# Date 2008-01-16 Time 06:19:23 PST -0800 (1200493163.27 s)
#phil __OFF__

Command line arguments: "../1101.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1784
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1101

-------------------------------------------------------------------------------
  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: (71.655, 45.9914, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96037
Completeness in resolution range: 0.94729
Completeness with d_max=infinity: 0.944549

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9604

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: (71.655, 45.9914, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96037
Completeness in resolution range: 0.94729
Completeness with d_max=infinity: 0.944549

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1963 [2166/2193]  1954   212   9.8%
  bin  2:  4.1963 -  3.3425 [2091/2111]  1879   212  10.1%
  bin  3:  3.3425 -  2.9235 [2044/2063]  1836   208  10.2%
  bin  4:  2.9235 -  2.6577 [2035/2065]  1839   196   9.6%
  bin  5:  2.6577 -  2.4681 [2041/2060]  1837   204  10.0%
  bin  6:  2.4681 -  2.3232 [2016/2041]  1806   210  10.4%
  bin  7:  2.3232 -  2.2072 [2022/2050]  1816   206  10.2%
  bin  8:  2.2072 -  2.1114 [1988/2024]  1796   192   9.7%
  bin  9:  2.1114 -  2.0303 [1968/2024]  1778   190   9.7%
  bin 10:  2.0303 -  1.9604 [1218/2048]  1089   129  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.43 -     2.12: 16
        2.12 -     2.82: 892
        2.82 -     3.51: 4530
        3.51 -     4.21: 9445
        4.21 -     4.90: 13758
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.428 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.623 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.894 3.120 -x,y-1/2,-z+1/2
  ... (remaining 28636 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_1101/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 = 71.655 45.9914 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4880   r_free= 0.4903   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.289840                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6810 0.99   1410  160 0.3893 0.4035      6.5734      6.6103|
|  2:  4.6810 -  3.7339 0.99   1354  145 0.4286 0.4155      6.8409      6.8207|
|  3:  3.7339 -  3.2673 0.99   1319  145 0.4625 0.4366      6.6898      6.7422|
|  4:  3.2673 -  2.9710 0.99   1331  158 0.4811 0.5029      6.5552      6.5202|
|  5:  2.9710 -  2.7595 0.99   1323  136 0.5136 0.5286       6.378      6.3744|
|  6:  2.7595 -  2.5976 0.99   1299  151 0.5233 0.5157      6.2941      6.2851|
|  7:  2.5976 -  2.4681 0.99   1309  137 0.5265 0.4889      6.2554      6.1987|
|  8:  2.4681 -  2.3611 0.98   1269  151 0.5318 0.5281      6.1736      6.1938|
|  9:  2.3611 -  2.2705 0.98   1294  146 0.5273 0.5431      6.1396      6.1391|
| 10:  2.2705 -  2.1924 1.00   1299  146 0.5274 0.5459      6.0943      6.1155|
| 11:  2.1924 -  2.1240 0.98   1299  137 0.5365 0.5645      6.0543      6.0605|
| 12:  2.1240 -  2.0635 0.98   1264  149 0.5336 0.5934      5.9609      6.0009|
| 13:  2.0635 -  2.0093 0.93   1199  131 0.5398 0.5244       5.883      5.8297|
| 14:  2.0093 -  1.9604 0.49    661   67 0.5519 0.4809      5.8383      5.8112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6810  1410   160  0.68  36.02   0.81     0.74      77593.92|
|  2:  4.6810 -  3.7339  1354   145  0.67  37.93   0.89     0.79     120714.97|
|  3:  3.7339 -  3.2673  1319   145  0.54  48.73   0.91     0.73     132504.31|
|  4:  3.2673 -  2.9710  1331   158  0.42  57.91   0.91     0.60     123544.28|
|  5:  2.9710 -  2.7595  1323   136  0.31  66.93   0.86     0.45      97664.83|
|  6:  2.7595 -  2.5976  1299   151  0.29  68.40   0.88     0.42      83713.45|
|  7:  2.5976 -  2.4681  1309   137  0.29  68.18   0.90     0.41      71122.71|
|  8:  2.4681 -  2.3611  1269   151  0.32  66.04   0.88     0.47      62530.55|
|  9:  2.3611 -  2.2705  1294   146  0.30  67.60   0.91     0.44      57743.00|
| 10:  2.2705 -  2.1924  1299   146  0.24  71.95   0.92     0.37      56137.40|
| 11:  2.1924 -  2.1240  1299   137  0.17  77.64   0.95     0.26      55599.61|
| 12:  2.1240 -  2.0635  1264   149  0.17  77.78   0.93     0.27      50171.60|
| 13:  2.0635 -  2.0093  1199   131  0.21  74.13   0.92     0.35      41330.95|
| 14:  2.0093 -  1.9604   661    67  0.32  66.23   0.92     0.49      31526.36|
|alpha:            min =        0.26 max =            0.79 mean =         0.49|
|beta:             min =    31526.36 max =       132504.31 mean =     78057.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.77|
|phase err.(test): min =        0.00 max =           89.99 mean =        63.05|
|-----------------------------------------------------------------------------|

============================== 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 = 13.715435             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.723   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.947562              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.519   (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 |  1.428 -  1.775:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.775 -  2.122:       14 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.122 -  2.469:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.469 -  2.817:      848 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.817 -  3.164:     2090 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.164 -  3.511:     2440 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.511 -  3.858:     4642 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.858 -  4.206:     4803 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6256 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7502 |
|-----------------------------------------------------------------------------|
|-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 |        0.182 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.428 |       0.495 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4880   r_free= 0.4903   ksol= 0.00   Bsol= 0.00   scale= 0.884    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.289840                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4810   r_free= 0.4846   ksol= 0.30   Bsol= 20.00   scale= 0.920   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,0.93,0.59,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.287981                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.404330             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.843   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.634317              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.178   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4810      final r-factor (work) = 0.3930          |
| start r-factor (free) = 0.4846      final r-factor (free) = 0.4277          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8704 = 10.40 * 0.50 * 6.2835 + 1.00 * 0.1824                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.4126 = 10.40 * 0.50 * 6.2068 + 1.00 * 0.1236                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3930      final r-factor (work) = 0.3560          |
| start r-factor (free) = 0.4277      final r-factor (free) = 0.4353          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1501 = 1.63 * 1.00 * 6.2068 + 1.00 * 0.0061                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0250 = 1.63 * 1.00 * 6.1198 + 1.00 * 0.0234                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.84  19.97    None  None   None       |
|    all(noH): 2823   0      0.00    107.84  19.97    None  None   None       |
|    Sol.    : 438    0      0.00    107.84  36.80    None  None   None       |
|    Mac.    : 2385   0      0.00    89.65   16.88    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 -  10.784:  909   |   5:    53.921 -  64.706:   65        |
|      1:    10.784 -  21.569:  889   |   6:    64.706 -  75.490:   29        |
|      2:    21.569 -  32.353:  522   |   7:    75.490 -  86.274:   11        |
|      3:    32.353 -  43.137:  251   |   8:    86.274 -  97.058:    5        |
|      4:    43.137 -  53.921:  140   |   9:    97.058 - 107.843:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3560 r_free = 0.4353             target_work(ml) = 6.122         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3553 r_free = 0.4351             target_work(ml) = 6.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3553   r_free= 0.4351   ksol= 0.30   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,0.93,0.59,0.00,0.00,0.00); trace/3= 0.48                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.121082                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3555   r_free= 0.4343   ksol= 0.34   Bsol= 53.19   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,0.13,0.58,0.00,0.00,0.00); trace/3= 0.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.121921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.081377             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.146   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.847567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.504  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3555      final r-factor (work) = 0.2785          |
| start r-factor (free) = 0.4343      final r-factor (free) = 0.3529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.0353 = 11.08 * 0.50 * 6.1205 + 1.00 * 0.1236                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.5766 = 11.08 * 0.50 * 6.0423 + 1.00 * 0.0979                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2785      final r-factor (work) = 0.2556          |
| start r-factor (free) = 0.3529      final r-factor (free) = 0.3379          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1457 = 0.85 * 1.00 * 6.0423 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0219 = 0.85 * 1.00 * 5.8959 + 1.00 * 0.0248                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.09  19.18    None  None   None       |
|    all(noH): 2823   0      0.00    108.09  19.18    None  None   None       |
|    Sol.    : 438    0      0.00    108.09  40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    92.91   15.25    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 -  10.809: 1000   |   5:    54.043 -  64.851:   71        |
|      1:    10.809 -  21.617:  944   |   6:    64.851 -  75.660:   35        |
|      2:    21.617 -  32.426:  415   |   7:    75.660 -  86.468:   13        |
|      3:    32.426 -  43.234:  222   |   8:    86.468 -  97.277:    4        |
|      4:    43.234 -  54.043:  115   |   9:    97.277 - 108.085:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2556 r_free = 0.3379             target_work(ml) = 5.876         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2554 r_free = 0.3376             target_work(ml) = 5.875         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2554   r_free= 0.3376   ksol= 0.34   Bsol= 53.19   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,0.13,0.58,0.00,0.00,0.00); trace/3= 0.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.874808                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2556   r_free= 0.3363   ksol= 0.36   Bsol= 65.57   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.94,-0.16,-0.00,-0.00,-0.00); trace/3= -0.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.873617                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.118226              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.490   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.438142              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.881   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2556      final r-factor (work) = 0.2081          |
| start r-factor (free) = 0.3363      final r-factor (free) = 0.2790          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2396 = 4.12 * 0.50 * 5.8966 + 1.00 * 0.0979                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9918 = 4.12 * 0.50 * 5.7965 + 1.00 * 0.0562                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2081      final r-factor (work) = 0.1935          |
| start r-factor (free) = 0.2790      final r-factor (free) = 0.2588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5576 = 0.44 * 1.00 * 5.7965 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4950 = 0.44 * 1.00 * 5.6699 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.45    101.43  18.26    None  None   None       |
|    all(noH): 2823   0      1.45    101.43  18.26    None  None   None       |
|    Sol.    : 438    0      3.76    101.43  42.62    None  None   None       |
|    Mac.    : 2385   0      1.45    91.21   13.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.445 -  11.443: 1223   |   5:    51.435 -  61.433:   98        |
|      1:    11.443 -  21.441:  891   |   6:    61.433 -  71.431:   38        |
|      2:    21.441 -  31.439:  259   |   7:    71.431 -  81.429:   13        |
|      3:    31.439 -  41.437:  149   |   8:    81.429 -  91.427:    6        |
|      4:    41.437 -  51.435:  142   |   9:    91.427 - 101.425:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1935 r_free = 0.2588             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1932 r_free = 0.2577             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1932   r_free= 0.2577   ksol= 0.36   Bsol= 65.57   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,-0.94,-0.16,-0.00,-0.00,-0.00); trace/3= -0.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.631318                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1931   r_free= 0.2567   ksol= 0.33   Bsol= 56.51   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.08,-1.08,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.630090                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.526452              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.748  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389585              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.607  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1931      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.2567      final r-factor (free) = 0.2027          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8955 = 4.53 * 0.50 * 5.6730 + 1.00 * 0.0562                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5807 = 4.53 * 0.50 * 5.5296 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1495      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2027      final r-factor (free) = 0.1885          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1650 = 0.39 * 1.00 * 5.5296 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0980 = 0.39 * 1.00 * 5.3606 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.83    95.36   17.83    None  None   None       |
|    all(noH): 2823   0      0.83    95.36   17.83    None  None   None       |
|    Sol.    : 438    0      5.53    95.36   43.68    None  None   None       |
|    Mac.    : 2385   0      0.83    94.36   13.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.834 -  10.287: 1105   |   5:    48.096 -  57.548:  105        |
|      1:    10.287 -  19.739: 1033   |   6:    57.548 -  67.000:   66        |
|      2:    19.739 -  29.191:  234   |   7:    67.000 -  76.453:   30        |
|      3:    29.191 -  38.643:  121   |   8:    76.453 -  85.905:   10        |
|      4:    38.643 -  48.096:  112   |   9:    85.905 -  95.357:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1379 r_free = 0.1885             target_work(ml) = 5.319         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1377 r_free = 0.1880             target_work(ml) = 5.318         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1880   ksol= 0.33   Bsol= 56.51   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.39,-2.08,-1.08,-0.00,-0.00,-0.00); trace/3= -1.52                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.318211                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1378   r_free= 0.1873   ksol= 0.32   Bsol= 51.23   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.58,-1.56,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.316903                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.302862              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.430  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.141162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1378      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1873      final r-factor (free) = 0.1725          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2398 = 2.30 * 0.50 * 5.3619 + 1.00 * 0.0659                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1353 = 2.30 * 0.50 * 5.2794 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1725      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7548 = 0.14 * 1.00 * 5.2794 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7457 = 0.14 * 1.00 * 5.2309 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.70    99.26   17.04    None  None   None       |
|    all(noH): 2823   0      1.70    99.26   17.04    None  None   None       |
|    Sol.    : 438    0      6.23    99.26   40.01    None  None   None       |
|    Mac.    : 2385   0      1.70    91.05   12.82    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.695 -  11.452: 1358   |   5:    50.479 -  60.236:   76        |
|      1:    11.452 -  21.209:  881   |   6:    60.236 -  69.992:   37        |
|      2:    21.209 -  30.965:  195   |   7:    69.992 -  79.749:   13        |
|      3:    30.965 -  40.722:  134   |   8:    79.749 -  89.506:    4        |
|      4:    40.722 -  50.479:  123   |   9:    89.506 -  99.262:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1676             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1673             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1673   ksol= 0.32   Bsol= 51.23   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.80,-2.58,-1.56,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.216490                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6810 0.99   1410  160 0.1026 0.1342      5.4062         5.6|
|  2:  4.6810 -  3.7339 0.99   1354  145 0.0928 0.1213      5.5118      5.7475|
|  3:  3.7339 -  3.2673 0.99   1319  145 0.1182 0.1633      5.5602      5.8909|
|  4:  3.2673 -  2.9710 0.99   1331  158 0.1410 0.1726      5.5685      5.6741|
|  5:  2.9710 -  2.7595 0.99   1323  136 0.1493 0.1890      5.3917       5.596|
|  6:  2.7595 -  2.5976 0.99   1299  151 0.1329 0.1684      5.2451      5.4377|
|  7:  2.5976 -  2.4681 0.99   1309  137 0.1408 0.1793      5.2215       5.411|
|  8:  2.4681 -  2.3611 0.98   1269  151 0.1310 0.1866      5.1226      5.4026|
|  9:  2.3611 -  2.2705 0.98   1294  146 0.1276 0.1866      5.0964      5.3517|
| 10:  2.2705 -  2.1924 1.00   1299  146 0.1229 0.1882      5.0127      5.2975|
| 11:  2.1924 -  2.1240 0.98   1299  137 0.1221 0.1940      5.0222      5.3662|
| 12:  2.1240 -  2.0635 0.98   1264  149 0.1233 0.1816      4.9293      5.1479|
| 13:  2.0635 -  2.0093 0.93   1199  131 0.1298 0.1875      4.8781      5.1257|
| 14:  2.0093 -  1.9604 0.49    661   67 0.1188 0.1537      4.7559      4.9636|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6810  1410   160  0.94   9.44   0.98     0.96       7519.92|
|  2:  4.6810 -  3.7339  1354   145  0.95   8.63   1.02     1.01      10158.18|
|  3:  3.7339 -  3.2673  1319   145  0.92  12.65   1.04     1.03      12174.87|
|  4:  3.2673 -  2.9710  1331   158  0.90  15.93   1.01     0.98      12404.62|
|  5:  2.9710 -  2.7595  1323   136  0.90  15.93   1.00     0.99       8347.04|
|  6:  2.7595 -  2.5976  1299   151  0.90  15.98   0.99     0.98       7072.98|
|  7:  2.5976 -  2.4681  1309   137  0.90  15.73   1.00     0.98       6387.86|
|  8:  2.4681 -  2.3611  1269   151  0.90  16.46   0.99     0.97       5714.11|
|  9:  2.3611 -  2.2705  1294   146  0.90  16.58   1.02     0.98       5565.64|
| 10:  2.2705 -  2.1924  1299   146  0.90  16.35   1.01     0.99       4828.65|
| 11:  2.1924 -  2.1240  1299   137  0.89  17.81   1.01     0.96       5127.35|
| 12:  2.1240 -  2.0635  1264   149  0.90  16.90   1.01     1.00       4427.33|
| 13:  2.0635 -  2.0093  1199   131  0.89  17.56   1.02     1.01       3914.53|
| 14:  2.0093 -  1.9604   661    67  0.90  16.40   1.00     0.97       3058.63|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     3058.63 max =        12404.62 mean =      7102.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.05|
|phase err.(test): min =        0.00 max =           88.92 mean =        14.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1673   ksol= 0.32   Bsol= 51.17   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.71,-1.73,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.216460                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1673   ksol= 0.32   Bsol= 51.17   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.71,-1.73,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.216460                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6810 0.99   1410  160 0.1027 0.1339      5.4066      5.5984|
|  2:  4.6810 -  3.7339 0.99   1354  145 0.0927 0.1213      5.5109      5.7471|
|  3:  3.7339 -  3.2673 0.99   1319  145 0.1182 0.1632        5.56      5.8905|
|  4:  3.2673 -  2.9710 0.99   1331  158 0.1410 0.1726      5.5684       5.674|
|  5:  2.9710 -  2.7595 0.99   1323  136 0.1493 0.1890      5.3918      5.5962|
|  6:  2.7595 -  2.5976 0.99   1299  151 0.1329 0.1686      5.2454      5.4384|
|  7:  2.5976 -  2.4681 0.99   1309  137 0.1409 0.1793      5.2218      5.4113|
|  8:  2.4681 -  2.3611 0.98   1269  151 0.1310 0.1867      5.1227      5.4028|
|  9:  2.3611 -  2.2705 0.98   1294  146 0.1276 0.1866      5.0965      5.3518|
| 10:  2.2705 -  2.1924 1.00   1299  146 0.1229 0.1883      5.0127      5.2977|
| 11:  2.1924 -  2.1240 0.98   1299  137 0.1221 0.1939      5.0221      5.3658|
| 12:  2.1240 -  2.0635 0.98   1264  149 0.1233 0.1815      4.9291      5.1475|
| 13:  2.0635 -  2.0093 0.93   1199  131 0.1298 0.1875      4.8782      5.1263|
| 14:  2.0093 -  1.9604 0.49    661   67 0.1188 0.1539       4.756      4.9637|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1245 -  4.6810  1410   160  0.94   9.44   0.98     0.96       7516.46|
|  2:  4.6810 -  3.7339  1354   145  0.95   8.62   1.02     1.01      10145.54|
|  3:  3.7339 -  3.2673  1319   145  0.92  12.64   1.03     1.03      12164.77|
|  4:  3.2673 -  2.9710  1331   158  0.90  15.92   1.01     0.97      12397.07|
|  5:  2.9710 -  2.7595  1323   136  0.90  15.93   1.00     0.98       8354.60|
|  6:  2.7595 -  2.5976  1299   151  0.90  15.98   0.99     0.97       7078.16|
|  7:  2.5976 -  2.4681  1309   137  0.90  15.73   0.99     0.97       6393.76|
|  8:  2.4681 -  2.3611  1269   151  0.90  16.46   0.98     0.96       5717.02|
|  9:  2.3611 -  2.2705  1294   146  0.90  16.58   1.01     0.97       5568.80|
| 10:  2.2705 -  2.1924  1299   146  0.90  16.35   1.00     0.98       4829.29|
| 11:  2.1924 -  2.1240  1299   137  0.89  17.81   1.00     0.95       5127.83|
| 12:  2.1240 -  2.0635  1264   149  0.90  16.89   1.00     0.99       4424.19|
| 13:  2.0635 -  2.0093  1199   131  0.89  17.56   1.01     1.00       3913.10|
| 14:  2.0093 -  1.9604   661    67  0.90  16.39   0.99     0.96       3058.59|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3058.59 max =        12397.07 mean =      7101.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.04|
|phase err.(test): min =        0.00 max =           88.96 mean =        14.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    99.20   16.98    None  None   None       |
|    all(noH): 2823   0      1.63    99.20   16.98    None  None   None       |
|    Sol.    : 438    0      6.17    99.20   39.95    None  None   None       |
|    Mac.    : 2385   0      1.63    90.99   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.635 -  11.391: 1358   |   5:    50.418 -  60.175:   76        |
|      1:    11.391 -  21.148:  881   |   6:    60.175 -  69.932:   37        |
|      2:    21.148 -  30.905:  195   |   7:    69.932 -  79.688:   13        |
|      3:    30.905 -  40.662:  134   |   8:    79.688 -  89.445:    4        |
|      4:    40.662 -  50.418:  123   |   9:    89.445 -  99.202:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.679 - 5.839
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 326 from: 327
   mapped sites are within: 0.742 - 5.839

peak=    6.044 closest distance to " O   HOH Z   7 " =    1.913
peak=    6.011 closest distance to " NE2 GLN A  11 " =    1.388
peak=    5.873 closest distance to " O   HOH Z 214 " =    1.793
peak=    5.519 closest distance to " O   HOH Z 222 " =    1.251
peak=    5.449 closest distance to " O   HOH Z 144 " =    1.769
peak=    5.427 closest distance to " O   HOH Z 126 " =    2.040
peak=    5.267 closest distance to " CG  PRO A  54 " =    1.366
peak=    5.237 closest distance to " CB  GLN A 223 " =    1.493
peak=    5.184 closest distance to " NH2BARG A 102 " =    1.032
peak=    5.150 closest distance to " O   HOH Z  65 " =    1.167
peak=    5.137 closest distance to " O   HOH Z 278 " =    1.202
peak=    4.958 closest distance to " O   HOH Z  49 " =    1.487
peak=    4.865 closest distance to " O   HOH Z 425 " =    1.661
peak=    4.768 closest distance to " O   HOH Z 183 " =    1.641
peak=    4.752 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.726 closest distance to " CG  PRO A 198 " =    1.377
peak=    4.713 closest distance to " O   HOH Z 221 " =    1.760
peak=    4.697 closest distance to " NH2 ARG A  56 " =    2.024
peak=    4.647 closest distance to " O   HOH Z  63 " =    1.677
peak=    4.612 closest distance to " O   HOH Z 427 " =    1.304
peak=    4.611 closest distance to " O   HOH Z 182 " =    1.468
peak=    4.610 closest distance to " O   HOH Z  97 " =    1.356
peak=    4.583 closest distance to " CB  SER A  63 " =    1.311
peak=    4.566 closest distance to " O   HOH Z 134 " =    1.680
peak=    4.507 closest distance to " O   HOH Z 423 " =    2.024
peak=    4.498 closest distance to " CB  ASN A 148 " =    1.296
peak=    4.458 closest distance to " CB  GLU A 128 " =    0.988
peak=    4.442 closest distance to " CB  SER A   3 " =    1.530
peak=    4.429 closest distance to " O   HOH Z 232 " =    2.252
peak=    4.429 closest distance to " O   HOH Z 403 " =    1.465
peak=    4.416 closest distance to " O   HOH Z 369 " =    2.035
peak=    4.395 closest distance to " O   HOH Z 427 " =    2.210
peak=    4.357 closest distance to " CB  GLU A 152 " =    1.294
peak=    4.347 closest distance to " CG  PRO A  90 " =    1.210
peak=    4.293 closest distance to " O   HOH Z 298 " =    2.046
peak=    4.278 closest distance to " O   HOH Z 313 " =    1.892
peak=    4.265 closest distance to " O   HOH Z 236 " =    2.147
peak=    4.258 closest distance to " O   HOH Z 133 " =    2.423
peak=    4.251 closest distance to " ND2 ASN A 187 " =    1.579
peak=    4.220 closest distance to " CG2 VAL A 257 " =    0.984
peak=    4.218 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.211 closest distance to " O   HOH Z  78 " =    1.594
peak=    4.210 closest distance to " O   HOH Z 193 " =    1.910
peak=    4.206 closest distance to " O   HOH Z 261 " =    2.153
peak=    4.206 closest distance to " O   SER A  87 " =    2.110
peak=    4.204 closest distance to " O   HOH Z 368 " =    1.986
peak=    4.201 closest distance to " O   HOH Z 126 " =    1.498
peak=    4.192 closest distance to " O   HOH Z 130 " =    0.843
peak=    4.189 closest distance to " O   HOH Z 103 " =    0.883
peak=    4.183 closest distance to " O   HOH Z   2 " =    2.116
peak=    4.116 closest distance to " O   HOH Z 272 " =    1.878
peak=    4.108 closest distance to " O   HOH Z 225 " =    1.483
peak=    4.078 closest distance to " O   HOH Z 258 " =    2.197
peak=    4.053 closest distance to " O   HOH Z 234 " =    3.907
peak=    4.053 closest distance to " O   HOH Z  61 " =    1.642
peak=    4.051 closest distance to " O   HOH Z 147 " =    1.365
peak=    4.043 closest distance to " CA  TYR A  30 " =    1.066
peak=    4.042 closest distance to " O   HOH Z   9 " =    2.158
peak=    4.037 closest distance to " CB  ASN A 148 " =    1.770
peak=    4.033 closest distance to " O   HOH Z 139 " =    1.482
peak=    4.028 closest distance to " O   HOH Z 108 " =    2.112
peak=    4.025 closest distance to " O   HOH Z  48 " =    1.721
peak=    4.021 closest distance to " O   HOH Z  68 " =    1.818
peak=    4.014 closest distance to " O   HOH Z 414 " =    1.435
peak=    4.013 closest distance to " CD BLYS A 290 " =    1.091
peak=    3.996 closest distance to " O   HOH Z 411 " =    3.408
peak=    3.994 closest distance to " O   HOH Z 316 " =    3.102
peak=    3.988 closest distance to " O   HOH Z  61 " =    1.604
peak=    3.986 closest distance to " NE AARG A 275 " =    1.562
peak=    3.986 closest distance to " CB  TYR A 169 " =    0.779
peak=    3.961 closest distance to " O   HOH Z 193 " =    1.732
peak=    3.951 closest distance to " O   HOH Z 145 " =    1.678
peak=    3.949 closest distance to " O   HOH Z  37 " =    1.272
peak=    3.935 closest distance to " CB  GLN A 183 " =    1.123
peak=    3.923 closest distance to " O   HOH Z 380 " =    1.890
peak=    3.909 closest distance to " CA  SER A  87 " =    0.913
peak=    3.894 closest distance to " CB  SER A 216 " =    0.908
peak=    3.880 closest distance to " O   HOH Z 417 " =    1.357
peak=    3.874 closest distance to " O   HOH Z   1 " =    1.832
peak=    3.872 closest distance to " O   HOH Z 389 " =    1.964
peak=    3.872 closest distance to " CB  LEU A 300 " =    0.994
peak=    3.871 closest distance to " O   HOH Z 155 " =    1.929
peak=    3.845 closest distance to " N   GLN A 278 " =    0.938
peak=    3.844 closest distance to " O   HOH Z 263 " =    2.346
peak=    3.840 closest distance to " CD BARG A 102 " =    1.249
peak=    3.838 closest distance to " CG1 ILE A  33 " =    1.174
peak=    3.831 closest distance to " O   HOH Z 135 " =    1.661
peak=    3.827 closest distance to " CE3 TRP A 274 " =    2.168
peak=    3.825 closest distance to " O   HOH Z 302 " =    1.519
peak=    3.820 closest distance to " O   HOH Z 260 " =    1.301
peak=    3.808 closest distance to " NZ  LYS A 117 " =    1.323
peak=    3.799 closest distance to " O   HOH Z 217 " =    2.701
peak=    3.787 closest distance to " O   HOH Z 437 " =    2.313
peak=    3.786 closest distance to " CB  ASN A 187 " =    0.937
peak=    3.785 closest distance to " O   HOH Z 186 " =    1.270
peak=    3.776 closest distance to " CG  GLN A  55 " =    1.790
peak=    3.767 closest distance to " OD1BASN A 224 " =    2.222
peak=    3.764 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.758 closest distance to " CB  ARG A 139 " =    1.200
peak=    3.749 closest distance to " O   HOH Z 124 " =    1.266
peak=    3.746 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.743 closest distance to " O   HOH Z  10 " =    1.865
peak=    3.738 closest distance to " NH1AARG A 145 " =    1.056
peak=    3.737 closest distance to " O   HOH Z 211 " =    1.283
peak=    3.736 closest distance to " CG  ARG A 159 " =    0.833
peak=    3.732 closest distance to " O   HOH Z 120 " =    0.957
peak=    3.729 closest distance to " CG  LEU A 167 " =    1.249
peak=    3.726 closest distance to " OG BSER A 258 " =    0.808
peak=    3.720 closest distance to " O   HOH Z 132 " =    2.031
peak=    3.718 closest distance to " O   HOH Z 133 " =    1.595
peak=    3.714 closest distance to " CB  VAL A 265 " =    1.300
peak=    3.701 closest distance to " O   HOH Z 409 " =    1.966
peak=    3.684 closest distance to " O   HOH Z 171 " =    2.637
peak=    3.683 closest distance to " CA  TYR A 186 " =    1.524
peak=    3.683 closest distance to " O   HOH Z 132 " =    1.073
peak=    3.678 closest distance to " OD1 ASN A  69 " =    2.458
peak=    3.677 closest distance to " CA  LEU A 282 " =    1.132
peak=    3.659 closest distance to " O   HOH Z 247 " =    1.367
peak=    3.655 closest distance to " O   HOH Z 390 " =    1.164
peak=    3.655 closest distance to " O   HOH Z 116 " =    1.657
peak=    3.651 closest distance to " O   HOH Z  40 " =    2.238
peak=    3.644 closest distance to " O   HOH Z 373 " =    2.115
peak=    3.636 closest distance to " CB  TRP A 179 " =    1.446
peak=    3.629 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.626 closest distance to " OD2 ASP A 286 " =    2.800
peak=    3.622 closest distance to " O   HOH Z 333 " =    2.555
peak=    3.619 closest distance to " O   HOH Z  59 " =    2.051
peak=    3.616 closest distance to " O   HOH Z 344 " =    1.168
peak=    3.599 closest distance to " O   HOH Z 148 " =    1.711
peak=    3.599 closest distance to " O   HOH Z  88 " =    3.122
peak=    3.593 closest distance to " CB  ALA A  21 " =    1.677
peak=    3.588 closest distance to " CB  MET A  47 " =    1.075
peak=    3.586 closest distance to " CA  ALA A  21 " =    1.150
peak=    3.582 closest distance to " CB  ALA A  34 " =    1.221
peak=    3.578 closest distance to " CZ3 TRP A 123 " =    1.259
peak=    3.570 closest distance to " ND1 HIS A  86 " =    1.824
peak=    3.568 closest distance to " O   HOH Z  44 " =    3.065
peak=    3.562 closest distance to " O   HOH Z 207 " =    2.097
peak=    3.559 closest distance to " O   HOH Z 244 " =    1.614
peak=    3.552 closest distance to " O   HOH Z 380 " =    3.410
peak=    3.550 closest distance to " O   HOH Z 371 " =    1.808
peak=    3.544 closest distance to " CA  ALA A 299 " =    0.931
peak=    3.537 closest distance to " CZ  PHE A 192 " =    0.930
peak=    3.534 closest distance to " O   HOH Z 288 " =    2.011
peak=    3.533 closest distance to " CA  THR A 264 " =    0.775
peak=    3.532 closest distance to " CA  ILE A 234 " =    1.025
peak=    3.531 closest distance to " CA  ASP A 191 " =    0.746
peak=    3.528 closest distance to " ND2 ASN A  60 " =    3.026
peak=    3.526 closest distance to " O   HOH Z 236 " =    1.623
peak=    3.525 closest distance to " O   HOH Z 358 " =    1.374
peak=    3.524 closest distance to " O   HOH Z 175 " =    3.652
peak=    3.517 closest distance to " O   HOH Z 139 " =    2.070
peak=    3.516 closest distance to " CG  GLN A  88 " =    1.033
peak=    3.511 closest distance to " CD  LYS A 166 " =    1.444
peak=    3.508 closest distance to " O   HOH Z 334 " =    2.800
peak=    3.503 closest distance to " CG  GLN A 278 " =    3.876
peak=    3.501 closest distance to " O   HOH Z 362 " =    2.083
peak=    3.501 closest distance to " NE2 GLN A  58 " =    3.342
peak=    3.500 closest distance to " OD1 ASN A 217 " =    1.542
peak=    3.496 closest distance to " CA  GLU A 152 " =    1.233
peak=    3.488 closest distance to " O   HOH Z 352 " =    1.688
peak=    3.484 closest distance to " O   HOH Z 250 " =    1.444
peak=    3.483 closest distance to " CB  LEU A 228 " =    0.964
peak=    3.480 closest distance to " CD2 TRP A 179 " =    2.136
peak=    3.478 closest distance to " N   GLY A 196 " =    1.036
peak=    3.477 closest distance to " O   HOH Z 106 " =    2.384
peak=    3.473 closest distance to " O   HOH Z 209 " =    2.398
peak=    3.472 closest distance to " N   PHE A 130 " =    1.199
peak=    3.467 closest distance to " CD1 ILE A  33 " =    1.612
peak=    3.467 closest distance to " O   HOH Z 413 " =    1.593
peak=    3.463 closest distance to " CB  THR A 157 " =    1.040
peak=    3.463 closest distance to " O   HOH Z 148 " =    3.432
peak=    3.460 closest distance to " CB  GLU A 236 " =    1.331
peak=    3.454 closest distance to " N   ARG A 156 " =    1.295
peak=    3.452 closest distance to " O   HOH Z 281 " =    4.440
peak=    3.446 closest distance to " CB  TYR A 116 " =    1.081
peak=    3.444 closest distance to " O   HOH Z 344 " =    3.184
peak=    3.437 closest distance to " O   HOH Z 392 " =    1.354
peak=    3.435 closest distance to " CA  ASP A  50 " =    1.081
peak=    3.434 closest distance to " O   PRO A 198 " =    1.555
peak=    3.432 closest distance to " O   HOH Z 271 " =    2.416
peak=    3.430 closest distance to " NH2AARG A 190 " =    1.508
peak=    3.430 closest distance to " NH2 ARG A 219 " =    1.679
peak=    3.427 closest distance to " O   HOH Z 419 " =    2.326
peak=    3.427 closest distance to " NE1 TRP A 274 " =    1.001
peak=    3.425 closest distance to " O   HOH Z 365 " =    5.839
peak=    3.414 closest distance to " O   HOH Z 227 " =    1.688
peak=    3.413 closest distance to " CB  VAL A 202 " =    1.599
peak=    3.408 closest distance to " CB  ASP A 124 " =    0.840
peak=    3.406 closest distance to " O   HOH Z 156 " =    2.750
peak=    3.404 closest distance to " O   HOH Z 195 " =    1.583
peak=    3.403 closest distance to " O   HOH Z 276 " =    1.287
peak=    3.403 closest distance to " CD2 LEU A 255 " =    0.871
peak=    3.395 closest distance to " O   HOH Z 345 " =    1.778
peak=    3.393 closest distance to " N   ALA A   1 " =    1.880
peak=    3.390 closest distance to " O   HOH Z 411 " =    2.179
peak=    3.389 closest distance to " NH2BARG A 190 " =    1.682
peak=    3.387 closest distance to " CA  GLY A 267 " =    1.265
peak=    3.383 closest distance to " OD1 ASP A 231 " =    1.734
peak=    3.381 closest distance to " O   HOH Z  88 " =    2.793
peak=    3.381 closest distance to " O   HOH Z 345 " =    3.516
peak=    3.381 closest distance to " N   TYR A  15 " =    0.962
peak=    3.380 closest distance to " O   HOH Z 180 " =    2.038
peak=    3.377 closest distance to " O   HOH Z 217 " =    1.644
peak=    3.375 closest distance to " O   HOH Z 117 " =    1.432
peak=    3.371 closest distance to " O   GLN A 278 " =    1.359
peak=    3.369 closest distance to " O   ALA A 233 " =    1.791
peak=    3.364 closest distance to " O   HOH Z 141 " =    1.749
peak=    3.364 closest distance to " O   HOH Z  32 " =    2.101
peak=    3.363 closest distance to " O   HOH Z 434 " =    1.409
peak=    3.356 closest distance to " CG  GLN A  77 " =    2.323
peak=    3.356 closest distance to " CB  ARG A 102 " =    0.770
peak=    3.355 closest distance to " O   HOH Z 152 " =    2.436
peak=    3.355 closest distance to " O   HOH Z 410 " =    1.784
peak=    3.354 closest distance to " NZ ALYS A 290 " =    1.058
peak=    3.352 closest distance to " CG  GLU A   2 " =    1.223
peak=    3.349 closest distance to " O   HOH Z   1 " =    1.550
peak=    3.347 closest distance to " CB  SER A 276 " =    1.125
peak=    3.347 closest distance to " CG  GLN A 144 " =    1.025
peak=    3.345 closest distance to " CD1 LEU A 300 " =    1.232
peak=    3.339 closest distance to " O   HOH Z 166 " =    1.243
peak=    3.331 closest distance to " O   HOH Z 303 " =    1.702
peak=    3.330 closest distance to " O   HOH Z 220 " =    1.387
peak=    3.328 closest distance to " O   HOH Z 116 " =    2.969
peak=    3.323 closest distance to " CD  GLN A 240 " =    1.702
peak=    3.323 closest distance to " O   HOH Z 130 " =    2.108
peak=    3.322 closest distance to " O   ASN A 209 " =    1.593
peak=    3.321 closest distance to " CG1 VAL A 153 " =    0.870
peak=    3.320 closest distance to " O   HOH Z 193 " =    2.148
peak=    3.319 closest distance to " CG  PRO A 243 " =    1.075
peak=    3.317 closest distance to " O   HOH Z 119 " =    1.579
peak=    3.316 closest distance to " O   HOH Z 175 " =    2.205
peak=    3.315 closest distance to " CA  SER A  32 " =    1.585
peak=    3.314 closest distance to " O   HOH Z 128 " =    1.950
peak=    3.312 closest distance to " O   HOH Z 151 " =    1.726
peak=    3.309 closest distance to " O   HOH Z 281 " =    2.155
peak=    3.309 closest distance to " CA  LYS A  48 " =    1.415
peak=    3.302 closest distance to " O   HOH Z 383 " =    2.503
peak=    3.298 closest distance to " NE  ARG A  66 " =    3.321
peak=    3.295 closest distance to " O   HOH Z 286 " =    2.398
peak=    3.293 closest distance to " O   HOH Z  73 " =    1.671
peak=    3.292 closest distance to " O   HOH Z 418 " =    1.680
peak=    3.288 closest distance to " OG  SER A  62 " =    2.949
peak=    3.282 closest distance to " NH1 ARG A  56 " =    1.182
peak=    3.281 closest distance to " O   HOH Z  68 " =    2.022
peak=    3.280 closest distance to " CB  LEU A 237 " =    0.808
peak=    3.280 closest distance to " CH2 TRP A 150 " =    1.132
peak=    3.279 closest distance to " O   HOH Z  51 " =    1.835
peak=    3.277 closest distance to " CA  ASN A 215 " =    1.224
peak=    3.270 closest distance to " O   HOH Z  44 " =    1.749
peak=    3.266 closest distance to " O   GLY A 302 " =    1.534
peak=    3.263 closest distance to " NH1 ARG A  14 " =    0.998
peak=    3.262 closest distance to " OG1 THR A 246 " =    3.216
peak=    3.261 closest distance to " O   HOH Z 128 " =    2.051
peak=    3.260 closest distance to " O   HOH Z 371 " =    2.738
peak=    3.258 closest distance to " O   HOH Z 216 " =    1.798
peak=    3.256 closest distance to " CD  GLN A  58 " =    5.645
peak=    3.254 closest distance to " CE BMET A  47 " =    1.363
peak=    3.253 closest distance to " N   ASN A 127 " =    1.464
peak=    3.250 closest distance to " O   HOH Z  50 " =    1.685
peak=    3.249 closest distance to " OH  TYR A 186 " =    1.055
peak=    3.245 closest distance to " O   HOH Z 112 " =    2.558
peak=    3.244 closest distance to " O   TYR A 116 " =    1.408
peak=    3.242 closest distance to " CA  THR A 221 " =    0.904
peak=    3.227 closest distance to " O   HOH Z 213 " =    1.939
peak=    3.220 closest distance to " O   HOH Z 393 " =    1.395
peak=    3.219 closest distance to " CG2 ILE A 151 " =    0.867
peak=    3.219 closest distance to " O   HOH Z 154 " =    1.969
peak=    3.213 closest distance to " CB  ALA A 184 " =    1.087
peak=    3.212 closest distance to " O   HOH Z  59 " =    1.475
peak=    3.209 closest distance to " O   ALA A   1 " =    1.537
peak=    3.209 closest distance to " CE  MET A  93 " =    1.369
peak=    3.207 closest distance to " O   HOH Z 373 " =    1.541
peak=    3.206 closest distance to " CA  PHE A 208 " =    0.914
peak=    3.205 closest distance to " O   HOH Z 158 " =    2.744
peak=    3.204 closest distance to " CA  ALA A 154 " =    0.918
peak=    3.204 closest distance to " O   HOH Z 255 " =    1.598
peak=    3.203 closest distance to " O   ARG A  56 " =    1.739
peak=    3.202 closest distance to " O   HOH Z  88 " =    3.747
peak=    3.201 closest distance to " OD1 ASP A 238 " =    0.888
peak=    3.200 closest distance to " O   HOH Z 295 " =    1.530
peak=    3.196 closest distance to " O   HOH Z 374 " =    2.873
peak=    3.195 closest distance to " O   HOH Z 122 " =    1.606
peak=    3.195 closest distance to " CA  ALA A  51 " =    1.059
peak=    3.186 closest distance to " O   HOH Z 368 " =    3.686
peak=    3.183 closest distance to " N   SER A  62 " =    1.131
peak=    3.182 closest distance to " O   HOH Z 112 " =    1.024
peak=    3.179 closest distance to " N   ASN A  39 " =    1.254
peak=    3.175 closest distance to " O   HOH Z 215 " =    1.421
peak=    3.170 closest distance to " O   GLY A 229 " =    1.594
peak=    3.167 closest distance to " CD  LYS A 119 " =    1.275
peak=    3.167 closest distance to " O   HOH Z 140 " =    1.835
peak=    3.158 closest distance to " CA  VAL A  41 " =    0.972
peak=    3.152 closest distance to " CB  SER A 210 " =    0.806
peak=    3.145 closest distance to " O   HOH Z 296 " =    1.546
peak=    3.142 closest distance to " O   HOH Z 115 " =    1.903
peak=    3.141 closest distance to " C   GLU A 277 " =    1.388
peak=    3.135 closest distance to " O   HOH Z 184 " =    1.982
peak=    3.134 closest distance to " O   HOH Z 394 " =    1.746
peak=    3.131 closest distance to " SD  MET A  93 " =    1.181
peak=    3.130 closest distance to " O   HOH Z 104 " =    1.565
peak=    3.125 closest distance to " CG1 ILE A  49 " =    1.209
peak=    3.125 closest distance to " O   HOH Z 346 " =    1.407
peak=    3.124 closest distance to " CD1 LEU A 228 " =    1.724
peak=    3.123 closest distance to " OG BSER A  99 " =    2.337
peak=    3.122 closest distance to " O   HOH Z 284 " =    1.472
peak=    3.118 closest distance to " O   HOH Z 108 " =    1.702
peak=    3.116 closest distance to " CB  ARG A 190 " =    1.733
peak=    3.115 closest distance to " CB  LYS A 117 " =    1.178
peak=    3.113 closest distance to " ND1 HIS A  81 " =    1.617
peak=    3.109 closest distance to " O   HOH Z 259 " =    2.393
peak=    3.108 closest distance to " CB  ASN A 170 " =    1.353
peak=    3.108 closest distance to " NH2 ARG A 159 " =    1.379
peak=    3.107 closest distance to " CD  ARG A  66 " =    2.210
peak=    3.094 closest distance to " CB  MET A  40 " =    0.872
peak=    3.091 closest distance to " CE AMET A  47 " =    1.347
peak=    3.089 closest distance to " N   CYS A 260 " =    0.742
peak=    3.081 closest distance to " CG  LYS A  76 " =    1.506
peak=    3.078 closest distance to " O   THR A 220 " =    1.502
peak=    3.075 closest distance to " NH2BARG A 145 " =    2.085
peak=    3.074 closest distance to " O   HOH Z 153 " =    3.916
peak=    3.071 closest distance to " CB  ILE A 120 " =    1.313
peak=    3.064 closest distance to " O   PRO A 198 " =    1.350
peak=    3.051 closest distance to " CA  ILE A 106 " =    0.827
peak=    3.046 closest distance to " O   HOH Z   9 " =    1.545
peak=    3.042 closest distance to " N   GLU A   2 " =    1.266

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.222 - 5.656
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 210
   mapped sites are within: 0.735 - 5.656

peak=   -5.204 closest distance to " O   HOH Z 290 " =    1.011
peak=   -4.914 closest distance to " CG  MET A 105 " =    0.965
peak=   -4.719 closest distance to " OE1 GLN A  88 " =    0.910
peak=   -4.557 closest distance to " CD  ARG A  14 " =    3.199
peak=   -4.453 closest distance to " O   HOH Z  65 " =    0.916
peak=   -4.449 closest distance to " O   PRO A 198 " =    1.296
peak=   -4.216 closest distance to " O   HOH Z 377 " =    1.102
peak=   -4.168 closest distance to " OD1 ASN A  39 " =    2.124
peak=   -4.163 closest distance to " O   HOH Z 438 " =    0.805
peak=   -4.159 closest distance to " O   HOH Z 166 " =    1.007
peak=   -4.129 closest distance to " O   HOH Z 124 " =    1.006
peak=   -4.118 closest distance to " CG  GLN A  88 " =    0.841
peak=   -4.093 closest distance to " O   HOH Z  43 " =    1.360
peak=   -4.072 closest distance to " C   ASN A 285 " =    2.336
peak=   -4.067 closest distance to " CB  PRO A 243 " =    2.546
peak=   -4.047 closest distance to " CD2 LEU A 143 " =    2.575
peak=   -4.025 closest distance to " O   HOH Z  76 " =    0.949
peak=   -4.010 closest distance to " O   HOH Z  60 " =    1.562
peak=   -3.994 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.944 closest distance to " O   HOH Z  98 " =    1.937
peak=   -3.925 closest distance to " O   HOH Z 231 " =    1.501
peak=   -3.897 closest distance to " O   HOH Z  28 " =    1.590
peak=   -3.889 closest distance to " O   HOH Z 185 " =    2.362
peak=   -3.889 closest distance to " O   ALA A   1 " =    1.072
peak=   -3.876 closest distance to " O   HOH Z 409 " =    3.394
peak=   -3.872 closest distance to " O   HOH Z 372 " =    2.425
peak=   -3.861 closest distance to " O   HOH Z  97 " =    1.268
peak=   -3.808 closest distance to " O   HOH Z 205 " =    0.864
peak=   -3.789 closest distance to " N   GLN A  58 " =    1.633
peak=   -3.783 closest distance to " O   HOH Z 351 " =    1.271
peak=   -3.774 closest distance to " CA  ASP A  27 " =    2.312
peak=   -3.774 closest distance to " O   HOH Z 388 " =    1.812
peak=   -3.755 closest distance to " CZ  PHE A  59 " =    1.390
peak=   -3.743 closest distance to " CD1 LEU A 101 " =    2.422
peak=   -3.726 closest distance to " CG  ARG A 219 " =    2.316
peak=   -3.709 closest distance to " N   THR A 157 " =    1.576
peak=   -3.703 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.698 closest distance to " CD  LYS A 289 " =    2.468
peak=   -3.692 closest distance to " O   HOH Z  71 " =    0.738
peak=   -3.685 closest distance to " CD2 TYR A 293 " =    1.979
peak=   -3.667 closest distance to " OD1 ASN A 301 " =    1.939
peak=   -3.662 closest distance to " OG  SER A  87 " =    1.188
peak=   -3.655 closest distance to " O   HOH Z  52 " =    1.185
peak=   -3.653 closest distance to " CB  ALA A 291 " =    2.146
peak=   -3.635 closest distance to " CD2 LEU A 237 " =    2.724
peak=   -3.634 closest distance to " OG1 THR A 279 " =    1.524
peak=   -3.618 closest distance to " O   HOH Z  39 " =    1.279
peak=   -3.604 closest distance to " OD2 ASP A 171 " =    1.691
peak=   -3.593 closest distance to " O   HOH Z 404 " =    0.901
peak=   -3.593 closest distance to " CA  GLY A 241 " =    2.174
peak=   -3.590 closest distance to " O   HOH Z 337 " =    0.965
peak=   -3.588 closest distance to " CD1 TRP A 179 " =    0.955
peak=   -3.583 closest distance to " CB  ALA A 248 " =    1.909
peak=   -3.583 closest distance to " O   HOH Z  51 " =    0.989
peak=   -3.580 closest distance to " O   HOH Z 278 " =    1.039
peak=   -3.576 closest distance to " OG  SER A  26 " =    0.832
peak=   -3.574 closest distance to " OG ASER A 134 " =    1.185
peak=   -3.569 closest distance to " O   VAL A 189 " =    2.401
peak=   -3.562 closest distance to " O   HOH Z 385 " =    0.964
peak=   -3.538 closest distance to " O   PRO A 243 " =    2.329
peak=   -3.537 closest distance to " N   HIS A 115 " =    2.023
peak=   -3.532 closest distance to " O   HOH Z 137 " =    1.274
peak=   -3.532 closest distance to " CB  CYS A 201 " =    2.379
peak=   -3.528 closest distance to " OG BSER A 134 " =    1.422
peak=   -3.521 closest distance to " OD1 ASP A 191 " =    1.870
peak=   -3.520 closest distance to " O   HOH Z 298 " =    1.146
peak=   -3.517 closest distance to " CE  LYS A 166 " =    1.026
peak=   -3.516 closest distance to " CE2 TYR A  30 " =    2.678
peak=   -3.516 closest distance to " CD2 LEU A 237 " =    2.284
peak=   -3.509 closest distance to " O   HOH Z  20 " =    2.500
peak=   -3.507 closest distance to " O   HOH Z 266 " =    4.336
peak=   -3.498 closest distance to " CZ3 TRP A 123 " =    1.519
peak=   -3.475 closest distance to " CB  PHE A 283 " =    2.614
peak=   -3.468 closest distance to " O   HOH Z  13 " =    1.244
peak=   -3.468 closest distance to " O   HOH Z  24 " =    1.392
peak=   -3.462 closest distance to " ND2 ASN A  45 " =    0.984
peak=   -3.461 closest distance to " OG  SER A  97 " =    2.160
peak=   -3.449 closest distance to " CE  LYS A  76 " =    2.877
peak=   -3.447 closest distance to " O   HOH Z 275 " =    1.534
peak=   -3.446 closest distance to " CD  ARG A 156 " =    1.991
peak=   -3.416 closest distance to " N   GLN A 122 " =    1.520
peak=   -3.415 closest distance to " CD2 LEU A 237 " =    2.507
peak=   -3.400 closest distance to " OE1 GLN A  11 " =    0.866
peak=   -3.400 closest distance to " O   HOH Z 247 " =    1.387
peak=   -3.399 closest distance to " O   HOH Z 102 " =    1.887
peak=   -3.396 closest distance to " O   VAL A 174 " =    2.166
peak=   -3.395 closest distance to " O   HOH Z 211 " =    1.743
peak=   -3.384 closest distance to " O   SER A  62 " =    2.356
peak=   -3.383 closest distance to " CA  GLY A 133 " =    2.005
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.242
peak=   -3.381 closest distance to " OXT GLY A 302 " =    3.105
peak=   -3.375 closest distance to " O   HOH Z 113 " =    2.533
peak=   -3.375 closest distance to " O   HOH Z 426 " =    2.078
peak=   -3.372 closest distance to " CD  GLN A  58 " =    1.105
peak=   -3.363 closest distance to " O   HOH Z 409 " =    5.542
peak=   -3.358 closest distance to " O   GLN A 194 " =    1.278
peak=   -3.354 closest distance to " O   HOH Z 213 " =    1.019
peak=   -3.353 closest distance to " N   ALA A  43 " =    2.317
peak=   -3.346 closest distance to " O   VAL A  67 " =    2.671
peak=   -3.346 closest distance to " CE1 TYR A 169 " =    2.503
peak=   -3.328 closest distance to " NH1 ARG A 195 " =    2.201
peak=   -3.327 closest distance to " CB  TRP A  85 " =    2.332
peak=   -3.327 closest distance to " CG  PRO A 163 " =    2.366
peak=   -3.326 closest distance to " O   ALA A 180 " =    1.213
peak=   -3.325 closest distance to " O   SER A 135 " =    1.494
peak=   -3.323 closest distance to " OE1 GLN A 223 " =    2.628
peak=   -3.320 closest distance to " O   HOH Z  97 " =    0.796
peak=   -3.315 closest distance to " O   HOH Z 152 " =    4.885
peak=   -3.315 closest distance to " CZ  TYR A 169 " =    1.838
peak=   -3.313 closest distance to " O   HOH Z 432 " =    3.853
peak=   -3.313 closest distance to " CB  ASP A  27 " =    2.463
peak=   -3.304 closest distance to " OG BSER A 134 " =    1.648
peak=   -3.303 closest distance to " C   ARG A 190 " =    1.095
peak=   -3.300 closest distance to " O   HOH Z 403 " =    0.735
peak=   -3.299 closest distance to " N   ALA A   1 " =    1.233
peak=   -3.298 closest distance to " O   HOH Z 222 " =    1.288
peak=   -3.296 closest distance to " CD1 LEU A 255 " =    2.967
peak=   -3.289 closest distance to " C   GLY A  13 " =    1.050
peak=   -3.285 closest distance to " OG  SER A 245 " =    0.988
peak=   -3.284 closest distance to " O   HOH Z 412 " =    4.992
peak=   -3.283 closest distance to " O   HOH Z 209 " =    2.648
peak=   -3.282 closest distance to " C   PHE A  59 " =    1.260
peak=   -3.279 closest distance to " O   TRP A  70 " =    1.417
peak=   -3.279 closest distance to " O   HOH Z 211 " =    0.920
peak=   -3.271 closest distance to " O   HOH Z 410 " =    2.274
peak=   -3.270 closest distance to " CG  GLU A 152 " =    0.750
peak=   -3.264 closest distance to " O   PRO A 198 " =    1.138
peak=   -3.259 closest distance to " O   HOH Z 298 " =    2.551
peak=   -3.258 closest distance to " O   PRO A 163 " =    1.856
peak=   -3.249 closest distance to " CB  PRO A  54 " =    2.392
peak=   -3.248 closest distance to " CD  GLN A 223 " =    1.103
peak=   -3.248 closest distance to " CA  GLY A 203 " =    2.079
peak=   -3.245 closest distance to " OD1 ASN A 170 " =    2.163
peak=   -3.244 closest distance to " O   HOH Z 384 " =    3.142
peak=   -3.244 closest distance to " CA  TYR A 247 " =    1.442
peak=   -3.234 closest distance to " O   HOH Z 111 " =    2.337
peak=   -3.232 closest distance to " OD1 ASN A 148 " =    1.741
peak=   -3.231 closest distance to " NH2 ARG A  79 " =    1.816
peak=   -3.231 closest distance to " CG  GLN A 223 " =    1.823
peak=   -3.225 closest distance to " CG1 VAL A  78 " =    2.357
peak=   -3.223 closest distance to " O   HOH Z 140 " =    4.453
peak=   -3.216 closest distance to " O   HOH Z 317 " =    2.434
peak=   -3.215 closest distance to " O   HOH Z 414 " =    1.523
peak=   -3.215 closest distance to " O   HOH Z 221 " =    1.773
peak=   -3.213 closest distance to " O   ALA A 161 " =    1.743
peak=   -3.209 closest distance to " O   HOH Z 111 " =    0.817
peak=   -3.206 closest distance to " NH2AARG A 275 " =    5.656
peak=   -3.203 closest distance to " O   HOH Z  90 " =    2.705
peak=   -3.200 closest distance to " N   ALA A   1 " =    3.070
peak=   -3.198 closest distance to " CG  GLU A 152 " =    2.218
peak=   -3.194 closest distance to " O   HOH Z 234 " =    4.327
peak=   -3.194 closest distance to " CG2 THR A  29 " =    2.291
peak=   -3.191 closest distance to " C   LEU A 143 " =    1.488
peak=   -3.187 closest distance to " O   HOH Z 212 " =    0.804
peak=   -3.185 closest distance to " CD  GLU A 277 " =    0.794
peak=   -3.184 closest distance to " CB  ALA A 227 " =    2.357
peak=   -3.182 closest distance to " CE  MET A  93 " =    1.047
peak=   -3.182 closest distance to " CB  PHE A 192 " =    1.654
peak=   -3.181 closest distance to " O   HOH Z 390 " =    2.409
peak=   -3.181 closest distance to " O   HOH Z 417 " =    2.672
peak=   -3.180 closest distance to " O   HOH Z 436 " =    0.867
peak=   -3.180 closest distance to " CZ2 TRP A 179 " =    2.250
peak=   -3.177 closest distance to " CE2 TYR A 186 " =    1.805
peak=   -3.177 closest distance to " O   HOH Z 368 " =    2.540
peak=   -3.175 closest distance to " O   HOH Z  88 " =    2.126
peak=   -3.173 closest distance to " O   HOH Z 130 " =    0.785
peak=   -3.169 closest distance to " O   HOH Z 208 " =    0.863
peak=   -3.163 closest distance to " O   HOH Z 103 " =    2.375
peak=   -3.157 closest distance to " O   HOH Z 148 " =    2.566
peak=   -3.155 closest distance to " CA  SER A 146 " =    2.307
peak=   -3.145 closest distance to " O   VAL A 153 " =    2.405
peak=   -3.144 closest distance to " CD  GLN A 223 " =    1.428
peak=   -3.140 closest distance to " O   HOH Z  22 " =    2.471
peak=   -3.140 closest distance to " O   HOH Z 198 " =    1.560
peak=   -3.138 closest distance to " OG1 THR A 246 " =    1.533
peak=   -3.137 closest distance to " O   HOH Z 435 " =    0.752
peak=   -3.137 closest distance to " CD  LYS A 166 " =    2.327
peak=   -3.130 closest distance to " OG  SER A   3 " =    1.455
peak=   -3.129 closest distance to " CA  GLY A  23 " =    2.712
peak=   -3.124 closest distance to " O   HOH Z 120 " =    3.136
peak=   -3.108 closest distance to " N   ASP A 171 " =    2.451
peak=   -3.108 closest distance to " CA  HIS A  86 " =    2.062
peak=   -3.107 closest distance to " O   HOH Z 207 " =    2.058
peak=   -3.105 closest distance to " O   HOH Z 417 " =    2.121
peak=   -3.104 closest distance to " CG1BVAL A  41 " =    2.771
peak=   -3.103 closest distance to " O   HOH Z 414 " =    2.477
peak=   -3.096 closest distance to " N   SER A  12 " =    1.227
peak=   -3.096 closest distance to " O   HOH Z  56 " =    0.803
peak=   -3.093 closest distance to " O   HOH Z 318 " =    1.392
peak=   -3.093 closest distance to " O   HOH Z 389 " =    4.447
peak=   -3.079 closest distance to " CB  ASP A  50 " =    2.418
peak=   -3.078 closest distance to " N   VAL A  72 " =    1.371
peak=   -3.071 closest distance to " O   ILE A  49 " =    1.597
peak=   -3.056 closest distance to " O   SER A  62 " =    1.489
peak=   -3.055 closest distance to " C   HIS A 108 " =    1.228
peak=   -3.054 closest distance to " O   HOH Z 119 " =    4.180
peak=   -3.016 closest distance to " O   HOH Z  52 " =    2.203
peak=   -3.007 closest distance to " O   HOH Z  92 " =    1.260

================= 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    :  0.4880 0.4903   6.289840e+00   6.289699e+00
   1_bss:  0.4810 0.4846   6.287981e+00   6.282698e+00
   1_xyz:  0.3930 0.4277   6.166978e+00   6.217146e+00
   1_adp:  0.3560 0.4353   6.122365e+00   6.225029e+00
   1_occ:  0.3553 0.4351   6.121082e+00   6.224103e+00
   2_bss:  0.3555 0.4343   6.121921e+00   6.222793e+00
   2_xyz:  0.2785 0.3529   5.927231e+00   6.086356e+00
   2_adp:  0.2556 0.3379   5.875706e+00   6.053099e+00
   2_occ:  0.2554 0.3376   5.874808e+00   6.052092e+00
   3_bss:  0.2556 0.3363   5.873617e+00   6.050888e+00
   3_xyz:  0.2081 0.2790   5.697582e+00   5.899483e+00
   3_adp:  0.1935 0.2588   5.633185e+00   5.841610e+00
   3_occ:  0.1932 0.2577   5.631318e+00   5.839485e+00
   4_bss:  0.1931 0.2567   5.630090e+00   5.837380e+00
   4_xyz:  0.1495 0.2027   5.393352e+00   5.628962e+00
   4_adp:  0.1379 0.1885   5.319451e+00   5.557090e+00
   4_occ:  0.1377 0.1880   5.318211e+00   5.555758e+00
   5_bss:  0.1378 0.1873   5.316903e+00   5.553986e+00
   5_xyz:  0.1250 0.1725   5.232407e+00   5.473323e+00
   5_adp:  0.1237 0.1676   5.217692e+00   5.452993e+00
   5_occ:  0.1235 0.1673   5.216490e+00   5.451937e+00
   5_bss:  0.1235 0.1673   5.216460e+00   5.451844e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000  -0.066   0.929   0.591   0.000   0.000   0.000
   1_xyz:  0.300  20.000  -0.066   0.929   0.591   0.000   0.000   0.000
   1_adp:  0.300  20.000  -0.066   0.929   0.591   0.000   0.000   0.000
   1_occ:  0.300  20.000  -0.066   0.929   0.591   0.000   0.000   0.000
   2_bss:  0.344  53.185   0.076   0.132   0.575   0.000   0.000   0.000
   2_xyz:  0.344  53.185   0.076   0.132   0.575   0.000   0.000   0.000
   2_adp:  0.344  53.185   0.076   0.132   0.575   0.000   0.000   0.000
   2_occ:  0.344  53.185   0.076   0.132   0.575   0.000   0.000   0.000
   3_bss:  0.355  65.574  -0.471  -0.937  -0.159  -0.000  -0.000  -0.000
   3_xyz:  0.355  65.574  -0.471  -0.937  -0.159  -0.000  -0.000  -0.000
   3_adp:  0.355  65.574  -0.471  -0.937  -0.159  -0.000  -0.000  -0.000
   3_occ:  0.355  65.574  -0.471  -0.937  -0.159  -0.000  -0.000  -0.000
   4_bss:  0.331  56.510  -1.387  -2.081  -1.080  -0.000  -0.000  -0.000
   4_xyz:  0.331  56.510  -1.387  -2.081  -1.080  -0.000  -0.000  -0.000
   4_adp:  0.331  56.510  -1.387  -2.081  -1.080  -0.000  -0.000  -0.000
   4_occ:  0.331  56.510  -1.387  -2.081  -1.080  -0.000  -0.000  -0.000
   5_bss:  0.321  51.228  -1.796  -2.580  -1.560  -0.000  -0.000  -0.000
   5_xyz:  0.321  51.228  -1.796  -2.580  -1.560  -0.000  -0.000  -0.000
   5_adp:  0.321  51.228  -1.796  -2.580  -1.560  -0.000  -0.000  -0.000
   5_occ:  0.321  51.228  -1.796  -2.580  -1.560  -0.000  -0.000  -0.000
   5_bss:  0.325  51.167  -1.910  -2.706  -1.731  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.802 0.3567  0.4883    78061.952
   1_bss:  62.240 0.3624  0.5087    75499.915
   1_xyz:  49.452 0.5264  0.7262    54609.629
   1_adp:  50.374 0.5141  0.7175    55759.265
   1_occ:  50.345 0.5144  0.7165    55577.961
   2_bss:  50.163 0.5166  0.7163    55279.133
   2_xyz:  37.984 0.6650  0.9034    33820.674
   2_adp:  35.464 0.6952  0.9210    30907.712
   2_occ:  35.435 0.6955  0.9205    30800.982
   3_bss:  35.293 0.6968  0.8962    30508.984
   3_xyz:  28.330 0.7753  0.9728    20386.876
   3_adp:  25.602 0.8055  0.9879    17524.283
   3_occ:  25.521 0.8063  0.9880    17401.937
   4_bss:  25.444 0.8070  0.9533    17263.545
   4_xyz:  19.566 0.8651  0.9897    10544.878
   4_adp:  17.644 0.8837  0.9937     9102.702
   4_occ:  17.605 0.8840  0.9937     9057.064
   5_bss:  17.564 0.8843  0.9771     9003.681
   5_xyz:  15.649 0.9010  0.9856     7429.851
   5_adp:  15.030 0.9068  0.9869     7131.950
   5_occ:  14.997 0.9071  0.9869     7103.811
   5_bss:  14.994 0.9071  0.9799     7102.818
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.8237e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.8237e-01
   1_xyz:   1.507  0.011  0.100 15.866  0.005  4.106   1.2363e-01
   1_adp:   1.507  0.011  0.100 15.866  0.005  4.106   1.2363e-01
   1_occ:   1.507  0.011  0.100 15.866  0.005  4.106   1.2363e-01
   2_bss:   1.507  0.011  0.100 15.866  0.005  4.106   1.2363e-01
   2_xyz:   1.308  0.011  0.093 15.444  0.005  4.108   9.7903e-02
   2_adp:   1.308  0.011  0.093 15.444  0.005  4.108   9.7903e-02
   2_occ:   1.308  0.011  0.093 15.444  0.005  4.108   9.7903e-02
   3_bss:   1.308  0.011  0.093 15.444  0.005  4.108   9.7903e-02
   3_xyz:   0.926  0.006  0.066 14.516  0.003  4.106   5.6213e-02
   3_adp:   0.926  0.006  0.066 14.516  0.003  4.106   5.6213e-02
   3_occ:   0.926  0.006  0.066 14.516  0.003  4.106   5.6213e-02
   4_bss:   0.926  0.006  0.066 14.516  0.003  4.106   5.6213e-02
   4_xyz:   1.070  0.007  0.074 14.726  0.004  4.115   6.5944e-02
   4_adp:   1.070  0.007  0.074 14.726  0.004  4.115   6.5944e-02
   4_occ:   1.070  0.007  0.074 14.726  0.004  4.115   6.5944e-02
   5_bss:   1.070  0.007  0.074 14.726  0.004  4.115   6.5944e-02
   5_xyz:   0.955  0.006  0.067 14.673  0.004  4.110   5.6401e-02
   5_adp:   0.955  0.006  0.067 14.673  0.004  4.110   5.6401e-02
   5_occ:   0.955  0.006  0.067 14.673  0.004  4.110   5.6401e-02
   5_bss:   0.955  0.006  0.067 14.673  0.004  4.110   5.6401e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.428   2.3944e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.428   2.3944e-01
   1_xyz:  10.526  0.080  0.489 88.774  0.031  1.960   8.3520e-02
   1_adp:  10.526  0.080  0.489 88.774  0.031  1.960   8.3520e-02
   1_occ:  10.526  0.080  0.489 88.774  0.031  1.960   8.3520e-02
   2_bss:  10.526  0.080  0.489 88.774  0.031  1.960   8.3520e-02
   2_xyz:  10.501  0.063  0.312 87.704  0.040  2.203   1.0859e-01
   2_adp:  10.501  0.063  0.312 87.704  0.040  2.203   1.0859e-01
   2_occ:  10.501  0.063  0.312 87.704  0.040  2.203   1.0859e-01
   3_bss:  10.501  0.063  0.312 87.704  0.040  2.203   1.0859e-01
   3_xyz:   7.847  0.038  0.248 82.072  0.019  2.253   5.9806e-02
   3_adp:   7.847  0.038  0.248 82.072  0.019  2.253   5.9806e-02
   3_occ:   7.847  0.038  0.248 82.072  0.019  2.253   5.9806e-02
   4_bss:   7.847  0.038  0.248 82.072  0.019  2.253   5.9806e-02
   4_xyz:   7.957  0.043  0.270 84.355  0.029  2.220   4.9263e-02
   4_adp:   7.957  0.043  0.270 84.355  0.029  2.220   4.9263e-02
   4_occ:   7.957  0.043  0.270 84.355  0.029  2.220   4.9263e-02
   5_bss:   7.957  0.043  0.270 84.355  0.029  2.220   4.9263e-02
   5_xyz:   8.043  0.034  0.218 84.350  0.035  2.313   6.8953e-02
   5_adp:   8.043  0.034  0.218 84.350  0.035  2.313   6.8953e-02
   5_occ:   8.043  0.034  0.218 84.350  0.035  2.313   6.8953e-02
   5_bss:   8.043  0.034  0.218 84.350  0.035  2.313   6.8953e-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: 107.84   0.00  19.97  89.65   0.00  16.88 107.84   0.00  36.80
   1_occ: 107.84   0.00  19.97  89.65   0.00  16.88 107.84   0.00  36.80
   2_bss: 107.84   0.00  19.97  89.65   0.00  16.88 107.84   0.00  36.80
   2_xyz: 107.84   0.00  19.97  89.65   0.00  16.88 107.84   0.00  36.80
   2_adp: 108.09   0.00  19.18  92.91   0.00  15.25 108.09   0.00  40.60
   2_occ: 108.09   0.00  19.18  92.91   0.00  15.25 108.09   0.00  40.60
   3_bss: 108.09   0.00  19.18  92.91   0.00  15.25 108.09   0.00  40.60
   3_xyz: 108.09   0.00  19.18  92.91   0.00  15.25 108.09   0.00  40.60
   3_adp: 101.43   1.45  18.26  91.21   1.45  13.79 101.43   3.76  42.62
   3_occ: 101.43   1.45  18.26  91.21   1.45  13.79 101.43   3.76  42.62
   4_bss: 101.43   1.45  18.26  91.21   1.45  13.79 101.43   3.76  42.62
   4_xyz: 101.43   1.45  18.26  91.21   1.45  13.79 101.43   3.76  42.62
   4_adp:  95.36   0.83  17.83  94.36   0.83  13.08  95.36   5.53  43.68
   4_occ:  95.36   0.83  17.83  94.36   0.83  13.08  95.36   5.53  43.68
   5_bss:  95.36   0.83  17.83  94.36   0.83  13.08  95.36   5.53  43.68
   5_xyz:  95.36   0.83  17.83  94.36   0.83  13.08  95.36   5.53  43.68
   5_adp:  99.26   1.70  17.04  91.05   1.70  12.82  99.26   6.23  40.01
   5_occ:  99.26   1.70  17.04  91.05   1.70  12.82  99.26   6.23  40.01
   5_bss:  99.20   1.63  16.98  90.99   1.63  12.76  99.20   6.17  39.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.976    0.015    0.321
   1_adp:    1.976    0.015    0.321
   1_occ:    1.976    0.015    0.321
   2_bss:    1.976    0.015    0.321
   2_xyz:    1.534    0.068    0.569
   2_adp:    1.534    0.068    0.569
   2_occ:    1.534    0.068    0.569
   3_bss:    1.534    0.068    0.569
   3_xyz:    1.687    0.020    0.679
   3_adp:    1.687    0.020    0.679
   3_occ:    1.687    0.020    0.679
   4_bss:    1.687    0.020    0.679
   4_xyz:    1.730    0.074    0.794
   4_adp:    1.730    0.074    0.794
   4_occ:    1.730    0.074    0.794
   5_bss:    1.730    0.074    0.794
   5_xyz:    1.780    0.065    0.819
   5_adp:    1.780    0.065    0.819
   5_occ:    1.780    0.065    0.819
   5_bss:    1.780    0.065    0.819
------------------------------------------------------------------------

CPU time actual refinement: 351.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/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_1101/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1101/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 351.10 
  Macro-tasks:
    bulk solvent and scale       = 45.28  
    individual site refinement   = 138.85 
    weights calculation          = 30.24  
    collect and process          = 6.43   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 220.92 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 113.39 
    alpha_beta                      = 8.18   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 120.03 
    fmodel                         = 7.29   
    r_factors                      = 0.23   
    phase_errors                   = 10.27  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 263.24 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.058 micro seconds
Total CPU time: 6.08 minutes
from_scatterers_fft:    632 calls, 113.00 s
gradients_fft:          577 calls, 107.77 s

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

# Date 2008-01-16 Time 06:25:27 PST -0800 (1200493527.54 s)
Start R-work = 0.4880, R-free = 0.4903 (no bulk solvent and anisotropic scale)
Final R-work = 0.1475, R-free = 0.1894 (no bulk solvent and anisotropic scale)

Start R-work = 0.4810, R-free = 0.4846
Final R-work = 0.1235, R-free = 0.1673