# Date 2008-01-16 Time 05:30:27 PST -0800 (1200490227.18 s)
#phil __OFF__

Command line arguments: "../762.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23891
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 762

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.4607, 85.5261, 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: 3.23, per 1000 atoms: 1.14


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98037
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.968697

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98037
Completeness in resolution range: 0.971677
Completeness with d_max=infinity: 0.968697

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2376 [2112/2137]  1902   210   9.9%
  bin  2:  4.2376 -  3.3761 [2038/2058]  1833   205  10.1%
  bin  3:  3.3761 -  2.9530 [2004/2023]  1801   203  10.1%
  bin  4:  2.9530 -  2.6847 [1990/2020]  1798   192   9.6%
  bin  5:  2.6847 -  2.4932 [1984/2003]  1786   198  10.0%
  bin  6:  2.4932 -  2.3468 [1964/1989]  1765   199  10.1%
  bin  7:  2.3468 -  2.2297 [1947/1975]  1747   200  10.3%
  bin  8:  2.2297 -  2.1329 [1959/1995]  1765   194   9.9%
  bin  9:  2.1329 -  2.0510 [1949/1991]  1759   190   9.7%
  bin 10:  2.0510 -  1.9804 [1642/1969]  1474   168  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/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: 22
        2.42 -     3.04: 2210
        3.04 -     3.66: 4739
        3.66 -     4.28: 9112
        4.28 -     4.90: 12399
  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 204 " - " O   HOH Z 296 "  2.159 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.283 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  ... (remaining 28477 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_762/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/model_refine_001.geo

CPU time processing inputs: 9.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3230   r_free= 0.3207   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.035140                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7264 0.99   1380  154 0.2858 0.2800      6.3501      6.2944|
|  2:  4.7264 -  3.7711 0.99   1325  146 0.2556 0.2460      6.4281      6.3894|
|  3:  3.7711 -  3.3002 0.99   1288  142 0.2712 0.2588      6.3064      6.4188|
|  4:  3.3002 -  3.0011 0.99   1283  147 0.2876 0.3267      6.2192      6.2443|
|  5:  3.0011 -  2.7874 0.99   1291  140 0.3306 0.3072      6.0962      6.0638|
|  6:  2.7874 -  2.6240 0.99   1278  142 0.3323 0.3547      6.0302      6.0184|
|  7:  2.6240 -  2.4932 0.99   1275  137 0.3429 0.3134      5.9951      5.9483|
|  8:  2.4932 -  2.3851 0.98   1256  146 0.3600 0.3551      5.9759      5.9867|
|  9:  2.3851 -  2.2936 0.98   1253  137 0.3523 0.3383       5.911       5.861|
| 10:  2.2936 -  2.2147 1.00   1270  142 0.3570 0.3552      5.8913      5.8901|
| 11:  2.2147 -  2.1457 0.97   1248  136 0.3784 0.3652      5.8742      5.8935|
| 12:  2.1457 -  2.0845 0.98   1241  142 0.3788 0.3926       5.821      5.8604|
| 13:  2.0845 -  2.0298 1.00   1260  136 0.3789 0.3780      5.7316      5.6905|
| 14:  2.0298 -  1.9804 0.77    982  112 0.4013 0.3871       5.729      5.6169|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7264  1380   154  0.80  25.52   0.87     0.82      40969.62|
|  2:  4.7264 -  3.7711  1325   146  0.85  21.75   0.98     0.93      45442.26|
|  3:  3.7711 -  3.3002  1288   142  0.81  25.59   1.01     0.97      45248.39|
|  4:  3.3002 -  3.0011  1283   147  0.78  28.48   1.00     0.95      40543.94|
|  5:  3.0011 -  2.7874  1291   140  0.73  32.77   0.99     0.93      33148.66|
|  6:  2.7874 -  2.6240  1278   142  0.74  32.41   1.00     0.93      28421.28|
|  7:  2.6240 -  2.4932  1275   137  0.73  33.05   1.01     0.94      25426.57|
|  8:  2.4932 -  2.3851  1256   146  0.72  34.41   1.01     0.94      23985.30|
|  9:  2.3851 -  2.2936  1253   137  0.72  33.89   1.03     0.94      22260.47|
| 10:  2.2936 -  2.2147  1270   142  0.70  35.68   1.05     0.95      21875.64|
| 11:  2.2147 -  2.1457  1248   136  0.68  37.82   1.06     0.94      21433.11|
| 12:  2.1457 -  2.0845  1241   142  0.67  38.31   1.06     0.94      20459.10|
| 13:  2.0845 -  2.0298  1260   136  0.65  40.06   1.05     0.90      17757.32|
| 14:  2.0298 -  1.9804   982   112  0.67  38.36   1.03     0.88      14292.81|
|alpha:            min =        0.82 max =            0.97 mean =         0.92|
|beta:             min =    14292.81 max =        45442.26 mean =     29094.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.73|
|phase err.(work): min =        0.00 max =           90.00 mean =        32.52|
|phase err.(test): min =        0.00 max =           89.41 mean =        32.50|
|-----------------------------------------------------------------------------|

============================== 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 = 4.759785              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.404   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.639   (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:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      209 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2001 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1875 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2864 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4671 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4441 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5632 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6767 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.175 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3230   r_free= 0.3207   ksol= 0.00   Bsol= 0.00   scale= 0.979    |
|                                                                             |
| 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:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.035140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3088   r_free= 0.3064   ksol= 0.32   Bsol= 35.40   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-0.06,-0.55,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 6.017201                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.113393              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.339584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.520   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3088      final r-factor (work) = 0.1680          |
| start r-factor (free) = 0.3064      final r-factor (free) = 0.1913          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5523 = 4.11 * 0.50 * 6.0247 + 1.00 * 0.1614                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7850 = 4.11 * 0.50 * 5.7000 + 1.00 * 0.0618                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1537          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1962          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9417 = 0.34 * 1.00 * 5.7000 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8383 = 0.34 * 1.00 * 5.3884 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.70   17.05    None  None   None       |
|    all(noH): 2823   0      0.00    71.70   17.05    None  None   None       |
|    Sol.    : 438    0      6.82    71.70   38.90    None  None   None       |
|    Mac.    : 2385   0      0.00    67.57   13.04    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 -   7.170:  350   |   5:    35.851 -  43.021:  112        |
|      1:     7.170 -  14.340: 1391   |   6:    43.021 -  50.191:  101        |
|      2:    14.340 -  21.510:  481   |   7:    50.191 -  57.361:   68        |
|      3:    21.510 -  28.680:  162   |   8:    57.361 -  64.531:   40        |
|      4:    28.680 -  35.851:  108   |   9:    64.531 -  71.701:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1537 r_free = 0.1962             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1533 r_free = 0.1963             target_work(ml) = 5.401         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1533   r_free= 0.1963   ksol= 0.32   Bsol= 35.40   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.65,-0.06,-0.55,-0.00,-0.00,-0.00); trace/3= -1.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.401259                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1526   r_free= 0.1941   ksol= 0.33   Bsol= 45.95   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.19,-1.62,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.395883                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.191592              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.018  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.176907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.594  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1526      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1941      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6841 = 3.19 * 0.50 * 5.4031 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5014 = 3.19 * 0.50 * 5.2907 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1192      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1617      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9445 = 0.18 * 1.00 * 5.2907 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9213 = 0.18 * 1.00 * 5.1679 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.16    72.07   16.79    None  None   None       |
|    all(noH): 2823   0      2.16    72.07   16.79    None  None   None       |
|    Sol.    : 438    0      6.32    70.32   37.81    None  None   None       |
|    Mac.    : 2385   0      2.16    72.07   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.161 -   9.151:  729   |   5:    37.114 -  44.104:  105        |
|      1:     9.151 -  16.142: 1220   |   6:    44.104 -  51.095:   84        |
|      2:    16.142 -  23.132:  354   |   7:    51.095 -  58.085:   65        |
|      3:    23.132 -  30.123:  113   |   8:    58.085 -  65.076:   22        |
|      4:    30.123 -  37.114:  120   |   9:    65.076 -  72.067:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1549             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1549             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1549   ksol= 0.33   Bsol= 45.95   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-2.19,-1.62,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143401                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1545   ksol= 0.33   Bsol= 45.95   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.51,-1.63,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.142334                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.231846              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.788  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.609367              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.577  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1513          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8245 = 2.23 * 0.50 * 5.1670 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7735 = 2.23 * 0.50 * 5.1209 + 1.00 * 0.0590                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1513      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1275 = 0.61 * 1.00 * 5.1209 + 1.00 * 0.0070                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1177 = 0.61 * 1.00 * 5.1030 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    75.90   16.86    None  None   None       |
|    all(noH): 2823   0      1.23    75.90   16.86    None  None   None       |
|    Sol.    : 438    0      6.05    73.38   38.58    None  None   None       |
|    Mac.    : 2385   0      1.23    75.90   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.233 -   8.700:  678   |   5:    38.566 -  46.032:  117        |
|      1:     8.700 -  16.166: 1272   |   6:    46.032 -  53.499:   88        |
|      2:    16.166 -  23.633:  352   |   7:    53.499 -  60.965:   57        |
|      3:    23.633 -  31.099:  122   |   8:    60.965 -  68.432:   22        |
|      4:    31.099 -  38.566:  109   |   9:    68.432 -  75.898:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1519             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1075 r_free = 0.1520             target_work(ml) = 5.106         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1520   ksol= 0.33   Bsol= 45.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.66,-2.51,-1.63,-0.00,-0.00,-0.00); trace/3= -2.27                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106211                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1075   r_free= 0.1519   ksol= 0.33   Bsol= 45.95   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.46,-1.52,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106139                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.840110              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.693  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.652545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1077          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1526          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7542 = 1.84 * 0.50 * 5.1032 + 1.00 * 0.0590                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7525 = 1.84 * 0.50 * 5.1064 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1077      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1526      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6593 = 3.65 * 1.00 * 5.1064 + 1.00 * 0.0081                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.6558 = 3.65 * 1.00 * 5.1050 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    91.16   17.15    None  None   None       |
|    all(noH): 2823   0      0.24    91.16   17.15    None  None   None       |
|    Sol.    : 438    0      6.48    82.19   40.18    None  None   None       |
|    Mac.    : 2385   0      0.24    91.16   12.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.240 -   9.332:  901   |   5:    45.700 -  54.792:   97        |
|      1:     9.332 -  18.424: 1209   |   6:    54.792 -  63.884:   64        |
|      2:    18.424 -  27.516:  242   |   7:    63.884 -  72.976:   27        |
|      3:    27.516 -  36.608:  145   |   8:    72.976 -  82.068:   14        |
|      4:    36.608 -  45.700:  120   |   9:    82.068 -  91.160:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1071 r_free = 0.1543             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1070 r_free = 0.1543             target_work(ml) = 5.111         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1070   r_free= 0.1543   ksol= 0.33   Bsol= 45.95   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.47,-2.46,-1.52,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.110978                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1543   ksol= 0.33   Bsol= 45.95   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.26,-1.29,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111092                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.177747              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 164.221  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446006              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1069      final r-factor (work) = 0.1037          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1673 = 3.18 * 0.50 * 5.1061 + 1.00 * 0.0543                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1682 = 3.18 * 0.50 * 5.0981 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1037      final r-factor (work) = 0.1039          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2835 = 0.45 * 1.00 * 5.0981 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2820 = 0.45 * 1.00 * 5.0967 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    92.24   16.75    None  None   None       |
|    all(noH): 2823   0      0.70    92.24   16.75    None  None   None       |
|    Sol.    : 438    0      6.29    83.03   38.97    None  None   None       |
|    Mac.    : 2385   0      0.70    92.24   12.67    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:     0.701 -   9.855: 1060   |   5:    46.471 -  55.625:   98        |
|      1:     9.855 -  19.009: 1095   |   6:    55.625 -  64.779:   52        |
|      2:    19.009 -  28.163:  220   |   7:    64.779 -  73.933:   16        |
|      3:    28.163 -  37.317:  145   |   8:    73.933 -  83.087:   11        |
|      4:    37.317 -  46.471:  122   |   9:    83.087 -  92.242:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1039 r_free = 0.1539             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1038 r_free = 0.1539             target_work(ml) = 5.093         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1038   r_free= 0.1539   ksol= 0.33   Bsol= 45.95   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.26,-1.29,-0.00,-0.00,-0.00); trace/3= -1.92                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.093135                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7264 0.99   1380  154 0.0948 0.1226      5.3483      5.5001|
|  2:  4.7264 -  3.7711 0.99   1325  146 0.0804 0.1103       5.398         5.6|
|  3:  3.7711 -  3.3002 0.99   1288  142 0.0985 0.1519      5.4305      5.8607|
|  4:  3.3002 -  3.0011 0.99   1283  147 0.1146 0.1516       5.423      5.5608|
|  5:  3.0011 -  2.7874 0.99   1291  140 0.1225 0.1763      5.2826      5.5572|
|  6:  2.7874 -  2.6240 0.99   1278  142 0.1099 0.1722      5.1645      5.3787|
|  7:  2.6240 -  2.4932 0.99   1275  137 0.1180 0.1571      5.1183      5.3499|
|  8:  2.4932 -  2.3851 0.98   1256  146 0.1063 0.1681      4.9967      5.3145|
|  9:  2.3851 -  2.2936 0.98   1253  137 0.1080 0.1620      4.9813      5.2114|
| 10:  2.2936 -  2.2147 1.00   1270  142 0.1006 0.1812      4.9031      5.2643|
| 11:  2.2147 -  2.1457 0.97   1248  136 0.1041 0.1630      4.9039      5.2161|
| 12:  2.1457 -  2.0845 0.98   1241  142 0.1049 0.1663      4.8421      5.1703|
| 13:  2.0845 -  2.0298 1.00   1260  136 0.1022 0.1739      4.7418      5.0731|
| 14:  2.0298 -  1.9804 0.77    982  112 0.0962 0.1622      4.5954      4.8481|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7264  1380   154  0.94   8.84   0.98     0.95       6690.00|
|  2:  4.7264 -  3.7711  1325   146  0.95   7.62   1.02     1.01       8657.80|
|  3:  3.7711 -  3.3002  1288   142  0.94  10.74   1.03     1.02       9792.84|
|  4:  3.3002 -  3.0011  1283   147  0.92  13.22   1.01     0.99       9946.44|
|  5:  3.0011 -  2.7874  1291   140  0.90  15.57   1.00     0.97       7939.40|
|  6:  2.7874 -  2.6240  1278   142  0.91  15.00   0.99     0.96       6711.43|
|  7:  2.6240 -  2.4932  1275   137  0.91  15.03   0.99     0.96       5768.15|
|  8:  2.4932 -  2.3851  1256   146  0.92  14.16   0.99     0.97       4700.46|
|  9:  2.3851 -  2.2936  1253   137  0.92  14.24   1.00     0.98       4553.58|
| 10:  2.2936 -  2.2147  1270   142  0.91  14.46   1.00     0.96       3994.19|
| 11:  2.2147 -  2.1457  1248   136  0.90  16.07   1.00     0.97       4228.23|
| 12:  2.1457 -  2.0845  1241   142  0.92  14.32   1.00     0.99       3739.58|
| 13:  2.0845 -  2.0298  1260   136  0.91  15.02   1.00     0.99       3104.83|
| 14:  2.0298 -  1.9804   982   112  0.92  13.35   0.98     0.95       2246.04|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2246.04 max =         9946.44 mean =      5954.45|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.35|
|phase err.(test): min =        0.00 max =           88.94 mean =        12.89|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1037   r_free= 0.1540   ksol= 0.33   Bsol= 45.93   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.09,-1.10,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.093219                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1037   r_free= 0.1540   ksol= 0.33   Bsol= 45.93   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.01,-2.09,-1.10,-0.00,-0.00,-0.00); trace/3= -1.73                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.093219                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7264 0.99   1380  154 0.0948 0.1227      5.3491      5.5012|
|  2:  4.7264 -  3.7711 0.99   1325  146 0.0804 0.1103      5.3984      5.5998|
|  3:  3.7711 -  3.3002 0.99   1288  142 0.0985 0.1519      5.4305      5.8609|
|  4:  3.3002 -  3.0011 0.99   1283  147 0.1146 0.1516       5.423      5.5609|
|  5:  3.0011 -  2.7874 0.99   1291  140 0.1225 0.1763      5.2825      5.5569|
|  6:  2.7874 -  2.6240 0.99   1278  142 0.1099 0.1722      5.1644      5.3785|
|  7:  2.6240 -  2.4932 0.99   1275  137 0.1180 0.1572      5.1184      5.3502|
|  8:  2.4932 -  2.3851 0.98   1256  146 0.1064 0.1680      4.9967      5.3142|
|  9:  2.3851 -  2.2936 0.98   1253  137 0.1080 0.1619      4.9814      5.2114|
| 10:  2.2936 -  2.2147 1.00   1270  142 0.1006 0.1813      4.9032      5.2648|
| 11:  2.2147 -  2.1457 0.97   1248  136 0.1042 0.1630       4.904       5.216|
| 12:  2.1457 -  2.0845 0.98   1241  142 0.1048 0.1664       4.842      5.1704|
| 13:  2.0845 -  2.0298 1.00   1260  136 0.1022 0.1739      4.7417      5.0728|
| 14:  2.0298 -  1.9804 0.77    982  112 0.0962 0.1622      4.5953      4.8477|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0074 -  4.7264  1380   154  0.94   8.85   0.98     0.95       6703.82|
|  2:  4.7264 -  3.7711  1325   146  0.95   7.63   1.02     1.01       8667.73|
|  3:  3.7711 -  3.3002  1288   142  0.94  10.74   1.03     1.03       9794.16|
|  4:  3.3002 -  3.0011  1283   147  0.92  13.22   1.02     1.00       9944.92|
|  5:  3.0011 -  2.7874  1291   140  0.90  15.57   1.00     0.97       7936.40|
|  6:  2.7874 -  2.6240  1278   142  0.91  15.00   1.00     0.97       6709.77|
|  7:  2.6240 -  2.4932  1275   137  0.91  15.03   1.00     0.96       5767.68|
|  8:  2.4932 -  2.3851  1256   146  0.92  14.16   1.00     0.98       4699.78|
|  9:  2.3851 -  2.2936  1253   137  0.92  14.24   1.01     0.99       4554.22|
| 10:  2.2936 -  2.2147  1270   142  0.91  14.47   1.00     0.97       3994.79|
| 11:  2.2147 -  2.1457  1248   136  0.90  16.08   1.01     0.98       4229.65|
| 12:  2.1457 -  2.0845  1241   142  0.92  14.32   1.01     0.99       3739.34|
| 13:  2.0845 -  2.0298  1260   136  0.91  15.03   1.01     1.00       3103.73|
| 14:  2.0298 -  1.9804   982   112  0.92  13.35   0.99     0.96       2244.35|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2244.35 max =         9944.92 mean =      5955.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.35|
|phase err.(test): min =        0.00 max =           88.94 mean =        12.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.748)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    92.22   16.73    None  None   None       |
|    all(noH): 2823   0      0.68    92.22   16.73    None  None   None       |
|    Sol.    : 438    0      6.27    83.01   38.95    None  None   None       |
|    Mac.    : 2385   0      0.68    92.22   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.677 -   9.831: 1060   |   5:    46.448 -  55.602:   98        |
|      1:     9.831 -  18.985: 1095   |   6:    55.602 -  64.756:   52        |
|      2:    18.985 -  28.140:  220   |   7:    64.756 -  73.910:   16        |
|      3:    28.140 -  37.294:  145   |   8:    73.910 -  83.064:   11        |
|      4:    37.294 -  46.448:  122   |   9:    83.064 -  92.218:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 276         
Filter by distance & map next to the model:
   mapped sites are within: 0.415 - 4.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 272 from: 276
   mapped sites are within: 0.737 - 4.606

peak=    5.998 closest distance to " NE2 GLN A  11 " =    1.184
peak=    5.609 closest distance to " O   HOH Z 126 " =    1.951
peak=    5.290 closest distance to " O   HOH Z 144 " =    1.741
peak=    5.286 closest distance to " CG  PRO A  54 " =    1.219
peak=    5.182 closest distance to " NH2 ARG A  56 " =    2.167
peak=    5.121 closest distance to " CB  SER A  63 " =    1.185
peak=    5.052 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.993 closest distance to " CB  GLN A 223 " =    1.467
peak=    4.704 closest distance to " O   HOH Z 236 " =    2.037
peak=    4.690 closest distance to " CB  ARG A 275 " =    0.893
peak=    4.680 closest distance to " CG  PRO A 213 " =    1.193
peak=    4.665 closest distance to " C   PRO A 198 " =    1.470
peak=    4.663 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.596 closest distance to " O   HOH Z  78 " =    1.794
peak=    4.581 closest distance to " O   HOH Z  15 " =    2.279
peak=    4.501 closest distance to " O   HOH Z 427 " =    2.838
peak=    4.456 closest distance to " CB  GLU A 152 " =    1.239
peak=    4.453 closest distance to " ND2 ASN A 187 " =    1.483
peak=    4.450 closest distance to " O   HOH Z 369 " =    2.055
peak=    4.439 closest distance to " CB  PRO A  54 " =    0.898
peak=    4.409 closest distance to " O   HOH Z 193 " =    1.751
peak=    4.331 closest distance to " O   HOH Z 298 " =    1.907
peak=    4.307 closest distance to " CB  ARG A  79 " =    1.421
peak=    4.288 closest distance to " OD1 ASN A  69 " =    2.579
peak=    4.284 closest distance to " CB  ASN A 148 " =    1.353
peak=    4.254 closest distance to " O   HOH Z 209 " =    2.279
peak=    4.249 closest distance to " O   HOH Z 303 " =    2.166
peak=    4.231 closest distance to " O   HOH Z 144 " =    2.263
peak=    4.223 closest distance to " CB  LEU A 228 " =    1.083
peak=    4.200 closest distance to " O   HOH Z 132 " =    2.304
peak=    4.186 closest distance to " O   HOH Z 234 " =    3.690
peak=    4.168 closest distance to " CA  TYR A  30 " =    0.940
peak=    4.166 closest distance to " O   HOH Z 272 " =    1.819
peak=    4.144 closest distance to " CB  VAL A 265 " =    1.333
peak=    4.143 closest distance to " O   HOH Z  61 " =    1.633
peak=    4.143 closest distance to " O   HOH Z 158 " =    3.064
peak=    4.105 closest distance to " O   HOH Z 203 " =    1.785
peak=    4.062 closest distance to " CB  SER A   3 " =    1.339
peak=    4.023 closest distance to " CB  TYR A 169 " =    0.768
peak=    4.018 closest distance to " O   HOH Z 346 " =    1.698
peak=    4.017 closest distance to " O   HOH Z 316 " =    3.041
peak=    4.014 closest distance to " O   HOH Z  44 " =    1.704
peak=    4.012 closest distance to " CA  ASN A 215 " =    1.217
peak=    4.005 closest distance to " O   HOH Z   1 " =    1.877
peak=    4.000 closest distance to " CD  ARG A  66 " =    2.373
peak=    3.992 closest distance to " NZ  LYS A 117 " =    3.234
peak=    3.967 closest distance to " O   HOH Z 128 " =    2.175
peak=    3.962 closest distance to " CB  GLU A 128 " =    1.034
peak=    3.956 closest distance to " CG2 VAL A 257 " =    0.885
peak=    3.952 closest distance to " CG1 ILE A  33 " =    1.201
peak=    3.936 closest distance to " CB  ARG A 190 " =    1.613
peak=    3.921 closest distance to " O   HOH Z 368 " =    1.965
peak=    3.915 closest distance to " O   HOH Z  66 " =    2.109
peak=    3.910 closest distance to " O   HOH Z 425 " =    2.095
peak=    3.908 closest distance to " O   HOH Z  61 " =    1.491
peak=    3.902 closest distance to " O   SER A  87 " =    2.184
peak=    3.899 closest distance to " O   HOH Z 403 " =    1.717
peak=    3.891 closest distance to " OD2 ASP A 286 " =    2.801
peak=    3.886 closest distance to " O   HOH Z 193 " =    1.675
peak=    3.882 closest distance to " O   HOH Z 250 " =    1.448
peak=    3.863 closest distance to " O   HOH Z 214 " =    2.042
peak=    3.856 closest distance to " CD2 TRP A 179 " =    1.355
peak=    3.851 closest distance to " O   HOH Z   9 " =    2.034
peak=    3.847 closest distance to " O   HOH Z 386 " =    3.248
peak=    3.836 closest distance to " O   HOH Z  40 " =    1.890
peak=    3.833 closest distance to " O   HOH Z 344 " =    3.163
peak=    3.825 closest distance to " CB  TRP A 179 " =    1.391
peak=    3.825 closest distance to " CD  ARG A  66 " =    2.325
peak=    3.814 closest distance to " OG BSER A 164 " =    2.319
peak=    3.794 closest distance to " O   HOH Z 327 " =    1.640
peak=    3.788 closest distance to " CB  ARG A 139 " =    0.978
peak=    3.788 closest distance to " O   HOH Z 133 " =    1.557
peak=    3.787 closest distance to " O   HOH Z 189 " =    1.937
peak=    3.772 closest distance to " O   HOH Z  64 " =    2.288
peak=    3.763 closest distance to " ND1 HIS A  86 " =    1.746
peak=    3.754 closest distance to " O   HOH Z 368 " =    3.591
peak=    3.754 closest distance to " O   HOH Z 419 " =    2.051
peak=    3.752 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.746 closest distance to " O   HOH Z 389 " =    1.882
peak=    3.733 closest distance to " O   HOH Z 234 " =    3.771
peak=    3.732 closest distance to " CB  ASP A 140 " =    0.921
peak=    3.718 closest distance to " O   HOH Z 245 " =    1.303
peak=    3.693 closest distance to " CA  THR A 264 " =    0.843
peak=    3.692 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.688 closest distance to " CD BLYS A 290 " =    1.224
peak=    3.680 closest distance to " NH1AARG A 145 " =    1.138
peak=    3.678 closest distance to " O   HOH Z 280 " =    3.000
peak=    3.672 closest distance to " O   HOH Z 305 " =    3.568
peak=    3.670 closest distance to " CB  SER A 212 " =    1.061
peak=    3.665 closest distance to " O   HOH Z 371 " =    3.020
peak=    3.645 closest distance to " O   HOH Z  10 " =    1.864
peak=    3.634 closest distance to " O   HOH Z 147 " =    1.751
peak=    3.619 closest distance to " CB  SER A 216 " =    0.822
peak=    3.616 closest distance to " O   HOH Z  21 " =    1.715
peak=    3.612 closest distance to " CB  GLN A  88 " =    1.268
peak=    3.612 closest distance to " NH2BARG A 145 " =    2.097
peak=    3.609 closest distance to " O   HOH Z 371 " =    1.650
peak=    3.601 closest distance to " CA  ALA A  21 " =    1.148
peak=    3.595 closest distance to " O   HOH Z 180 " =    2.165
peak=    3.593 closest distance to " O   HOH Z 141 " =    1.695
peak=    3.593 closest distance to " O   HOH Z 426 " =    1.600
peak=    3.579 closest distance to " O   HOH Z 207 " =    1.804
peak=    3.579 closest distance to " O   HOH Z 407 " =    2.315
peak=    3.576 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.561 closest distance to " OG  SER A  22 " =    2.779
peak=    3.556 closest distance to " OD1BASN A 224 " =    2.261
peak=    3.552 closest distance to " CD2 LEU A 255 " =    1.524
peak=    3.551 closest distance to " CB  THR A 157 " =    1.095
peak=    3.547 closest distance to " O   HOH Z 213 " =    1.781
peak=    3.544 closest distance to " CA  THR A 221 " =    1.027
peak=    3.541 closest distance to " O   HOH Z 163 " =    1.879
peak=    3.538 closest distance to " O   HOH Z 248 " =    1.662
peak=    3.536 closest distance to " O   HOH Z   3 " =    1.838
peak=    3.536 closest distance to " O   HOH Z 219 " =    2.158
peak=    3.533 closest distance to " O   HOH Z 108 " =    2.096
peak=    3.531 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.519 closest distance to " CB  VAL A 202 " =    1.606
peak=    3.518 closest distance to " CD2 LEU A 297 " =    0.890
peak=    3.514 closest distance to " O   HOH Z  89 " =    2.167
peak=    3.510 closest distance to " CB  ALA A  34 " =    1.115
peak=    3.508 closest distance to " ND1 HIS A  81 " =    1.580
peak=    3.502 closest distance to " O   HOH Z 353 " =    2.697
peak=    3.500 closest distance to " O   HOH Z 193 " =    2.025
peak=    3.496 closest distance to " O   HOH Z 273 " =    2.721
peak=    3.496 closest distance to " CZ  PHE A 218 " =    1.009
peak=    3.491 closest distance to " CG2 THR A 221 " =    1.128
peak=    3.487 closest distance to " O   HOH Z 128 " =    2.106
peak=    3.482 closest distance to " NH2AARG A 275 " =    3.709
peak=    3.478 closest distance to " CB  GLU A 277 " =    3.525
peak=    3.476 closest distance to " N   PHE A 130 " =    1.287
peak=    3.475 closest distance to " CA  ALA A 158 " =    1.135
peak=    3.468 closest distance to " CB  ASN A 224 " =    1.000
peak=    3.468 closest distance to " O   HOH Z 345 " =    3.418
peak=    3.466 closest distance to " O   HOH Z 423 " =    2.722
peak=    3.462 closest distance to " CG  PRO A 243 " =    1.102
peak=    3.459 closest distance to " O   HOH Z 437 " =    1.476
peak=    3.457 closest distance to " O   HOH Z 329 " =    3.724
peak=    3.452 closest distance to " O   HOH Z  43 " =    1.764
peak=    3.452 closest distance to " O   HOH Z  97 " =    1.964
peak=    3.445 closest distance to " CA  ALA A 291 " =    0.900
peak=    3.443 closest distance to " O   HOH Z   1 " =    1.689
peak=    3.441 closest distance to " O   HOH Z  93 " =    2.445
peak=    3.440 closest distance to " O   HOH Z 286 " =    2.320
peak=    3.439 closest distance to " CB  LEU A 143 " =    1.113
peak=    3.439 closest distance to " O   HOH Z  59 " =    1.705
peak=    3.433 closest distance to " O   HOH Z 298 " =    2.567
peak=    3.431 closest distance to " O   HOH Z 133 " =    2.470
peak=    3.429 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.424 closest distance to " N   ARG A 156 " =    1.282
peak=    3.424 closest distance to " CG2 ILE A 120 " =    1.212
peak=    3.424 closest distance to " CB  SER A  62 " =    1.268
peak=    3.420 closest distance to " CD1 LEU A 300 " =    1.265
peak=    3.417 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.416 closest distance to " O   HOH Z 411 " =    3.780
peak=    3.409 closest distance to " O   HOH Z  71 " =    2.209
peak=    3.401 closest distance to " O   HOH Z 172 " =    3.299
peak=    3.397 closest distance to " N   SER A 134 " =    1.332
peak=    3.397 closest distance to " O   HOH Z 175 " =    2.145
peak=    3.393 closest distance to " CB  LYS A 117 " =    1.170
peak=    3.392 closest distance to " CA  PHE A 283 " =    1.271
peak=    3.391 closest distance to " O   HOH Z 417 " =    3.149
peak=    3.390 closest distance to " CA  ALA A  84 " =    1.420
peak=    3.382 closest distance to " O   HOH Z 199 " =    1.584
peak=    3.379 closest distance to " CB  ASN A  39 " =    0.883
peak=    3.378 closest distance to " O   MET A 105 " =    1.792
peak=    3.378 closest distance to " CD1 ILE A 106 " =    0.861
peak=    3.374 closest distance to " OG BSER A 134 " =    2.823
peak=    3.370 closest distance to " O   HOH Z 402 " =    1.435
peak=    3.368 closest distance to " O   HOH Z 261 " =    2.273
peak=    3.366 closest distance to " O   HOH Z   6 " =    2.028
peak=    3.361 closest distance to " CA  MET A  40 " =    1.090
peak=    3.360 closest distance to " O   HOH Z 265 " =    2.420
peak=    3.360 closest distance to " CB  MET A  40 " =    0.839
peak=    3.358 closest distance to " CB  ALA A   1 " =    4.606
peak=    3.354 closest distance to " O   HOH Z 391 " =    2.876
peak=    3.352 closest distance to " O   HOH Z 271 " =    2.402
peak=    3.345 closest distance to " CB  ASN A 142 " =    0.938
peak=    3.345 closest distance to " O   HOH Z  85 " =    2.166
peak=    3.339 closest distance to " CB  ALA A 233 " =    1.358
peak=    3.334 closest distance to " O   HOH Z 135 " =    1.656
peak=    3.331 closest distance to " CB  LEU A 255 " =    0.781
peak=    3.329 closest distance to " O   HOH Z 405 " =    1.089
peak=    3.327 closest distance to " O   HOH Z 163 " =    1.608
peak=    3.318 closest distance to " O  BHOH Z 338 " =    2.350
peak=    3.314 closest distance to " O   HOH Z  66 " =    2.114
peak=    3.314 closest distance to " O   HOH Z 234 " =    1.730
peak=    3.307 closest distance to " CD  PRO A 243 " =    1.542
peak=    3.307 closest distance to " CB  GLN A  89 " =    1.374
peak=    3.301 closest distance to " CA  ALA A 233 " =    1.047
peak=    3.299 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.297 closest distance to " O   HOH Z 406 " =    1.637
peak=    3.292 closest distance to " O   HOH Z 411 " =    1.754
peak=    3.288 closest distance to " N   ASN A 127 " =    1.293
peak=    3.287 closest distance to " O   HOH Z 173 " =    1.819
peak=    3.282 closest distance to " O   HOH Z 291 " =    1.577
peak=    3.281 closest distance to " CG  PRO A  90 " =    1.057
peak=    3.276 closest distance to " CG  MET A 113 " =    1.219
peak=    3.276 closest distance to " CD1 ILE A 263 " =    1.340
peak=    3.274 closest distance to " O   HOH Z 425 " =    1.239
peak=    3.274 closest distance to " CD  ARG A 269 " =    0.960
peak=    3.273 closest distance to " NH2 ARG A 219 " =    1.834
peak=    3.270 closest distance to " NH1BARG A 145 " =    1.190
peak=    3.268 closest distance to " CA  ARG A 195 " =    1.177
peak=    3.267 closest distance to " CB  ALA A   9 " =    1.591
peak=    3.265 closest distance to " O   HOH Z  88 " =    3.153
peak=    3.261 closest distance to " CB  TYR A 116 " =    0.826
peak=    3.260 closest distance to " CG  GLN A  89 " =    1.481
peak=    3.259 closest distance to " CB  ARG A 138 " =    0.963
peak=    3.256 closest distance to " OG  SER A  62 " =    2.912
peak=    3.253 closest distance to " OD1 ASN A 217 " =    1.733
peak=    3.252 closest distance to " CB  MET A  47 " =    1.132
peak=    3.251 closest distance to " CA  ALA A  51 " =    0.933
peak=    3.250 closest distance to " CB  ALA A 248 " =    0.915
peak=    3.250 closest distance to " O   HOH Z 435 " =    1.863
peak=    3.248 closest distance to " O   HOH Z 188 " =    2.059
peak=    3.246 closest distance to " O   HOH Z 433 " =    1.789
peak=    3.245 closest distance to " O   HOH Z 153 " =    1.589
peak=    3.244 closest distance to " CB  ILE A 120 " =    1.302
peak=    3.241 closest distance to " O   HOH Z 313 " =    1.897
peak=    3.240 closest distance to " CB  SER A  26 " =    1.598
peak=    3.235 closest distance to " NH2 ARG A 156 " =    1.194
peak=    3.231 closest distance to " CG1 ILE A 151 " =    0.939
peak=    3.226 closest distance to " CB  ASP A 171 " =    1.328
peak=    3.223 closest distance to " O   HOH Z 409 " =    2.545
peak=    3.217 closest distance to " CG  PRO A 198 " =    1.247
peak=    3.216 closest distance to " CB  ASN A 110 " =    1.127
peak=    3.212 closest distance to " CA  ASN A 127 " =    1.058
peak=    3.211 closest distance to " CG1BVAL A  72 " =    1.520
peak=    3.209 closest distance to " CG2 VAL A 197 " =    1.140
peak=    3.208 closest distance to " O   HOH Z 295 " =    1.539
peak=    3.203 closest distance to " NE2 GLN A  73 " =    3.723
peak=    3.198 closest distance to " O   HOH Z 422 " =    2.698
peak=    3.194 closest distance to " CG  LYS A  76 " =    1.003
peak=    3.194 closest distance to " O   ASN A 209 " =    1.331
peak=    3.193 closest distance to " CA  ASN A  74 " =    1.244
peak=    3.192 closest distance to " CA  SER A  87 " =    1.032
peak=    3.185 closest distance to " O   HOH Z 148 " =    3.301
peak=    3.184 closest distance to " O   HOH Z 299 " =    4.339
peak=    3.184 closest distance to " O   HOH Z  96 " =    2.131
peak=    3.177 closest distance to " O   HOH Z  44 " =    3.032
peak=    3.174 closest distance to " CG  MET A 185 " =    1.208
peak=    3.165 closest distance to " CD  ARG A  79 " =    2.350
peak=    3.165 closest distance to " O   HOH Z 336 " =    1.997
peak=    3.157 closest distance to " CB  GLN A 278 " =    0.826
peak=    3.156 closest distance to " CA  LYS A 290 " =    1.295
peak=    3.156 closest distance to " CD  LYS A 166 " =    1.245
peak=    3.155 closest distance to " CD  ARG A 219 " =    1.112
peak=    3.153 closest distance to " CB  THR A 294 " =    1.659
peak=    3.152 closest distance to " O   ALA A   1 " =    1.687
peak=    3.152 closest distance to " O   HOH Z 359 " =    1.361
peak=    3.145 closest distance to " O   HOH Z 146 " =    1.645
peak=    3.144 closest distance to " CB  ALA A 291 " =    1.434
peak=    3.143 closest distance to " CZ2 TRP A 179 " =    1.618
peak=    3.142 closest distance to " O   HOH Z 217 " =    1.363
peak=    3.138 closest distance to " O   HOH Z 263 " =    1.715
peak=    3.138 closest distance to " N   SER A 146 " =    1.705
peak=    3.128 closest distance to " CB  TRP A 150 " =    1.315
peak=    3.125 closest distance to " O   HOH Z 366 " =    2.893
peak=    3.122 closest distance to " O   HOH Z 266 " =    3.059
peak=    3.118 closest distance to " OG  SER A 206 " =    1.309
peak=    3.110 closest distance to " OG BSER A  99 " =    2.168
peak=    3.109 closest distance to " CG BARG A 102 " =    1.784
peak=    3.101 closest distance to " N   GLN A 278 " =    1.175
peak=    3.090 closest distance to " O   HOH Z 218 " =    2.327
peak=    3.087 closest distance to " O   HOH Z 357 " =    1.820
peak=    3.081 closest distance to " O   HOH Z  49 " =    2.054
peak=    3.079 closest distance to " CB  LYS A 290 " =    1.077
peak=    3.064 closest distance to " CA  ALA A 248 " =    1.235
peak=    3.058 closest distance to " CB  VAL A 126 " =    1.077
peak=    3.054 closest distance to " OE2 GLU A  53 " =    2.195
peak=    3.052 closest distance to " O   HOH Z  59 " =    1.841
peak=    3.018 closest distance to " O   HOH Z 371 " =    3.377

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.312
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.748 - 5.312

peak=   -4.852 closest distance to " CB  PRO A 243 " =    2.595
peak=   -4.715 closest distance to " O   HOH Z 266 " =    4.723
peak=   -4.622 closest distance to " O   HOH Z 377 " =    2.104
peak=   -4.609 closest distance to " CD  ARG A 156 " =    2.040
peak=   -4.345 closest distance to " O   HOH Z 435 " =    2.756
peak=   -4.318 closest distance to " CG  GLN A 223 " =    1.920
peak=   -4.312 closest distance to " OG BSER A 134 " =    1.246
peak=   -4.306 closest distance to " SG  CYS A 254 " =    3.333
peak=   -4.228 closest distance to " O   HOH Z 389 " =    1.935
peak=   -4.227 closest distance to " CG1 VAL A 112 " =    2.845
peak=   -4.199 closest distance to " O   VAL A  67 " =    2.688
peak=   -4.177 closest distance to " CE2 PHE A 218 " =    2.438
peak=   -4.176 closest distance to " C   HIS A 108 " =    1.138
peak=   -4.153 closest distance to " O   HOH Z 290 " =    1.223
peak=   -4.128 closest distance to " CE  MET A 105 " =    2.302
peak=   -4.119 closest distance to " O   VAL A  67 " =    2.713
peak=   -4.012 closest distance to " O   HOH Z 231 " =    2.185
peak=   -3.962 closest distance to " O   HOH Z 313 " =    1.895
peak=   -3.946 closest distance to " CZ  PHE A  59 " =    1.538
peak=   -3.944 closest distance to " O   HOH Z 372 " =    2.481
peak=   -3.886 closest distance to " O   ILE A 109 " =    2.553
peak=   -3.855 closest distance to " O   HOH Z 198 " =    2.045
peak=   -3.852 closest distance to " ND2 ASN A  45 " =    1.760
peak=   -3.841 closest distance to " CE2 TYR A  30 " =    2.791
peak=   -3.840 closest distance to " OXT GLY A 302 " =    2.825
peak=   -3.821 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.820 closest distance to " N   ALA A  43 " =    2.606
peak=   -3.808 closest distance to " CG  PHE A 283 " =    2.690
peak=   -3.803 closest distance to " O   HOH Z 114 " =    2.998
peak=   -3.797 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.787 closest distance to " O   HOH Z  52 " =    1.277
peak=   -3.779 closest distance to " CD1 PHE A  59 " =    1.869
peak=   -3.773 closest distance to " O   HOH Z 407 " =    3.090
peak=   -3.749 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.740 closest distance to " O   HOH Z 198 " =    1.442
peak=   -3.737 closest distance to " NH2BARG A 275 " =    1.789
peak=   -3.735 closest distance to " CD  ARG A 139 " =    1.561
peak=   -3.735 closest distance to " O   HOH Z 185 " =    2.208
peak=   -3.710 closest distance to " CZ  TYR A 169 " =    1.636
peak=   -3.703 closest distance to " O   HOH Z  10 " =    1.461
peak=   -3.702 closest distance to " CB  ALA A 291 " =    2.308
peak=   -3.699 closest distance to " O   SER A 135 " =    1.477
peak=   -3.692 closest distance to " NH1 ARG A 195 " =    2.592
peak=   -3.688 closest distance to " CZ3 TRP A 179 " =    1.138
peak=   -3.671 closest distance to " CA  GLY A  98 " =    1.890
peak=   -3.666 closest distance to " O   PRO A 198 " =    1.250
peak=   -3.665 closest distance to " OD1 ASN A 148 " =    1.605
peak=   -3.662 closest distance to " O   HOH Z  43 " =    1.673
peak=   -3.661 closest distance to " O   ARG A 145 " =    1.550
peak=   -3.661 closest distance to " O   HOH Z 126 " =    1.828
peak=   -3.654 closest distance to " N   GLN A  58 " =    1.594
peak=   -3.649 closest distance to " O   HOH Z 395 " =    5.138
peak=   -3.645 closest distance to " CB  TYR A  15 " =    2.191
peak=   -3.641 closest distance to " O   HOH Z  60 " =    2.393
peak=   -3.641 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.614 closest distance to " NE  ARG A  36 " =    1.950
peak=   -3.609 closest distance to " N   ASP A 286 " =    2.387
peak=   -3.591 closest distance to " O   HOH Z  13 " =    1.556
peak=   -3.579 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.564 closest distance to " ND2 ASN A  45 " =    1.097
peak=   -3.564 closest distance to " C   ALA A 158 " =    1.349
peak=   -3.562 closest distance to " CB  ASN A  39 " =    2.225
peak=   -3.557 closest distance to " O   HOH Z 211 " =    1.635
peak=   -3.554 closest distance to " OD1 ASN A 187 " =    1.612
peak=   -3.551 closest distance to " O   HOH Z 351 " =    1.525
peak=   -3.549 closest distance to " CD  GLN A  58 " =    1.102
peak=   -3.535 closest distance to " CD1 LEU A 228 " =    2.231
peak=   -3.518 closest distance to " CD2 PHE A 192 " =    1.983
peak=   -3.516 closest distance to " O   SER A  95 " =    1.479
peak=   -3.506 closest distance to " OD1 ASP A 191 " =    1.824
peak=   -3.506 closest distance to " CB  ALA A 248 " =    2.381
peak=   -3.504 closest distance to " N   ALA A 248 " =    1.567
peak=   -3.501 closest distance to " CB  TRP A  85 " =    2.513
peak=   -3.492 closest distance to " SG ACYS A 201 " =    1.806
peak=   -3.490 closest distance to " CB  ASP A 132 " =    2.373
peak=   -3.483 closest distance to " C   LEU A 143 " =    1.175
peak=   -3.477 closest distance to " NH2 ARG A  79 " =    1.914
peak=   -3.468 closest distance to " O   HOH Z 298 " =    1.289
peak=   -3.467 closest distance to " OG BSER A 134 " =    1.664
peak=   -3.458 closest distance to " NH2AARG A 275 " =    5.312
peak=   -3.457 closest distance to " NZ  LYS A 119 " =    3.397
peak=   -3.456 closest distance to " CG  ARG A 269 " =    2.328
peak=   -3.452 closest distance to " ND2 ASN A 249 " =    2.104
peak=   -3.451 closest distance to " O   HOH Z  44 " =    2.255
peak=   -3.444 closest distance to " O   HOH Z 353 " =    2.160
peak=   -3.444 closest distance to " O   VAL A 189 " =    2.526
peak=   -3.438 closest distance to " CB  PHE A 208 " =    2.231
peak=   -3.436 closest distance to " O   HOH Z  98 " =    2.297
peak=   -3.431 closest distance to " O   SER A 210 " =    2.006
peak=   -3.429 closest distance to " OG  SER A  62 " =    1.588
peak=   -3.426 closest distance to " O   HOH Z 196 " =    2.199
peak=   -3.424 closest distance to " O   HOH Z 385 " =    1.996
peak=   -3.422 closest distance to " O   HOH Z 253 " =    3.840
peak=   -3.421 closest distance to " CA  GLY A 203 " =    2.179
peak=   -3.416 closest distance to " CB  CYS A 254 " =    2.325
peak=   -3.416 closest distance to " O   PRO A 243 " =    2.503
peak=   -3.406 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.405 closest distance to " OD2 ASP A 171 " =    2.319
peak=   -3.402 closest distance to " CE3 TRP A 274 " =    2.385
peak=   -3.400 closest distance to " O   PHE A 218 " =    1.587
peak=   -3.397 closest distance to " O   HOH Z 263 " =    2.969
peak=   -3.394 closest distance to " OG  SER A  97 " =    2.139
peak=   -3.389 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.387 closest distance to " CD2 LEU A 300 " =    2.809
peak=   -3.386 closest distance to " O   HOH Z 311 " =    3.626
peak=   -3.362 closest distance to " CB  ALA A 131 " =    2.003
peak=   -3.359 closest distance to " O   HOH Z 394 " =    1.402
peak=   -3.357 closest distance to " N   THR A 235 " =    1.371
peak=   -3.356 closest distance to " O   HOH Z  90 " =    2.547
peak=   -3.352 closest distance to " O   HOH Z 137 " =    1.467
peak=   -3.345 closest distance to " O   HOH Z 359 " =    3.286
peak=   -3.345 closest distance to " OE1 GLN A 223 " =    1.987
peak=   -3.338 closest distance to " O   HOH Z  38 " =    1.567
peak=   -3.336 closest distance to " CG1 VAL A 197 " =    2.151
peak=   -3.331 closest distance to " CD2 PHE A 225 " =    1.151
peak=   -3.329 closest distance to " O   HOH Z 102 " =    1.567
peak=   -3.325 closest distance to " CB  ASP A 286 " =    2.190
peak=   -3.314 closest distance to " O   HOH Z 266 " =    4.574
peak=   -3.308 closest distance to " OD1 ASP A 191 " =    1.505
peak=   -3.307 closest distance to " CG2 ILE A 263 " =    2.260
peak=   -3.303 closest distance to " OH  TYR A 214 " =    1.232
peak=   -3.302 closest distance to " CD2 LEU A 237 " =    2.665
peak=   -3.301 closest distance to " CA  GLY A 133 " =    1.978
peak=   -3.301 closest distance to " CG1 VAL A 230 " =    2.000
peak=   -3.297 closest distance to " O   VAL A 174 " =    2.135
peak=   -3.294 closest distance to " CB  PRO A 163 " =    2.533
peak=   -3.290 closest distance to " CG  GLU A   2 " =    1.991
peak=   -3.284 closest distance to " O   HOH Z  73 " =    2.283
peak=   -3.284 closest distance to " O   HOH Z 281 " =    2.695
peak=   -3.279 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.274 closest distance to " OD2 ASP A 191 " =    1.461
peak=   -3.268 closest distance to " CD1 LEU A 101 " =    2.307
peak=   -3.268 closest distance to " O   ALA A 161 " =    1.633
peak=   -3.260 closest distance to " O   HOH Z 322 " =    1.625
peak=   -3.259 closest distance to " OG  SER A  26 " =    1.174
peak=   -3.257 closest distance to " CB  ALA A 248 " =    1.984
peak=   -3.249 closest distance to " OXT GLY A 302 " =    3.506
peak=   -3.249 closest distance to " O   HOH Z  51 " =    1.277
peak=   -3.249 closest distance to " O   HOH Z  93 " =    2.146
peak=   -3.248 closest distance to " O   HOH Z 377 " =    0.866
peak=   -3.247 closest distance to " O   ALA A  51 " =    1.382
peak=   -3.242 closest distance to " O   HOH Z  11 " =    2.087
peak=   -3.238 closest distance to " O   HOH Z 111 " =    2.218
peak=   -3.236 closest distance to " O   HOH Z 244 " =    1.985
peak=   -3.234 closest distance to " CA  GLY A 241 " =    3.128
peak=   -3.233 closest distance to " O   GLY A  80 " =    2.432
peak=   -3.233 closest distance to " O   GLN A 240 " =    2.375
peak=   -3.231 closest distance to " O   HOH Z 317 " =    2.394
peak=   -3.229 closest distance to " CD1 LEU A 297 " =    2.436
peak=   -3.228 closest distance to " O   HOH Z  63 " =    1.584
peak=   -3.226 closest distance to " O   GLY A 211 " =    1.435
peak=   -3.224 closest distance to " CG1 VAL A 250 " =    2.617
peak=   -3.223 closest distance to " CG2 VAL A 189 " =    1.962
peak=   -3.216 closest distance to " O   HOH Z  24 " =    1.417
peak=   -3.210 closest distance to " O   HOH Z 414 " =    1.875
peak=   -3.209 closest distance to " CG  TRP A 266 " =    1.889
peak=   -3.202 closest distance to " O   MET A  40 " =    2.724
peak=   -3.201 closest distance to " O   HOH Z  89 " =    2.970
peak=   -3.201 closest distance to " CE3 TRP A 123 " =    1.250
peak=   -3.200 closest distance to " O   LEU A 101 " =    2.606
peak=   -3.196 closest distance to " O   VAL A 189 " =    1.588
peak=   -3.191 closest distance to " CG  GLU A 152 " =    1.214
peak=   -3.181 closest distance to " CB  CYS A 201 " =    2.568
peak=   -3.180 closest distance to " ND2 ASN A  69 " =    1.510
peak=   -3.178 closest distance to " CB  ASP A 286 " =    1.851
peak=   -3.177 closest distance to " O   TRP A  70 " =    1.524
peak=   -3.173 closest distance to " N   SER A 276 " =    1.261
peak=   -3.170 closest distance to " OD2 ASP A  50 " =    1.672
peak=   -3.169 closest distance to " O   HOH Z 174 " =    2.499
peak=   -3.166 closest distance to " CD  LYS A 289 " =    2.361
peak=   -3.164 closest distance to " OD2 ASP A 171 " =    1.719
peak=   -3.160 closest distance to " NE2 GLN A 278 " =    1.659
peak=   -3.158 closest distance to " CE1 TYR A 169 " =    2.485
peak=   -3.155 closest distance to " O   TYR A  30 " =    2.868
peak=   -3.153 closest distance to " O   HOH Z 148 " =    1.785
peak=   -3.148 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.145 closest distance to " ND2 ASN A  60 " =    1.418
peak=   -3.144 closest distance to " O   HOH Z 137 " =    1.414
peak=   -3.139 closest distance to " CG1BVAL A  41 " =    2.897
peak=   -3.136 closest distance to " N   LYS A 289 " =    1.515
peak=   -3.134 closest distance to " O   HOH Z 337 " =    1.703
peak=   -3.133 closest distance to " O   ALA A 292 " =    1.991
peak=   -3.132 closest distance to " CG1 VAL A 125 " =    2.380
peak=   -3.129 closest distance to " O   SER A  22 " =    2.259
peak=   -3.124 closest distance to " CG  PRO A 163 " =    2.576
peak=   -3.122 closest distance to " O   HOH Z 103 " =    1.832
peak=   -3.122 closest distance to " O   HOH Z 369 " =    2.219
peak=   -3.121 closest distance to " OE1 GLN A  88 " =    1.205
peak=   -3.117 closest distance to " O   HOH Z 295 " =    1.494
peak=   -3.105 closest distance to " OD1AASN A 224 " =    1.804
peak=   -3.096 closest distance to " NE2 GLN A  88 " =    1.828
peak=   -3.091 closest distance to " O   HOH Z 139 " =    2.893
peak=   -3.088 closest distance to " O   HOH Z 357 " =    2.001
peak=   -3.086 closest distance to " CG  ASN A 301 " =    1.907
peak=   -3.084 closest distance to " O   PRO A 198 " =    1.647
peak=   -3.082 closest distance to " O   ASN A 249 " =    1.507
peak=   -3.080 closest distance to " O   HOH Z 323 " =    1.346
peak=   -3.078 closest distance to " O   HOH Z 166 " =    1.454
peak=   -3.077 closest distance to " CD1 ILE A 151 " =    2.228
peak=   -3.074 closest distance to " C   MET A 188 " =    1.475
peak=   -3.069 closest distance to " OG BSER A 210 " =    2.024
peak=   -3.066 closest distance to " O   HOH Z 168 " =    1.786
peak=   -3.065 closest distance to " CG  ARG A 269 " =    2.035
peak=   -3.054 closest distance to " CH2 TRP A 179 " =    2.148
peak=   -3.048 closest distance to " C   LYS A  76 " =    1.728

================= 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    :  0.3230 0.3207   6.035140e+00   6.023543e+00
   1_bss:  0.3088 0.3064   6.017201e+00   5.992885e+00
   1_xyz:  0.1680 0.1913   5.455497e+00   5.565869e+00
   1_adp:  0.1537 0.1962   5.402720e+00   5.602556e+00
   1_occ:  0.1533 0.1963   5.401259e+00   5.601483e+00
   2_bss:  0.1526 0.1941   5.395883e+00   5.593428e+00
   2_xyz:  0.1192 0.1617   5.183635e+00   5.418171e+00
   2_adp:  0.1148 0.1549   5.143730e+00   5.371870e+00
   2_occ:  0.1146 0.1549   5.143401e+00   5.371954e+00
   3_bss:  0.1148 0.1545   5.142334e+00   5.369502e+00
   3_xyz:  0.1092 0.1513   5.110749e+00   5.351183e+00
   3_adp:  0.1076 0.1519   5.106168e+00   5.354410e+00
   3_occ:  0.1075 0.1520   5.106211e+00   5.354603e+00
   4_bss:  0.1075 0.1519   5.106139e+00   5.354584e+00
   4_xyz:  0.1077 0.1526   5.108840e+00   5.359215e+00
   4_adp:  0.1071 0.1543   5.110877e+00   5.366702e+00
   4_occ:  0.1070 0.1543   5.110978e+00   5.367009e+00
   5_bss:  0.1069 0.1543   5.111092e+00   5.367088e+00
   5_xyz:  0.1037 0.1549   5.097070e+00   5.367667e+00
   5_adp:  0.1039 0.1539   5.093064e+00   5.361142e+00
   5_occ:  0.1038 0.1539   5.093135e+00   5.361359e+00
   5_bss:  0.1037 0.1540   5.093219e+00   5.361413e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.324  35.402  -2.649  -0.060  -0.550  -0.000  -0.000  -0.000
   1_xyz:  0.324  35.402  -2.649  -0.060  -0.550  -0.000  -0.000  -0.000
   1_adp:  0.324  35.402  -2.649  -0.060  -0.550  -0.000  -0.000  -0.000
   1_occ:  0.324  35.402  -2.649  -0.060  -0.550  -0.000  -0.000  -0.000
   2_bss:  0.326  45.954  -2.788  -2.186  -1.616  -0.000  -0.000  -0.000
   2_xyz:  0.326  45.954  -2.788  -2.186  -1.616  -0.000  -0.000  -0.000
   2_adp:  0.326  45.954  -2.788  -2.186  -1.616  -0.000  -0.000  -0.000
   2_occ:  0.326  45.954  -2.788  -2.186  -1.616  -0.000  -0.000  -0.000
   3_bss:  0.326  45.954  -2.661  -2.509  -1.632  -0.000  -0.000  -0.000
   3_xyz:  0.326  45.954  -2.661  -2.509  -1.632  -0.000  -0.000  -0.000
   3_adp:  0.326  45.954  -2.661  -2.509  -1.632  -0.000  -0.000  -0.000
   3_occ:  0.326  45.954  -2.661  -2.509  -1.632  -0.000  -0.000  -0.000
   4_bss:  0.326  45.954  -2.470  -2.463  -1.524  -0.000  -0.000  -0.000
   4_xyz:  0.326  45.954  -2.470  -2.463  -1.524  -0.000  -0.000  -0.000
   4_adp:  0.326  45.954  -2.470  -2.463  -1.524  -0.000  -0.000  -0.000
   4_occ:  0.326  45.954  -2.470  -2.463  -1.524  -0.000  -0.000  -0.000
   5_bss:  0.326  45.954  -2.209  -2.262  -1.294  -0.000  -0.000  -0.000
   5_xyz:  0.326  45.954  -2.209  -2.262  -1.294  -0.000  -0.000  -0.000
   5_adp:  0.326  45.954  -2.209  -2.262  -1.294  -0.000  -0.000  -0.000
   5_occ:  0.326  45.954  -2.209  -2.262  -1.294  -0.000  -0.000  -0.000
   5_bss:  0.326  45.931  -2.012  -2.094  -1.097  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.514 0.7335  0.9244    29093.574
   1_bss:  31.140 0.7465  0.9050    25587.636
   1_xyz:  17.542 0.8863  1.0078     9386.489
   1_adp:  18.437 0.8776  1.0038     9987.611
   1_occ:  18.424 0.8777  1.0035     9951.757
   2_bss:  18.173 0.8799  0.9670     9726.159
   2_xyz:  14.552 0.9101  0.9848     6641.021
   2_adp:  13.635 0.9176  0.9862     6147.796
   2_occ:  13.636 0.9176  0.9861     6143.898
   3_bss:  13.600 0.9178  0.9838     6110.488
   3_xyz:  13.152 0.9216  0.9834     5843.060
   3_adp:  13.194 0.9215  0.9774     5859.864
   3_occ:  13.199 0.9214  0.9773     5862.384
   4_bss:  13.199 0.9214  0.9815     5863.340
   4_xyz:  13.287 0.9207  0.9811     5929.335
   4_adp:  13.445 0.9196  0.9747     6006.324
   4_occ:  13.450 0.9195  0.9746     6011.701
   5_bss:  13.452 0.9195  0.9829     6014.078
   5_xyz:  13.426 0.9197  0.9830     6027.913
   5_adp:  13.299 0.9206  0.9773     5952.999
   5_occ:  13.305 0.9206  0.9772     5954.155
   5_bss:  13.307 0.9206  0.9831     5955.544
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6138e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6138e-01
   1_xyz:   1.022  0.007  0.070 14.995  0.005  4.109   6.1810e-02
   1_adp:   1.022  0.007  0.070 14.995  0.005  4.109   6.1810e-02
   1_occ:   1.022  0.007  0.070 14.995  0.005  4.109   6.1810e-02
   2_bss:   1.022  0.007  0.070 14.995  0.005  4.109   6.1810e-02
   2_xyz:   0.997  0.006  0.074 14.797  0.004  4.114   5.8501e-02
   2_adp:   0.997  0.006  0.074 14.797  0.004  4.114   5.8501e-02
   2_occ:   0.997  0.006  0.074 14.797  0.004  4.114   5.8501e-02
   3_bss:   0.997  0.006  0.074 14.797  0.004  4.114   5.8501e-02
   3_xyz:   0.980  0.007  0.075 14.821  0.004  4.116   5.8977e-02
   3_adp:   0.980  0.007  0.075 14.821  0.004  4.116   5.8977e-02
   3_occ:   0.980  0.007  0.075 14.821  0.004  4.116   5.8977e-02
   4_bss:   0.980  0.007  0.075 14.821  0.004  4.116   5.8977e-02
   4_xyz:   0.938  0.006  0.072 14.573  0.004  4.116   5.4325e-02
   4_adp:   0.938  0.006  0.072 14.573  0.004  4.116   5.4325e-02
   4_occ:   0.938  0.006  0.072 14.573  0.004  4.116   5.4325e-02
   5_bss:   0.938  0.006  0.072 14.573  0.004  4.116   5.4325e-02
   5_xyz:   1.064  0.008  0.080 14.943  0.005  4.117   6.8014e-02
   5_adp:   1.064  0.008  0.080 14.943  0.005  4.117   6.8014e-02
   5_occ:   1.064  0.008  0.080 14.943  0.005  4.117   6.8014e-02
   5_bss:   1.064  0.008  0.080 14.943  0.005  4.117   6.8014e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3964e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3964e-01
   1_xyz:   7.511  0.053  0.348 85.485  0.043  2.267   5.7085e-02
   1_adp:   7.511  0.053  0.348 85.485  0.043  2.267   5.7085e-02
   1_occ:   7.511  0.053  0.348 85.485  0.043  2.267   5.7085e-02
   2_bss:   7.511  0.053  0.348 85.485  0.043  2.267   5.7085e-02
   2_xyz:   7.544  0.039  0.222 84.922  0.040  2.322   4.4342e-02
   2_adp:   7.544  0.039  0.222 84.922  0.040  2.322   4.4342e-02
   2_occ:   7.544  0.039  0.222 84.922  0.040  2.322   4.4342e-02
   3_bss:   7.544  0.039  0.222 84.922  0.040  2.322   4.4342e-02
   3_xyz:   6.985  0.042  0.236 84.842  0.036  2.297   4.3991e-02
   3_adp:   6.985  0.042  0.236 84.842  0.036  2.297   4.3991e-02
   3_occ:   6.985  0.042  0.236 84.842  0.036  2.297   4.3991e-02
   4_bss:   6.985  0.042  0.236 84.842  0.036  2.297   4.3991e-02
   4_xyz:   6.690  0.040  0.229 84.470  0.041  2.345   3.8061e-02
   4_adp:   6.690  0.040  0.229 84.470  0.041  2.345   3.8061e-02
   4_occ:   6.690  0.040  0.229 84.470  0.041  2.345   3.8061e-02
   5_bss:   6.690  0.040  0.229 84.470  0.041  2.345   3.8061e-02
   5_xyz:   6.587  0.046  0.256 83.824  0.037  2.276   5.8366e-02
   5_adp:   6.587  0.046  0.256 83.824  0.037  2.276   5.8366e-02
   5_occ:   6.587  0.046  0.256 83.824  0.037  2.276   5.8366e-02
   5_bss:   6.587  0.046  0.256 83.824  0.037  2.276   5.8366e-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:  71.70   0.00  17.05  67.57   0.00  13.04  71.70   6.82  38.90
   1_occ:  71.70   0.00  17.05  67.57   0.00  13.04  71.70   6.82  38.90
   2_bss:  71.70   0.00  17.05  67.57   0.00  13.04  71.70   6.82  38.90
   2_xyz:  71.70   0.00  17.05  67.57   0.00  13.04  71.70   6.82  38.90
   2_adp:  72.07   2.16  16.79  72.07   2.16  12.92  70.32   6.32  37.81
   2_occ:  72.07   2.16  16.79  72.07   2.16  12.92  70.32   6.32  37.81
   3_bss:  72.07   2.16  16.79  72.07   2.16  12.92  70.32   6.32  37.81
   3_xyz:  72.07   2.16  16.79  72.07   2.16  12.92  70.32   6.32  37.81
   3_adp:  75.90   1.23  16.86  75.90   1.23  12.87  73.38   6.05  38.58
   3_occ:  75.90   1.23  16.86  75.90   1.23  12.87  73.38   6.05  38.58
   4_bss:  75.90   1.23  16.86  75.90   1.23  12.87  73.38   6.05  38.58
   4_xyz:  75.90   1.23  16.86  75.90   1.23  12.87  73.38   6.05  38.58
   4_adp:  91.16   0.24  17.15  91.16   0.24  12.92  82.19   6.48  40.18
   4_occ:  91.16   0.24  17.15  91.16   0.24  12.92  82.19   6.48  40.18
   5_bss:  91.16   0.24  17.15  91.16   0.24  12.92  82.19   6.48  40.18
   5_xyz:  91.16   0.24  17.15  91.16   0.24  12.92  82.19   6.48  40.18
   5_adp:  92.24   0.70  16.75  92.24   0.70  12.67  83.03   6.29  38.97
   5_occ:  92.24   0.70  16.75  92.24   0.70  12.67  83.03   6.29  38.97
   5_bss:  92.22   0.68  16.73  92.22   0.68  12.65  83.01   6.27  38.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.047    0.026    0.312
   1_adp:    1.047    0.026    0.312
   1_occ:    1.047    0.026    0.312
   2_bss:    1.047    0.026    0.312
   2_xyz:    0.703    0.041    0.366
   2_adp:    0.703    0.041    0.366
   2_occ:    0.703    0.041    0.366
   3_bss:    0.703    0.041    0.366
   3_xyz:    0.821    0.024    0.391
   3_adp:    0.821    0.024    0.391
   3_occ:    0.821    0.024    0.391
   4_bss:    0.821    0.024    0.391
   4_xyz:    0.961    0.019    0.396
   4_adp:    0.961    0.019    0.396
   4_occ:    0.961    0.019    0.396
   5_bss:    0.961    0.019    0.396
   5_xyz:    1.057    0.025    0.403
   5_adp:    1.057    0.025    0.403
   5_occ:    1.057    0.025    0.403
   5_bss:    1.057    0.025    0.403
------------------------------------------------------------------------

CPU time actual refinement: 319.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/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_762/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_762/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.98 
  Macro-tasks:
    bulk solvent and scale       = 36.77  
    individual site refinement   = 127.96 
    weights calculation          = 28.27  
    collect and process          = 6.43   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 199.52 
  Micro-tasks:
    mask                            = 1.15   
    f_calc                          = 102.54 
    alpha_beta                      = 7.55   
    target                          = 1.08   
    gradients_wrt_atomic_parameters = 110.88 
    fmodel                         = 6.30   
    r_factors                      = 0.16   
    phase_errors                   = 11.20  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 241.16 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.547 micro seconds
Total CPU time: 5.54 minutes
from_scatterers_fft:    657 calls, 102.15 s
gradients_fft:          602 calls,  97.58 s

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

# Date 2008-01-16 Time 05:35:57 PST -0800 (1200490557.96 s)
Start R-work = 0.3230, R-free = 0.3207 (no bulk solvent and anisotropic scale)
Final R-work = 0.1280, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.3088, R-free = 0.3064
Final R-work = 0.1037, R-free = 0.1540