# Date 2008-01-16 Time 06:15:40 PST -0800 (1200492940.01 s)
#phil __OFF__

Command line arguments: "../1068.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10662
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1068

-------------------------------------------------------------------------------
  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: (71.3037, 47.8686, 84.6622, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96152
Completeness in resolution range: 0.917303
Completeness with d_max=infinity: 0.914605

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0711
                             d_min =   1.9615

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: (71.3037, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0711 1.96152
Completeness in resolution range: 0.917303
Completeness with d_max=infinity: 0.914605

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0715 -  4.1984 [2241/2270]  2018   223  10.0%
  bin  2:  4.1984 -  3.3443 [2149/2172]  1933   216  10.1%
  bin  3:  3.3443 -  2.9251 [2111/2136]  1898   213  10.1%
  bin  4:  2.9251 -  2.6593 [2104/2121]  1897   207   9.8%
  bin  5:  2.6593 -  2.4695 [2087/2130]  1882   205   9.8%
  bin  6:  2.4695 -  2.3245 [2082/2110]  1875   207   9.9%
  bin  7:  2.3245 -  2.2085 [2070/2106]  1857   213  10.3%
  bin  8:  2.2085 -  2.1126 [2057/2099]  1854   203   9.9%
  bin  9:  2.1126 -  2.0315 [2039/2106]  1833   206  10.1%
  bin 10:  2.0315 -  1.9615 [ 649/2105]   583    66  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 20
        2.22 -     2.89: 1319
        2.89 -     3.56: 4414
        3.56 -     4.23: 9167
        4.23 -     4.90: 13277
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.546 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.556 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.586 3.120 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.646 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.700 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28192 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_1068/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/model_refine_001.geo

CPU time processing inputs: 9.60


============================ 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 = 71.30375 47.8686 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4631   r_free= 0.4540   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.272655                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.3595 0.3712      6.5341      6.5261|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.3924 0.3805      6.8065      6.7948|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.4333 0.3984      6.6435        6.63|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.4582 0.4464      6.4939      6.4788|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.4770 0.4750      6.3366      6.3309|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.5070 0.4856      6.2726      6.1676|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.4996 0.4367      6.2303      6.1767|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.5208 0.5257      6.1468       6.204|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.5360 0.5166      6.1401      6.1016|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.5089 0.5424      6.0679      6.1229|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.5285 0.5597       6.026      5.9908|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.5087 0.5307      5.9285      5.9889|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.5131 0.4332      5.8709      5.8201|
| 14:  2.0105 -  1.9615 0.20    282   28 0.5730 0.4761      5.7921      5.7749|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6832  1457   165  0.71  33.02   0.83     0.74      67610.45|
|  2:  4.6832 -  3.7358  1393   151  0.72  33.70   0.91     0.80      94906.45|
|  3:  3.7358 -  3.2691  1375   152  0.62  42.50   0.90     0.78     103665.84|
|  4:  3.2691 -  2.9727  1359   151  0.52  49.92   0.91     0.72      94778.41|
|  5:  2.9727 -  2.7610  1357   152  0.45  55.49   0.87     0.65      77026.65|
|  6:  2.7610 -  2.5991  1348   155  0.44  57.12   0.89     0.61      64772.40|
|  7:  2.5991 -  2.4695  1339   138  0.43  57.54   0.91     0.59      58461.68|
|  8:  2.4695 -  2.3625  1337   149  0.38  61.48   0.87     0.56      57164.72|
|  9:  2.3625 -  2.2718  1334   154  0.35  63.97   0.91     0.52      54160.54|
| 10:  2.2718 -  2.1937  1337   149  0.31  67.22   0.93     0.46      53198.12|
| 11:  2.1937 -  2.1253  1318   141  0.26  70.76   0.91     0.39      50416.17|
| 12:  2.1253 -  2.0647  1320   146  0.23  73.17   0.92     0.37      47644.85|
| 13:  2.0647 -  2.0105  1074   128  0.27  70.17   0.93     0.42      38890.53|
| 14:  2.0105 -  1.9615   282    28  0.33  65.19   0.86     0.53      29367.73|
|alpha:            min =        0.37 max =            0.80 mean =         0.59|
|beta:             min =    29367.73 max =       103665.84 mean =     66441.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.25|
|phase err.(test): min =        0.00 max =           89.99 mean =        56.32|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.537046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.348   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.861541              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.487   (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 |  1.546 -  1.881:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.881 -  2.217:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.217 -  2.552:       37 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.552 -  2.887:     1282 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.887 -  3.223:     1891 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.223 -  3.558:     2523 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.558 -  3.894:     4659 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.894 -  4.229:     4508 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.229 -  4.565:     6062 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.565 -  4.900:     7215 |
|-----------------------------------------------------------------------------|
|-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 |        0.184 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.546 |       0.489 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4631   r_free= 0.4540   ksol= 0.00   Bsol= 0.00   scale= 0.890    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.272655                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4555   r_free= 0.4474   ksol= 0.29   Bsol= 27.04   scale= 0.935   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,3.29,0.77,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.267247                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.806240              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.303   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.254660              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.184   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4555      final r-factor (work) = 0.3700          |
| start r-factor (free) = 0.4474      final r-factor (free) = 0.3992          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5033 = 6.81 * 0.50 * 6.2646 + 1.00 * 0.1842                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.0760 = 6.81 * 0.50 * 6.1605 + 1.00 * 0.1111                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3700      final r-factor (work) = 0.3365          |
| start r-factor (free) = 0.3992      final r-factor (free) = 0.4085          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7354 = 1.25 * 1.00 * 6.1605 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6489 = 1.25 * 1.00 * 6.0808 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.60  19.23    None  None   None       |
|    all(noH): 2823   0      0.00    105.60  19.23    None  None   None       |
|    Sol.    : 438    0      0.00    105.60  38.04    None  None   None       |
|    Mac.    : 2385   0      0.00    88.00   15.77    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 -  10.560:  957   |   5:    52.800 -  63.360:   74        |
|      1:    10.560 -  21.120:  910   |   6:    63.360 -  73.920:   43        |
|      2:    21.120 -  31.680:  466   |   7:    73.920 -  84.480:   16        |
|      3:    31.680 -  42.240:  239   |   8:    84.480 -  95.040:    3        |
|      4:    42.240 -  52.800:  114   |   9:    95.040 - 105.600:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3365 r_free = 0.4085             target_work(ml) = 6.087         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3363 r_free = 0.4093             target_work(ml) = 6.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3363   r_free= 0.4093   ksol= 0.29   Bsol= 27.04   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.22,3.29,0.77,0.00,0.00,0.00); trace/3= 0.95                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.086862                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3359   r_free= 0.4064   ksol= 0.32   Bsol= 57.66   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,1.73,0.10,0.00,0.00,0.00); trace/3= 0.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.087441                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.256046              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.680905              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.061  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3359      final r-factor (work) = 0.2671          |
| start r-factor (free) = 0.4064      final r-factor (free) = 0.3407          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2144 = 8.26 * 0.50 * 6.0812 + 1.00 * 0.1111                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.8761 = 8.26 * 0.50 * 6.0058 + 1.00 * 0.0841                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2671      final r-factor (work) = 0.2532          |
| start r-factor (free) = 0.3407      final r-factor (free) = 0.3268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1089 = 0.68 * 1.00 * 6.0058 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0253 = 0.68 * 1.00 * 5.8880 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.29  18.69    None  None   None       |
|    all(noH): 2823   0      0.00    106.29  18.69    None  None   None       |
|    Sol.    : 438    0      1.34    106.29  39.00    None  None   None       |
|    Mac.    : 2385   0      0.00    87.00   14.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.629: 1026   |   5:    53.145 -  63.774:   72        |
|      1:    10.629 -  21.258:  947   |   6:    63.774 -  74.403:   28        |
|      2:    21.258 -  31.887:  385   |   7:    74.403 -  85.032:   19        |
|      3:    31.887 -  42.516:  221   |   8:    85.032 -  95.661:    3        |
|      4:    42.516 -  53.145:  121   |   9:    95.661 - 106.290:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2532 r_free = 0.3268             target_work(ml) = 5.869         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2530 r_free = 0.3265             target_work(ml) = 5.869         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2530   r_free= 0.3265   ksol= 0.32   Bsol= 57.66   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.92,1.73,0.10,0.00,0.00,0.00); trace/3= 0.30                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.868749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2531   r_free= 0.3259   ksol= 0.32   Bsol= 59.78   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,0.71,-0.67,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.867976                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.194548              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.155   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.768502              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.561  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2531      final r-factor (work) = 0.1936          |
| start r-factor (free) = 0.3259      final r-factor (free) = 0.2462          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3220 = 6.19 * 0.50 * 5.8884 + 1.00 * 0.0841                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9597 = 6.19 * 0.50 * 5.7720 + 1.00 * 0.0824                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1936      final r-factor (work) = 0.1686          |
| start r-factor (free) = 0.2462      final r-factor (free) = 0.2180          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4564 = 0.77 * 1.00 * 5.7720 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2786 = 0.77 * 1.00 * 5.5509 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.74  18.44    None  None   None       |
|    all(noH): 2823   0      0.00    100.74  18.44    None  None   None       |
|    Sol.    : 438    0      5.13    100.74  44.55    None  None   None       |
|    Mac.    : 2385   0      0.00    100.50  13.65    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 -  10.074: 1070   |   5:    50.369 -  60.443:   96        |
|      1:    10.074 -  20.148: 1006   |   6:    60.443 -  70.517:   62        |
|      2:    20.148 -  30.221:  276   |   7:    70.517 -  80.590:   31        |
|      3:    30.221 -  40.295:  138   |   8:    80.590 -  90.664:   14        |
|      4:    40.295 -  50.369:  123   |   9:    90.664 - 100.738:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1686 r_free = 0.2180             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1684 r_free = 0.2179             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1684   r_free= 0.2179   ksol= 0.32   Bsol= 59.78   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,0.71,-0.67,0.00,-0.00,-0.00); trace/3= -0.30                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.494631                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1682   r_free= 0.2183   ksol= 0.33   Bsol= 69.63   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-0.68,-1.43,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.495411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.631010              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.624   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.355569              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.754  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1682      final r-factor (work) = 0.1384          |
| start r-factor (free) = 0.2183      final r-factor (free) = 0.1852          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1714 = 3.63 * 0.50 * 5.5572 + 1.00 * 0.0824                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8943 = 3.63 * 0.50 * 5.4120 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1384      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1852      final r-factor (free) = 0.1769          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9371 = 0.36 * 1.00 * 5.4120 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8946 = 0.36 * 1.00 * 5.2988 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.40    103.13  17.73    None  None   None       |
|    all(noH): 2823   0      1.40    103.13  17.73    None  None   None       |
|    Sol.    : 438    0      5.36    97.77   43.54    None  None   None       |
|    Mac.    : 2385   0      1.40    103.13  12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.404 -  11.577: 1388   |   5:    52.268 -  62.441:   83        |
|      1:    11.577 -  21.750:  842   |   6:    62.441 -  72.614:   50        |
|      2:    21.750 -  31.923:  185   |   7:    72.614 -  82.787:   24        |
|      3:    31.923 -  42.096:  118   |   8:    82.787 -  92.960:    7        |
|      4:    42.096 -  52.268:  119   |   9:    92.960 - 103.133:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1769             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1769             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1769   ksol= 0.33   Bsol= 69.63   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,-0.68,-1.43,-0.00,-0.00,-0.00); trace/3= -1.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.274518                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1305   r_free= 0.1771   ksol= 0.32   Bsol= 63.97   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.25,-1.63,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.276419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.645010              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.182094              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.618  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1771      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4282 = 1.65 * 0.50 * 5.3002 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3828 = 1.65 * 0.50 * 5.2657 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9693 = 0.18 * 1.00 * 5.2657 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9640 = 0.18 * 1.00 * 5.2477 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.21    100.49  17.01    None  None   None       |
|    all(noH): 2823   0      2.21    100.49  17.01    None  None   None       |
|    Sol.    : 438    0      4.60    92.11   40.63    None  None   None       |
|    Mac.    : 2385   0      2.21    100.49  12.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.209 -  12.038: 1520   |   5:    51.352 -  61.180:   77        |
|      1:    12.038 -  21.866:  752   |   6:    61.180 -  71.009:   36        |
|      2:    21.866 -  31.695:  167   |   7:    71.009 -  80.837:   18        |
|      3:    31.695 -  41.523:  133   |   8:    80.837 -  90.666:    4        |
|      4:    41.523 -  51.352:  110   |   9:    90.666 - 100.495:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1262 r_free = 0.1697             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1261 r_free = 0.1696             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1696   ksol= 0.32   Bsol= 63.97   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-1.25,-1.63,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241943                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.1017 0.1292      5.3957       5.559|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.0924 0.1102      5.4787      5.6834|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.1177 0.1775      5.5499      5.9204|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.1454 0.1673      5.5685       5.699|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.1552 0.1988      5.4468      5.6044|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.1453 0.2125      5.3207      5.5077|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.1381 0.1754      5.2492      5.4272|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.1376 0.1940      5.1709      5.4021|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.1327 0.1987       5.114        5.35|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.1297 0.1754      5.0543      5.2994|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.1250 0.1857       4.979      5.2272|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.1311 0.1842       4.938      5.1666|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.1298 0.1862      4.8595      5.0773|
| 14:  2.0105 -  1.9615 0.20    282   28 0.1291 0.1831      4.7462      5.0111|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6832  1457   165  0.94   8.83   0.97     0.94       6848.15|
|  2:  4.6832 -  3.7358  1393   151  0.95   8.43   1.00     0.99       9279.15|
|  3:  3.7358 -  3.2691  1375   152  0.92  12.85   1.02     1.01      12062.47|
|  4:  3.2691 -  2.9727  1359   151  0.90  16.29   1.00     0.97      12593.64|
|  5:  2.9727 -  2.7610  1357   152  0.87  18.89   0.99     0.97      10639.09|
|  6:  2.7610 -  2.5991  1348   155  0.89  17.78   0.99     0.96       8404.71|
|  7:  2.5991 -  2.4695  1339   138  0.90  16.77   0.99     0.96       7102.16|
|  8:  2.4695 -  2.3625  1337   149  0.88  18.19   1.00     0.96       6613.55|
|  9:  2.3625 -  2.2718  1334   154  0.89  17.56   1.00     0.96       5748.77|
| 10:  2.2718 -  2.1937  1337   149  0.90  16.84   0.98     0.94       5135.79|
| 11:  2.1937 -  2.1253  1318   141  0.90  16.69   0.98     0.94       4464.67|
| 12:  2.1253 -  2.0647  1320   146  0.89  17.40   0.99     0.98       4398.14|
| 13:  2.0647 -  2.0105  1074   128  0.89  17.45   0.99     0.97       3747.02|
| 14:  2.0105 -  1.9615   282    28  0.88  18.02   0.97     0.94       3013.27|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3013.27 max =        12593.64 mean =      7477.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.63|
|phase err.(test): min =        0.00 max =           89.06 mean =        15.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1695   ksol= 0.32   Bsol= 58.31   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.33,-1.58,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1695   ksol= 0.32   Bsol= 58.31   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.95,-1.33,-1.58,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241699                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0715 -  4.6832 0.99   1457  165 0.1015 0.1287      5.3939      5.5538|
|  2:  4.6832 -  3.7358 0.99   1393  151 0.0920 0.1097      5.4746      5.6777|
|  3:  3.7358 -  3.2691 0.99   1375  152 0.1175 0.1772      5.5476      5.9199|
|  4:  3.2691 -  2.9727 0.99   1359  151 0.1455 0.1669      5.5686      5.6982|
|  5:  2.9727 -  2.7610 0.99   1357  152 0.1554 0.1988      5.4475      5.6051|
|  6:  2.7610 -  2.5991 0.99   1348  155 0.1455 0.2125      5.3213      5.5084|
|  7:  2.5991 -  2.4695 0.98   1339  138 0.1382 0.1754      5.2498      5.4275|
|  8:  2.4695 -  2.3625 0.98   1337  149 0.1376 0.1943      5.1718      5.4035|
|  9:  2.3625 -  2.2718 0.99   1334  154 0.1327 0.1988      5.1144       5.351|
| 10:  2.2718 -  2.1937 0.98   1337  149 0.1298 0.1754       5.055      5.3001|
| 11:  2.1937 -  2.1253 0.97   1318  141 0.1250 0.1857      4.9791      5.2272|
| 12:  2.1253 -  2.0647 0.98   1320  146 0.1312 0.1845      4.9389      5.1684|
| 13:  2.0647 -  2.0105 0.81   1074  128 0.1298 0.1861      4.8599      5.0767|
| 14:  2.0105 -  1.9615 0.20    282   28 0.1292 0.1830      4.7461      5.0101|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0715 -  4.6832  1457   165  0.94   8.78   0.97     0.94       6789.87|
|  2:  4.6832 -  3.7358  1393   151  0.95   8.39   1.00     0.99       9182.69|
|  3:  3.7358 -  3.2691  1375   152  0.92  12.76   1.01     1.01      11958.01|
|  4:  3.2691 -  2.9727  1359   151  0.90  16.27   1.00     0.97      12577.62|
|  5:  2.9727 -  2.7610  1357   152  0.87  18.88   0.99     0.96      10634.70|
|  6:  2.7610 -  2.5991  1348   155  0.89  17.79   0.98     0.96       8412.80|
|  7:  2.5991 -  2.4695  1339   138  0.90  16.78   0.98     0.96       7110.06|
|  8:  2.4695 -  2.3625  1337   149  0.88  18.21   0.99     0.95       6628.21|
|  9:  2.3625 -  2.2718  1334   154  0.89  17.57   0.99     0.95       5761.82|
| 10:  2.2718 -  2.1937  1337   149  0.90  16.85   0.98     0.94       5145.87|
| 11:  2.1937 -  2.1253  1318   141  0.90  16.70   0.98     0.94       4468.62|
| 12:  2.1253 -  2.0647  1320   146  0.89  17.41   0.98     0.98       4406.19|
| 13:  2.0647 -  2.0105  1074   128  0.89  17.46   0.98     0.97       3748.54|
| 14:  2.0105 -  1.9615   282    28  0.88  18.01   0.97     0.94       3008.40|
|alpha:            min =        0.94 max =            1.01 mean =         0.96|
|beta:             min =     3008.40 max =        12577.62 mean =      7460.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.62|
|phase err.(test): min =        0.00 max =           89.07 mean =        14.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.048)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.13    100.41  16.93    None  None   None       |
|    all(noH): 2823   0      2.13    100.41  16.93    None  None   None       |
|    Sol.    : 438    0      4.52    92.03   40.55    None  None   None       |
|    Mac.    : 2385   0      2.13    100.41  12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.129 -  11.958: 1520   |   5:    51.272 -  61.100:   77        |
|      1:    11.958 -  21.786:  752   |   6:    61.100 -  70.929:   36        |
|      2:    21.786 -  31.615:  167   |   7:    70.929 -  80.758:   18        |
|      3:    31.615 -  41.443:  133   |   8:    80.758 -  90.586:    4        |
|      4:    41.443 -  51.272:  110   |   9:    90.586 - 100.415:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.525 - 5.916
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 330
   mapped sites are within: 0.714 - 5.916

peak=    5.542 closest distance to " CB  SER A  63 " =    1.342
peak=    5.487 closest distance to " CB  GLN A 223 " =    1.455
peak=    5.408 closest distance to " CG  PRO A  54 " =    1.303
peak=    5.305 closest distance to " O   HOH Z 111 " =    2.136
peak=    5.295 closest distance to " CG  PRO A 280 " =    0.871
peak=    5.053 closest distance to " CG  PRO A 198 " =    1.340
peak=    4.965 closest distance to " O   HOH Z 134 " =    1.898
peak=    4.909 closest distance to " CG  PRO A  90 " =    1.231
peak=    4.794 closest distance to " NH2BARG A 102 " =    0.991
peak=    4.736 closest distance to " O   HOH Z  15 " =    2.102
peak=    4.705 closest distance to " CA  TYR A  30 " =    1.040
peak=    4.668 closest distance to " CB  PRO A  54 " =    0.831
peak=    4.667 closest distance to " O   PRO A 198 " =    1.567
peak=    4.651 closest distance to " O   HOH Z 132 " =    1.301
peak=    4.625 closest distance to " CB  ARG A 275 " =    0.869
peak=    4.607 closest distance to " O   HOH Z 126 " =    1.802
peak=    4.584 closest distance to " CG  PRO A 213 " =    1.296
peak=    4.556 closest distance to " O   HOH Z  80 " =    2.042
peak=    4.524 closest distance to " O   HOH Z 214 " =    1.220
peak=    4.508 closest distance to " O   HOH Z 234 " =    3.880
peak=    4.506 closest distance to " O   HOH Z 154 " =    1.516
peak=    4.491 closest distance to " OE1 GLN A  11 " =    1.977
peak=    4.476 closest distance to " O   HOH Z 210 " =    1.266
peak=    4.464 closest distance to " O   HOH Z 247 " =    1.508
peak=    4.389 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.372 closest distance to " O   HOH Z  48 " =    1.902
peak=    4.285 closest distance to " CB  GLU A 128 " =    1.131
peak=    4.275 closest distance to " N   ASN A  39 " =    1.285
peak=    4.273 closest distance to " CB  LEU A 228 " =    1.123
peak=    4.252 closest distance to " NH2 ARG A 156 " =    1.259
peak=    4.247 closest distance to " O   HOH Z  40 " =    2.043
peak=    4.226 closest distance to " CB  PRO A 198 " =    0.990
peak=    4.195 closest distance to " O   HOH Z 433 " =    1.621
peak=    4.165 closest distance to " O   HOH Z  47 " =    1.591
peak=    4.159 closest distance to " CB  GLN A 183 " =    1.242
peak=    4.150 closest distance to " O   HOH Z 124 " =    1.453
peak=    4.130 closest distance to " O   HOH Z  67 " =    1.930
peak=    4.128 closest distance to " CB  GLU A 152 " =    1.178
peak=    4.128 closest distance to " O   HOH Z 196 " =    1.442
peak=    4.120 closest distance to " O   HOH Z 163 " =    1.703
peak=    4.112 closest distance to " OD1 ASN A 217 " =    1.616
peak=    4.110 closest distance to " O   HOH Z 132 " =    2.038
peak=    4.107 closest distance to " O   HOH Z 193 " =    2.059
peak=    4.102 closest distance to " O   HOH Z 403 " =    1.825
peak=    4.092 closest distance to " CB  TRP A 179 " =    1.383
peak=    4.090 closest distance to " CB  PRO A  54 " =    1.336
peak=    4.065 closest distance to " O   HOH Z 394 " =    1.697
peak=    4.062 closest distance to " O   HOH Z 189 " =    2.186
peak=    4.061 closest distance to " CA  GLU A 152 " =    0.912
peak=    4.060 closest distance to " CG  PRO A 243 " =    1.100
peak=    4.057 closest distance to " O   HOH Z 395 " =    1.529
peak=    4.056 closest distance to " CG1 ILE A  33 " =    1.290
peak=    4.052 closest distance to " CB  VAL A 202 " =    1.515
peak=    4.041 closest distance to " ND2 ASN A 110 " =    1.870
peak=    4.035 closest distance to " O   HOH Z  43 " =    1.593
peak=    4.010 closest distance to " CG  ARG A  66 " =    2.659
peak=    4.008 closest distance to " O   HOH Z 108 " =    1.471
peak=    4.006 closest distance to " CG2 THR A 221 " =    0.979
peak=    4.004 closest distance to " CG  GLN A  77 " =    0.842
peak=    3.993 closest distance to " O   HOH Z  78 " =    2.226
peak=    3.989 closest distance to " O   HOH Z 132 " =    2.445
peak=    3.989 closest distance to " CB  SER A   3 " =    1.441
peak=    3.982 closest distance to " O   HOH Z 118 " =    1.779
peak=    3.978 closest distance to " O   HOH Z  44 " =    2.367
peak=    3.972 closest distance to " O   HOH Z 374 " =    2.692
peak=    3.969 closest distance to " O   HOH Z 411 " =    3.224
peak=    3.966 closest distance to " CD  ARG A 269 " =    0.951
peak=    3.953 closest distance to " CA  ASP A 191 " =    0.836
peak=    3.953 closest distance to " O   HOH Z 389 " =    1.852
peak=    3.931 closest distance to " O   HOH Z 127 " =    1.087
peak=    3.926 closest distance to " CB  TYR A 169 " =    0.901
peak=    3.916 closest distance to " CG2 VAL A  78 " =    1.026
peak=    3.913 closest distance to " O   HOH Z 112 " =    1.505
peak=    3.899 closest distance to " C   SER A  32 " =    1.065
peak=    3.897 closest distance to " CB  GLN A  58 " =    0.872
peak=    3.895 closest distance to " O   HOH Z  61 " =    1.625
peak=    3.894 closest distance to " O   HOH Z 108 " =    2.222
peak=    3.893 closest distance to " O   SER A  87 " =    2.108
peak=    3.885 closest distance to " O   HOH Z  88 " =    3.575
peak=    3.879 closest distance to " CA  GLN A 223 " =    0.923
peak=    3.879 closest distance to " CB  ARG A  79 " =    1.340
peak=    3.877 closest distance to " O   HOH Z  11 " =    1.307
peak=    3.876 closest distance to " O   HOH Z 287 " =    2.020
peak=    3.873 closest distance to " CD BLYS A 290 " =    0.993
peak=    3.867 closest distance to " O   HOH Z 369 " =    2.074
peak=    3.856 closest distance to " O   HOH Z 279 " =    2.263
peak=    3.841 closest distance to " CB  ILE A 199 " =    1.105
peak=    3.840 closest distance to " O   HOH Z 215 " =    1.468
peak=    3.839 closest distance to " CB  SER A 141 " =    1.053
peak=    3.829 closest distance to " O   HOH Z  97 " =    1.951
peak=    3.821 closest distance to " O   HOH Z 260 " =    1.357
peak=    3.819 closest distance to " O   HOH Z 371 " =    3.341
peak=    3.817 closest distance to " NE2 HIS A 115 " =    0.959
peak=    3.805 closest distance to " CB  SER A  62 " =    0.885
peak=    3.798 closest distance to " O   HOH Z 145 " =    2.291
peak=    3.790 closest distance to " CB  GLU A 277 " =    3.700
peak=    3.788 closest distance to " CB  PHE A  16 " =    1.039
peak=    3.785 closest distance to " O   HOH Z 313 " =    2.150
peak=    3.784 closest distance to " O   HOH Z 404 " =    1.432
peak=    3.780 closest distance to " O   HOH Z 154 " =    2.300
peak=    3.780 closest distance to " O   HOH Z 368 " =    2.026
peak=    3.779 closest distance to " O   HOH Z 298 " =    1.948
peak=    3.777 closest distance to " CA  ASP A 124 " =    0.780
peak=    3.771 closest distance to " O   HOH Z 387 " =    2.427
peak=    3.771 closest distance to " CB  ASN A 148 " =    1.156
peak=    3.767 closest distance to " O   HOH Z  20 " =    2.069
peak=    3.763 closest distance to " CG1 VAL A 153 " =    1.046
peak=    3.747 closest distance to " CD1 TRP A 266 " =    1.142
peak=    3.743 closest distance to " CB  ASN A 187 " =    1.096
peak=    3.741 closest distance to " CA  ARG A  36 " =    1.154
peak=    3.739 closest distance to " OD2 ASP A 286 " =    2.976
peak=    3.729 closest distance to " CB  ARG A 190 " =    1.763
peak=    3.729 closest distance to " O   HOH Z  30 " =    1.668
peak=    3.728 closest distance to " O   HOH Z 272 " =    1.962
peak=    3.724 closest distance to " CD1 LEU A 300 " =    1.259
peak=    3.723 closest distance to " CA  ALA A  21 " =    1.376
peak=    3.710 closest distance to " CD  ARG A 159 " =    0.830
peak=    3.709 closest distance to " O   HOH Z 227 " =    1.722
peak=    3.706 closest distance to " CD  LYS A 166 " =    1.487
peak=    3.700 closest distance to " CB  ARG A 139 " =    1.014
peak=    3.698 closest distance to " O   HOH Z  39 " =    1.497
peak=    3.695 closest distance to " O   HOH Z 133 " =    1.570
peak=    3.695 closest distance to " O   HOH Z 197 " =    1.950
peak=    3.694 closest distance to " CD2 LEU A 297 " =    0.907
peak=    3.676 closest distance to " CD  LYS A 119 " =    1.362
peak=    3.674 closest distance to " OD1 ASN A  69 " =    2.432
peak=    3.672 closest distance to " CB  ASN A 285 " =    0.864
peak=    3.669 closest distance to " CG2BVAL A  41 " =    1.017
peak=    3.669 closest distance to " O   HOH Z 265 " =    2.178
peak=    3.664 closest distance to " O   HOH Z 192 " =    1.903
peak=    3.659 closest distance to " O   HOH Z  49 " =    1.896
peak=    3.658 closest distance to " NH1 ARG A 269 " =    0.811
peak=    3.650 closest distance to " O   HOH Z 357 " =    2.108
peak=    3.643 closest distance to " CB  TRP A 266 " =    0.950
peak=    3.642 closest distance to " O   HOH Z  21 " =    1.811
peak=    3.639 closest distance to " CB  MET A  47 " =    1.077
peak=    3.635 closest distance to " O   HOH Z  54 " =    1.717
peak=    3.632 closest distance to " CA  GLY A 196 " =    0.919
peak=    3.627 closest distance to " CZ  PHE A 218 " =    1.060
peak=    3.625 closest distance to " O   HOH Z 142 " =    1.556
peak=    3.622 closest distance to " O   HOH Z 200 " =    1.547
peak=    3.612 closest distance to " CB  GLN A 194 " =    0.925
peak=    3.609 closest distance to " O   HOH Z 316 " =    3.051
peak=    3.602 closest distance to " C   GLY A  80 " =    1.194
peak=    3.599 closest distance to " O   HOH Z 432 " =    1.816
peak=    3.595 closest distance to " O   HOH Z  22 " =    2.438
peak=    3.570 closest distance to " NH2BARG A 145 " =    1.961
peak=    3.569 closest distance to " O   HOH Z 352 " =    1.925
peak=    3.569 closest distance to " NZ  LYS A 117 " =    3.173
peak=    3.567 closest distance to " CE  LYS A 119 " =    1.151
peak=    3.566 closest distance to " O   HOH Z  63 " =    1.861
peak=    3.562 closest distance to " CG2 VAL A 197 " =    1.164
peak=    3.559 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.553 closest distance to " O   TRP A 274 " =    1.612
peak=    3.536 closest distance to " O   HOH Z   6 " =    2.145
peak=    3.533 closest distance to " O   HOH Z 426 " =    1.508
peak=    3.533 closest distance to " O   HOH Z 174 " =    2.141
peak=    3.533 closest distance to " CD2 LEU A 255 " =    1.217
peak=    3.532 closest distance to " O   HOH Z 344 " =    3.150
peak=    3.523 closest distance to " O   THR A 251 " =    1.302
peak=    3.520 closest distance to " CZ  PHE A 192 " =    0.937
peak=    3.516 closest distance to " NZ  LYS A  76 " =    1.361
peak=    3.514 closest distance to " O   HOH Z  87 " =    1.842
peak=    3.512 closest distance to " O   HOH Z 261 " =    1.864
peak=    3.510 closest distance to " CB  ASP A 140 " =    0.735
peak=    3.509 closest distance to " CB  ALA A 100 " =    1.459
peak=    3.508 closest distance to " NH2AARG A 190 " =    1.452
peak=    3.499 closest distance to " O   HOH Z 245 " =    1.381
peak=    3.495 closest distance to " CA  ARG A 195 " =    1.133
peak=    3.492 closest distance to " O   HOH Z 345 " =    3.179
peak=    3.482 closest distance to " CA  ALA A 160 " =    0.908
peak=    3.478 closest distance to " CG AARG A 275 " =    1.069
peak=    3.476 closest distance to " O   HOH Z 406 " =    1.533
peak=    3.473 closest distance to " CB  GLN A  73 " =    1.008
peak=    3.471 closest distance to " CB  ALA A 291 " =    1.259
peak=    3.470 closest distance to " ND1 HIS A  81 " =    1.483
peak=    3.470 closest distance to " O   HOH Z 336 " =    1.598
peak=    3.468 closest distance to " O   HOH Z 362 " =    3.227
peak=    3.466 closest distance to " O   HOH Z 425 " =    1.516
peak=    3.465 closest distance to " O   HOH Z 383 " =    1.994
peak=    3.465 closest distance to " N   SER A 164 " =    1.088
peak=    3.463 closest distance to " O   HOH Z 437 " =    1.675
peak=    3.456 closest distance to " N   THR A  52 " =    1.119
peak=    3.453 closest distance to " O   HOH Z  66 " =    2.197
peak=    3.452 closest distance to " O   HOH Z 423 " =    1.804
peak=    3.447 closest distance to " OD1 ASP A 238 " =    0.928
peak=    3.445 closest distance to " O   GLY A  91 " =    1.122
peak=    3.441 closest distance to " CA  THR A 221 " =    0.884
peak=    3.436 closest distance to " CA  ASP A 162 " =    1.212
peak=    3.433 closest distance to " O   HOH Z 301 " =    1.518
peak=    3.433 closest distance to " O   HOH Z 221 " =    1.467
peak=    3.432 closest distance to " OE1 GLN A  58 " =    5.916
peak=    3.425 closest distance to " N   ARG A 156 " =    1.473
peak=    3.422 closest distance to " O   HOH Z 147 " =    1.727
peak=    3.415 closest distance to " O   HOH Z 248 " =    1.659
peak=    3.410 closest distance to " CA  ILE A 263 " =    0.996
peak=    3.407 closest distance to " ND2 ASN A 187 " =    1.519
peak=    3.399 closest distance to " O   GLY A 211 " =    1.334
peak=    3.397 closest distance to " CB  MET A  40 " =    0.714
peak=    3.393 closest distance to " NE AARG A 275 " =    1.415
peak=    3.391 closest distance to " O   HOH Z 326 " =    1.417
peak=    3.390 closest distance to " O   HOH Z 373 " =    1.652
peak=    3.388 closest distance to " CB  LEU A 143 " =    1.041
peak=    3.387 closest distance to " O   HOH Z 402 " =    1.498
peak=    3.382 closest distance to " O   HOH Z  19 " =    1.830
peak=    3.374 closest distance to " O   HOH Z 102 " =    1.287
peak=    3.373 closest distance to " O   HOH Z  48 " =    2.027
peak=    3.368 closest distance to " O   HOH Z 128 " =    2.272
peak=    3.362 closest distance to " CG1BVAL A  72 " =    1.673
peak=    3.358 closest distance to " O   GLY A  23 " =    2.340
peak=    3.354 closest distance to " OG  SER A  97 " =    3.571
peak=    3.351 closest distance to " CB  GLU A 277 " =    0.981
peak=    3.349 closest distance to " CB  SER A 216 " =    0.735
peak=    3.348 closest distance to " CA  ILE A 106 " =    0.847
peak=    3.348 closest distance to " CA  PRO A  90 " =    0.957
peak=    3.348 closest distance to " O   HOH Z 156 " =    2.520
peak=    3.343 closest distance to " O   HOH Z 207 " =    2.077
peak=    3.337 closest distance to " O   SER A  26 " =    1.732
peak=    3.336 closest distance to " O   HOH Z 281 " =    4.005
peak=    3.335 closest distance to " O   HOH Z 155 " =    2.857
peak=    3.334 closest distance to " CA  SER A  87 " =    0.836
peak=    3.330 closest distance to " CG  LEU A 167 " =    1.078
peak=    3.327 closest distance to " CB  ASP A 124 " =    0.747
peak=    3.327 closest distance to " CB  TRP A 123 " =    1.145
peak=    3.326 closest distance to " CE3 TRP A 274 " =    3.611
peak=    3.326 closest distance to " CA  VAL A  41 " =    0.819
peak=    3.325 closest distance to " CA  GLN A  88 " =    1.254
peak=    3.324 closest distance to " O   HOH Z 386 " =    2.295
peak=    3.320 closest distance to " O   HOH Z 139 " =    4.512
peak=    3.308 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.306 closest distance to " NE1 TRP A 274 " =    0.839
peak=    3.303 closest distance to " O   HOH Z 211 " =    1.173
peak=    3.302 closest distance to " CG2 THR A 220 " =    0.729
peak=    3.301 closest distance to " CA  GLU A  46 " =    0.775
peak=    3.295 closest distance to " CG  ASP A 231 " =    1.124
peak=    3.295 closest distance to " CG1 ILE A 120 " =    1.074
peak=    3.295 closest distance to " O   HOH Z 255 " =    1.848
peak=    3.289 closest distance to " CG2 ILE A 106 " =    1.069
peak=    3.288 closest distance to " O   HOH Z 291 " =    1.620
peak=    3.286 closest distance to " O   HOH Z 426 " =    3.165
peak=    3.280 closest distance to " CA  THR A 221 " =    1.360
peak=    3.279 closest distance to " CA  LYS A  48 " =    1.404
peak=    3.278 closest distance to " CA  LEU A 282 " =    1.166
peak=    3.277 closest distance to " O   HOH Z  87 " =    2.491
peak=    3.276 closest distance to " O   VAL A  72 " =    3.407
peak=    3.273 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.270 closest distance to " O   HOH Z 368 " =    2.548
peak=    3.266 closest distance to " CD  ARG A 195 " =    1.088
peak=    3.266 closest distance to " O   HOH Z   1 " =    2.799
peak=    3.265 closest distance to " CB  ARG A 269 " =    0.958
peak=    3.264 closest distance to " CB  ALA A  71 " =    1.241
peak=    3.263 closest distance to " O   HOH Z 104 " =    3.216
peak=    3.260 closest distance to " NZ  LYS A 193 " =    1.495
peak=    3.257 closest distance to " O   HOH Z  44 " =    1.730
peak=    3.256 closest distance to " N   HIS A 108 " =    1.903
peak=    3.255 closest distance to " CA  GLY A  75 " =    0.992
peak=    3.251 closest distance to " CA  ALA A  51 " =    0.956
peak=    3.249 closest distance to " CB  ALA A 248 " =    1.036
peak=    3.249 closest distance to " CB  MET A 105 " =    1.264
peak=    3.247 closest distance to " OH  TYR A  30 " =    1.350
peak=    3.246 closest distance to " O   HOH Z 263 " =    2.174
peak=    3.244 closest distance to " CG  GLN A  11 " =    1.343
peak=    3.244 closest distance to " O   HOH Z 173 " =    1.980
peak=    3.244 closest distance to " CB  ILE A 120 " =    1.225
peak=    3.243 closest distance to " O   HOH Z 345 " =    1.766
peak=    3.239 closest distance to " CB  ALA A 244 " =    0.909
peak=    3.238 closest distance to " O   HOH Z 409 " =    3.023
peak=    3.233 closest distance to " CB  VAL A 265 " =    1.249
peak=    3.228 closest distance to " O   HOH Z 363 " =    1.155
peak=    3.228 closest distance to " O   HOH Z 418 " =    1.522
peak=    3.226 closest distance to " O   HOH Z 109 " =    2.460
peak=    3.219 closest distance to " CD  ARG A 219 " =    0.931
peak=    3.217 closest distance to " O   HOH Z 427 " =    3.016
peak=    3.215 closest distance to " CA  ASP A 140 " =    1.256
peak=    3.214 closest distance to " O   HOH Z 428 " =    1.414
peak=    3.210 closest distance to " NH1BARG A 145 " =    0.830
peak=    3.209 closest distance to " CG  GLN A  58 " =    2.318
peak=    3.206 closest distance to " NH1 ARG A  14 " =    1.210
peak=    3.206 closest distance to " CB  PRO A  90 " =    1.133
peak=    3.201 closest distance to " O   HOH Z  50 " =    3.350
peak=    3.198 closest distance to " O   HOH Z 117 " =    1.084
peak=    3.191 closest distance to " O   HOH Z 116 " =    1.781
peak=    3.190 closest distance to " O   HOH Z 327 " =    2.511
peak=    3.190 closest distance to " CD  ARG A  66 " =    3.157
peak=    3.188 closest distance to " O   HOH Z  88 " =    1.685
peak=    3.184 closest distance to " N   PHE A 130 " =    1.402
peak=    3.184 closest distance to " N   LYS A 166 " =    0.800
peak=    3.181 closest distance to " CA  ASN A 215 " =    1.112
peak=    3.180 closest distance to " NZ  LYS A 119 " =    1.598
peak=    3.178 closest distance to " O   HOH Z  63 " =    1.379
peak=    3.175 closest distance to " NH1 ARG A  56 " =    1.282
peak=    3.173 closest distance to " CB  ASN A 148 " =    1.786
peak=    3.171 closest distance to " CA  GLY A 211 " =    1.064
peak=    3.170 closest distance to " O   HOH Z 420 " =    2.000
peak=    3.169 closest distance to " O   HOH Z 214 " =    1.575
peak=    3.166 closest distance to " CD  PRO A 280 " =    1.005
peak=    3.160 closest distance to " O   HOH Z 124 " =    3.168
peak=    3.159 closest distance to " O   HOH Z 420 " =    5.780
peak=    3.153 closest distance to " CD  LYS A 119 " =    1.975
peak=    3.148 closest distance to " CH2 TRP A 274 " =    2.024
peak=    3.145 closest distance to " OG1 THR A 294 " =    2.500
peak=    3.144 closest distance to " O   HOH Z 183 " =    1.503
peak=    3.139 closest distance to " CG2 ILE A 120 " =    1.038
peak=    3.138 closest distance to " CA  ILE A  33 " =    1.576
peak=    3.133 closest distance to " CA  MET A  40 " =    1.079
peak=    3.126 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.123 closest distance to " O   HOH Z 343 " =    2.406
peak=    3.121 closest distance to " NZ  LYS A 166 " =    3.126
peak=    3.120 closest distance to " O   HOH Z 296 " =    1.590
peak=    3.112 closest distance to " CG2 VAL A 257 " =    0.807
peak=    3.110 closest distance to " NZ  LYS A 117 " =    1.460
peak=    3.110 closest distance to " CG  MET A 188 " =    0.832
peak=    3.110 closest distance to " CD2 TRP A 179 " =    1.315
peak=    3.109 closest distance to " CD1 PHE A  59 " =    1.705
peak=    3.109 closest distance to " CB  TYR A 247 " =    1.031
peak=    3.100 closest distance to " O   HOH Z 261 " =    1.696
peak=    3.089 closest distance to " OE1 GLN A  58 " =    3.580
peak=    3.064 closest distance to " O   HOH Z 346 " =    1.543
peak=    3.063 closest distance to " O   HOH Z 244 " =    1.715
peak=    3.062 closest distance to " CD1 TYR A 169 " =    1.354
peak=    3.027 closest distance to " ND2 ASN A 285 " =    2.975
peak=    3.022 closest distance to " O   HOH Z   2 " =    2.104

                           ----------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: 0.676 - 5.392
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 211
   mapped sites are within: 0.703 - 5.392

peak=   -4.498 closest distance to " O   HOH Z 290 " =    0.878
peak=   -4.350 closest distance to " NH2 ARG A  66 " =    1.240
peak=   -4.259 closest distance to " O   HOH Z 266 " =    4.531
peak=   -4.249 closest distance to " O   HOH Z  52 " =    1.955
peak=   -4.238 closest distance to " O   HOH Z 166 " =    1.719
peak=   -4.220 closest distance to " O   HOH Z  71 " =    1.242
peak=   -4.200 closest distance to " O   HOH Z 377 " =    0.824
peak=   -4.099 closest distance to " N   ALA A  43 " =    2.588
peak=   -4.092 closest distance to " C   ASN A 285 " =    2.547
peak=   -4.067 closest distance to " O   HOH Z 221 " =    1.004
peak=   -4.043 closest distance to " O   HOH Z  13 " =    1.591
peak=   -4.012 closest distance to " O   HOH Z 109 " =    3.816
peak=   -3.957 closest distance to " O   HOH Z  17 " =    1.142
peak=   -3.953 closest distance to " O   HOH Z  91 " =    2.194
peak=   -3.933 closest distance to " CB  LEU A 167 " =    2.199
peak=   -3.923 closest distance to " OG  SER A  97 " =    2.246
peak=   -3.922 closest distance to " OXT GLY A 302 " =    2.774
peak=   -3.895 closest distance to " CZ  ARG A  66 " =    1.011
peak=   -3.884 closest distance to " O   HOH Z 308 " =    1.590
peak=   -3.870 closest distance to " O   HOH Z  58 " =    0.703
peak=   -3.850 closest distance to " CD  GLN A  88 " =    0.769
peak=   -3.846 closest distance to " OG  SER A  32 " =    1.092
peak=   -3.830 closest distance to " OG ASER A 134 " =    1.252
peak=   -3.824 closest distance to " O   HOH Z  19 " =    2.099
peak=   -3.815 closest distance to " CD2 LEU A 300 " =    3.014
peak=   -3.814 closest distance to " CD2 PHE A  59 " =    2.478
peak=   -3.800 closest distance to " CG  ASP A 231 " =    0.776
peak=   -3.771 closest distance to " CD1 PHE A  59 " =    1.851
peak=   -3.763 closest distance to " O   HOH Z 418 " =    1.271
peak=   -3.755 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.747 closest distance to " OE2 GLU A   2 " =    1.252
peak=   -3.746 closest distance to " OH  TYR A 169 " =    0.957
peak=   -3.742 closest distance to " CG  GLU A  53 " =    1.334
peak=   -3.737 closest distance to " O   HOH Z 351 " =    1.368
peak=   -3.725 closest distance to " CD  ARG A 156 " =    1.947
peak=   -3.715 closest distance to " CA  VAL A 197 " =    1.004
peak=   -3.715 closest distance to " O   HOH Z 283 " =    1.771
peak=   -3.715 closest distance to " CB  TYR A  15 " =    2.364
peak=   -3.710 closest distance to " CG  GLN A  58 " =    1.140
peak=   -3.706 closest distance to " CB  CYS A 254 " =    2.515
peak=   -3.697 closest distance to " OD1 ASP A 191 " =    1.622
peak=   -3.694 closest distance to " CE  MET A  93 " =    1.106
peak=   -3.693 closest distance to " CH2 TRP A 179 " =    1.074
peak=   -3.692 closest distance to " O   VAL A  67 " =    2.648
peak=   -3.677 closest distance to " CG1 VAL A 112 " =    2.658
peak=   -3.671 closest distance to " O   HOH Z 222 " =    1.195
peak=   -3.668 closest distance to " O   HOH Z  15 " =    1.676
peak=   -3.661 closest distance to " O   HOH Z 185 " =    2.504
peak=   -3.651 closest distance to " OD2 ASP A 171 " =    2.209
peak=   -3.650 closest distance to " C   HIS A 108 " =    1.075
peak=   -3.648 closest distance to " CD2 LEU A 237 " =    2.464
peak=   -3.635 closest distance to " O   HOH Z 385 " =    3.917
peak=   -3.633 closest distance to " O   HOH Z  10 " =    1.615
peak=   -3.618 closest distance to " CE2 TYR A  30 " =    2.692
peak=   -3.605 closest distance to " CG  ASP A  50 " =    2.423
peak=   -3.599 closest distance to " CA  SER A 164 " =    2.136
peak=   -3.564 closest distance to " CA  SER A 276 " =    1.369
peak=   -3.558 closest distance to " NE2 GLN A  58 " =    0.862
peak=   -3.547 closest distance to " N   GLN A  58 " =    1.634
peak=   -3.544 closest distance to " C   ALA A 158 " =    1.149
peak=   -3.543 closest distance to " O   HOH Z 234 " =    4.351
peak=   -3.542 closest distance to " CD1 LEU A 228 " =    2.484
peak=   -3.538 closest distance to " N   ALA A 226 " =    2.106
peak=   -3.535 closest distance to " CG2 THR A   4 " =    1.874
peak=   -3.535 closest distance to " CG  ARG A 269 " =    2.335
peak=   -3.527 closest distance to " O   HOH Z 241 " =    1.010
peak=   -3.524 closest distance to " O   HOH Z 151 " =    1.499
peak=   -3.524 closest distance to " O   HOH Z  38 " =    1.083
peak=   -3.524 closest distance to " O   ALA A 256 " =    1.455
peak=   -3.521 closest distance to " OD2 ASP A 171 " =    1.904
peak=   -3.517 closest distance to " O   HOH Z  11 " =    1.522
peak=   -3.516 closest distance to " ND2 ASN A  45 " =    0.973
peak=   -3.514 closest distance to " N   ARG A 275 " =    1.451
peak=   -3.512 closest distance to " CA  VAL A  67 " =    2.805
peak=   -3.503 closest distance to " O   GLY A 196 " =    1.099
peak=   -3.501 closest distance to " O   HOH Z 423 " =    2.318
peak=   -3.501 closest distance to " O   HOH Z 423 " =    1.056
peak=   -3.495 closest distance to " O   HOH Z 184 " =    1.256
peak=   -3.489 closest distance to " O   HOH Z  93 " =    1.496
peak=   -3.482 closest distance to " CB  ARG A 219 " =    2.390
peak=   -3.482 closest distance to " C   SER A 206 " =    1.567
peak=   -3.479 closest distance to " O   HOH Z 231 " =    1.422
peak=   -3.479 closest distance to " O   HOH Z 150 " =    1.213
peak=   -3.473 closest distance to " OE1 GLN A  88 " =    0.980
peak=   -3.472 closest distance to " O   GLY A 118 " =    2.244
peak=   -3.465 closest distance to " OG1 THR A  82 " =    2.142
peak=   -3.452 closest distance to " O   HOH Z 259 " =    0.983
peak=   -3.436 closest distance to " CB  SER A 146 " =    2.219
peak=   -3.436 closest distance to " CD2 LEU A 167 " =    1.742
peak=   -3.436 closest distance to " C   THR A 279 " =    1.195
peak=   -3.435 closest distance to " NH2AARG A 275 " =    5.255
peak=   -3.432 closest distance to " O   HOH Z  37 " =    1.559
peak=   -3.430 closest distance to " CD1 LEU A 101 " =    2.950
peak=   -3.423 closest distance to " CA  GLY A 241 " =    2.265
peak=   -3.415 closest distance to " O   HOH Z 292 " =    4.358
peak=   -3.415 closest distance to " O   HOH Z  98 " =    1.912
peak=   -3.415 closest distance to " CD1 LEU A  25 " =    2.470
peak=   -3.414 closest distance to " OD1 ASN A 148 " =    1.708
peak=   -3.403 closest distance to " O   HOH Z 407 " =    0.871
peak=   -3.402 closest distance to " O   HOH Z 380 " =    4.667
peak=   -3.399 closest distance to " CD  GLN A  88 " =    0.825
peak=   -3.397 closest distance to " O   HOH Z 100 " =    0.845
peak=   -3.397 closest distance to " O   HOH Z  43 " =    1.707
peak=   -3.394 closest distance to " CB  ALA A 291 " =    2.233
peak=   -3.391 closest distance to " O   HOH Z 396 " =    1.682
peak=   -3.384 closest distance to " CE  MET A 105 " =    1.958
peak=   -3.381 closest distance to " O   HOH Z 275 " =    1.515
peak=   -3.381 closest distance to " O   HOH Z 377 " =    2.061
peak=   -3.364 closest distance to " CB  GLU A 277 " =    1.278
peak=   -3.364 closest distance to " O   HOH Z 414 " =    1.307
peak=   -3.363 closest distance to " ND2 ASN A  45 " =    1.142
peak=   -3.356 closest distance to " CD1 TRP A 179 " =    0.975
peak=   -3.350 closest distance to " C   ASN A 187 " =    1.934
peak=   -3.349 closest distance to " O   HOH Z 231 " =    2.162
peak=   -3.333 closest distance to " O   HOH Z 103 " =    1.916
peak=   -3.325 closest distance to " O   HOH Z 165 " =    2.029
peak=   -3.324 closest distance to " O   HOH Z 118 " =    3.126
peak=   -3.323 closest distance to " O   HOH Z 422 " =    1.303
peak=   -3.323 closest distance to " O  BHOH Z 338 " =    1.338
peak=   -3.318 closest distance to " C   LEU A 101 " =    0.917
peak=   -3.318 closest distance to " O   HOH Z  92 " =    1.495
peak=   -3.317 closest distance to " CA  PRO A 198 " =    1.116
peak=   -3.315 closest distance to " O   HOH Z 231 " =    0.884
peak=   -3.313 closest distance to " CA  GLY A 203 " =    2.267
peak=   -3.311 closest distance to " CA  ASP A 298 " =    1.057
peak=   -3.309 closest distance to " O   HOH Z 417 " =    3.000
peak=   -3.308 closest distance to " CD  LYS A 119 " =    0.979
peak=   -3.301 closest distance to " CH2 TRP A 177 " =    1.910
peak=   -3.291 closest distance to " CD  ARG A 139 " =    1.579
peak=   -3.288 closest distance to " O   HOH Z 176 " =    1.005
peak=   -3.283 closest distance to " O   HOH Z 368 " =    2.098
peak=   -3.283 closest distance to " CD1 TYR A 247 " =    2.397
peak=   -3.282 closest distance to " O   HOH Z 146 " =    0.966
peak=   -3.281 closest distance to " ND2 ASN A  60 " =    1.560
peak=   -3.280 closest distance to " O   HOH Z 111 " =    1.113
peak=   -3.277 closest distance to " CD  GLN A 223 " =    1.236
peak=   -3.272 closest distance to " ND2 ASN A  60 " =    1.416
peak=   -3.270 closest distance to " OG  SER A  62 " =    1.422
peak=   -3.267 closest distance to " CD2 PHE A  61 " =    1.785
peak=   -3.266 closest distance to " CB  ASN A  39 " =    2.167
peak=   -3.264 closest distance to " NE1 TRP A 266 " =    2.242
peak=   -3.264 closest distance to " CG  MET A 105 " =    0.876
peak=   -3.264 closest distance to " O   HOH Z  94 " =    2.136
peak=   -3.262 closest distance to " O   HOH Z 434 " =    4.164
peak=   -3.257 closest distance to " CD2 TYR A 293 " =    2.025
peak=   -3.244 closest distance to " O   HOH Z 251 " =    1.599
peak=   -3.243 closest distance to " CB  ALA A 161 " =    2.654
peak=   -3.242 closest distance to " O   TRP A  92 " =    1.851
peak=   -3.242 closest distance to " O   HOH Z 384 " =    2.303
peak=   -3.241 closest distance to " O   HOH Z 136 " =    1.418
peak=   -3.231 closest distance to " O   VAL A 121 " =    0.987
peak=   -3.226 closest distance to " O   PHE A 218 " =    1.399
peak=   -3.218 closest distance to " SG  CYS A 254 " =    3.081
peak=   -3.216 closest distance to " CB  ALA A  43 " =    2.671
peak=   -3.216 closest distance to " O   HOH Z 348 " =    2.303
peak=   -3.216 closest distance to " OH  TYR A 172 " =    1.580
peak=   -3.211 closest distance to " C   SER A 271 " =    1.239
peak=   -3.211 closest distance to " CD  GLU A 236 " =    1.057
peak=   -3.209 closest distance to " CG  LYS A 193 " =    2.698
peak=   -3.203 closest distance to " O   HOH Z 166 " =    1.980
peak=   -3.201 closest distance to " O   HOH Z 298 " =    2.827
peak=   -3.194 closest distance to " O   HOH Z 424 " =    2.825
peak=   -3.193 closest distance to " SG ACYS A 201 " =    2.243
peak=   -3.193 closest distance to " O   HOH Z 325 " =    1.604
peak=   -3.191 closest distance to " O   HOH Z  58 " =    0.791
peak=   -3.190 closest distance to " O   ARG A 275 " =    2.061
peak=   -3.189 closest distance to " OG  SER A  63 " =    1.259
peak=   -3.189 closest distance to " CD2 LEU A 237 " =    2.656
peak=   -3.188 closest distance to " CB  PRO A 243 " =    2.636
peak=   -3.188 closest distance to " NH1 ARG A 195 " =    2.680
peak=   -3.185 closest distance to " O   HOH Z 265 " =    1.815
peak=   -3.184 closest distance to " O   HOH Z 313 " =    1.140
peak=   -3.184 closest distance to " N   THR A 235 " =    1.181
peak=   -3.180 closest distance to " CA  GLU A  37 " =    1.353
peak=   -3.176 closest distance to " O   HOH Z 252 " =    4.282
peak=   -3.175 closest distance to " CE2 TRP A  85 " =    1.036
peak=   -3.175 closest distance to " O   ALA A  10 " =    1.776
peak=   -3.173 closest distance to " O   HOH Z 196 " =    2.559
peak=   -3.172 closest distance to " CD  ARG A 195 " =    5.118
peak=   -3.169 closest distance to " NH2 ARG A  66 " =    5.392
peak=   -3.165 closest distance to " CB  ALA A   9 " =    2.726
peak=   -3.163 closest distance to " C   GLU A  46 " =    1.017
peak=   -3.162 closest distance to " O   HOH Z  97 " =    1.526
peak=   -3.162 closest distance to " CE  MET A 105 " =    2.084
peak=   -3.161 closest distance to " C   GLN A 194 " =    1.281
peak=   -3.154 closest distance to " CB  ALA A 248 " =    1.972
peak=   -3.151 closest distance to " O   HOH Z 148 " =    3.432
peak=   -3.141 closest distance to " CD  PRO A 198 " =    1.083
peak=   -3.137 closest distance to " SG  CYS A 168 " =    1.065
peak=   -3.134 closest distance to " O   HOH Z  76 " =    2.008
peak=   -3.134 closest distance to " CG2AVAL A 121 " =    2.231
peak=   -3.127 closest distance to " NH2 ARG A 156 " =    1.226
peak=   -3.123 closest distance to " O   HOH Z 390 " =    2.313
peak=   -3.122 closest distance to " O   VAL A 197 " =    1.195
peak=   -3.121 closest distance to " O   HOH Z 389 " =    1.951
peak=   -3.116 closest distance to " O   ALA A  34 " =    2.025
peak=   -3.113 closest distance to " C   VAL A 257 " =    1.196
peak=   -3.110 closest distance to " O   HOH Z   6 " =    1.556
peak=   -3.107 closest distance to " NZ  LYS A 117 " =    1.723
peak=   -3.103 closest distance to " CB  GLN A  55 " =    1.429
peak=   -3.095 closest distance to " NH1 ARG A 195 " =    2.294
peak=   -3.092 closest distance to " O   HOH Z 399 " =    2.274
peak=   -3.080 closest distance to " O   HOH Z 407 " =    1.741
peak=   -3.079 closest distance to " OG  SER A  87 " =    1.519
peak=   -3.076 closest distance to " O   HOH Z 366 " =    1.686
peak=   -3.061 closest distance to " CB  PRO A 163 " =    2.850
peak=   -3.026 closest distance to " O   HOH Z  48 " =    1.022
peak=   -3.015 closest distance to " CE2 TRP A 274 " =    1.082
peak=   -3.012 closest distance to " CG  ASP A 298 " =    0.886

================= 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    :  0.4631 0.4540   6.272655e+00   6.259140e+00
   1_bss:  0.4555 0.4474   6.267247e+00   6.247693e+00
   1_xyz:  0.3700 0.3992   6.129401e+00   6.182105e+00
   1_adp:  0.3365 0.4085   6.087473e+00   6.194181e+00
   1_occ:  0.3363 0.4093   6.086862e+00   6.194674e+00
   2_bss:  0.3359 0.4064   6.087441e+00   6.193526e+00
   2_xyz:  0.2671 0.3407   5.907849e+00   6.074799e+00
   2_adp:  0.2532 0.3268   5.869214e+00   6.044371e+00
   2_occ:  0.2530 0.3265   5.868749e+00   6.043802e+00
   3_bss:  0.2531 0.3259   5.867976e+00   6.042564e+00
   3_xyz:  0.1936 0.2462   5.610690e+00   5.804540e+00
   3_adp:  0.1686 0.2180   5.494965e+00   5.701729e+00
   3_occ:  0.1684 0.2179   5.494631e+00   5.701091e+00
   4_bss:  0.1682 0.2183   5.495411e+00   5.701009e+00
   4_xyz:  0.1384 0.1852   5.320726e+00   5.545475e+00
   4_adp:  0.1303 0.1769   5.274612e+00   5.500777e+00
   4_occ:  0.1302 0.1769   5.274518e+00   5.500877e+00
   5_bss:  0.1305 0.1771   5.276419e+00   5.501729e+00
   5_xyz:  0.1261 0.1712   5.245975e+00   5.465779e+00
   5_adp:  0.1262 0.1697   5.242217e+00   5.457127e+00
   5_occ:  0.1261 0.1696   5.241943e+00   5.457066e+00
   5_bss:  0.1261 0.1695   5.241699e+00   5.456520e+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:  0.287  27.040  -1.220   3.285   0.772   0.000   0.000   0.000
   1_xyz:  0.287  27.040  -1.220   3.285   0.772   0.000   0.000   0.000
   1_adp:  0.287  27.040  -1.220   3.285   0.772   0.000   0.000   0.000
   1_occ:  0.287  27.040  -1.220   3.285   0.772   0.000   0.000   0.000
   2_bss:  0.321  57.661  -0.922   1.728   0.096   0.000   0.000   0.000
   2_xyz:  0.321  57.661  -0.922   1.728   0.096   0.000   0.000   0.000
   2_adp:  0.321  57.661  -0.922   1.728   0.096   0.000   0.000   0.000
   2_occ:  0.321  57.661  -0.922   1.728   0.096   0.000   0.000   0.000
   3_bss:  0.319  59.782  -0.953   0.714  -0.666   0.000  -0.000  -0.000
   3_xyz:  0.319  59.782  -0.953   0.714  -0.666   0.000  -0.000  -0.000
   3_adp:  0.319  59.782  -0.953   0.714  -0.666   0.000  -0.000  -0.000
   3_occ:  0.319  59.782  -0.953   0.714  -0.666   0.000  -0.000  -0.000
   4_bss:  0.328  69.632  -1.792  -0.679  -1.426  -0.000  -0.000  -0.000
   4_xyz:  0.328  69.632  -1.792  -0.679  -1.426  -0.000  -0.000  -0.000
   4_adp:  0.328  69.632  -1.792  -0.679  -1.426  -0.000  -0.000  -0.000
   4_occ:  0.328  69.632  -1.792  -0.679  -1.426  -0.000  -0.000  -0.000
   5_bss:  0.323  63.971  -1.982  -1.246  -1.625  -0.000  -0.000  -0.000
   5_xyz:  0.323  63.971  -1.982  -1.246  -1.625  -0.000  -0.000  -0.000
   5_adp:  0.323  63.971  -1.982  -1.246  -1.625  -0.000  -0.000  -0.000
   5_occ:  0.323  63.971  -1.982  -1.246  -1.625  -0.000  -0.000  -0.000
   5_bss:  0.320  58.305  -1.950  -1.331  -1.580  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.256 0.4411  0.5908    66434.831
   1_bss:  55.071 0.4545  0.6301    63053.517
   1_xyz:  45.945 0.5695  0.7796    47419.955
   1_adp:  47.490 0.5497  0.7615    49685.337
   1_occ:  47.596 0.5482  0.7573    49711.097
   2_bss:  47.375 0.5509  0.7475    49396.483
   2_xyz:  37.755 0.6670  0.8899    32890.958
   2_adp:  35.334 0.6963  0.9066    29919.968
   2_occ:  35.315 0.6965  0.9063    29884.916
   3_bss:  35.171 0.6980  0.8890    29679.898
   3_xyz:  25.061 0.8094  0.9817    15858.975
   3_adp:  21.592 0.8454  0.9887    12535.781
   3_occ:  21.585 0.8456  0.9886    12536.148
   4_bss:  21.528 0.8461  0.9557    12509.951
   4_xyz:  17.761 0.8817  0.9781     8832.333
   4_adp:  16.644 0.8925  0.9782     8151.908
   4_occ:  16.645 0.8925  0.9780     8163.086
   5_bss:  16.673 0.8922  0.9674     8195.129
   5_xyz:  15.818 0.8998  0.9691     7537.546
   5_adp:  15.568 0.9022  0.9649     7469.593
   5_occ:  15.564 0.9023  0.9649     7476.667
   5_bss:  15.555 0.9023  0.9622     7459.518
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8419e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8419e-01
   1_xyz:   1.446  0.011  0.089 15.431  0.005  4.114   1.1110e-01
   1_adp:   1.446  0.011  0.089 15.431  0.005  4.114   1.1110e-01
   1_occ:   1.446  0.011  0.089 15.431  0.005  4.114   1.1110e-01
   2_bss:   1.446  0.011  0.089 15.431  0.005  4.114   1.1110e-01
   2_xyz:   1.253  0.009  0.084 14.636  0.005  4.111   8.4083e-02
   2_adp:   1.253  0.009  0.084 14.636  0.005  4.111   8.4083e-02
   2_occ:   1.253  0.009  0.084 14.636  0.005  4.111   8.4083e-02
   3_bss:   1.253  0.009  0.084 14.636  0.005  4.111   8.4083e-02
   3_xyz:   1.167  0.010  0.074 14.518  0.005  4.112   8.2368e-02
   3_adp:   1.167  0.010  0.074 14.518  0.005  4.112   8.2368e-02
   3_occ:   1.167  0.010  0.074 14.518  0.005  4.112   8.2368e-02
   4_bss:   1.167  0.010  0.074 14.518  0.005  4.112   8.2368e-02
   4_xyz:   1.100  0.009  0.076 14.492  0.004  4.122   6.8758e-02
   4_adp:   1.100  0.009  0.076 14.492  0.004  4.122   6.8758e-02
   4_occ:   1.100  0.009  0.076 14.492  0.004  4.122   6.8758e-02
   5_bss:   1.100  0.009  0.076 14.492  0.004  4.122   6.8758e-02
   5_xyz:   0.930  0.006  0.067 14.193  0.003  4.125   5.1707e-02
   5_adp:   0.930  0.006  0.067 14.193  0.003  4.125   5.1707e-02
   5_occ:   0.930  0.006  0.067 14.193  0.003  4.125   5.1707e-02
   5_bss:   0.930  0.006  0.067 14.193  0.003  4.125   5.1707e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.546   2.4289e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.546   2.4289e-01
   1_xyz:   9.115  0.070  0.367 88.717  0.027  1.938   8.1407e-02
   1_adp:   9.115  0.070  0.367 88.717  0.027  1.938   8.1407e-02
   1_occ:   9.115  0.070  0.367 88.717  0.027  1.938   8.1407e-02
   2_bss:   9.115  0.070  0.367 88.717  0.027  1.938   8.1407e-02
   2_xyz:   6.824  0.046  0.244 79.357  0.034  2.265   9.8549e-02
   2_adp:   6.824  0.046  0.244 79.357  0.034  2.265   9.8549e-02
   2_occ:   6.824  0.046  0.244 79.357  0.034  2.265   9.8549e-02
   3_bss:   6.824  0.046  0.244 79.357  0.034  2.265   9.8549e-02
   3_xyz:   7.885  0.084  0.272 82.344  0.060  2.229   1.6571e-01
   3_adp:   7.885  0.084  0.272 82.344  0.060  2.229   1.6571e-01
   3_occ:   7.885  0.084  0.272 82.344  0.060  2.229   1.6571e-01
   4_bss:   7.885  0.084  0.272 82.344  0.060  2.229   1.6571e-01
   4_xyz:   7.985  0.061  0.267 83.657  0.037  2.320   5.1923e-02
   4_adp:   7.985  0.061  0.267 83.657  0.037  2.320   5.1923e-02
   4_occ:   7.985  0.061  0.267 83.657  0.037  2.320   5.1923e-02
   5_bss:   7.985  0.061  0.267 83.657  0.037  2.320   5.1923e-02
   5_xyz:   7.690  0.042  0.223 82.688  0.037  2.424   3.3150e-02
   5_adp:   7.690  0.042  0.223 82.688  0.037  2.424   3.3150e-02
   5_occ:   7.690  0.042  0.223 82.688  0.037  2.424   3.3150e-02
   5_bss:   7.690  0.042  0.223 82.688  0.037  2.424   3.3150e-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: 105.60   0.00  19.23  88.00   0.00  15.77 105.60   0.00  38.04
   1_occ: 105.60   0.00  19.23  88.00   0.00  15.77 105.60   0.00  38.04
   2_bss: 105.60   0.00  19.23  88.00   0.00  15.77 105.60   0.00  38.04
   2_xyz: 105.60   0.00  19.23  88.00   0.00  15.77 105.60   0.00  38.04
   2_adp: 106.29   0.00  18.69  87.00   0.00  14.96 106.29   1.34  39.00
   2_occ: 106.29   0.00  18.69  87.00   0.00  14.96 106.29   1.34  39.00
   3_bss: 106.29   0.00  18.69  87.00   0.00  14.96 106.29   1.34  39.00
   3_xyz: 106.29   0.00  18.69  87.00   0.00  14.96 106.29   1.34  39.00
   3_adp: 100.74   0.00  18.44 100.50   0.00  13.65 100.74   5.13  44.55
   3_occ: 100.74   0.00  18.44 100.50   0.00  13.65 100.74   5.13  44.55
   4_bss: 100.74   0.00  18.44 100.50   0.00  13.65 100.74   5.13  44.55
   4_xyz: 100.74   0.00  18.44 100.50   0.00  13.65 100.74   5.13  44.55
   4_adp: 103.13   1.40  17.73 103.13   1.40  12.99  97.77   5.36  43.54
   4_occ: 103.13   1.40  17.73 103.13   1.40  12.99  97.77   5.36  43.54
   5_bss: 103.13   1.40  17.73 103.13   1.40  12.99  97.77   5.36  43.54
   5_xyz: 103.13   1.40  17.73 103.13   1.40  12.99  97.77   5.36  43.54
   5_adp: 100.49   2.21  17.01 100.49   2.21  12.67  92.11   4.60  40.63
   5_occ: 100.49   2.21  17.01 100.49   2.21  12.67  92.11   4.60  40.63
   5_bss: 100.41   2.13  16.93 100.41   2.13  12.59  92.03   4.52  40.55
------------------------------------------------------------------------
 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:    1.932    0.014    0.298
   1_adp:    1.932    0.014    0.298
   1_occ:    1.932    0.014    0.298
   2_bss:    1.932    0.014    0.298
   2_xyz:    1.571    0.031    0.501
   2_adp:    1.571    0.031    0.501
   2_occ:    1.571    0.031    0.501
   3_bss:    1.571    0.031    0.501
   3_xyz:    1.731    0.040    0.703
   3_adp:    1.731    0.040    0.703
   3_occ:    1.731    0.040    0.703
   4_bss:    1.731    0.040    0.703
   4_xyz:    1.481    0.070    0.761
   4_adp:    1.481    0.070    0.761
   4_occ:    1.481    0.070    0.761
   5_bss:    1.481    0.070    0.761
   5_xyz:    1.439    0.019    0.781
   5_adp:    1.439    0.019    0.781
   5_occ:    1.439    0.019    0.781
   5_bss:    1.439    0.019    0.781
------------------------------------------------------------------------

CPU time actual refinement: 353.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/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_1068/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1068/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.46 
  Macro-tasks:
    bulk solvent and scale       = 38.54  
    individual site refinement   = 150.39 
    weights calculation          = 30.29  
    collect and process          = 6.42   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 225.77 
  Micro-tasks:
    mask                            = 2.58   
    f_calc                          = 117.08 
    alpha_beta                      = 8.26   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 125.12 
    fmodel                         = 6.41   
    r_factors                      = 0.18   
    phase_errors                   = 10.05  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 271.13 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.040 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    634 calls, 116.72 s
gradients_fft:          579 calls, 112.25 s

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

# Date 2008-01-16 Time 06:21:46 PST -0800 (1200493306.37 s)
Start R-work = 0.4631, R-free = 0.4540 (no bulk solvent and anisotropic scale)
Final R-work = 0.1463, R-free = 0.1887 (no bulk solvent and anisotropic scale)

Start R-work = 0.4555, R-free = 0.4474
Final R-work = 0.1261, R-free = 0.1695