# Date 2008-01-16 Time 06:11:21 PST -0800 (1200492681.92 s)
#phil __OFF__

Command line arguments: "../1041.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8735
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1041

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.1647, 87.2539, 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: 3.29, 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: (71.3037, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.01158
Completeness in resolution range: 0.973657
Completeness with d_max=infinity: 0.970617

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0116

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.01158
Completeness in resolution range: 0.973657
Completeness with d_max=infinity: 0.970617

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.3041 [2108/2132]  1898   210  10.0%
  bin  2:  4.3041 -  3.4292 [2032/2052]  1828   204  10.0%
  bin  3:  3.4292 -  2.9995 [2004/2023]  1802   202  10.1%
  bin  4:  2.9995 -  2.7270 [1986/2016]  1791   195   9.8%
  bin  5:  2.7270 -  2.5325 [1982/2001]  1784   198  10.0%
  bin  6:  2.5325 -  2.3838 [1957/1982]  1756   201  10.3%
  bin  7:  2.3838 -  2.2648 [1948/1976]  1754   194  10.0%
  bin  8:  2.2648 -  2.1665 [1953/1989]  1760   193   9.9%
  bin  9:  2.1665 -  2.0833 [1930/1972]  1738   192   9.9%
  bin 10:  2.0833 -  2.0116 [1689/1976]  1519   170  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 7
        2.42 -     3.04: 2169
        3.04 -     3.66: 4583
        3.66 -     4.28: 8894
        4.28 -     4.90: 12224
  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
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.822 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 27872 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_1041/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/model_refine_001.geo

CPU time processing inputs: 9.74


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.16465 87.2539 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: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3251   r_free= 0.3152   ksol= 0.00   Bsol= 0.00   scale= 0.959    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.030443                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.2787 0.2619      6.3245      6.2358|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.2510 0.2337       6.415      6.3586|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.2765 0.2587      6.3172      6.3291|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.2921 0.3076      6.2071      6.2069|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.3330 0.3246      6.0981      6.1196|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.3457 0.3323      6.0397      5.9475|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.3567 0.3332      5.9962      6.0588|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.3601 0.3479      5.9862      5.9587|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.3597 0.3422      5.9089      5.8903|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.3690 0.3511      5.9087      5.8895|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.3834 0.3742       5.882      5.9098|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.3891 0.4051      5.8108      5.8923|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.3887 0.3732      5.7365      5.6716|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.3791 0.3733      5.6617      5.6389|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8004  1378   152  0.80  24.81   0.86     0.82      38338.58|
|  2:  4.8004 -  3.8303  1314   147  0.85  20.70   0.97     0.91      40520.54|
|  3:  3.8303 -  3.3521  1294   143  0.82  24.54   0.98     0.92      40481.45|
|  4:  3.3521 -  3.0483  1277   146  0.79  27.45   0.98     0.90      36904.11|
|  5:  3.0483 -  2.8313  1287   142  0.72  33.64   0.97     0.87      32371.13|
|  6:  2.8313 -  2.6653  1277   139  0.72  33.82   0.98     0.87      28167.09|
|  7:  2.6653 -  2.5325  1276   140  0.70  35.31   0.98     0.87      26126.98|
|  8:  2.5325 -  2.4227  1244   142  0.71  34.79   1.00     0.89      24513.34|
|  9:  2.4227 -  2.3298  1266   139  0.71  35.03   1.00     0.89      22878.96|
| 10:  2.3298 -  2.2496  1253   143  0.68  37.17   1.04     0.88      21936.25|
| 11:  2.2496 -  2.1795  1251   133  0.67  38.08   1.01     0.88      21715.65|
| 12:  2.1795 -  2.1174  1244   141  0.67  38.79   1.02     0.90      20764.27|
| 13:  2.1174 -  2.0618  1266   141  0.67  38.84   1.01     0.91      17657.29|
| 14:  2.0618 -  2.0116  1003   111  0.70  36.16   1.01     0.88      13224.78|
|alpha:            min =        0.82 max =            0.92 mean =         0.88|
|beta:             min =    13224.78 max =        40520.54 mean =     27913.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.73|
|phase err.(work): min =        0.00 max =           89.99 mean =        32.63|
|phase err.(test): min =        0.00 max =           89.20 mean =        32.13|
|-----------------------------------------------------------------------------|

============================== 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 = 3.090241              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.946   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.667361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.719   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      177 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1992 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1814 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2769 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4578 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4316 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5576 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6648 |
|-----------------------------------------------------------------------------|
|-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 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.115    4.900  1.806 |       0.141 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    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: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3251   r_free= 0.3152   ksol= 0.00   Bsol= 0.00   scale= 0.959    |
|                                                                             |
| 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:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.030443                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3135   r_free= 0.3054   ksol= 0.32   Bsol= 64.54   scale= 0.969   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-2.10,0.28,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 6.010033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.807541              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.036   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.379398              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.462   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3135      final r-factor (work) = 0.1908          |
| start r-factor (free) = 0.3054      final r-factor (free) = 0.2080          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6077 = 2.81 * 0.50 * 6.0166 + 1.00 * 0.1618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1237 = 2.81 * 0.50 * 5.7425 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1908      final r-factor (work) = 0.1761          |
| start r-factor (free) = 0.2080      final r-factor (free) = 0.2130          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1851 = 0.38 * 1.00 * 5.7425 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1246 = 0.38 * 1.00 * 5.5045 + 1.00 * 0.0362                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.58   16.79    None  None   None       |
|    all(noH): 2823   0      0.00    66.58   16.79    None  None   None       |
|    Sol.    : 438    0      4.99    64.94   37.91    None  None   None       |
|    Mac.    : 2385   0      0.00    66.58   12.91    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 -   6.658:  323   |   5:    33.288 -  39.945:   95        |
|      1:     6.658 -  13.315: 1216   |   6:    39.945 -  46.603:  103        |
|      2:    13.315 -  19.973:  602   |   7:    46.603 -  53.260:   83        |
|      3:    19.973 -  26.630:  224   |   8:    53.260 -  59.918:   47        |
|      4:    26.630 -  33.288:  121   |   9:    59.918 -  66.575:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1761 r_free = 0.2130             target_work(ml) = 5.512         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1756 r_free = 0.2126             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1756   r_free= 0.2126   ksol= 0.32   Bsol= 64.54   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-2.10,0.28,-0.00,0.00,0.00); trace/3= -0.72                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.509926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1749   r_free= 0.2113   ksol= 0.33   Bsol= 69.63   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.59,-1.11,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.510886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.623582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.369   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298213              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.498   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1749      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.2113      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5417 = 1.62 * 0.50 * 5.5175 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4385 = 1.62 * 0.50 * 5.4013 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1385      final r-factor (work) = 0.1311          |
| start r-factor (free) = 0.1752      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6325 = 0.30 * 1.00 * 5.4013 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6000 = 0.30 * 1.00 * 5.2768 + 1.00 * 0.0264                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.22   17.14    None  None   None       |
|    all(noH): 2823   0      0.00    78.22   17.14    None  None   None       |
|    Sol.    : 438    0      6.09    75.36   39.72    None  None   None       |
|    Mac.    : 2385   0      0.00    78.22   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.822:  542   |   5:    39.112 -  46.934:   97        |
|      1:     7.822 -  15.645: 1354   |   6:    46.934 -  54.756:   92        |
|      2:    15.645 -  23.467:  393   |   7:    54.756 -  62.579:   73        |
|      3:    23.467 -  31.289:  141   |   8:    62.579 -  70.401:   19        |
|      4:    31.289 -  39.112:  104   |   9:    70.401 -  78.223:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1311 r_free = 0.1690             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1311 r_free = 0.1689             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1689   ksol= 0.33   Bsol= 69.63   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.96,-2.59,-1.11,-0.00,-0.00,-0.00); trace/3= -1.89                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.259418                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1311   r_free= 0.1688   ksol= 0.33   Bsol= 69.61   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.37,-0.99,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.259280                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.142333              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.293  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.251531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.915   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1311      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7061 = 2.14 * 0.50 * 5.2768 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6408 = 2.14 * 0.50 * 5.2056 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1605      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3194 = 0.25 * 1.00 * 5.2056 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3093 = 0.25 * 1.00 * 5.1708 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.13   16.90    None  None   None       |
|    all(noH): 2823   0      0.00    79.13   16.90    None  None   None       |
|    Sol.    : 438    0      0.00    76.25   39.35    None  None   None       |
|    Mac.    : 2385   0      0.93    79.13   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.913:  558   |   5:    39.566 -  47.479:   95        |
|      1:     7.913 -  15.826: 1375   |   6:    47.479 -  55.392:   93        |
|      2:    15.826 -  23.739:  369   |   7:    55.392 -  63.305:   62        |
|      3:    23.739 -  31.653:  131   |   8:    63.305 -  71.218:   18        |
|      4:    31.653 -  39.566:  117   |   9:    71.218 -  79.131:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1161 r_free = 0.1590             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1589             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1589   ksol= 0.33   Bsol= 69.61   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.17,-2.37,-0.99,-0.00,-0.00,-0.00); trace/3= -1.84                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164088                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1590   ksol= 0.33   Bsol= 63.67   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.12,-0.84,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.164265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.512939              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.916940              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.305  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5621 = 2.51 * 0.50 * 5.1711 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5398 = 2.51 * 0.50 * 5.1486 + 1.00 * 0.0707                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1603          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7296 = 0.92 * 1.00 * 5.1486 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7267 = 0.92 * 1.00 * 5.1444 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.59   16.81    None  None   None       |
|    all(noH): 2823   0      0.00    80.59   16.81    None  None   None       |
|    Sol.    : 438    0      0.00    77.52   39.61    None  None   None       |
|    Mac.    : 2385   0      0.00    80.59   12.63    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.059:  650   |   5:    40.294 -  48.352:   93        |
|      1:     8.059 -  16.118: 1303   |   6:    48.352 -  56.411:   91        |
|      2:    16.118 -  24.176:  349   |   7:    56.411 -  64.470:   61        |
|      3:    24.176 -  32.235:  142   |   8:    64.470 -  72.528:   18        |
|      4:    32.235 -  40.294:  111   |   9:    72.528 -  80.587:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1603             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1603             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1603   ksol= 0.33   Bsol= 63.67   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.09,-2.12,-0.84,-0.00,-0.00,-0.00); trace/3= -1.68                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149230                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1602   ksol= 0.33   Bsol= 63.67   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.88,-0.64,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.149332                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.572528              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.009  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 9.878042              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.468   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1602      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6881 = 2.57 * 0.50 * 5.1447 + 1.00 * 0.0707                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6904 = 2.57 * 0.50 * 5.1477 + 1.00 * 0.0691                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.8590 = 9.88 * 1.00 * 5.1477 + 1.00 * 0.0096                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 50.8703 = 9.88 * 1.00 * 5.1487 + 1.00 * 0.0114                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   16.93    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   16.93    None  None   None       |
|    Sol.    : 438    0      1.10    84.02   40.68    None  None   None       |
|    Mac.    : 2385   0      0.00    90.51   12.57    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 -   9.051:  956   |   5:    45.253 -  54.303:   87        |
|      1:     9.051 -  18.101: 1143   |   6:    54.303 -  63.354:   77        |
|      2:    18.101 -  27.152:  261   |   7:    63.354 -  72.404:   42        |
|      3:    27.152 -  36.202:  133   |   8:    72.404 -  81.455:   11        |
|      4:    36.202 -  45.253:  106   |   9:    81.455 -  90.505:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1627             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1107 r_free = 0.1627             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1107   r_free= 0.1627   ksol= 0.33   Bsol= 63.67   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.88,-0.64,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.153338                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.0998 0.1349      5.4016      5.5371|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.0830 0.1106      5.4307      5.6241|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.1025 0.1519      5.4687      5.8766|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.1191 0.1589       5.461      5.6038|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.1322 0.1877      5.3478       5.613|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.1197 0.1931       5.234      5.4823|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.1279 0.1595      5.1781      5.3594|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.1118 0.1744      5.0632      5.3729|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.1134 0.1720      5.0338      5.2753|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.1102 0.1862      4.9703      5.2977|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.1154 0.1765       4.967      5.2494|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.1120 0.1817      4.9078       5.264|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.1137 0.1792      4.8309      5.1021|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.1048 0.1832      4.7018      4.9969|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8004  1378   152  0.94   9.71   0.97     0.94       7721.05|
|  2:  4.8004 -  3.8303  1314   147  0.95   8.01   1.00     0.98       9279.79|
|  3:  3.8303 -  3.3521  1294   143  0.93  11.19   1.02     1.01      10457.23|
|  4:  3.3521 -  3.0483  1277   146  0.92  13.74   1.00     0.98      10671.13|
|  5:  3.0483 -  2.8313  1287   142  0.90  16.29   0.99     0.96       8914.48|
|  6:  2.8313 -  2.6653  1277   139  0.90  16.42   0.98     0.95       7631.55|
|  7:  2.6653 -  2.5325  1276   140  0.90  16.16   0.98     0.95       6492.61|
|  8:  2.5325 -  2.4227  1244   142  0.91  14.82   0.98     0.96       5300.91|
|  9:  2.4227 -  2.3298  1266   139  0.91  15.35   0.98     0.94       5104.16|
| 10:  2.3298 -  2.2496  1253   143  0.90  15.44   0.98     0.93       4478.98|
| 11:  2.2496 -  2.1795  1251   133  0.89  17.18   0.97     0.93       4689.21|
| 12:  2.1795 -  2.1174  1244   141  0.91  15.72   0.99     0.97       4255.34|
| 13:  2.1174 -  2.0618  1266   141  0.90  16.66   0.97     0.94       3721.10|
| 14:  2.0618 -  2.0116  1003   111  0.91  15.40   0.94     0.90       2855.23|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     2855.23 max =        10671.13 mean =      6630.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.36 mean =        13.90|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1613   ksol= 0.32   Bsol= 65.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-1.61,-0.39,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.151659                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1613   ksol= 0.32   Bsol= 65.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.62,-1.61,-0.39,-0.00,-0.00,-0.00); trace/3= -1.21                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.151659                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8004 0.99   1378  152 0.1001 0.1287      5.3967      5.5142|
|  2:  4.8004 -  3.8303 0.99   1314  147 0.0837 0.1085      5.4276      5.6139|
|  3:  3.8303 -  3.3521 0.99   1294  143 0.1028 0.1496      5.4645      5.8608|
|  4:  3.3521 -  3.0483 0.99   1277  146 0.1186 0.1581      5.4554      5.6017|
|  5:  3.0483 -  2.8313 0.99   1287  142 0.1322 0.1867      5.3455      5.6082|
|  6:  2.8313 -  2.6653 0.99   1277  139 0.1196 0.1927      5.2324      5.4808|
|  7:  2.6653 -  2.5325 0.99   1276  140 0.1278 0.1593      5.1778      5.3592|
|  8:  2.5325 -  2.4227 0.98   1244  142 0.1117 0.1746      5.0627      5.3727|
|  9:  2.4227 -  2.3298 0.98   1266  139 0.1133 0.1723      5.0337      5.2753|
| 10:  2.3298 -  2.2496 1.00   1253  143 0.1101 0.1862      4.9703      5.2985|
| 11:  2.2496 -  2.1795 0.97   1251  133 0.1154 0.1768      4.9669      5.2498|
| 12:  2.1795 -  2.1174 0.98   1244  141 0.1120 0.1816      4.9077      5.2632|
| 13:  2.1174 -  2.0618 0.99   1266  141 0.1137 0.1794      4.8309      5.1021|
| 14:  2.0618 -  2.0116 0.80   1003  111 0.1048 0.1832       4.702      4.9972|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.8004  1378   152  0.94   9.40   0.97     0.94       7325.40|
|  2:  4.8004 -  3.8303  1314   147  0.95   7.85   1.00     0.99       8964.12|
|  3:  3.8303 -  3.3521  1294   143  0.94  11.02   1.02     1.02      10233.29|
|  4:  3.3521 -  3.0483  1277   146  0.92  13.63   1.00     0.99      10507.70|
|  5:  3.0483 -  2.8313  1287   142  0.90  16.22   1.00     0.97       8855.27|
|  6:  2.8313 -  2.6653  1277   139  0.90  16.40   0.99     0.96       7599.03|
|  7:  2.6653 -  2.5325  1276   140  0.90  16.15   0.99     0.96       6488.01|
|  8:  2.5325 -  2.4227  1244   142  0.91  14.81   0.99     0.97       5297.28|
|  9:  2.4227 -  2.3298  1266   139  0.91  15.36   0.99     0.95       5105.95|
| 10:  2.3298 -  2.2496  1253   143  0.90  15.44   0.99     0.94       4481.03|
| 11:  2.2496 -  2.1795  1251   133  0.89  17.18   0.99     0.94       4689.40|
| 12:  2.1795 -  2.1174  1244   141  0.91  15.72   1.00     0.99       4254.63|
| 13:  2.1174 -  2.0618  1266   141  0.90  16.66   0.98     0.96       3720.60|
| 14:  2.0618 -  2.0116  1003   111  0.91  15.41   0.96     0.92       2858.65|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2858.65 max =        10507.70 mean =      6541.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.82 mean =        14.30|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.81|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.271)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.51   16.93    None  None   None       |
|    all(noH): 2823   0      0.00    90.51   16.93    None  None   None       |
|    Sol.    : 438    0      1.11    84.02   40.68    None  None   None       |
|    Mac.    : 2385   0      0.00    90.51   12.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.054:  956   |   5:    45.256 -  54.306:   87        |
|      1:     9.054 -  18.104: 1143   |   6:    54.306 -  63.357:   77        |
|      2:    18.104 -  27.155:  261   |   7:    63.357 -  72.407:   42        |
|      3:    27.155 -  36.205:  133   |   8:    72.407 -  81.458:   11        |
|      4:    36.205 -  45.256:  106   |   9:    81.458 -  90.508:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.447 - 4.799
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 294 from: 301
   mapped sites are within: 0.706 - 4.799

peak=    5.703 closest distance to " O   HOH Z 111 " =    2.228
peak=    5.514 closest distance to " CB  GLN A 223 " =    1.420
peak=    5.157 closest distance to " CG  PRO A  54 " =    1.329
peak=    5.027 closest distance to " O   HOH Z 232 " =    2.279
peak=    4.901 closest distance to " CB  SER A  63 " =    1.206
peak=    4.860 closest distance to " CB  GLN A 183 " =    1.258
peak=    4.666 closest distance to " NE2 GLN A  11 " =    1.049
peak=    4.657 closest distance to " CG  PRO A 213 " =    1.177
peak=    4.641 closest distance to " O   HOH Z  15 " =    2.193
peak=    4.632 closest distance to " O   HOH Z  78 " =    1.689
peak=    4.623 closest distance to " CB  ARG A  79 " =    1.402
peak=    4.599 closest distance to " CB  PRO A  54 " =    0.933
peak=    4.566 closest distance to " CB  ARG A 190 " =    1.627
peak=    4.563 closest distance to " O   HOH Z 298 " =    2.003
peak=    4.526 closest distance to " CB  ARG A 275 " =    0.933
peak=    4.497 closest distance to " CA  TYR A  30 " =    0.978
peak=    4.430 closest distance to " CG  PRO A 198 " =    1.239
peak=    4.419 closest distance to " O   HOH Z 369 " =    2.158
peak=    4.414 closest distance to " O   HOH Z 126 " =    1.883
peak=    4.411 closest distance to " CZ  PHE A 218 " =    1.064
peak=    4.392 closest distance to " CB  LEU A 228 " =    1.097
peak=    4.251 closest distance to " CG  PRO A  90 " =    1.079
peak=    4.248 closest distance to " O   HOH Z 368 " =    2.164
peak=    4.226 closest distance to " O   HOH Z 261 " =    1.955
peak=    4.220 closest distance to " O   HOH Z 189 " =    2.649
peak=    4.216 closest distance to " C   PRO A 198 " =    1.504
peak=    4.204 closest distance to " O   HOH Z 427 " =    3.114
peak=    4.182 closest distance to " CB  TYR A 169 " =    0.748
peak=    4.153 closest distance to " CB  TRP A 266 " =    0.979
peak=    4.134 closest distance to " CB  ASN A 148 " =    1.457
peak=    4.128 closest distance to " O   HOH Z 180 " =    2.175
peak=    4.126 closest distance to " CB  GLU A 277 " =    3.733
peak=    4.087 closest distance to " CB  GLU A 128 " =    1.063
peak=    4.085 closest distance to " CD1 LEU A 300 " =    1.214
peak=    4.052 closest distance to " O   HOH Z  53 " =    2.498
peak=    4.045 closest distance to " CG  PRO A 243 " =    1.027
peak=    4.034 closest distance to " O   HOH Z 142 " =    1.597
peak=    4.031 closest distance to " OD1 ASN A  69 " =    2.593
peak=    4.025 closest distance to " CE  LYS A  76 " =    0.830
peak=    4.005 closest distance to " ND2 ASN A 187 " =    1.351
peak=    3.981 closest distance to " O   HOH Z 158 " =    3.031
peak=    3.980 closest distance to " O   HOH Z 133 " =    2.341
peak=    3.974 closest distance to " O   HOH Z 287 " =    2.081
peak=    3.973 closest distance to " CB  ASP A 124 " =    0.714
peak=    3.963 closest distance to " CG2 VAL A 257 " =    0.884
peak=    3.956 closest distance to " CD ALYS A 290 " =    0.941
peak=    3.928 closest distance to " O   HOH Z 234 " =    3.842
peak=    3.927 closest distance to " CB  ASP A 140 " =    1.017
peak=    3.910 closest distance to " O   HOH Z 250 " =    1.525
peak=    3.896 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.890 closest distance to " CB  VAL A 202 " =    1.626
peak=    3.887 closest distance to " O   HOH Z 346 " =    1.646
peak=    3.877 closest distance to " O   HOH Z 303 " =    2.133
peak=    3.872 closest distance to " NZ  LYS A 117 " =    3.379
peak=    3.859 closest distance to " O   HOH Z 203 " =    1.735
peak=    3.855 closest distance to " O   HOH Z 193 " =    1.741
peak=    3.844 closest distance to " CB  GLU A 152 " =    1.159
peak=    3.842 closest distance to " O   HOH Z 316 " =    3.136
peak=    3.836 closest distance to " O   HOH Z  43 " =    1.887
peak=    3.834 closest distance to " NH1AARG A 145 " =    1.281
peak=    3.820 closest distance to " CD  ARG A 269 " =    0.924
peak=    3.806 closest distance to " C   ILE A 106 " =    1.892
peak=    3.805 closest distance to " O   HOH Z  63 " =    1.995
peak=    3.804 closest distance to " NH2 ARG A 156 " =    1.181
peak=    3.796 closest distance to " CA  ALA A  51 " =    0.905
peak=    3.785 closest distance to " CA  ASP A 124 " =    0.706
peak=    3.780 closest distance to " CB  VAL A 265 " =    1.247
peak=    3.776 closest distance to " O   HOH Z  54 " =    2.360
peak=    3.776 closest distance to " O   HOH Z  40 " =    1.704
peak=    3.773 closest distance to " CD  ARG A  66 " =    2.333
peak=    3.770 closest distance to " CA  ARG A  36 " =    1.154
peak=    3.764 closest distance to " O   HOH Z  21 " =    1.825
peak=    3.758 closest distance to " O   HOH Z 214 " =    2.068
peak=    3.751 closest distance to " O   HOH Z 193 " =    1.960
peak=    3.747 closest distance to " CG1 ILE A  33 " =    1.210
peak=    3.740 closest distance to " CB  SER A 212 " =    1.103
peak=    3.712 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.711 closest distance to " CB  TYR A 116 " =    0.795
peak=    3.702 closest distance to " O   HOH Z 147 " =    1.815
peak=    3.701 closest distance to " O   HOH Z 272 " =    1.907
peak=    3.688 closest distance to " CB  SER A   3 " =    1.309
peak=    3.688 closest distance to " CA  MET A  40 " =    1.182
peak=    3.684 closest distance to " CD2 LEU A 297 " =    0.879
peak=    3.671 closest distance to " CG2 THR A 221 " =    1.110
peak=    3.660 closest distance to " O   SER A  87 " =    2.332
peak=    3.659 closest distance to " CA  ASN A 215 " =    1.179
peak=    3.659 closest distance to " CA  MET A 105 " =    1.042
peak=    3.657 closest distance to " CG  LEU A 167 " =    1.258
peak=    3.652 closest distance to " O   HOH Z 313 " =    1.959
peak=    3.648 closest distance to " O   HOH Z  44 " =    2.261
peak=    3.645 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.645 closest distance to " CD  ARG A 159 " =    0.791
peak=    3.639 closest distance to " O   HOH Z 285 " =    2.525
peak=    3.637 closest distance to " O   HOH Z 411 " =    3.801
peak=    3.637 closest distance to " O   HOH Z   1 " =    2.179
peak=    3.625 closest distance to " O   HOH Z 368 " =    3.705
peak=    3.615 closest distance to " O   HOH Z 280 " =    2.961
peak=    3.611 closest distance to " O   HOH Z 423 " =    1.897
peak=    3.608 closest distance to " CA  TYR A  30 " =    1.048
peak=    3.606 closest distance to " CB  ASN A  39 " =    0.924
peak=    3.604 closest distance to " O   HOH Z 172 " =    3.642
peak=    3.601 closest distance to " O   HOH Z 197 " =    3.085
peak=    3.598 closest distance to " O   HOH Z 108 " =    2.860
peak=    3.597 closest distance to " O   HOH Z 403 " =    1.385
peak=    3.591 closest distance to " N   ASN A 127 " =    1.278
peak=    3.589 closest distance to " NE2 HIS A 207 " =    1.292
peak=    3.587 closest distance to " CD  LYS A 166 " =    1.284
peak=    3.585 closest distance to " O   HOH Z 135 " =    1.720
peak=    3.580 closest distance to " O   HOH Z  66 " =    2.149
peak=    3.580 closest distance to " CB  GLU A  46 " =    1.003
peak=    3.579 closest distance to " O   HOH Z 426 " =    1.655
peak=    3.570 closest distance to " CD1 LEU A  96 " =    0.712
peak=    3.554 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.552 closest distance to " O   HOH Z 291 " =    1.624
peak=    3.547 closest distance to " O   HOH Z 213 " =    2.019
peak=    3.546 closest distance to " CB  TRP A 179 " =    1.496
peak=    3.546 closest distance to " O   THR A 220 " =    1.201
peak=    3.544 closest distance to " O   HOH Z 406 " =    1.591
peak=    3.540 closest distance to " O   HOH Z 391 " =    2.894
peak=    3.527 closest distance to " CB  ASN A 187 " =    1.427
peak=    3.526 closest distance to " ND2 ASN A 110 " =    1.591
peak=    3.525 closest distance to " O   HOH Z 128 " =    2.130
peak=    3.525 closest distance to " O   HOH Z 245 " =    1.252
peak=    3.524 closest distance to " O   ALA A 165 " =    1.510
peak=    3.518 closest distance to " O   HOH Z 353 " =    2.687
peak=    3.516 closest distance to " CG1BVAL A  72 " =    1.779
peak=    3.514 closest distance to " CZ  PHE A  38 " =    1.256
peak=    3.513 closest distance to " CA  THR A 221 " =    0.958
peak=    3.510 closest distance to " O   HOH Z 305 " =    3.618
peak=    3.504 closest distance to " O   HOH Z 359 " =    1.485
peak=    3.502 closest distance to " CB  MET A  47 " =    1.044
peak=    3.502 closest distance to " O   HOH Z 132 " =    2.685
peak=    3.496 closest distance to " O   HOH Z 325 " =    2.487
peak=    3.491 closest distance to " OG BSER A 164 " =    2.320
peak=    3.490 closest distance to " ND2 ASN A 249 " =    0.859
peak=    3.489 closest distance to " O   HOH Z 403 " =    1.625
peak=    3.485 closest distance to " CD2 TRP A 179 " =    1.355
peak=    3.484 closest distance to " O   HOH Z  59 " =    2.159
peak=    3.471 closest distance to " CB  ALA A  34 " =    0.979
peak=    3.470 closest distance to " O   HOH Z 126 " =    1.631
peak=    3.469 closest distance to " CG2 ILE A 120 " =    1.065
peak=    3.467 closest distance to " CB  ILE A 120 " =    1.282
peak=    3.463 closest distance to " N   ARG A 156 " =    1.393
peak=    3.457 closest distance to " CE1 TYR A 186 " =    1.409
peak=    3.452 closest distance to " O   HOH Z 148 " =    3.404
peak=    3.449 closest distance to " CA  ALA A 154 " =    1.015
peak=    3.448 closest distance to " CD  GLU A 152 " =    0.794
peak=    3.443 closest distance to " O   HOH Z 134 " =    1.284
peak=    3.440 closest distance to " CB  LEU A 143 " =    1.160
peak=    3.438 closest distance to " CG2 ILE A 234 " =    0.831
peak=    3.436 closest distance to " CA  THR A 264 " =    0.895
peak=    3.436 closest distance to " O   HOH Z 193 " =    2.149
peak=    3.433 closest distance to " O   HOH Z 128 " =    2.371
peak=    3.430 closest distance to " CD  ARG A  66 " =    2.327
peak=    3.428 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.424 closest distance to " CA  ASN A 176 " =    1.830
peak=    3.422 closest distance to " CA  ALA A 158 " =    1.197
peak=    3.417 closest distance to " CD  LYS A 119 " =    1.248
peak=    3.417 closest distance to " CB  GLN A  89 " =    1.291
peak=    3.411 closest distance to " CD  LYS A  76 " =    2.068
peak=    3.409 closest distance to " CA  ALA A 160 " =    0.919
peak=    3.409 closest distance to " O   TYR A 116 " =    1.304
peak=    3.406 closest distance to " CA  ALA A  21 " =    1.210
peak=    3.406 closest distance to " CA  VAL A 125 " =    1.176
peak=    3.404 closest distance to " ND1 HIS A  86 " =    1.763
peak=    3.403 closest distance to " CB  THR A  82 " =    1.453
peak=    3.401 closest distance to " O   ALA A 158 " =    1.266
peak=    3.400 closest distance to " O   HOH Z  66 " =    2.210
peak=    3.395 closest distance to " ND2 ASN A 249 " =    1.901
peak=    3.393 closest distance to " OE1 GLN A  11 " =    2.117
peak=    3.392 closest distance to " O   HOH Z   9 " =    2.098
peak=    3.392 closest distance to " CA  ALA A 295 " =    1.130
peak=    3.391 closest distance to " O   HOH Z 171 " =    3.886
peak=    3.389 closest distance to " CB  ARG A 139 " =    0.902
peak=    3.386 closest distance to " O   HOH Z 365 " =    2.911
peak=    3.382 closest distance to " CB  MET A  40 " =    0.792
peak=    3.377 closest distance to " O   THR A 251 " =    1.318
peak=    3.375 closest distance to " CB  ASN A 142 " =    1.048
peak=    3.367 closest distance to " O   HOH Z 383 " =    2.134
peak=    3.366 closest distance to " O   HOH Z  88 " =    4.036
peak=    3.363 closest distance to " O   HOH Z 294 " =    1.564
peak=    3.354 closest distance to " O   HOH Z 344 " =    3.285
peak=    3.353 closest distance to " O   HOH Z 425 " =    1.319
peak=    3.353 closest distance to " CB  SER A 141 " =    0.993
peak=    3.352 closest distance to " O   HOH Z 166 " =    3.821
peak=    3.351 closest distance to " O   HOH Z 371 " =    3.219
peak=    3.350 closest distance to " CB  ALA A 291 " =    1.289
peak=    3.350 closest distance to " O   HOH Z 329 " =    3.988
peak=    3.349 closest distance to " CA  SER A  87 " =    1.076
peak=    3.345 closest distance to " O   HOH Z  80 " =    1.571
peak=    3.335 closest distance to " O   HOH Z 290 " =    0.885
peak=    3.332 closest distance to " O   ASN A  74 " =    1.548
peak=    3.327 closest distance to " OD2 ASP A 286 " =    2.901
peak=    3.323 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.322 closest distance to " O   HOH Z 299 " =    4.531
peak=    3.321 closest distance to " ND1 HIS A  81 " =    1.608
peak=    3.318 closest distance to " N   VAL A 126 " =    1.376
peak=    3.310 closest distance to " O   HOH Z 425 " =    1.917
peak=    3.309 closest distance to " O   HOH Z 133 " =    3.253
peak=    3.306 closest distance to " CA  ASP A 191 " =    0.867
peak=    3.304 closest distance to " O   HOH Z 417 " =    3.208
peak=    3.304 closest distance to " CB  ALA A   1 " =    4.799
peak=    3.303 closest distance to " CG BARG A 275 " =    1.443
peak=    3.302 closest distance to " O   HOH Z 402 " =    1.378
peak=    3.301 closest distance to " N   ASN A  39 " =    1.367
peak=    3.291 closest distance to " CB  ARG A 138 " =    0.989
peak=    3.287 closest distance to " CB  SER A 216 " =    0.894
peak=    3.286 closest distance to " O   HOH Z  20 " =    1.669
peak=    3.283 closest distance to " O   HOH Z  40 " =    1.322
peak=    3.282 closest distance to " CG  MET A 185 " =    1.180
peak=    3.282 closest distance to " CE  LYS A  48 " =    1.016
peak=    3.267 closest distance to " CB  LYS A 193 " =    0.925
peak=    3.265 closest distance to " CD  ARG A 219 " =    1.077
peak=    3.263 closest distance to " O   HOH Z 273 " =    2.890
peak=    3.263 closest distance to " NE  ARG A  79 " =    1.103
peak=    3.262 closest distance to " CB  ALA A   9 " =    1.610
peak=    3.261 closest distance to " CB  ALA A 242 " =    0.911
peak=    3.256 closest distance to " CA  ALA A 233 " =    1.539
peak=    3.255 closest distance to " CA  ALA A 100 " =    1.142
peak=    3.253 closest distance to " CB  ALA A 248 " =    0.980
peak=    3.252 closest distance to " OG  SER A  22 " =    2.806
peak=    3.251 closest distance to " O  BHOH Z  74 " =    1.252
peak=    3.250 closest distance to " OG BSER A 134 " =    2.941
peak=    3.250 closest distance to " O   HOH Z 163 " =    1.733
peak=    3.249 closest distance to " CZ3 TRP A 266 " =    1.155
peak=    3.248 closest distance to " N   ARG A 190 " =    1.040
peak=    3.245 closest distance to " CB  LEU A  83 " =    0.778
peak=    3.243 closest distance to " O   HOH Z 185 " =    1.870
peak=    3.241 closest distance to " CB  GLN A 103 " =    0.839
peak=    3.240 closest distance to " O   THR A 251 " =    1.901
peak=    3.240 closest distance to " O   HOH Z 124 " =    1.801
peak=    3.239 closest distance to " CB  ASP A 200 " =    1.094
peak=    3.238 closest distance to " O   HOH Z 422 " =    2.749
peak=    3.238 closest distance to " CZ  PHE A 192 " =    0.894
peak=    3.238 closest distance to " O   HOH Z  90 " =    2.374
peak=    3.237 closest distance to " O   HOH Z 327 " =    1.784
peak=    3.231 closest distance to " CB  THR A  31 " =    1.770
peak=    3.231 closest distance to " CD1 ILE A 106 " =    0.789
peak=    3.228 closest distance to " C   TYR A 214 " =    1.553
peak=    3.225 closest distance to " CB  GLN A  88 " =    1.240
peak=    3.224 closest distance to " CA  ASN A 217 " =    1.226
peak=    3.218 closest distance to " CB  ALA A 104 " =    0.748
peak=    3.217 closest distance to " CA  ALA A 291 " =    0.809
peak=    3.214 closest distance to " O   HOH Z 109 " =    2.709
peak=    3.205 closest distance to " CD1AILE A 234 " =    0.918
peak=    3.204 closest distance to " O   HOH Z 285 " =    1.670
peak=    3.203 closest distance to " OE2 GLU A  53 " =    2.077
peak=    3.200 closest distance to " NH2AARG A 275 " =    3.599
peak=    3.198 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.197 closest distance to " O   HOH Z 213 " =    2.456
peak=    3.197 closest distance to " CG  GLU A  37 " =    0.868
peak=    3.189 closest distance to " O   HOH Z 421 " =    1.910
peak=    3.188 closest distance to " CA  ALA A  84 " =    1.379
peak=    3.186 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.185 closest distance to " O   HOH Z 409 " =    3.100
peak=    3.185 closest distance to " O   HOH Z  44 " =    3.183
peak=    3.183 closest distance to " CB  LYS A 117 " =    1.158
peak=    3.180 closest distance to " CA  SER A 146 " =    1.758
peak=    3.179 closest distance to " CG2 ILE A  20 " =    1.240
peak=    3.178 closest distance to " O   HOH Z  97 " =    2.042
peak=    3.177 closest distance to " CZ2 TRP A 179 " =    1.698
peak=    3.177 closest distance to " O   HOH Z 258 " =    1.703
peak=    3.167 closest distance to " CA  ARG A 159 " =    1.263
peak=    3.166 closest distance to " CG2 VAL A 197 " =    1.142
peak=    3.166 closest distance to " CB  SER A  26 " =    1.776
peak=    3.165 closest distance to " O   HOH Z 163 " =    1.593
peak=    3.163 closest distance to " NH1BARG A 145 " =    0.990
peak=    3.161 closest distance to " O   HOH Z 339 " =    2.237
peak=    3.158 closest distance to " CE2 PHE A  16 " =    0.899
peak=    3.153 closest distance to " N   GLY A  98 " =    1.123
peak=    3.142 closest distance to " CA  ARG A 102 " =    1.145
peak=    3.139 closest distance to " O   HOH Z 261 " =    1.570
peak=    3.138 closest distance to " CG  GLN A  11 " =    1.573
peak=    3.133 closest distance to " O   HOH Z 183 " =    1.252
peak=    3.129 closest distance to " O   HOH Z 430 " =    3.885
peak=    3.126 closest distance to " CA  GLU A  46 " =    0.780
peak=    3.124 closest distance to " O   HOH Z 419 " =    1.909
peak=    3.118 closest distance to " CG  LYS A  76 " =    0.937
peak=    3.115 closest distance to " O   HOH Z 116 " =    1.868
peak=    3.113 closest distance to " CG  ARG A 159 " =    0.884
peak=    3.098 closest distance to " O   THR A 182 " =    1.405
peak=    3.097 closest distance to " CB  TYR A 169 " =    1.228
peak=    3.096 closest distance to " CA  ALA A 154 " =    1.095
peak=    3.091 closest distance to " O   HOH Z 421 " =    2.954
peak=    3.089 closest distance to " CB  TRP A 150 " =    1.274
peak=    3.086 closest distance to " O   HOH Z 327 " =    1.947
peak=    3.067 closest distance to " O   HOH Z  49 " =    2.259
peak=    3.066 closest distance to " O   HOH Z  88 " =    1.939
peak=    3.066 closest distance to " N   TYR A 247 " =    1.070
peak=    3.064 closest distance to " O   HOH Z 188 " =    2.338
peak=    3.062 closest distance to " O   HOH Z 248 " =    1.586
peak=    3.034 closest distance to " O   TRP A 274 " =    1.840
peak=    3.027 closest distance to " O   GLN A 278 " =    1.549
peak=    3.018 closest distance to " CB  VAL A 265 " =    1.991

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.822 - 5.812
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 219
   mapped sites are within: 0.822 - 5.812

peak=   -4.517 closest distance to " CD  GLN A  58 " =    0.958
peak=   -4.502 closest distance to " CD  ARG A 156 " =    2.040
peak=   -4.432 closest distance to " CD  ARG A  14 " =    3.505
peak=   -4.419 closest distance to " CB  PRO A 243 " =    2.652
peak=   -4.409 closest distance to " O   HOH Z 266 " =    5.339
peak=   -4.358 closest distance to " CG1 VAL A 112 " =    2.643
peak=   -4.284 closest distance to " OE1 GLN A 223 " =    2.023
peak=   -4.280 closest distance to " O   VAL A  67 " =    2.752
peak=   -4.276 closest distance to " O   HOH Z 231 " =    2.257
peak=   -4.263 closest distance to " O   HOH Z 377 " =    2.038
peak=   -4.134 closest distance to " CE2 TYR A  30 " =    2.720
peak=   -4.122 closest distance to " N   ALA A  43 " =    2.697
peak=   -4.022 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -4.018 closest distance to " OG  SER A  97 " =    2.210
peak=   -4.011 closest distance to " CB  ALA A 161 " =    2.652
peak=   -4.003 closest distance to " CA  GLY A 241 " =    3.213
peak=   -4.002 closest distance to " O   HOH Z  10 " =    1.535
peak=   -3.997 closest distance to " CG1 VAL A 250 " =    2.660
peak=   -3.994 closest distance to " O   HOH Z 198 " =    2.099
peak=   -3.973 closest distance to " C   HIS A 108 " =    1.081
peak=   -3.939 closest distance to " O   HOH Z 196 " =    1.985
peak=   -3.906 closest distance to " CD2 TYR A 293 " =    1.967
peak=   -3.879 closest distance to " OG BSER A 134 " =    1.306
peak=   -3.848 closest distance to " O   HOH Z 389 " =    1.985
peak=   -3.834 closest distance to " O   PRO A 198 " =    1.341
peak=   -3.815 closest distance to " NE2 GLN A  88 " =    1.937
peak=   -3.814 closest distance to " CG1 VAL A 112 " =    2.932
peak=   -3.810 closest distance to " O   HOH Z  73 " =    2.180
peak=   -3.778 closest distance to " CG2 ILE A  49 " =    2.772
peak=   -3.765 closest distance to " OD1 ASN A 148 " =    1.508
peak=   -3.743 closest distance to " CB  ALA A 291 " =    2.336
peak=   -3.742 closest distance to " O   HOH Z 372 " =    2.405
peak=   -3.723 closest distance to " NH2AARG A 275 " =    5.493
peak=   -3.693 closest distance to " CD1 LEU A 101 " =    2.441
peak=   -3.691 closest distance to " O   HOH Z  38 " =    1.288
peak=   -3.685 closest distance to " CE  MET A 105 " =    2.325
peak=   -3.683 closest distance to " O   HOH Z 166 " =    1.896
peak=   -3.679 closest distance to " CA  GLY A 203 " =    2.411
peak=   -3.676 closest distance to " CD1 PHE A  59 " =    1.943
peak=   -3.659 closest distance to " O   HOH Z 185 " =    2.336
peak=   -3.648 closest distance to " OXT GLY A 302 " =    3.030
peak=   -3.646 closest distance to " C   ASN A 187 " =    1.906
peak=   -3.645 closest distance to " CG2 ILE A 263 " =    2.400
peak=   -3.638 closest distance to " O   HOH Z  51 " =    1.585
peak=   -3.633 closest distance to " O   HOH Z 393 " =    1.365
peak=   -3.622 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.622 closest distance to " O   HOH Z  43 " =    1.626
peak=   -3.614 closest distance to " O   HOH Z  52 " =    1.470
peak=   -3.610 closest distance to " O   GLY A 211 " =    1.441
peak=   -3.608 closest distance to " O   HOH Z 407 " =    3.363
peak=   -3.607 closest distance to " ND2 ASN A  45 " =    1.085
peak=   -3.606 closest distance to " O   HOH Z 435 " =    2.812
peak=   -3.598 closest distance to " O   HOH Z 394 " =    1.485
peak=   -3.594 closest distance to " O   HOH Z 114 " =    3.382
peak=   -3.593 closest distance to " CG  ARG A 269 " =    2.538
peak=   -3.583 closest distance to " ND2 ASN A  45 " =    1.839
peak=   -3.568 closest distance to " O   PRO A 163 " =    2.142
peak=   -3.564 closest distance to " CB  ALA A 129 " =    2.441
peak=   -3.563 closest distance to " CD2 PHE A 192 " =    2.018
peak=   -3.554 closest distance to " O   HOH Z 353 " =    2.118
peak=   -3.547 closest distance to " C   ASN A 285 " =    2.507
peak=   -3.544 closest distance to " NH2 ARG A  79 " =    1.529
peak=   -3.541 closest distance to " C   GLY A  17 " =    1.187
peak=   -3.537 closest distance to " CA  GLY A 241 " =    2.307
peak=   -3.533 closest distance to " CG2 VAL A 189 " =    2.212
peak=   -3.527 closest distance to " O   HOH Z 211 " =    1.559
peak=   -3.508 closest distance to " CG  HIS A  86 " =    1.061
peak=   -3.507 closest distance to " O   VAL A 189 " =    2.569
peak=   -3.496 closest distance to " CB  ASN A  39 " =    2.367
peak=   -3.494 closest distance to " ND2 ASN A  45 " =    1.323
peak=   -3.490 closest distance to " OD2 ASP A 171 " =    1.838
peak=   -3.490 closest distance to " O   HOH Z 348 " =    2.255
peak=   -3.489 closest distance to " C   LEU A 143 " =    1.172
peak=   -3.486 closest distance to " O   HOH Z   6 " =    2.295
peak=   -3.485 closest distance to " CZ  PHE A  59 " =    1.723
peak=   -3.482 closest distance to " O   HOH Z 290 " =    1.324
peak=   -3.481 closest distance to " CG1 VAL A 125 " =    1.946
peak=   -3.480 closest distance to " CA  GLY A 241 " =    2.865
peak=   -3.478 closest distance to " CG  MET A 105 " =    0.971
peak=   -3.470 closest distance to " ND2 ASN A 249 " =    2.507
peak=   -3.466 closest distance to " O   ALA A  10 " =    1.693
peak=   -3.464 closest distance to " NE2 GLN A 194 " =    1.840
peak=   -3.463 closest distance to " ND2 ASN A  60 " =    1.417
peak=   -3.453 closest distance to " CG  GLU A 277 " =    1.109
peak=   -3.452 closest distance to " CB  ALA A 291 " =    2.280
peak=   -3.449 closest distance to " CB  ASP A 132 " =    2.339
peak=   -3.443 closest distance to " O   HOH Z 292 " =    4.677
peak=   -3.440 closest distance to " O   HOH Z  60 " =    2.512
peak=   -3.430 closest distance to " CB  ALA A  43 " =    2.670
peak=   -3.428 closest distance to " CG  ARG A  66 " =    2.366
peak=   -3.421 closest distance to " CG  GLU A  53 " =    1.545
peak=   -3.419 closest distance to " O   HOH Z  44 " =    2.284
peak=   -3.414 closest distance to " O   HOH Z 114 " =    1.432
peak=   -3.411 closest distance to " CE2 PHE A 218 " =    2.396
peak=   -3.410 closest distance to " O   HOH Z 198 " =    1.485
peak=   -3.406 closest distance to " CD2 TYR A 293 " =    2.142
peak=   -3.405 closest distance to " CD1 LEU A 228 " =    2.388
peak=   -3.403 closest distance to " CE BMET A  47 " =    1.812
peak=   -3.403 closest distance to " CA  VAL A  67 " =    2.937
peak=   -3.399 closest distance to " CD  ARG A 195 " =    5.134
peak=   -3.396 closest distance to " CE3 TRP A 150 " =    2.188
peak=   -3.395 closest distance to " O   HOH Z 103 " =    1.802
peak=   -3.392 closest distance to " O   HOH Z   6 " =    1.492
peak=   -3.387 closest distance to " CB  TYR A  15 " =    2.230
peak=   -3.385 closest distance to " OD1 ASP A 171 " =    1.562
peak=   -3.384 closest distance to " O   HOH Z 243 " =    2.153
peak=   -3.373 closest distance to " CE2 PHE A  61 " =    2.636
peak=   -3.368 closest distance to " O   HOH Z 311 " =    3.779
peak=   -3.366 closest distance to " OD1 ASP A 191 " =    1.658
peak=   -3.362 closest distance to " CA  GLY A 133 " =    2.326
peak=   -3.355 closest distance to " NH2 ARG A 159 " =    2.367
peak=   -3.355 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.355 closest distance to " O   HOH Z 111 " =    1.946
peak=   -3.354 closest distance to " CG  PHE A 283 " =    2.720
peak=   -3.342 closest distance to " C   SER A 206 " =    1.518
peak=   -3.340 closest distance to " O   HOH Z 396 " =    1.747
peak=   -3.340 closest distance to " CD2 PHE A 225 " =    1.141
peak=   -3.339 closest distance to " O   HOH Z 351 " =    1.487
peak=   -3.337 closest distance to " O   PHE A 218 " =    1.507
peak=   -3.335 closest distance to " N   ALA A 226 " =    2.151
peak=   -3.333 closest distance to " CD2 TYR A 247 " =    2.398
peak=   -3.330 closest distance to " N   ALA A 248 " =    1.625
peak=   -3.330 closest distance to " SG ACYS A 201 " =    2.055
peak=   -3.326 closest distance to " O   SER A 210 " =    1.975
peak=   -3.324 closest distance to " CG  GLN A  11 " =    1.705
peak=   -3.320 closest distance to " ND2BASN A 224 " =    1.734
peak=   -3.316 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.315 closest distance to " O   HOH Z 426 " =    1.694
peak=   -3.315 closest distance to " O   HOH Z 216 " =    1.781
peak=   -3.309 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.305 closest distance to " N   MET A 105 " =    2.621
peak=   -3.302 closest distance to " ND2 ASN A  69 " =    1.738
peak=   -3.302 closest distance to " NE2 GLN A 103 " =    1.736
peak=   -3.298 closest distance to " O   HOH Z 322 " =    1.593
peak=   -3.296 closest distance to " O   HOH Z 232 " =    1.731
peak=   -3.289 closest distance to " O   HOH Z 313 " =    1.976
peak=   -3.288 closest distance to " CB  TRP A  85 " =    2.381
peak=   -3.288 closest distance to " O   HOH Z 295 " =    1.538
peak=   -3.286 closest distance to " OG BSER A 134 " =    1.870
peak=   -3.278 closest distance to " O   HOH Z 323 " =    1.500
peak=   -3.276 closest distance to " O   HOH Z 253 " =    4.124
peak=   -3.274 closest distance to " O   HOH Z 350 " =    1.998
peak=   -3.273 closest distance to " CB  PHE A  16 " =    2.589
peak=   -3.269 closest distance to " O   HOH Z 106 " =    1.857
peak=   -3.267 closest distance to " O   HOH Z 298 " =    1.306
peak=   -3.260 closest distance to " OE1 GLN A 223 " =    2.158
peak=   -3.260 closest distance to " O   SER A  95 " =    1.660
peak=   -3.251 closest distance to " N   THR A 264 " =    1.345
peak=   -3.245 closest distance to " O   HOH Z 193 " =    1.644
peak=   -3.243 closest distance to " O   HOH Z 166 " =    1.706
peak=   -3.239 closest distance to " O   HOH Z 324 " =    2.246
peak=   -3.237 closest distance to " CB  ASP A 286 " =    2.149
peak=   -3.228 closest distance to " CD  ARG A 139 " =    1.640
peak=   -3.226 closest distance to " CG  PRO A 243 " =    1.797
peak=   -3.224 closest distance to " CB  PRO A 163 " =    2.521
peak=   -3.221 closest distance to " CD1 ILE A 239 " =    2.112
peak=   -3.216 closest distance to " OD1 ASN A 187 " =    1.536
peak=   -3.214 closest distance to " O   ALA A  34 " =    2.578
peak=   -3.213 closest distance to " OH  TYR A 247 " =    1.843
peak=   -3.207 closest distance to " O   HOH Z  90 " =    1.722
peak=   -3.207 closest distance to " C   PHE A  59 " =    1.352
peak=   -3.205 closest distance to " O   HOH Z 139 " =    2.997
peak=   -3.205 closest distance to " OE1 GLN A  88 " =    1.192
peak=   -3.204 closest distance to " O   HOH Z 191 " =    5.812
peak=   -3.203 closest distance to " CG  ASP A 231 " =    0.822
peak=   -3.202 closest distance to " O   HOH Z 265 " =    2.284
peak=   -3.199 closest distance to " O   SER A 135 " =    1.478
peak=   -3.194 closest distance to " CB  ALA A 100 " =    2.114
peak=   -3.192 closest distance to " O   HOH Z 241 " =    1.440
peak=   -3.188 closest distance to " CG1BVAL A  41 " =    2.841
peak=   -3.181 closest distance to " O   HOH Z 275 " =    1.576
peak=   -3.180 closest distance to " CZ  PHE A 155 " =    1.338
peak=   -3.179 closest distance to " ND2 ASN A  60 " =    4.122
peak=   -3.175 closest distance to " CZ  TYR A 169 " =    1.798
peak=   -3.171 closest distance to " O   HOH Z 264 " =    1.815
peak=   -3.169 closest distance to " O   HOH Z 252 " =    4.186
peak=   -3.162 closest distance to " C   GLY A  13 " =    0.977
peak=   -3.157 closest distance to " CG1 VAL A 125 " =    2.319
peak=   -3.154 closest distance to " O   HOH Z 175 " =    4.040
peak=   -3.152 closest distance to " CB  PRO A  54 " =    2.507
peak=   -3.148 closest distance to " O   HOH Z 322 " =    1.321
peak=   -3.148 closest distance to " CG1AVAL A  41 " =    2.804
peak=   -3.144 closest distance to " OG  SER A  87 " =    1.521
peak=   -3.144 closest distance to " CB  ALA A 248 " =    2.426
peak=   -3.138 closest distance to " C   MET A 188 " =    1.349
peak=   -3.136 closest distance to " CD  ARG A  79 " =    1.096
peak=   -3.136 closest distance to " O   HOH Z 234 " =    4.350
peak=   -3.134 closest distance to " CG  ASN A 301 " =    2.001
peak=   -3.133 closest distance to " O   HOH Z 298 " =    2.471
peak=   -3.132 closest distance to " N   VAL A 232 " =    2.297
peak=   -3.129 closest distance to " O   HOH Z  11 " =    1.752
peak=   -3.128 closest distance to " O   HOH Z 134 " =    2.827
peak=   -3.128 closest distance to " CD2 LEU A 300 " =    2.679
peak=   -3.128 closest distance to " CD1 LEU A 297 " =    2.506
peak=   -3.123 closest distance to " CG1 VAL A 197 " =    2.284
peak=   -3.122 closest distance to " OD2 ASP A 191 " =    1.588
peak=   -3.122 closest distance to " O   GLY A 203 " =    2.360
peak=   -3.119 closest distance to " O   HOH Z 414 " =    1.714
peak=   -3.115 closest distance to " O   GLY A  80 " =    2.502
peak=   -3.108 closest distance to " O   HOH Z  76 " =    1.967
peak=   -3.106 closest distance to " O   HOH Z 123 " =    2.482
peak=   -3.101 closest distance to " O   TRP A  70 " =    1.472
peak=   -3.096 closest distance to " O   HOH Z 174 " =    3.058
peak=   -3.093 closest distance to " CE3 TRP A  70 " =    1.845
peak=   -3.092 closest distance to " SD  MET A 188 " =    2.289
peak=   -3.083 closest distance to " OG ASER A 134 " =    1.232
peak=   -3.083 closest distance to " O   HOH Z 317 " =    2.240
peak=   -3.081 closest distance to " O   GLN A 240 " =    2.503
peak=   -3.081 closest distance to " CG2 THR A 221 " =    2.302
peak=   -3.078 closest distance to " O   HOH Z 184 " =    1.601
peak=   -3.076 closest distance to " CD2 PHE A  59 " =    2.523
peak=   -3.072 closest distance to " O   GLY A  80 " =    2.640
peak=   -3.064 closest distance to " CB  ALA A  10 " =    2.247
peak=   -3.064 closest distance to " CD2 LEU A 237 " =    2.901
peak=   -3.050 closest distance to " NH2BARG A 275 " =    1.922
peak=   -3.048 closest distance to " NH2 ARG A  66 " =    2.157
peak=   -3.047 closest distance to " O   ARG A  24 " =    1.609
peak=   -3.041 closest distance to " O   HOH Z  70 " =    2.227
peak=   -3.016 closest distance to " O   HOH Z 357 " =    2.037

================= 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    :  0.3251 0.3152   6.030443e+00   6.016968e+00
   1_bss:  0.3135 0.3054   6.010033e+00   5.990792e+00
   1_xyz:  0.1908 0.2080   5.567142e+00   5.643284e+00
   1_adp:  0.1761 0.2130   5.512117e+00   5.668226e+00
   1_occ:  0.1756 0.2126   5.509926e+00   5.666866e+00
   2_bss:  0.1749 0.2113   5.510886e+00   5.667018e+00
   2_xyz:  0.1385 0.1752   5.305383e+00   5.494065e+00
   2_adp:  0.1311 0.1690   5.259789e+00   5.459196e+00
   2_occ:  0.1311 0.1689   5.259418e+00   5.458966e+00
   3_bss:  0.1311 0.1688   5.259280e+00   5.457641e+00
   3_xyz:  0.1174 0.1605   5.176760e+00   5.406117e+00
   3_adp:  0.1161 0.1590   5.164466e+00   5.394721e+00
   3_occ:  0.1160 0.1589   5.164088e+00   5.394495e+00
   4_bss:  0.1160 0.1590   5.164265e+00   5.394727e+00
   4_xyz:  0.1121 0.1592   5.148687e+00   5.393657e+00
   4_adp:  0.1115 0.1603   5.149194e+00   5.399407e+00
   4_occ:  0.1114 0.1603   5.149230e+00   5.399841e+00
   5_bss:  0.1113 0.1602   5.149332e+00   5.399902e+00
   5_xyz:  0.1109 0.1615   5.152212e+00   5.408510e+00
   5_adp:  0.1107 0.1627   5.153240e+00   5.413000e+00
   5_occ:  0.1107 0.1627   5.153338e+00   5.413239e+00
   5_bss:  0.1106 0.1613   5.151659e+00   5.408953e+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:  0.316  64.539  -0.334  -2.096   0.284  -0.000   0.000   0.000
   1_xyz:  0.316  64.539  -0.334  -2.096   0.284  -0.000   0.000   0.000
   1_adp:  0.316  64.539  -0.334  -2.096   0.284  -0.000   0.000   0.000
   1_occ:  0.316  64.539  -0.334  -2.096   0.284  -0.000   0.000   0.000
   2_bss:  0.334  69.626  -1.957  -2.593  -1.109  -0.000  -0.000  -0.000
   2_xyz:  0.334  69.626  -1.957  -2.593  -1.109  -0.000  -0.000  -0.000
   2_adp:  0.334  69.626  -1.957  -2.593  -1.109  -0.000  -0.000  -0.000
   2_occ:  0.334  69.626  -1.957  -2.593  -1.109  -0.000  -0.000  -0.000
   3_bss:  0.332  69.607  -2.174  -2.368  -0.986  -0.000  -0.000  -0.000
   3_xyz:  0.332  69.607  -2.174  -2.368  -0.986  -0.000  -0.000  -0.000
   3_adp:  0.332  69.607  -2.174  -2.368  -0.986  -0.000  -0.000  -0.000
   3_occ:  0.332  69.607  -2.174  -2.368  -0.986  -0.000  -0.000  -0.000
   4_bss:  0.327  63.673  -2.085  -2.124  -0.841  -0.000  -0.000  -0.000
   4_xyz:  0.327  63.673  -2.085  -2.124  -0.841  -0.000  -0.000  -0.000
   4_adp:  0.327  63.673  -2.085  -2.124  -0.841  -0.000  -0.000  -0.000
   4_occ:  0.327  63.673  -2.085  -2.124  -0.841  -0.000  -0.000  -0.000
   5_bss:  0.327  63.673  -1.879  -1.884  -0.643  -0.000  -0.000  -0.000
   5_xyz:  0.327  63.673  -1.879  -1.884  -0.643  -0.000  -0.000  -0.000
   5_adp:  0.327  63.673  -1.879  -1.884  -0.643  -0.000  -0.000  -0.000
   5_occ:  0.327  63.673  -1.879  -1.884  -0.643  -0.000  -0.000  -0.000
   5_bss:  0.324  65.000  -1.622  -1.611  -0.391  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.580 0.7321  0.8840    27914.458
   1_bss:  31.581 0.7418  0.8801    25595.922
   1_xyz:  19.490 0.8682  0.9898    10957.453
   1_adp:  20.226 0.8605  0.9848    11472.053
   1_occ:  20.192 0.8607  0.9846    11408.140
   2_bss:  20.174 0.8610  0.9442    11432.679
   2_xyz:  16.183 0.8968  0.9640     7787.200
   2_adp:  15.308 0.9045  0.9605     7213.432
   2_occ:  15.305 0.9045  0.9604     7207.712
   3_bss:  15.284 0.9047  0.9615     7170.978
   3_xyz:  14.235 0.9132  0.9669     6487.899
   3_adp:  13.938 0.9158  0.9616     6368.058
   3_occ:  13.935 0.9158  0.9615     6364.671
   4_bss:  13.943 0.9158  0.9668     6365.298
   4_xyz:  13.937 0.9158  0.9681     6383.257
   4_adp:  14.048 0.9150  0.9595     6443.641
   4_occ:  14.059 0.9149  0.9593     6447.191
   5_bss:  14.061 0.9149  0.9667     6448.334
   5_xyz:  14.207 0.9137  0.9651     6583.938
   5_adp:  14.316 0.9128  0.9558     6628.652
   5_occ:  14.320 0.9128  0.9557     6630.892
   5_bss:  14.254 0.9133  0.9645     6541.283
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.115   1.6179e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.115   1.6179e-01
   1_xyz:   1.032  0.008  0.068 15.195  0.004  4.115   6.2633e-02
   1_adp:   1.032  0.008  0.068 15.195  0.004  4.115   6.2633e-02
   1_occ:   1.032  0.008  0.068 15.195  0.004  4.115   6.2633e-02
   2_bss:   1.032  0.008  0.068 15.195  0.004  4.115   6.2633e-02
   2_xyz:   0.972  0.006  0.071 14.370  0.004  4.128   5.3695e-02
   2_adp:   0.972  0.006  0.071 14.370  0.004  4.128   5.3695e-02
   2_occ:   0.972  0.006  0.071 14.370  0.004  4.128   5.3695e-02
   3_bss:   0.972  0.006  0.071 14.370  0.004  4.128   5.3695e-02
   3_xyz:   1.038  0.009  0.077 14.537  0.004  4.115   6.4761e-02
   3_adp:   1.038  0.009  0.077 14.537  0.004  4.115   6.4761e-02
   3_occ:   1.038  0.009  0.077 14.537  0.004  4.115   6.4761e-02
   4_bss:   1.038  0.009  0.077 14.537  0.004  4.115   6.4761e-02
   4_xyz:   1.074  0.010  0.082 14.637  0.004  4.119   7.0684e-02
   4_adp:   1.074  0.010  0.082 14.637  0.004  4.119   7.0684e-02
   4_occ:   1.074  0.010  0.082 14.637  0.004  4.119   7.0684e-02
   5_bss:   1.074  0.010  0.082 14.637  0.004  4.119   7.0684e-02
   5_xyz:   1.059  0.010  0.081 14.571  0.004  4.120   6.9117e-02
   5_adp:   1.059  0.010  0.081 14.571  0.004  4.120   6.9117e-02
   5_occ:   1.059  0.010  0.081 14.571  0.004  4.120   6.9117e-02
   5_bss:   1.059  0.010  0.081 14.571  0.004  4.120   6.9117e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4377e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4377e-01
   1_xyz:   8.099  0.044  0.237 85.005  0.031  2.281   6.5618e-02
   1_adp:   8.099  0.044  0.237 85.005  0.031  2.281   6.5618e-02
   1_occ:   8.099  0.044  0.237 85.005  0.031  2.281   6.5618e-02
   2_bss:   8.099  0.044  0.237 85.005  0.031  2.281   6.5618e-02
   2_xyz:   7.013  0.040  0.212 81.145  0.037  2.379   4.1938e-02
   2_adp:   7.013  0.040  0.212 81.145  0.037  2.379   4.1938e-02
   2_occ:   7.013  0.040  0.212 81.145  0.037  2.379   4.1938e-02
   3_bss:   7.013  0.040  0.212 81.145  0.037  2.379   4.1938e-02
   3_xyz:   7.563  0.044  0.235 83.090  0.036  2.374   4.7095e-02
   3_adp:   7.563  0.044  0.235 83.090  0.036  2.374   4.7095e-02
   3_occ:   7.563  0.044  0.235 83.090  0.036  2.374   4.7095e-02
   4_bss:   7.563  0.044  0.235 83.090  0.036  2.374   4.7095e-02
   4_xyz:   7.336  0.046  0.264 83.112  0.037  2.356   5.0408e-02
   4_adp:   7.336  0.046  0.264 83.112  0.037  2.356   5.0408e-02
   4_occ:   7.336  0.046  0.264 83.112  0.037  2.356   5.0408e-02
   5_bss:   7.336  0.046  0.264 83.112  0.037  2.356   5.0408e-02
   5_xyz:   7.368  0.050  0.261 83.028  0.036  2.368   4.9251e-02
   5_adp:   7.368  0.050  0.261 83.028  0.036  2.368   4.9251e-02
   5_occ:   7.368  0.050  0.261 83.028  0.036  2.368   4.9251e-02
   5_bss:   7.368  0.050  0.261 83.028  0.036  2.368   4.9251e-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:  66.58   0.00  16.79  66.58   0.00  12.91  64.94   4.99  37.91
   1_occ:  66.58   0.00  16.79  66.58   0.00  12.91  64.94   4.99  37.91
   2_bss:  66.58   0.00  16.79  66.58   0.00  12.91  64.94   4.99  37.91
   2_xyz:  66.58   0.00  16.79  66.58   0.00  12.91  64.94   4.99  37.91
   2_adp:  78.22   0.00  17.14  78.22   0.00  13.00  75.36   6.09  39.72
   2_occ:  78.22   0.00  17.14  78.22   0.00  13.00  75.36   6.09  39.72
   3_bss:  78.22   0.00  17.14  78.22   0.00  13.00  75.36   6.09  39.72
   3_xyz:  78.22   0.00  17.14  78.22   0.00  13.00  75.36   6.09  39.72
   3_adp:  79.13   0.00  16.90  79.13   0.93  12.78  76.25   0.00  39.35
   3_occ:  79.13   0.00  16.90  79.13   0.93  12.78  76.25   0.00  39.35
   4_bss:  79.13   0.00  16.90  79.13   0.93  12.78  76.25   0.00  39.35
   4_xyz:  79.13   0.00  16.90  79.13   0.93  12.78  76.25   0.00  39.35
   4_adp:  80.59   0.00  16.81  80.59   0.00  12.63  77.52   0.00  39.61
   4_occ:  80.59   0.00  16.81  80.59   0.00  12.63  77.52   0.00  39.61
   5_bss:  80.59   0.00  16.81  80.59   0.00  12.63  77.52   0.00  39.61
   5_xyz:  80.59   0.00  16.81  80.59   0.00  12.63  77.52   0.00  39.61
   5_adp:  90.51   0.00  16.93  90.51   0.00  12.57  84.02   1.10  40.68
   5_occ:  90.51   0.00  16.93  90.51   0.00  12.57  84.02   1.10  40.68
   5_bss:  90.51   0.00  16.93  90.51   0.00  12.57  84.02   1.11  40.68
------------------------------------------------------------------------
 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:    1.264    0.021    0.261
   1_adp:    1.264    0.021    0.261
   1_occ:    1.264    0.021    0.261
   2_bss:    1.264    0.021    0.261
   2_xyz:    0.938    0.018    0.319
   2_adp:    0.938    0.018    0.319
   2_occ:    0.938    0.018    0.319
   3_bss:    0.938    0.018    0.319
   3_xyz:    0.915    0.039    0.365
   3_adp:    0.915    0.039    0.365
   3_occ:    0.915    0.039    0.365
   4_bss:    0.915    0.039    0.365
   4_xyz:    1.044    0.048    0.381
   4_adp:    1.044    0.048    0.381
   4_occ:    1.044    0.048    0.381
   5_bss:    1.044    0.048    0.381
   5_xyz:    1.149    0.060    0.389
   5_adp:    1.149    0.060    0.389
   5_occ:    1.149    0.060    0.389
   5_bss:    1.149    0.060    0.389
------------------------------------------------------------------------

CPU time actual refinement: 364.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/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_1041/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1041/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 364.72 
  Macro-tasks:
    bulk solvent and scale       = 38.53  
    individual site refinement   = 166.23 
    weights calculation          = 29.84  
    collect and process          = 6.76   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 241.48 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 118.85 
    alpha_beta                      = 8.14   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 132.02 
    fmodel                         = 6.91   
    r_factors                      = 0.26   
    phase_errors                   = 10.99  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 280.35 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.892 micro seconds
Total CPU time: 6.31 minutes
from_scatterers_fft:    709 calls, 118.48 s
gradients_fft:          654 calls, 115.74 s

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

# Date 2008-01-16 Time 06:17:41 PST -0800 (1200493061.22 s)
Start R-work = 0.3251, R-free = 0.3152 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1779 (no bulk solvent and anisotropic scale)

Start R-work = 0.3135, R-free = 0.3054
Final R-work = 0.1106, R-free = 0.1613