# Date 2008-01-16 Time 04:19:31 PST -0800 (1200485971.34 s)
#phil __OFF__

Command line arguments: "../267.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4836
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 267

-------------------------------------------------------------------------------
  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: (69.1963, 46.2261, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.32, per 1000 atoms: 1.18


================================== 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: (69.1963, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.97009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7893
                             d_min =   1.9701

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: (69.1963, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7893 1.97009
Completeness in resolution range: 0.981314
Completeness with d_max=infinity: 0.978178

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7897 -  4.2147 [2096/2119]  1886   210  10.0%
  bin  2:  4.2147 -  3.3582 [2024/2044]  1822   202  10.0%
  bin  3:  3.3582 -  2.9375 [1989/2008]  1791   198  10.0%
  bin  4:  2.9375 -  2.6707 [1954/1984]  1758   196  10.0%
  bin  5:  2.6707 -  2.4802 [1970/1989]  1773   197  10.0%
  bin  6:  2.4802 -  2.3346 [1950/1975]  1753   197  10.1%
  bin  7:  2.3346 -  2.2181 [1929/1957]  1737   192  10.0%
  bin  8:  2.2181 -  2.1218 [1931/1967]  1737   194  10.0%
  bin  9:  2.1218 -  2.0403 [1922/1964]  1732   190   9.9%
  bin 10:  2.0403 -  1.9701 [1824/1955]  1641   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 14
        2.12 -     2.81: 861
        2.81 -     3.51: 4585
        3.51 -     4.20: 9517
        4.20 -     4.90: 13933
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.420 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.621 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.858 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.864 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28905 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_267/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/model_refine_001.geo

CPU time processing inputs: 8.97


============================ 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 = 69.19625 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4111   r_free= 0.4081   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.202308                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.3313 0.3265       6.457      6.4356|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.3356 0.3162      6.6501      6.6066|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.3726 0.3468      6.5759      6.6418|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.3828 0.4130      6.4223      6.4681|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.4283 0.4003      6.2874      6.2372|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.4381 0.4343      6.2232       6.183|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.4371 0.4362      6.1725        6.11|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.4539 0.4694      6.1403      6.1769|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.4631 0.4558      6.0868      6.0731|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.4603 0.4822      6.0564      6.0645|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.4610 0.4903      5.9869      6.0445|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.4784 0.4571      5.9715      5.9802|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.4631 0.4544       5.865      5.8234|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.4837 0.4461      5.8387       5.718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.74  30.56   0.85     0.78      57078.71|
|  2:  4.7005 -  3.7510  1299   146  0.77  28.56   0.96     0.88      75610.32|
|  3:  3.7510 -  3.2828  1286   141  0.70  35.22   0.98     0.89      80497.72|
|  4:  3.2828 -  2.9853  1283   142  0.64  40.34   0.98     0.84      73162.77|
|  5:  2.9853 -  2.7728  1258   141  0.58  45.52   0.94     0.79      58535.48|
|  6:  2.7728 -  2.6103  1268   141  0.58  45.93   0.94     0.79      50456.35|
|  7:  2.6103 -  2.4802  1265   140  0.56  47.19   0.96     0.77      46798.91|
|  8:  2.4802 -  2.3727  1248   137  0.53  49.56   0.99     0.75      44876.17|
|  9:  2.3727 -  2.2817  1242   141  0.52  50.79   0.95     0.72      41752.63|
| 10:  2.2817 -  2.2032  1242   139  0.51  51.36   1.01     0.73      38300.44|
| 11:  2.2032 -  2.1345  1251   138  0.50  52.09   0.99     0.74      35654.18|
| 12:  2.1345 -  2.0737  1239   138  0.51  51.75   1.02     0.76      31770.19|
| 13:  2.0737 -  2.0192  1248   137  0.52  50.49   1.01     0.76      26716.10|
| 14:  2.0192 -  1.9701  1130   126  0.56  47.66   0.99     0.76      20268.75|
|alpha:            min =        0.72 max =            0.89 mean =         0.78|
|beta:             min =    20268.75 max =        80497.72 mean =     49139.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.99 mean =        44.59|
|phase err.(test): min =        0.00 max =           89.76 mean =        44.46|
|-----------------------------------------------------------------------------|

============================== 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 = 4.997085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.714   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.354886              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.599   (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 |  1.420 -  1.768:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.768 -  2.116:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.116 -  2.464:       46 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.464 -  2.812:      815 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.812 -  3.160:     2093 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.160 -  3.508:     2492 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.508 -  3.856:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.856 -  4.204:     4845 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.204 -  4.552:     6318 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.552 -  4.900:     7615 |
|-----------------------------------------------------------------------------|
|-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 |        0.179 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.420 |       0.466 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    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 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4111   r_free= 0.4081   ksol= 0.00   Bsol= 0.00   scale= 0.947    |
|                                                                             |
| 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:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.202308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4000   r_free= 0.3956   ksol= 0.33   Bsol= 15.81   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.75,-0.67,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.191047                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.172711              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.542   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.741698              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.412   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4000      final r-factor (work) = 0.2697          |
| start r-factor (free) = 0.3956      final r-factor (free) = 0.3000          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0944 = 4.17 * 0.50 * 6.1904 + 1.00 * 0.1790                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5978 = 4.17 * 0.50 * 5.9939 + 1.00 * 0.0924                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2697      final r-factor (work) = 0.2458          |
| start r-factor (free) = 0.3000      final r-factor (free) = 0.3082          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4517 = 0.74 * 1.00 * 5.9939 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3289 = 0.74 * 1.00 * 5.8181 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.67   18.01    None  None   None       |
|    all(noH): 2823   0      0.00    85.67   18.01    None  None   None       |
|    Sol.    : 438    0      3.21    85.67   39.18    None  None   None       |
|    Mac.    : 2385   0      0.00    83.37   14.12    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 -   8.567:  737   |   5:    42.835 -  51.403:  111        |
|      1:     8.567 -  17.134: 1044   |   6:    51.403 -  59.970:   70        |
|      2:    17.134 -  25.701:  456   |   7:    59.970 -  68.537:   40        |
|      3:    25.701 -  34.268:  210   |   8:    68.537 -  77.104:   11        |
|      4:    34.268 -  42.835:  142   |   9:    77.104 -  85.671:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2458 r_free = 0.3082             target_work(ml) = 5.832         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2455 r_free = 0.3086             target_work(ml) = 5.831         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2455   r_free= 0.3086   ksol= 0.33   Bsol= 15.81   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.41,1.75,-0.67,0.00,-0.00,-0.00); trace/3= -0.11                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.831464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2433   r_free= 0.3074   ksol= 0.32   Bsol= 30.42   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-0.57,-1.19,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.826036                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.567352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.598   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175825              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.345  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2433      final r-factor (work) = 0.1753          |
| start r-factor (free) = 0.3074      final r-factor (free) = 0.2227          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4715 = 3.57 * 0.50 * 5.8190 + 1.00 * 0.0924                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2129 = 3.57 * 0.50 * 5.6858 + 1.00 * 0.0713                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1753      final r-factor (work) = 0.1574          |
| start r-factor (free) = 0.2227      final r-factor (free) = 0.2023          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0134 = 0.18 * 1.00 * 5.6858 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9679 = 0.18 * 1.00 * 5.4640 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.52    81.21   17.03    None  None   None       |
|    all(noH): 2823   0      1.52    81.21   17.03    None  None   None       |
|    Sol.    : 438    0      6.46    80.21   38.13    None  None   None       |
|    Mac.    : 2385   0      1.52    81.21   13.16    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:     1.524 -   9.493:  839   |   5:    41.368 -  49.337:  120        |
|      1:     9.493 -  17.462: 1178   |   6:    49.337 -  57.306:   69        |
|      2:    17.462 -  25.431:  298   |   7:    57.306 -  65.275:   28        |
|      3:    25.431 -  33.400:  127   |   8:    65.275 -  73.244:   10        |
|      4:    33.400 -  41.368:  152   |   9:    73.244 -  81.212:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1574 r_free = 0.2023             target_work(ml) = 5.423         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1570 r_free = 0.2018             target_work(ml) = 5.421         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1570   r_free= 0.2018   ksol= 0.32   Bsol= 30.42   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.35,-0.57,-1.19,-0.00,-0.00,-0.00); trace/3= -1.37                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.421341                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1570   r_free= 0.2009   ksol= 0.31   Bsol= 30.42   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-1.86,-1.19,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.417176                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.626486              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.466   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.332509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.886  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1570      final r-factor (work) = 0.1313          |
| start r-factor (free) = 0.2009      final r-factor (free) = 0.1738          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5149 = 1.63 * 0.50 * 5.4641 + 1.00 * 0.0713                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3811 = 1.63 * 0.50 * 5.3295 + 1.00 * 0.0469                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1313      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1738      final r-factor (free) = 0.1693          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7793 = 0.33 * 1.00 * 5.3295 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7489 = 0.33 * 1.00 * 5.2352 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    85.98   17.17    None  None   None       |
|    all(noH): 2823   0      0.76    85.98   17.17    None  None   None       |
|    Sol.    : 438    0      4.19    80.99   40.01    None  None   None       |
|    Mac.    : 2385   0      0.76    85.98   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.757 -   9.279:  818   |   5:    43.367 -  51.889:  111        |
|      1:     9.279 -  17.801: 1247   |   6:    51.889 -  60.411:   78        |
|      2:    17.801 -  26.323:  272   |   7:    60.411 -  68.933:   30        |
|      3:    26.323 -  34.845:  125   |   8:    68.933 -  77.455:    8        |
|      4:    34.845 -  43.367:  130   |   9:    77.455 -  85.977:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1693             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1693             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1693   ksol= 0.31   Bsol= 30.42   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.58,-1.86,-1.19,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.222573                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1690   ksol= 0.32   Bsol= 36.84   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.39,-1.44,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.222004                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.639761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.238  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.573049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9584 = 2.64 * 0.50 * 5.2369 + 1.00 * 0.0464                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8836 = 2.64 * 0.50 * 5.1707 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1096          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9712 = 0.57 * 1.00 * 5.1707 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9451 = 0.57 * 1.00 * 5.1245 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.32    87.73   17.03    None  None   None       |
|    all(noH): 2823   0      0.32    87.73   17.03    None  None   None       |
|    Sol.    : 438    0      4.92    81.93   39.98    None  None   None       |
|    Mac.    : 2385   0      0.32    87.73   12.82    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:     0.325 -   9.066:  818   |   5:    44.030 -  52.770:  117        |
|      1:     9.066 -  17.807: 1263   |   6:    52.770 -  61.511:   71        |
|      2:    17.807 -  26.548:  268   |   7:    61.511 -  70.252:   30        |
|      3:    26.548 -  35.289:  119   |   8:    70.252 -  78.993:    6        |
|      4:    35.289 -  44.030:  126   |   9:    78.993 -  87.734:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1096 r_free = 0.1561             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1095 r_free = 0.1561             target_work(ml) = 5.119         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1561   ksol= 0.32   Bsol= 36.84   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.86,-2.39,-1.44,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.118682                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1095   r_free= 0.1561   ksol= 0.31   Bsol= 36.84   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.31,-1.29,-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: 5.118591                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.221682              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.698  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.253998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.731  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7516 = 2.22 * 0.50 * 5.1246 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7334 = 2.22 * 0.50 * 5.1112 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1076      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.7516 = 4.25 * 1.00 * 5.1112 + 1.00 * 0.0085                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.7231 = 4.25 * 1.00 * 5.1043 + 1.00 * 0.0096                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.58   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    96.58   17.07    None  None   None       |
|    Sol.    : 438    0      6.32    87.71   40.56    None  None   None       |
|    Mac.    : 2385   0      0.00    96.58   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.658: 1023   |   5:    48.291 -  57.950:   99        |
|      1:     9.658 -  19.317: 1146   |   6:    57.950 -  67.608:   46        |
|      2:    19.317 -  28.975:  218   |   7:    67.608 -  77.266:   24        |
|      3:    28.975 -  38.633:  130   |   8:    77.266 -  86.925:    8        |
|      4:    38.633 -  48.291:  125   |   9:    86.925 -  96.583:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1561             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1562             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1562   ksol= 0.31   Bsol= 36.84   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.72,-2.31,-1.29,-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: 5.109389                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.0971 0.1218      5.3617      5.5049|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.0818 0.1142       5.416      5.6205|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.1029 0.1506      5.4627      5.8515|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.1155 0.1550       5.422      5.5864|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.1219 0.1804      5.2854      5.5315|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.1139 0.1667      5.1779      5.3971|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.1180 0.1593       5.122      5.3371|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.1116 0.1732      5.0478      5.3636|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.1094 0.1647      4.9928      5.2262|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.1050 0.1775      4.9349        5.22|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.1087 0.1743      4.9234       5.247|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.1078 0.1656      4.8512      5.2136|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.1060 0.1650      4.7746      5.0233|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.0991 0.1800      4.6537       4.953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.94   8.81   0.98     0.96       6715.01|
|  2:  4.7005 -  3.7510  1299   146  0.95   7.74   1.03     1.02       8865.82|
|  3:  3.7510 -  3.2828  1286   141  0.94  10.88   1.04     1.03      10119.69|
|  4:  3.2828 -  2.9853  1283   142  0.93  12.79   1.02     1.01       9775.91|
|  5:  2.9853 -  2.7728  1258   141  0.91  15.04   1.01     0.98       7889.56|
|  6:  2.7728 -  2.6103  1268   141  0.91  15.35   0.99     0.96       6692.13|
|  7:  2.6103 -  2.4802  1265   140  0.91  15.25   0.99     0.95       5845.34|
|  8:  2.4802 -  2.3727  1248   137  0.92  14.23   1.00     0.98       5022.35|
|  9:  2.3727 -  2.2817  1242   141  0.91  14.88   1.01     0.99       4761.12|
| 10:  2.2817 -  2.2032  1242   139  0.91  14.91   1.00     0.96       4190.59|
| 11:  2.2032 -  2.1345  1251   138  0.90  15.82   1.00     0.97       4327.87|
| 12:  2.1345 -  2.0737  1239   138  0.91  15.15   1.02     1.00       3785.95|
| 13:  2.0737 -  2.0192  1248   137  0.91  14.93   1.01     1.00       3259.46|
| 14:  2.0192 -  1.9701  1130   126  0.92  14.36   0.99     0.95       2561.09|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2561.09 max =        10119.69 mean =      6042.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.52|
|phase err.(test): min =        0.00 max =           88.11 mean =        13.21|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1561   ksol= 0.32   Bsol= 40.33   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.16,-1.09,-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: 5.109041                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.79 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1067   r_free= 0.1561   ksol= 0.32   Bsol= 40.33   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.51,-2.16,-1.09,-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: 5.109041                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7897 -  4.7005 0.99   1371  152 0.0972 0.1221      5.3631      5.5066|
|  2:  4.7005 -  3.7510 0.99   1299  146 0.0820 0.1143      5.4181      5.6218|
|  3:  3.7510 -  3.2828 0.99   1286  141 0.1031 0.1507      5.4637      5.8526|
|  4:  3.2828 -  2.9853 0.99   1283  142 0.1155 0.1549      5.4216      5.5857|
|  5:  2.9853 -  2.7728 0.99   1258  141 0.1218 0.1800      5.2843      5.5298|
|  6:  2.7728 -  2.6103 0.99   1268  141 0.1137 0.1663      5.1765      5.3951|
|  7:  2.6103 -  2.4802 0.99   1265  140 0.1180 0.1591      5.1204      5.3358|
|  8:  2.4802 -  2.3727 0.98   1248  137 0.1115 0.1730      5.0467      5.3615|
|  9:  2.3727 -  2.2817 0.98   1242  141 0.1093 0.1647      4.9921      5.2263|
| 10:  2.2817 -  2.2032 1.00   1242  139 0.1050 0.1776      4.9347      5.2203|
| 11:  2.2032 -  2.1345 0.97   1251  138 0.1087 0.1741      4.9227      5.2465|
| 12:  2.1345 -  2.0737 0.98   1239  138 0.1077 0.1655      4.8507      5.2124|
| 13:  2.0737 -  2.0192 0.99   1248  137 0.1060 0.1651       4.774       5.023|
| 14:  2.0192 -  1.9701 0.91   1130  126 0.0990 0.1798      4.6523      4.9516|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7897 -  4.7005  1371   152  0.94   8.84   0.99     0.96       6747.18|
|  2:  4.7005 -  3.7510  1299   146  0.95   7.75   1.03     1.02       8891.44|
|  3:  3.7510 -  3.2828  1286   141  0.94  10.89   1.04     1.03      10131.18|
|  4:  3.2828 -  2.9853  1283   142  0.93  12.79   1.02     1.01       9763.67|
|  5:  2.9853 -  2.7728  1258   141  0.91  15.03   1.01     0.98       7869.24|
|  6:  2.7728 -  2.6103  1268   141  0.91  15.32   1.00     0.97       6669.98|
|  7:  2.6103 -  2.4802  1265   140  0.91  15.22   0.99     0.96       5820.01|
|  8:  2.4802 -  2.3727  1248   137  0.92  14.22   1.01     0.99       5008.91|
|  9:  2.3727 -  2.2817  1242   141  0.91  14.88   1.02     0.99       4756.41|
| 10:  2.2817 -  2.2032  1242   139  0.91  14.90   1.01     0.97       4188.98|
| 11:  2.2032 -  2.1345  1251   138  0.90  15.81   1.01     0.98       4321.09|
| 12:  2.1345 -  2.0737  1239   138  0.91  15.13   1.03     1.01       3781.19|
| 13:  2.0737 -  2.0192  1248   137  0.91  14.92   1.02     1.01       3253.05|
| 14:  2.0192 -  1.9701  1130   126  0.92  14.33   1.00     0.97       2552.16|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2552.16 max =        10131.18 mean =      6039.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.84 mean =        13.51|
|phase err.(test): min =        0.00 max =           88.12 mean =        13.20|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.425)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.59   17.07    None  None   None       |
|    all(noH): 2823   0      0.00    96.59   17.07    None  None   None       |
|    Sol.    : 438    0      6.32    87.71   40.56    None  None   None       |
|    Mac.    : 2385   0      0.00    96.59   12.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.661: 1023   |   5:    48.294 -  57.953:   99        |
|      1:     9.661 -  19.320: 1146   |   6:    57.953 -  67.611:   46        |
|      2:    19.320 -  28.978:  218   |   7:    67.611 -  77.269:   24        |
|      3:    28.978 -  38.636:  130   |   8:    77.269 -  86.927:    8        |
|      4:    38.636 -  48.294:  125   |   9:    86.927 -  96.586:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 295         
Filter by distance & map next to the model:
   mapped sites are within: 0.412 - 4.521
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 295
   mapped sites are within: 0.713 - 4.521

peak=    6.237 closest distance to " NE2 GLN A  11 " =    1.206
peak=    6.105 closest distance to " O   HOH Z 144 " =    1.818
peak=    5.938 closest distance to " O   HOH Z 126 " =    1.917
peak=    5.490 closest distance to " O   HOH Z 236 " =    1.472
peak=    5.432 closest distance to " CG  PRO A  54 " =    1.259
peak=    5.338 closest distance to " CB  ARG A 275 " =    0.925
peak=    5.336 closest distance to " CG  PRO A 213 " =    1.268
peak=    4.952 closest distance to " NH2 ARG A  56 " =    2.087
peak=    4.903 closest distance to " O   HOH Z  78 " =    1.759
peak=    4.897 closest distance to " O   HOH Z 427 " =    2.670
peak=    4.891 closest distance to " O   HOH Z 232 " =    2.338
peak=    4.761 closest distance to " O   HOH Z 209 " =    2.200
peak=    4.658 closest distance to " O   HOH Z 193 " =    1.722
peak=    4.640 closest distance to " O   HOH Z 287 " =    1.768
peak=    4.618 closest distance to " CB  SER A  63 " =    1.179
peak=    4.567 closest distance to " C   PRO A 198 " =    1.460
peak=    4.546 closest distance to " O   HOH Z  44 " =    1.816
peak=    4.479 closest distance to " O   HOH Z 425 " =    2.058
peak=    4.464 closest distance to " OG BSER A 164 " =    2.243
peak=    4.456 closest distance to " O   HOH Z 371 " =    1.799
peak=    4.438 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.429 closest distance to " CB  GLN A 223 " =    1.538
peak=    4.412 closest distance to " CG  ARG A  66 " =    2.432
peak=    4.401 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.371 closest distance to " CG2 VAL A 257 " =    0.830
peak=    4.322 closest distance to " O   HOH Z  78 " =    2.099
peak=    4.316 closest distance to " O   HOH Z 316 " =    2.913
peak=    4.312 closest distance to " O   HOH Z 272 " =    1.881
peak=    4.310 closest distance to " NZ  LYS A 117 " =    2.976
peak=    4.304 closest distance to " CB  PRO A  54 " =    0.980
peak=    4.292 closest distance to " CB  ASN A 148 " =    1.364
peak=    4.268 closest distance to " CB  ARG A  79 " =    1.348
peak=    4.267 closest distance to " CB  GLU A 152 " =    1.279
peak=    4.223 closest distance to " O   HOH Z 368 " =    3.600
peak=    4.179 closest distance to " O   HOH Z 369 " =    2.236
peak=    4.161 closest distance to " O   HOH Z 303 " =    2.183
peak=    4.137 closest distance to " O   HOH Z 203 " =    1.813
peak=    4.137 closest distance to " O   HOH Z 298 " =    1.838
peak=    4.119 closest distance to " O   HOH Z 112 " =    1.249
peak=    4.119 closest distance to " O   HOH Z   9 " =    2.290
peak=    4.110 closest distance to " O   SER A  87 " =    2.261
peak=    4.103 closest distance to " CG  PRO A 280 " =    0.726
peak=    4.087 closest distance to " O   HOH Z 250 " =    1.457
peak=    4.074 closest distance to " O   HOH Z  61 " =    1.564
peak=    4.071 closest distance to " CB  SER A   3 " =    1.311
peak=    4.065 closest distance to " O   HOH Z 234 " =    3.539
peak=    4.065 closest distance to " ND2 ASN A 187 " =    1.338
peak=    4.043 closest distance to " CD2 TRP A 179 " =    1.366
peak=    4.032 closest distance to " CB  VAL A 265 " =    1.291
peak=    4.029 closest distance to " CG  PRO A  90 " =    1.124
peak=    4.022 closest distance to " O   HOH Z 128 " =    1.987
peak=    4.018 closest distance to " CG  PRO A 198 " =    1.224
peak=    4.016 closest distance to " CB  SER A  26 " =    1.645
peak=    4.005 closest distance to " O   HOH Z 289 " =    1.617
peak=    4.003 closest distance to " CG  PRO A 243 " =    1.072
peak=    4.001 closest distance to " O   HOH Z 403 " =    1.717
peak=    3.989 closest distance to " O   HOH Z 344 " =    3.202
peak=    3.949 closest distance to " O   HOH Z 132 " =    2.171
peak=    3.915 closest distance to " O   HOH Z 144 " =    2.018
peak=    3.911 closest distance to " O   HOH Z 368 " =    1.978
peak=    3.899 closest distance to " O   HOH Z 327 " =    1.676
peak=    3.892 closest distance to " O   HOH Z   1 " =    1.830
peak=    3.889 closest distance to " O   HOH Z 419 " =    2.117
peak=    3.884 closest distance to " CG1 ILE A  33 " =    1.245
peak=    3.870 closest distance to " O   HOH Z  61 " =    1.475
peak=    3.850 closest distance to " O   HOH Z 425 " =    1.292
peak=    3.842 closest distance to " O   HOH Z 423 " =    2.459
peak=    3.839 closest distance to " CB  ARG A 190 " =    1.667
peak=    3.837 closest distance to " CG2 ILE A 120 " =    1.076
peak=    3.833 closest distance to " O   HOH Z 189 " =    1.885
peak=    3.829 closest distance to " CB  GLU A 128 " =    1.053
peak=    3.824 closest distance to " NH1AARG A 145 " =    1.206
peak=    3.812 closest distance to " O   HOH Z 222 " =    2.395
peak=    3.804 closest distance to " O   HOH Z 417 " =    1.077
peak=    3.802 closest distance to " CD2 LEU A 297 " =    1.001
peak=    3.793 closest distance to " O   HOH Z 124 " =    1.274
peak=    3.783 closest distance to " CA  ASN A 215 " =    1.147
peak=    3.782 closest distance to " NH1BARG A 145 " =    1.291
peak=    3.782 closest distance to " O   HOH Z 389 " =    3.019
peak=    3.766 closest distance to " O   HOH Z 380 " =    1.587
peak=    3.764 closest distance to " O   HOH Z  97 " =    1.988
peak=    3.760 closest distance to " O   HOH Z  66 " =    2.141
peak=    3.756 closest distance to " O   HOH Z   1 " =    1.555
peak=    3.733 closest distance to " CB  TRP A 179 " =    1.228
peak=    3.732 closest distance to " O   HOH Z 286 " =    2.213
peak=    3.731 closest distance to " O   HOH Z 158 " =    2.923
peak=    3.726 closest distance to " O   HOH Z  59 " =    1.559
peak=    3.718 closest distance to " O   HOH Z   3 " =    1.935
peak=    3.717 closest distance to " O   HOH Z   6 " =    2.200
peak=    3.714 closest distance to " O  BHOH Z 338 " =    2.359
peak=    3.712 closest distance to " CE  LYS A  76 " =    0.825
peak=    3.711 closest distance to " O   HOH Z 407 " =    2.184
peak=    3.677 closest distance to " O   HOH Z 365 " =    2.725
peak=    3.638 closest distance to " CB  ARG A 139 " =    1.029
peak=    3.632 closest distance to " OG BSER A  99 " =    2.381
peak=    3.627 closest distance to " O   HOH Z  54 " =    1.678
peak=    3.626 closest distance to " O   HOH Z  93 " =    2.083
peak=    3.622 closest distance to " CD BLYS A 290 " =    1.220
peak=    3.606 closest distance to " O   HOH Z 402 " =    1.356
peak=    3.604 closest distance to " CB  LEU A 228 " =    1.090
peak=    3.600 closest distance to " CB  TYR A 169 " =    0.833
peak=    3.589 closest distance to " OD1 ASN A  69 " =    2.542
peak=    3.585 closest distance to " NZ  LYS A 119 " =    2.844
peak=    3.578 closest distance to " NE2 GLN A  73 " =    3.520
peak=    3.575 closest distance to " O   HOH Z 405 " =    1.129
peak=    3.568 closest distance to " CA  LYS A 290 " =    1.365
peak=    3.568 closest distance to " CB  THR A  31 " =    1.742
peak=    3.552 closest distance to " CB  VAL A 202 " =    1.590
peak=    3.551 closest distance to " CE AMET A  47 " =    1.355
peak=    3.549 closest distance to " O   HOH Z 146 " =    1.684
peak=    3.547 closest distance to " OG  SER A  62 " =    2.843
peak=    3.546 closest distance to " O   HOH Z 371 " =    3.041
peak=    3.545 closest distance to " O   HOH Z  40 " =    2.002
peak=    3.542 closest distance to " O   HOH Z 193 " =    2.014
peak=    3.539 closest distance to " O   HOH Z 128 " =    2.079
peak=    3.537 closest distance to " O   HOH Z 353 " =    2.443
peak=    3.536 closest distance to " O   HOH Z 357 " =    1.795
peak=    3.529 closest distance to " O   HOH Z  10 " =    1.746
peak=    3.520 closest distance to " O   HOH Z 173 " =    2.016
peak=    3.519 closest distance to " CB  THR A 157 " =    1.038
peak=    3.517 closest distance to " CB  ILE A 120 " =    1.330
peak=    3.514 closest distance to " CB  LYS A 117 " =    1.163
peak=    3.513 closest distance to " CG AARG A 275 " =    0.988
peak=    3.513 closest distance to " O   HOH Z 193 " =    1.780
peak=    3.511 closest distance to " O   HOH Z 394 " =    1.624
peak=    3.504 closest distance to " O   HOH Z 245 " =    1.262
peak=    3.503 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.499 closest distance to " O   HOH Z 437 " =    1.598
peak=    3.497 closest distance to " CZ  PHE A 218 " =    1.012
peak=    3.496 closest distance to " O   HOH Z 284 " =    2.808
peak=    3.495 closest distance to " ND1 HIS A  86 " =    1.815
peak=    3.495 closest distance to " CB  GLN A  89 " =    1.432
peak=    3.493 closest distance to " CA  ALA A  21 " =    1.109
peak=    3.490 closest distance to " O   HOH Z 415 " =    3.523
peak=    3.487 closest distance to " O   HOH Z 423 " =    1.343
peak=    3.484 closest distance to " O   HOH Z 213 " =    1.689
peak=    3.480 closest distance to " NH2BARG A 145 " =    2.020
peak=    3.461 closest distance to " CB  TRP A 266 " =    1.092
peak=    3.456 closest distance to " OE2 GLU A  53 " =    2.064
peak=    3.452 closest distance to " O   HOH Z 337 " =    3.497
peak=    3.447 closest distance to " O   HOH Z  71 " =    1.850
peak=    3.446 closest distance to " N   GLU A   2 " =    1.416
peak=    3.443 closest distance to " O  BHOH Z  74 " =    1.419
peak=    3.443 closest distance to " O   HOH Z  40 " =    1.913
peak=    3.439 closest distance to " O   HOH Z 313 " =    1.923
peak=    3.438 closest distance to " O   HOH Z 305 " =    3.491
peak=    3.437 closest distance to " O   HOH Z 336 " =    1.859
peak=    3.436 closest distance to " CB  ALA A  34 " =    1.154
peak=    3.435 closest distance to " O   HOH Z  88 " =    2.507
peak=    3.434 closest distance to " OD1BASN A 224 " =    2.182
peak=    3.433 closest distance to " O   HOH Z 147 " =    1.685
peak=    3.432 closest distance to " O   HOH Z 153 " =    1.585
peak=    3.431 closest distance to " O   HOH Z 389 " =    1.673
peak=    3.428 closest distance to " CA  ASP A 162 " =    1.063
peak=    3.428 closest distance to " CB  SER A 216 " =    0.805
peak=    3.426 closest distance to " O   HOH Z 175 " =    1.955
peak=    3.425 closest distance to " O   HOH Z 261 " =    2.264
peak=    3.413 closest distance to " O   HOH Z 290 " =    0.930
peak=    3.406 closest distance to " CA  PHE A 283 " =    1.304
peak=    3.404 closest distance to " CB  ASN A  39 " =    0.804
peak=    3.402 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.400 closest distance to " O   HOH Z 207 " =    1.600
peak=    3.394 closest distance to " O   HOH Z  64 " =    2.480
peak=    3.387 closest distance to " CB  ALA A  21 " =    1.919
peak=    3.386 closest distance to " O   HOH Z 426 " =    1.824
peak=    3.385 closest distance to " CA  ALA A  84 " =    1.313
peak=    3.380 closest distance to " CG  GLN A  77 " =    2.274
peak=    3.379 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.371 closest distance to " O   HOH Z 298 " =    2.550
peak=    3.369 closest distance to " O   HOH Z 244 " =    1.753
peak=    3.367 closest distance to " O   HOH Z 257 " =    2.184
peak=    3.363 closest distance to " O   HOH Z  80 " =    1.948
peak=    3.361 closest distance to " CA  ALA A 299 " =    0.953
peak=    3.353 closest distance to " O   ASN A  74 " =    1.496
peak=    3.351 closest distance to " N   ARG A 156 " =    1.285
peak=    3.350 closest distance to " N   ASN A  39 " =    1.214
peak=    3.347 closest distance to " O   HOH Z 433 " =    1.853
peak=    3.344 closest distance to " O   HOH Z  21 " =    1.774
peak=    3.342 closest distance to " O   HOH Z 345 " =    3.355
peak=    3.342 closest distance to " CB  TYR A 116 " =    0.833
peak=    3.341 closest distance to " CA  MET A  40 " =    1.049
peak=    3.341 closest distance to " OD2 ASP A 286 " =    2.620
peak=    3.338 closest distance to " N   ASN A 127 " =    1.218
peak=    3.335 closest distance to " O   HOH Z 180 " =    2.244
peak=    3.332 closest distance to " N   SER A 134 " =    1.403
peak=    3.331 closest distance to " CG1BVAL A  72 " =    1.330
peak=    3.330 closest distance to " O   HOH Z 409 " =    2.480
peak=    3.329 closest distance to " O   HOH Z 423 " =    1.808
peak=    3.326 closest distance to " CG2BVAL A  41 " =    0.749
peak=    3.322 closest distance to " O   HOH Z 283 " =    2.338
peak=    3.320 closest distance to " O   HOH Z 214 " =    2.264
peak=    3.318 closest distance to " CA  LEU A 300 " =    0.952
peak=    3.318 closest distance to " O   HOH Z  44 " =    3.046
peak=    3.317 closest distance to " O   HOH Z 128 " =    1.966
peak=    3.316 closest distance to " O   HOH Z 411 " =    3.596
peak=    3.313 closest distance to " CB  LEU A 255 " =    0.752
peak=    3.312 closest distance to " O   HOH Z   9 " =    2.189
peak=    3.312 closest distance to " O   HOH Z 112 " =    2.395
peak=    3.301 closest distance to " O   HOH Z 406 " =    1.626
peak=    3.300 closest distance to " CB  VAL A 126 " =    1.146
peak=    3.298 closest distance to " CE  LYS A 119 " =    1.238
peak=    3.296 closest distance to " CA  THR A 264 " =    0.802
peak=    3.296 closest distance to " CG2 THR A 221 " =    1.190
peak=    3.292 closest distance to " N   GLN A 278 " =    1.049
peak=    3.291 closest distance to " CB  ALA A   1 " =    4.521
peak=    3.291 closest distance to " N   PHE A 130 " =    1.251
peak=    3.290 closest distance to " O   HOH Z  89 " =    2.107
peak=    3.288 closest distance to " O   HOH Z  63 " =    1.334
peak=    3.288 closest distance to " O   HOH Z 227 " =    1.832
peak=    3.287 closest distance to " CA  ILE A 234 " =    1.051
peak=    3.284 closest distance to " N   ASP A 162 " =    1.160
peak=    3.279 closest distance to " CD  PRO A 243 " =    1.603
peak=    3.278 closest distance to " CG2 VAL A 197 " =    1.088
peak=    3.276 closest distance to " O   HOH Z 422 " =    2.601
peak=    3.271 closest distance to " O   HOH Z 291 " =    1.487
peak=    3.269 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.268 closest distance to " O   HOH Z  92 " =    1.146
peak=    3.268 closest distance to " O   HOH Z 119 " =    4.414
peak=    3.266 closest distance to " O   HOH Z 108 " =    2.203
peak=    3.262 closest distance to " CB  SER A  62 " =    1.368
peak=    3.261 closest distance to " CB  ALA A 233 " =    1.381
peak=    3.260 closest distance to " O   HOH Z 435 " =    1.901
peak=    3.259 closest distance to " O   HOH Z  30 " =    1.657
peak=    3.256 closest distance to " O   HOH Z 391 " =    2.949
peak=    3.252 closest distance to " O   HOH Z 292 " =    1.660
peak=    3.249 closest distance to " O   HOH Z 271 " =    2.096
peak=    3.247 closest distance to " CD1 ILE A 106 " =    0.903
peak=    3.246 closest distance to " CA  ALA A 158 " =    1.197
peak=    3.246 closest distance to " O   HOH Z 109 " =    2.528
peak=    3.241 closest distance to " O   HOH Z  85 " =    2.319
peak=    3.236 closest distance to " O   HOH Z 251 " =    1.717
peak=    3.235 closest distance to " O   ALA A   1 " =    1.684
peak=    3.234 closest distance to " CG  MET A 185 " =    1.399
peak=    3.223 closest distance to " O   HOH Z 432 " =    1.782
peak=    3.221 closest distance to " O   ARG A 145 " =    1.797
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.324
peak=    3.221 closest distance to " O   ASP A 124 " =    1.286
peak=    3.217 closest distance to " CB  THR A 279 " =    1.698
peak=    3.216 closest distance to " O   HOH Z 421 " =    1.822
peak=    3.212 closest distance to " O   HOH Z 272 " =    2.090
peak=    3.211 closest distance to " O   HOH Z 329 " =    3.658
peak=    3.210 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.205 closest distance to " O   HOH Z 114 " =    4.234
peak=    3.203 closest distance to " CG  MET A 113 " =    0.983
peak=    3.200 closest distance to " CB  SER A 276 " =    1.132
peak=    3.199 closest distance to " CB  ASN A 110 " =    1.040
peak=    3.198 closest distance to " CB  MET A  47 " =    1.164
peak=    3.189 closest distance to " O   HOH Z 189 " =    2.104
peak=    3.189 closest distance to " O   HOH Z  88 " =    2.363
peak=    3.188 closest distance to " CG  LYS A  76 " =    0.988
peak=    3.180 closest distance to " CA  ASN A 127 " =    1.011
peak=    3.176 closest distance to " O   HOH Z 185 " =    1.773
peak=    3.171 closest distance to " O   HOH Z 218 " =    2.142
peak=    3.170 closest distance to " CB  ALA A 114 " =    1.431
peak=    3.169 closest distance to " CB  VAL A 265 " =    2.295
peak=    3.165 closest distance to " O   HOH Z 172 " =    3.109
peak=    3.162 closest distance to " O   HOH Z 213 " =    1.870
peak=    3.158 closest distance to " O   HOH Z 128 " =    1.606
peak=    3.158 closest distance to " O   HOH Z 106 " =    2.655
peak=    3.155 closest distance to " O   HOH Z 299 " =    4.242
peak=    3.155 closest distance to " OG  SER A  22 " =    2.672
peak=    3.151 closest distance to " O   HOH Z 383 " =    1.783
peak=    3.151 closest distance to " N   TYR A 116 " =    1.616
peak=    3.149 closest distance to " CB  LEU A 300 " =    0.909
peak=    3.148 closest distance to " O   HOH Z  43 " =    2.236
peak=    3.141 closest distance to " O   HOH Z 302 " =    1.494
peak=    3.138 closest distance to " CG  ARG A 269 " =    1.409
peak=    3.130 closest distance to " CG  GLN A  89 " =    1.502
peak=    3.130 closest distance to " CG1 ILE A 151 " =    0.958
peak=    3.127 closest distance to " CB  ASN A 215 " =    1.071
peak=    3.120 closest distance to " O   HOH Z 261 " =    1.386
peak=    3.118 closest distance to " CD  LYS A 166 " =    1.299
peak=    3.112 closest distance to " O   HOH Z  59 " =    1.894
peak=    3.108 closest distance to " CA  ALA A 233 " =    0.939
peak=    3.107 closest distance to " O   PRO A  90 " =    1.480
peak=    3.105 closest distance to " CG AARG A 275 " =    1.087
peak=    3.103 closest distance to " O   HOH Z 163 " =    1.730
peak=    3.098 closest distance to " CA  ALA A 291 " =    0.857
peak=    3.077 closest distance to " OG1 THR A   4 " =    2.478
peak=    3.077 closest distance to " O   HOH Z  43 " =    2.688
peak=    3.076 closest distance to " O   HOH Z  85 " =    1.329
peak=    3.075 closest distance to " NH1 ARG A 138 " =    1.178
peak=    3.072 closest distance to " CB  MET A 188 " =    1.572
peak=    3.067 closest distance to " O   HOH Z 291 " =    1.820
peak=    3.061 closest distance to " CA  ARG A 102 " =    1.037
peak=    3.057 closest distance to " NE2 GLN A  58 " =    3.612
peak=    3.057 closest distance to " CG1BVAL A  72 " =    1.221
peak=    3.056 closest distance to " CA  ARG A 195 " =    1.229
peak=    3.053 closest distance to " CZ2 TRP A 179 " =    1.593
peak=    3.050 closest distance to " O   HOH Z  55 " =    2.143
peak=    3.041 closest distance to " O   HOH Z 151 " =    1.359
peak=    3.032 closest distance to " CD1AILE A 234 " =    0.922

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.763 - 5.952
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.763 - 5.952

peak=   -4.551 closest distance to " O   HOH Z 377 " =    2.069
peak=   -4.519 closest distance to " CD  ARG A 156 " =    2.054
peak=   -4.510 closest distance to " C   HIS A 108 " =    1.097
peak=   -4.483 closest distance to " O   HOH Z 266 " =    4.686
peak=   -4.312 closest distance to " CG  GLN A 223 " =    1.771
peak=   -4.302 closest distance to " OG BSER A 134 " =    1.331
peak=   -4.283 closest distance to " CD1 LEU A 255 " =    2.847
peak=   -4.249 closest distance to " CA  VAL A  67 " =    2.875
peak=   -4.238 closest distance to " O   VAL A  67 " =    2.634
peak=   -4.212 closest distance to " SG  CYS A 254 " =    3.392
peak=   -4.195 closest distance to " CB  PRO A 243 " =    2.606
peak=   -4.143 closest distance to " CG1 VAL A 112 " =    2.768
peak=   -4.111 closest distance to " O   HOH Z 372 " =    2.480
peak=   -4.045 closest distance to " O   HOH Z 198 " =    1.932
peak=   -4.034 closest distance to " ND2 ASN A  45 " =    1.122
peak=   -4.018 closest distance to " CZ  PHE A  59 " =    1.463
peak=   -4.013 closest distance to " OD1 ASN A 187 " =    1.658
peak=   -4.005 closest distance to " O   ALA A 161 " =    1.567
peak=   -3.995 closest distance to " O   HOH Z 185 " =    2.086
peak=   -3.978 closest distance to " CE  MET A 105 " =    2.182
peak=   -3.959 closest distance to " OD2 ASP A 191 " =    1.397
peak=   -3.951 closest distance to " O   PRO A 198 " =    1.325
peak=   -3.898 closest distance to " N   GLN A  58 " =    1.662
peak=   -3.896 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.872 closest distance to " CG  PHE A 283 " =    2.583
peak=   -3.866 closest distance to " O   HOH Z 407 " =    2.930
peak=   -3.854 closest distance to " CA  GLY A  98 " =    1.784
peak=   -3.845 closest distance to " CB  ASN A  39 " =    2.309
peak=   -3.840 closest distance to " CZ  TYR A 169 " =    1.648
peak=   -3.837 closest distance to " O   HOH Z 313 " =    1.817
peak=   -3.817 closest distance to " OD2 ASP A 171 " =    2.294
peak=   -3.809 closest distance to " CB  ALA A 291 " =    2.140
peak=   -3.797 closest distance to " O   HOH Z 290 " =    1.154
peak=   -3.776 closest distance to " O   HOH Z 389 " =    1.917
peak=   -3.775 closest distance to " O   HOH Z 126 " =    1.887
peak=   -3.770 closest distance to " N   ALA A 248 " =    1.575
peak=   -3.767 closest distance to " O   HOH Z 317 " =    1.498
peak=   -3.764 closest distance to " O   HOH Z 231 " =    2.206
peak=   -3.753 closest distance to " O   PHE A 218 " =    1.457
peak=   -3.747 closest distance to " O   HOH Z 102 " =    1.626
peak=   -3.738 closest distance to " O   HOH Z 395 " =    5.080
peak=   -3.732 closest distance to " O   HOH Z 351 " =    1.576
peak=   -3.720 closest distance to " O   PRO A 198 " =    1.269
peak=   -3.703 closest distance to " O   ARG A 145 " =    1.557
peak=   -3.698 closest distance to " CG  GLN A  58 " =    1.107
peak=   -3.691 closest distance to " CB  PHE A 192 " =    1.847
peak=   -3.686 closest distance to " O   SER A  95 " =    1.400
peak=   -3.685 closest distance to " O   HOH Z 263 " =    2.928
peak=   -3.677 closest distance to " CB  ILE A  33 " =    2.829
peak=   -3.676 closest distance to " OD1 ASP A 191 " =    1.864
peak=   -3.666 closest distance to " CD1 PHE A  59 " =    1.958
peak=   -3.635 closest distance to " O   SER A 135 " =    1.492
peak=   -3.631 closest distance to " CG  PRO A 243 " =    1.584
peak=   -3.631 closest distance to " O   HOH Z  13 " =    1.496
peak=   -3.623 closest distance to " O   ALA A  51 " =    1.239
peak=   -3.621 closest distance to " N   ALA A  43 " =    2.405
peak=   -3.614 closest distance to " CD2 PHE A 225 " =    1.231
peak=   -3.613 closest distance to " O   HOH Z  63 " =    1.723
peak=   -3.592 closest distance to " O   SER A 146 " =    1.018
peak=   -3.590 closest distance to " O   HOH Z 111 " =    2.498
peak=   -3.582 closest distance to " CD1 LEU A 101 " =    2.246
peak=   -3.579 closest distance to " CD1 LEU A 228 " =    2.004
peak=   -3.579 closest distance to " O   HOH Z  52 " =    1.323
peak=   -3.569 closest distance to " N   HIS A 115 " =    2.023
peak=   -3.569 closest distance to " O   HOH Z 211 " =    1.577
peak=   -3.565 closest distance to " O   HOH Z  37 " =    1.723
peak=   -3.561 closest distance to " CD1 ILE A 239 " =    2.506
peak=   -3.556 closest distance to " CA  GLY A  57 " =    2.118
peak=   -3.555 closest distance to " OXT GLY A 302 " =    2.822
peak=   -3.538 closest distance to " CB  ALA A   7 " =    2.035
peak=   -3.523 closest distance to " NE2 GLN A 278 " =    1.698
peak=   -3.522 closest distance to " OE2 GLU A 152 " =    1.191
peak=   -3.517 closest distance to " CB  ALA A 248 " =    2.011
peak=   -3.514 closest distance to " O   HOH Z 131 " =    4.071
peak=   -3.511 closest distance to " O   HOH Z 166 " =    1.229
peak=   -3.506 closest distance to " O   HOH Z  90 " =    2.323
peak=   -3.502 closest distance to " CE2 TYR A  30 " =    2.732
peak=   -3.501 closest distance to " CB  PHE A 208 " =    2.203
peak=   -3.486 closest distance to " O   HOH Z  24 " =    1.249
peak=   -3.481 closest distance to " O   HOH Z 385 " =    1.943
peak=   -3.479 closest distance to " CB  ALA A 291 " =    2.295
peak=   -3.476 closest distance to " CB  ALA A 161 " =    2.416
peak=   -3.472 closest distance to " CB  ALA A 248 " =    2.255
peak=   -3.466 closest distance to " O   HOH Z  60 " =    1.857
peak=   -3.457 closest distance to " O   GLN A  89 " =    1.549
peak=   -3.452 closest distance to " CA  GLY A 133 " =    1.918
peak=   -3.449 closest distance to " O   ALA A 292 " =    1.939
peak=   -3.441 closest distance to " CE2 PHE A 218 " =    2.382
peak=   -3.439 closest distance to " N   ASP A 286 " =    2.362
peak=   -3.439 closest distance to " O   HOH Z 114 " =    2.943
peak=   -3.431 closest distance to " ND2 ASN A  69 " =    1.493
peak=   -3.423 closest distance to " O   TRP A  70 " =    1.440
peak=   -3.420 closest distance to " O   PRO A 163 " =    1.889
peak=   -3.416 closest distance to " O   SER A  22 " =    2.382
peak=   -3.414 closest distance to " O   HOH Z 388 " =    2.024
peak=   -3.413 closest distance to " OE1 GLU A 277 " =    2.027
peak=   -3.402 closest distance to " O   HOH Z 250 " =    1.331
peak=   -3.401 closest distance to " OE1 GLN A 223 " =    1.921
peak=   -3.389 closest distance to " O   HOH Z 348 " =    1.789
peak=   -3.386 closest distance to " CB  ASP A 132 " =    2.328
peak=   -3.386 closest distance to " O   HOH Z 148 " =    1.797
peak=   -3.386 closest distance to " CG  ASP A 231 " =    0.763
peak=   -3.385 closest distance to " O   HOH Z  43 " =    1.828
peak=   -3.383 closest distance to " O   HOH Z 244 " =    2.109
peak=   -3.383 closest distance to " C   ALA A 158 " =    1.321
peak=   -3.381 closest distance to " O   HOH Z 140 " =    1.861
peak=   -3.378 closest distance to " O   HOH Z 362 " =    5.952
peak=   -3.374 closest distance to " OD1 ASN A 148 " =    1.600
peak=   -3.367 closest distance to " CB  ALA A 244 " =    1.999
peak=   -3.366 closest distance to " CE3 TRP A 274 " =    2.259
peak=   -3.362 closest distance to " CZ2 TRP A 274 " =    0.988
peak=   -3.354 closest distance to " OG  SER A  87 " =    1.298
peak=   -3.353 closest distance to " O   HOH Z  11 " =    1.867
peak=   -3.353 closest distance to " CB  PRO A 163 " =    2.507
peak=   -3.351 closest distance to " O   HOH Z 266 " =    4.410
peak=   -3.350 closest distance to " O   PRO A 198 " =    1.575
peak=   -3.346 closest distance to " O   HOH Z 191 " =    5.650
peak=   -3.346 closest distance to " O   HOH Z 236 " =    1.999
peak=   -3.344 closest distance to " NH1 ARG A 195 " =    2.594
peak=   -3.338 closest distance to " OE1 GLN A  88 " =    1.148
peak=   -3.335 closest distance to " ND2 ASN A  39 " =    1.387
peak=   -3.334 closest distance to " CD  ARG A  36 " =    1.909
peak=   -3.333 closest distance to " O   SER A 146 " =    0.961
peak=   -3.330 closest distance to " CE1 TYR A 169 " =    2.428
peak=   -3.328 closest distance to " O   ASP A 162 " =    2.151
peak=   -3.325 closest distance to " O   ASN A 249 " =    1.375
peak=   -3.320 closest distance to " OD1 ASP A 171 " =    1.567
peak=   -3.320 closest distance to " O   VAL A 189 " =    2.464
peak=   -3.319 closest distance to " O   HOH Z 309 " =    2.512
peak=   -3.319 closest distance to " NE2 GLN A 194 " =    2.792
peak=   -3.318 closest distance to " CG2 ILE A 263 " =    2.274
peak=   -3.318 closest distance to " CD  ARG A 139 " =    1.553
peak=   -3.313 closest distance to " CG2 VAL A 189 " =    1.956
peak=   -3.313 closest distance to " O   HOH Z 213 " =    1.344
peak=   -3.310 closest distance to " NH2 ARG A  79 " =    2.021
peak=   -3.301 closest distance to " CA  GLY A 203 " =    2.140
peak=   -3.282 closest distance to " CZ3 TRP A 179 " =    1.233
peak=   -3.282 closest distance to " N   ASN A 127 " =    1.507
peak=   -3.281 closest distance to " O   MET A  40 " =    2.633
peak=   -3.268 closest distance to " OG  SER A 245 " =    1.329
peak=   -3.268 closest distance to " O   HOH Z 393 " =    3.427
peak=   -3.258 closest distance to " CG1 VAL A 230 " =    1.948
peak=   -3.254 closest distance to " CD  LYS A 289 " =    2.361
peak=   -3.252 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.252 closest distance to " O   HOH Z 385 " =    1.849
peak=   -3.251 closest distance to " NH2AARG A 275 " =    5.015
peak=   -3.248 closest distance to " ND2 ASN A 187 " =    1.538
peak=   -3.243 closest distance to " CE  MET A  93 " =    1.077
peak=   -3.240 closest distance to " CD2 TYR A 293 " =    1.860
peak=   -3.238 closest distance to " CE3 TRP A 123 " =    1.300
peak=   -3.233 closest distance to " O   VAL A 174 " =    2.110
peak=   -3.230 closest distance to " N   PRO A 163 " =    1.627
peak=   -3.227 closest distance to " CD  GLN A  88 " =    0.887
peak=   -3.222 closest distance to " O   HOH Z 427 " =    1.535
peak=   -3.215 closest distance to " CD2 LEU A 237 " =    2.634
peak=   -3.215 closest distance to " O   HOH Z 345 " =    1.850
peak=   -3.215 closest distance to " CG1 VAL A 197 " =    2.114
peak=   -3.213 closest distance to " O   HOH Z 326 " =    1.588
peak=   -3.212 closest distance to " ND2 ASN A 252 " =    1.711
peak=   -3.212 closest distance to " N   SER A 212 " =    1.949
peak=   -3.209 closest distance to " OG1 THR A 178 " =    1.151
peak=   -3.208 closest distance to " O   ALA A  10 " =    1.713
peak=   -3.207 closest distance to " O   HOH Z 198 " =    1.613
peak=   -3.205 closest distance to " CB  ASP A 132 " =    2.194
peak=   -3.201 closest distance to " O   HOH Z 438 " =    1.193
peak=   -3.198 closest distance to " O   HOH Z  44 " =    2.232
peak=   -3.197 closest distance to " O   ALA A  34 " =    2.319
peak=   -3.193 closest distance to " N   PHE A  59 " =    1.811
peak=   -3.188 closest distance to " ND2 ASN A 209 " =    1.709
peak=   -3.186 closest distance to " O   ASN A 127 " =    2.101
peak=   -3.182 closest distance to " O   VAL A 197 " =    1.451
peak=   -3.175 closest distance to " O   HOH Z  93 " =    1.848
peak=   -3.175 closest distance to " CD1 ILE A 263 " =    2.674
peak=   -3.174 closest distance to " CA  TRP A  70 " =    2.386
peak=   -3.170 closest distance to " CB  ALA A  43 " =    2.363
peak=   -3.169 closest distance to " N   GLN A  77 " =    1.681
peak=   -3.169 closest distance to " NZ  LYS A 119 " =    3.392
peak=   -3.157 closest distance to " CA  ASP A  27 " =    2.360
peak=   -3.155 closest distance to " O   GLY A  80 " =    2.324
peak=   -3.150 closest distance to " CG  GLU A   2 " =    2.086
peak=   -3.146 closest distance to " N   LYS A 289 " =    1.518
peak=   -3.144 closest distance to " CD1 LEU A   5 " =    2.329
peak=   -3.141 closest distance to " OG  SER A  97 " =    2.048
peak=   -3.140 closest distance to " O   ALA A 180 " =    1.078
peak=   -3.139 closest distance to " O   HOH Z  60 " =    2.018
peak=   -3.136 closest distance to " O   HOH Z 137 " =    1.421
peak=   -3.132 closest distance to " O   ILE A 106 " =    2.003
peak=   -3.116 closest distance to " O   ASN A 224 " =    0.968
peak=   -3.114 closest distance to " CD  GLN A  77 " =    1.370
peak=   -3.107 closest distance to " O   HOH Z 281 " =    2.775
peak=   -3.103 closest distance to " CG  GLU A 152 " =    1.160
peak=   -3.098 closest distance to " CG  GLU A 277 " =    1.244
peak=   -3.088 closest distance to " O   HOH Z 134 " =    3.041
peak=   -3.088 closest distance to " ND2 ASN A 249 " =    2.400
peak=   -3.087 closest distance to " CB  ASP A 286 " =    1.662
peak=   -3.087 closest distance to " C   MET A 188 " =    1.483
peak=   -3.085 closest distance to " O   HOH Z 298 " =    2.345
peak=   -3.084 closest distance to " O   HOH Z 137 " =    1.466
peak=   -3.084 closest distance to " CE  LYS A  76 " =    2.879
peak=   -3.082 closest distance to " CA  GLY A 241 " =    3.025
peak=   -3.048 closest distance to " SG ACYS A 201 " =    1.654
peak=   -3.036 closest distance to " CZ3 TRP A 123 " =    1.782

================= 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    :  0.4111 0.4081   6.202308e+00   6.190692e+00
   1_bss:  0.4000 0.3956   6.191047e+00   6.166465e+00
   1_xyz:  0.2697 0.3000   5.887398e+00   5.953005e+00
   1_adp:  0.2458 0.3082   5.831965e+00   5.983420e+00
   1_occ:  0.2455 0.3086   5.831464e+00   5.983868e+00
   2_bss:  0.2433 0.3074   5.826036e+00   5.979238e+00
   2_xyz:  0.1753 0.2227   5.515255e+00   5.706359e+00
   2_adp:  0.1574 0.2023   5.423303e+00   5.620944e+00
   2_occ:  0.1570 0.2018   5.421341e+00   5.618401e+00
   3_bss:  0.1570 0.2009   5.417176e+00   5.611745e+00
   3_xyz:  0.1313 0.1738   5.259130e+00   5.469730e+00
   3_adp:  0.1252 0.1693   5.223104e+00   5.445900e+00
   3_occ:  0.1251 0.1693   5.222573e+00   5.445189e+00
   4_bss:  0.1251 0.1690   5.222004e+00   5.444498e+00
   4_xyz:  0.1116 0.1575   5.132457e+00   5.375172e+00
   4_adp:  0.1096 0.1561   5.118902e+00   5.364919e+00
   4_occ:  0.1095 0.1561   5.118682e+00   5.364660e+00
   5_bss:  0.1095 0.1561   5.118591e+00   5.364559e+00
   5_xyz:  0.1076 0.1553   5.108575e+00   5.361687e+00
   5_adp:  0.1068 0.1561   5.109449e+00   5.368562e+00
   5_occ:  0.1068 0.1562   5.109389e+00   5.368513e+00
   5_bss:  0.1067 0.1561   5.109041e+00   5.368045e+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:  0.328  15.808  -1.407   1.747  -0.668   0.000  -0.000  -0.000
   1_xyz:  0.328  15.808  -1.407   1.747  -0.668   0.000  -0.000  -0.000
   1_adp:  0.328  15.808  -1.407   1.747  -0.668   0.000  -0.000  -0.000
   1_occ:  0.328  15.808  -1.407   1.747  -0.668   0.000  -0.000  -0.000
   2_bss:  0.322  30.423  -2.349  -0.572  -1.187  -0.000  -0.000  -0.000
   2_xyz:  0.322  30.423  -2.349  -0.572  -1.187  -0.000  -0.000  -0.000
   2_adp:  0.322  30.423  -2.349  -0.572  -1.187  -0.000  -0.000  -0.000
   2_occ:  0.322  30.423  -2.349  -0.572  -1.187  -0.000  -0.000  -0.000
   3_bss:  0.307  30.423  -2.581  -1.858  -1.185  -0.000  -0.000  -0.000
   3_xyz:  0.307  30.423  -2.581  -1.858  -1.185  -0.000  -0.000  -0.000
   3_adp:  0.307  30.423  -2.581  -1.858  -1.185  -0.000  -0.000  -0.000
   3_occ:  0.307  30.423  -2.581  -1.858  -1.185  -0.000  -0.000  -0.000
   4_bss:  0.315  36.837  -2.861  -2.387  -1.444  -0.000  -0.000  -0.000
   4_xyz:  0.315  36.837  -2.861  -2.387  -1.444  -0.000  -0.000  -0.000
   4_adp:  0.315  36.837  -2.861  -2.387  -1.444  -0.000  -0.000  -0.000
   4_occ:  0.315  36.837  -2.861  -2.387  -1.444  -0.000  -0.000  -0.000
   5_bss:  0.314  36.837  -2.715  -2.307  -1.290  -0.000  -0.000  -0.000
   5_xyz:  0.314  36.837  -2.715  -2.307  -1.290  -0.000  -0.000  -0.000
   5_adp:  0.314  36.837  -2.715  -2.307  -1.290  -0.000  -0.000  -0.000
   5_occ:  0.314  36.837  -2.715  -2.307  -1.290  -0.000  -0.000  -0.000
   5_bss:  0.318  40.334  -2.512  -2.159  -1.093  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.576 0.5899  0.7838    49138.416
   1_bss:  43.330 0.6030  0.7952    44999.670
   1_xyz:  29.416 0.7656  0.9642    23119.786
   1_adp:  30.911 0.7482  0.9455    24900.062
   1_occ:  30.939 0.7479  0.9446    24917.463
   2_bss:  30.591 0.7516  0.9099    24424.009
   2_xyz:  21.369 0.8479  0.9936    12226.065
   2_adp:  18.772 0.8741  1.0092    10216.203
   2_occ:  18.722 0.8745  1.0090    10144.644
   3_bss:  18.529 0.8760  0.9920     9907.935
   3_xyz:  15.705 0.9005  1.0010     7437.552
   3_adp:  15.091 0.9061  0.9978     7137.711
   3_occ:  15.078 0.9062  0.9978     7122.665
   4_bss:  15.041 0.9066  0.9851     7121.588
   4_xyz:  13.754 0.9166  0.9902     6108.808
   4_adp:  13.493 0.9189  0.9858     6001.327
   4_occ:  13.492 0.9189  0.9857     5995.138
   5_bss:  13.489 0.9189  0.9905     5993.577
   5_xyz:  13.376 0.9200  0.9896     5976.548
   5_adp:  13.491 0.9192  0.9822     6043.211
   5_occ:  13.491 0.9192  0.9821     6042.805
   5_bss:  13.482 0.9192  0.9893     6039.042
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   1.7903e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   1.7903e-01
   1_xyz:   1.279  0.010  0.081 14.830  0.005  4.103   9.2369e-02
   1_adp:   1.279  0.010  0.081 14.830  0.005  4.103   9.2369e-02
   1_occ:   1.279  0.010  0.081 14.830  0.005  4.103   9.2369e-02
   2_bss:   1.279  0.010  0.081 14.830  0.005  4.103   9.2369e-02
   2_xyz:   1.099  0.008  0.075 14.187  0.004  4.108   7.1254e-02
   2_adp:   1.099  0.008  0.075 14.187  0.004  4.108   7.1254e-02
   2_occ:   1.099  0.008  0.075 14.187  0.004  4.108   7.1254e-02
   3_bss:   1.099  0.008  0.075 14.187  0.004  4.108   7.1254e-02
   3_xyz:   0.862  0.005  0.062 14.247  0.003  4.104   4.6916e-02
   3_adp:   0.862  0.005  0.062 14.247  0.003  4.104   4.6916e-02
   3_occ:   0.862  0.005  0.062 14.247  0.003  4.104   4.6916e-02
   4_bss:   0.862  0.005  0.062 14.247  0.003  4.104   4.6916e-02
   4_xyz:   1.003  0.006  0.073 14.703  0.004  4.112   5.8895e-02
   4_adp:   1.003  0.006  0.073 14.703  0.004  4.112   5.8895e-02
   4_occ:   1.003  0.006  0.073 14.703  0.004  4.112   5.8895e-02
   5_bss:   1.003  0.006  0.073 14.703  0.004  4.112   5.8895e-02
   5_xyz:   0.970  0.006  0.071 14.511  0.004  4.112   5.5669e-02
   5_adp:   0.970  0.006  0.071 14.511  0.004  4.112   5.5669e-02
   5_occ:   0.970  0.006  0.071 14.511  0.004  4.112   5.5669e-02
   5_bss:   0.970  0.006  0.071 14.511  0.004  4.112   5.5669e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.420   2.3755e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.420   2.3755e-01
   1_xyz:   9.162  0.054  0.326 89.215  0.047  2.049   8.7240e-02
   1_adp:   9.162  0.054  0.326 89.215  0.047  2.049   8.7240e-02
   1_occ:   9.162  0.054  0.326 89.215  0.047  2.049   8.7240e-02
   2_bss:   9.162  0.054  0.326 89.215  0.047  2.049   8.7240e-02
   2_xyz:   6.427  0.059  0.248 80.655  0.040  2.333   1.6662e-01
   2_adp:   6.427  0.059  0.248 80.655  0.040  2.333   1.6662e-01
   2_occ:   6.427  0.059  0.248 80.655  0.040  2.333   1.6662e-01
   3_bss:   6.427  0.059  0.248 80.655  0.040  2.333   1.6662e-01
   3_xyz:   6.939  0.045  0.187 82.168  0.035  2.378   3.5878e-02
   3_adp:   6.939  0.045  0.187 82.168  0.035  2.378   3.5878e-02
   3_occ:   6.939  0.045  0.187 82.168  0.035  2.378   3.5878e-02
   4_bss:   6.939  0.045  0.187 82.168  0.035  2.378   3.5878e-02
   4_xyz:   6.654  0.036  0.237 84.639  0.044  2.277   4.7287e-02
   4_adp:   6.654  0.036  0.237 84.639  0.044  2.277   4.7287e-02
   4_occ:   6.654  0.036  0.237 84.639  0.044  2.277   4.7287e-02
   5_bss:   6.654  0.036  0.237 84.639  0.044  2.277   4.7287e-02
   5_xyz:   6.563  0.034  0.224 84.273  0.042  2.304   4.4221e-02
   5_adp:   6.563  0.034  0.224 84.273  0.042  2.304   4.4221e-02
   5_occ:   6.563  0.034  0.224 84.273  0.042  2.304   4.4221e-02
   5_bss:   6.563  0.034  0.224 84.273  0.042  2.304   4.4221e-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:  85.67   0.00  18.01  83.37   0.00  14.12  85.67   3.21  39.18
   1_occ:  85.67   0.00  18.01  83.37   0.00  14.12  85.67   3.21  39.18
   2_bss:  85.67   0.00  18.01  83.37   0.00  14.12  85.67   3.21  39.18
   2_xyz:  85.67   0.00  18.01  83.37   0.00  14.12  85.67   3.21  39.18
   2_adp:  81.21   1.52  17.03  81.21   1.52  13.16  80.21   6.46  38.13
   2_occ:  81.21   1.52  17.03  81.21   1.52  13.16  80.21   6.46  38.13
   3_bss:  81.21   1.52  17.03  81.21   1.52  13.16  80.21   6.46  38.13
   3_xyz:  81.21   1.52  17.03  81.21   1.52  13.16  80.21   6.46  38.13
   3_adp:  85.98   0.76  17.17  85.98   0.76  12.98  80.99   4.19  40.01
   3_occ:  85.98   0.76  17.17  85.98   0.76  12.98  80.99   4.19  40.01
   4_bss:  85.98   0.76  17.17  85.98   0.76  12.98  80.99   4.19  40.01
   4_xyz:  85.98   0.76  17.17  85.98   0.76  12.98  80.99   4.19  40.01
   4_adp:  87.73   0.32  17.03  87.73   0.32  12.82  81.93   4.92  39.98
   4_occ:  87.73   0.32  17.03  87.73   0.32  12.82  81.93   4.92  39.98
   5_bss:  87.73   0.32  17.03  87.73   0.32  12.82  81.93   4.92  39.98
   5_xyz:  87.73   0.32  17.03  87.73   0.32  12.82  81.93   4.92  39.98
   5_adp:  96.58   0.00  17.07  96.58   0.00  12.76  87.71   6.32  40.56
   5_occ:  96.58   0.00  17.07  96.58   0.00  12.76  87.71   6.32  40.56
   5_bss:  96.59   0.00  17.07  96.59   0.00  12.76  87.71   6.32  40.56
------------------------------------------------------------------------
 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:    1.701    0.021    0.306
   1_adp:    1.701    0.021    0.306
   1_occ:    1.701    0.021    0.306
   2_bss:    1.701    0.021    0.306
   2_xyz:    1.155    0.018    0.483
   2_adp:    1.155    0.018    0.483
   2_occ:    1.155    0.018    0.483
   3_bss:    1.155    0.018    0.483
   3_xyz:    1.098    0.023    0.532
   3_adp:    1.098    0.023    0.532
   3_occ:    1.098    0.023    0.532
   4_bss:    1.098    0.023    0.532
   4_xyz:    1.116    0.062    0.573
   4_adp:    1.116    0.062    0.573
   4_occ:    1.116    0.062    0.573
   5_bss:    1.116    0.062    0.573
   5_xyz:    1.195    0.080    0.585
   5_adp:    1.195    0.080    0.585
   5_occ:    1.195    0.080    0.585
   5_bss:    1.195    0.080    0.585
------------------------------------------------------------------------

CPU time actual refinement: 332.54


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/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_267/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_267/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.41 
  Macro-tasks:
    bulk solvent and scale       = 45.91  
    individual site refinement   = 128.27 
    weights calculation          = 30.03  
    collect and process          = 6.66   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 210.96 
  Micro-tasks:
    mask                            = 1.66   
    f_calc                          = 105.50 
    alpha_beta                      = 8.01   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 107.84 
    fmodel                         = 7.52   
    r_factors                      = 0.19   
    phase_errors                   = 11.81  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 243.95 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.764 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    634 calls, 105.00 s
gradients_fft:          579 calls,  96.85 s

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

# Date 2008-01-16 Time 04:25:17 PST -0800 (1200486317.07 s)
Start R-work = 0.4111, R-free = 0.4081 (no bulk solvent and anisotropic scale)
Final R-work = 0.1316, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.4000, R-free = 0.3956
Final R-work = 0.1067, R-free = 0.1561