# Date 2008-01-16 Time 05:01:49 PST -0800 (1200488509.24 s)
#phil __OFF__

Command line arguments: "../563.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24327
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 563

-------------------------------------------------------------------------------
  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: (69.8988, 47.3993, 85.0941, 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: 3.26, per 1000 atoms: 1.15


================================== 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: (69.8988, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97129
Completeness in resolution range: 0.954816
Completeness with d_max=infinity: 0.951846

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8779
                             d_min =   1.9713

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: (69.8988, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97129
Completeness in resolution range: 0.954816
Completeness with d_max=infinity: 0.951846

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8783 -  4.2178 [2154/2182]  1939   215  10.0%
  bin  2:  4.2178 -  3.3605 [2063/2086]  1855   208  10.1%
  bin  3:  3.3605 -  2.9394 [2048/2070]  1843   205  10.0%
  bin  4:  2.9394 -  2.6723 [2022/2041]  1827   195   9.6%
  bin  5:  2.6723 -  2.4817 [2019/2048]  1809   210  10.4%
  bin  6:  2.4817 -  2.3360 [1980/2021]  1791   189   9.5%
  bin  7:  2.3360 -  2.2194 [1984/2019]  1782   202  10.2%
  bin  8:  2.2194 -  2.1231 [1996/2035]  1795   201  10.1%
  bin  9:  2.1231 -  2.0416 [1985/2016]  1791   194   9.8%
  bin 10:  2.0416 -  1.9713 [1338/1998]  1198   140  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 31
        2.42 -     3.04: 2200
        3.04 -     3.66: 4721
        3.66 -     4.28: 9052
        4.28 -     4.90: 12437
  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 100 " - " O   HOH Z 352 "  1.916 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.954 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.965 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.036 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28436 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_563/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 = 69.89875 47.3993 85.09415 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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3496   r_free= 0.3446   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.099011                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7041 0.99   1395  154 0.2948 0.3067       6.377      6.3709|
|  2:  4.7041 -  3.7536 0.99   1356  148 0.2778 0.2679      6.4933      6.4778|
|  3:  3.7536 -  3.2849 0.99   1319  155 0.2969 0.2841      6.3866      6.4426|
|  4:  3.2849 -  2.9872 0.99   1316  138 0.3237 0.3073      6.2721      6.2133|
|  5:  2.9872 -  2.7746 0.98   1293  147 0.3440 0.2973      6.1445      6.0807|
|  6:  2.7746 -  2.6119 0.98   1295  149 0.3707 0.3681      6.0933      5.9983|
|  7:  2.6119 -  2.4817 0.99   1299  142 0.3720 0.3221      6.0805       5.967|
|  8:  2.4817 -  2.3742 0.99   1285  145 0.3814 0.4330      6.0194      6.0743|
|  9:  2.3742 -  2.2831 0.98   1294  135 0.4044 0.3909       6.001      6.0335|
| 10:  2.2831 -  2.2046 0.98   1264  147 0.4009 0.4568      5.9701      6.0447|
| 11:  2.2046 -  2.1358 0.98   1274  139 0.4105 0.4117      5.9191      5.9759|
| 12:  2.1358 -  2.0750 0.99   1263  142 0.4058 0.4288      5.8605      5.9062|
| 13:  2.0750 -  2.0205 0.97   1265  137 0.4260 0.4068      5.7829      5.7629|
| 14:  2.0205 -  1.9713 0.55    712   81 0.4446 0.3998      5.7693      5.6424|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.7041  1395   154  0.77  27.96   0.87     0.78      48307.63|
|  2:  4.7041 -  3.7536  1356   148  0.82  24.12   0.97     0.90      52021.82|
|  3:  3.7536 -  3.2849  1319   155  0.79  27.36   0.98     0.94      49764.77|
|  4:  3.2849 -  2.9872  1316   138  0.76  30.33   0.99     0.94      42478.74|
|  5:  2.9872 -  2.7746  1293   147  0.72  33.76   0.98     0.92      34703.07|
|  6:  2.7746 -  2.6119  1295   149  0.70  35.37   0.99     0.91      30553.09|
|  7:  2.6119 -  2.4817  1299   142  0.71  35.03   0.98     0.91      28837.92|
|  8:  2.4817 -  2.3742  1285   145  0.66  39.39   1.00     0.87      30341.85|
|  9:  2.3742 -  2.2831  1294   135  0.62  42.72   1.01     0.82      30007.96|
| 10:  2.2831 -  2.2046  1264   147  0.58  45.39   1.02     0.79      30919.05|
| 11:  2.2046 -  2.1358  1274   139  0.57  46.33   1.03     0.81      29149.24|
| 12:  2.1358 -  2.0750  1263   142  0.58  45.85   1.04     0.84      27137.87|
| 13:  2.0750 -  2.0205  1265   137  0.58  45.60   1.01     0.85      22115.38|
| 14:  2.0205 -  1.9713   712    81  0.63  42.14   1.00     0.84      17048.94|
|alpha:            min =        0.78 max =            0.94 mean =         0.87|
|beta:             min =    17048.94 max =        52021.82 mean =     34588.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.68|
|phase err.(work): min =        0.00 max =           89.95 mean =        36.90|
|phase err.(test): min =        0.00 max =           89.79 mean =        36.71|
|-----------------------------------------------------------------------------|

============================== 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 = 4.959040              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.583   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.853001              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.250   (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:        8 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      190 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2010 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1889 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2832 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4630 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4422 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5685 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6752 |
|-----------------------------------------------------------------------------|
|-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 |        0.167 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.806 |       0.249 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3496   r_free= 0.3446   ksol= 0.00   Bsol= 0.00   scale= 0.965    |
|                                                                             |
| 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:   0.42 A                  |
| x-ray target function (ml) for work reflections: 6.099011                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3367   r_free= 0.3298   ksol= 0.30   Bsol= 28.55   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,0.49,0.98,0.00,0.00,0.00); trace/3= -0.55                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 6.080170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.411392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.447   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.457063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.156   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3367      final r-factor (work) = 0.1875          |
| start r-factor (free) = 0.3298      final r-factor (free) = 0.2072          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5910 = 4.41 * 0.50 * 6.0862 + 1.00 * 0.1666                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8473 = 4.41 * 0.50 * 5.7916 + 1.00 * 0.0727                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1875      final r-factor (work) = 0.1707          |
| start r-factor (free) = 0.2072      final r-factor (free) = 0.2154          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6533 = 0.46 * 1.00 * 5.7916 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5131 = 0.46 * 1.00 * 5.4778 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.38   17.34    None  None   None       |
|    all(noH): 2823   0      0.00    80.38   17.34    None  None   None       |
|    Sol.    : 438    0      7.77    72.16   39.23    None  None   None       |
|    Mac.    : 2385   0      0.00    80.38   13.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.038:  570   |   5:    40.191 -  48.230:  121        |
|      1:     8.038 -  16.077: 1306   |   6:    48.230 -  56.268:   88        |
|      2:    16.077 -  24.115:  398   |   7:    56.268 -  64.306:   45        |
|      3:    24.115 -  32.153:  142   |   8:    64.306 -  72.345:   20        |
|      4:    32.153 -  40.191:  131   |   9:    72.345 -  80.383:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1707 r_free = 0.2154             target_work(ml) = 5.491         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1704 r_free = 0.2156             target_work(ml) = 5.490         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1704   r_free= 0.2156   ksol= 0.30   Bsol= 28.55   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,0.49,0.98,0.00,0.00,0.00); trace/3= -0.55                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.489945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1681   r_free= 0.2131   ksol= 0.32   Bsol= 44.01   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-1.39,-1.18,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.483495                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.893030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.544   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170594              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.765  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1681      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.2131      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0168 = 2.89 * 0.50 * 5.4919 + 1.00 * 0.0727                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8176 = 2.89 * 0.50 * 5.3642 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1273      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9245 = 0.17 * 1.00 * 5.3642 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8974 = 0.17 * 1.00 * 5.2185 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.23    79.59   16.81    None  None   None       |
|    all(noH): 2823   0      2.23    79.59   16.81    None  None   None       |
|    Sol.    : 438    0      5.96    69.82   37.79    None  None   None       |
|    Mac.    : 2385   0      2.23    79.59   12.95    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:     2.232 -   9.968:  956   |   5:    40.911 -  48.646:  113        |
|      1:     9.968 -  17.703: 1110   |   6:    48.646 -  56.382:   85        |
|      2:    17.703 -  25.439:  266   |   7:    56.382 -  64.118:   25        |
|      3:    25.439 -  33.175:  129   |   8:    64.118 -  71.853:   15        |
|      4:    33.175 -  40.911:  122   |   9:    71.853 -  79.589:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1612             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1609             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1609   ksol= 0.32   Bsol= 44.01   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-1.39,-1.18,-0.00,-0.00,-0.00); trace/3= -1.93                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.192042                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1600   ksol= 0.32   Bsol= 44.53   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.80,-1.58,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191351                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.541797              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.403  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.241193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.621  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1600      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6901 = 2.54 * 0.50 * 5.2184 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6109 = 2.54 * 0.50 * 5.1515 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1091          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1536          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2496 = 0.24 * 1.00 * 5.1515 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2420 = 0.24 * 1.00 * 5.1188 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    82.07   16.69    None  None   None       |
|    all(noH): 2823   0      1.99    82.07   16.69    None  None   None       |
|    Sol.    : 438    0      5.77    71.50   37.79    None  None   None       |
|    Mac.    : 2385   0      1.99    82.07   12.81    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:     1.988 -   9.997:  997   |   5:    42.029 -  50.037:  116        |
|      1:     9.997 -  18.005: 1103   |   6:    50.037 -  58.046:   77        |
|      2:    18.005 -  26.013:  249   |   7:    58.046 -  66.054:   24        |
|      3:    26.013 -  34.021:  131   |   8:    66.054 -  74.062:    8        |
|      4:    34.021 -  42.029:  115   |   9:    74.062 -  82.070:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1091 r_free = 0.1536             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1090 r_free = 0.1536             target_work(ml) = 5.120         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1536   ksol= 0.32   Bsol= 44.53   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-1.80,-1.58,-0.00,-0.00,-0.00); trace/3= -2.10                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119772                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1090   r_free= 0.1536   ksol= 0.32   Bsol= 44.53   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.89,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.119566                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.515888              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.152  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.339544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.634  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1536      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5027 = 2.52 * 0.50 * 5.1186 + 1.00 * 0.0639                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4951 = 2.52 * 0.50 * 5.1120 + 1.00 * 0.0645                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1067          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7431 = 0.34 * 1.00 * 5.1120 + 1.00 * 0.0074                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7423 = 0.34 * 1.00 * 5.1086 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.55    82.51   16.57    None  None   None       |
|    all(noH): 2823   0      1.55    82.51   16.57    None  None   None       |
|    Sol.    : 438    0      5.48    71.41   37.81    None  None   None       |
|    Mac.    : 2385   0      1.55    82.51   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:     1.549 -   9.644:  948   |   5:    42.028 -  50.123:  117        |
|      1:     9.644 -  17.740: 1134   |   6:    50.123 -  58.219:   74        |
|      2:    17.740 -  25.836:  266   |   7:    58.219 -  66.315:   27        |
|      3:    25.836 -  33.932:  127   |   8:    66.315 -  74.411:    7        |
|      4:    33.932 -  42.028:  120   |   9:    74.411 -  82.507:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1067 r_free = 0.1539             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1539             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1539   ksol= 0.32   Bsol= 44.53   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,-1.89,-1.60,-0.00,-0.00,-0.00); trace/3= -2.09                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.111888                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1539   ksol= 0.32   Bsol= 44.66   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.76,-1.45,-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: 5.111944                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.049268              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 165.517  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.678924              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.553  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1066      final r-factor (work) = 0.1075          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2996 = 2.05 * 0.50 * 5.1093 + 1.00 * 0.0645                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2998 = 2.05 * 0.50 * 5.1160 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1075      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.9450 = 4.68 * 1.00 * 5.1160 + 1.00 * 0.0077                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 23.9510 = 4.68 * 1.00 * 5.1169 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    94.70   16.85    None  None   None       |
|    all(noH): 2823   0      0.25    94.70   16.85    None  None   None       |
|    Sol.    : 438    0      5.42    76.26   39.59    None  None   None       |
|    Mac.    : 2385   0      0.25    94.70   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:     0.247 -   9.693: 1027   |   5:    47.473 -  56.918:  100        |
|      1:     9.693 -  19.138: 1134   |   6:    56.918 -  66.364:   60        |
|      2:    19.138 -  28.583:  221   |   7:    66.364 -  75.809:   14        |
|      3:    28.583 -  38.028:  135   |   8:    75.809 -  85.254:    5        |
|      4:    38.028 -  47.473:  124   |   9:    85.254 -  94.699:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1566             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1567             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1567   ksol= 0.32   Bsol= 44.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.56,-1.76,-1.45,-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: 5.124383                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7041 0.99   1395  154 0.0959 0.1254      5.3542      5.5015|
|  2:  4.7041 -  3.7536 0.99   1356  148 0.0818 0.1103      5.4001      5.6102|
|  3:  3.7536 -  3.2849 0.99   1319  155 0.1006 0.1499      5.4399      5.8314|
|  4:  3.2849 -  2.9872 0.99   1316  138 0.1176 0.1557      5.4364      5.6118|
|  5:  2.9872 -  2.7746 0.98   1293  147 0.1239 0.1694      5.2948       5.512|
|  6:  2.7746 -  2.6119 0.98   1295  149 0.1191 0.1844      5.1964      5.4159|
|  7:  2.6119 -  2.4817 0.99   1299  142 0.1167 0.1586      5.1161      5.3675|
|  8:  2.4817 -  2.3742 0.99   1285  145 0.1096 0.1773      5.0445      5.2844|
|  9:  2.3742 -  2.2831 0.98   1294  135 0.1116 0.1770      5.0021      5.3228|
| 10:  2.2831 -  2.2046 0.98   1264  147 0.1061 0.1839      4.9469      5.2246|
| 11:  2.2046 -  2.1358 0.98   1274  139 0.1088 0.1729      4.9162      5.2494|
| 12:  2.1358 -  2.0750 0.99   1263  142 0.1038 0.1642      4.8513      5.1377|
| 13:  2.0750 -  2.0205 0.97   1265  137 0.1096 0.1797      4.7861      5.1054|
| 14:  2.0205 -  1.9713 0.55    712   81 0.1039 0.1692       4.702      4.8976|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.7041  1395   154  0.94   8.78   0.98     0.96       6745.24|
|  2:  4.7041 -  3.7536  1356   148  0.95   7.80   1.02     1.00       8448.79|
|  3:  3.7536 -  3.2849  1319   155  0.94  10.78   1.03     1.02       9861.11|
|  4:  3.2849 -  2.9872  1316   138  0.92  13.72   1.01     0.99      10333.42|
|  5:  2.9872 -  2.7746  1293   147  0.90  15.64   0.99     0.97       8073.73|
|  6:  2.7746 -  2.6119  1295   149  0.90  15.76   0.98     0.95       6971.73|
|  7:  2.6119 -  2.4817  1299   142  0.91  14.94   0.98     0.96       5737.44|
|  8:  2.4817 -  2.3742  1285   145  0.91  15.10   0.99     0.96       5321.96|
|  9:  2.3742 -  2.2831  1294   135  0.91  15.08   0.99     0.96       4780.84|
| 10:  2.2831 -  2.2046  1264   147  0.90  15.54   0.99     0.95       4444.93|
| 11:  2.2046 -  2.1358  1274   139  0.90  16.10   0.99     0.95       4241.06|
| 12:  2.1358 -  2.0750  1263   142  0.92  14.82   1.00     0.98       3859.21|
| 13:  2.0750 -  2.0205  1265   137  0.90  16.49   0.99     0.98       3473.52|
| 14:  2.0205 -  1.9713   712    81  0.91  15.51   0.97     0.93       2855.08|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2855.08 max =        10333.42 mean =      6224.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.89|
|phase err.(test): min =        0.00 max =           89.32 mean =        13.44|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1567   ksol= 0.32   Bsol= 47.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.55,-1.25,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.124210                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1567   ksol= 0.32   Bsol= 47.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.31,-1.55,-1.25,-0.00,-0.00,-0.00); trace/3= -1.70                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.124210                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7041 0.99   1395  154 0.0960 0.1257      5.3553      5.5037|
|  2:  4.7041 -  3.7536 0.99   1356  148 0.0821 0.1104      5.4026      5.6116|
|  3:  3.7536 -  3.2849 0.99   1319  155 0.1008 0.1500      5.4408      5.8321|
|  4:  3.2849 -  2.9872 0.99   1316  138 0.1175 0.1554      5.4358      5.6107|
|  5:  2.9872 -  2.7746 0.98   1293  147 0.1237 0.1692      5.2931      5.5109|
|  6:  2.7746 -  2.6119 0.98   1295  149 0.1188 0.1840      5.1952      5.4144|
|  7:  2.6119 -  2.4817 0.99   1299  142 0.1166 0.1584      5.1151      5.3673|
|  8:  2.4817 -  2.3742 0.99   1285  145 0.1096 0.1770      5.0439      5.2828|
|  9:  2.3742 -  2.2831 0.98   1294  135 0.1116 0.1773      5.0019      5.3239|
| 10:  2.2831 -  2.2046 0.98   1264  147 0.1061 0.1838      4.9467      5.2237|
| 11:  2.2046 -  2.1358 0.98   1274  139 0.1087 0.1727      4.9159      5.2494|
| 12:  2.1358 -  2.0750 0.99   1263  142 0.1038 0.1641      4.8508      5.1371|
| 13:  2.0750 -  2.0205 0.97   1265  137 0.1096 0.1795      4.7856      5.1043|
| 14:  2.0205 -  1.9713 0.55    712   81 0.1039 0.1692      4.7014      4.8977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8783 -  4.7041  1395   154  0.94   8.80   0.98     0.96       6766.49|
|  2:  4.7041 -  3.7536  1356   148  0.95   7.82   1.02     1.00       8475.87|
|  3:  3.7536 -  3.2849  1319   155  0.94  10.80   1.03     1.03       9880.99|
|  4:  3.2849 -  2.9872  1316   138  0.92  13.71   1.01     1.00      10323.35|
|  5:  2.9872 -  2.7746  1293   147  0.90  15.62   1.00     0.97       8054.50|
|  6:  2.7746 -  2.6119  1295   149  0.90  15.74   0.99     0.96       6953.33|
|  7:  2.6119 -  2.4817  1299   142  0.91  14.93   0.99     0.97       5722.40|
|  8:  2.4817 -  2.3742  1285   145  0.91  15.09   1.00     0.97       5312.98|
|  9:  2.3742 -  2.2831  1294   135  0.91  15.07   1.00     0.97       4777.96|
| 10:  2.2831 -  2.2046  1264   147  0.90  15.54   1.00     0.96       4442.82|
| 11:  2.2046 -  2.1358  1274   139  0.90  16.09   1.00     0.96       4236.51|
| 12:  2.1358 -  2.0750  1263   142  0.92  14.81   1.01     1.00       3853.59|
| 13:  2.0750 -  2.0205  1265   137  0.90  16.47   1.01     1.00       3468.64|
| 14:  2.0205 -  1.9713   712    81  0.91  15.50   0.98     0.94       2850.72|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2850.72 max =        10323.35 mean =      6222.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.88|
|phase err.(test): min =        0.00 max =           89.18 mean =        13.43|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.24    94.69   16.84    None  None   None       |
|    all(noH): 2823   0      0.24    94.69   16.84    None  None   None       |
|    Sol.    : 438    0      5.41    76.26   39.58    None  None   None       |
|    Mac.    : 2385   0      0.24    94.69   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:     0.241 -   9.686: 1027   |   5:    47.467 -  56.912:  100        |
|      1:     9.686 -  19.131: 1134   |   6:    56.912 -  66.357:   60        |
|      2:    19.131 -  28.577:  221   |   7:    66.357 -  75.802:   14        |
|      3:    28.577 -  38.022:  135   |   8:    75.802 -  85.248:    5        |
|      4:    38.022 -  47.467:  124   |   9:    85.248 -  94.693:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.597 - 4.506
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 289 from: 291
   mapped sites are within: 0.739 - 4.506

peak=    5.827 closest distance to " NH2 ARG A  56 " =    2.278
peak=    5.575 closest distance to " CG  PRO A  54 " =    1.228
peak=    5.533 closest distance to " CB  GLN A 223 " =    1.412
peak=    5.428 closest distance to " CB  ARG A 275 " =    0.943
peak=    5.172 closest distance to " CB  SER A  63 " =    1.150
peak=    5.005 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.876 closest distance to " CB  GLN A 183 " =    1.321
peak=    4.831 closest distance to " O   HOH Z 298 " =    1.873
peak=    4.782 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.762 closest distance to " O   HOH Z 126 " =    1.793
peak=    4.749 closest distance to " O   HOH Z  78 " =    1.801
peak=    4.696 closest distance to " O   HOH Z 232 " =    2.347
peak=    4.653 closest distance to " O   HOH Z 142 " =    1.669
peak=    4.606 closest distance to " CG  PRO A  90 " =    1.118
peak=    4.573 closest distance to " NE2 GLN A  11 " =    1.023
peak=    4.556 closest distance to " OD1 ASN A  69 " =    2.530
peak=    4.510 closest distance to " C   PRO A 198 " =    1.471
peak=    4.467 closest distance to " CB  PRO A  54 " =    0.889
peak=    4.463 closest distance to " CB  GLU A 152 " =    1.172
peak=    4.438 closest distance to " CB  TYR A 169 " =    0.798
peak=    4.408 closest distance to " CA  ALA A  21 " =    1.254
peak=    4.378 closest distance to " O   HOH Z 234 " =    3.727
peak=    4.374 closest distance to " O   HOH Z 403 " =    1.682
peak=    4.360 closest distance to " NZ  LYS A 117 " =    3.219
peak=    4.343 closest distance to " CB  GLU A 128 " =    1.191
peak=    4.338 closest distance to " O   HOH Z 193 " =    1.810
peak=    4.328 closest distance to " O   HOH Z 236 " =    2.004
peak=    4.305 closest distance to " O   HOH Z 203 " =    1.809
peak=    4.284 closest distance to " CB  ASN A 148 " =    1.478
peak=    4.266 closest distance to " CG  PRO A 198 " =    1.209
peak=    4.261 closest distance to " OD2 ASP A 286 " =    2.792
peak=    4.249 closest distance to " O   HOH Z  15 " =    2.099
peak=    4.228 closest distance to " CB  ARG A  79 " =    1.369
peak=    4.222 closest distance to " CG1 ILE A  33 " =    1.259
peak=    4.217 closest distance to " O   HOH Z 272 " =    1.820
peak=    4.200 closest distance to " O   HOH Z 427 " =    2.844
peak=    4.141 closest distance to " CB  GLU A 277 " =    3.517
peak=    4.138 closest distance to " NH2BARG A 145 " =    2.124
peak=    4.116 closest distance to " O   HOH Z 316 " =    2.968
peak=    4.113 closest distance to " CB  SER A   3 " =    1.264
peak=    4.098 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.075 closest distance to " O   HOH Z 368 " =    1.987
peak=    4.074 closest distance to " O   HOH Z 144 " =    2.182
peak=    4.068 closest distance to " O   HOH Z 369 " =    2.187
peak=    4.068 closest distance to " O   HOH Z  54 " =    1.807
peak=    4.066 closest distance to " O   HOH Z  97 " =    1.892
peak=    4.040 closest distance to " O   HOH Z  40 " =    1.818
peak=    4.034 closest distance to " CB  ARG A 190 " =    1.717
peak=    3.976 closest distance to " CB  VAL A 265 " =    1.231
peak=    3.961 closest distance to " OG BSER A 164 " =    2.281
peak=    3.946 closest distance to " O   HOH Z 108 " =    2.408
peak=    3.946 closest distance to " O   HOH Z 158 " =    2.957
peak=    3.927 closest distance to " CB  TRP A 179 " =    1.279
peak=    3.904 closest distance to " O   HOH Z 284 " =    2.962
peak=    3.903 closest distance to " O   HOH Z 209 " =    2.219
peak=    3.893 closest distance to " CA  ASN A 176 " =    1.161
peak=    3.888 closest distance to " O   HOH Z 156 " =    3.378
peak=    3.887 closest distance to " O   HOH Z  61 " =    1.592
peak=    3.882 closest distance to " O   HOH Z 245 " =    1.294
peak=    3.877 closest distance to " O   HOH Z 289 " =    1.698
peak=    3.875 closest distance to " ND2 ASN A 187 " =    1.427
peak=    3.867 closest distance to " CB  LEU A 228 " =    1.112
peak=    3.867 closest distance to " O   HOH Z 327 " =    1.647
peak=    3.866 closest distance to " CG  ARG A  66 " =    2.492
peak=    3.865 closest distance to " O   HOH Z 344 " =    3.056
peak=    3.860 closest distance to " CA  ASN A 215 " =    1.175
peak=    3.855 closest distance to " O   HOH Z 147 " =    1.759
peak=    3.854 closest distance to " O   SER A  87 " =    2.245
peak=    3.848 closest distance to " OE1 GLU A   2 " =    2.232
peak=    3.847 closest distance to " O   MET A 105 " =    1.868
peak=    3.841 closest distance to " CD2 LEU A 297 " =    0.898
peak=    3.838 closest distance to " O   HOH Z 183 " =    1.477
peak=    3.838 closest distance to " CG2 ILE A 120 " =    1.187
peak=    3.825 closest distance to " O   HOH Z  43 " =    2.022
peak=    3.822 closest distance to " CG1BVAL A  72 " =    1.625
peak=    3.821 closest distance to " O   HOH Z 132 " =    2.631
peak=    3.817 closest distance to " OD2 ASP A 298 " =    3.943
peak=    3.816 closest distance to " O   HOH Z 250 " =    1.409
peak=    3.811 closest distance to " O   HOH Z  97 " =    2.604
peak=    3.803 closest distance to " CA  THR A 221 " =    0.957
peak=    3.800 closest distance to " CG  GLN A  58 " =    2.632
peak=    3.798 closest distance to " O   HOH Z 303 " =    1.996
peak=    3.797 closest distance to " O   HOH Z 389 " =    1.864
peak=    3.786 closest distance to " O   HOH Z 426 " =    1.525
peak=    3.773 closest distance to " O   HOH Z  44 " =    2.019
peak=    3.769 closest distance to " CD  ARG A 269 " =    0.979
peak=    3.765 closest distance to " NH2 ARG A 156 " =    1.154
peak=    3.739 closest distance to " O   HOH Z  19 " =    2.142
peak=    3.734 closest distance to " O   HOH Z 402 " =    1.435
peak=    3.732 closest distance to " O   HOH Z 132 " =    2.525
peak=    3.726 closest distance to " CA  ARG A  36 " =    1.073
peak=    3.719 closest distance to " CB  TRP A 266 " =    0.939
peak=    3.713 closest distance to " CD2 TRP A 179 " =    1.433
peak=    3.702 closest distance to " CB  ALA A 291 " =    1.322
peak=    3.696 closest distance to " O   HOH Z 197 " =    2.959
peak=    3.688 closest distance to " O   HOH Z 411 " =    3.729
peak=    3.688 closest distance to " CB  ASN A 148 " =    1.164
peak=    3.687 closest distance to " CG2 THR A 221 " =    1.133
peak=    3.684 closest distance to " CA  ASP A 140 " =    1.139
peak=    3.675 closest distance to " O   HOH Z 180 " =    2.253
peak=    3.667 closest distance to " O   HOH Z 279 " =    2.118
peak=    3.667 closest distance to " O   HOH Z 134 " =    1.284
peak=    3.663 closest distance to " CG2 VAL A 257 " =    0.860
peak=    3.661 closest distance to " O   HOH Z 128 " =    1.979
peak=    3.652 closest distance to " O   HOH Z  59 " =    2.215
peak=    3.649 closest distance to " O   HOH Z 345 " =    3.101
peak=    3.648 closest distance to " CE  LYS A  76 " =    0.859
peak=    3.638 closest distance to " O   HOH Z 214 " =    2.173
peak=    3.634 closest distance to " CG2 ILE A  20 " =    1.352
peak=    3.630 closest distance to " CB  ASP A 140 " =    0.965
peak=    3.628 closest distance to " O   HOH Z 193 " =    2.165
peak=    3.626 closest distance to " CB  TYR A 169 " =    0.870
peak=    3.625 closest distance to " O   HOH Z 173 " =    1.993
peak=    3.620 closest distance to " O   HOH Z 423 " =    1.991
peak=    3.619 closest distance to " CB  ARG A 139 " =    0.876
peak=    3.618 closest distance to " O   HOH Z  68 " =    1.760
peak=    3.613 closest distance to " O   HOH Z 416 " =    2.839
peak=    3.612 closest distance to " O   HOH Z 357 " =    1.935
peak=    3.603 closest distance to " O   HOH Z  21 " =    1.745
peak=    3.603 closest distance to " CA  MET A  40 " =    1.049
peak=    3.585 closest distance to " CZ  PHE A 218 " =    1.056
peak=    3.585 closest distance to " CB  SER A 141 " =    1.033
peak=    3.569 closest distance to " CB  VAL A 202 " =    1.531
peak=    3.569 closest distance to " O   HOH Z 374 " =    2.594
peak=    3.561 closest distance to " ND2 ASN A 110 " =    1.677
peak=    3.557 closest distance to " O   HOH Z 185 " =    1.676
peak=    3.555 closest distance to " N   ASN A  39 " =    1.267
peak=    3.548 closest distance to " CD1 LEU A 300 " =    1.255
peak=    3.547 closest distance to " O   HOH Z  49 " =    2.114
peak=    3.514 closest distance to " CD1 ILE A 106 " =    0.824
peak=    3.513 closest distance to " O   HOH Z 291 " =    1.555
peak=    3.511 closest distance to " CA  LYS A 117 " =    1.216
peak=    3.508 closest distance to " CG  LYS A  76 " =    1.071
peak=    3.504 closest distance to " O   TRP A 274 " =    1.954
peak=    3.504 closest distance to " O   HOH Z 247 " =    1.263
peak=    3.500 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.500 closest distance to " CZ2 TRP A 179 " =    1.675
peak=    3.491 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.488 closest distance to " CA  ARG A 195 " =    1.265
peak=    3.486 closest distance to " NH1AARG A 145 " =    1.168
peak=    3.482 closest distance to " O   HOH Z 337 " =    3.690
peak=    3.474 closest distance to " O   HOH Z 281 " =    4.506
peak=    3.473 closest distance to " O   HOH Z 214 " =    2.335
peak=    3.466 closest distance to " CB  ASN A  39 " =    0.868
peak=    3.456 closest distance to " CD  ARG A 159 " =    0.760
peak=    3.455 closest distance to " CD1 LEU A  96 " =    0.772
peak=    3.455 closest distance to " O   HOH Z 189 " =    2.086
peak=    3.452 closest distance to " O   HOH Z  10 " =    1.825
peak=    3.448 closest distance to " O   HOH Z 421 " =    1.750
peak=    3.447 closest distance to " O   HOH Z 425 " =    2.040
peak=    3.445 closest distance to " O   HOH Z  88 " =    3.227
peak=    3.441 closest distance to " CA  ALA A 291 " =    0.862
peak=    3.438 closest distance to " O   HOH Z 368 " =    3.665
peak=    3.435 closest distance to " O   HOH Z 286 " =    2.222
peak=    3.432 closest distance to " O   HOH Z 368 " =    2.594
peak=    3.431 closest distance to " CG2 VAL A 197 " =    1.122
peak=    3.428 closest distance to " O   HOH Z  68 " =    1.991
peak=    3.414 closest distance to " O   HOH Z 411 " =    1.694
peak=    3.408 closest distance to " O   HOH Z 417 " =    2.981
peak=    3.407 closest distance to " CG2BVAL A  41 " =    0.792
peak=    3.399 closest distance to " O   SER A  26 " =    1.703
peak=    3.393 closest distance to " O   HOH Z 365 " =    2.962
peak=    3.390 closest distance to " CB  ILE A 120 " =    1.351
peak=    3.384 closest distance to " CD2 HIS A  81 " =    1.183
peak=    3.380 closest distance to " CA  GLY A  80 " =    1.006
peak=    3.379 closest distance to " O   HOH Z 406 " =    1.625
peak=    3.374 closest distance to " CA  ALA A  51 " =    0.939
peak=    3.373 closest distance to " CB  SER A  26 " =    1.615
peak=    3.372 closest distance to " O   HOH Z 148 " =    3.173
peak=    3.370 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.358 closest distance to " O   HOH Z 403 " =    1.280
peak=    3.349 closest distance to " O   HOH Z 427 " =    3.076
peak=    3.349 closest distance to " C   SER A  32 " =    1.045
peak=    3.348 closest distance to " O   HOH Z  64 " =    2.241
peak=    3.348 closest distance to " O   HOH Z 299 " =    2.445
peak=    3.347 closest distance to " CA  ALA A  84 " =    1.301
peak=    3.347 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.346 closest distance to " ND1 HIS A  81 " =    1.622
peak=    3.346 closest distance to " CB  SER A 216 " =    0.838
peak=    3.342 closest distance to " O   HOH Z 359 " =    1.363
peak=    3.342 closest distance to " N   ARG A 156 " =    1.356
peak=    3.335 closest distance to " O   HOH Z 423 " =    3.335
peak=    3.334 closest distance to " O   HOH Z 305 " =    3.652
peak=    3.333 closest distance to " CD BLYS A 290 " =    1.168
peak=    3.329 closest distance to " NH2 ARG A 219 " =    1.940
peak=    3.324 closest distance to " CB  ALA A 295 " =    1.099
peak=    3.322 closest distance to " CG2 VAL A  78 " =    0.885
peak=    3.318 closest distance to " O   HOH Z 163 " =    1.402
peak=    3.307 closest distance to " O   HOH Z  89 " =    2.147
peak=    3.304 closest distance to " CB  MET A  47 " =    1.006
peak=    3.301 closest distance to " CA  MET A 105 " =    1.050
peak=    3.294 closest distance to " O   HOH Z 227 " =    1.578
peak=    3.294 closest distance to " CB  SER A 212 " =    1.066
peak=    3.293 closest distance to " O   HOH Z 163 " =    1.633
peak=    3.289 closest distance to " O   THR A 251 " =    1.167
peak=    3.288 closest distance to " CG2 VAL A 202 " =    1.107
peak=    3.288 closest distance to " O   HOH Z 383 " =    1.951
peak=    3.288 closest distance to " CA  ASP A 162 " =    1.150
peak=    3.283 closest distance to " CB  SER A  62 " =    0.791
peak=    3.277 closest distance to " O   HOH Z 261 " =    2.166
peak=    3.275 closest distance to " O   HOH Z 292 " =    1.587
peak=    3.274 closest distance to " O   HOH Z  63 " =    1.964
peak=    3.274 closest distance to " CA  ILE A  33 " =    1.442
peak=    3.273 closest distance to " O   HOH Z 258 " =    2.269
peak=    3.273 closest distance to " O   HOH Z 353 " =    2.735
peak=    3.271 closest distance to " CG1 ILE A 151 " =    0.907
peak=    3.270 closest distance to " CA  VAL A  41 " =    0.914
peak=    3.269 closest distance to " O   HOH Z 124 " =    1.317
peak=    3.262 closest distance to " CG  GLU A 277 " =    2.126
peak=    3.259 closest distance to " O   ALA A 165 " =    1.403
peak=    3.258 closest distance to " OG  SER A  62 " =    2.870
peak=    3.252 closest distance to " NZ  LYS A 119 " =    1.447
peak=    3.251 closest distance to " O   HOH Z 325 " =    2.368
peak=    3.251 closest distance to " O   HOH Z  35 " =    2.459
peak=    3.251 closest distance to " CB  SER A 273 " =    0.806
peak=    3.250 closest distance to " CB  ALA A 242 " =    1.008
peak=    3.247 closest distance to " O   HOH Z 250 " =    1.647
peak=    3.246 closest distance to " O   HOH Z  66 " =    2.126
peak=    3.246 closest distance to " O   HOH Z 273 " =    2.758
peak=    3.241 closest distance to " CB  LEU A 255 " =    0.739
peak=    3.241 closest distance to " O   HOH Z 145 " =    2.290
peak=    3.240 closest distance to " CG1 VAL A 153 " =    0.995
peak=    3.237 closest distance to " O   HOH Z 417 " =    2.201
peak=    3.236 closest distance to " O   THR A 220 " =    1.246
peak=    3.235 closest distance to " O   HOH Z 163 " =    1.841
peak=    3.234 closest distance to " O   HOH Z 391 " =    2.976
peak=    3.230 closest distance to " CE  LYS A 119 " =    1.111
peak=    3.229 closest distance to " CD2 LEU A 255 " =    1.273
peak=    3.228 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.225 closest distance to " N   ALA A 154 " =    1.166
peak=    3.224 closest distance to " CB  THR A 157 " =    1.045
peak=    3.216 closest distance to " O   HOH Z  50 " =    2.013
peak=    3.213 closest distance to " O   HOH Z 171 " =    2.125
peak=    3.211 closest distance to " CB  GLN A 278 " =    0.883
peak=    3.211 closest distance to " CG  GLN A  77 " =    2.247
peak=    3.207 closest distance to " O   HOH Z 341 " =    1.840
peak=    3.207 closest distance to " CD  LYS A 119 " =    1.204
peak=    3.206 closest distance to " O   HOH Z  54 " =    2.401
peak=    3.203 closest distance to " CA  MET A 188 " =    0.970
peak=    3.200 closest distance to " N   TYR A 116 " =    1.538
peak=    3.198 closest distance to " O   HOH Z 267 " =    2.014
peak=    3.196 closest distance to " CD1AILE A 234 " =    0.954
peak=    3.195 closest distance to " O   HOH Z   1 " =    2.114
peak=    3.191 closest distance to " CB  ASN A 215 " =    1.144
peak=    3.190 closest distance to " O   HOH Z 189 " =    2.750
peak=    3.190 closest distance to " CG  MET A 185 " =    1.131
peak=    3.187 closest distance to " CA  ASN A 217 " =    1.274
peak=    3.186 closest distance to " O   HOH Z 329 " =    2.648
peak=    3.182 closest distance to " O   HOH Z 393 " =    3.398
peak=    3.180 closest distance to " O   HOH Z 255 " =    1.558
peak=    3.179 closest distance to " CB  TYR A 116 " =    0.819
peak=    3.176 closest distance to " O   HOH Z 435 " =    1.873
peak=    3.174 closest distance to " O   HOH Z 336 " =    1.731
peak=    3.170 closest distance to " O   HOH Z 286 " =    2.488
peak=    3.167 closest distance to " CG  GLN A  58 " =    2.665
peak=    3.167 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.166 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.158 closest distance to " O   HOH Z 299 " =    4.455
peak=    3.156 closest distance to " O   HOH Z  80 " =    1.599
peak=    3.155 closest distance to " CD  GLN A 240 " =    1.495
peak=    3.153 closest distance to " CA  THR A 264 " =    0.855
peak=    3.149 closest distance to " O   HOH Z  71 " =    2.342
peak=    3.145 closest distance to " O   HOH Z 392 " =    2.031
peak=    3.136 closest distance to " N   ARG A 190 " =    0.984
peak=    3.136 closest distance to " CG2 VAL A 296 " =    1.005
peak=    3.134 closest distance to " CB  ALA A  34 " =    1.161
peak=    3.132 closest distance to " O   HOH Z  85 " =    1.323
peak=    3.123 closest distance to " O   HOH Z  46 " =    1.469
peak=    3.123 closest distance to " CG1 VAL A 202 " =    2.112
peak=    3.114 closest distance to " O   HOH Z 133 " =    1.381
peak=    3.111 closest distance to " CB  GLN A 103 " =    0.936
peak=    3.109 closest distance to " O   HOH Z 422 " =    2.685
peak=    3.109 closest distance to " O   HOH Z 367 " =    3.595
peak=    3.106 closest distance to " NZ  LYS A 166 " =    3.025
peak=    3.106 closest distance to " CB  ALA A  71 " =    1.256
peak=    3.105 closest distance to " O   HOH Z 334 " =    1.439
peak=    3.104 closest distance to " C   TYR A 214 " =    1.391
peak=    3.103 closest distance to " OG  SER A  22 " =    2.702
peak=    3.098 closest distance to " O   HOH Z 380 " =    2.023
peak=    3.098 closest distance to " CA  ILE A 234 " =    0.953
peak=    3.092 closest distance to " CB  TRP A 150 " =    1.556
peak=    3.085 closest distance to " O   HOH Z 211 " =    2.810
peak=    3.077 closest distance to " O   HOH Z 102 " =    1.248
peak=    3.073 closest distance to " O   HOH Z 329 " =    3.696
peak=    3.068 closest distance to " CA  SER A  87 " =    1.003
peak=    3.068 closest distance to " CD  ARG A  66 " =    2.666
peak=    3.053 closest distance to " CA  ALA A 158 " =    1.185
peak=    3.049 closest distance to " CA  ASP A 191 " =    1.042
peak=    3.044 closest distance to " NZ  LYS A  76 " =    1.391

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.870 - 5.707
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 211
   mapped sites are within: 0.870 - 5.707

peak=   -5.084 closest distance to " O   HOH Z 266 " =    4.480
peak=   -4.412 closest distance to " CB  PRO A 243 " =    2.635
peak=   -4.347 closest distance to " C   HIS A 108 " =    1.075
peak=   -4.318 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.316 closest distance to " O   HOH Z 372 " =    2.308
peak=   -4.210 closest distance to " O   HOH Z 377 " =    2.059
peak=   -4.186 closest distance to " SG  CYS A 254 " =    3.291
peak=   -4.142 closest distance to " O   VAL A  67 " =    2.758
peak=   -4.139 closest distance to " CB  ALA A 161 " =    2.588
peak=   -4.118 closest distance to " OXT GLY A 302 " =    2.788
peak=   -4.110 closest distance to " O   HOH Z  13 " =    1.690
peak=   -4.085 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -4.054 closest distance to " OG  SER A  97 " =    2.173
peak=   -4.049 closest distance to " OG BSER A 134 " =    1.214
peak=   -4.038 closest distance to " CG  ASP A 231 " =    0.870
peak=   -4.029 closest distance to " CG  GLN A 223 " =    2.023
peak=   -3.970 closest distance to " O   PRO A 163 " =    2.062
peak=   -3.966 closest distance to " O   HOH Z 231 " =    2.250
peak=   -3.944 closest distance to " O   HOH Z 165 " =    2.016
peak=   -3.913 closest distance to " O   HOH Z 353 " =    2.187
peak=   -3.913 closest distance to " ND2 ASN A  45 " =    0.970
peak=   -3.907 closest distance to " N   ALA A 248 " =    1.721
peak=   -3.901 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -3.894 closest distance to " O   HOH Z 198 " =    2.090
peak=   -3.876 closest distance to " CG  ASP A 132 " =    2.335
peak=   -3.862 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.845 closest distance to " CD1 LEU A 228 " =    2.206
peak=   -3.843 closest distance to " N   GLN A  58 " =    1.646
peak=   -3.839 closest distance to " CZ  PHE A  59 " =    1.656
peak=   -3.833 closest distance to " O   PRO A 198 " =    1.298
peak=   -3.833 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.833 closest distance to " O   HOH Z 126 " =    1.906
peak=   -3.830 closest distance to " O   HOH Z 196 " =    1.998
peak=   -3.821 closest distance to " CZ3 TRP A 179 " =    1.267
peak=   -3.815 closest distance to " N   SER A 212 " =    2.012
peak=   -3.803 closest distance to " O   HOH Z 185 " =    2.287
peak=   -3.800 closest distance to " CB  TYR A  15 " =    2.257
peak=   -3.792 closest distance to " O   HOH Z 118 " =    3.308
peak=   -3.788 closest distance to " CA  ASP A 298 " =    1.032
peak=   -3.784 closest distance to " N   ALA A  43 " =    2.611
peak=   -3.766 closest distance to " O   HOH Z 407 " =    3.007
peak=   -3.756 closest distance to " CD1 LEU A  25 " =    2.476
peak=   -3.737 closest distance to " OG  SER A  62 " =    1.603
peak=   -3.727 closest distance to " O   HOH Z  52 " =    1.428
peak=   -3.718 closest distance to " O   HOH Z 292 " =    4.491
peak=   -3.707 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.704 closest distance to " O   HOH Z  11 " =    2.083
peak=   -3.672 closest distance to " O   VAL A  67 " =    2.783
peak=   -3.670 closest distance to " CD  GLN A  58 " =    1.184
peak=   -3.665 closest distance to " O   HOH Z 389 " =    1.741
peak=   -3.660 closest distance to " O   PHE A 218 " =    1.604
peak=   -3.651 closest distance to " O   HOH Z 166 " =    1.556
peak=   -3.647 closest distance to " CD  ARG A 139 " =    1.557
peak=   -3.641 closest distance to " CG1 VAL A 112 " =    2.797
peak=   -3.638 closest distance to " NH1 ARG A 195 " =    2.558
peak=   -3.618 closest distance to " OD1 ASN A 187 " =    1.774
peak=   -3.612 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.609 closest distance to " C   LEU A 143 " =    1.086
peak=   -3.608 closest distance to " O   HOH Z 290 " =    1.174
peak=   -3.584 closest distance to " CB  ASN A  39 " =    2.255
peak=   -3.578 closest distance to " CB  ALA A 291 " =    2.323
peak=   -3.573 closest distance to " ND2 ASN A 187 " =    1.502
peak=   -3.572 closest distance to " O   HOH Z 361 " =    3.415
peak=   -3.563 closest distance to " O   HOH Z 166 " =    1.759
peak=   -3.562 closest distance to " O   MET A  40 " =    2.638
peak=   -3.558 closest distance to " CB  PHE A 192 " =    2.027
peak=   -3.557 closest distance to " OD1 ASN A 148 " =    1.579
peak=   -3.545 closest distance to " O   HOH Z 234 " =    4.143
peak=   -3.543 closest distance to " N   THR A 235 " =    1.365
peak=   -3.520 closest distance to " CG1 VAL A 250 " =    2.586
peak=   -3.497 closest distance to " CA  GLY A 203 " =    2.239
peak=   -3.489 closest distance to " CG2 ILE A 263 " =    2.290
peak=   -3.481 closest distance to " OG BSER A 134 " =    1.740
peak=   -3.480 closest distance to " O   LEU A 167 " =    1.538
peak=   -3.480 closest distance to " NH2AARG A 275 " =    5.209
peak=   -3.479 closest distance to " O   ALA A 160 " =    1.468
peak=   -3.478 closest distance to " CG  PHE A 283 " =    2.496
peak=   -3.478 closest distance to " CD  ARG A 195 " =    5.143
peak=   -3.477 closest distance to " CD2 LEU A 300 " =    2.842
peak=   -3.466 closest distance to " N   ALA A 248 " =    2.234
peak=   -3.457 closest distance to " CE  MET A 105 " =    2.111
peak=   -3.456 closest distance to " O   HOH Z  43 " =    1.558
peak=   -3.454 closest distance to " OG BSER A 210 " =    2.016
peak=   -3.453 closest distance to " CB  PHE A 208 " =    2.221
peak=   -3.452 closest distance to " O   HOH Z 243 " =    2.111
peak=   -3.442 closest distance to " C   ALA A 158 " =    1.243
peak=   -3.437 closest distance to " CG  GLU A  53 " =    1.424
peak=   -3.437 closest distance to " O   HOH Z 311 " =    3.607
peak=   -3.435 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.430 closest distance to " NH2 ARG A 159 " =    2.304
peak=   -3.429 closest distance to " O   HOH Z 417 " =    2.479
peak=   -3.421 closest distance to " O   VAL A 174 " =    2.051
peak=   -3.415 closest distance to " NE2 GLN A  88 " =    1.825
peak=   -3.408 closest distance to " SG ACYS A 201 " =    2.062
peak=   -3.407 closest distance to " O   HOH Z 283 " =    2.047
peak=   -3.400 closest distance to " NH2 ARG A  66 " =    5.233
peak=   -3.400 closest distance to " OD1 ASP A 171 " =    1.567
peak=   -3.399 closest distance to " CB  ASP A 286 " =    1.944
peak=   -3.386 closest distance to " C   MET A 188 " =    1.645
peak=   -3.385 closest distance to " O   HOH Z 191 " =    5.707
peak=   -3.381 closest distance to " CD  LYS A 289 " =    2.484
peak=   -3.378 closest distance to " O   TRP A  92 " =    1.797
peak=   -3.372 closest distance to " O   HOH Z 252 " =    3.688
peak=   -3.370 closest distance to " O   HOH Z 298 " =    1.265
peak=   -3.364 closest distance to " O   HOH Z  37 " =    1.751
peak=   -3.362 closest distance to " O   ALA A  34 " =    2.288
peak=   -3.358 closest distance to " O   HOH Z 211 " =    1.657
peak=   -3.358 closest distance to " C   SER A 206 " =    1.670
peak=   -3.355 closest distance to " O   HOH Z  88 " =    2.445
peak=   -3.350 closest distance to " O   HOH Z  44 " =    2.157
peak=   -3.347 closest distance to " O   HOH Z  38 " =    1.605
peak=   -3.345 closest distance to " NH2 ARG A  79 " =    1.991
peak=   -3.337 closest distance to " OD1 ASP A 191 " =    1.667
peak=   -3.337 closest distance to " CB  ALA A  10 " =    2.239
peak=   -3.336 closest distance to " O   HOH Z 351 " =    1.458
peak=   -3.331 closest distance to " CD2 TYR A 247 " =    2.479
peak=   -3.320 closest distance to " OG  SER A  26 " =    1.294
peak=   -3.320 closest distance to " OD2 ASP A 171 " =    2.304
peak=   -3.320 closest distance to " O   HOH Z   6 " =    1.696
peak=   -3.320 closest distance to " OG1 THR A 178 " =    1.313
peak=   -3.317 closest distance to " OD2 ASP A  50 " =    2.336
peak=   -3.313 closest distance to " O   HOH Z 385 " =    1.964
peak=   -3.312 closest distance to " CB  PRO A 163 " =    2.577
peak=   -3.306 closest distance to " OD2 ASP A 191 " =    1.558
peak=   -3.304 closest distance to " O   HOH Z 148 " =    3.643
peak=   -3.302 closest distance to " O   HOH Z  90 " =    2.896
peak=   -3.301 closest distance to " CB  ALA A 248 " =    2.008
peak=   -3.300 closest distance to " O   HOH Z  15 " =    1.556
peak=   -3.298 closest distance to " O   SER A 135 " =    1.525
peak=   -3.292 closest distance to " CG1 VAL A 125 " =    2.337
peak=   -3.290 closest distance to " CA  PRO A 243 " =    2.363
peak=   -3.281 closest distance to " OE2 GLU A   2 " =    1.797
peak=   -3.278 closest distance to " NE2 GLN A 103 " =    1.641
peak=   -3.274 closest distance to " CA  GLY A 133 " =    1.941
peak=   -3.272 closest distance to " O   HOH Z 388 " =    2.032
peak=   -3.270 closest distance to " OE1 GLN A 223 " =    1.957
peak=   -3.269 closest distance to " CB  ALA A 291 " =    2.267
peak=   -3.265 closest distance to " N   GLN A 122 " =    1.474
peak=   -3.265 closest distance to " O   GLY A 111 " =    1.213
peak=   -3.265 closest distance to " CB  GLN A  11 " =    1.820
peak=   -3.261 closest distance to " CE  MET A  93 " =    1.202
peak=   -3.260 closest distance to " O   HOH Z  11 " =    1.764
peak=   -3.259 closest distance to " O   HOH Z 435 " =    2.715
peak=   -3.258 closest distance to " OD2 ASP A 171 " =    1.735
peak=   -3.257 closest distance to " O   HOH Z   9 " =    2.014
peak=   -3.257 closest distance to " N   ASP A 286 " =    2.397
peak=   -3.256 closest distance to " CG1 VAL A 112 " =    2.944
peak=   -3.248 closest distance to " CD1 ILE A 239 " =    2.090
peak=   -3.242 closest distance to " N   ALA A   9 " =    1.575
peak=   -3.242 closest distance to " CG  GLU A 277 " =    1.153
peak=   -3.241 closest distance to " C   GLN A 205 " =    1.869
peak=   -3.235 closest distance to " C   GLY A  80 " =    2.432
peak=   -3.222 closest distance to " OG ASER A 134 " =    1.141
peak=   -3.220 closest distance to " O   HOH Z  71 " =    1.680
peak=   -3.220 closest distance to " O   HOH Z 198 " =    1.425
peak=   -3.214 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.213 closest distance to " CG  GLU A 152 " =    2.153
peak=   -3.213 closest distance to " O   LYS A 117 " =    1.660
peak=   -3.208 closest distance to " CB  SER A 245 " =    2.404
peak=   -3.207 closest distance to " O   HOH Z 193 " =    1.779
peak=   -3.207 closest distance to " O   HOH Z 377 " =    1.790
peak=   -3.206 closest distance to " O   HOH Z 414 " =    1.534
peak=   -3.204 closest distance to " CZ2 TRP A 274 " =    1.051
peak=   -3.200 closest distance to " O   GLY A 196 " =    0.986
peak=   -3.199 closest distance to " OH  TYR A 169 " =    0.998
peak=   -3.196 closest distance to " ND2 ASN A 249 " =    2.092
peak=   -3.196 closest distance to " O   GLY A 211 " =    1.559
peak=   -3.193 closest distance to " CZ  PHE A 130 " =    0.980
peak=   -3.191 closest distance to " NE2 GLN A  58 " =    1.191
peak=   -3.189 closest distance to " O   HOH Z 422 " =    1.575
peak=   -3.187 closest distance to " O   HOH Z 436 " =    1.530
peak=   -3.179 closest distance to " N   ALA A 226 " =    2.021
peak=   -3.178 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.175 closest distance to " CD1 LEU A 297 " =    2.504
peak=   -3.175 closest distance to " CG  PRO A 243 " =    1.706
peak=   -3.170 closest distance to " O   HOH Z 262 " =    2.527
peak=   -3.162 closest distance to " CG2 VAL A 189 " =    2.240
peak=   -3.161 closest distance to " O   HOH Z 427 " =    1.429
peak=   -3.155 closest distance to " O   ALA A  10 " =    1.802
peak=   -3.153 closest distance to " O   GLY A  80 " =    2.503
peak=   -3.149 closest distance to " O   ASN A  45 " =    1.833
peak=   -3.146 closest distance to " O   HOH Z 171 " =    1.901
peak=   -3.145 closest distance to " NH2 ARG A  66 " =    2.018
peak=   -3.139 closest distance to " CD2 PHE A 225 " =    1.264
peak=   -3.134 closest distance to " O   HOH Z  61 " =    1.634
peak=   -3.130 closest distance to " CA  GLY A  98 " =    2.009
peak=   -3.127 closest distance to " O   TYR A 186 " =    1.484
peak=   -3.125 closest distance to " CD1 TYR A 247 " =    2.392
peak=   -3.121 closest distance to " O   ILE A 106 " =    1.797
peak=   -3.118 closest distance to " O   ASN A 301 " =    1.325
peak=   -3.113 closest distance to " N   SER A 276 " =    1.360
peak=   -3.112 closest distance to " CA  TYR A  68 " =    3.214
peak=   -3.110 closest distance to " O   GLY A  75 " =    1.915
peak=   -3.103 closest distance to " O   HOH Z 265 " =    2.184
peak=   -3.095 closest distance to " CD  ARG A  36 " =    1.897
peak=   -3.089 closest distance to " O   HOH Z 324 " =    2.159
peak=   -3.086 closest distance to " CA  GLY A 241 " =    3.154
peak=   -3.073 closest distance to " CE3 TRP A 274 " =    2.446
peak=   -3.071 closest distance to " O   HOH Z 263 " =    2.884
peak=   -3.066 closest distance to " CB  TRP A  85 " =    2.426
peak=   -3.063 closest distance to " OD1 ASP A 200 " =    1.344
peak=   -3.059 closest distance to " CB  ALA A   9 " =    2.557
peak=   -3.054 closest distance to " O   HOH Z  97 " =    1.561
peak=   -3.053 closest distance to " N   ASP A 171 " =    2.411
peak=   -3.042 closest distance to " CG1AVAL A  41 " =    2.763
peak=   -3.039 closest distance to " O   HOH Z 411 " =    3.545
peak=   -3.027 closest distance to " O   ALA A  51 " =    1.405
peak=   -3.018 closest distance to " CD2 LEU A 300 " =    2.630
peak=   -3.007 closest distance to " CG  GLU A 152 " =    1.456
peak=   -3.005 closest distance to " CG1 VAL A  78 " =    2.591

================= 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    :  0.3496 0.3446   6.099011e+00   6.090119e+00
   1_bss:  0.3367 0.3298   6.080170e+00   6.059112e+00
   1_xyz:  0.1875 0.2072   5.545389e+00   5.638863e+00
   1_adp:  0.1707 0.2154   5.490711e+00   5.672722e+00
   1_occ:  0.1704 0.2156   5.489945e+00   5.672239e+00
   2_bss:  0.1681 0.2131   5.483495e+00   5.663616e+00
   2_xyz:  0.1273 0.1687   5.239706e+00   5.454685e+00
   2_adp:  0.1214 0.1612   5.193442e+00   5.404823e+00
   2_occ:  0.1212 0.1609   5.192042e+00   5.403275e+00
   3_bss:  0.1214 0.1600   5.191351e+00   5.400958e+00
   3_xyz:  0.1108 0.1534   5.126827e+00   5.358875e+00
   3_adp:  0.1091 0.1536   5.119950e+00   5.359490e+00
   3_occ:  0.1090 0.1536   5.119772e+00   5.359575e+00
   4_bss:  0.1090 0.1536   5.119566e+00   5.359389e+00
   4_xyz:  0.1070 0.1534   5.111164e+00   5.358021e+00
   4_adp:  0.1067 0.1539   5.111908e+00   5.362337e+00
   4_occ:  0.1066 0.1539   5.111888e+00   5.362506e+00
   5_bss:  0.1066 0.1539   5.111944e+00   5.362547e+00
   5_xyz:  0.1075 0.1553   5.120943e+00   5.371786e+00
   5_adp:  0.1068 0.1566   5.124387e+00   5.381882e+00
   5_occ:  0.1068 0.1567   5.124383e+00   5.382065e+00
   5_bss:  0.1067 0.1567   5.124210e+00   5.381889e+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:  0.303  28.551  -3.111   0.485   0.976   0.000   0.000   0.000
   1_xyz:  0.303  28.551  -3.111   0.485   0.976   0.000   0.000   0.000
   1_adp:  0.303  28.551  -3.111   0.485   0.976   0.000   0.000   0.000
   1_occ:  0.303  28.551  -3.111   0.485   0.976   0.000   0.000   0.000
   2_bss:  0.320  44.009  -3.233  -1.388  -1.183  -0.000  -0.000  -0.000
   2_xyz:  0.320  44.009  -3.233  -1.388  -1.183  -0.000  -0.000  -0.000
   2_adp:  0.320  44.009  -3.233  -1.388  -1.183  -0.000  -0.000  -0.000
   2_occ:  0.320  44.009  -3.233  -1.388  -1.183  -0.000  -0.000  -0.000
   3_bss:  0.321  44.533  -2.914  -1.805  -1.577  -0.000  -0.000  -0.000
   3_xyz:  0.321  44.533  -2.914  -1.805  -1.577  -0.000  -0.000  -0.000
   3_adp:  0.321  44.533  -2.914  -1.805  -1.577  -0.000  -0.000  -0.000
   3_occ:  0.321  44.533  -2.914  -1.805  -1.577  -0.000  -0.000  -0.000
   4_bss:  0.322  44.533  -2.770  -1.886  -1.599  -0.000  -0.000  -0.000
   4_xyz:  0.322  44.533  -2.770  -1.886  -1.599  -0.000  -0.000  -0.000
   4_adp:  0.322  44.533  -2.770  -1.886  -1.599  -0.000  -0.000  -0.000
   4_occ:  0.322  44.533  -2.770  -1.886  -1.599  -0.000  -0.000  -0.000
   5_bss:  0.323  44.662  -2.559  -1.760  -1.455  -0.000  -0.000  -0.000
   5_xyz:  0.323  44.662  -2.559  -1.760  -1.455  -0.000  -0.000  -0.000
   5_adp:  0.323  44.662  -2.559  -1.760  -1.455  -0.000  -0.000  -0.000
   5_occ:  0.323  44.662  -2.559  -1.760  -1.455  -0.000  -0.000  -0.000
   5_bss:  0.324  47.783  -2.310  -1.552  -1.251  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  36.883 0.6820  0.8670    34589.432
   1_bss:  35.399 0.6972  0.8676    30688.541
   1_xyz:  19.496 0.8676  1.0126    10737.035
   1_adp:  20.552 0.8565  1.0038    11478.571
   1_occ:  20.556 0.8564  1.0035    11472.875
   2_bss:  20.224 0.8597  0.9597    11209.607
   2_xyz:  15.569 0.9015  0.9837     7199.916
   2_adp:  14.480 0.9110  0.9846     6592.749
   2_occ:  14.456 0.9112  0.9847     6566.018
   3_bss:  14.404 0.9116  0.9794     6541.473
   3_xyz:  13.492 0.9189  0.9827     5985.436
   3_adp:  13.458 0.9194  0.9785     6000.902
   3_occ:  13.457 0.9194  0.9784     6000.027
   4_bss:  13.453 0.9194  0.9791     6000.152
   4_xyz:  13.410 0.9198  0.9784     5966.966
   4_adp:  13.483 0.9192  0.9726     6009.624
   4_occ:  13.485 0.9192  0.9726     6010.588
   5_bss:  13.486 0.9192  0.9783     6012.148
   5_xyz:  13.627 0.9182  0.9780     6120.830
   5_adp:  13.839 0.9166  0.9707     6222.087
   5_occ:  13.842 0.9165  0.9707     6224.882
   5_bss:  13.838 0.9166  0.9784     6223.238
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6662e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6662e-01
   1_xyz:   1.110  0.009  0.073 15.057  0.005  4.113   7.2705e-02
   1_adp:   1.110  0.009  0.073 15.057  0.005  4.113   7.2705e-02
   1_occ:   1.110  0.009  0.073 15.057  0.005  4.113   7.2705e-02
   2_bss:   1.110  0.009  0.073 15.057  0.005  4.113   7.2705e-02
   2_xyz:   1.011  0.006  0.072 14.601  0.004  4.119   5.8191e-02
   2_adp:   1.011  0.006  0.072 14.601  0.004  4.119   5.8191e-02
   2_occ:   1.011  0.006  0.072 14.601  0.004  4.119   5.8191e-02
   3_bss:   1.011  0.006  0.072 14.601  0.004  4.119   5.8191e-02
   3_xyz:   1.042  0.008  0.077 14.865  0.004  4.118   6.3861e-02
   3_adp:   1.042  0.008  0.077 14.865  0.004  4.118   6.3861e-02
   3_occ:   1.042  0.008  0.077 14.865  0.004  4.118   6.3861e-02
   4_bss:   1.042  0.008  0.077 14.865  0.004  4.118   6.3861e-02
   4_xyz:   1.049  0.008  0.078 14.737  0.004  4.118   6.4511e-02
   4_adp:   1.049  0.008  0.078 14.737  0.004  4.118   6.4511e-02
   4_occ:   1.049  0.008  0.078 14.737  0.004  4.118   6.4511e-02
   5_bss:   1.049  0.008  0.078 14.737  0.004  4.118   6.4511e-02
   5_xyz:   0.990  0.007  0.074 14.552  0.004  4.118   5.7755e-02
   5_adp:   0.990  0.007  0.074 14.552  0.004  4.118   5.7755e-02
   5_occ:   0.990  0.007  0.074 14.552  0.004  4.118   5.7755e-02
   5_bss:   0.990  0.007  0.074 14.552  0.004  4.118   5.7755e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4016e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4016e-01
   1_xyz:   6.772  0.097  0.256 85.136  0.021  2.367   1.1543e-01
   1_adp:   6.772  0.097  0.256 85.136  0.021  2.367   1.1543e-01
   1_occ:   6.772  0.097  0.256 85.136  0.021  2.367   1.1543e-01
   2_bss:   6.772  0.097  0.256 85.136  0.021  2.367   1.1543e-01
   2_xyz:   6.736  0.048  0.226 82.516  0.037  2.325   3.9451e-02
   2_adp:   6.736  0.048  0.226 82.516  0.037  2.325   3.9451e-02
   2_occ:   6.736  0.048  0.226 82.516  0.037  2.325   3.9451e-02
   3_bss:   6.736  0.048  0.226 82.516  0.037  2.325   3.9451e-02
   3_xyz:   7.687  0.044  0.256 82.895  0.038  2.334   5.6127e-02
   3_adp:   7.687  0.044  0.256 82.895  0.038  2.334   5.6127e-02
   3_occ:   7.687  0.044  0.256 82.895  0.038  2.334   5.6127e-02
   4_bss:   7.687  0.044  0.256 82.895  0.038  2.334   5.6127e-02
   4_xyz:   7.426  0.048  0.248 82.368  0.039  2.310   4.9198e-02
   4_adp:   7.426  0.048  0.248 82.368  0.039  2.310   4.9198e-02
   4_occ:   7.426  0.048  0.248 82.368  0.039  2.310   4.9198e-02
   5_bss:   7.426  0.048  0.248 82.368  0.039  2.310   4.9198e-02
   5_xyz:   7.082  0.043  0.245 82.732  0.037  2.360   3.9925e-02
   5_adp:   7.082  0.043  0.245 82.732  0.037  2.360   3.9925e-02
   5_occ:   7.082  0.043  0.245 82.732  0.037  2.360   3.9925e-02
   5_bss:   7.082  0.043  0.245 82.732  0.037  2.360   3.9925e-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:  80.38   0.00  17.34  80.38   0.00  13.32  72.16   7.77  39.23
   1_occ:  80.38   0.00  17.34  80.38   0.00  13.32  72.16   7.77  39.23
   2_bss:  80.38   0.00  17.34  80.38   0.00  13.32  72.16   7.77  39.23
   2_xyz:  80.38   0.00  17.34  80.38   0.00  13.32  72.16   7.77  39.23
   2_adp:  79.59   2.23  16.81  79.59   2.23  12.95  69.82   5.96  37.79
   2_occ:  79.59   2.23  16.81  79.59   2.23  12.95  69.82   5.96  37.79
   3_bss:  79.59   2.23  16.81  79.59   2.23  12.95  69.82   5.96  37.79
   3_xyz:  79.59   2.23  16.81  79.59   2.23  12.95  69.82   5.96  37.79
   3_adp:  82.07   1.99  16.69  82.07   1.99  12.81  71.50   5.77  37.79
   3_occ:  82.07   1.99  16.69  82.07   1.99  12.81  71.50   5.77  37.79
   4_bss:  82.07   1.99  16.69  82.07   1.99  12.81  71.50   5.77  37.79
   4_xyz:  82.07   1.99  16.69  82.07   1.99  12.81  71.50   5.77  37.79
   4_adp:  82.51   1.55  16.57  82.51   1.55  12.67  71.41   5.48  37.81
   4_occ:  82.51   1.55  16.57  82.51   1.55  12.67  71.41   5.48  37.81
   5_bss:  82.51   1.55  16.57  82.51   1.55  12.67  71.41   5.48  37.81
   5_xyz:  82.51   1.55  16.57  82.51   1.55  12.67  71.41   5.48  37.81
   5_adp:  94.70   0.25  16.85  94.70   0.25  12.67  76.26   5.42  39.59
   5_occ:  94.70   0.25  16.85  94.70   0.25  12.67  76.26   5.42  39.59
   5_bss:  94.69   0.24  16.84  94.69   0.24  12.67  76.26   5.41  39.58
------------------------------------------------------------------------
 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:    1.430    0.005    0.337
   1_adp:    1.430    0.005    0.337
   1_occ:    1.430    0.005    0.337
   2_bss:    1.430    0.005    0.337
   2_xyz:    0.962    0.031    0.416
   2_adp:    0.962    0.031    0.416
   2_occ:    0.962    0.031    0.416
   3_bss:    0.962    0.031    0.416
   3_xyz:    1.090    0.060    0.450
   3_adp:    1.090    0.060    0.450
   3_occ:    1.090    0.060    0.450
   4_bss:    1.090    0.060    0.450
   4_xyz:    1.145    0.030    0.459
   4_adp:    1.145    0.030    0.459
   4_occ:    1.145    0.030    0.459
   5_bss:    1.145    0.030    0.459
   5_xyz:    1.293    0.080    0.465
   5_adp:    1.293    0.080    0.465
   5_occ:    1.293    0.080    0.465
   5_bss:    1.293    0.080    0.465
------------------------------------------------------------------------

CPU time actual refinement: 341.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/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_563/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_563/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.74 
  Macro-tasks:
    bulk solvent and scale       = 37.41  
    individual site refinement   = 142.38 
    weights calculation          = 30.06  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 216.61 
  Micro-tasks:
    mask                            = 1.19   
    f_calc                          = 110.88 
    alpha_beta                      = 8.19   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 120.54 
    fmodel                         = 6.50   
    r_factors                      = 0.14   
    phase_errors                   = 11.12  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 259.99 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.773 micro seconds
Total CPU time: 5.92 minutes
from_scatterers_fft:    674 calls, 110.40 s
gradients_fft:          619 calls, 106.48 s

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

# Date 2008-01-16 Time 05:07:44 PST -0800 (1200488864.74 s)
Start R-work = 0.3496, R-free = 0.3446 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1752 (no bulk solvent and anisotropic scale)

Start R-work = 0.3367, R-free = 0.3298
Final R-work = 0.1067, R-free = 0.1567