# Date 2008-01-16 Time 06:21:28 PST -0800 (1200493288.00 s)
#phil __OFF__

Command line arguments: "../1109.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13730
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1109

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 45.9914, 88.1178, 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: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.96432
Completeness in resolution range: 0.916102
Completeness with d_max=infinity: 0.913538

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   1.9643

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.96432
Completeness in resolution range: 0.916102
Completeness with d_max=infinity: 0.913538

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.2054 [2242/2269]  2018   224  10.0%
  bin  2:  4.2054 -  3.3495 [2164/2184]  1952   212   9.8%
  bin  3:  3.3495 -  2.9295 [2116/2135]  1897   219  10.3%
  bin  4:  2.9295 -  2.6632 [2097/2127]  1885   212  10.1%
  bin  5:  2.6632 -  2.4731 [2115/2134]  1907   208   9.8%
  bin  6:  2.4731 -  2.3279 [2092/2117]  1879   213  10.2%
  bin  7:  2.3279 -  2.2116 [2070/2098]  1863   207  10.0%
  bin  8:  2.2116 -  2.1156 [2064/2100]  1860   204   9.9%
  bin  9:  2.1156 -  2.0344 [2037/2110]  1840   197   9.7%
  bin 10:  2.0344 -  1.9643 [ 592/2109]   529    63  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/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: 0.16 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:
        1.81 -     2.42: 31
        2.42 -     3.04: 2202
        3.04 -     3.66: 4661
        3.66 -     4.28: 8961
        4.28 -     4.90: 12216
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.982 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 324 " - " O   HOH Z 374 "  1.985 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28066 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_1109/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/model_refine_001.geo

CPU time processing inputs: 9.75


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 45.9914 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4850   r_free= 0.4875   ksol= 0.00   Bsol= 0.00   scale= 0.870    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.294600                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.6916 0.99   1455  163 0.3901 0.3665      6.6062      6.5546|
|  2:  4.6916 -  3.7418 0.99   1404  155 0.4259 0.4244        6.85      6.8295|
|  3:  3.7418 -  3.2741 0.99   1366  151 0.4487 0.4197      6.6655      6.6504|
|  4:  3.2741 -  2.9772 0.99   1377  154 0.4847 0.5260      6.5337      6.5333|
|  5:  2.9772 -  2.7651 0.99   1353  150 0.5194 0.5300      6.3688      6.3999|
|  6:  2.7651 -  2.6029 0.99   1350  152 0.5131 0.5185      6.2789      6.2217|
|  7:  2.6029 -  2.4731 0.99   1354  150 0.5246 0.5109      6.2346      6.1802|
|  8:  2.4731 -  2.3659 0.98   1331  148 0.5451 0.5714      6.1778      6.1618|
|  9:  2.3659 -  2.2751 0.98   1332  148 0.5319 0.5573      6.1346      6.1916|
| 10:  2.2751 -  2.1968 1.00   1350  156 0.5358 0.5440      6.0591      6.0649|
| 11:  2.1968 -  2.1283 0.98   1324  143 0.5278 0.5329      6.0296      6.0501|
| 12:  2.1283 -  2.0676 0.98   1337  143 0.5328 0.5382      5.9308      5.9436|
| 13:  2.0676 -  2.0133 0.79   1064  121 0.5326 0.4934      5.8791       5.787|
| 14:  2.0133 -  1.9643 0.17    233   25 0.5187 0.5135      5.8604      5.9423|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.6916  1455   163  0.72  32.09   0.81     0.77      66033.23|
|  2:  4.6916 -  3.7418  1404   155  0.70  35.64   0.88     0.80     112011.86|
|  3:  3.7418 -  3.2741  1366   151  0.54  49.09   0.90     0.72     128163.33|
|  4:  3.2741 -  2.9772  1377   154  0.40  59.61   0.87     0.57     124766.82|
|  5:  2.9772 -  2.7651  1353   150  0.31  66.32   0.85     0.47      97237.05|
|  6:  2.7651 -  2.6029  1350   152  0.28  68.66   0.88     0.42      83469.94|
|  7:  2.6029 -  2.4731  1354   150  0.28  68.96   0.88     0.40      72004.65|
|  8:  2.4731 -  2.3659  1331   148  0.25  71.03   0.87     0.38      65497.94|
|  9:  2.3659 -  2.2751  1332   148  0.27  69.51   0.91     0.41      60159.62|
| 10:  2.2751 -  2.1968  1350   156  0.27  70.20   0.88     0.41      53288.91|
| 11:  2.1968 -  2.1283  1324   143  0.25  71.73   0.92     0.38      52377.03|
| 12:  2.1283 -  2.0676  1337   143  0.22  73.84   0.89     0.35      46908.19|
| 13:  2.0676 -  2.0133  1064   121  0.23  72.61   0.91     0.39      41295.87|
| 14:  2.0133 -  1.9643   233    25  0.37  62.15   0.96     0.53      29739.10|
|alpha:            min =        0.35 max =            0.80 mean =         0.50|
|beta:             min =    29739.10 max =       128163.33 mean =     77376.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.77|
|phase err.(test): min =        0.00 max =           89.98 mean =        62.06|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.233991             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.858   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.604217              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.607   (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 |  1.806 -  2.115:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       22 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      199 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2003 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1854 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2807 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4611 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4350 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5561 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6655 |
|-----------------------------------------------------------------------------|
|-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 |        0.172 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.806 |       0.297 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4850   r_free= 0.4875   ksol= 0.00   Bsol= 0.00   scale= 0.870    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.294600                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4782   r_free= 0.4848   ksol= 0.32   Bsol= 60.09   scale= 0.913   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,0.50,2.06,0.00,0.00,0.00); trace/3= 0.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.292802                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.438443             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.743   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.635248              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.141   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4782      final r-factor (work) = 0.3863          |
| start r-factor (free) = 0.4848      final r-factor (free) = 0.4237          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.2653 = 12.44 * 0.50 * 6.2859 + 1.00 * 0.1717                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.7147 = 12.44 * 0.50 * 6.2036 + 1.00 * 0.1333                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3863      final r-factor (work) = 0.3498          |
| start r-factor (free) = 0.4237      final r-factor (free) = 0.4372          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1506 = 1.64 * 1.00 * 6.2036 + 1.00 * 0.0062                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0160 = 1.64 * 1.00 * 6.1107 + 1.00 * 0.0235                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.44  20.41    None  None   None       |
|    all(noH): 2823   0      0.00    100.44  20.41    None  None   None       |
|    Sol.    : 438    0      0.00    100.44  39.52    None  None   None       |
|    Mac.    : 2385   0      0.00    77.86   16.90    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 -  10.045:  839   |   5:    50.222 -  60.267:  103        |
|      1:    10.045 -  20.089:  816   |   6:    60.267 -  70.311:   51        |
|      2:    20.089 -  30.133:  552   |   7:    70.311 -  80.356:   26        |
|      3:    30.133 -  40.178:  288   |   8:    80.356 -  90.400:    7        |
|      4:    40.178 -  50.222:  140   |   9:    90.400 - 100.444:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3498 r_free = 0.4372             target_work(ml) = 6.119         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3494 r_free = 0.4381             target_work(ml) = 6.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3494   r_free= 0.4381   ksol= 0.32   Bsol= 60.09   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,0.50,2.06,0.00,0.00,0.00); trace/3= 0.74                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.118547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3502   r_free= 0.4364   ksol= 0.36   Bsol= 91.48   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,-0.27,1.61,-0.00,0.00,0.00); trace/3= 0.40                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.120279                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.095505             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.595   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3502      final r-factor (work) = 0.2766          |
| start r-factor (free) = 0.4364      final r-factor (free) = 0.3508          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.1545 = 13.10 * 0.50 * 6.1122 + 1.00 * 0.1333                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.7103 = 13.10 * 0.50 * 6.0485 + 1.00 * 0.1059                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2766      final r-factor (work) = 0.2575          |
| start r-factor (free) = 0.3508      final r-factor (free) = 0.3370          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0406 = 0.66 * 1.00 * 6.0485 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9348 = 0.66 * 1.00 * 5.9005 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.77   20.28    None  None   None       |
|    all(noH): 2823   0      0.00    99.77   20.28    None  None   None       |
|    Sol.    : 438    0      0.00    99.77   41.27    None  None   None       |
|    Mac.    : 2385   0      0.00    76.18   16.43    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 -   9.977:  792   |   5:    49.885 -  59.862:   91        |
|      1:     9.977 -  19.954:  938   |   6:    59.862 -  69.839:   51        |
|      2:    19.954 -  29.931:  510   |   7:    69.839 -  79.816:   27        |
|      3:    29.931 -  39.908:  271   |   8:    79.816 -  89.793:    5        |
|      4:    39.908 -  49.885:  137   |   9:    89.793 -  99.770:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2575 r_free = 0.3370             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2573 r_free = 0.3372             target_work(ml) = 5.884         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2573   r_free= 0.3372   ksol= 0.36   Bsol= 91.48   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.13,-0.27,1.61,-0.00,0.00,0.00); trace/3= 0.40                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.883721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2573   r_free= 0.3373   ksol= 0.35   Bsol= 80.83   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-1.43,0.16,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.883866                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.125364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.559   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 15.073307             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.746  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2573      final r-factor (work) = 0.2172          |
| start r-factor (free) = 0.3373      final r-factor (free) = 0.2892          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2777 = 4.13 * 0.50 * 5.9009 + 1.00 * 0.1059                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0644 = 4.13 * 0.50 * 5.8204 + 1.00 * 0.0587                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2172      final r-factor (work) = 0.1968          |
| start r-factor (free) = 0.2892      final r-factor (free) = 0.2799          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 87.7494 = 15.07 * 1.00 * 5.8204 + 1.00 * 0.0160                             |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 85.9208 = 15.07 * 1.00 * 5.6986 + 1.00 * 0.0233                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    126.01  21.62    None  None   None       |
|    all(noH): 2823   0      0.00    126.01  21.62    None  None   None       |
|    Sol.    : 438    0      3.38    126.01  53.09    None  None   None       |
|    Mac.    : 2385   0      0.00    107.72  15.84    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 -  12.601: 1238   |   5:    63.005 -  75.606:   95        |
|      1:    12.601 -  25.202:  848   |   6:    75.606 -  88.207:   63        |
|      2:    25.202 -  37.803:  273   |   7:    88.207 - 100.808:   22        |
|      3:    37.803 -  50.404:  152   |   8:   100.808 - 113.409:   15        |
|      4:    50.404 -  63.005:  115   |   9:   113.409 - 126.010:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1968 r_free = 0.2799             target_work(ml) = 5.682         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1968 r_free = 0.2799             target_work(ml) = 5.682         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1968   r_free= 0.2799   ksol= 0.35   Bsol= 80.83   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.12,-1.43,0.16,-0.00,0.00,0.00); trace/3= -0.80                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.681763                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1970   r_free= 0.2803   ksol= 0.35   Bsol= 94.98   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.03,-0.15,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.681876                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.410037              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.349  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.715035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.702  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1970      final r-factor (work) = 0.1623          |
| start r-factor (free) = 0.2803      final r-factor (free) = 0.2336          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3269 = 6.41 * 0.50 * 5.6999 + 1.00 * 0.0587                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0412 = 6.41 * 0.50 * 5.6068 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1623      final r-factor (work) = 0.1476          |
| start r-factor (free) = 0.2336      final r-factor (free) = 0.2104          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6389 = 1.72 * 1.00 * 5.6068 + 1.00 * 0.0231                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3903 = 1.72 * 1.00 * 5.4652 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    134.06  20.36    None  None   None       |
|    all(noH): 2823   0      0.00    134.06  20.36    None  None   None       |
|    Sol.    : 438    0      6.03    134.06  53.23    None  None   None       |
|    Mac.    : 2385   0      0.00    110.07  14.33    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 -  13.406: 1504   |   5:    67.030 -  80.436:   80        |
|      1:    13.406 -  26.812:  746   |   6:    80.436 -  93.842:   53        |
|      2:    26.812 -  40.218:  204   |   7:    93.842 - 107.248:   22        |
|      3:    40.218 -  53.624:  110   |   8:   107.248 - 120.654:    7        |
|      4:    53.624 -  67.030:   96   |   9:   120.654 - 134.061:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1476 r_free = 0.2104             target_work(ml) = 5.406         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1476 r_free = 0.2103             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.2103   ksol= 0.35   Bsol= 94.98   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.55,-2.03,-0.15,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.405419                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1480   r_free= 0.2102   ksol= 0.34   Bsol= 87.31   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-2.44,-0.48,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.405483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.964053              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.844  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338442              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.363  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1480      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2102      final r-factor (free) = 0.1973          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4395 = 1.96 * 0.50 * 5.4665 + 1.00 * 0.0712                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3424 = 1.96 * 0.50 * 5.3906 + 1.00 * 0.0487                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.1973      final r-factor (free) = 0.1893          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8416 = 0.34 * 1.00 * 5.3906 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8240 = 0.34 * 1.00 * 5.3487 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.99    130.89  19.68    None  None   None       |
|    all(noH): 2823   0      0.99    130.89  19.68    None  None   None       |
|    Sol.    : 438    0      6.55    130.89  51.57    None  None   None       |
|    Mac.    : 2385   0      0.99    108.03  13.83    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:     0.990 -  13.980: 1679   |   5:    65.938 -  78.928:   74        |
|      1:    13.980 -  26.969:  629   |   6:    78.928 -  91.918:   45        |
|      2:    26.969 -  39.959:  158   |   7:    91.918 - 104.907:   23        |
|      3:    39.959 -  52.949:  105   |   8:   104.907 - 117.897:    8        |
|      4:    52.949 -  65.938:  101   |   9:   117.897 - 130.887:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1372 r_free = 0.1893             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1371 r_free = 0.1892             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1892   ksol= 0.34   Bsol= 87.31   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.77,-2.44,-0.48,-0.00,-0.00,-0.00); trace/3= -1.56                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.324108                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.6916 0.99   1455  163 0.0994 0.1485      5.4273      5.6662|
|  2:  4.6916 -  3.7418 0.99   1404  155 0.0904 0.1287      5.5158      5.7641|
|  3:  3.7418 -  3.2741 0.99   1366  151 0.1241 0.1783      5.6005      5.9066|
|  4:  3.2741 -  2.9772 0.99   1377  154 0.1606 0.2084      5.6498       5.811|
|  5:  2.9772 -  2.7651 0.99   1353  150 0.1641 0.2170      5.5124      5.7287|
|  6:  2.7651 -  2.6029 0.99   1350  152 0.1597 0.2333      5.4049      5.6287|
|  7:  2.6029 -  2.4731 0.99   1354  150 0.1526 0.2046      5.3294      5.5079|
|  8:  2.4731 -  2.3659 0.98   1331  148 0.1537 0.1994      5.2742      5.4752|
|  9:  2.3659 -  2.2751 0.98   1332  148 0.1546 0.2165      5.2464      5.4824|
| 10:  2.2751 -  2.1968 1.00   1350  156 0.1458 0.1931      5.1318      5.3064|
| 11:  2.1968 -  2.1283 0.98   1324  143 0.1447 0.2032      5.1015      5.4209|
| 12:  2.1283 -  2.0676 0.98   1337  143 0.1486 0.2225      5.0404       5.284|
| 13:  2.0676 -  2.0133 0.79   1064  121 0.1388 0.1923      4.9515      5.1127|
| 14:  2.0133 -  1.9643 0.17    233   25 0.1238 0.1822      4.8247      5.1476|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.6916  1455   163  0.93  10.14   0.96     0.93       8541.02|
|  2:  4.6916 -  3.7418  1404   155  0.94   9.42   1.02     1.00      10977.39|
|  3:  3.7418 -  3.2741  1366   151  0.91  14.01   1.05     1.05      13661.23|
|  4:  3.2741 -  2.9772  1377   154  0.88  18.48   1.03     1.00      15224.41|
|  5:  2.9772 -  2.7651  1353   150  0.87  19.66   1.02     0.99      12273.59|
|  6:  2.7651 -  2.6029  1350   152  0.86  20.41   1.00     0.96      10208.18|
|  7:  2.6029 -  2.4731  1354   150  0.87  19.31   1.02     0.99       8926.49|
|  8:  2.4731 -  2.3659  1331   148  0.86  20.27   1.02     0.98       8055.59|
|  9:  2.3659 -  2.2751  1332   148  0.87  19.95   1.02     0.95       7399.82|
| 10:  2.2751 -  2.1968  1350   156  0.87  19.53   1.02     0.99       6206.78|
| 11:  2.1968 -  2.1283  1324   143  0.87  19.27   1.01     0.95       5714.53|
| 12:  2.1283 -  2.0676  1337   143  0.87  19.72   1.01     1.00       5405.69|
| 13:  2.0676 -  2.0133  1064   121  0.86  20.52   1.01     0.98       4756.76|
| 14:  2.0133 -  1.9643   233    25  0.90  16.68   1.00     0.97       3627.96|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     3627.96 max =        15224.41 mean =      9052.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.61|
|phase err.(test): min =        0.00 max =           89.63 mean =        17.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1892   ksol= 0.33   Bsol= 79.97   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.88,-0.76,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1369   r_free= 0.1892   ksol= 0.33   Bsol= 79.97   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.12,-2.88,-0.76,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323540                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.6916 0.99   1455  163 0.0990 0.1479      5.4242      5.6615|
|  2:  4.6916 -  3.7418 0.99   1404  155 0.0903 0.1285      5.5136      5.7611|
|  3:  3.7418 -  3.2741 0.99   1366  151 0.1240 0.1781      5.5997      5.9058|
|  4:  3.2741 -  2.9772 0.99   1377  154 0.1607 0.2086      5.6501      5.8115|
|  5:  2.9772 -  2.7651 0.99   1353  150 0.1643 0.2170      5.5129      5.7298|
|  6:  2.7651 -  2.6029 0.99   1350  152 0.1596 0.2333      5.4046      5.6279|
|  7:  2.6029 -  2.4731 0.99   1354  150 0.1527 0.2046      5.3295      5.5081|
|  8:  2.4731 -  2.3659 0.98   1331  148 0.1538 0.1996      5.2742      5.4761|
|  9:  2.3659 -  2.2751 0.98   1332  148 0.1545 0.2163       5.246      5.4808|
| 10:  2.2751 -  2.1968 1.00   1350  156 0.1458 0.1933      5.1317      5.3083|
| 11:  2.1968 -  2.1283 0.98   1324  143 0.1446 0.2035      5.1008      5.4212|
| 12:  2.1283 -  2.0676 0.98   1337  143 0.1486 0.2226      5.0409      5.2843|
| 13:  2.0676 -  2.0133 0.79   1064  121 0.1387 0.1914      4.9507      5.1114|
| 14:  2.0133 -  1.9643 0.17    233   25 0.1240 0.1821      4.8231      5.1445|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2943 -  4.6916  1455   163  0.93  10.11   0.96     0.93       8496.57|
|  2:  4.6916 -  3.7418  1404   155  0.94   9.38   1.02     1.00      10926.98|
|  3:  3.7418 -  3.2741  1366   151  0.91  13.98   1.04     1.04      13613.85|
|  4:  3.2741 -  2.9772  1377   154  0.88  18.46   1.02     0.99      15207.45|
|  5:  2.9772 -  2.7651  1353   150  0.87  19.64   1.01     0.98      12268.73|
|  6:  2.7651 -  2.6029  1350   152  0.86  20.40   0.99     0.94      10206.16|
|  7:  2.6029 -  2.4731  1354   150  0.87  19.30   1.01     0.98       8925.48|
|  8:  2.4731 -  2.3659  1331   148  0.86  20.26   1.00     0.96       8056.45|
|  9:  2.3659 -  2.2751  1332   148  0.87  19.94   1.00     0.94       7398.72|
| 10:  2.2751 -  2.1968  1350   156  0.87  19.53   1.00     0.97       6209.29|
| 11:  2.1968 -  2.1283  1324   143  0.87  19.27   0.99     0.93       5721.41|
| 12:  2.1283 -  2.0676  1337   143  0.87  19.72   0.99     0.98       5410.55|
| 13:  2.0676 -  2.0133  1064   121  0.86  20.49   0.98     0.95       4750.61|
| 14:  2.0133 -  1.9643   233    25  0.90  16.60   0.97     0.95       3606.38|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3606.38 max =        15207.45 mean =      9039.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.59|
|phase err.(test): min =        0.00 max =           89.93 mean =        17.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.049)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.96    130.85  19.65    None  None   None       |
|    all(noH): 2823   0      0.96    130.85  19.65    None  None   None       |
|    Sol.    : 438    0      6.52    130.85  51.54    None  None   None       |
|    Mac.    : 2385   0      0.96    108.00  13.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.956 -  13.946: 1679   |   5:    65.904 -  78.894:   74        |
|      1:    13.946 -  26.935:  629   |   6:    78.894 -  91.884:   45        |
|      2:    26.935 -  39.925:  158   |   7:    91.884 - 104.873:   23        |
|      3:    39.925 -  52.915:  105   |   8:   104.873 - 117.863:    8        |
|      4:    52.915 -  65.904:  101   |   9:   117.863 - 130.853:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.659
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 345 from: 349
   mapped sites are within: 0.712 - 5.659

peak=    7.976 closest distance to " O   HOH Z 103 " =    1.034
peak=    6.168 closest distance to " O   HOH Z 245 " =    1.103
peak=    5.685 closest distance to " O   HOH Z 222 " =    1.480
peak=    5.219 closest distance to " CG  PRO A  54 " =    1.462
peak=    5.214 closest distance to " CG  PRO A  90 " =    1.340
peak=    4.963 closest distance to " OE1 GLN A  73 " =    2.157
peak=    4.955 closest distance to " O   HOH Z 417 " =    2.373
peak=    4.932 closest distance to " O   HOH Z  11 " =    1.249
peak=    4.932 closest distance to " CB  SER A 216 " =    1.153
peak=    4.876 closest distance to " O   HOH Z 295 " =    1.253
peak=    4.863 closest distance to " O   HOH Z  63 " =    1.688
peak=    4.861 closest distance to " O   HOH Z  65 " =    1.124
peak=    4.807 closest distance to " O   HOH Z 287 " =    2.308
peak=    4.794 closest distance to " CB  ASN A 148 " =    1.320
peak=    4.751 closest distance to " O   HOH Z   7 " =    1.788
peak=    4.697 closest distance to " NE2 GLN A  11 " =    1.168
peak=    4.673 closest distance to " CB  GLN A 223 " =    1.541
peak=    4.658 closest distance to " O   TYR A 116 " =    1.304
peak=    4.655 closest distance to " O   HOH Z  46 " =    1.066
peak=    4.644 closest distance to " CB  SER A  63 " =    1.458
peak=    4.636 closest distance to " O   HOH Z 403 " =    1.388
peak=    4.580 closest distance to " O   PRO A 198 " =    1.311
peak=    4.550 closest distance to " O   HOH Z 414 " =    2.144
peak=    4.525 closest distance to " CB  PRO A  54 " =    1.246
peak=    4.455 closest distance to " NH1AARG A 145 " =    1.212
peak=    4.386 closest distance to " CG  PRO A 198 " =    1.330
peak=    4.375 closest distance to " O   HOH Z 105 " =    1.117
peak=    4.359 closest distance to " O   HOH Z 427 " =    2.323
peak=    4.344 closest distance to " O   HOH Z 375 " =    1.155
peak=    4.338 closest distance to " O   HOH Z 126 " =    2.066
peak=    4.272 closest distance to " CB  PRO A  90 " =    1.218
peak=    4.258 closest distance to " O   HOH Z  39 " =    1.122
peak=    4.251 closest distance to " O   HOH Z 296 " =    1.260
peak=    4.230 closest distance to " CG2 ILE A 120 " =    1.064
peak=    4.226 closest distance to " CB  ALA A 114 " =    0.861
peak=    4.223 closest distance to " O   HOH Z 130 " =    0.991
peak=    4.214 closest distance to " CE3 TRP A 274 " =    1.499
peak=    4.203 closest distance to " O   HOH Z 139 " =    1.105
peak=    4.203 closest distance to " NZ  LYS A 166 " =    0.936
peak=    4.182 closest distance to " CA  ALA A  51 " =    1.017
peak=    4.179 closest distance to " O   HOH Z 316 " =    3.104
peak=    4.162 closest distance to " CG2 THR A 221 " =    1.263
peak=    4.153 closest distance to " O   HOH Z 158 " =    1.192
peak=    4.151 closest distance to " O   HOH Z  66 " =    1.030
peak=    4.149 closest distance to " O   HOH Z  49 " =    1.472
peak=    4.144 closest distance to " CZ3 TRP A 266 " =    1.192
peak=    4.138 closest distance to " O   HOH Z 147 " =    1.089
peak=    4.125 closest distance to " CZ  PHE A 218 " =    1.157
peak=    4.056 closest distance to " O   HOH Z 369 " =    2.142
peak=    4.055 closest distance to " OE1 GLN A 240 " =    1.683
peak=    4.052 closest distance to " CB  MET A  47 " =    1.009
peak=    4.049 closest distance to " O   HOH Z 232 " =    2.066
peak=    4.039 closest distance to " O   HOH Z  97 " =    1.454
peak=    4.037 closest distance to " O   HOH Z  69 " =    1.457
peak=    4.029 closest distance to " CA  TYR A  30 " =    1.165
peak=    4.012 closest distance to " O   HOH Z 361 " =    1.494
peak=    4.010 closest distance to " CB  ASP A 124 " =    0.918
peak=    4.007 closest distance to " CB  MET A  40 " =    0.860
peak=    4.000 closest distance to " O   HOH Z 117 " =    0.712
peak=    3.999 closest distance to " OE2 GLU A  53 " =    1.133
peak=    3.972 closest distance to " CG  LEU A 167 " =    1.338
peak=    3.969 closest distance to " CD  ARG A 159 " =    0.865
peak=    3.969 closest distance to " O   HOH Z 425 " =    1.720
peak=    3.957 closest distance to " ND2 ASN A  60 " =    2.834
peak=    3.947 closest distance to " CA  ARG A 195 " =    1.508
peak=    3.938 closest distance to " O   HOH Z   9 " =    1.918
peak=    3.935 closest distance to " O   HOH Z 427 " =    1.234
peak=    3.916 closest distance to " NE2 HIS A 207 " =    1.034
peak=    3.914 closest distance to " CB  TRP A 266 " =    1.011
peak=    3.901 closest distance to " O   HOH Z 182 " =    1.139
peak=    3.900 closest distance to " O   HOH Z 298 " =    2.351
peak=    3.891 closest distance to " N   TYR A  15 " =    1.074
peak=    3.886 closest distance to " CB  GLU A 128 " =    0.987
peak=    3.883 closest distance to " CA  VAL A 125 " =    1.142
peak=    3.881 closest distance to " CB  SER A 210 " =    0.959
peak=    3.876 closest distance to " NZ  LYS A 119 " =    2.455
peak=    3.873 closest distance to " CB  SER A   3 " =    1.534
peak=    3.871 closest distance to " O   HOH Z 131 " =    1.375
peak=    3.867 closest distance to " CA  ALA A 160 " =    1.116
peak=    3.861 closest distance to " O   HOH Z 422 " =    0.863
peak=    3.861 closest distance to " CB  TYR A  30 " =    1.285
peak=    3.860 closest distance to " O   HOH Z 217 " =    2.959
peak=    3.855 closest distance to " CB  LYS A 290 " =    0.907
peak=    3.851 closest distance to " N   GLN A 278 " =    1.053
peak=    3.844 closest distance to " O   HOH Z 183 " =    1.610
peak=    3.842 closest distance to " CZ  PHE A  38 " =    1.310
peak=    3.841 closest distance to " O   HOH Z 411 " =    3.210
peak=    3.830 closest distance to " CA  ASN A 127 " =    1.080
peak=    3.821 closest distance to " CB  PRO A 213 " =    1.397
peak=    3.819 closest distance to " CB  ASN A  60 " =    0.992
peak=    3.811 closest distance to " O   HOH Z  61 " =    1.907
peak=    3.785 closest distance to " OE1 GLN A  77 " =    1.244
peak=    3.782 closest distance to " CB  PHE A  61 " =    1.204
peak=    3.756 closest distance to " C   ASN A 209 " =    1.562
peak=    3.750 closest distance to " O   HOH Z 414 " =    1.287
peak=    3.749 closest distance to " CD  LYS A  76 " =    1.695
peak=    3.741 closest distance to " ND2BASN A 224 " =    0.854
peak=    3.738 closest distance to " CG  PRO A 243 " =    1.131
peak=    3.729 closest distance to " NZ ALYS A 290 " =    0.929
peak=    3.729 closest distance to " O   HOH Z 126 " =    1.510
peak=    3.722 closest distance to " O   HOH Z 218 " =    1.621
peak=    3.711 closest distance to " CA  ILE A 234 " =    1.087
peak=    3.709 closest distance to " CB  ASP A  50 " =    1.104
peak=    3.704 closest distance to " O   HOH Z  27 " =    1.010
peak=    3.698 closest distance to " O   HOH Z  58 " =    1.992
peak=    3.698 closest distance to " CA  ARG A  36 " =    1.234
peak=    3.696 closest distance to " CB  SER A  62 " =    0.937
peak=    3.695 closest distance to " OD1 ASP A 238 " =    0.970
peak=    3.683 closest distance to " O   THR A 294 " =    1.017
peak=    3.681 closest distance to " N   VAL A 296 " =    1.838
peak=    3.679 closest distance to " O   HOH Z 437 " =    1.672
peak=    3.674 closest distance to " CA  TRP A  92 " =    1.139
peak=    3.672 closest distance to " O   HOH Z 193 " =    1.538
peak=    3.671 closest distance to " O   HOH Z  40 " =    2.035
peak=    3.670 closest distance to " O   HOH Z  28 " =    1.014
peak=    3.669 closest distance to " CA  GLU A 152 " =    1.007
peak=    3.657 closest distance to " CB  GLN A  89 " =    1.195
peak=    3.655 closest distance to " O   HOH Z 380 " =    1.846
peak=    3.654 closest distance to " O   HOH Z 207 " =    0.830
peak=    3.654 closest distance to " CB  ALA A  43 " =    0.927
peak=    3.650 closest distance to " O   HOH Z 145 " =    2.029
peak=    3.650 closest distance to " N   SER A  97 " =    0.886
peak=    3.649 closest distance to " CD1 LEU A 300 " =    1.077
peak=    3.648 closest distance to " O   HOH Z 258 " =    2.011
peak=    3.645 closest distance to " CZ  PHE A 192 " =    0.950
peak=    3.634 closest distance to " O   HOH Z 434 " =    1.664
peak=    3.631 closest distance to " CB  VAL A 202 " =    1.530
peak=    3.629 closest distance to " O   HOH Z 171 " =    2.466
peak=    3.624 closest distance to " O   HOH Z  88 " =    3.626
peak=    3.623 closest distance to " O   HOH Z 273 " =    1.260
peak=    3.623 closest distance to " OG ASER A 212 " =    1.463
peak=    3.622 closest distance to " O   HOH Z 211 " =    1.570
peak=    3.602 closest distance to " O   HOH Z  26 " =    1.432
peak=    3.601 closest distance to " O   HOH Z 272 " =    1.897
peak=    3.591 closest distance to " O   HOH Z 419 " =    1.957
peak=    3.585 closest distance to " NE  ARG A  66 " =    3.199
peak=    3.582 closest distance to " CG2 ILE A  20 " =    1.502
peak=    3.582 closest distance to " O   HOH Z  30 " =    1.686
peak=    3.574 closest distance to " O   HOH Z  67 " =    1.702
peak=    3.571 closest distance to " CD  GLU A 152 " =    0.780
peak=    3.568 closest distance to " CB  SER A 276 " =    1.114
peak=    3.567 closest distance to " O   HOH Z 394 " =    1.768
peak=    3.556 closest distance to " O   HOH Z 359 " =    1.325
peak=    3.555 closest distance to " CB  PHE A 225 " =    1.417
peak=    3.555 closest distance to " ND1 HIS A  86 " =    1.817
peak=    3.549 closest distance to " O   GLN A  55 " =    1.645
peak=    3.547 closest distance to " OG  SER A  26 " =    1.425
peak=    3.546 closest distance to " CA  ASN A 284 " =    0.950
peak=    3.545 closest distance to " O   HOH Z 410 " =    1.370
peak=    3.544 closest distance to " O   HOH Z 390 " =    1.333
peak=    3.542 closest distance to " CG  GLU A 277 " =    2.018
peak=    3.537 closest distance to " O   HOH Z 422 " =    2.487
peak=    3.537 closest distance to " CG2 THR A  29 " =    1.538
peak=    3.535 closest distance to " O   HOH Z 293 " =    1.417
peak=    3.533 closest distance to " CB  LEU A 228 " =    1.207
peak=    3.517 closest distance to " NE2 GLN A  55 " =    1.084
peak=    3.515 closest distance to " CE  MET A  93 " =    1.423
peak=    3.514 closest distance to " CG  GLN A  88 " =    0.960
peak=    3.512 closest distance to " CB  ALA A 233 " =    1.135
peak=    3.509 closest distance to " O   HOH Z 207 " =    2.498
peak=    3.500 closest distance to " CE  LYS A  76 " =    0.894
peak=    3.497 closest distance to " CB  ALA A  10 " =    1.044
peak=    3.489 closest distance to " O   HOH Z  91 " =    2.333
peak=    3.489 closest distance to " O   HOH Z 217 " =    1.295
peak=    3.487 closest distance to " CA  ILE A 263 " =    1.079
peak=    3.486 closest distance to " O   HOH Z 255 " =    1.169
peak=    3.486 closest distance to " CB  ASN A  39 " =    0.851
peak=    3.482 closest distance to " O  BHOH Z  74 " =    1.071
peak=    3.476 closest distance to " C   PRO A  54 " =    0.732
peak=    3.472 closest distance to " O   HOH Z 393 " =    1.532
peak=    3.471 closest distance to " CG2BVAL A  41 " =    1.111
peak=    3.466 closest distance to " CA  SER A  95 " =    0.912
peak=    3.465 closest distance to " O   HOH Z 132 " =    0.986
peak=    3.465 closest distance to " CB  ARG A 275 " =    1.105
peak=    3.462 closest distance to " N   CYS A 260 " =    0.901
peak=    3.458 closest distance to " CA  ARG A 102 " =    1.119
peak=    3.450 closest distance to " CD BLYS A 290 " =    1.099
peak=    3.445 closest distance to " O   HOH Z 290 " =    1.020
peak=    3.442 closest distance to " CB  GLU A 152 " =    1.085
peak=    3.440 closest distance to " CA  PHE A 283 " =    1.218
peak=    3.439 closest distance to " O   HOH Z  53 " =    2.337
peak=    3.438 closest distance to " O   HOH Z 378 " =    1.072
peak=    3.435 closest distance to " CD  LYS A 119 " =    1.607
peak=    3.430 closest distance to " CB  ASN A 187 " =    1.021
peak=    3.423 closest distance to " O   HOH Z  76 " =    1.183
peak=    3.416 closest distance to " CE3 TRP A  85 " =    0.997
peak=    3.411 closest distance to " O   HOH Z 362 " =    1.938
peak=    3.405 closest distance to " O   HOH Z 153 " =    3.720
peak=    3.398 closest distance to " CA  ASP A 124 " =    0.848
peak=    3.397 closest distance to " O   THR A 251 " =    1.294
peak=    3.397 closest distance to " N   ARG A  66 " =    1.137
peak=    3.395 closest distance to " O   HOH Z 171 " =    1.882
peak=    3.394 closest distance to " N   SER A 271 " =    1.077
peak=    3.388 closest distance to " CG1 ILE A 151 " =    0.999
peak=    3.387 closest distance to " O   HOH Z 148 " =    1.527
peak=    3.387 closest distance to " O   HOH Z 368 " =    3.781
peak=    3.381 closest distance to " CD  LYS A 166 " =    1.454
peak=    3.380 closest distance to " CA  GLY A 196 " =    0.901
peak=    3.376 closest distance to " CA  ARG A 156 " =    1.063
peak=    3.372 closest distance to " OE2 GLU A  53 " =    1.850
peak=    3.372 closest distance to " CA  ALA A   7 " =    0.944
peak=    3.370 closest distance to " CD  ARG A 269 " =    0.927
peak=    3.369 closest distance to " CB  HIS A  86 " =    1.006
peak=    3.367 closest distance to " O   HOH Z 120 " =    0.962
peak=    3.366 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.365 closest distance to " O   HOH Z 180 " =    2.156
peak=    3.365 closest distance to " CB  ARG A 156 " =    1.062
peak=    3.364 closest distance to " O   HOH Z 287 " =    1.915
peak=    3.360 closest distance to " O   HOH Z 276 " =    1.034
peak=    3.359 closest distance to " CE3 TRP A 150 " =    1.306
peak=    3.358 closest distance to " OD1 ASN A 217 " =    1.330
peak=    3.355 closest distance to " CB  ARG A  79 " =    1.085
peak=    3.350 closest distance to " CH2 TRP A 150 " =    1.152
peak=    3.348 closest distance to " CD  ARG A 195 " =    3.503
peak=    3.346 closest distance to " CG  TRP A 179 " =    2.205
peak=    3.344 closest distance to " OD1 ASN A  60 " =    1.016
peak=    3.341 closest distance to " CG2 VAL A 257 " =    0.921
peak=    3.339 closest distance to " O   HOH Z 201 " =    1.995
peak=    3.337 closest distance to " O   HOH Z 189 " =    3.526
peak=    3.337 closest distance to " N   GLU A 152 " =    1.411
peak=    3.336 closest distance to " O   HOH Z 244 " =    1.647
peak=    3.336 closest distance to " CD  ARG A  66 " =    2.076
peak=    3.333 closest distance to " CG  GLN A  89 " =    1.519
peak=    3.331 closest distance to " O   HOH Z 111 " =    1.493
peak=    3.331 closest distance to " O   HOH Z 285 " =    2.402
peak=    3.329 closest distance to " O   HOH Z  78 " =    1.660
peak=    3.328 closest distance to " O   HOH Z 329 " =    4.105
peak=    3.325 closest distance to " OE1 GLN A 278 " =    0.992
peak=    3.323 closest distance to " CB  LEU A 300 " =    0.959
peak=    3.322 closest distance to " NE2 GLN A  58 " =    4.494
peak=    3.319 closest distance to " O   HOH Z 389 " =    1.896
peak=    3.315 closest distance to " O   HOH Z 251 " =    1.442
peak=    3.312 closest distance to " N   SER A 135 " =    1.383
peak=    3.311 closest distance to " CA  TYR A 116 " =    1.318
peak=    3.310 closest distance to " CB  GLU A 175 " =    1.020
peak=    3.307 closest distance to " CB  SER A  99 " =    0.844
peak=    3.303 closest distance to " O   HOH Z 170 " =    1.031
peak=    3.298 closest distance to " CD1 ILE A  33 " =    1.758
peak=    3.298 closest distance to " CB  GLN A 183 " =    1.158
peak=    3.290 closest distance to " O   HOH Z 282 " =    2.031
peak=    3.289 closest distance to " CG1 VAL A 296 " =    1.197
peak=    3.281 closest distance to " O   HOH Z 240 " =    1.955
peak=    3.281 closest distance to " CA  SER A  87 " =    0.971
peak=    3.277 closest distance to " CD1AILE A 234 " =    0.968
peak=    3.274 closest distance to " NZ  LYS A 117 " =    1.347
peak=    3.271 closest distance to " N   ARG A 156 " =    1.296
peak=    3.266 closest distance to " O   HOH Z 225 " =    1.665
peak=    3.265 closest distance to " O   HOH Z 421 " =    2.972
peak=    3.263 closest distance to " O   HOH Z 127 " =    0.928
peak=    3.263 closest distance to " CB  ALA A 161 " =    1.036
peak=    3.261 closest distance to " CA  ASP A 191 " =    1.045
peak=    3.260 closest distance to " CB  VAL A 296 " =    1.486
peak=    3.259 closest distance to " OE1 GLU A  46 " =    1.147
peak=    3.258 closest distance to " O   HOH Z 313 " =    1.575
peak=    3.256 closest distance to " O   HOH Z  68 " =    1.826
peak=    3.251 closest distance to " CB  VAL A 265 " =    1.277
peak=    3.250 closest distance to " O   HOH Z 158 " =    2.899
peak=    3.248 closest distance to " O   GLY A 302 " =    2.373
peak=    3.245 closest distance to " CB  ARG A 102 " =    0.880
peak=    3.244 closest distance to " CA  THR A 264 " =    0.914
peak=    3.242 closest distance to " CA  GLU A  46 " =    0.798
peak=    3.242 closest distance to " CG1 ILE A  20 " =    1.343
peak=    3.241 closest distance to " CA  ILE A 106 " =    0.882
peak=    3.240 closest distance to " O   HOH Z   7 " =    3.287
peak=    3.239 closest distance to " O   HOH Z   1 " =    1.684
peak=    3.239 closest distance to " N   GLU A   2 " =    1.540
peak=    3.238 closest distance to " O   ASP A 124 " =    1.209
peak=    3.235 closest distance to " OH  TYR A 116 " =    1.903
peak=    3.234 closest distance to " CA  ALA A 154 " =    1.103
peak=    3.232 closest distance to " CB  TYR A 169 " =    0.999
peak=    3.231 closest distance to " N   ALA A   1 " =    1.953
peak=    3.229 closest distance to " O   HOH Z 200 " =    2.411
peak=    3.227 closest distance to " O   HOH Z 352 " =    1.786
peak=    3.226 closest distance to " CB  TRP A 274 " =    1.025
peak=    3.225 closest distance to " CD  ARG A  79 " =    1.024
peak=    3.225 closest distance to " CB  ALA A 104 " =    0.803
peak=    3.224 closest distance to " O   MET A 105 " =    1.720
peak=    3.223 closest distance to " CB  LEU A  83 " =    0.769
peak=    3.222 closest distance to " O   HOH Z  59 " =    1.711
peak=    3.221 closest distance to " O   HOH Z  88 " =    2.982
peak=    3.219 closest distance to " CG  ARG A 138 " =    1.472
peak=    3.218 closest distance to " O   HOH Z 154 " =    2.299
peak=    3.215 closest distance to " CD1 LEU A   5 " =    1.215
peak=    3.214 closest distance to " O   HOH Z   6 " =    1.608
peak=    3.212 closest distance to " CB  TRP A 150 " =    1.080
peak=    3.212 closest distance to " CA  VAL A 121 " =    0.968
peak=    3.212 closest distance to " O   HOH Z 175 " =    3.843
peak=    3.210 closest distance to " O   HOH Z 288 " =    1.851
peak=    3.210 closest distance to " CG  ARG A 159 " =    0.732
peak=    3.210 closest distance to " CB  ASP A 171 " =    0.890
peak=    3.209 closest distance to " CB  GLU A 277 " =    3.622
peak=    3.209 closest distance to " CB  SER A  62 " =    3.771
peak=    3.203 closest distance to " NH2AARG A 190 " =    1.835
peak=    3.203 closest distance to " CE2 PHE A  16 " =    1.017
peak=    3.200 closest distance to " O   HOH Z 365 " =    5.659
peak=    3.199 closest distance to " O   HOH Z 332 " =    1.584
peak=    3.196 closest distance to " NH1 ARG A  14 " =    1.189
peak=    3.189 closest distance to " CA  ALA A 295 " =    1.168
peak=    3.186 closest distance to " CG2 ILE A 151 " =    0.864
peak=    3.186 closest distance to " O   HOH Z 213 " =    2.288
peak=    3.182 closest distance to " O   HOH Z 216 " =    4.161
peak=    3.177 closest distance to " CB  LEU A 237 " =    0.900
peak=    3.177 closest distance to " CA  ALA A 161 " =    1.063
peak=    3.177 closest distance to " O   HOH Z 438 " =    2.207
peak=    3.177 closest distance to " O   HOH Z 122 " =    2.130
peak=    3.176 closest distance to " OG ASER A 212 " =    1.977
peak=    3.175 closest distance to " N   ASN A 127 " =    1.436
peak=    3.173 closest distance to " N   TRP A  70 " =    0.992
peak=    3.172 closest distance to " O   HOH Z 145 " =    1.781
peak=    3.172 closest distance to " O   HOH Z 302 " =    1.499
peak=    3.169 closest distance to " N   SER A 210 " =    1.111
peak=    3.167 closest distance to " O   THR A 220 " =    1.323
peak=    3.166 closest distance to " CA  ASP A 162 " =    0.961
peak=    3.164 closest distance to " O   HOH Z 431 " =    1.167
peak=    3.159 closest distance to " O   HOH Z 368 " =    1.914
peak=    3.157 closest distance to " O   HOH Z 234 " =    4.018
peak=    3.154 closest distance to " C   HIS A 115 " =    1.059
peak=    3.153 closest distance to " CG  MET A 113 " =    1.371
peak=    3.148 closest distance to " O   HOH Z 215 " =    1.564
peak=    3.143 closest distance to " C   GLN A  73 " =    1.070
peak=    3.141 closest distance to " CA  ASP A 149 " =    1.408
peak=    3.136 closest distance to " O   HOH Z 279 " =    4.254
peak=    3.134 closest distance to " O   ASP A  50 " =    1.405
peak=    3.125 closest distance to " O   HOH Z 172 " =    2.255
peak=    3.123 closest distance to " O   HOH Z 172 " =    5.092
peak=    3.123 closest distance to " O   HOH Z 325 " =    2.228
peak=    3.114 closest distance to " O   HOH Z 298 " =    3.979
peak=    3.113 closest distance to " NH2 ARG A 269 " =    1.014
peak=    3.109 closest distance to " CA  ALA A 100 " =    1.085
peak=    3.108 closest distance to " CB  ILE A 120 " =    1.365
peak=    3.103 closest distance to " CG2 VAL A 268 " =    0.862
peak=    3.100 closest distance to " CZ  PHE A 208 " =    1.052
peak=    3.098 closest distance to " OE1 GLU A 236 " =    1.270
peak=    3.096 closest distance to " CD2 LEU A   5 " =    1.310
peak=    3.090 closest distance to " NE2 HIS A  81 " =    1.114
peak=    3.089 closest distance to " O   HOH Z  70 " =    0.923
peak=    3.081 closest distance to " CA  SER A 271 " =    0.779
peak=    3.076 closest distance to " CB  ALA A 291 " =    1.192
peak=    3.074 closest distance to " O   ASN A 142 " =    1.021
peak=    3.071 closest distance to " O   HOH Z  60 " =    1.184
peak=    3.061 closest distance to " O   HOH Z 409 " =    3.540
peak=    3.045 closest distance to " O   HOH Z 153 " =    4.131
peak=    3.037 closest distance to " O   HOH Z 287 " =    2.287
peak=    3.025 closest distance to " O   HOH Z 140 " =    1.925
peak=    3.017 closest distance to " CA  ASP A  65 " =    1.052

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.655 - 5.633
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.722 - 5.633

peak=   -4.873 closest distance to " O   PRO A 198 " =    1.247
peak=   -4.300 closest distance to " O   ALA A  10 " =    1.528
peak=   -4.300 closest distance to " CD  ARG A 156 " =    1.981
peak=   -4.293 closest distance to " CG  GLN A  88 " =    0.903
peak=   -4.293 closest distance to " CD  ARG A  14 " =    3.188
peak=   -4.211 closest distance to " O   HOH Z 216 " =    1.309
peak=   -4.130 closest distance to " CD2 TYR A 293 " =    1.877
peak=   -4.076 closest distance to " O   HOH Z  32 " =    1.725
peak=   -4.054 closest distance to " CG  MET A 105 " =    0.934
peak=   -4.021 closest distance to " O   VAL A 125 " =    2.296
peak=   -4.004 closest distance to " O   HOH Z 111 " =    1.749
peak=   -4.000 closest distance to " O   GLN A 240 " =    3.146
peak=   -3.993 closest distance to " CD1 TYR A 247 " =    2.746
peak=   -3.988 closest distance to " OE1 GLN A  88 " =    1.111
peak=   -3.975 closest distance to " O   PRO A 163 " =    1.889
peak=   -3.944 closest distance to " O   HOH Z 404 " =    1.071
peak=   -3.910 closest distance to " CG2 ILE A  49 " =    2.841
peak=   -3.902 closest distance to " CB  ASP A  27 " =    2.510
peak=   -3.899 closest distance to " CB  ALA A 291 " =    2.331
peak=   -3.879 closest distance to " O   HOH Z  24 " =    0.979
peak=   -3.857 closest distance to " CB  PRO A 243 " =    2.551
peak=   -3.853 closest distance to " CD2 TYR A 116 " =    2.172
peak=   -3.850 closest distance to " OG  SER A  97 " =    2.045
peak=   -3.843 closest distance to " O   HOH Z 374 " =    1.970
peak=   -3.838 closest distance to " O   HOH Z 389 " =    2.277
peak=   -3.833 closest distance to " CD1 TRP A 179 " =    1.196
peak=   -3.827 closest distance to " OE1 GLU A  44 " =    1.706
peak=   -3.827 closest distance to " CB  GLN A  55 " =    1.297
peak=   -3.804 closest distance to " OG BSER A 134 " =    1.654
peak=   -3.796 closest distance to " O   HOH Z  60 " =    1.336
peak=   -3.785 closest distance to " CB  ALA A  43 " =    2.649
peak=   -3.769 closest distance to " O   HOH Z  52 " =    2.191
peak=   -3.768 closest distance to " C   PHE A  59 " =    1.097
peak=   -3.753 closest distance to " C   ILE A 239 " =    1.917
peak=   -3.743 closest distance to " O   HOH Z  28 " =    1.156
peak=   -3.742 closest distance to " CA  GLY A  98 " =    1.855
peak=   -3.731 closest distance to " O   HOH Z  39 " =    0.946
peak=   -3.715 closest distance to " CZ3 TRP A 179 " =    1.263
peak=   -3.697 closest distance to " O   HOH Z 275 " =    1.754
peak=   -3.695 closest distance to " CA  HIS A 207 " =    1.105
peak=   -3.689 closest distance to " O   HOH Z 103 " =    1.419
peak=   -3.683 closest distance to " O   HOH Z 231 " =    2.056
peak=   -3.670 closest distance to " NE2 GLN A 122 " =    0.957
peak=   -3.665 closest distance to " N   ALA A  43 " =    2.457
peak=   -3.657 closest distance to " CB  ALA A   9 " =    2.515
peak=   -3.653 closest distance to " CG1 VAL A  78 " =    2.583
peak=   -3.611 closest distance to " CA  GLY A 203 " =    2.433
peak=   -3.599 closest distance to " O   HOH Z 316 " =    1.846
peak=   -3.594 closest distance to " O   GLY A 203 " =    2.563
peak=   -3.593 closest distance to " O   HOH Z 318 " =    1.374
peak=   -3.588 closest distance to " O   HOH Z 166 " =    1.895
peak=   -3.582 closest distance to " CG  GLN A 223 " =    2.408
peak=   -3.580 closest distance to " O   ASP A 253 " =    1.805
peak=   -3.573 closest distance to " CB  ALA A 131 " =    1.942
peak=   -3.573 closest distance to " O   HOH Z 298 " =    2.331
peak=   -3.564 closest distance to " O   GLY A  80 " =    2.557
peak=   -3.559 closest distance to " CB  ALA A 160 " =    2.207
peak=   -3.534 closest distance to " O   HOH Z 313 " =    1.603
peak=   -3.532 closest distance to " O   HOH Z 368 " =    1.826
peak=   -3.526 closest distance to " O   SER A 135 " =    1.385
peak=   -3.512 closest distance to " O   HOH Z 286 " =    1.471
peak=   -3.498 closest distance to " O   HOH Z 368 " =    1.580
peak=   -3.495 closest distance to " O   HOH Z 371 " =    2.330
peak=   -3.493 closest distance to " O   SER A  22 " =    2.883
peak=   -3.492 closest distance to " OG  SER A  32 " =    0.998
peak=   -3.488 closest distance to " CD  LYS A 166 " =    2.509
peak=   -3.481 closest distance to " CD2 PHE A  61 " =    2.081
peak=   -3.474 closest distance to " O   HOH Z 410 " =    2.308
peak=   -3.460 closest distance to " CG2 THR A 221 " =    2.283
peak=   -3.448 closest distance to " C   VAL A  72 " =    0.920
peak=   -3.445 closest distance to " CG2BVAL A  41 " =    1.286
peak=   -3.439 closest distance to " CG1 VAL A 265 " =    2.532
peak=   -3.434 closest distance to " O   HOH Z 282 " =    4.430
peak=   -3.433 closest distance to " NE2 GLN A 223 " =    1.616
peak=   -3.430 closest distance to " N   LEU A 282 " =    2.247
peak=   -3.428 closest distance to " OG1 THR A 157 " =    1.722
peak=   -3.427 closest distance to " O   HOH Z 290 " =    1.198
peak=   -3.423 closest distance to " O   HOH Z  37 " =    1.242
peak=   -3.413 closest distance to " OD1 ASN A 148 " =    1.326
peak=   -3.408 closest distance to " OG  SER A  63 " =    1.217
peak=   -3.404 closest distance to " O   HOH Z 132 " =    4.963
peak=   -3.401 closest distance to " CG  LEU A  83 " =    2.299
peak=   -3.400 closest distance to " CG2 THR A 178 " =    2.198
peak=   -3.400 closest distance to " NH2AARG A 275 " =    5.633
peak=   -3.399 closest distance to " CE3 TRP A  70 " =    1.746
peak=   -3.397 closest distance to " CB  ALA A 100 " =    2.356
peak=   -3.396 closest distance to " O   HOH Z 198 " =    2.105
peak=   -3.393 closest distance to " CD  LYS A 289 " =    2.357
peak=   -3.383 closest distance to " CD1 LEU A 101 " =    2.353
peak=   -3.380 closest distance to " NH1AARG A 275 " =    1.940
peak=   -3.379 closest distance to " O   ALA A  51 " =    1.254
peak=   -3.378 closest distance to " CB  PRO A  54 " =    2.363
peak=   -3.378 closest distance to " CA  ASN A 110 " =    0.956
peak=   -3.375 closest distance to " CG1BVAL A  41 " =    2.712
peak=   -3.369 closest distance to " CA  GLY A 133 " =    1.991
peak=   -3.366 closest distance to " O   HOH Z  85 " =    2.348
peak=   -3.365 closest distance to " ND2 ASN A 285 " =    2.165
peak=   -3.364 closest distance to " O   HOH Z 108 " =    1.188
peak=   -3.364 closest distance to " O   SER A  99 " =    1.292
peak=   -3.363 closest distance to " N   PRO A  54 " =    1.023
peak=   -3.360 closest distance to " O   HOH Z 163 " =    1.612
peak=   -3.356 closest distance to " C   ASN A 285 " =    2.369
peak=   -3.343 closest distance to " N   ASP A 191 " =    1.194
peak=   -3.340 closest distance to " NZ  LYS A 166 " =    1.389
peak=   -3.338 closest distance to " CB  TYR A  15 " =    1.921
peak=   -3.335 closest distance to " OD2 ASP A  27 " =    1.625
peak=   -3.333 closest distance to " O   LEU A 300 " =    2.268
peak=   -3.333 closest distance to " O   ALA A 158 " =    2.220
peak=   -3.327 closest distance to " O   HOH Z 276 " =    1.078
peak=   -3.325 closest distance to " CG2 VAL A 232 " =    2.140
peak=   -3.324 closest distance to " O   HOH Z 348 " =    1.995
peak=   -3.320 closest distance to " CE1 PHE A 225 " =    1.996
peak=   -3.319 closest distance to " N   GLN A  58 " =    1.461
peak=   -3.314 closest distance to " O   GLU A 152 " =    1.706
peak=   -3.309 closest distance to " NZ  LYS A 119 " =    0.722
peak=   -3.307 closest distance to " O   HOH Z 351 " =    1.627
peak=   -3.306 closest distance to " OE1 GLN A 278 " =    1.158
peak=   -3.306 closest distance to " CB  TYR A  68 " =    1.064
peak=   -3.300 closest distance to " O   HOH Z 188 " =    0.970
peak=   -3.298 closest distance to " O   HOH Z 275 " =    1.654
peak=   -3.298 closest distance to " CB  TRP A  85 " =    1.991
peak=   -3.290 closest distance to " O   HOH Z  76 " =    1.633
peak=   -3.290 closest distance to " O   ILE A  49 " =    1.634
peak=   -3.288 closest distance to " NH2 ARG A  79 " =    2.153
peak=   -3.286 closest distance to " CD2 TYR A 169 " =    2.306
peak=   -3.285 closest distance to " CB  PHE A 130 " =    1.200
peak=   -3.285 closest distance to " O   HOH Z  69 " =    1.601
peak=   -3.284 closest distance to " O   HOH Z 165 " =    2.326
peak=   -3.282 closest distance to " O   HOH Z 143 " =    1.542
peak=   -3.275 closest distance to " CA  GLY A 241 " =    2.223
peak=   -3.269 closest distance to " O   HOH Z 413 " =    3.588
peak=   -3.268 closest distance to " CB  ASP A 132 " =    2.552
peak=   -3.266 closest distance to " CG2 VAL A 112 " =    2.605
peak=   -3.261 closest distance to " O   TRP A  70 " =    1.576
peak=   -3.261 closest distance to " CA  ILE A 120 " =    1.163
peak=   -3.261 closest distance to " O   HOH Z 139 " =    3.184
peak=   -3.257 closest distance to " O   HOH Z 407 " =    3.308
peak=   -3.257 closest distance to " CZ  PHE A 130 " =    1.117
peak=   -3.247 closest distance to " CE1 PHE A  16 " =    2.711
peak=   -3.244 closest distance to " CB  CYS A 254 " =    1.893
peak=   -3.242 closest distance to " O   HOH Z 131 " =    3.791
peak=   -3.241 closest distance to " OG ASER A 134 " =    1.294
peak=   -3.241 closest distance to " CG2 ILE A 120 " =    0.985
peak=   -3.240 closest distance to " CB  HIS A  86 " =    1.181
peak=   -3.240 closest distance to " NE2 HIS A  81 " =    1.263
peak=   -3.239 closest distance to " CA  GLY A 241 " =    2.213
peak=   -3.238 closest distance to " O   HOH Z 102 " =    1.800
peak=   -3.237 closest distance to " ND2 ASN A 217 " =    2.118
peak=   -3.237 closest distance to " CZ  PHE A  38 " =    2.483
peak=   -3.234 closest distance to " O   HOH Z  68 " =    1.538
peak=   -3.232 closest distance to " CD2 HIS A 207 " =    1.540
peak=   -3.231 closest distance to " O   HOH Z  27 " =    0.776
peak=   -3.231 closest distance to " O   HOH Z  37 " =    2.088
peak=   -3.226 closest distance to " OG1 THR A  82 " =    1.232
peak=   -3.225 closest distance to " OE2 GLU A 152 " =    1.186
peak=   -3.224 closest distance to " CD  GLU A 236 " =    1.097
peak=   -3.223 closest distance to " CD2 PHE A  16 " =    2.386
peak=   -3.222 closest distance to " O   ALA A 180 " =    1.162
peak=   -3.222 closest distance to " O   HOH Z 292 " =    1.846
peak=   -3.221 closest distance to " CG1 VAL A 125 " =    1.823
peak=   -3.216 closest distance to " O   HOH Z 201 " =    1.740
peak=   -3.216 closest distance to " O   MET A  47 " =    2.763
peak=   -3.214 closest distance to " O   HOH Z 285 " =    1.663
peak=   -3.210 closest distance to " O   HOH Z 181 " =    1.532
peak=   -3.209 closest distance to " CD1 LEU A   5 " =    2.442
peak=   -3.209 closest distance to " CG  GLN A  55 " =    1.174
peak=   -3.207 closest distance to " O   HOH Z 251 " =    0.983
peak=   -3.207 closest distance to " O   HOH Z 390 " =    2.343
peak=   -3.203 closest distance to " ND2 ASN A 249 " =    2.153
peak=   -3.201 closest distance to " CD2 LEU A 143 " =    2.514
peak=   -3.201 closest distance to " O   HOH Z 259 " =    3.817
peak=   -3.199 closest distance to " O   HOH Z 300 " =    2.179
peak=   -3.199 closest distance to " CA  SER A  62 " =    2.632
peak=   -3.197 closest distance to " CG2 VAL A 189 " =    2.661
peak=   -3.194 closest distance to " O   HOH Z  58 " =    0.775
peak=   -3.174 closest distance to " CG  PRO A 213 " =    2.025
peak=   -3.172 closest distance to " O   HOH Z  42 " =    2.368
peak=   -3.170 closest distance to " O   HOH Z 128 " =    2.496
peak=   -3.168 closest distance to " O   HOH Z  11 " =    1.653
peak=   -3.165 closest distance to " O   ASP A  27 " =    1.829
peak=   -3.159 closest distance to " O   HOH Z 270 " =    2.922
peak=   -3.156 closest distance to " O   HOH Z 126 " =    1.700
peak=   -3.152 closest distance to " O   HOH Z 281 " =    2.874
peak=   -3.146 closest distance to " OE2 GLU A 152 " =    2.296
peak=   -3.145 closest distance to " O   HOH Z 165 " =    1.822
peak=   -3.143 closest distance to " SG BCYS A 201 " =    2.113
peak=   -3.141 closest distance to " N   ARG A 159 " =    2.080
peak=   -3.139 closest distance to " CA  GLY A 241 " =    3.221
peak=   -3.135 closest distance to " O   HOH Z 241 " =    1.467
peak=   -3.135 closest distance to " CE3 TRP A 150 " =    2.078
peak=   -3.134 closest distance to " CG2BVAL A  41 " =    2.936
peak=   -3.131 closest distance to " O   HOH Z 425 " =    0.927
peak=   -3.121 closest distance to " O   ALA A   1 " =    1.362
peak=   -3.119 closest distance to " CB  SER A  63 " =    3.347
peak=   -3.110 closest distance to " O   HOH Z 257 " =    1.273
peak=   -3.105 closest distance to " O   HOH Z 133 " =    1.564
peak=   -3.099 closest distance to " O   PHE A 218 " =    1.579
peak=   -3.093 closest distance to " O   HOH Z 364 " =    2.491
peak=   -3.087 closest distance to " N   TRP A 274 " =    1.142
peak=   -3.082 closest distance to " OE1 GLN A 183 " =    1.824
peak=   -3.077 closest distance to " OD2 ASP A  50 " =    2.363
peak=   -3.077 closest distance to " CB  ALA A  10 " =    2.334
peak=   -3.065 closest distance to " O   HOH Z  69 " =    1.824
peak=   -3.065 closest distance to " CB  ALA A 158 " =    1.800
peak=   -3.063 closest distance to " CE2 TYR A  30 " =    2.455
peak=   -3.053 closest distance to " O   HOH Z 323 " =    1.936
peak=   -3.051 closest distance to " O   HOH Z 211 " =    2.418
peak=   -3.023 closest distance to " CE  LYS A  76 " =    2.941

================= 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    :  0.4850 0.4875   6.294600e+00   6.282977e+00
   1_bss:  0.4782 0.4848   6.292802e+00   6.279868e+00
   1_xyz:  0.3863 0.4237   6.157441e+00   6.207155e+00
   1_adp:  0.3498 0.4372   6.118545e+00   6.223182e+00
   1_occ:  0.3494 0.4381   6.118547e+00   6.223573e+00
   2_bss:  0.3502 0.4364   6.120279e+00   6.223214e+00
   2_xyz:  0.2766 0.3508   5.926286e+00   6.079474e+00
   2_adp:  0.2575 0.3370   5.884266e+00   6.053366e+00
   2_occ:  0.2573 0.3372   5.883721e+00   6.053557e+00
   3_bss:  0.2573 0.3373   5.883866e+00   6.052720e+00
   3_xyz:  0.2172 0.2892   5.738187e+00   5.937808e+00
   3_adp:  0.1968 0.2799   5.681911e+00   5.904144e+00
   3_occ:  0.1968 0.2799   5.681763e+00   5.904498e+00
   4_bss:  0.1970 0.2803   5.681876e+00   5.904120e+00
   4_xyz:  0.1623 0.2336   5.493211e+00   5.750540e+00
   4_adp:  0.1476 0.2104   5.405855e+00   5.652888e+00
   4_occ:  0.1476 0.2103   5.405419e+00   5.652483e+00
   5_bss:  0.1480 0.2102   5.405483e+00   5.651320e+00
   5_xyz:  0.1407 0.1973   5.355472e+00   5.591695e+00
   5_adp:  0.1372 0.1893   5.324603e+00   5.550741e+00
   5_occ:  0.1371 0.1892   5.324108e+00   5.550036e+00
   5_bss:  0.1369 0.1892   5.323540e+00   5.549447e+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:  0.324  60.089  -0.332   0.503   2.058   0.000   0.000   0.000
   1_xyz:  0.324  60.089  -0.332   0.503   2.058   0.000   0.000   0.000
   1_adp:  0.324  60.089  -0.332   0.503   2.058   0.000   0.000   0.000
   1_occ:  0.324  60.089  -0.332   0.503   2.058   0.000   0.000   0.000
   2_bss:  0.363  91.475  -0.133  -0.269   1.612  -0.000   0.000   0.000
   2_xyz:  0.363  91.475  -0.133  -0.269   1.612  -0.000   0.000   0.000
   2_adp:  0.363  91.475  -0.133  -0.269   1.612  -0.000   0.000   0.000
   2_occ:  0.363  91.475  -0.133  -0.269   1.612  -0.000   0.000   0.000
   3_bss:  0.349  80.829  -1.124  -1.427   0.160  -0.000   0.000   0.000
   3_xyz:  0.349  80.829  -1.124  -1.427   0.160  -0.000   0.000   0.000
   3_adp:  0.349  80.829  -1.124  -1.427   0.160  -0.000   0.000   0.000
   3_occ:  0.349  80.829  -1.124  -1.427   0.160  -0.000   0.000   0.000
   4_bss:  0.345  94.976  -1.548  -2.029  -0.150  -0.000  -0.000  -0.000
   4_xyz:  0.345  94.976  -1.548  -2.029  -0.150  -0.000  -0.000  -0.000
   4_adp:  0.345  94.976  -1.548  -2.029  -0.150  -0.000  -0.000  -0.000
   4_occ:  0.345  94.976  -1.548  -2.029  -0.150  -0.000  -0.000  -0.000
   5_bss:  0.335  87.308  -1.766  -2.436  -0.483  -0.000  -0.000  -0.000
   5_xyz:  0.335  87.308  -1.766  -2.436  -0.483  -0.000  -0.000  -0.000
   5_adp:  0.335  87.308  -1.766  -2.436  -0.483  -0.000  -0.000  -0.000
   5_occ:  0.335  87.308  -1.766  -2.436  -0.483  -0.000  -0.000  -0.000
   5_bss:  0.327  79.966  -2.115  -2.885  -0.759  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.798 0.3694  0.5036    77377.837
   1_bss:  61.536 0.3718  0.5279    76684.101
   1_xyz:  49.016 0.5318  0.7338    53660.510
   1_adp:  50.491 0.5129  0.7272    56986.073
   1_occ:  50.624 0.5111  0.7244    57177.384
   2_bss:  50.485 0.5129  0.7187    56967.749
   2_xyz:  37.791 0.6673  0.9091    34062.560
   2_adp:  36.102 0.6874  0.9298    31578.734
   2_occ:  36.093 0.6875  0.9294    31554.175
   3_bss:  36.004 0.6884  0.8925    31457.360
   3_xyz:  29.916 0.7572  0.9580    22358.478
   3_adp:  28.565 0.7720  0.9484    20457.971
   3_occ:  28.571 0.7719  0.9482    20459.518
   4_bss:  28.553 0.7721  0.9340    20453.249
   4_xyz:  23.281 0.8270  0.9771    13784.055
   4_adp:  20.370 0.8572  0.9849    11231.039
   4_occ:  20.360 0.8573  0.9848    11215.183
   5_bss:  20.330 0.8576  0.9741    11181.764
   5_xyz:  18.631 0.8742  0.9813     9771.925
   5_adp:  17.559 0.8847  0.9823     9069.869
   5_occ:  17.548 0.8848  0.9823     9053.086
   5_bss:  17.531 0.8849  0.9691     9040.203
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.7169e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.7169e-01
   1_xyz:   1.549  0.011  0.103 16.083  0.006  4.107   1.3325e-01
   1_adp:   1.549  0.011  0.103 16.083  0.006  4.107   1.3325e-01
   1_occ:   1.549  0.011  0.103 16.083  0.006  4.107   1.3325e-01
   2_bss:   1.549  0.011  0.103 16.083  0.006  4.107   1.3325e-01
   2_xyz:   1.406  0.010  0.096 15.436  0.006  4.110   1.0595e-01
   2_adp:   1.406  0.010  0.096 15.436  0.006  4.110   1.0595e-01
   2_occ:   1.406  0.010  0.096 15.436  0.006  4.110   1.0595e-01
   3_bss:   1.406  0.010  0.096 15.436  0.006  4.110   1.0595e-01
   3_xyz:   0.987  0.007  0.070 14.587  0.004  4.121   5.8675e-02
   3_adp:   0.987  0.007  0.070 14.587  0.004  4.121   5.8675e-02
   3_occ:   0.987  0.007  0.070 14.587  0.004  4.121   5.8675e-02
   4_bss:   0.987  0.007  0.070 14.587  0.004  4.121   5.8675e-02
   4_xyz:   1.094  0.009  0.080 14.699  0.004  4.113   7.1219e-02
   4_adp:   1.094  0.009  0.080 14.699  0.004  4.113   7.1219e-02
   4_occ:   1.094  0.009  0.080 14.699  0.004  4.113   7.1219e-02
   5_bss:   1.094  0.009  0.080 14.699  0.004  4.113   7.1219e-02
   5_xyz:   0.886  0.006  0.066 14.256  0.003  4.119   4.8679e-02
   5_adp:   0.886  0.006  0.066 14.256  0.003  4.119   4.8679e-02
   5_occ:   0.886  0.006  0.066 14.256  0.003  4.119   4.8679e-02
   5_bss:   0.886  0.006  0.066 14.256  0.003  4.119   4.8679e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4267e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4267e-01
   1_xyz:   9.157  0.054  0.321 82.529  0.033  2.033   1.0310e-01
   1_adp:   9.157  0.054  0.321 82.529  0.033  2.033   1.0310e-01
   1_occ:   9.157  0.054  0.321 82.529  0.033  2.033   1.0310e-01
   2_bss:   9.157  0.054  0.321 82.529  0.033  2.033   1.0310e-01
   2_xyz:  10.772  0.052  0.304 81.869  0.048  2.126   1.0546e-01
   2_adp:  10.772  0.052  0.304 81.869  0.048  2.126   1.0546e-01
   2_occ:  10.772  0.052  0.304 81.869  0.048  2.126   1.0546e-01
   3_bss:  10.772  0.052  0.304 81.869  0.048  2.126   1.0546e-01
   3_xyz:   7.881  0.043  0.256 80.464  0.030  2.355   6.3073e-02
   3_adp:   7.881  0.043  0.256 80.464  0.030  2.355   6.3073e-02
   3_occ:   7.881  0.043  0.256 80.464  0.030  2.355   6.3073e-02
   4_bss:   7.881  0.043  0.256 80.464  0.030  2.355   6.3073e-02
   4_xyz:   7.772  0.060  0.246 81.519  0.038  2.342   5.3730e-02
   4_adp:   7.772  0.060  0.246 81.519  0.038  2.342   5.3730e-02
   4_occ:   7.772  0.060  0.246 81.519  0.038  2.342   5.3730e-02
   5_bss:   7.772  0.060  0.246 81.519  0.038  2.342   5.3730e-02
   5_xyz:   8.198  0.040  0.250 79.576  0.036  2.388   3.1560e-02
   5_adp:   8.198  0.040  0.250 79.576  0.036  2.388   3.1560e-02
   5_occ:   8.198  0.040  0.250 79.576  0.036  2.388   3.1560e-02
   5_bss:   8.198  0.040  0.250 79.576  0.036  2.388   3.1560e-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: 100.44   0.00  20.41  77.86   0.00  16.90 100.44   0.00  39.52
   1_occ: 100.44   0.00  20.41  77.86   0.00  16.90 100.44   0.00  39.52
   2_bss: 100.44   0.00  20.41  77.86   0.00  16.90 100.44   0.00  39.52
   2_xyz: 100.44   0.00  20.41  77.86   0.00  16.90 100.44   0.00  39.52
   2_adp:  99.77   0.00  20.28  76.18   0.00  16.43  99.77   0.00  41.27
   2_occ:  99.77   0.00  20.28  76.18   0.00  16.43  99.77   0.00  41.27
   3_bss:  99.77   0.00  20.28  76.18   0.00  16.43  99.77   0.00  41.27
   3_xyz:  99.77   0.00  20.28  76.18   0.00  16.43  99.77   0.00  41.27
   3_adp: 126.01   0.00  21.62 107.72   0.00  15.84 126.01   3.38  53.09
   3_occ: 126.01   0.00  21.62 107.72   0.00  15.84 126.01   3.38  53.09
   4_bss: 126.01   0.00  21.62 107.72   0.00  15.84 126.01   3.38  53.09
   4_xyz: 126.01   0.00  21.62 107.72   0.00  15.84 126.01   3.38  53.09
   4_adp: 134.06   0.00  20.36 110.07   0.00  14.33 134.06   6.03  53.23
   4_occ: 134.06   0.00  20.36 110.07   0.00  14.33 134.06   6.03  53.23
   5_bss: 134.06   0.00  20.36 110.07   0.00  14.33 134.06   6.03  53.23
   5_xyz: 134.06   0.00  20.36 110.07   0.00  14.33 134.06   6.03  53.23
   5_adp: 130.89   0.99  19.68 108.03   0.99  13.83 130.89   6.55  51.57
   5_occ: 130.89   0.99  19.68 108.03   0.99  13.83 130.89   6.55  51.57
   5_bss: 130.85   0.96  19.65 108.00   0.96  13.79 130.85   6.52  51.54
------------------------------------------------------------------------
 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:    1.667    0.023    0.350
   1_adp:    1.667    0.023    0.350
   1_occ:    1.667    0.023    0.350
   2_bss:    1.667    0.023    0.350
   2_xyz:    1.390    0.075    0.577
   2_adp:    1.390    0.075    0.577
   2_occ:    1.390    0.075    0.577
   3_bss:    1.390    0.075    0.577
   3_xyz:    1.357    0.052    0.672
   3_adp:    1.357    0.052    0.672
   3_occ:    1.357    0.052    0.672
   4_bss:    1.357    0.052    0.672
   4_xyz:    1.417    0.024    0.776
   4_adp:    1.417    0.024    0.776
   4_occ:    1.417    0.024    0.776
   5_bss:    1.417    0.024    0.776
   5_xyz:    1.464    0.074    0.800
   5_adp:    1.464    0.074    0.800
   5_occ:    1.464    0.074    0.800
   5_bss:    1.464    0.074    0.800
------------------------------------------------------------------------

CPU time actual refinement: 374.84


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/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_1109/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1109/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 374.68 
  Macro-tasks:
    bulk solvent and scale       = 61.26  
    individual site refinement   = 146.09 
    weights calculation          = 30.24  
    collect and process          = 6.40   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 244.11 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 117.81 
    alpha_beta                      = 8.18   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 123.97 
    fmodel                         = 9.13   
    r_factors                      = 0.39   
    phase_errors                   = 10.05  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 273.54 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.348 micro seconds
Total CPU time: 6.48 minutes
from_scatterers_fft:    623 calls, 117.49 s
gradients_fft:          568 calls, 111.49 s

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

# Date 2008-01-16 Time 06:27:55 PST -0800 (1200493675.77 s)
Start R-work = 0.4850, R-free = 0.4875 (no bulk solvent and anisotropic scale)
Final R-work = 0.1574, R-free = 0.2054 (no bulk solvent and anisotropic scale)

Start R-work = 0.4782, R-free = 0.4848
Final R-work = 0.1369, R-free = 0.1892