# Date 2008-01-16 Time 06:16:47 PST -0800 (1200493007.06 s)
#phil __OFF__

Command line arguments: "../1078.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5230
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1078

-------------------------------------------------------------------------------
  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, 48.1033, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.77, per 1000 atoms: 0.98


================================== 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, 48.1033, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95165
Completeness in resolution range: 0.904344
Completeness with d_max=infinity: 0.901722

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0490
                             d_min =   1.9516

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 48.1033, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.049 1.95165
Completeness in resolution range: 0.904344
Completeness with d_max=infinity: 0.901722

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0495 -  4.1775 [2275/2304]  2048   227  10.0%
  bin  2:  4.1775 -  3.3276 [2181/2204]  1961   220  10.1%
  bin  3:  3.3276 -  2.9104 [2150/2175]  1937   213   9.9%
  bin  4:  2.9104 -  2.6459 [2127/2160]  1918   209   9.8%
  bin  5:  2.6459 -  2.4571 [2110/2137]  1901   209   9.9%
  bin  6:  2.4571 -  2.3128 [2126/2154]  1908   218  10.3%
  bin  7:  2.3128 -  2.1974 [2104/2140]  1891   213  10.1%
  bin  8:  2.1974 -  2.1020 [2082/2124]  1875   207   9.9%
  bin  9:  2.1020 -  2.0212 [1922/2145]  1732   190   9.9%
  bin 10:  2.0212 -  1.9516 [ 512/2118]   459    53  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/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: 0.12 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:
        1.28 -     2.01: 16
        2.01 -     2.73: 227
        2.73 -     3.45: 4590
        3.45 -     4.18: 9363
        4.18 -     4.90: 14047
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.283 3.040 -x+1/2,-y+1,z-1/2
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.291 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.317 3.040 -x+1/2,-y+1,z+1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  1.334 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.610 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28238 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_1078/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/model_refine_001.geo

CPU time processing inputs: 7.83


============================ 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 48.10325 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4914   r_free= 0.4800   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.300516                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6601 0.99   1479  166 0.3966 0.4113      6.6117      6.6215|
|  2:  4.6601 -  3.7172 0.99   1416  157 0.4377 0.4214       6.865       6.851|
|  3:  3.7172 -  3.2527 0.99   1387  149 0.4741 0.4350      6.6926      6.6899|
|  4:  3.2527 -  2.9578 0.98   1383  162 0.4969 0.4848      6.5331      6.5061|
|  5:  2.9578 -  2.7472 0.99   1386  148 0.5197 0.4974      6.3702      6.3352|
|  6:  2.7472 -  2.5861 0.99   1364  160 0.5281 0.4984      6.2818      6.1809|
|  7:  2.5861 -  2.4571 0.98   1350  136 0.5212 0.4942      6.2458      6.2196|
|  8:  2.4571 -  2.3506 0.98   1364  157 0.5329 0.5209      6.1475      6.1875|
|  9:  2.3506 -  2.2604 0.98   1341  148 0.5474 0.5411      6.1456      6.1129|
| 10:  2.2604 -  2.1827 0.99   1360  156 0.5308 0.5288      6.0793       6.119|
| 11:  2.1827 -  2.1146 0.98   1336  144 0.5287 0.5752      6.0145      5.9891|
| 12:  2.1146 -  2.0543 0.97   1338  143 0.5103 0.5255      5.9171      5.9856|
| 13:  2.0543 -  2.0003 0.67    894  113 0.5469 0.4526       5.868      5.8184|
| 14:  2.0003 -  1.9516 0.16    232   20 0.5729 0.3975      5.7701      5.6971|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6601  1479   166  0.66  37.55   0.81     0.70      83937.56|
|  2:  4.6601 -  3.7172  1416   157  0.66  38.91   0.88     0.75     120559.63|
|  3:  3.7172 -  3.2527  1387   149  0.54  48.98   0.88     0.71     129442.62|
|  4:  3.2527 -  2.9578  1383   162  0.44  56.64   0.87     0.63     114379.40|
|  5:  2.9578 -  2.7472  1386   148  0.39  60.87   0.84     0.58      87637.04|
|  6:  2.7472 -  2.5861  1364   160  0.38  61.14   0.86     0.55      70685.39|
|  7:  2.5861 -  2.4571  1350   136  0.38  61.72   0.90     0.52      63361.26|
|  8:  2.4571 -  2.3506  1364   157  0.33  65.12   0.87     0.50      61249.82|
|  9:  2.3506 -  2.2604  1341   148  0.31  67.15   0.91     0.47      57318.40|
| 10:  2.2604 -  2.1827  1360   156  0.28  69.06   0.92     0.43      54409.48|
| 11:  2.1827 -  2.1146  1336   144  0.24  71.96   0.92     0.37      50737.23|
| 12:  2.1146 -  2.0543  1338   143  0.20  74.88   0.92     0.34      48420.49|
| 13:  2.0543 -  2.0003   894   113  0.21  74.27   0.90     0.35      40784.76|
| 14:  2.0003 -  1.9516   232    20  0.24  72.32   0.85     0.41      33795.92|
|alpha:            min =        0.34 max =            0.75 mean =         0.54|
|beta:             min =    33795.92 max =       129442.62 mean =     76419.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.97 mean =        60.14|
|phase err.(test): min =        0.00 max =           89.90 mean =        60.12|
|-----------------------------------------------------------------------------|

============================== 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 = 21.114745             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.298   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.724628              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.482   (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 |  1.283 -  1.644:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.644 -  2.006:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.006 -  2.368:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.368 -  2.730:      201 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.730 -  3.091:     2317 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.091 -  3.453:     2273 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.453 -  3.815:     4171 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.815 -  4.177:     5192 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.177 -  4.538:     6311 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.538 -  4.900:     7736 |
|-----------------------------------------------------------------------------|
|-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 |        0.211 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.283 |       0.884 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4914   r_free= 0.4800   ksol= 0.00   Bsol= 0.00   scale= 0.869    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.300516                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4846   r_free= 0.4736   ksol= 0.28   Bsol= 14.13   scale= 0.908   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,3.02,0.69,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.298318                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.531914             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.131   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.561977              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4846      final r-factor (work) = 0.3985          |
| start r-factor (free) = 0.4736      final r-factor (free) = 0.4397          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.2409 = 16.53 * 0.50 * 6.2945 + 1.00 * 0.2110                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4602 = 16.53 * 0.50 * 6.2036 + 1.00 * 0.1812                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3985      final r-factor (work) = 0.3652          |
| start r-factor (free) = 0.4397      final r-factor (free) = 0.4463          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6961 = 1.56 * 1.00 * 6.2036 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6159 = 1.56 * 1.00 * 6.1431 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.24   19.50    None  None   None       |
|    all(noH): 2823   0      0.00    94.24   19.50    None  None   None       |
|    Sol.    : 438    0      0.00    94.24   35.58    None  None   None       |
|    Mac.    : 2385   0      0.00    90.66   16.54    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.424:  747   |   5:    47.121 -  56.545:   81        |
|      1:     9.424 -  18.848:  897   |   6:    56.545 -  65.969:   50        |
|      2:    18.848 -  28.272:  550   |   7:    65.969 -  75.393:   25        |
|      3:    28.272 -  37.696:  310   |   8:    75.393 -  84.817:    5        |
|      4:    37.696 -  47.121:  153   |   9:    84.817 -  94.241:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3652 r_free = 0.4463             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3649 r_free = 0.4465             target_work(ml) = 6.148         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3649   r_free= 0.4465   ksol= 0.28   Bsol= 14.13   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.47,3.02,0.69,0.00,0.00,0.00); trace/3= 0.75                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.148241                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3641   r_free= 0.4430   ksol= 0.32   Bsol= 56.01   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,1.52,0.12,0.00,0.00,0.00); trace/3= 0.27                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.147728                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.337375             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.094  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.683265              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.176  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3641      final r-factor (work) = 0.2980          |
| start r-factor (free) = 0.4430      final r-factor (free) = 0.3732          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.5882 = 19.34 * 0.50 * 6.1442 + 1.00 * 0.1819                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 58.9712 = 19.34 * 0.50 * 6.0837 + 1.00 * 0.1499                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2980      final r-factor (work) = 0.2723          |
| start r-factor (free) = 0.3732      final r-factor (free) = 0.3546          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2609 = 1.68 * 1.00 * 6.0837 + 1.00 * 0.0204                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0422 = 1.68 * 1.00 * 5.9534 + 1.00 * 0.0210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.06  20.23    None  None   None       |
|    all(noH): 2823   0      0.00    112.06  20.23    None  None   None       |
|    Sol.    : 438    0      0.00    112.06  42.34    None  None   None       |
|    Mac.    : 2385   0      0.00    99.35   16.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.206: 1068   |   5:    56.029 -  67.235:   71        |
|      1:    11.206 -  22.412:  854   |   6:    67.235 -  78.441:   44        |
|      2:    22.412 -  33.618:  396   |   7:    78.441 -  89.647:   27        |
|      3:    33.618 -  44.824:  209   |   8:    89.647 - 100.853:    8        |
|      4:    44.824 -  56.029:  142   |   9:   100.853 - 112.059:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2723 r_free = 0.3546             target_work(ml) = 5.934         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2722 r_free = 0.3541             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2722   r_free= 0.3541   ksol= 0.32   Bsol= 56.01   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.83,1.52,0.12,0.00,0.00,0.00); trace/3= 0.27                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.933302                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2716   r_free= 0.3530   ksol= 0.33   Bsol= 60.12   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,0.87,-0.24,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.930186                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.200463              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.798   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.443147              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.852  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2716      final r-factor (work) = 0.2393          |
| start r-factor (free) = 0.3530      final r-factor (free) = 0.3096          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6277 = 5.20 * 0.50 * 5.9525 + 1.00 * 0.1497                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3660 = 5.20 * 0.50 * 5.8851 + 1.00 * 0.0633                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2393      final r-factor (work) = 0.2311          |
| start r-factor (free) = 0.3096      final r-factor (free) = 0.2927          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6290 = 0.44 * 1.00 * 5.8851 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5839 = 0.44 * 1.00 * 5.8035 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.39  18.87    None  None   None       |
|    all(noH): 2823   0      0.00    107.39  18.87    None  None   None       |
|    Sol.    : 438    0      2.82    107.39  41.90    None  None   None       |
|    Mac.    : 2385   0      0.00    95.76   14.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.739: 1110   |   5:    53.695 -  64.434:   71        |
|      1:    10.739 -  21.478:  915   |   6:    64.434 -  75.173:   38        |
|      2:    21.478 -  32.217:  325   |   7:    75.173 -  85.912:   23        |
|      3:    32.217 -  42.956:  201   |   8:    85.912 -  96.651:    6        |
|      4:    42.956 -  53.695:  130   |   9:    96.651 - 107.390:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2311 r_free = 0.2927             target_work(ml) = 5.779         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2310 r_free = 0.2923             target_work(ml) = 5.778         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2310   r_free= 0.2923   ksol= 0.33   Bsol= 60.12   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.39,0.87,-0.24,0.00,-0.00,-0.00); trace/3= 0.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.778474                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2310   r_free= 0.2921   ksol= 0.32   Bsol= 61.28   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.06,-1.18,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.778933                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.031234              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.760  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.065812              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.420  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2310      final r-factor (work) = 0.1868          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.2371          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8605 = 3.03 * 0.50 * 5.8044 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6969 = 3.03 * 0.50 * 5.6953 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1868      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.2371      final r-factor (free) = 0.2254          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7774 = 2.07 * 1.00 * 5.6953 + 1.00 * 0.0121                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4627 = 2.07 * 1.00 * 5.5407 + 1.00 * 0.0166                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.70  19.52    None  None   None       |
|    all(noH): 2823   0      0.00    118.70  19.52    None  None   None       |
|    Sol.    : 438    0      5.15    110.09  49.93    None  None   None       |
|    Mac.    : 2385   0      0.00    118.70  13.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.870: 1370   |   5:    59.351 -  71.221:   94        |
|      1:    11.870 -  23.740:  814   |   6:    71.221 -  83.091:   54        |
|      2:    23.740 -  35.611:  211   |   7:    83.091 -  94.962:   29        |
|      3:    35.611 -  47.481:  117   |   8:    94.962 - 106.832:   15        |
|      4:    47.481 -  59.351:  112   |   9:   106.832 - 118.702:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1708 r_free = 0.2254             target_work(ml) = 5.518         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1707 r_free = 0.2253             target_work(ml) = 5.518         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1707   r_free= 0.2253   ksol= 0.32   Bsol= 61.28   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.28,0.06,-1.18,0.00,-0.00,-0.00); trace/3= -0.80                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.517676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1711   r_free= 0.2258   ksol= 0.33   Bsol= 68.55   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.45,-1.43,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.519444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.342081              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.440  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.141238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.623  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1711      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.1979          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0984 = 4.34 * 0.50 * 5.5427 + 1.00 * 0.0651                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8925 = 4.34 * 0.50 * 5.4438 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1391          |
| start r-factor (free) = 0.1979      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7855 = 0.14 * 1.00 * 5.4438 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7681 = 0.14 * 1.00 * 5.3649 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.15  18.23    None  None   None       |
|    all(noH): 2823   0      0.00    113.15  18.23    None  None   None       |
|    Sol.    : 438    0      5.67    102.40  45.78    None  None   None       |
|    Mac.    : 2385   0      0.00    113.15  13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.316: 1373   |   5:    56.578 -  67.893:   76        |
|      1:    11.316 -  22.631:  886   |   6:    67.893 -  79.209:   43        |
|      2:    22.631 -  33.947:  165   |   7:    79.209 -  90.524:   24        |
|      3:    33.947 -  45.262:  120   |   8:    90.524 - 101.839:   12        |
|      4:    45.262 -  56.578:  117   |   9:   101.839 - 113.155:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1391 r_free = 0.1847             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1390 r_free = 0.1849             target_work(ml) = 5.330         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1849   ksol= 0.33   Bsol= 68.55   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.67,-0.45,-1.43,-0.00,-0.00,-0.00); trace/3= -1.18                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.329940                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6601 0.99   1479  166 0.0986 0.1345      5.4226      5.6337|
|  2:  4.6601 -  3.7172 0.99   1416  157 0.0944 0.1216      5.5092      5.7685|
|  3:  3.7172 -  3.2527 0.99   1387  149 0.1269 0.1875      5.6108      5.9878|
|  4:  3.2527 -  2.9578 0.98   1383  162 0.1662 0.1946      5.6558      5.8017|
|  5:  2.9578 -  2.7472 0.99   1386  148 0.1722 0.2031      5.5295      5.6315|
|  6:  2.7472 -  2.5861 0.99   1364  160 0.1560 0.2409      5.4053      5.6066|
|  7:  2.5861 -  2.4571 0.98   1350  136 0.1560 0.2069      5.3466       5.576|
|  8:  2.4571 -  2.3506 0.98   1364  157 0.1608 0.1883      5.2864      5.4349|
|  9:  2.3506 -  2.2604 0.98   1341  148 0.1527 0.2272      5.2094      5.4391|
| 10:  2.2604 -  2.1827 0.99   1360  156 0.1472 0.1992        5.16      5.3906|
| 11:  2.1827 -  2.1146 0.98   1336  144 0.1412 0.1977      5.0814      5.2836|
| 12:  2.1146 -  2.0543 0.97   1338  143 0.1487 0.2212      5.0233      5.2713|
| 13:  2.0543 -  2.0003 0.67    894  113 0.1496 0.1904      4.9585      5.1375|
| 14:  2.0003 -  1.9516 0.16    232   20 0.1579 0.1609      4.8713      5.0432|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6601  1479   166  0.93  10.21   0.96     0.94       8536.89|
|  2:  4.6601 -  3.7172  1416   157  0.94   9.39   1.01     0.99      10602.18|
|  3:  3.7172 -  3.2527  1387   149  0.91  14.25   1.03     1.03      13352.50|
|  4:  3.2527 -  2.9578  1383   162  0.88  18.52   1.02     1.00      15157.37|
|  5:  2.9578 -  2.7472  1386   148  0.85  20.93   1.02     0.99      12744.80|
|  6:  2.7472 -  2.5861  1364   160  0.86  20.24   1.01     0.98      10430.04|
|  7:  2.5861 -  2.4571  1350   136  0.87  19.50   1.00     0.96       8954.91|
|  8:  2.4571 -  2.3506  1364   157  0.87  20.16   1.02     0.98       8175.92|
|  9:  2.3506 -  2.2604  1341   148  0.87  19.98   1.01     0.96       7066.06|
| 10:  2.2604 -  2.1827  1360   156  0.87  19.33   1.00     0.96       6418.58|
| 11:  2.1827 -  2.1146  1336   144  0.87  19.33   1.00     0.96       5758.53|
| 12:  2.1146 -  2.0543  1338   143  0.87  20.11   1.00     0.97       5276.66|
| 13:  2.0543 -  2.0003   894   113  0.86  20.32   1.00     1.00       4541.11|
| 14:  2.0003 -  1.9516   232    20  0.86  20.47   0.99     0.97       3665.93|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3665.93 max =        15157.37 mean =      9082.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.75|
|phase err.(test): min =        0.00 max =           89.49 mean =        16.97|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1851   ksol= 0.32   Bsol= 61.40   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.10,-1.76,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331798                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1393   r_free= 0.1851   ksol= 0.32   Bsol= 61.40   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.05,-1.10,-1.76,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331798                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0495 -  4.6601 0.99   1479  166 0.1005 0.1367      5.4396      5.6303|
|  2:  4.6601 -  3.7172 0.99   1416  157 0.0949 0.1211      5.5121      5.7676|
|  3:  3.7172 -  3.2527 0.99   1387  149 0.1273 0.1876      5.6119      5.9923|
|  4:  3.2527 -  2.9578 0.98   1383  162 0.1662 0.1953      5.6568      5.8033|
|  5:  2.9578 -  2.7472 0.99   1386  148 0.1725 0.2034      5.5306      5.6334|
|  6:  2.7472 -  2.5861 0.99   1364  160 0.1563 0.2397      5.4054      5.6048|
|  7:  2.5861 -  2.4571 0.98   1350  136 0.1559 0.2072      5.3464      5.5759|
|  8:  2.4571 -  2.3506 0.98   1364  157 0.1606 0.1888       5.286      5.4365|
|  9:  2.3506 -  2.2604 0.98   1341  148 0.1526 0.2274      5.2092      5.4394|
| 10:  2.2604 -  2.1827 0.99   1360  156 0.1472 0.1993      5.1602      5.3911|
| 11:  2.1827 -  2.1146 0.98   1336  144 0.1412 0.1981      5.0805      5.2824|
| 12:  2.1146 -  2.0543 0.97   1338  143 0.1488 0.2221      5.0244      5.2741|
| 13:  2.0543 -  2.0003 0.67    894  113 0.1497 0.1896      4.9584      5.1347|
| 14:  2.0003 -  1.9516 0.16    232   20 0.1579 0.1612      4.8703      5.0395|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0495 -  4.6601  1479   166  0.93  10.45   0.96     0.93       8696.44|
|  2:  4.6601 -  3.7172  1416   157  0.94   9.34   1.01     0.99      10570.90|
|  3:  3.7172 -  3.2527  1387   149  0.91  14.12   1.03     1.02      13205.31|
|  4:  3.2527 -  2.9578  1383   162  0.88  18.56   1.01     0.99      15223.47|
|  5:  2.9578 -  2.7472  1386   148  0.85  20.92   1.00     0.98      12742.54|
|  6:  2.7472 -  2.5861  1364   160  0.86  20.22   0.99     0.96      10415.56|
|  7:  2.5861 -  2.4571  1350   136  0.87  19.45   0.98     0.95       8936.87|
|  8:  2.4571 -  2.3506  1364   157  0.87  20.14   1.00     0.96       8173.26|
|  9:  2.3506 -  2.2604  1341   148  0.87  19.98   0.99     0.95       7083.81|
| 10:  2.2604 -  2.1827  1360   156  0.87  19.32   0.98     0.94       6423.91|
| 11:  2.1827 -  2.1146  1336   144  0.87  19.31   0.98     0.94       5755.17|
| 12:  2.1146 -  2.0543  1338   143  0.87  20.11   0.97     0.95       5286.51|
| 13:  2.0543 -  2.0003   894   113  0.86  20.30   0.97     0.97       4535.26|
| 14:  2.0003 -  1.9516   232    20  0.86  20.41   0.97     0.94       3645.31|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     3645.31 max =        15223.47 mean =      9085.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.75|
|phase err.(test): min =        0.00 max =           89.17 mean =        16.98|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.004)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.16  18.23    None  None   None       |
|    all(noH): 2823   0      0.00    113.16  18.23    None  None   None       |
|    Sol.    : 438    0      5.67    102.40  45.78    None  None   None       |
|    Mac.    : 2385   0      0.00    113.16  13.17    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  11.319: 1373   |   5:    56.580 -  67.896:   76        |
|      1:    11.319 -  22.634:  886   |   6:    67.896 -  79.211:   43        |
|      2:    22.634 -  33.950:  165   |   7:    79.211 -  90.527:   24        |
|      3:    33.950 -  45.265:  120   |   8:    90.527 - 101.842:   12        |
|      4:    45.265 -  56.580:  117   |   9:   101.842 - 113.158:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.636 - 5.856
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 348
   mapped sites are within: 0.711 - 5.856

peak=    7.652 closest distance to " O   HOH Z  41 " =    1.268
peak=    7.069 closest distance to " O   HOH Z 332 " =    1.385
peak=    6.432 closest distance to " O   HOH Z 130 " =    0.962
peak=    6.105 closest distance to " O   HOH Z 120 " =    1.131
peak=    5.945 closest distance to " CG  GLN A  77 " =    0.927
peak=    5.228 closest distance to " NH2BARG A 102 " =    1.067
peak=    5.221 closest distance to " O   HOH Z 352 " =    1.448
peak=    5.215 closest distance to " O   HOH Z  61 " =    1.628
peak=    5.130 closest distance to " O   HOH Z 192 " =    1.635
peak=    5.094 closest distance to " O   HOH Z 221 " =    1.382
peak=    5.087 closest distance to " O   HOH Z 127 " =    1.238
peak=    5.061 closest distance to " O   HOH Z 210 " =    1.673
peak=    4.993 closest distance to " O   HOH Z 117 " =    1.296
peak=    4.989 closest distance to " CB  SER A  62 " =    0.950
peak=    4.979 closest distance to " O   HOH Z 350 " =    1.103
peak=    4.965 closest distance to " CG  PRO A  54 " =    1.273
peak=    4.917 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.909 closest distance to " OG ASER A 164 " =    0.985
peak=    4.895 closest distance to " O   HOH Z 272 " =    1.412
peak=    4.887 closest distance to " O   HOH Z 400 " =    0.929
peak=    4.874 closest distance to " O   ARG A 275 " =    0.788
peak=    4.798 closest distance to " OE1 GLN A  77 " =    1.046
peak=    4.798 closest distance to " O   HOH Z 124 " =    1.522
peak=    4.767 closest distance to " CB  GLN A  73 " =    0.954
peak=    4.756 closest distance to " O   HOH Z 126 " =    2.111
peak=    4.744 closest distance to " O   HOH Z 111 " =    2.189
peak=    4.737 closest distance to " O   HOH Z  15 " =    2.063
peak=    4.733 closest distance to " CA  TYR A  30 " =    1.074
peak=    4.705 closest distance to " O   HOH Z  54 " =    1.312
peak=    4.705 closest distance to " O   HOH Z 433 " =    2.056
peak=    4.700 closest distance to " CB  SER A  63 " =    1.403
peak=    4.693 closest distance to " O   PRO A 198 " =    1.558
peak=    4.684 closest distance to " NE2 HIS A 115 " =    0.886
peak=    4.636 closest distance to " O   HOH Z  80 " =    2.319
peak=    4.617 closest distance to " CB  GLN A 194 " =    0.908
peak=    4.615 closest distance to " O   HOH Z 404 " =    1.505
peak=    4.571 closest distance to " CB  PRO A  54 " =    0.711
peak=    4.567 closest distance to " O   HOH Z  47 " =    1.789
peak=    4.553 closest distance to " O   HOH Z   7 " =    1.175
peak=    4.535 closest distance to " O   HOH Z 182 " =    1.297
peak=    4.534 closest distance to " O   HOH Z 142 " =    1.710
peak=    4.509 closest distance to " O   HOH Z 389 " =    1.908
peak=    4.487 closest distance to " O   HOH Z 134 " =    2.468
peak=    4.486 closest distance to " O   HOH Z 133 " =    1.869
peak=    4.462 closest distance to " O   HOH Z 422 " =    1.277
peak=    4.448 closest distance to " O   HOH Z 211 " =    1.687
peak=    4.430 closest distance to " CG  PRO A 198 " =    1.471
peak=    4.383 closest distance to " CB  GLU A 277 " =    0.883
peak=    4.370 closest distance to " O   HOH Z  63 " =    1.636
peak=    4.347 closest distance to " CG2BVAL A  41 " =    1.030
peak=    4.342 closest distance to " O   HOH Z   4 " =    1.366
peak=    4.334 closest distance to " O   HOH Z 406 " =    1.575
peak=    4.315 closest distance to " O   HOH Z 193 " =    1.930
peak=    4.278 closest distance to " O   HOH Z 261 " =    1.512
peak=    4.273 closest distance to " O   HOH Z  11 " =    1.216
peak=    4.271 closest distance to " CA  GLY A 196 " =    1.032
peak=    4.268 closest distance to " O   HOH Z 217 " =    1.404
peak=    4.241 closest distance to " CB  TRP A 179 " =    1.402
peak=    4.228 closest distance to " O   HOH Z 132 " =    1.754
peak=    4.223 closest distance to " O   HOH Z 363 " =    1.221
peak=    4.220 closest distance to " O   HOH Z 232 " =    2.152
peak=    4.191 closest distance to " O   HOH Z 271 " =    1.792
peak=    4.175 closest distance to " O   HOH Z  97 " =    1.601
peak=    4.160 closest distance to " O   HOH Z 214 " =    1.378
peak=    4.153 closest distance to " O   HOH Z 324 " =    1.807
peak=    4.140 closest distance to " CG  PRO A 280 " =    1.021
peak=    4.136 closest distance to " O   HOH Z 431 " =    1.327
peak=    4.104 closest distance to " O   HOH Z 368 " =    1.078
peak=    4.075 closest distance to " CD2 LEU A 297 " =    1.051
peak=    4.070 closest distance to " O   HOH Z 156 " =    3.310
peak=    4.055 closest distance to " CB  GLN A  88 " =    1.086
peak=    4.049 closest distance to " O   HOH Z 163 " =    1.827
peak=    4.028 closest distance to " CB  GLN A 183 " =    1.202
peak=    4.018 closest distance to " O   HOH Z 369 " =    2.136
peak=    4.014 closest distance to " CD  LYS A 119 " =    1.228
peak=    4.009 closest distance to " OE1 GLN A  11 " =    2.073
peak=    4.006 closest distance to " CG1 VAL A 153 " =    1.131
peak=    4.002 closest distance to " NZ  LYS A 193 " =    1.441
peak=    4.001 closest distance to " CG AARG A 275 " =    1.010
peak=    3.996 closest distance to " O   HOH Z 272 " =    1.357
peak=    3.987 closest distance to " CA  ALA A  21 " =    1.480
peak=    3.982 closest distance to " O   HOH Z 192 " =    2.373
peak=    3.975 closest distance to " O   HOH Z 243 " =    0.945
peak=    3.970 closest distance to " CG  PRO A 213 " =    1.314
peak=    3.964 closest distance to " O   HOH Z  68 " =    1.767
peak=    3.956 closest distance to " CB  GLN A 223 " =    1.423
peak=    3.948 closest distance to " CG1 ILE A  33 " =    1.282
peak=    3.945 closest distance to " O   HOH Z 246 " =    1.582
peak=    3.938 closest distance to " O   HOH Z  47 " =    1.673
peak=    3.927 closest distance to " CB  PRO A 198 " =    1.000
peak=    3.926 closest distance to " O   HOH Z 215 " =    1.572
peak=    3.919 closest distance to " O   HOH Z 137 " =    1.995
peak=    3.908 closest distance to " O   HOH Z  39 " =    2.247
peak=    3.895 closest distance to " CD BLYS A 290 " =    1.010
peak=    3.891 closest distance to " CB  PHE A  61 " =    0.756
peak=    3.886 closest distance to " CB  GLU A 152 " =    1.163
peak=    3.883 closest distance to " O   HOH Z 326 " =    1.459
peak=    3.881 closest distance to " O   HOH Z  28 " =    2.347
peak=    3.878 closest distance to " O   HOH Z 207 " =    2.233
peak=    3.878 closest distance to " CA  ILE A 106 " =    0.802
peak=    3.871 closest distance to " CB  TRP A 266 " =    1.042
peak=    3.869 closest distance to " O   HOH Z  44 " =    2.351
peak=    3.859 closest distance to " O   HOH Z 292 " =    1.632
peak=    3.858 closest distance to " CB  LEU A 228 " =    1.132
peak=    3.858 closest distance to " CA  ARG A 195 " =    1.185
peak=    3.857 closest distance to " O   HOH Z 234 " =    3.694
peak=    3.852 closest distance to " CE BMET A  47 " =    1.210
peak=    3.844 closest distance to " CB  TRP A 179 " =    1.590
peak=    3.827 closest distance to " O   HOH Z 418 " =    1.755
peak=    3.824 closest distance to " N   ASN A  39 " =    1.219
peak=    3.816 closest distance to " O   HOH Z 394 " =    1.736
peak=    3.816 closest distance to " O   HOH Z 260 " =    1.430
peak=    3.810 closest distance to " N   GLU A 277 " =    1.090
peak=    3.792 closest distance to " NZ  LYS A 117 " =    3.094
peak=    3.791 closest distance to " NH2AARG A 145 " =    0.973
peak=    3.790 closest distance to " O   HOH Z 411 " =    3.079
peak=    3.778 closest distance to " O   HOH Z 139 " =    4.459
peak=    3.776 closest distance to " CG1 ILE A 120 " =    1.173
peak=    3.772 closest distance to " O   HOH Z  44 " =    1.747
peak=    3.767 closest distance to " O   HOH Z 240 " =    1.890
peak=    3.762 closest distance to " O   HOH Z  43 " =    2.060
peak=    3.759 closest distance to " CG  PRO A  90 " =    1.215
peak=    3.759 closest distance to " O   HOH Z 154 " =    1.397
peak=    3.753 closest distance to " O   HOH Z  88 " =    3.596
peak=    3.745 closest distance to " O   HOH Z  78 " =    2.127
peak=    3.743 closest distance to " CB  TYR A 116 " =    1.474
peak=    3.739 closest distance to " CA  ARG A  66 " =    1.071
peak=    3.738 closest distance to " O   HOH Z 132 " =    1.699
peak=    3.724 closest distance to " CG2 VAL A  78 " =    1.037
peak=    3.713 closest distance to " CB  ASN A 148 " =    1.365
peak=    3.711 closest distance to " O   ALA A 165 " =    1.193
peak=    3.710 closest distance to " CB  ALA A 100 " =    1.476
peak=    3.703 closest distance to " O  BHOH Z 338 " =    0.982
peak=    3.701 closest distance to " O   HOH Z 132 " =    2.188
peak=    3.699 closest distance to " O   GLY A  91 " =    1.218
peak=    3.690 closest distance to " N   VAL A 296 " =    1.633
peak=    3.683 closest distance to " OD1 ASN A 148 " =    2.099
peak=    3.683 closest distance to " O   HOH Z 361 " =    2.966
peak=    3.682 closest distance to " CG2 VAL A 197 " =    1.357
peak=    3.680 closest distance to " NH1AARG A 145 " =    1.036
peak=    3.677 closest distance to " O   HOH Z 183 " =    1.452
peak=    3.675 closest distance to " CA  ASN A 176 " =    1.819
peak=    3.673 closest distance to " CG  PRO A 243 " =    1.174
peak=    3.669 closest distance to " O   HOH Z 416 " =    1.468
peak=    3.667 closest distance to " OG  SER A  97 " =    3.281
peak=    3.649 closest distance to " O   HOH Z 301 " =    1.554
peak=    3.643 closest distance to " O   HOH Z 316 " =    3.109
peak=    3.642 closest distance to " O   HOH Z 202 " =    1.673
peak=    3.638 closest distance to " CB  SER A  26 " =    0.957
peak=    3.638 closest distance to " O   HOH Z   1 " =    3.232
peak=    3.638 closest distance to " O   HOH Z 142 " =    1.785
peak=    3.631 closest distance to " CD1 TRP A 274 " =    1.054
peak=    3.625 closest distance to " CA  ALA A 295 " =    0.984
peak=    3.625 closest distance to " CA  ALA A 100 " =    1.200
peak=    3.623 closest distance to " CE  LYS A 119 " =    1.323
peak=    3.619 closest distance to " O   HOH Z 196 " =    2.547
peak=    3.619 closest distance to " CA  VAL A 197 " =    1.138
peak=    3.611 closest distance to " O   HOH Z 437 " =    1.756
peak=    3.606 closest distance to " O   HOH Z 349 " =    1.159
peak=    3.604 closest distance to " O   HOH Z 402 " =    1.675
peak=    3.600 closest distance to " OE1 GLN A  88 " =    0.766
peak=    3.599 closest distance to " O   HOH Z 139 " =    3.369
peak=    3.597 closest distance to " CB  SER A 276 " =    0.879
peak=    3.595 closest distance to " CB  VAL A 202 " =    1.483
peak=    3.592 closest distance to " O   HOH Z 331 " =    1.368
peak=    3.587 closest distance to " CB  MET A  47 " =    1.039
peak=    3.583 closest distance to " CA  GLN A 223 " =    0.856
peak=    3.574 closest distance to " N   GLN A  55 " =    0.780
peak=    3.571 closest distance to " CB  GLN A  58 " =    0.916
peak=    3.567 closest distance to " O   HOH Z 215 " =    1.933
peak=    3.565 closest distance to " O   SER A 276 " =    1.143
peak=    3.560 closest distance to " ND2 ASN A  45 " =    1.199
peak=    3.557 closest distance to " CB  ASN A 187 " =    1.126
peak=    3.554 closest distance to " O   HOH Z 223 " =    1.359
peak=    3.542 closest distance to " CG2 THR A 221 " =    1.028
peak=    3.533 closest distance to " CG2 THR A  42 " =    0.889
peak=    3.524 closest distance to " O   HOH Z 336 " =    1.605
peak=    3.511 closest distance to " O   HOH Z 119 " =    2.348
peak=    3.508 closest distance to " O   SER A 164 " =    1.309
peak=    3.507 closest distance to " O   HOH Z 155 " =    2.829
peak=    3.500 closest distance to " O   HOH Z 428 " =    1.162
peak=    3.499 closest distance to " ND2 ASN A 110 " =    1.648
peak=    3.499 closest distance to " CA  VAL A  41 " =    0.769
peak=    3.498 closest distance to " O   HOH Z 203 " =    1.589
peak=    3.498 closest distance to " N   TYR A 116 " =    1.900
peak=    3.496 closest distance to " CB  TYR A  30 " =    1.158
peak=    3.494 closest distance to " O   HOH Z 395 " =    1.363
peak=    3.489 closest distance to " CA  ALA A 248 " =    1.237
peak=    3.488 closest distance to " O   HOH Z 156 " =    2.344
peak=    3.487 closest distance to " O   HOH Z 299 " =    1.700
peak=    3.477 closest distance to " O   HOH Z 128 " =    2.161
peak=    3.476 closest distance to " CG  ARG A  66 " =    3.001
peak=    3.475 closest distance to " CB  ASN A 127 " =    0.889
peak=    3.471 closest distance to " CB  ALA A   1 " =    1.295
peak=    3.469 closest distance to " CE3 TRP A 274 " =    3.498
peak=    3.457 closest distance to " O   HOH Z 112 " =    1.549
peak=    3.451 closest distance to " O   HOH Z 102 " =    1.383
peak=    3.450 closest distance to " CB  ASN A 285 " =    0.947
peak=    3.445 closest distance to " CG2 THR A 220 " =    0.754
peak=    3.441 closest distance to " CA  LEU A 282 " =    1.114
peak=    3.439 closest distance to " O   HOH Z 189 " =    1.802
peak=    3.433 closest distance to " O   HOH Z  98 " =    2.150
peak=    3.428 closest distance to " CB  PHE A 283 " =    1.083
peak=    3.428 closest distance to " O   THR A 251 " =    1.372
peak=    3.427 closest distance to " CG  GLN A  11 " =    1.595
peak=    3.423 closest distance to " CD  LYS A 166 " =    1.566
peak=    3.415 closest distance to " OH  TYR A  30 " =    1.588
peak=    3.414 closest distance to " CH2 TRP A 274 " =    2.021
peak=    3.411 closest distance to " O   HOH Z 183 " =    1.542
peak=    3.410 closest distance to " O   HOH Z 118 " =    2.134
peak=    3.406 closest distance to " CB  ILE A 120 " =    1.397
peak=    3.402 closest distance to " O   ALA A  71 " =    1.021
peak=    3.400 closest distance to " CA  ALA A 160 " =    1.073
peak=    3.397 closest distance to " O   HOH Z  38 " =    3.784
peak=    3.394 closest distance to " CA  ASP A 149 " =    1.523
peak=    3.391 closest distance to " NZ  LYS A 166 " =    3.214
peak=    3.387 closest distance to " CB  ALA A 137 " =    1.313
peak=    3.384 closest distance to " O   HOH Z 184 " =    0.957
peak=    3.382 closest distance to " O   HOH Z 225 " =    2.011
peak=    3.381 closest distance to " O   HOH Z 357 " =    2.008
peak=    3.380 closest distance to " CB  SER A 141 " =    0.921
peak=    3.375 closest distance to " O   HOH Z 427 " =    1.178
peak=    3.365 closest distance to " O   HOH Z 358 " =    1.807
peak=    3.360 closest distance to " O   HOH Z 425 " =    1.589
peak=    3.360 closest distance to " O   HOH Z 267 " =    1.283
peak=    3.359 closest distance to " CB  ASN A 170 " =    1.212
peak=    3.359 closest distance to " O   HOH Z  63 " =    2.034
peak=    3.358 closest distance to " CG2 THR A 251 " =    1.138
peak=    3.354 closest distance to " O   HOH Z  50 " =    3.432
peak=    3.351 closest distance to " O   HOH Z  14 " =    1.596
peak=    3.349 closest distance to " CB  PHE A  16 " =    1.418
peak=    3.347 closest distance to " CB  THR A  31 " =    1.660
peak=    3.347 closest distance to " CB  GLU A 128 " =    1.041
peak=    3.346 closest distance to " OD1 ASP A 238 " =    0.954
peak=    3.343 closest distance to " CB  LEU A  83 " =    0.748
peak=    3.342 closest distance to " O   HOH Z  59 " =    1.887
peak=    3.339 closest distance to " O   HOH Z 126 " =    2.114
peak=    3.334 closest distance to " O   HOH Z 403 " =    1.834
peak=    3.328 closest distance to " CA  THR A 221 " =    0.949
peak=    3.327 closest distance to " O   HOH Z  49 " =    0.994
peak=    3.326 closest distance to " CZ3 TRP A 274 " =    4.770
peak=    3.326 closest distance to " O   HOH Z 368 " =    1.369
peak=    3.326 closest distance to " O   HOH Z 271 " =    1.876
peak=    3.324 closest distance to " O   HOH Z  22 " =    2.079
peak=    3.317 closest distance to " ND2 ASN A  60 " =    1.372
peak=    3.308 closest distance to " O   HOH Z 334 " =    1.767
peak=    3.308 closest distance to " CA  SER A  87 " =    0.780
peak=    3.307 closest distance to " NE2 GLN A  89 " =    1.196
peak=    3.306 closest distance to " CA  ARG A 139 " =    1.442
peak=    3.300 closest distance to " CA  VAL A 296 " =    1.614
peak=    3.299 closest distance to " O   HOH Z 214 " =    1.802
peak=    3.293 closest distance to " O   HOH Z 250 " =    1.439
peak=    3.292 closest distance to " O   HOH Z 379 " =    1.612
peak=    3.291 closest distance to " O   HOH Z 380 " =    1.967
peak=    3.290 closest distance to " CB  TRP A 150 " =    1.053
peak=    3.287 closest distance to " CA  SER A  12 " =    1.408
peak=    3.282 closest distance to " O   HOH Z 409 " =    3.051
peak=    3.282 closest distance to " CB  LEU A 167 " =    1.327
peak=    3.282 closest distance to " NH1BARG A 145 " =    1.916
peak=    3.276 closest distance to " ND1 HIS A  81 " =    1.159
peak=    3.275 closest distance to " CA  ASP A 124 " =    0.907
peak=    3.274 closest distance to " CG  ARG A  66 " =    0.827
peak=    3.271 closest distance to " O   HOH Z 435 " =    1.998
peak=    3.269 closest distance to " O   HOH Z 200 " =    1.281
peak=    3.266 closest distance to " O   HOH Z 135 " =    1.599
peak=    3.264 closest distance to " CA  GLU A 152 " =    1.085
peak=    3.263 closest distance to " O   HOH Z 146 " =    1.881
peak=    3.256 closest distance to " O   SER A  87 " =    2.334
peak=    3.251 closest distance to " O   HOH Z 150 " =    2.011
peak=    3.249 closest distance to " O   HOH Z  64 " =    2.225
peak=    3.249 closest distance to " CB  VAL A 230 " =    1.420
peak=    3.246 closest distance to " CB  ARG A 190 " =    1.740
peak=    3.243 closest distance to " N   TYR A  15 " =    0.884
peak=    3.241 closest distance to " CG2 VAL A 112 " =    1.482
peak=    3.241 closest distance to " CD2 PHE A  59 " =    1.857
peak=    3.239 closest distance to " OD2 ASP A 286 " =    2.943
peak=    3.236 closest distance to " CG ALYS A 290 " =    1.213
peak=    3.236 closest distance to " CB  ARG A 275 " =    1.123
peak=    3.235 closest distance to " O   HOH Z  39 " =    2.353
peak=    3.235 closest distance to " CD2 LEU A 255 " =    1.107
peak=    3.234 closest distance to " O   HOH Z 344 " =    3.433
peak=    3.228 closest distance to " O   HOH Z 427 " =    3.458
peak=    3.225 closest distance to " O   HOH Z 108 " =    1.762
peak=    3.223 closest distance to " O   HOH Z 426 " =    1.391
peak=    3.220 closest distance to " CD2 TRP A 179 " =    1.226
peak=    3.218 closest distance to " CB  ARG A 102 " =    0.783
peak=    3.217 closest distance to " OG  SER A 245 " =    1.501
peak=    3.216 closest distance to " O   HOH Z 174 " =    1.369
peak=    3.213 closest distance to " N   HIS A 108 " =    1.939
peak=    3.211 closest distance to " O   HOH Z 303 " =    2.019
peak=    3.208 closest distance to " CB  ALA A 256 " =    1.166
peak=    3.208 closest distance to " CD1 LEU A 300 " =    1.221
peak=    3.200 closest distance to " CD  GLN A  73 " =    0.959
peak=    3.199 closest distance to " O   HOH Z 372 " =    1.200
peak=    3.196 closest distance to " O   HOH Z 327 " =    1.536
peak=    3.192 closest distance to " CE  MET A 105 " =    1.485
peak=    3.190 closest distance to " O   HOH Z 154 " =    2.158
peak=    3.188 closest distance to " NH2BARG A 145 " =    1.892
peak=    3.178 closest distance to " N   ASN A 252 " =    1.183
peak=    3.176 closest distance to " CA  ARG A  36 " =    1.155
peak=    3.173 closest distance to " OE1 GLN A  58 " =    5.856
peak=    3.169 closest distance to " CG  GLU A 277 " =    2.497
peak=    3.168 closest distance to " CD  ARG A 195 " =    1.012
peak=    3.166 closest distance to " O   HOH Z 145 " =    1.693
peak=    3.161 closest distance to " CB  ASP A 124 " =    0.965
peak=    3.160 closest distance to " CB  TYR A 169 " =    0.986
peak=    3.160 closest distance to " CB  ALA A  71 " =    1.339
peak=    3.160 closest distance to " O   HOH Z 398 " =    1.425
peak=    3.155 closest distance to " CA  ASP A 162 " =    1.178
peak=    3.153 closest distance to " O   HOH Z 259 " =    1.944
peak=    3.152 closest distance to " O   HOH Z 287 " =    2.160
peak=    3.152 closest distance to " O   HOH Z  69 " =    1.148
peak=    3.152 closest distance to " O   HOH Z  38 " =    1.308
peak=    3.151 closest distance to " O   HOH Z 261 " =    2.176
peak=    3.151 closest distance to " CD  LYS A  76 " =    1.773
peak=    3.145 closest distance to " O   HOH Z 408 " =    2.600
peak=    3.142 closest distance to " O   HOH Z 194 " =    1.739
peak=    3.139 closest distance to " O   HOH Z 298 " =    2.004
peak=    3.135 closest distance to " O   HOH Z 432 " =    1.833
peak=    3.132 closest distance to " O   SER A  26 " =    1.558
peak=    3.127 closest distance to " O   HOH Z 186 " =    1.144
peak=    3.126 closest distance to " O   HOH Z 410 " =    1.472
peak=    3.126 closest distance to " OG ASER A 134 " =    1.215
peak=    3.126 closest distance to " CA  ALA A 158 " =    1.097
peak=    3.125 closest distance to " NE2 GLN A  11 " =    1.180
peak=    3.111 closest distance to " CA  GLN A  73 " =    1.424
peak=    3.105 closest distance to " OD1 ASN A  69 " =    2.254
peak=    3.102 closest distance to " NH2BARG A 145 " =    1.262
peak=    3.097 closest distance to " O   HOH Z 281 " =    3.872
peak=    3.095 closest distance to " CD  ARG A 139 " =    1.347
peak=    3.079 closest distance to " O   HOH Z 420 " =    5.258
peak=    3.078 closest distance to " O   HOH Z 374 " =    2.620
peak=    3.072 closest distance to " O  BHOH Z 338 " =    2.524
peak=    3.067 closest distance to " CB  PRO A 213 " =    1.643
peak=    3.065 closest distance to " O   HOH Z 172 " =    2.070
peak=    3.064 closest distance to " O   HOH Z  22 " =    1.086
peak=    3.056 closest distance to " CD  ARG A 269 " =    0.879
peak=    3.042 closest distance to " O   HOH Z 428 " =    3.800
peak=    3.033 closest distance to " CA  ASP A 191 " =    0.876
peak=    3.032 closest distance to " O   HOH Z 200 " =    3.828
peak=    3.011 closest distance to " O   HOH Z  66 " =    1.655

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.489 - 5.401
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 218
   mapped sites are within: 0.706 - 5.401

peak=   -5.427 closest distance to " N   ARG A 275 " =    0.810
peak=   -4.646 closest distance to " O   HOH Z  52 " =    2.104
peak=   -4.445 closest distance to " NH2 ARG A  66 " =    1.113
peak=   -4.281 closest distance to " CD2 HIS A 115 " =    1.107
peak=   -4.276 closest distance to " O   HOH Z 166 " =    1.848
peak=   -4.241 closest distance to " O   HOH Z 151 " =    1.512
peak=   -4.180 closest distance to " C   ASN A 285 " =    2.643
peak=   -4.134 closest distance to " CB  LEU A 167 " =    2.048
peak=   -4.060 closest distance to " O   ALA A  34 " =    1.913
peak=   -4.014 closest distance to " O   HOH Z 290 " =    0.968
peak=   -4.009 closest distance to " OG1 THR A  82 " =    1.913
peak=   -3.964 closest distance to " O   HOH Z  93 " =    1.745
peak=   -3.953 closest distance to " O  BHOH Z 338 " =    1.355
peak=   -3.950 closest distance to " OG  SER A  97 " =    2.325
peak=   -3.922 closest distance to " O   PRO A 198 " =    1.360
peak=   -3.922 closest distance to " O   HOH Z 120 " =    1.024
peak=   -3.916 closest distance to " O   HOH Z 221 " =    1.167
peak=   -3.914 closest distance to " OG ASER A 134 " =    1.245
peak=   -3.912 closest distance to " N   SER A 134 " =    1.198
peak=   -3.895 closest distance to " O   HOH Z 148 " =    2.962
peak=   -3.890 closest distance to " O   HOH Z  69 " =    0.905
peak=   -3.889 closest distance to " O   HOH Z 400 " =    1.053
peak=   -3.867 closest distance to " CG2 THR A 221 " =    2.275
peak=   -3.864 closest distance to " O   HOH Z 198 " =    1.589
peak=   -3.862 closest distance to " N   ALA A  43 " =    2.653
peak=   -3.817 closest distance to " CA  VAL A 197 " =    0.938
peak=   -3.813 closest distance to " CE  MET A 105 " =    2.230
peak=   -3.811 closest distance to " O   THR A  52 " =    2.132
peak=   -3.807 closest distance to " CA  VAL A  67 " =    2.913
peak=   -3.802 closest distance to " O   HOH Z 340 " =    0.966
peak=   -3.801 closest distance to " O   HOH Z  71 " =    1.221
peak=   -3.798 closest distance to " CD1 PHE A  59 " =    1.853
peak=   -3.784 closest distance to " CB  GLN A  55 " =    1.525
peak=   -3.780 closest distance to " O   HOH Z 377 " =    2.010
peak=   -3.766 closest distance to " O   HOH Z 282 " =    1.682
peak=   -3.753 closest distance to " O   HOH Z 325 " =    2.004
peak=   -3.743 closest distance to " CA  GLU A 277 " =    1.185
peak=   -3.738 closest distance to " O   HOH Z  37 " =    1.608
peak=   -3.735 closest distance to " ND2 ASN A  60 " =    5.401
peak=   -3.731 closest distance to " CD2 PHE A  59 " =    2.208
peak=   -3.722 closest distance to " O   HOH Z 210 " =    1.042
peak=   -3.710 closest distance to " O   HOH Z 274 " =    2.801
peak=   -3.706 closest distance to " CD1 TYR A 247 " =    2.277
peak=   -3.703 closest distance to " NH2 ARG A  66 " =    1.008
peak=   -3.698 closest distance to " O   HOH Z  58 " =    0.725
peak=   -3.695 closest distance to " O   HOH Z 109 " =    3.659
peak=   -3.694 closest distance to " O   HOH Z  11 " =    1.213
peak=   -3.683 closest distance to " CG2BVAL A  41 " =    2.490
peak=   -3.678 closest distance to " O   HOH Z 124 " =    1.448
peak=   -3.651 closest distance to " CE  MET A  93 " =    1.232
peak=   -3.645 closest distance to " O   HOH Z 259 " =    0.859
peak=   -3.643 closest distance to " CD  GLN A 223 " =    1.086
peak=   -3.640 closest distance to " CA  SER A 164 " =    1.850
peak=   -3.634 closest distance to " O   HOH Z 401 " =    1.354
peak=   -3.631 closest distance to " O   HOH Z 136 " =    1.516
peak=   -3.631 closest distance to " O   HOH Z 155 " =    1.214
peak=   -3.630 closest distance to " OH  TYR A 169 " =    0.909
peak=   -3.614 closest distance to " CG  GLN A  73 " =    1.108
peak=   -3.613 closest distance to " O   HOH Z  91 " =    2.219
peak=   -3.611 closest distance to " OG  SER A 276 " =    0.856
peak=   -3.587 closest distance to " O   ALA A   1 " =    2.112
peak=   -3.571 closest distance to " CA  GLY A 118 " =    2.418
peak=   -3.566 closest distance to " O   HOH Z  38 " =    1.302
peak=   -3.549 closest distance to " O   HOH Z 430 " =    1.303
peak=   -3.544 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -3.541 closest distance to " CA  SER A 276 " =    1.352
peak=   -3.539 closest distance to " C   THR A 279 " =    1.068
peak=   -3.528 closest distance to " CD1 TRP A 179 " =    1.011
peak=   -3.517 closest distance to " O   HOH Z 266 " =    4.554
peak=   -3.516 closest distance to " O   THR A  18 " =    1.528
peak=   -3.513 closest distance to " O   HOH Z 407 " =    1.671
peak=   -3.506 closest distance to " NH2 ARG A  79 " =    1.679
peak=   -3.505 closest distance to " CD  LYS A 289 " =    2.408
peak=   -3.504 closest distance to " CD  ARG A  14 " =    3.542
peak=   -3.504 closest distance to " O   HOH Z 166 " =    2.217
peak=   -3.502 closest distance to " O   ARG A  66 " =    1.362
peak=   -3.500 closest distance to " O   HOH Z 127 " =    1.654
peak=   -3.495 closest distance to " C   SER A 206 " =    1.546
peak=   -3.495 closest distance to " C   SER A 271 " =    1.282
peak=   -3.493 closest distance to " O   HOH Z   7 " =    1.314
peak=   -3.483 closest distance to " CG2 ILE A  49 " =    2.604
peak=   -3.482 closest distance to " O   HOH Z 380 " =    4.199
peak=   -3.473 closest distance to " O   HOH Z  53 " =    2.413
peak=   -3.473 closest distance to " O   HOH Z 350 " =    0.833
peak=   -3.466 closest distance to " NH2AARG A 275 " =    5.203
peak=   -3.464 closest distance to " O   HOH Z 414 " =    1.560
peak=   -3.455 closest distance to " CD2 LEU A 237 " =    2.359
peak=   -3.453 closest distance to " CB  ALA A 227 " =    2.342
peak=   -3.450 closest distance to " CB  ALA A 161 " =    2.590
peak=   -3.448 closest distance to " C   ASN A 187 " =    2.108
peak=   -3.443 closest distance to " CD2 TRP A 274 " =    2.284
peak=   -3.431 closest distance to " O   HOH Z 111 " =    1.075
peak=   -3.427 closest distance to " CD1 LEU A 228 " =    2.595
peak=   -3.422 closest distance to " O   HOH Z 215 " =    3.142
peak=   -3.420 closest distance to " O   HOH Z  92 " =    1.226
peak=   -3.414 closest distance to " O   HOH Z  29 " =    1.006
peak=   -3.413 closest distance to " O   HOH Z 402 " =    1.063
peak=   -3.413 closest distance to " CA  GLY A  23 " =    2.277
peak=   -3.396 closest distance to " O   HOH Z 158 " =    1.662
peak=   -3.394 closest distance to " CD  PRO A 198 " =    1.121
peak=   -3.394 closest distance to " CE2 TYR A  30 " =    2.794
peak=   -3.387 closest distance to " O   HOH Z 132 " =    1.493
peak=   -3.383 closest distance to " O   HOH Z 349 " =    0.727
peak=   -3.381 closest distance to " NZ  LYS A 119 " =    1.473
peak=   -3.379 closest distance to " OD2 ASP A 171 " =    2.389
peak=   -3.377 closest distance to " O   HOH Z 434 " =    4.292
peak=   -3.376 closest distance to " CA  ALA A 291 " =    2.859
peak=   -3.376 closest distance to " O   TYR A  15 " =    1.371
peak=   -3.373 closest distance to " OD1 ASN A 148 " =    1.569
peak=   -3.365 closest distance to " O   ARG A 275 " =    0.949
peak=   -3.362 closest distance to " O   HOH Z 150 " =    1.909
peak=   -3.358 closest distance to " O   HOH Z 423 " =    1.150
peak=   -3.358 closest distance to " O   HOH Z 150 " =    2.116
peak=   -3.347 closest distance to " CD2 LEU A 237 " =    2.519
peak=   -3.341 closest distance to " CB  ALA A  43 " =    2.535
peak=   -3.339 closest distance to " N   GLY A  17 " =    1.628
peak=   -3.332 closest distance to " O   HOH Z 292 " =    1.490
peak=   -3.318 closest distance to " O   HOH Z 119 " =    3.133
peak=   -3.316 closest distance to " O   HOH Z 369 " =    2.145
peak=   -3.303 closest distance to " N   LEU A 282 " =    2.413
peak=   -3.294 closest distance to " CG2 VAL A 296 " =    1.788
peak=   -3.293 closest distance to " O   HOH Z 436 " =    1.262
peak=   -3.290 closest distance to " OD2 ASP A 171 " =    1.922
peak=   -3.289 closest distance to " N   GLY A  75 " =    1.291
peak=   -3.281 closest distance to " O   GLY A 196 " =    1.160
peak=   -3.281 closest distance to " CD  GLU A 236 " =    0.943
peak=   -3.275 closest distance to " CD  GLN A  77 " =    0.979
peak=   -3.269 closest distance to " O   ILE A 120 " =    0.763
peak=   -3.269 closest distance to " O   HOH Z 416 " =    0.821
peak=   -3.266 closest distance to " CD1 LEU A  25 " =    2.580
peak=   -3.265 closest distance to " O   HOH Z 428 " =    1.373
peak=   -3.265 closest distance to " OG  SER A  87 " =    1.693
peak=   -3.264 closest distance to " O   HOH Z  50 " =    1.520
peak=   -3.264 closest distance to " OE1 GLU A 277 " =    2.187
peak=   -3.263 closest distance to " O   HOH Z 378 " =    1.209
peak=   -3.262 closest distance to " CG  LYS A 193 " =    2.700
peak=   -3.258 closest distance to " C   MET A 113 " =    1.083
peak=   -3.256 closest distance to " O   HOH Z 119 " =    3.010
peak=   -3.256 closest distance to " O   HOH Z 310 " =    1.053
peak=   -3.250 closest distance to " O   ALA A 256 " =    1.651
peak=   -3.246 closest distance to " CG  GLU A   2 " =    1.383
peak=   -3.240 closest distance to " CB  ASP A  50 " =    2.498
peak=   -3.235 closest distance to " CA  ASN A 110 " =    0.941
peak=   -3.232 closest distance to " CD2 TYR A  30 " =    2.855
peak=   -3.230 closest distance to " N   VAL A  72 " =    1.191
peak=   -3.228 closest distance to " O   HOH Z 140 " =    0.872
peak=   -3.228 closest distance to " O   HOH Z 193 " =    1.174
peak=   -3.228 closest distance to " O   HOH Z  98 " =    1.754
peak=   -3.225 closest distance to " O   HOH Z 396 " =    1.669
peak=   -3.223 closest distance to " O   HOH Z 184 " =    0.876
peak=   -3.222 closest distance to " O   HOH Z  33 " =    0.841
peak=   -3.215 closest distance to " ND1 HIS A 115 " =    1.177
peak=   -3.213 closest distance to " O   HOH Z 213 " =    1.628
peak=   -3.209 closest distance to " SD  MET A  93 " =    1.820
peak=   -3.208 closest distance to " CA  ASP A 298 " =    1.033
peak=   -3.207 closest distance to " O   HOH Z 105 " =    2.006
peak=   -3.207 closest distance to " CD  LYS A 119 " =    0.984
peak=   -3.206 closest distance to " O   HOH Z 423 " =    2.347
peak=   -3.204 closest distance to " NE2 GLN A  58 " =    0.978
peak=   -3.192 closest distance to " O   HOH Z 182 " =    0.796
peak=   -3.190 closest distance to " ND2 ASN A  60 " =    1.503
peak=   -3.189 closest distance to " O   HOH Z 219 " =    2.463
peak=   -3.185 closest distance to " OD2 ASP A 270 " =    2.259
peak=   -3.184 closest distance to " O   LEU A 143 " =    1.232
peak=   -3.180 closest distance to " O   ASP A 132 " =    2.229
peak=   -3.179 closest distance to " C   GLN A 194 " =    1.156
peak=   -3.178 closest distance to " N   GLU A 277 " =    0.734
peak=   -3.177 closest distance to " CG1AVAL A  41 " =    2.607
peak=   -3.173 closest distance to " O   HOH Z 418 " =    1.740
peak=   -3.172 closest distance to " O   VAL A 125 " =    2.090
peak=   -3.171 closest distance to " O   HOH Z 298 " =    3.003
peak=   -3.171 closest distance to " C   LEU A 101 " =    0.816
peak=   -3.170 closest distance to " O   HOH Z 366 " =    1.094
peak=   -3.165 closest distance to " N   ALA A 226 " =    2.212
peak=   -3.163 closest distance to " OD1 ASP A 298 " =    2.002
peak=   -3.161 closest distance to " O   SER A 146 " =    0.847
peak=   -3.161 closest distance to " CD2 TRP A  85 " =    1.191
peak=   -3.160 closest distance to " O   HOH Z 308 " =    1.727
peak=   -3.160 closest distance to " N   THR A 235 " =    1.133
peak=   -3.156 closest distance to " O   GLY A  80 " =    2.135
peak=   -3.150 closest distance to " CG  GLN A  58 " =    1.192
peak=   -3.139 closest distance to " O   HOH Z   7 " =    1.418
peak=   -3.134 closest distance to " ND2 ASN A 127 " =    1.461
peak=   -3.134 closest distance to " O   GLY A 262 " =    2.173
peak=   -3.130 closest distance to " SG  CYS A 168 " =    1.064
peak=   -3.130 closest distance to " O   HOH Z 426 " =    2.264
peak=   -3.125 closest distance to " CD2 LEU A 300 " =    2.542
peak=   -3.124 closest distance to " O   HOH Z  40 " =    3.380
peak=   -3.123 closest distance to " O   HOH Z 329 " =    2.881
peak=   -3.119 closest distance to " ND2 ASN A 285 " =    2.213
peak=   -3.108 closest distance to " ND2 ASN A  60 " =    1.448
peak=   -3.108 closest distance to " CE2 TRP A 274 " =    0.986
peak=   -3.107 closest distance to " O   HOH Z 427 " =    1.509
peak=   -3.105 closest distance to " CD1 PHE A 283 " =    2.105
peak=   -3.102 closest distance to " CD  GLN A  88 " =    0.914
peak=   -3.100 closest distance to " O   ASN A 285 " =    2.585
peak=   -3.094 closest distance to " CE3 TRP A 150 " =    1.717
peak=   -3.093 closest distance to " O   HOH Z 231 " =    1.930
peak=   -3.091 closest distance to " O  BHOH Z 338 " =    0.706
peak=   -3.091 closest distance to " N   ALA A 114 " =    1.019
peak=   -3.090 closest distance to " CZ  ARG A 156 " =    1.093
peak=   -3.086 closest distance to " O   HOH Z 134 " =    2.027
peak=   -3.084 closest distance to " O   HOH Z 185 " =    2.037
peak=   -3.081 closest distance to " CH2 TRP A 177 " =    2.011
peak=   -3.077 closest distance to " N   ASP A 286 " =    1.367
peak=   -3.069 closest distance to " N   GLN A  58 " =    1.655
peak=   -3.065 closest distance to " N   THR A 157 " =    1.835
peak=   -3.065 closest distance to " O   HOH Z 406 " =    1.161
peak=   -3.054 closest distance to " O   HOH Z  19 " =    1.932
peak=   -3.050 closest distance to " CG  ARG A  36 " =    2.845
peak=   -3.000 closest distance to " CA  TYR A  68 " =    2.655

================= 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    :  0.4914 0.4800   6.300516e+00   6.288144e+00
   1_bss:  0.4846 0.4736   6.298318e+00   6.279534e+00
   1_xyz:  0.3985 0.4397   6.180754e+00   6.237116e+00
   1_adp:  0.3652 0.4463   6.148591e+00   6.244186e+00
   1_occ:  0.3649 0.4465   6.148241e+00   6.244460e+00
   2_bss:  0.3641 0.4430   6.147728e+00   6.242311e+00
   2_xyz:  0.2980 0.3732   5.988756e+00   6.134928e+00
   2_adp:  0.2723 0.3546   5.933640e+00   6.104703e+00
   2_occ:  0.2722 0.3541   5.933302e+00   6.104252e+00
   3_bss:  0.2716 0.3530   5.930186e+00   6.102356e+00
   3_xyz:  0.2393 0.3096   5.811470e+00   5.996809e+00
   3_adp:  0.2311 0.2927   5.778985e+00   5.955457e+00
   3_occ:  0.2310 0.2923   5.778474e+00   5.954664e+00
   4_bss:  0.2310 0.2921   5.778933e+00   5.955298e+00
   4_xyz:  0.1868 0.2371   5.583607e+00   5.772996e+00
   4_adp:  0.1708 0.2254   5.518163e+00   5.728257e+00
   4_occ:  0.1707 0.2253   5.517676e+00   5.727713e+00
   5_bss:  0.1711 0.2258   5.519444e+00   5.729293e+00
   5_xyz:  0.1437 0.1979   5.371435e+00   5.605724e+00
   5_adp:  0.1391 0.1847   5.329881e+00   5.541331e+00
   5_occ:  0.1390 0.1849   5.329940e+00   5.542116e+00
   5_bss:  0.1393 0.1851   5.331798e+00   5.542316e+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:  0.281  14.130  -1.468   3.017   0.691   0.000   0.000   0.000
   1_xyz:  0.281  14.130  -1.468   3.017   0.691   0.000   0.000   0.000
   1_adp:  0.281  14.130  -1.468   3.017   0.691   0.000   0.000   0.000
   1_occ:  0.281  14.130  -1.468   3.017   0.691   0.000   0.000   0.000
   2_bss:  0.323  56.013  -0.831   1.515   0.116   0.000   0.000   0.000
   2_xyz:  0.323  56.013  -0.831   1.515   0.116   0.000   0.000   0.000
   2_adp:  0.323  56.013  -0.831   1.515   0.116   0.000   0.000   0.000
   2_occ:  0.323  56.013  -0.831   1.515   0.116   0.000   0.000   0.000
   3_bss:  0.326  60.116  -0.387   0.873  -0.239   0.000  -0.000  -0.000
   3_xyz:  0.326  60.116  -0.387   0.873  -0.239   0.000  -0.000  -0.000
   3_adp:  0.326  60.116  -0.387   0.873  -0.239   0.000  -0.000  -0.000
   3_occ:  0.326  60.116  -0.387   0.873  -0.239   0.000  -0.000  -0.000
   4_bss:  0.324  61.281  -1.277   0.065  -1.177   0.000  -0.000  -0.000
   4_xyz:  0.324  61.281  -1.277   0.065  -1.177   0.000  -0.000  -0.000
   4_adp:  0.324  61.281  -1.277   0.065  -1.177   0.000  -0.000  -0.000
   4_occ:  0.324  61.281  -1.277   0.065  -1.177   0.000  -0.000  -0.000
   5_bss:  0.327  68.551  -1.669  -0.453  -1.429  -0.000  -0.000  -0.000
   5_xyz:  0.327  68.551  -1.669  -0.453  -1.429  -0.000  -0.000  -0.000
   5_adp:  0.327  68.551  -1.669  -0.453  -1.429  -0.000  -0.000  -0.000
   5_occ:  0.327  68.551  -1.669  -0.453  -1.429  -0.000  -0.000  -0.000
   5_bss:  0.323  61.397  -2.046  -1.100  -1.761  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.138 0.3920  0.5377    76418.078
   1_bss:  59.048 0.4047  0.5692    73190.856
   1_xyz:  52.064 0.4934  0.6900    59078.039
   1_adp:  53.439 0.4753  0.6797    61090.266
   1_occ:  53.550 0.4739  0.6759    61111.144
   2_bss:  53.214 0.4780  0.6752    60392.228
   2_xyz:  41.990 0.6171  0.8510    40158.159
   2_adp:  39.472 0.6476  0.8630    36527.468
   2_occ:  39.490 0.6473  0.8621    36500.203
   3_bss:  39.329 0.6490  0.8583    36122.342
   3_xyz:  33.108 0.7216  0.9287    26515.232
   3_adp:  30.522 0.7518  0.9457    23655.100
   3_occ:  30.494 0.7522  0.9462    23625.912
   4_bss:  30.450 0.7526  0.9180    23606.718
   4_xyz:  23.773 0.8233  0.9683    14776.740
   4_adp:  22.182 0.8398  0.9653    13341.004
   4_occ:  22.172 0.8399  0.9654    13331.667
   5_bss:  22.190 0.8398  0.9525    13374.150
   5_xyz:  19.237 0.8681  0.9728    10182.687
   5_adp:  17.659 0.8834  0.9773     9055.129
   5_occ:  17.671 0.8834  0.9773     9082.774
   5_bss:  17.673 0.8834  0.9624     9086.140
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   2.1099e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   2.1099e-01
   1_xyz:   1.787  0.014  0.113 16.913  0.007  4.109   1.8116e-01
   1_adp:   1.787  0.014  0.113 16.913  0.007  4.109   1.8116e-01
   1_occ:   1.787  0.014  0.113 16.913  0.007  4.109   1.8116e-01
   2_bss:   1.787  0.014  0.113 16.913  0.007  4.109   1.8116e-01
   2_xyz:   1.642  0.012  0.107 16.073  0.006  4.108   1.4993e-01
   2_adp:   1.642  0.012  0.107 16.073  0.006  4.108   1.4993e-01
   2_occ:   1.642  0.012  0.107 16.073  0.006  4.108   1.4993e-01
   3_bss:   1.642  0.012  0.107 16.073  0.006  4.108   1.4993e-01
   3_xyz:   1.034  0.007  0.067 14.818  0.004  4.115   6.3261e-02
   3_adp:   1.034  0.007  0.067 14.818  0.004  4.115   6.3261e-02
   3_occ:   1.034  0.007  0.067 14.818  0.004  4.115   6.3261e-02
   4_bss:   1.034  0.007  0.067 14.818  0.004  4.115   6.3261e-02
   4_xyz:   1.090  0.007  0.075 14.141  0.004  4.112   6.5055e-02
   4_adp:   1.090  0.007  0.075 14.141  0.004  4.112   6.5055e-02
   4_occ:   1.090  0.007  0.075 14.141  0.004  4.112   6.5055e-02
   5_bss:   1.090  0.007  0.075 14.141  0.004  4.112   6.5055e-02
   5_xyz:   1.143  0.009  0.078 14.648  0.004  4.122   7.3799e-02
   5_adp:   1.143  0.009  0.078 14.648  0.004  4.122   7.3799e-02
   5_occ:   1.143  0.009  0.078 14.648  0.004  4.122   7.3799e-02
   5_bss:   1.143  0.009  0.078 14.648  0.004  4.122   7.3799e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.283   2.4497e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.283   2.4497e-01
   1_xyz:  10.568  0.084  0.440 88.124  0.033  1.712   1.0543e-01
   1_adp:  10.568  0.084  0.440 88.124  0.033  1.712   1.0543e-01
   1_occ:  10.568  0.084  0.440 88.124  0.033  1.712   1.0543e-01
   2_bss:  10.568  0.084  0.440 88.124  0.033  1.712   1.0543e-01
   2_xyz:   8.603  0.069  0.327 82.410  0.040  2.088   2.0143e-01
   2_adp:   8.603  0.069  0.327 82.410  0.040  2.088   2.0143e-01
   2_occ:   8.603  0.069  0.327 82.410  0.040  2.088   2.0143e-01
   3_bss:   8.603  0.069  0.327 82.410  0.040  2.088   2.0143e-01
   3_xyz:   7.433  0.043  0.252 83.935  0.033  2.266   4.3728e-02
   3_adp:   7.433  0.043  0.252 83.935  0.033  2.266   4.3728e-02
   3_occ:   7.433  0.043  0.252 83.935  0.033  2.266   4.3728e-02
   4_bss:   7.433  0.043  0.252 83.935  0.033  2.266   4.3728e-02
   4_xyz:   8.774  0.057  0.248 89.802  0.026  2.320   5.1888e-02
   4_adp:   8.774  0.057  0.248 89.802  0.026  2.320   5.1888e-02
   4_occ:   8.774  0.057  0.248 89.802  0.026  2.320   5.1888e-02
   5_bss:   8.774  0.057  0.248 89.802  0.026  2.320   5.1888e-02
   5_xyz:   7.551  0.047  0.227 82.714  0.024  2.298   5.4048e-02
   5_adp:   7.551  0.047  0.227 82.714  0.024  2.298   5.4048e-02
   5_occ:   7.551  0.047  0.227 82.714  0.024  2.298   5.4048e-02
   5_bss:   7.551  0.047  0.227 82.714  0.024  2.298   5.4048e-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:  94.24   0.00  19.50  90.66   0.00  16.54  94.24   0.00  35.58
   1_occ:  94.24   0.00  19.50  90.66   0.00  16.54  94.24   0.00  35.58
   2_bss:  94.24   0.00  19.50  90.66   0.00  16.54  94.24   0.00  35.58
   2_xyz:  94.24   0.00  19.50  90.66   0.00  16.54  94.24   0.00  35.58
   2_adp: 112.06   0.00  20.23  99.35   0.00  16.17 112.06   0.00  42.34
   2_occ: 112.06   0.00  20.23  99.35   0.00  16.17 112.06   0.00  42.34
   3_bss: 112.06   0.00  20.23  99.35   0.00  16.17 112.06   0.00  42.34
   3_xyz: 112.06   0.00  20.23  99.35   0.00  16.17 112.06   0.00  42.34
   3_adp: 107.39   0.00  18.87  95.76   0.00  14.64 107.39   2.82  41.90
   3_occ: 107.39   0.00  18.87  95.76   0.00  14.64 107.39   2.82  41.90
   4_bss: 107.39   0.00  18.87  95.76   0.00  14.64 107.39   2.82  41.90
   4_xyz: 107.39   0.00  18.87  95.76   0.00  14.64 107.39   2.82  41.90
   4_adp: 118.70   0.00  19.52 118.70   0.00  13.93 110.09   5.15  49.93
   4_occ: 118.70   0.00  19.52 118.70   0.00  13.93 110.09   5.15  49.93
   5_bss: 118.70   0.00  19.52 118.70   0.00  13.93 110.09   5.15  49.93
   5_xyz: 118.70   0.00  19.52 118.70   0.00  13.93 110.09   5.15  49.93
   5_adp: 113.15   0.00  18.23 113.15   0.00  13.17 102.40   5.67  45.78
   5_occ: 113.15   0.00  18.23 113.15   0.00  13.17 102.40   5.67  45.78
   5_bss: 113.16   0.00  18.23 113.16   0.00  13.17 102.40   5.67  45.78
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    2.957    0.017    0.418
   1_adp:    2.957    0.017    0.418
   1_occ:    2.957    0.017    0.418
   2_bss:    2.957    0.017    0.418
   2_xyz:    2.883    0.066    0.694
   2_adp:    2.883    0.066    0.694
   2_occ:    2.883    0.066    0.694
   3_bss:    2.883    0.066    0.694
   3_xyz:    2.827    0.099    0.763
   3_adp:    2.827    0.099    0.763
   3_occ:    2.827    0.099    0.763
   4_bss:    2.827    0.099    0.763
   4_xyz:    2.741    0.100    0.875
   4_adp:    2.741    0.100    0.875
   4_occ:    2.741    0.100    0.875
   5_bss:    2.741    0.100    0.875
   5_xyz:    2.605    0.086    0.939
   5_adp:    2.605    0.086    0.939
   5_occ:    2.605    0.086    0.939
   5_bss:    2.605    0.086    0.939
------------------------------------------------------------------------

CPU time actual refinement: 300.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/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_1078/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1078/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 300.60 
  Macro-tasks:
    bulk solvent and scale       = 37.58  
    individual site refinement   = 125.81 
    weights calculation          = 26.37  
    collect and process          = 5.33   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 195.19 
  Micro-tasks:
    mask                            = 2.62   
    f_calc                          = 97.62  
    alpha_beta                      = 7.03   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 103.93 
    fmodel                         = 5.98   
    r_factors                      = 0.20   
    phase_errors                   = 8.32   
    foms                           = 0.14   
    TOTAL for micro-tasks          = 226.79 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.315 micro seconds
Total CPU time: 5.20 minutes
from_scatterers_fft:    608 calls, 97.38 s
gradients_fft:          553 calls, 92.97 s

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

# Date 2008-01-16 Time 06:21:58 PST -0800 (1200493318.56 s)
Start R-work = 0.4914, R-free = 0.4800 (no bulk solvent and anisotropic scale)
Final R-work = 0.1588, R-free = 0.2048 (no bulk solvent and anisotropic scale)

Start R-work = 0.4846, R-free = 0.4736
Final R-work = 0.1393, R-free = 0.1851