# Date 2008-01-16 Time 05:25:53 PST -0800 (1200489953.34 s)
#phil __OFF__

Command line arguments: "../734.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4240
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 734

-------------------------------------------------------------------------------
  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: (70.6012, 45.7567, 87.6859, 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: 3.27, 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: (70.6012, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.95378
Completeness in resolution range: 0.925144
Completeness with d_max=infinity: 0.922486

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9538

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: (70.6012, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.95378
Completeness in resolution range: 0.925144
Completeness with d_max=infinity: 0.922486

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.1823 [2220/2246]  1997   223  10.0%
  bin  2:  4.1823 -  3.3313 [2146/2166]  1934   212   9.9%
  bin  3:  3.3313 -  2.9137 [2101/2120]  1891   210  10.0%
  bin  4:  2.9137 -  2.6488 [2091/2121]  1875   216  10.3%
  bin  5:  2.6488 -  2.4598 [2088/2107]  1884   204   9.8%
  bin  6:  2.4598 -  2.3153 [2069/2094]  1858   211  10.2%
  bin  7:  2.3153 -  2.1998 [2056/2084]  1847   209  10.2%
  bin  8:  2.1998 -  2.1043 [2033/2069]  1828   205  10.1%
  bin  9:  2.1043 -  2.0235 [2043/2094]  1855   188   9.2%
  bin 10:  2.0235 -  1.9538 [ 742/2073]   661    81  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 34
        2.32 -     2.97: 1778
        2.97 -     3.61: 4584
        3.61 -     4.26: 9184
        4.26 -     4.90: 12804
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.786 3.040 -x+1/2,-y+1,z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28379 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_734/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 = 70.60125 45.75675 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4549   r_free= 0.4558   ksol= 0.00   Bsol= 0.00   scale= 0.896    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.274407                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6656 0.99   1441  158 0.3783 0.3733      6.5861      6.5643|
|  2:  4.6656 -  3.7214 0.99   1389  158 0.3960 0.3812      6.8088      6.7542|
|  3:  3.7214 -  3.2564 0.99   1368  150 0.4221 0.4147      6.6567      6.6579|
|  4:  3.2564 -  2.9611 0.99   1346  155 0.4554 0.4856      6.5234      6.5374|
|  5:  2.9611 -  2.7502 0.99   1353  147 0.4843 0.4573      6.3465      6.3697|
|  6:  2.7502 -  2.5889 0.99   1345  148 0.4830 0.4973        6.25      6.1945|
|  7:  2.5889 -  2.4598 0.99   1339  149 0.4795 0.4773      6.2192      6.1524|
|  8:  2.4598 -  2.3532 0.98   1318  149 0.5036 0.5031      6.1625      6.1549|
|  9:  2.3532 -  2.2629 0.98   1321  145 0.4898 0.5463      6.1077      6.1886|
| 10:  2.2629 -  2.1850 1.00   1342  145 0.5032 0.5295      6.0634      6.0789|
| 11:  2.1850 -  2.1169 0.98   1316  149 0.4905 0.4884      6.0121      6.0245|
| 12:  2.1169 -  2.0565 0.98   1307  142 0.4964 0.4715      5.9208      5.9279|
| 13:  2.0565 -  2.0025 0.88   1170  131 0.5018 0.4960      5.8742      5.8013|
| 14:  2.0025 -  1.9538 0.21    275   33 0.5282 0.4810      5.8599      5.8199|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6656  1441   158  0.72  32.53   0.82     0.77      67903.41|
|  2:  4.6656 -  3.7214  1389   158  0.70  35.08   0.90     0.81     108769.58|
|  3:  3.7214 -  3.2564  1368   150  0.57  45.98   0.93     0.76     118525.59|
|  4:  3.2564 -  2.9611  1346   155  0.47  53.88   0.90     0.66     110885.63|
|  5:  2.9611 -  2.7502  1353   147  0.42  58.46   0.88     0.61      82311.02|
|  6:  2.7502 -  2.5889  1345   148  0.40  59.88   0.90     0.57      69873.10|
|  7:  2.5889 -  2.4598  1339   149  0.40  59.94   0.93     0.56      61700.51|
|  8:  2.4598 -  2.3532  1318   149  0.37  62.32   0.92     0.53      57207.02|
|  9:  2.3532 -  2.2629  1321   145  0.36  62.88   0.93     0.54      54677.22|
| 10:  2.2629 -  2.1850  1342   145  0.36  62.96   0.93     0.54      48156.62|
| 11:  2.1850 -  2.1169  1316   149  0.35  63.68   0.98     0.55      47042.79|
| 12:  2.1169 -  2.0565  1307   142  0.36  63.02   0.94     0.56      40657.26|
| 13:  2.0565 -  2.0025  1170   131  0.36  63.45   0.96     0.59      35565.01|
| 14:  2.0025 -  1.9538   275    33  0.43  57.53   1.01     0.63      27103.49|
|alpha:            min =        0.53 max =            0.81 mean =         0.62|
|beta:             min =    27103.49 max =       118525.59 mean =     69464.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.41|
|phase err.(test): min =        0.00 max =           89.92 mean =        55.89|
|-----------------------------------------------------------------------------|

============================== 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 = 18.300673             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.562   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.720299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.479   (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 |  1.681 -  2.003:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.003 -  2.325:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.325 -  2.647:       74 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.647 -  2.969:     1704 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.969 -  3.290:     1916 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.290 -  3.612:     2668 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.612 -  3.934:     4757 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.934 -  4.256:     4427 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.256 -  4.578:     5840 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.578 -  4.900:     6964 |
|-----------------------------------------------------------------------------|
|-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 |        0.186 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.681 |       0.525 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4549   r_free= 0.4558   ksol= 0.00   Bsol= 0.00   scale= 0.896    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.274407                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4445   r_free= 0.4489   ksol= 0.35   Bsol= 50.00   scale= 0.926   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,2.34,1.16,0.00,0.00,0.00); trace/3= 0.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.268442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.921871             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.474   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.355012              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4445      final r-factor (work) = 0.3484          |
| start r-factor (free) = 0.4489      final r-factor (free) = 0.3978          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.9168 = 14.92 * 0.50 * 6.2634 + 1.00 * 0.1857                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0812 = 14.92 * 0.50 * 6.1552 + 1.00 * 0.1579                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3484      final r-factor (work) = 0.3182          |
| start r-factor (free) = 0.3978      final r-factor (free) = 0.4071          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3465 = 1.36 * 1.00 * 6.1552 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2274 = 1.36 * 1.00 * 6.0574 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.36   18.26    None  None   None       |
|    all(noH): 2823   0      0.00    77.36   18.26    None  None   None       |
|    Sol.    : 438    0      0.00    77.36   36.06    None  None   None       |
|    Mac.    : 2385   0      0.00    67.86   15.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.736:  636   |   5:    38.680 -  46.417:  104        |
|      1:     7.736 -  15.472:  852   |   6:    46.417 -  54.153:   81        |
|      2:    15.472 -  23.208:  552   |   7:    54.153 -  61.889:   48        |
|      3:    23.208 -  30.944:  325   |   8:    61.889 -  69.625:   21        |
|      4:    30.944 -  38.680:  197   |   9:    69.625 -  77.361:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3182 r_free = 0.4071             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3178 r_free = 0.4072             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3178   r_free= 0.4072   ksol= 0.35   Bsol= 50.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,2.34,1.16,0.00,0.00,0.00); trace/3= 0.15                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.066394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3171   r_free= 0.4047   ksol= 0.36   Bsol= 77.05   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,0.34,0.52,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.066023                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.290430              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.100  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.554162              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.401  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3171      final r-factor (work) = 0.2656          |
| start r-factor (free) = 0.4047      final r-factor (free) = 0.3383          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2712 = 8.29 * 0.50 * 6.0584 + 1.00 * 0.1577                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9868 = 8.29 * 0.50 * 6.0083 + 1.00 * 0.0809                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2656      final r-factor (work) = 0.2514          |
| start r-factor (free) = 0.3383      final r-factor (free) = 0.3244          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3488 = 0.55 * 1.00 * 6.0083 + 1.00 * 0.0192                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2773 = 0.55 * 1.00 * 5.8914 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.55   18.17    None  None   None       |
|    all(noH): 2823   0      0.00    81.55   18.17    None  None   None       |
|    Sol.    : 438    0      1.37    81.55   37.91    None  None   None       |
|    Mac.    : 2385   0      0.00    75.36   14.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.155:  701   |   5:    40.775 -  48.930:  109        |
|      1:     8.155 -  16.310:  928   |   6:    48.930 -  57.085:   71        |
|      2:    16.310 -  24.465:  511   |   7:    57.085 -  65.240:   39        |
|      3:    24.465 -  32.620:  268   |   8:    65.240 -  73.395:   14        |
|      4:    32.620 -  40.775:  177   |   9:    73.395 -  81.550:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2514 r_free = 0.3244             target_work(ml) = 5.876         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2513 r_free = 0.3242             target_work(ml) = 5.876         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2513   r_free= 0.3242   ksol= 0.36   Bsol= 77.05   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.48,0.34,0.52,0.00,0.00,0.00); trace/3= -0.21                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.875546                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2515   r_free= 0.3235   ksol= 0.33   Bsol= 69.06   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-0.52,0.39,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.873769                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.738688              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.800  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.209362              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.033  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2515      final r-factor (work) = 0.2070          |
| start r-factor (free) = 0.3235      final r-factor (free) = 0.2712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0933 = 3.74 * 0.50 * 5.8910 + 1.00 * 0.0809                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8922 = 3.74 * 0.50 * 5.7941 + 1.00 * 0.0610                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2070      final r-factor (work) = 0.1908          |
| start r-factor (free) = 0.2712      final r-factor (free) = 0.2583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0196 = 1.21 * 1.00 * 5.7941 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8572 = 1.21 * 1.00 * 5.6568 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.02  19.08    None  None   None       |
|    all(noH): 2823   0      0.00    100.02  19.08    None  None   None       |
|    Sol.    : 438    0      3.49    97.11   46.84    None  None   None       |
|    Mac.    : 2385   0      0.00    100.02  13.98    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 -  10.002: 1064   |   5:    50.009 -  60.011:   84        |
|      1:    10.002 -  20.004:  938   |   6:    60.011 -  70.013:   71        |
|      2:    20.004 -  30.006:  294   |   7:    70.013 -  80.015:   47        |
|      3:    30.006 -  40.008:  173   |   8:    80.015 -  90.017:   20        |
|      4:    40.008 -  50.009:  126   |   9:    90.017 - 100.019:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1908 r_free = 0.2583             target_work(ml) = 5.632         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1907 r_free = 0.2583             target_work(ml) = 5.632         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1907   r_free= 0.2583   ksol= 0.33   Bsol= 69.06   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-0.52,0.39,-0.00,0.00,0.00); trace/3= -0.48                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.632022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1908   r_free= 0.2584   ksol= 0.33   Bsol= 71.33   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-1.39,0.13,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.632226                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.374684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.078  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.232656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.070  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1908      final r-factor (work) = 0.1617          |
| start r-factor (free) = 0.2584      final r-factor (free) = 0.2216          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7791 = 2.37 * 0.50 * 5.6581 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6549 = 2.37 * 0.50 * 5.5622 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1617      final r-factor (work) = 0.1552          |
| start r-factor (free) = 0.2216      final r-factor (free) = 0.2069          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3102 = 0.23 * 1.00 * 5.5622 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2821 = 0.23 * 1.00 * 5.4652 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.75   17.81    None  None   None       |
|    all(noH): 2823   0      0.00    98.75   17.81    None  None   None       |
|    Sol.    : 438    0      5.69    92.68   44.43    None  None   None       |
|    Mac.    : 2385   0      0.00    98.75   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.875: 1082   |   5:    49.377 -  59.252:   90        |
|      1:     9.875 -  19.751: 1047   |   6:    59.252 -  69.128:   63        |
|      2:    19.751 -  29.626:  240   |   7:    69.128 -  79.003:   38        |
|      3:    29.626 -  39.502:  135   |   8:    79.003 -  88.879:   15        |
|      4:    39.502 -  49.377:  109   |   9:    88.879 -  98.754:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1552 r_free = 0.2069             target_work(ml) = 5.433         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1550 r_free = 0.2067             target_work(ml) = 5.432         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1550   r_free= 0.2067   ksol= 0.33   Bsol= 71.33   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-1.39,0.13,-0.00,0.00,0.00); trace/3= -0.96                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.432015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2065   ksol= 0.33   Bsol= 71.33   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.05,-0.21,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.431342                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.035221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.395  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.669566              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.582  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1552      final r-factor (work) = 0.1361          |
| start r-factor (free) = 0.2065      final r-factor (free) = 0.1832          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6129 = 2.04 * 0.50 * 5.4659 + 1.00 * 0.0507                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5201 = 2.04 * 0.50 * 5.3741 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1361      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1832      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9829 = 1.67 * 1.00 * 5.3741 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8437 = 1.67 * 1.00 * 5.2895 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.45  18.03    None  None   None       |
|    all(noH): 2823   0      0.00    101.45  18.03    None  None   None       |
|    Sol.    : 438    0      0.00    99.18   47.29    None  None   None       |
|    Mac.    : 2385   0      0.00    101.45  12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.145: 1193   |   5:    50.726 -  60.871:   90        |
|      1:    10.145 -  20.290:  971   |   6:    60.871 -  71.016:   60        |
|      2:    20.290 -  30.435:  225   |   7:    71.016 -  81.161:   62        |
|      3:    30.435 -  40.580:  115   |   8:    81.161 -  91.306:   17        |
|      4:    40.580 -  50.726:   82   |   9:    91.306 - 101.451:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1312 r_free = 0.1804             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1804             target_work(ml) = 5.281         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1804   ksol= 0.33   Bsol= 71.33   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.91,-2.05,-0.21,-0.00,-0.00,-0.00); trace/3= -1.39                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280855                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6656 0.99   1441  158 0.0998 0.1365      5.4055      5.6463|
|  2:  4.6656 -  3.7214 0.99   1389  158 0.0908 0.1171      5.4956      5.7035|
|  3:  3.7214 -  3.2564 0.99   1368  150 0.1247 0.1656      5.5923      5.8626|
|  4:  3.2564 -  2.9611 0.99   1346  155 0.1511 0.2028      5.6057      5.7724|
|  5:  2.9611 -  2.7502 0.99   1353  147 0.1592 0.2094      5.4751      5.7107|
|  6:  2.7502 -  2.5889 0.99   1345  148 0.1489 0.2153      5.3402      5.5417|
|  7:  2.5889 -  2.4598 0.99   1339  149 0.1461 0.1910      5.2971      5.4751|
|  8:  2.4598 -  2.3532 0.98   1318  149 0.1474 0.2016      5.2336      5.4935|
|  9:  2.3532 -  2.2629 0.98   1321  145 0.1465 0.2131      5.1954      5.4454|
| 10:  2.2629 -  2.1850 1.00   1342  145 0.1321 0.1751      5.0619      5.2734|
| 11:  2.1850 -  2.1169 0.98   1316  149 0.1308 0.2083      5.0564       5.419|
| 12:  2.1169 -  2.0565 0.98   1307  142 0.1373 0.2160      4.9977      5.2741|
| 13:  2.0565 -  2.0025 0.88   1170  131 0.1314 0.1760      4.9081       5.057|
| 14:  2.0025 -  1.9538 0.21    275   33 0.1194 0.1888      4.7909      5.1231|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6656  1441   158  0.93   9.81   0.97     0.94       7809.18|
|  2:  4.6656 -  3.7214  1389   158  0.95   8.51   1.02     1.01      10080.65|
|  3:  3.7214 -  3.2564  1368   150  0.92  13.30   1.04     1.04      12796.30|
|  4:  3.2564 -  2.9611  1346   155  0.89  17.08   1.02     0.99      13886.70|
|  5:  2.9611 -  2.7502  1353   147  0.88  18.80   1.00     0.98      11137.30|
|  6:  2.7502 -  2.5889  1345   148  0.87  19.14   0.99     0.96       9068.19|
|  7:  2.5889 -  2.4598  1339   149  0.88  18.32   1.00     0.96       8193.27|
|  8:  2.4598 -  2.3532  1318   149  0.87  19.17   1.00     0.97       7361.81|
|  9:  2.3532 -  2.2629  1321   145  0.87  19.10   0.99     0.93       6712.81|
| 10:  2.2629 -  2.1850  1342   145  0.88  17.95   1.00     0.97       5431.60|
| 11:  2.1850 -  2.1169  1316   149  0.88  18.67   0.99     0.93       5532.73|
| 12:  2.1169 -  2.0565  1307   142  0.88  18.68   1.00     0.99       5055.56|
| 13:  2.0565 -  2.0025  1170   131  0.87  19.64   0.99     0.97       4390.67|
| 14:  2.0025 -  1.9538   275    33  0.92  15.00   0.99     0.95       3150.29|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3150.29 max =        13886.70 mean =      8249.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        16.65|
|phase err.(test): min =        0.00 max =           89.63 mean =        16.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1803   ksol= 0.33   Bsol= 71.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.13,-0.17,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280696                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1803   ksol= 0.33   Bsol= 71.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.83,-2.13,-0.17,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.280696                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.6656 0.99   1441  158 0.0998 0.1365      5.4055      5.6466|
|  2:  4.6656 -  3.7214 0.99   1389  158 0.0908 0.1171       5.496      5.7038|
|  3:  3.7214 -  3.2564 0.99   1368  150 0.1247 0.1657      5.5926      5.8627|
|  4:  3.2564 -  2.9611 0.99   1346  155 0.1511 0.2028      5.6056      5.7724|
|  5:  2.9611 -  2.7502 0.99   1353  147 0.1592 0.2093      5.4748      5.7104|
|  6:  2.7502 -  2.5889 0.99   1345  148 0.1488 0.2151      5.3396      5.5414|
|  7:  2.5889 -  2.4598 0.99   1339  149 0.1461 0.1911      5.2969      5.4751|
|  8:  2.4598 -  2.3532 0.98   1318  149 0.1474 0.2018      5.2336      5.4939|
|  9:  2.3532 -  2.2629 0.98   1321  145 0.1464 0.2128      5.1955      5.4448|
| 10:  2.2629 -  2.1850 1.00   1342  145 0.1321 0.1751      5.0618      5.2742|
| 11:  2.1850 -  2.1169 0.98   1316  149 0.1307 0.2085      5.0561      5.4197|
| 12:  2.1169 -  2.0565 0.98   1307  142 0.1373 0.2157      4.9976      5.2735|
| 13:  2.0565 -  2.0025 0.88   1170  131 0.1314 0.1757      4.9071      5.0549|
| 14:  2.0025 -  1.9538 0.21    275   33 0.1194 0.1884      4.7884      5.1198|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1096 -  4.6656  1441   158  0.93   9.81   0.97     0.94       7810.80|
|  2:  4.6656 -  3.7214  1389   158  0.95   8.51   1.02     1.01      10084.66|
|  3:  3.7214 -  3.2564  1368   150  0.92  13.31   1.04     1.04      12807.70|
|  4:  3.2564 -  2.9611  1346   155  0.89  17.08   1.02     0.99      13881.55|
|  5:  2.9611 -  2.7502  1353   147  0.88  18.78   1.00     0.98      11128.02|
|  6:  2.7502 -  2.5889  1345   148  0.87  19.13   0.99     0.96       9056.06|
|  7:  2.5889 -  2.4598  1339   149  0.88  18.31   1.00     0.96       8188.72|
|  8:  2.4598 -  2.3532  1318   149  0.87  19.17   1.00     0.97       7361.91|
|  9:  2.3532 -  2.2629  1321   145  0.87  19.11   1.00     0.93       6718.70|
| 10:  2.2629 -  2.1850  1342   145  0.88  17.95   1.00     0.97       5432.22|
| 11:  2.1850 -  2.1169  1316   149  0.88  18.67   0.99     0.93       5534.73|
| 12:  2.1169 -  2.0565  1307   142  0.88  18.68   1.00     0.99       5054.02|
| 13:  2.0565 -  2.0025  1170   131  0.87  19.61   0.99     0.97       4378.59|
| 14:  2.0025 -  1.9538   275    33  0.92  14.87   0.98     0.95       3127.85|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3127.85 max =        13881.55 mean =      8247.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.84 mean =        16.64|
|phase err.(test): min =        0.00 max =           89.63 mean =        16.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.759)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.45  18.03    None  None   None       |
|    all(noH): 2823   0      0.00    101.45  18.03    None  None   None       |
|    Sol.    : 438    0      0.00    99.19   47.29    None  None   None       |
|    Mac.    : 2385   0      0.00    101.45  12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  10.148: 1193   |   5:    50.729 -  60.874:   90        |
|      1:    10.148 -  20.293:  971   |   6:    60.874 -  71.019:   60        |
|      2:    20.293 -  30.438:  225   |   7:    71.019 -  81.164:   62        |
|      3:    30.438 -  40.583:  115   |   8:    81.164 -  91.309:   17        |
|      4:    40.583 -  50.729:   82   |   9:    91.309 - 101.454:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 4.368
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 338
   mapped sites are within: 0.709 - 4.368

peak=    7.851 closest distance to " O   HOH Z 390 " =    1.299
peak=    6.858 closest distance to " O   HOH Z 245 " =    1.374
peak=    6.687 closest distance to " O   HOH Z 385 " =    1.534
peak=    5.904 closest distance to " O  BHOH Z  74 " =    1.140
peak=    5.738 closest distance to " O   HOH Z 222 " =    1.488
peak=    5.734 closest distance to " O   HOH Z 417 " =    2.580
peak=    5.709 closest distance to " O   HOH Z 422 " =    1.187
peak=    5.593 closest distance to " O   HOH Z 431 " =    1.592
peak=    5.482 closest distance to " O   HOH Z  77 " =    1.209
peak=    5.463 closest distance to " NE2 GLN A  11 " =    1.370
peak=    5.422 closest distance to " O   HOH Z 375 " =    1.310
peak=    5.290 closest distance to " O   HOH Z 278 " =    1.235
peak=    5.170 closest distance to " O   HOH Z  65 " =    1.557
peak=    5.140 closest distance to " O   HOH Z 287 " =    2.175
peak=    5.056 closest distance to " O   HOH Z 142 " =    2.093
peak=    5.039 closest distance to " O   HOH Z 126 " =    2.055
peak=    4.974 closest distance to " O   HOH Z 419 " =    2.483
peak=    4.907 closest distance to " CG  PRO A  90 " =    1.451
peak=    4.791 closest distance to " CG  PRO A  54 " =    1.465
peak=    4.785 closest distance to " O   HOH Z 139 " =    1.393
peak=    4.776 closest distance to " O   HOH Z  63 " =    1.717
peak=    4.763 closest distance to " O   HOH Z 105 " =    1.302
peak=    4.749 closest distance to " CB  PRO A  54 " =    1.216
peak=    4.743 closest distance to " O   PRO A 198 " =    1.295
peak=    4.735 closest distance to " O   HOH Z 293 " =    1.496
peak=    4.669 closest distance to " O   HOH Z   7 " =    1.779
peak=    4.651 closest distance to " O   HOH Z  69 " =    1.641
peak=    4.643 closest distance to " O   HOH Z 250 " =    2.276
peak=    4.624 closest distance to " O   HOH Z   9 " =    1.762
peak=    4.586 closest distance to " O   HOH Z  49 " =    1.336
peak=    4.583 closest distance to " CB  SER A 216 " =    1.016
peak=    4.581 closest distance to " O   HOH Z  46 " =    1.053
peak=    4.575 closest distance to " O   HOH Z  29 " =    1.336
peak=    4.549 closest distance to " NZ BLYS A 290 " =    1.003
peak=    4.542 closest distance to " O   HOH Z 145 " =    1.897
peak=    4.472 closest distance to " O   HOH Z  39 " =    1.218
peak=    4.453 closest distance to " O   HOH Z 403 " =    1.651
peak=    4.426 closest distance to " O   HOH Z 427 " =    2.174
peak=    4.411 closest distance to " O   HOH Z 414 " =    1.541
peak=    4.395 closest distance to " O   HOH Z 380 " =    2.074
peak=    4.390 closest distance to " CB  GLN A 223 " =    1.555
peak=    4.383 closest distance to " O   HOH Z 425 " =    1.303
peak=    4.376 closest distance to " O   HOH Z  66 " =    1.128
peak=    4.339 closest distance to " CB  ASN A 148 " =    1.488
peak=    4.300 closest distance to " O   HOH Z 276 " =    1.402
peak=    4.292 closest distance to " CB  ARG A 275 " =    1.091
peak=    4.280 closest distance to " N   GLN A 278 " =    1.021
peak=    4.279 closest distance to " O   HOH Z 130 " =    0.891
peak=    4.268 closest distance to " O   HOH Z 424 " =    1.209
peak=    4.260 closest distance to " O   HOH Z 158 " =    1.256
peak=    4.257 closest distance to " CB  SER A   3 " =    1.287
peak=    4.240 closest distance to " O   HOH Z  11 " =    1.122
peak=    4.239 closest distance to " O   HOH Z 371 " =    2.030
peak=    4.196 closest distance to " O   HOH Z 298 " =    2.099
peak=    4.177 closest distance to " N   GLU A   2 " =    1.354
peak=    4.153 closest distance to " O   HOH Z  78 " =    1.756
peak=    4.151 closest distance to " O   HOH Z 414 " =    2.158
peak=    4.146 closest distance to " O   HOH Z 133 " =    1.119
peak=    4.143 closest distance to " CB  SER A  63 " =    1.369
peak=    4.132 closest distance to " O   HOH Z 225 " =    1.721
peak=    4.115 closest distance to " O   HOH Z 359 " =    1.524
peak=    4.096 closest distance to " CB  ALA A 114 " =    1.070
peak=    4.095 closest distance to " O   HOH Z 316 " =    3.113
peak=    4.089 closest distance to " CB  ASN A  39 " =    0.974
peak=    4.062 closest distance to " NH2 ARG A  56 " =    2.049
peak=    4.032 closest distance to " CG  PRO A 198 " =    1.262
peak=    4.024 closest distance to " O   HOH Z 211 " =    1.288
peak=    4.020 closest distance to " O   HOH Z 127 " =    1.027
peak=    4.014 closest distance to " O   HOH Z 214 " =    2.209
peak=    4.007 closest distance to " O   HOH Z 394 " =    1.867
peak=    3.997 closest distance to " O   HOH Z 295 " =    1.119
peak=    3.997 closest distance to " CB  THR A 157 " =    1.157
peak=    3.994 closest distance to " O   HOH Z 361 " =    1.432
peak=    3.981 closest distance to " O   HOH Z 352 " =    1.625
peak=    3.980 closest distance to " O   HOH Z 418 " =    1.062
peak=    3.978 closest distance to " O   HOH Z 427 " =    1.101
peak=    3.974 closest distance to " CG2 ILE A 120 " =    1.119
peak=    3.972 closest distance to " O   HOH Z  91 " =    2.421
peak=    3.972 closest distance to " CA  TYR A  30 " =    1.057
peak=    3.971 closest distance to " NZ  LYS A 117 " =    3.191
peak=    3.965 closest distance to " CG2 THR A 221 " =    1.254
peak=    3.952 closest distance to " O   HOH Z 392 " =    1.353
peak=    3.948 closest distance to " CZ3 TRP A 266 " =    1.135
peak=    3.943 closest distance to " O   HOH Z 437 " =    2.051
peak=    3.939 closest distance to " O   HOH Z 415 " =    1.043
peak=    3.930 closest distance to " CB  ASP A 124 " =    0.961
peak=    3.928 closest distance to " CG2 VAL A 257 " =    0.849
peak=    3.911 closest distance to " CB  GLU A 128 " =    1.085
peak=    3.906 closest distance to " ND2 ASN A  60 " =    2.939
peak=    3.906 closest distance to " O   HOH Z 393 " =    1.325
peak=    3.901 closest distance to " NH1AARG A 145 " =    1.157
peak=    3.893 closest distance to " CG  ARG A 159 " =    0.864
peak=    3.890 closest distance to " CE3 TRP A 274 " =    1.450
peak=    3.884 closest distance to " NZ  LYS A 119 " =    2.351
peak=    3.882 closest distance to " O   HOH Z  59 " =    1.725
peak=    3.877 closest distance to " O   HOH Z 236 " =    1.492
peak=    3.874 closest distance to " CA  ALA A  51 " =    1.077
peak=    3.863 closest distance to " CB  SER A 276 " =    1.220
peak=    3.861 closest distance to " O   HOH Z 119 " =    1.492
peak=    3.860 closest distance to " CG  GLN A  58 " =    1.026
peak=    3.847 closest distance to " CB  TRP A 266 " =    0.990
peak=    3.846 closest distance to " CA  ILE A 234 " =    1.110
peak=    3.842 closest distance to " O   HOH Z  61 " =    1.645
peak=    3.840 closest distance to " CB  PRO A 213 " =    1.309
peak=    3.835 closest distance to " CG  TRP A 179 " =    2.166
peak=    3.820 closest distance to " O   HOH Z 378 " =    1.045
peak=    3.815 closest distance to " C   GLN A  73 " =    1.054
peak=    3.814 closest distance to " O   HOH Z 171 " =    1.863
peak=    3.802 closest distance to " O   HOH Z 416 " =    1.305
peak=    3.796 closest distance to " CG  LEU A 167 " =    1.325
peak=    3.790 closest distance to " OE1 GLN A  77 " =    1.230
peak=    3.773 closest distance to " ND2BASN A 224 " =    0.862
peak=    3.771 closest distance to " O   HOH Z 126 " =    1.451
peak=    3.771 closest distance to " OE1 GLU A   2 " =    2.159
peak=    3.767 closest distance to " CE3 TRP A 150 " =    1.179
peak=    3.762 closest distance to " O   VAL A  72 " =    0.981
peak=    3.747 closest distance to " O   HOH Z 381 " =    1.180
peak=    3.745 closest distance to " O   HOH Z  88 " =    3.562
peak=    3.734 closest distance to " O   HOH Z 193 " =    1.733
peak=    3.728 closest distance to " O   HOH Z  57 " =    1.121
peak=    3.721 closest distance to " O   HOH Z  43 " =    1.214
peak=    3.701 closest distance to " CB  GLN A 183 " =    1.178
peak=    3.692 closest distance to " O   HOH Z 390 " =    2.443
peak=    3.690 closest distance to " O   HOH Z  68 " =    1.950
peak=    3.688 closest distance to " CB  LYS A 290 " =    0.828
peak=    3.682 closest distance to " O   HOH Z 368 " =    3.622
peak=    3.681 closest distance to " O   HOH Z 365 " =    2.509
peak=    3.680 closest distance to " O   HOH Z 201 " =    1.786
peak=    3.679 closest distance to " O   HOH Z 358 " =    1.266
peak=    3.679 closest distance to " O   HOH Z 272 " =    1.802
peak=    3.676 closest distance to " CB  PRO A  90 " =    1.054
peak=    3.676 closest distance to " CA  ARG A 195 " =    1.353
peak=    3.676 closest distance to " CA  ARG A 102 " =    1.089
peak=    3.656 closest distance to " O   HOH Z  92 " =    1.256
peak=    3.650 closest distance to " CD  LYS A 166 " =    1.546
peak=    3.645 closest distance to " CZ  PHE A  38 " =    1.275
peak=    3.645 closest distance to " CB  GLU A 277 " =    3.652
peak=    3.640 closest distance to " CA  LEU A 282 " =    1.111
peak=    3.637 closest distance to " O   HOH Z 103 " =    0.982
peak=    3.617 closest distance to " O   HOH Z 426 " =    1.095
peak=    3.613 closest distance to " O   HOH Z  30 " =    1.907
peak=    3.608 closest distance to " O   HOH Z  44 " =    1.994
peak=    3.605 closest distance to " O   HOH Z 143 " =    1.373
peak=    3.601 closest distance to " O   TYR A 116 " =    1.245
peak=    3.598 closest distance to " CB  SER A 210 " =    0.938
peak=    3.590 closest distance to " CB  ARG A 190 " =    1.802
peak=    3.585 closest distance to " CA  VAL A 125 " =    1.116
peak=    3.569 closest distance to " O   HOH Z 371 " =    3.197
peak=    3.564 closest distance to " O   HOH Z 146 " =    1.648
peak=    3.561 closest distance to " OG BSER A  99 " =    2.312
peak=    3.561 closest distance to " N   TYR A  15 " =    1.141
peak=    3.547 closest distance to " O   HOH Z  58 " =    1.766
peak=    3.541 closest distance to " N   CYS A 260 " =    0.895
peak=    3.537 closest distance to " ND2 ASN A 249 " =    0.781
peak=    3.536 closest distance to " O   HOH Z 147 " =    1.528
peak=    3.535 closest distance to " CG  GLN A  11 " =    2.170
peak=    3.529 closest distance to " N   ALA A   1 " =    1.328
peak=    3.528 closest distance to " O   HOH Z 104 " =    1.581
peak=    3.528 closest distance to " CB  TRP A 150 " =    0.976
peak=    3.527 closest distance to " O   HOH Z 363 " =    1.057
peak=    3.525 closest distance to " O   HOH Z  90 " =    2.266
peak=    3.523 closest distance to " NH2AARG A 190 " =    1.864
peak=    3.522 closest distance to " O   HOH Z 410 " =    1.446
peak=    3.522 closest distance to " CB  GLU A 152 " =    1.256
peak=    3.521 closest distance to " CD  ARG A  66 " =    2.354
peak=    3.513 closest distance to " CB  LEU A 300 " =    0.892
peak=    3.511 closest distance to " CE  LYS A 119 " =    1.287
peak=    3.502 closest distance to " O   HOH Z 411 " =    3.630
peak=    3.499 closest distance to " CA  MET A  40 " =    1.250
peak=    3.498 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.497 closest distance to " O   HOH Z 222 " =    2.187
peak=    3.496 closest distance to " CD  ARG A 159 " =    0.821
peak=    3.490 closest distance to " CB  LEU A 228 " =    1.252
peak=    3.482 closest distance to " CA  ALA A 160 " =    0.952
peak=    3.478 closest distance to " O   HOH Z 244 " =    1.419
peak=    3.477 closest distance to " CE AMET A  47 " =    1.314
peak=    3.475 closest distance to " O   HOH Z 434 " =    1.398
peak=    3.475 closest distance to " NE1 TRP A 274 " =    1.020
peak=    3.469 closest distance to " O   HOH Z 258 " =    2.051
peak=    3.453 closest distance to " O   HOH Z 402 " =    1.557
peak=    3.450 closest distance to " CG  PRO A 243 " =    1.105
peak=    3.442 closest distance to " CA  SER A  95 " =    0.964
peak=    3.435 closest distance to " ND1 HIS A  86 " =    1.858
peak=    3.433 closest distance to " N   ARG A 156 " =    1.227
peak=    3.427 closest distance to " CA  VAL A 121 " =    0.919
peak=    3.427 closest distance to " CB  SER A  99 " =    0.846
peak=    3.420 closest distance to " O   HOH Z 218 " =    1.779
peak=    3.416 closest distance to " O   HOH Z 119 " =    4.195
peak=    3.415 closest distance to " CB  MET A  40 " =    0.782
peak=    3.412 closest distance to " O   HOH Z 233 " =    1.369
peak=    3.409 closest distance to " O   HOH Z 259 " =    2.353
peak=    3.408 closest distance to " O   HOH Z  40 " =    2.208
peak=    3.407 closest distance to " O   HOH Z   7 " =    3.332
peak=    3.400 closest distance to " CB  THR A  31 " =    1.628
peak=    3.399 closest distance to " O   HOH Z 422 " =    2.281
peak=    3.397 closest distance to " CA  GLY A 267 " =    1.173
peak=    3.389 closest distance to " CA  ARG A  36 " =    1.195
peak=    3.387 closest distance to " CB  SER A 273 " =    1.012
peak=    3.385 closest distance to " CD  ARG A 195 " =    3.568
peak=    3.380 closest distance to " CA  ALA A 180 " =    1.261
peak=    3.380 closest distance to " O   HOH Z  97 " =    1.436
peak=    3.376 closest distance to " NE2 GLN A 278 " =    3.718
peak=    3.371 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.368 closest distance to " CA  SER A  87 " =    1.156
peak=    3.368 closest distance to " C   SER A 135 " =    0.762
peak=    3.365 closest distance to " CG  GLN A  89 " =    1.583
peak=    3.364 closest distance to " O   HOH Z 172 " =    2.009
peak=    3.357 closest distance to " CB  LYS A 117 " =    1.271
peak=    3.353 closest distance to " CB  ARG A  79 " =    1.155
peak=    3.352 closest distance to " OG  SER A  26 " =    1.425
peak=    3.347 closest distance to " O   HOH Z 106 " =    3.967
peak=    3.346 closest distance to " CG2 THR A 279 " =    0.919
peak=    3.344 closest distance to " NZ  LYS A 117 " =    1.206
peak=    3.342 closest distance to " O   HOH Z 153 " =    3.669
peak=    3.342 closest distance to " CB  SER A 212 " =    1.336
peak=    3.341 closest distance to " CA  PHE A 283 " =    1.322
peak=    3.340 closest distance to " O   HOH Z 405 " =    1.744
peak=    3.340 closest distance to " O   HOH Z 389 " =    1.816
peak=    3.338 closest distance to " O   HOH Z 130 " =    2.119
peak=    3.332 closest distance to " CB  ASN A 215 " =    1.113
peak=    3.332 closest distance to " CA  ALA A 129 " =    1.219
peak=    3.330 closest distance to " CG2 VAL A 202 " =    1.506
peak=    3.330 closest distance to " CE  MET A  93 " =    1.397
peak=    3.328 closest distance to " CB  LEU A 237 " =    0.822
peak=    3.327 closest distance to " CB  ARG A 219 " =    0.831
peak=    3.325 closest distance to " CG2 VAL A 232 " =    1.159
peak=    3.324 closest distance to " O   HOH Z 368 " =    1.788
peak=    3.323 closest distance to " CB  ALA A  43 " =    0.859
peak=    3.321 closest distance to " OE2 GLU A  53 " =    2.020
peak=    3.319 closest distance to " N   VAL A 125 " =    1.460
peak=    3.319 closest distance to " O   THR A  52 " =    1.909
peak=    3.316 closest distance to " O   HOH Z 132 " =    2.303
peak=    3.312 closest distance to " CG  GLU A 277 " =    2.000
peak=    3.310 closest distance to " O   HOH Z  51 " =    1.857
peak=    3.310 closest distance to " NZ  LYS A 119 " =    1.418
peak=    3.308 closest distance to " O   HOH Z 373 " =    1.528
peak=    3.307 closest distance to " CG2 ILE A  20 " =    1.580
peak=    3.306 closest distance to " O   HOH Z 296 " =    1.099
peak=    3.304 closest distance to " CB  TYR A 116 " =    1.223
peak=    3.290 closest distance to " OG BSER A 164 " =    2.236
peak=    3.289 closest distance to " CB  ASP A 140 " =    0.965
peak=    3.289 closest distance to " O   HOH Z 148 " =    2.204
peak=    3.289 closest distance to " O   HOH Z 284 " =    1.412
peak=    3.279 closest distance to " CB  ALA A 114 " =    1.495
peak=    3.275 closest distance to " CD  ARG A  66 " =    2.314
peak=    3.274 closest distance to " CA  MET A 105 " =    0.886
peak=    3.273 closest distance to " O   HOH Z 424 " =    2.952
peak=    3.271 closest distance to " C   GLU A 277 " =    1.270
peak=    3.269 closest distance to " CA  TYR A 116 " =    1.502
peak=    3.268 closest distance to " N   VAL A  72 " =    1.671
peak=    3.267 closest distance to " N   SER A  97 " =    0.872
peak=    3.262 closest distance to " CA  ASN A 127 " =    1.080
peak=    3.260 closest distance to " CB  PHE A 130 " =    1.075
peak=    3.257 closest distance to " O   ASN A 142 " =    1.071
peak=    3.256 closest distance to " OD2 ASP A 286 " =    2.491
peak=    3.254 closest distance to " O   HOH Z 290 " =    0.999
peak=    3.253 closest distance to " CB  PHE A 225 " =    1.368
peak=    3.253 closest distance to " CB  ASP A 171 " =    0.852
peak=    3.253 closest distance to " CG  LYS A  76 " =    1.872
peak=    3.252 closest distance to " O   HOH Z 425 " =    2.205
peak=    3.251 closest distance to " CB  VAL A 265 " =    1.296
peak=    3.249 closest distance to " O   HOH Z 189 " =    2.870
peak=    3.247 closest distance to " CA  GLY A 196 " =    0.956
peak=    3.247 closest distance to " CG2BVAL A  41 " =    1.018
peak=    3.243 closest distance to " CD  ARG A 138 " =    0.830
peak=    3.241 closest distance to " CD BLYS A 290 " =    1.057
peak=    3.240 closest distance to " O   HOH Z 248 " =    1.787
peak=    3.238 closest distance to " C   VAL A 153 " =    1.077
peak=    3.231 closest distance to " CG1 VAL A 189 " =    1.353
peak=    3.230 closest distance to " CZ  PHE A 218 " =    1.183
peak=    3.228 closest distance to " CB  ARG A 138 " =    0.911
peak=    3.225 closest distance to " O   HOH Z 423 " =    1.598
peak=    3.224 closest distance to " CB  ALA A 292 " =    0.935
peak=    3.223 closest distance to " O   HOH Z 207 " =    2.336
peak=    3.223 closest distance to " N   ALA A   1 " =    2.677
peak=    3.222 closest distance to " O   THR A 294 " =    1.040
peak=    3.218 closest distance to " O   HOH Z 180 " =    2.314
peak=    3.216 closest distance to " O   HOH Z 357 " =    2.096
peak=    3.214 closest distance to " CG2 THR A 178 " =    1.162
peak=    3.211 closest distance to " O   HOH Z 260 " =    2.431
peak=    3.210 closest distance to " C   GLY A 302 " =    2.613
peak=    3.204 closest distance to " O   HOH Z 431 " =    1.494
peak=    3.204 closest distance to " O   HOH Z 155 " =    1.635
peak=    3.203 closest distance to " CE3 TRP A  85 " =    0.894
peak=    3.203 closest distance to " O   HOH Z 156 " =    2.811
peak=    3.198 closest distance to " O   THR A 220 " =    1.731
peak=    3.192 closest distance to " ND1 HIS A  81 " =    1.659
peak=    3.190 closest distance to " O   HOH Z 215 " =    1.489
peak=    3.188 closest distance to " O   HOH Z 362 " =    1.678
peak=    3.187 closest distance to " OG BSER A 258 " =    0.931
peak=    3.187 closest distance to " CZ3 TRP A 266 " =    0.932
peak=    3.187 closest distance to " O   HOH Z  76 " =    1.135
peak=    3.184 closest distance to " O   HOH Z 213 " =    1.906
peak=    3.182 closest distance to " CA  ILE A 106 " =    0.709
peak=    3.181 closest distance to " CG1 ILE A 120 " =    1.396
peak=    3.180 closest distance to " OD1 ASP A 171 " =    1.301
peak=    3.177 closest distance to " CB  ASP A 272 " =    1.061
peak=    3.174 closest distance to " CB  TRP A 274 " =    1.272
peak=    3.169 closest distance to " O   MET A 105 " =    1.713
peak=    3.166 closest distance to " O   HOH Z 371 " =    1.867
peak=    3.164 closest distance to " O   HOH Z 302 " =    1.523
peak=    3.163 closest distance to " O   HOH Z 299 " =    3.014
peak=    3.162 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.160 closest distance to " O   HOH Z 369 " =    1.728
peak=    3.156 closest distance to " O   HOH Z 219 " =    3.689
peak=    3.154 closest distance to " OG BSER A 134 " =    2.664
peak=    3.152 closest distance to " O   HOH Z   1 " =    1.510
peak=    3.147 closest distance to " N   VAL A 296 " =    1.777
peak=    3.145 closest distance to " N   ALA A 292 " =    1.156
peak=    3.137 closest distance to " N   GLN A  73 " =    1.063
peak=    3.136 closest distance to " CE2 PHE A  16 " =    0.826
peak=    3.127 closest distance to " O   HOH Z  27 " =    0.936
peak=    3.126 closest distance to " O   HOH Z 365 " =    1.468
peak=    3.126 closest distance to " CD2 PHE A 204 " =    1.108
peak=    3.125 closest distance to " CG1 VAL A 296 " =    1.216
peak=    3.118 closest distance to " O   HOH Z 145 " =    2.191
peak=    3.118 closest distance to " O   ALA A  71 " =    1.323
peak=    3.116 closest distance to " N   SER A 210 " =    1.052
peak=    3.110 closest distance to " O   HOH Z 412 " =    3.283
peak=    3.108 closest distance to " CB  VAL A 230 " =    0.835
peak=    3.107 closest distance to " CD2 LEU A   5 " =    1.274
peak=    3.105 closest distance to " OG BSER A 212 " =    2.806
peak=    3.102 closest distance to " CB  ASP A 200 " =    0.838
peak=    3.093 closest distance to " O   HOH Z 122 " =    2.068
peak=    3.093 closest distance to " CB  PHE A  61 " =    1.372
peak=    3.090 closest distance to " O   HOH Z 193 " =    1.955
peak=    3.082 closest distance to " NE2 GLN A  58 " =    4.368
peak=    3.072 closest distance to " N   ASN A 127 " =    1.315
peak=    3.065 closest distance to " CD2 LEU A 167 " =    1.110
peak=    3.065 closest distance to " O   HOH Z 344 " =    3.297
peak=    3.063 closest distance to " N   SER A 271 " =    1.132
peak=    3.041 closest distance to " CA  GLY A 136 " =    1.045
peak=    3.028 closest distance to " O   HOH Z  22 " =    1.232

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.797 - 4.965
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.797 - 4.965

peak=   -4.514 closest distance to " O   PRO A 198 " =    1.159
peak=   -4.455 closest distance to " N   THR A 157 " =    1.692
peak=   -4.320 closest distance to " CB  PRO A 243 " =    2.486
peak=   -4.208 closest distance to " O   ALA A  10 " =    1.627
peak=   -4.196 closest distance to " O   HOH Z  60 " =    1.588
peak=   -4.174 closest distance to " O   HOH Z  39 " =    0.894
peak=   -4.164 closest distance to " O   ASP A 191 " =    1.963
peak=   -4.132 closest distance to " OG  SER A  97 " =    2.005
peak=   -4.119 closest distance to " CD  LYS A 166 " =    2.519
peak=   -4.118 closest distance to " O   HOH Z 313 " =    1.125
peak=   -4.114 closest distance to " O   HOH Z  28 " =    1.180
peak=   -4.066 closest distance to " CD  ARG A  14 " =    3.333
peak=   -4.059 closest distance to " CG  MET A 105 " =    0.998
peak=   -4.050 closest distance to " O   HOH Z 385 " =    1.356
peak=   -4.007 closest distance to " CB  GLN A  55 " =    1.221
peak=   -3.947 closest distance to " OE1 GLU A  44 " =    1.962
peak=   -3.928 closest distance to " O   HOH Z 185 " =    2.012
peak=   -3.907 closest distance to " CB  ALA A 291 " =    2.115
peak=   -3.848 closest distance to " O   SER A  22 " =    2.722
peak=   -3.846 closest distance to " O   SER A 135 " =    1.576
peak=   -3.822 closest distance to " CE2 TYR A  30 " =    2.617
peak=   -3.808 closest distance to " O   HOH Z 298 " =    2.565
peak=   -3.800 closest distance to " N   ALA A  43 " =    2.577
peak=   -3.796 closest distance to " O   HOH Z 415 " =    1.073
peak=   -3.780 closest distance to " O   HOH Z  24 " =    1.000
peak=   -3.778 closest distance to " CA  GLY A 241 " =    2.188
peak=   -3.764 closest distance to " CB  ALA A   9 " =    2.398
peak=   -3.749 closest distance to " CD1 TRP A 179 " =    1.157
peak=   -3.748 closest distance to " O   HOH Z  69 " =    1.339
peak=   -3.746 closest distance to " NE2 GLN A  55 " =    0.851
peak=   -3.744 closest distance to " OE1 GLN A 223 " =    2.395
peak=   -3.742 closest distance to " CB  ALA A 131 " =    1.873
peak=   -3.722 closest distance to " OG  SER A  32 " =    0.991
peak=   -3.703 closest distance to " O   HOH Z 131 " =    3.935
peak=   -3.702 closest distance to " CA  HIS A 207 " =    1.210
peak=   -3.700 closest distance to " O   LYS A  76 " =    1.173
peak=   -3.695 closest distance to " OG BSER A 134 " =    1.582
peak=   -3.694 closest distance to " C   ILE A 239 " =    2.076
peak=   -3.683 closest distance to " O   PRO A 163 " =    1.449
peak=   -3.680 closest distance to " O   GLY A  80 " =    2.457
peak=   -3.676 closest distance to " O   HOH Z 163 " =    1.720
peak=   -3.675 closest distance to " N   GLN A  58 " =    1.257
peak=   -3.667 closest distance to " O   PHE A 218 " =    1.553
peak=   -3.647 closest distance to " CD1 LEU A 101 " =    2.219
peak=   -3.645 closest distance to " NE2 GLN A 223 " =    1.755
peak=   -3.641 closest distance to " O   HOH Z 351 " =    1.605
peak=   -3.641 closest distance to " CA  GLY A  98 " =    1.733
peak=   -3.635 closest distance to " CA  GLY A 133 " =    2.063
peak=   -3.630 closest distance to " OG  SER A 245 " =    1.416
peak=   -3.621 closest distance to " OG  SER A  63 " =    1.355
peak=   -3.608 closest distance to " O   HOH Z 266 " =    4.965
peak=   -3.606 closest distance to " O   HOH Z 111 " =    1.864
peak=   -3.594 closest distance to " CB  ASP A  27 " =    2.474
peak=   -3.578 closest distance to " CZ3 TRP A 179 " =    1.348
peak=   -3.572 closest distance to " OE1 GLU A 277 " =    2.337
peak=   -3.571 closest distance to " C   VAL A  72 " =    0.939
peak=   -3.562 closest distance to " O   HOH Z 129 " =    3.735
peak=   -3.549 closest distance to " NH2 ARG A 219 " =    1.974
peak=   -3.541 closest distance to " O   HOH Z 251 " =    1.012
peak=   -3.534 closest distance to " O   HOH Z 231 " =    1.049
peak=   -3.529 closest distance to " OE1 GLN A 183 " =    1.653
peak=   -3.515 closest distance to " O   HOH Z 425 " =    0.812
peak=   -3.503 closest distance to " O   HOH Z 407 " =    3.116
peak=   -3.493 closest distance to " O   HOH Z 427 " =    1.893
peak=   -3.492 closest distance to " OD2 ASP A 171 " =    2.187
peak=   -3.487 closest distance to " O   ILE A  49 " =    1.660
peak=   -3.480 closest distance to " CB  ALA A  43 " =    2.364
peak=   -3.480 closest distance to " CG1BVAL A  41 " =    2.764
peak=   -3.478 closest distance to " CD  ARG A 156 " =    1.947
peak=   -3.477 closest distance to " O   HOH Z 348 " =    1.891
peak=   -3.477 closest distance to " O   HOH Z 238 " =    0.935
peak=   -3.477 closest distance to " ND2 ASN A 249 " =    2.189
peak=   -3.475 closest distance to " CZ2 TRP A 274 " =    0.922
peak=   -3.472 closest distance to " O   HOH Z  49 " =    1.181
peak=   -3.472 closest distance to " CG  LEU A  83 " =    2.125
peak=   -3.469 closest distance to " O   HOH Z 288 " =    1.325
peak=   -3.465 closest distance to " O   HOH Z 276 " =    1.137
peak=   -3.464 closest distance to " O   HOH Z 275 " =    1.706
peak=   -3.459 closest distance to " O   HOH Z 166 " =    1.316
peak=   -3.458 closest distance to " O   HOH Z  88 " =    1.926
peak=   -3.457 closest distance to " CZ  TYR A 169 " =    1.987
peak=   -3.457 closest distance to " O   HOH Z  22 " =    2.502
peak=   -3.455 closest distance to " O   ASP A  27 " =    1.943
peak=   -3.450 closest distance to " O   HOH Z 231 " =    1.896
peak=   -3.448 closest distance to " CD2 TYR A 116 " =    2.145
peak=   -3.447 closest distance to " CD1 ILE A  49 " =    1.442
peak=   -3.445 closest distance to " O   HOH Z 216 " =    1.650
peak=   -3.444 closest distance to " O   HOH Z 414 " =    1.636
peak=   -3.443 closest distance to " NZ  LYS A 166 " =    1.331
peak=   -3.438 closest distance to " ND2 ASN A 209 " =    1.872
peak=   -3.433 closest distance to " CG1 VAL A 265 " =    2.449
peak=   -3.417 closest distance to " O   HOH Z 143 " =    1.153
peak=   -3.417 closest distance to " CD2 PHE A  61 " =    1.924
peak=   -3.415 closest distance to " O   HOH Z 324 " =    0.797
peak=   -3.414 closest distance to " N   ASP A 171 " =    2.463
peak=   -3.412 closest distance to " O   HOH Z 197 " =    3.617
peak=   -3.402 closest distance to " CG  ARG A 219 " =    2.460
peak=   -3.396 closest distance to " O   HOH Z 244 " =    1.549
peak=   -3.388 closest distance to " O   ARG A 145 " =    1.185
peak=   -3.388 closest distance to " O   HOH Z 368 " =    1.435
peak=   -3.386 closest distance to " O   HOH Z 155 " =    1.041
peak=   -3.386 closest distance to " O   HOH Z 432 " =    3.577
peak=   -3.385 closest distance to " CG  TRP A 266 " =    1.720
peak=   -3.382 closest distance to " O   HOH Z  56 " =    2.006
peak=   -3.380 closest distance to " CG2 ILE A  49 " =    2.778
peak=   -3.378 closest distance to " O   HOH Z 198 " =    1.723
peak=   -3.373 closest distance to " ND2 ASN A 285 " =    2.096
peak=   -3.372 closest distance to " O   GLU A 152 " =    1.301
peak=   -3.367 closest distance to " CB  ALA A 114 " =    2.533
peak=   -3.367 closest distance to " CA  GLY A 203 " =    2.465
peak=   -3.360 closest distance to " ND2 ASN A  60 " =    3.907
peak=   -3.357 closest distance to " CB  ALA A 158 " =    1.749
peak=   -3.356 closest distance to " ND2 ASN A 187 " =    1.539
peak=   -3.343 closest distance to " O   THR A  82 " =    1.393
peak=   -3.343 closest distance to " O   HOH Z 286 " =    1.513
peak=   -3.337 closest distance to " O   HOH Z 211 " =    1.135
peak=   -3.336 closest distance to " O   HOH Z 147 " =    2.039
peak=   -3.335 closest distance to " CG2 ILE A  20 " =    2.635
peak=   -3.327 closest distance to " OG  SER A  87 " =    1.804
peak=   -3.319 closest distance to " O   ASP A 162 " =    2.130
peak=   -3.317 closest distance to " OD2 ASP A 272 " =    1.542
peak=   -3.312 closest distance to " O   HOH Z 337 " =    1.594
peak=   -3.305 closest distance to " CG2 ILE A 120 " =    0.922
peak=   -3.305 closest distance to " O   HOH Z 323 " =    2.095
peak=   -3.301 closest distance to " O   HOH Z 275 " =    1.490
peak=   -3.296 closest distance to " CD2 TYR A 293 " =    1.850
peak=   -3.289 closest distance to " CZ  PHE A 130 " =    1.068
peak=   -3.284 closest distance to " O   HOH Z 292 " =    1.470
peak=   -3.283 closest distance to " O   HOH Z  70 " =    2.168
peak=   -3.283 closest distance to " O   HOH Z 105 " =    1.941
peak=   -3.279 closest distance to " O   HOH Z 100 " =    1.320
peak=   -3.278 closest distance to " CE3 TRP A 274 " =    2.318
peak=   -3.278 closest distance to " CD1 ILE A 239 " =    2.492
peak=   -3.276 closest distance to " OE2 GLU A 152 " =    1.129
peak=   -3.272 closest distance to " CG2 VAL A 112 " =    2.625
peak=   -3.267 closest distance to " N   ALA A   1 " =    1.488
peak=   -3.266 closest distance to " NH2 ARG A  79 " =    2.066
peak=   -3.264 closest distance to " CB  TRP A  85 " =    2.106
peak=   -3.264 closest distance to " O   HOH Z 435 " =    3.228
peak=   -3.248 closest distance to " O   HOH Z   5 " =    1.374
peak=   -3.247 closest distance to " O   HOH Z 412 " =    3.920
peak=   -3.244 closest distance to " CG2 VAL A 189 " =    1.966
peak=   -3.244 closest distance to " CG1 VAL A 265 " =    2.713
peak=   -3.243 closest distance to " O   HOH Z 352 " =    1.692
peak=   -3.243 closest distance to " CD1 TRP A 274 " =    1.209
peak=   -3.241 closest distance to " CZ  ARG A  36 " =    1.402
peak=   -3.241 closest distance to " C   GLU A   2 " =    1.862
peak=   -3.239 closest distance to " N   VAL A 232 " =    2.229
peak=   -3.237 closest distance to " CG1 VAL A 112 " =    3.186
peak=   -3.236 closest distance to " CB  ALA A 100 " =    1.958
peak=   -3.236 closest distance to " O   HOH Z 165 " =    2.214
peak=   -3.232 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.231 closest distance to " O   HOH Z  52 " =    1.072
peak=   -3.229 closest distance to " O   GLN A 240 " =    3.132
peak=   -3.228 closest distance to " CB  ALA A 248 " =    2.093
peak=   -3.226 closest distance to " CG2 THR A 178 " =    2.021
peak=   -3.224 closest distance to " O   HOH Z 282 " =    4.563
peak=   -3.220 closest distance to " CD  GLN A  77 " =    1.333
peak=   -3.217 closest distance to " CB  ASN A  45 " =    2.139
peak=   -3.216 closest distance to " OG  SER A   3 " =    1.634
peak=   -3.214 closest distance to " CG2 ILE A 151 " =    2.555
peak=   -3.212 closest distance to " CZ  PHE A  16 " =    2.142
peak=   -3.208 closest distance to " CE BMET A  47 " =    1.308
peak=   -3.204 closest distance to " O   ALA A 137 " =    0.993
peak=   -3.201 closest distance to " O   ALA A  84 " =    1.628
peak=   -3.195 closest distance to " O   HOH Z 102 " =    1.795
peak=   -3.194 closest distance to " O   HOH Z 359 " =    1.492
peak=   -3.191 closest distance to " CB  PRO A  54 " =    2.362
peak=   -3.187 closest distance to " CD2 LEU A  25 " =    2.265
peak=   -3.179 closest distance to " OH  TYR A 247 " =    1.550
peak=   -3.177 closest distance to " O   HOH Z 128 " =    2.418
peak=   -3.176 closest distance to " O   HOH Z 426 " =    1.616
peak=   -3.170 closest distance to " CA  ILE A 120 " =    1.114
peak=   -3.166 closest distance to " O   HOH Z 134 " =    3.986
peak=   -3.162 closest distance to " O   HOH Z 198 " =    2.317
peak=   -3.155 closest distance to " NE2 GLN A 122 " =    1.051
peak=   -3.154 closest distance to " CD2 LEU A 297 " =    2.101
peak=   -3.151 closest distance to " O   HOH Z 328 " =    1.017
peak=   -3.151 closest distance to " O   HOH Z 105 " =    1.379
peak=   -3.137 closest distance to " CG1 ILE A 234 " =    1.897
peak=   -3.134 closest distance to " O   HOH Z 352 " =    1.796
peak=   -3.130 closest distance to " OD2 ASP A  27 " =    1.632
peak=   -3.123 closest distance to " CA  ASN A 110 " =    0.909
peak=   -3.123 closest distance to " O   HOH Z 217 " =    1.736
peak=   -3.123 closest distance to " O   HOH Z 130 " =    1.019
peak=   -3.119 closest distance to " O   HOH Z  37 " =    1.399
peak=   -3.112 closest distance to " O   VAL A 125 " =    1.996
peak=   -3.109 closest distance to " O   SER A 271 " =    2.178
peak=   -3.100 closest distance to " OD2 ASP A 132 " =    2.326
peak=   -3.093 closest distance to " O   HOH Z 397 " =    1.308
peak=   -3.090 closest distance to " O   HOH Z 201 " =    1.877
peak=   -3.086 closest distance to " CG1 VAL A 197 " =    2.385
peak=   -3.083 closest distance to " OD2 ASP A 171 " =    1.666
peak=   -3.080 closest distance to " OG  SER A  87 " =    1.202
peak=   -3.074 closest distance to " CB  TYR A  15 " =    2.121
peak=   -3.055 closest distance to " O   HOH Z  68 " =    1.325
peak=   -3.052 closest distance to " O   HOH Z  26 " =    0.982

================= 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    :  0.4549 0.4558   6.274407e+00   6.265163e+00
   1_bss:  0.4445 0.4489   6.268442e+00   6.257680e+00
   1_xyz:  0.3484 0.3978   6.103337e+00   6.181646e+00
   1_adp:  0.3182 0.4071   6.066359e+00   6.196004e+00
   1_occ:  0.3178 0.4072   6.066394e+00   6.196638e+00
   2_bss:  0.3171 0.4047   6.066023e+00   6.196598e+00
   2_xyz:  0.2656 0.3383   5.909507e+00   6.070821e+00
   2_adp:  0.2514 0.3244   5.875690e+00   6.043333e+00
   2_occ:  0.2513 0.3242   5.875546e+00   6.043341e+00
   3_bss:  0.2515 0.3235   5.873769e+00   6.041702e+00
   3_xyz:  0.2070 0.2712   5.694580e+00   5.890048e+00
   3_adp:  0.1908 0.2583   5.632489e+00   5.846294e+00
   3_occ:  0.1907 0.2583   5.632022e+00   5.846006e+00
   4_bss:  0.1908 0.2584   5.632226e+00   5.845254e+00
   4_xyz:  0.1617 0.2216   5.477169e+00   5.711161e+00
   4_adp:  0.1552 0.2069   5.432853e+00   5.649897e+00
   4_occ:  0.1550 0.2067   5.432015e+00   5.648964e+00
   5_bss:  0.1552 0.2065   5.431342e+00   5.647839e+00
   5_xyz:  0.1361 0.1832   5.308229e+00   5.532504e+00
   5_adp:  0.1312 0.1804   5.280990e+00   5.514735e+00
   5_occ:  0.1311 0.1804   5.280855e+00   5.514769e+00
   5_bss:  0.1311 0.1803   5.280696e+00   5.514640e+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:  0.350  50.001  -3.044   2.339   1.163   0.000   0.000   0.000
   1_xyz:  0.350  50.001  -3.044   2.339   1.163   0.000   0.000   0.000
   1_adp:  0.350  50.001  -3.044   2.339   1.163   0.000   0.000   0.000
   1_occ:  0.350  50.001  -3.044   2.339   1.163   0.000   0.000   0.000
   2_bss:  0.358  77.051  -1.478   0.338   0.516   0.000   0.000   0.000
   2_xyz:  0.358  77.051  -1.478   0.338   0.516   0.000   0.000   0.000
   2_adp:  0.358  77.051  -1.478   0.338   0.516   0.000   0.000   0.000
   2_occ:  0.358  77.051  -1.478   0.338   0.516   0.000   0.000   0.000
   3_bss:  0.333  69.057  -1.315  -0.524   0.388  -0.000   0.000   0.000
   3_xyz:  0.333  69.057  -1.315  -0.524   0.388  -0.000   0.000   0.000
   3_adp:  0.333  69.057  -1.315  -0.524   0.388  -0.000   0.000   0.000
   3_occ:  0.333  69.057  -1.315  -0.524   0.388  -0.000   0.000   0.000
   4_bss:  0.332  71.332  -1.602  -1.389   0.126  -0.000   0.000   0.000
   4_xyz:  0.332  71.332  -1.602  -1.389   0.126  -0.000   0.000   0.000
   4_adp:  0.332  71.332  -1.602  -1.389   0.126  -0.000   0.000   0.000
   4_occ:  0.332  71.332  -1.602  -1.389   0.126  -0.000   0.000   0.000
   5_bss:  0.332  71.332  -1.907  -2.051  -0.207  -0.000  -0.000  -0.000
   5_xyz:  0.332  71.332  -1.907  -2.051  -0.207  -0.000  -0.000  -0.000
   5_adp:  0.332  71.332  -1.907  -2.051  -0.207  -0.000  -0.000  -0.000
   5_occ:  0.332  71.332  -1.907  -2.051  -0.207  -0.000  -0.000  -0.000
   5_bss:  0.332  71.335  -1.830  -2.127  -0.170  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.456 0.4525  0.6217    69474.659
   1_bss:  54.663 0.4616  0.6423    67418.694
   1_xyz:  45.100 0.5807  0.7838    47959.217
   1_adp:  46.386 0.5643  0.7655    50460.980
   1_occ:  46.504 0.5628  0.7627    50589.129
   2_bss:  46.114 0.5676  0.7606    50019.391
   2_xyz:  36.576 0.6816  0.8889    32403.365
   2_adp:  34.679 0.7044  0.9017    30071.336
   2_occ:  34.689 0.7043  0.9017    30078.506
   3_bss:  34.565 0.7055  0.8940    29814.561
   3_xyz:  27.770 0.7808  0.9613    19602.399
   3_adp:  25.863 0.8017  0.9624    17419.132
   3_occ:  25.849 0.8018  0.9621    17386.633
   4_bss:  25.814 0.8022  0.9467    17343.805
   4_xyz:  21.697 0.8440  0.9737    12443.381
   4_adp:  19.935 0.8622  0.9777    11039.188
   4_occ:  19.909 0.8625  0.9774    11004.774
   5_bss:  19.855 0.8629  0.9628    10947.553
   5_xyz:  17.112 0.8883  0.9767     8537.846
   5_adp:  16.594 0.8933  0.9715     8253.190
   5_occ:  16.593 0.8933  0.9713     8250.435
   5_bss:  16.589 0.8934  0.9719     8248.766
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.8568e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.8568e-01
   1_xyz:   1.690  0.013  0.114 16.635  0.007  4.111   1.5793e-01
   1_adp:   1.690  0.013  0.114 16.635  0.007  4.111   1.5793e-01
   1_occ:   1.690  0.013  0.114 16.635  0.007  4.111   1.5793e-01
   2_bss:   1.690  0.013  0.114 16.635  0.007  4.111   1.5793e-01
   2_xyz:   1.196  0.008  0.089 14.964  0.005  4.119   8.0895e-02
   2_adp:   1.196  0.008  0.089 14.964  0.005  4.119   8.0895e-02
   2_occ:   1.196  0.008  0.089 14.964  0.005  4.119   8.0895e-02
   3_bss:   1.196  0.008  0.089 14.964  0.005  4.119   8.0895e-02
   3_xyz:   1.011  0.007  0.069 14.550  0.004  4.110   6.1010e-02
   3_adp:   1.011  0.007  0.069 14.550  0.004  4.110   6.1010e-02
   3_occ:   1.011  0.007  0.069 14.550  0.004  4.110   6.1010e-02
   4_bss:   1.011  0.007  0.069 14.550  0.004  4.110   6.1010e-02
   4_xyz:   0.909  0.005  0.069 14.351  0.003  4.116   5.0732e-02
   4_adp:   0.909  0.005  0.069 14.351  0.003  4.116   5.0732e-02
   4_occ:   0.909  0.005  0.069 14.351  0.003  4.116   5.0732e-02
   5_bss:   0.909  0.005  0.069 14.351  0.003  4.116   5.0732e-02
   5_xyz:   0.917  0.006  0.068 14.505  0.003  4.110   5.1417e-02
   5_adp:   0.917  0.006  0.068 14.505  0.003  4.110   5.1417e-02
   5_occ:   0.917  0.006  0.068 14.505  0.003  4.110   5.1417e-02
   5_bss:   0.917  0.006  0.068 14.505  0.003  4.110   5.1417e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.681   2.4126e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.681   2.4126e-01
   1_xyz:  10.639  0.068  0.381 81.569  0.047  1.990   1.0531e-01
   1_adp:  10.639  0.068  0.381 81.569  0.047  1.990   1.0531e-01
   1_occ:  10.639  0.068  0.381 81.569  0.047  1.990   1.0531e-01
   2_bss:  10.639  0.068  0.381 81.569  0.047  1.990   1.0531e-01
   2_xyz:   9.320  0.051  0.256 82.185  0.040  2.090   7.4633e-02
   2_adp:   9.320  0.051  0.256 82.185  0.040  2.090   7.4633e-02
   2_occ:   9.320  0.051  0.256 82.185  0.040  2.090   7.4633e-02
   3_bss:   9.320  0.051  0.256 82.185  0.040  2.090   7.4633e-02
   3_xyz:   7.949  0.046  0.229 81.799  0.036  2.282   6.4464e-02
   3_adp:   7.949  0.046  0.229 81.799  0.036  2.282   6.4464e-02
   3_occ:   7.949  0.046  0.229 81.799  0.036  2.282   6.4464e-02
   4_bss:   7.949  0.046  0.229 81.799  0.036  2.282   6.4464e-02
   4_xyz:   6.504  0.037  0.211 78.180  0.035  2.386   3.7724e-02
   4_adp:   6.504  0.037  0.211 78.180  0.035  2.386   3.7724e-02
   4_occ:   6.504  0.037  0.211 78.180  0.035  2.386   3.7724e-02
   5_bss:   6.504  0.037  0.211 78.180  0.035  2.386   3.7724e-02
   5_xyz:   6.983  0.036  0.216 81.592  0.034  2.376   3.2674e-02
   5_adp:   6.983  0.036  0.216 81.592  0.034  2.376   3.2674e-02
   5_occ:   6.983  0.036  0.216 81.592  0.034  2.376   3.2674e-02
   5_bss:   6.983  0.036  0.216 81.592  0.034  2.376   3.2674e-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:  77.36   0.00  18.26  67.86   0.00  15.00  77.36   0.00  36.06
   1_occ:  77.36   0.00  18.26  67.86   0.00  15.00  77.36   0.00  36.06
   2_bss:  77.36   0.00  18.26  67.86   0.00  15.00  77.36   0.00  36.06
   2_xyz:  77.36   0.00  18.26  67.86   0.00  15.00  77.36   0.00  36.06
   2_adp:  81.55   0.00  18.17  75.36   0.00  14.55  81.55   1.37  37.91
   2_occ:  81.55   0.00  18.17  75.36   0.00  14.55  81.55   1.37  37.91
   3_bss:  81.55   0.00  18.17  75.36   0.00  14.55  81.55   1.37  37.91
   3_xyz:  81.55   0.00  18.17  75.36   0.00  14.55  81.55   1.37  37.91
   3_adp: 100.02   0.00  19.08 100.02   0.00  13.98  97.11   3.49  46.84
   3_occ: 100.02   0.00  19.08 100.02   0.00  13.98  97.11   3.49  46.84
   4_bss: 100.02   0.00  19.08 100.02   0.00  13.98  97.11   3.49  46.84
   4_xyz: 100.02   0.00  19.08 100.02   0.00  13.98  97.11   3.49  46.84
   4_adp:  98.75   0.00  17.81  98.75   0.00  12.92  92.68   5.69  44.43
   4_occ:  98.75   0.00  17.81  98.75   0.00  12.92  92.68   5.69  44.43
   5_bss:  98.75   0.00  17.81  98.75   0.00  12.92  92.68   5.69  44.43
   5_xyz:  98.75   0.00  17.81  98.75   0.00  12.92  92.68   5.69  44.43
   5_adp: 101.45   0.00  18.03 101.45   0.00  12.65  99.18   0.00  47.29
   5_occ: 101.45   0.00  18.03 101.45   0.00  12.65  99.18   0.00  47.29
   5_bss: 101.45   0.00  18.03 101.45   0.00  12.65  99.19   0.00  47.29
------------------------------------------------------------------------
 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:    1.774    0.029    0.438
   1_adp:    1.774    0.029    0.438
   1_occ:    1.774    0.029    0.438
   2_bss:    1.774    0.029    0.438
   2_xyz:    1.510    0.049    0.551
   2_adp:    1.510    0.049    0.551
   2_occ:    1.510    0.049    0.551
   3_bss:    1.510    0.049    0.551
   3_xyz:    1.555    0.062    0.678
   3_adp:    1.555    0.062    0.678
   3_occ:    1.555    0.062    0.678
   4_bss:    1.555    0.062    0.678
   4_xyz:    1.536    0.039    0.748
   4_adp:    1.536    0.039    0.748
   4_occ:    1.536    0.039    0.748
   5_bss:    1.536    0.039    0.748
   5_xyz:    1.614    0.060    0.797
   5_adp:    1.614    0.060    0.797
   5_occ:    1.614    0.060    0.797
   5_bss:    1.614    0.060    0.797
------------------------------------------------------------------------

CPU time actual refinement: 357.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/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_734/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_734/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.90 
  Macro-tasks:
    bulk solvent and scale       = 43.34  
    individual site refinement   = 148.73 
    weights calculation          = 29.10  
    collect and process          = 5.97   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 227.23 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 117.41 
    alpha_beta                      = 8.34   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 125.71 
    fmodel                         = 7.06   
    r_factors                      = 0.30   
    phase_errors                   = 10.49  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 273.15 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.054 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    647 calls, 117.00 s
gradients_fft:          592 calls, 112.39 s

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

# Date 2008-01-16 Time 05:32:03 PST -0800 (1200490323.21 s)
Start R-work = 0.4549, R-free = 0.4558 (no bulk solvent and anisotropic scale)
Final R-work = 0.1499, R-free = 0.1951 (no bulk solvent and anisotropic scale)

Start R-work = 0.4445, R-free = 0.4489
Final R-work = 0.1311, R-free = 0.1803