak=   -3.275 closest distance to " O   HOH Z 283 " =    2.035
peak=   -3.274 closest distance to " CB  ALA A 248 " =    2.102
peak=   -3.273 closest distance to " O   CYS A 260 " =    1.314
peak=   -3.267 closest distance to " O   ALA A  10 " =    1.480
peak=   -3.261 closest distance to " CE1 PHE A  16 " =    1.074
peak=   -3.261 closest distance to " O   HOH Z 185 " =    1.378
peak=   -3.260 closest distance to " ND2 ASN A 249 " =    2.363
peak=   -3.249 closest distance to " C   ARG A 156 " =    0.926
peak=   -3.249 closest distance to " N   ARG A 138 " =    1.835
peak=   -3.248 closest distance to " O   HOH Z  39 " =    1.249
peak=   -3.245 closest distance to " O   HOH Z 198 " =    2.204
peak=   -3.238 closest distance to " C   ILE A 120 " =    1.743
peak=   -3.236 closest distance to " O   HOH Z 216 " =    1.528
peak=   -3.236 closest distance to " CG  ASP A 231 " =    0.968
peak=   -3.235 closest distance to " CB  SER A  62 " =    5.191
peak=   -3.232 closest distance to " O   LYS A 117 " =    1.717
peak=   -3.231 closest distance to " OE2 GLU A 152 " =    1.260
peak=   -3.218 closest distance to " CB  SER A 210 " =    1.092
peak=   -3.216 closest distance to " N   GLN A  58 " =    1.001
peak=   -3.212 closest distance to " N   SER A 206 " =    1.727
peak=   -3.211 closest distance to " O   HOH Z 250 " =    0.996
peak=   -3.208 closest distance to " O   HOH Z 147 " =    1.666
peak=   -3.205 closest distance to " N   ALA A  19 " =    2.202
peak=   -3.200 closest distance to " OXT GLY A 302 " =    3.273
peak=   -3.199 closest distance to " N   ILE A 263 " =    0.835
peak=   -3.198 closest distance to " O   HOH Z 131 " =    4.130
peak=   -3.198 closest distance to " O   HOH Z 336 " =    5.145
peak=   -3.198 closest distance to " O   HOH Z 429 " =    1.734
peak=   -3.192 closest distance to " O   PRO A 163 " =    1.081
peak=   -3.192 closest distance to " O   HOH Z 358 " =    1.649
peak=   -3.190 closest distance to " O   HOH Z 126 " =    1.727
peak=   -3.189 closest distance to " CB  ASN A 249 " =    1.790
peak=   -3.189 closest distance to " CA  GLY A 203 " =    2.601
peak=   -3.189 closest distance to " OD2 ASP A 272 " =    1.360
peak=   -3.188 closest distance to " OD2 ASP A 171 " =    2.095
peak=   -3.188 closest distance to " O   SER A 273 " =    0.817
peak=   -3.185 closest distance to " O   HOH Z 395 " =    1.135
peak=   -3.181 closest distance to " N   ASN A  60 " =    0.876
peak=   -3.176 closest distance to " ND2 ASN A 127 " =    1.712
peak=   -3.176 closest distance to " NH1BARG A 145 " =    3.337
peak=   -3.172 closest distance to " O   HOH Z 278 " =    0.965
peak=   -3.166 closest distance to " CB  ARG A  79 " =    2.749
peak=   -3.165 closest distance to " SG  CYS A 168 " =    1.265
peak=   -3.163 closest distance to " OG1 THR A  82 " =    1.136
peak=   -3.159 closest distance to " CA  GLN A  58 " =    1.226
peak=   -3.153 closest distance to " O   HOH Z 387 " =    1.508
peak=   -3.149 closest distance to " CD2 HIS A 207 " =    1.452
peak=   -3.148 closest distance to " CG  ARG A  66 " =    1.932
peak=   -3.147 closest distance to " N   SER A  62 " =    2.438
peak=   -3.136 closest distance to " CA  GLY A 241 " =    2.149
peak=   -3.124 closest distance to " NE1 TRP A  70 " =    1.192
peak=   -3.119 closest distance to " CG  GLU A 128 " =    1.593
peak=   -3.118 closest distance to " NE2 GLN A 278 " =    1.429
peak=   -3.116 closest distance to " CG2 THR A 221 " =    2.239
peak=   -3.110 closest distance to " CG  ARG A  79 " =    0.785
peak=   -3.101 closest distance to " CD2 TYR A 116 " =    2.313
peak=   -3.099 closest distance to " CB  ALA A 100 " =    1.981
peak=   -3.094 closest distance to " CA  GLY A 133 " =    2.066
peak=   -3.090 closest distance to " O   HOH Z 215 " =    1.279
peak=   -3.084 closest distance to " OG1 THR A 251 " =    2.836
peak=   -3.074 closest distance to " CZ  PHE A  16 " =    1.859
peak=   -3.069 closest distance to " OG BSER A 210 " =    2.112
peak=   -3.045 closest distance to " O   HOH Z 428 " =    2.759
peak=   -3.037 closest distance to " NE2 GLN A  77 " =    0.970
peak=   -3.018 closest distance to " CE  LYS A  48 " =    1.569

================= 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    :  0.4849 0.4801   6.293633e+00   6.288199e+00
   1_bss:  0.4768 0.4748   6.289970e+00   6.277624e+00
   1_xyz:  0.4073 0.4466   6.202507e+00   6.243681e+00
   1_adp:  0.3729 0.4558   6.171332e+00   6.251589e+00
   1_occ:  0.3724 0.4565   6.171540e+00   6.252174e+00
   2_bss:  0.3726 0.4529   6.170965e+00   6.251112e+00
   2_xyz:  0.3235 0.4057   6.064508e+00   6.186485e+00
   2_adp:  0.3093 0.3970   6.041423e+00   6.171192e+00
   2_occ:  0.3091 0.3974   6.041791e+00   6.171579e+00
   3_bss:  0.3099 0.3965   6.041356e+00   6.170075e+00
   3_xyz:  0.2592 0.3393   5.886233e+00   6.054468e+00
   3_adp:  0.2381 0.3256   5.833990e+00   6.024749e+00
   3_occ:  0.2379 0.3249   5.832943e+00   6.023731e+00
   4_bss:  0.2379 0.3243   5.831561e+00   6.022487e+00
   4_xyz:  0.2004 0.2674   5.668469e+00   5.872353e+00
   4_adp:  0.1852 0.2518   5.602435e+00   5.817813e+00
   4_occ:  0.1850 0.2512   5.601014e+00   5.815998e+00
   5_bss:  0.1852 0.2506   5.599080e+00   5.814739e+00
   5_xyz:  0.1595 0.2193   5.458434e+00   5.692589e+00
   5_adp:  0.1519 0.2025   5.402301e+00   5.624687e+00
   5_occ:  0.1517 0.2020   5.400511e+00   5.622230e+00
   5_bss:  0.1517 0.2015   5.399613e+00   5.620811e+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:  0.344  20.001  -0.718   1.339  -0.307   0.000  -0.000  -0.000
   1_xyz:  0.344  20.001  -0.718   1.339  -0.307   0.000  -0.000  -0.000
   1_adp:  0.344  20.001  -0.718   1.339  -0.307   0.000  -0.000  -0.000
   1_occ:  0.344  20.001  -0.718   1.339  -0.307   0.000  -0.000  -0.000
   2_bss:  0.351  50.001  -0.343   1.337   0.838   0.000   0.000   0.000
   2_xyz:  0.351  50.001  -0.343   1.337   0.838   0.000   0.000   0.000
   2_adp:  0.351  50.001  -0.343   1.337   0.838   0.000   0.000   0.000
   2_occ:  0.351  50.001  -0.343   1.337   0.838   0.000   0.000   0.000
   3_bss:  0.344  57.799  -0.340   1.265   1.323   0.000   0.000   0.000
   3_xyz:  0.344  57.799  -0.340   1.265   1.323   0.000   0.000   0.000
   3_adp:  0.344  57.799  -0.340   1.265   1.323   0.000   0.000   0.000
   3_occ:  0.344  57.799  -0.340   1.265   1.323   0.000   0.000   0.000
   4_bss:  0.344  57.799  -0.854   0.171   1.014   0.000   0.000   0.000
   4_xyz:  0.344  57.799  -0.854   0.171   1.014   0.000   0.000   0.000
   4_adp:  0.344  57.799  -0.854   0.171   1.014   0.000   0.000   0.000
   4_occ:  0.344  57.799  -0.854   0.171   1.014   0.000   0.000   0.000
   5_bss:  0.330  57.799  -0.998  -0.289   1.118  -0.000   0.000   0.000
   5_xyz:  0.330  57.799  -0.998  -0.289   1.118  -0.000   0.000   0.000
   5_adp:  0.330  57.799  -0.998  -0.289   1.118  -0.000   0.000   0.000
   5_occ:  0.330  57.799  -0.998  -0.289   1.118  -0.000   0.000   0.000
   5_bss:  0.311  43.517  -1.334  -0.778   0.850  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.843 0.3835  0.5346    79422.324
   1_bss:  59.633 0.3980  0.5597    76012.673
   1_xyz:  53.657 0.4737  0.6539    63614.867
   1_adp:  54.873 0.4580  0.6323    66579.803
   1_occ:  55.046 0.4558  0.6281    66808.796
   2_bss:  54.767 0.4591  0.6453    66050.599
   2_xyz:  46.274 0.5655  0.7975    49699.740
   2_adp:  44.486 0.5879  0.8047    47111.332
   2_occ:  44.553 0.5870  0.8034    47206.422
   3_bss:  44.425 0.5885  0.8086    46902.305
   3_xyz:  35.924 0.6895  0.9285    31582.474
   3_adp:  33.938 0.7128  0.9348    28802.544
   3_occ:  33.875 0.7136  0.9354    28704.970
   4_bss:  33.769 0.7146  0.9154    28522.542
   4_xyz:  27.161 0.7880  0.9753    19096.968
   4_adp:  24.984 0.8117  0.9726    16664.705
   4_occ:  24.923 0.8123  0.9728    16570.484
   5_bss:  24.841 0.8130  0.9671    16434.487
   5_xyz:  21.248 0.8489  0.9920    12197.689
   5_adp:  19.208 0.8694  0.9949    10533.536
   5_occ:  19.154 0.8699  0.9950    10465.093
   5_bss:  19.137 0.8699  0.9814    10409.262
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.104   2.3801e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.104   2.3801e-01
   1_xyz:   1.491  0.011  0.100 15.507  0.006  4.109   1.3082e-01
   1_adp:   1.491  0.011  0.100 15.507  0.006  4.109   1.3082e-01
   1_occ:   1.491  0.011  0.100 15.507  0.006  4.109   1.3082e-01
   2_bss:   1.491  0.011  0.100 15.507  0.006  4.109   1.3082e-01
   2_xyz:   1.344  0.009  0.091 15.090  0.006  4.103   1.0178e-01
   2_adp:   1.344  0.009  0.091 15.090  0.006  4.103   1.0178e-01
   2_occ:   1.344  0.009  0.091 15.090  0.006  4.103   1.0178e-01
   3_bss:   1.344  0.009  0.091 15.090  0.006  4.103   1.0178e-01
   3_xyz:   1.180  0.008  0.083 14.776  0.005  4.103   8.1980e-02
   3_adp:   1.180  0.008  0.083 14.776  0.005  4.103   8.1980e-02
   3_occ:   1.180  0.008  0.083 14.776  0.005  4.103   8.1980e-02
   4_bss:   1.180  0.008  0.083 14.776  0.005  4.103   8.1980e-02
   4_xyz:   0.948  0.006  0.068 14.099  0.003  4.113   5.5107e-02
   4_adp:   0.948  0.006  0.068 14.099  0.003  4.113   5.5107e-02
   4_occ:   0.948  0.006  0.068 14.099  0.003  4.113   5.5107e-02
   5_bss:   0.948  0.006  0.068 14.099  0.003  4.113   5.5107e-02
   5_xyz:   0.911  0.005  0.064 14.025  0.003  4.108   5.0885e-02
   5_adp:   0.911  0.005  0.064 14.025  0.003  4.108   5.0885e-02
   5_occ:   0.911  0.005  0.064 14.025  0.003  4.108   5.0885e-02
   5_bss:   0.911  0.005  0.064 14.025  0.003  4.108   5.0885e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.336   2.4090e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.336   2.4090e-01
   1_xyz:  10.568  0.062  0.394 75.943  0.042  1.918   1.1245e-01
   1_adp:  10.568  0.062  0.394 75.943  0.042  1.918   1.1245e-01
   1_occ:  10.568  0.062  0.394 75.943  0.042  1.918   1.1245e-01
   2_bss:  10.568  0.062  0.394 75.943  0.042  1.918   1.1245e-01
   2_xyz:   9.436  0.056  0.311 75.643  0.056  2.007   8.8817e-02
   2_adp:   9.436  0.056  0.311 75.643  0.056  2.007   8.8817e-02
   2_occ:   9.436  0.056  0.311 75.643  0.056  2.007   8.8817e-02
   3_bss:   9.436  0.056  0.311 75.643  0.056  2.007   8.8817e-02
   3_xyz:   6.873  0.049  0.262 77.602  0.053  2.071   7.9846e-02
   3_adp:   6.873  0.049  0.262 77.602  0.053  2.071   7.9846e-02
   3_occ:   6.873  0.049  0.262 77.602  0.053  2.071   7.9846e-02
   4_bss:   6.873  0.049  0.262 77.602  0.053  2.071   7.9846e-02
   4_xyz:   6.908  0.035  0.214 81.950  0.025  2.287   4.2972e-02
   4_adp:   6.908  0.035  0.214 81.950  0.025  2.287   4.2972e-02
   4_occ:   6.908  0.035  0.214 81.950  0.025  2.287   4.2972e-02
   5_bss:   6.908  0.035  0.214 81.950  0.025  2.287   4.2972e-02
   5_xyz:   7.418  0.045  0.190 79.307  0.034  2.408   4.2850e-02
   5_adp:   7.418  0.045  0.190 79.307  0.034  2.408   4.2850e-02
   5_occ:   7.418  0.045  0.190 79.307  0.034  2.408   4.2850e-02
   5_bss:   7.418  0.045  0.190 79.307  0.034  2.408   4.2850e-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:  78.62   0.00  19.07  75.66   0.00  16.56  78.62   0.00  32.75
   1_occ:  78.62   0.00  19.07  75.66   0.00  16.56  78.62   0.00  32.75
   2_bss:  78.62   0.00  19.07  75.66   0.00  16.56  78.62   0.00  32.75
   2_xyz:  78.62   0.00  19.07  75.66   0.00  16.56  78.62   0.00  32.75
   2_adp:  85.39   0.00  18.12  85.39   0.00  15.41  75.56   0.00  32.84
   2_occ:  85.39   0.00  18.12  85.39   0.00  15.41  75.56   0.00  32.84
   3_bss:  85.39   0.00  18.12  85.39   0.00  15.41  75.56   0.00  32.84
   3_xyz:  85.39   0.00  18.12  85.39   0.00  15.41  75.56   0.00  32.84
   3_adp:  95.16   0.00  18.35  95.16   0.00  14.42  93.12   1.49  39.77
   3_occ:  95.16   0.00  18.35  95.16   0.00  14.42  93.12   1.49  39.77
   4_bss:  95.16   0.00  18.35  95.16   0.00  14.42  93.12   1.49  39.77
   4_xyz:  95.16   0.00  18.35  95.16   0.00  14.42  93.12   1.49  39.77
   4_adp: 110.71   0.00  18.81 110.71   0.00  13.52 105.75   4.17  47.66
   4_occ: 110.71   0.00  18.81 110.71   0.00  13.52 105.75   4.17  47.66
   5_bss: 110.71   0.00  18.81 110.71   0.00  13.52 105.75   4.17  47.66
   5_xyz: 110.71   0.00  18.81 110.71   0.00  13.52 105.75   4.17  47.66
   5_adp: 105.51   0.00  17.09 105.51   0.00  12.08 100.43   3.82  44.35
   5_occ: 105.51   0.00  17.09 105.51   0.00  12.08 100.43   3.82  44.35
   5_bss: 105.51   0.00  17.09 105.51   0.00  12.09 100.43   3.83  44.35
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.862    0.020    0.321
   1_adp:    1.862    0.020    0.321
   1_occ:    1.862    0.020    0.321
   2_bss:    1.862    0.020    0.321
   2_xyz:    1.603    0.038    0.506
   2_adp:    1.603    0.038    0.506
   2_occ:    1.603    0.038    0.506
   3_bss:    1.603    0.038    0.506
   3_xyz:    1.790    0.064    0.687
   3_adp:    1.790    0.064    0.687
   3_occ:    1.790    0.064    0.687
   4_bss:    1.790    0.064    0.687
   4_xyz:    2.029    0.047    0.788
   4_adp:    2.029    0.047    0.788
   4_occ:    2.029    0.047    0.788
   5_bss:    2.029    0.047    0.788
   5_xyz:    2.222    0.053    0.858
   5_adp:    2.222    0.053    0.858
   5_occ:    2.222    0.053    0.858
   5_bss:    2.222    0.053    0.858
------------------------------------------------------------------------

CPU time actual refinement: 353.36


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/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_7/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_7/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.23 
  Macro-tasks:
    bulk solvent and scale       = 47.78  
    individual site refinement   = 145.25 
    weights calculation          = 29.72  
    collect and process          = 6.48   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 229.32 
  Micro-tasks:
    mask                            = 2.80   
    f_calc                          = 113.81 
    alpha_beta                      = 8.74   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 117.20 
    fmodel                         = 7.69   
    r_factors                      = 0.12   
    phase_errors                   = 10.70  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 262.52 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.022 micro seconds
Total CPU time: 6.11 minutes
from_scatterers_fft:    639 calls, 113.33 s
gradients_fft:          584 calls, 106.22 s

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

# Date 2008-01-16 Time 03:46:33 PST -0800 (1200483993.03 s)
Start R-work = 0.4849, R-free = 0.4801 (no bulk solvent and anisotropic scale)
Final R-work = 0.1677, R-free = 0.2151 (no bulk solvent and anisotropic scale)

Start R-work = 0.4768, R-free = 0.4748
Final R-work = 0.1517, R-free = 0.2015